Package 'PLNmodels'

Title: Poisson Lognormal Models
Description: The Poisson-lognormal model and variants (Chiquet, Mariadassou and Robin, 2021 <doi:10.3389/fevo.2021.588292>) can be used for a variety of multivariate problems when count data are at play, including principal component analysis for count data, discriminant analysis, model-based clustering and network inference. Implements variational algorithms to fit such models accompanied with a set of functions for visualization and diagnostic.
Authors: Julien Chiquet [aut, cre] (ORCID: <https://orcid.org/0000-0002-3629-3429>), Mahendra Mariadassou [aut] (ORCID: <https://orcid.org/0000-0003-2986-354X>), Stéphane Robin [aut], François Gindraud [aut], Julie Aubert [ctb], Bastien Batardière [ctb], Giovanni Poggiato [ctb], Cole Trapnell [ctb], Maddy Duran [ctb]
Maintainer: Julien Chiquet <[email protected]>
License: GPL (>= 3)
Version: 1.2.2-9100
Built: 2026-06-09 07:27:29 UTC
Source: https://github.com/pln-team/plnmodels

Help Index

Barents fish data set

Description

This data set gives the abundance of 30 fish species observed in 89 sites in the Barents sea. For each site, 4 additional covariates are known. Subsample of the original datasets studied by Fossheim et al, 2006.

Usage

barents

Format

A data frame with 6 variables:

  • Abundance: A 30 fish species by 89 sites count matrix

  • Offset: A 30 fish species by 89 samples offset matrix, measuring the sampling effort in each site

  • 4 covariates for latitude, longitude, depth (in meters), temperature (in Celsius degrees).

Source

Data from M. Fossheim and coauthors.

References

Fossheim, Maria, Einar M. Nilssen, and Michaela Aschan. "Fish assemblages in the Barents Sea." Marine Biology Research 2.4 (2006). doi:10.1080/17451000600815698

Examples

data(barents)

Extract model coefficients

Description

Extracts model coefficients from objects returned by PLN() and its variants

Usage

## S3 method for class 'PLNfit'
coef(object, type = c("main", "covariance"), ...)

Arguments

object

an R6 object with class PLNfit
type

type of parameter that should be extracted. Either "main" (default) for

BB

or "covariance" for

Σ\Sigma

...

additional parameters for S3 compatibility. Not used

Value

A matrix of coefficients extracted from the PLNfit model.

See Also

sigma.PLNfit(), vcov.PLNfit(), standard_error.PLNfit()

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLN(Abundance ~ 1 + offset(log(Offset)), data = trichoptera)
coef(myPLN) ## B
coef(myPLN, type = "covariance") ## Sigma

Extracts model coefficients from objects returned by PLNLDA()

Description

The method for objects returned by PLNLDA() only returns coefficients associated to the

Θ\Theta

part of the model (see the PLNLDA vignette for mathematical details).

Usage

## S3 method for class 'PLNLDAfit'
coef(object, ...)

Arguments

object

an R6 object with class PLNLDAfit
...

additional parameters for S3 compatibility. Not used

Value

Either NULL or a matrix of coefficients extracted from the PLNLDAfit model.

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLNLDA <- PLNLDA(Abundance ~ Wind, grouping = Group, data = trichoptera)
coef(myPLNLDA)

Extract model coefficients

Description

Extracts model coefficients from objects returned by PLN() and its variants

Usage

## S3 method for class 'PLNmixturefit'
coef(object, type = c("main", "means", "covariance", "mixture"), ...)

Arguments

object

an R6 object with class PLNmixturefit
type

type of parameter that should be extracted. Either "main" (default) for

Θ\Theta

, "means" for

μ\mu

, "mixture" for

π\pi

or "covariance" for

Σ\Sigma

...

additional parameters for S3 compatibility. Not used

Value

A matrix of coefficients extracted from the PLNfit model.

See Also

sigma.PLNmixturefit()

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLNmixture(Abundance ~ 1 + offset(log(Offset)),
           data = trichoptera, control = PLNmixture_param(smoothing = "none"))  %>% getBestModel()
coef(myPLN) ## Theta - empty here
coef(myPLN, type = "mixture") ## pi
coef(myPLN, type = "means") ## mu
coef(myPLN, type = "covariance") ## Sigma

Extract model coefficients

Description

Extracts model coefficients from objects returned by ZIPLN() and its variants

Usage

## S3 method for class 'ZIPLNfit'
coef(object, type = c("count", "zero", "precision", "covariance"), ...)

Arguments

object

an R6 object with class ZIPLNfit
type

type of parameter that should be extracted. Either "count" (default) for BB, "zero" for B0B0, "precision" for Ω\Omega, "covariance" for Σ\Sigma
...

additional parameters for S3 compatibility. Not used

Value

A matrix of coefficients extracted from the ZIPLNfit model.

See Also

sigma.ZIPLNfit()

Examples

data(scRNA)
# data subsample: only 100 random cell and the 50 most varying transcript
subset <- sample.int(nrow(scRNA), 100)
myPLN  <- ZIPLN(counts[, 1:50] ~ 1 + offset(log(total_counts)), subset = subset, data = scRNA)

Extract the regularization path of a PLNnetwork fit

Description

Extract the regularization path of a PLNnetwork fit

Usage

coefficient_path(Robject, precision = TRUE, corr = TRUE)

Arguments

Robject

an object with class Networkfamily, i.e. an output from PLNnetwork()
precision

a logical, should the coefficients of the precision matrix Omega or the covariance matrix Sigma be sent back. Default is TRUE.
corr

a logical, should the correlation (partial in case precision = TRUE) be sent back. Default is TRUE.

Value

Sends back a tibble/data.frame.

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
head(coefficient_path(fits))

Compute offsets from a count data using one of several normalization schemes

Description

Computes offsets from the count table using one of several normalization schemes (TSS, CSS, RLE, GMPR, Wrench, TMM, etc) described in the literature.

Usage

compute_offset(
  counts,
  offset = c("TSS", "GMPR", "RLE", "CSS", "Wrench", "TMM", "none"),
  scale = c("none", "count"),
  ...
)

Arguments

counts

Required. An abundance count table, preferably with dimensions names and species as columns.
offset

Optional. Normalization scheme used to compute scaling factors used as offset during PLN inference. Available schemes are "TSS" (Total Sum Scaling, default), "CSS" (Cumulative Sum Scaling, used in metagenomeSeq), "RLE" (Relative Log Expression, used in DESeq2), "GMPR" (Geometric Mean of Pairwise Ratio, introduced in Chen et al., 2018), Wrench (introduced in Kumar et al., 2018) or "none". Alternatively the user can supply its own vector or matrix of offsets (see note for specification of the user-supplied offsets).
scale

Either "none" (default) or "count". Should the offset be normalized to be on the same scale as the counts ?
...

Additional parameters passed on to specific methods (for now CSS and RLE)

Details

RLE has additional pseudocounts and type arguments to add pseudocounts to the observed counts (defaults to 0L) and to compute offsets using only positive counts (if type == "poscounts"). This mimics the behavior of DESeq2::DESeq() when using sfType == "poscounts". CSS has an additional reference argument to choose the location function used to compute the reference quantiles (defaults to median as in the Nature publication but can be set to mean to reproduce behavior of functions cumNormStat* from metagenomeSeq). Wrench has two additional parameters: groups to specify sample groups and type to either reproduce exactly the default Wrench::wrench() behavior (type = "wrench", default) or to use simpler heuristics (type = "simple"). Note that (i) CSS normalization fails when the median absolute deviation around quantiles does not become instable for high quantiles (limited count variations both within and across samples) and/or one sample has less than two positive counts, (ii) RLE fails when there are no common species across all samples (unless type == "poscounts" has been specified) and (iii) GMPR fails if a sample does not share any species with all other samples. TMM code between two libraries is simplified and adapted from M. Robinson (edgeR:::.calcFactorTMM). The final output is however different from the one produced by edgeR:::.calcFactorTMM as they are intended to be used as such in the model (whereas they need to be multiplied by sequencing depths in edgeR)

Value

If offset = "none", NULL else a vector of length nrow(counts) with one offset per sample.

References

Chen, L., Reeve, J., Zhang, L., Huang, S., Wang, X. and Chen, J. (2018) GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data. PeerJ, 6, e4600 doi:10.7717/peerj.4600

Paulson, J. N., Colin Stine, O., Bravo, H. C. and Pop, M. (2013) Differential abundance analysis for microbial marker-gene surveys. Nature Methods, 10, 1200-1202 doi:10.1038/nmeth.2658

Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biology, 11, R106 doi:10.1186/gb-2010-11-10-r106

Kumar, M., Slud, E., Okrah, K. et al. (2018) Analysis and correction of compositional bias in sparse sequencing count data. BMC Genomics 19, 799 doi:10.1186/s12864-018-5160-5

Robinson, M.D., Oshlack, A. (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11, R25 doi:10.1186/gb-2010-11-3-r25

Examples

data(trichoptera)
counts <- trichoptera$Abundance
compute_offset(counts)
## Other normalization schemes
compute_offset(counts, offset = "RLE", pseudocounts = 1)
compute_offset(counts, offset = "Wrench", groups = trichoptera$Covariate$Group)
compute_offset(counts, offset = "GMPR")
compute_offset(counts, offset = "TMM")
## User supplied offsets
my_offset <- setNames(rep(1, nrow(counts)), rownames(counts))
compute_offset(counts, offset = my_offset)

Helper function for PLN initialization.

Description

Barebone function to compute starting points for B, M and S when fitting a PLN. Mostly intended for internal use.

Usage

compute_PLN_starting_point(Y, X, O, w, s = 0.1)

Arguments

Y

Response count matrix
X

Covariate matrix. Note that initialization will fail if the model matrix is singular.
O

Offset matrix (in log-scale)
w

Weight vector (defaults to 1)
s

Scale parameter for S (defaults to 0.1)

Details

The default strategy to estimate B and M is to fit a linear model with covariates X to the response count matrix (after adding a pseudocount of 1, scaling by the offset and taking the log). The regression matrix is used to initialize B and the residuals to initialize M. S is initialized as a constant conformable matrix with value s.

Value

a named list of starting values for model parameter B and variational parameters M and S used in the iterative optimization algorithm of PLN()

Examples

## Not run: 
data(barents)
Y <- barents$Abundance
X <- model.matrix(Abundance ~ Latitude + Longitude + Depth + Temperature, data = barents)
O <- log(barents$Offset)
w <-- rep(1, nrow(Y))
compute_PLN_starting_point(Y, X, O, w)

## End(Not run)

Extract edge selection frequency in bootstrap subsamples

Description

Extracts edge selection frequency in networks reconstructed from bootstrap subsamples during the stars stability selection procedure, as either a matrix or a named vector. In the latter case, edge names follow igraph naming convention.

Usage

extract_probs(
  Robject,
  penalty = NULL,
  index = NULL,
  crit = c("StARS", "BIC", "EBIC"),
  format = c("matrix", "vector"),
  tol = 1e-05
)

Arguments

Robject

an object with class PLNnetworkfamily, i.e. an output from PLNnetwork()
penalty

penalty used for the bootstrap subsamples
index

Integer index of the model to be returned. Only the first value is taken into account.
crit

a character for the criterion used to performed the selection. Either "BIC", "ICL", "EBIC", "StARS", "R_squared". Default is ICL for PLNPCA, and BIC for PLNnetwork. If StARS (Stability Approach to Regularization Selection) is chosen and stability selection was not yet performed, the function will call the method stability_selection() with default argument.
format

output format. Either a matrix (default) or a named vector.
tol

tolerance for rounding error when comparing penalties.

Value

Either a matrix or named vector of edge-wise probabilities. In the latter case, edge names follow igraph convention.

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
nets <- PLNnetwork(Abundance ~ 1 + offset(log(Offset)), data = trichoptera)
## Not run: 
stability_selection(nets)
probs <- extract_probs(nets, crit = "StARS", format = "vector")
probs

## End(Not run)

## Not run: 
## Add edge attributes to graph using igraph
net_stars <- getBestModel(nets, "StARS")
g <- plot(net_stars, type = "partial_cor", plot=F)
library(igraph)
E(g)$prob <- probs[as_ids(E(g))]
g

## End(Not run)

Extracts model fitted values from objects returned by PLN() and its variants

Description

Extracts model fitted values from objects returned by PLN() and its variants

Usage

## S3 method for class 'PLNfit'
fitted(object, ...)

Arguments

object

an R6 object with class PLNfit
...

additional parameters for S3 compatibility. Not used

Value

A matrix of Fitted values extracted from the object object.

Extracts model fitted values from objects returned by PLNmixture() and its variants

Description

Extracts model fitted values from objects returned by PLNmixture() and its variants

Usage

## S3 method for class 'PLNmixturefit'
fitted(object, ...)

Arguments

object

an R6 object with class PLNmixturefit
...

additional parameters for S3 compatibility. Not used

Value

A matrix of Fitted values extracted from the object object.

Extracts model fitted values from objects returned by ZIPLN() and its variants

Description

Extracts model fitted values from objects returned by ZIPLN() and its variants

Usage

## S3 method for class 'ZIPLNfit'
fitted(object, ...)

Arguments

object

an R6 object with class ZIPLNfit
...

additional parameters for S3 compatibility. Not used

Value

A matrix of Fitted values extracted from the object object.

Best model extraction from a collection of models

Description

Best model extraction from a collection of models

Usage

## S3 method for class 'PLNPCAfamily'
getBestModel(Robject, crit = c("ICL", "BIC"), ...)

getBestModel(Robject, crit, ...)

## S3 method for class 'PLNmixturefamily'
getBestModel(Robject, crit = c("ICL", "BIC"), ...)

## S3 method for class 'Networkfamily'
getBestModel(Robject, crit = c("BIC", "EBIC", "StARS"), ...)

## S3 method for class 'PLNnetworkfamily'
getBestModel(Robject, crit = c("BIC", "EBIC", "StARS"), ...)

## S3 method for class 'ZIPLNnetworkfamily'
getBestModel(Robject, crit = c("BIC", "EBIC", "StARS"), ...)

Arguments

Robject

an object with class PLNPCAfamilly ot PLNnetworkfamily
crit

a character for the criterion used to performed the selection. Either "BIC", "ICL", "EBIC", "StARS", "R_squared". Default is ICL for PLNPCA, and BIC for PLNnetwork. If StARS (Stability Approach to Regularization Selection) is chosen and stability selection was not yet performed, the function will call the method stability_selection() with default argument.
...

additional parameters for StARS criterion (only for PLNnetwork). stability, a scalar indicating the target stability (= 1 - 2 beta) at which the network is selected. Default is 0.9.

Value

Send back an object with class PLNPCAfit or PLNnetworkfit

Methods (by class)

Examples

## Not run: 
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPCA <- PLNPCA(Abundance ~ 1 + offset(log(Offset)), data = trichoptera, ranks = 1:4)
myModel <- getBestModel(myPCA)

## End(Not run)

Model extraction from a collection of models

Description

Model extraction from a collection of models

Usage

## S3 method for class 'PLNPCAfamily'
getModel(Robject, var, index = NULL)

getModel(Robject, var, index)

## S3 method for class 'PLNmixturefamily'
getModel(Robject, var, index = NULL)

## S3 method for class 'Networkfamily'
getModel(Robject, var, index = NULL)

## S3 method for class 'PLNnetworkfamily'
getModel(Robject, var, index = NULL)

## S3 method for class 'ZIPLNnetworkfamily'
getModel(Robject, var, index = NULL)

Arguments

Robject

an R6 object with class PLNPCAfamily or PLNnetworkfamily
var

value of the parameter (rank for PLNPCA, sparsity for PLNnetwork) that identifies the model to be extracted from the collection. If no exact match is found, the model with closest parameter value is returned with a warning.
index

Integer index of the model to be returned. Only the first value is taken into account.

Value

Sends back an object with class PLNPCAfit or PLNnetworkfit.

Methods (by class)

Examples

## Not run: 
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPCA <- PLNPCA(Abundance ~ 1 + offset(log(Offset)), data = trichoptera, ranks = 1:5)
myModel <- getModel(myPCA, 2)

## End(Not run)

Cow microbiome data set

Description

This data gives the evolution of the microbiota of 45 lactating cows before and after calving in terms of counts of Amplicon Sequence Variants (ASV) in various body sites. Three body sites (vagina, mouth, nose) in addition to the milk of the 4 teats were sampled at 4 times points: 1 week before calving (except for the milk), 1 month, 3 months and 7 months after calving. We present a reduced version of the original data consisting of 880 samples with sequencing depths ranging from 1,001 to 71,881 reads per sample (see doi:10.1186/s42523-023-00252-w for details). ASVs with prevalence in the dataset lower than 5% were filtered out and samples for which the total depth (after ASV filtering were removed), resulting in a count table of n = 880 samples with p = 259 ASV and a mean proportion of zeroes of 90.3%.

Usage

microcosm

Format

A data frame with 6 variables:

  • Abundance: A 880 samples by 259 taxa count matrix

  • sample: Unique sample id

  • Offset: sequencing depth

  • site: sampling site (O: oral; N: nasal; V: vaginal; M: milk)

  • time: sampling time (⁠-1W⁠: 1 week before calving; ⁠1M⁠: 1 month after calving; ⁠3M⁠: 3 months after calving; ⁠7M⁠: 7 months after calving)

  • site_time: factor of possible pairs of (site, time). The combination ⁠M -1W⁠ is absent.

Source

Data from M. Mariadassou and coauthors.

References

Mariadassou, M., Nouvel, L.X., Constant, F. et al. Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd. anim microbiome 5, 32 (2023). doi:10.1186/s42523-023-00252-w

See Also

prepare_data()

Examples

data(microcosm)
## Not run: 
my_ZIPLN <- ZIPLN(formula = Abundance ~ 0 + site + offset(log(Offset)) | 1, data = microcosm)

## End(Not run)

Mollusk data set

Description

This data set gives the abundance of 32 mollusk species in 163 samples. For each sample, 4 additional covariates are known.

Usage

mollusk

Format

A list with 2 two data frames:

Abundance

a 163 x 32 data frame of abundancies/counts (163 samples and 32 mollusk species)

Covariate

a 163 x 4 data frame of covariates:

site

a factor with 8 levels indicating the sampling site

season

a factor with 4 levels indicating the season

method

a factor with 2 levels for the method of sampling - wood or string

duration

a numeric with 3 levels for the time of exposure in week

In order to prepare the data for using formula in multivariate analysis (multiple outputs and inputs), use prepare_data(). Original data set has been extracted from ade4.

Source

Data from Richardot-Coulet, Chessel and Bournaud.

References

Richardot-Coulet, M., Chessel D. and Bournaud M. (1986) Typological value of the benthos of old beds of a large river. Methodological approach. Archiv fùr Hydrobiologie, 107, 363–383.

See Also

prepare_data()

Examples

data(mollusk)
mollusc <- prepare_data(mollusk$Abundance, mollusk$Covariate)

An R6 Class to virtually represent a collection of network fits

Description

The functions PLNnetwork() and ZIPLNnetwork() both produce an instance of this class, which can be thought of as a vector of PLNnetworkfits ZIPLNfit_sparses (indexed by penalty parameter)

This class comes with a set of methods mostly used to compare network fits (in terms of goodness of fit) or extract one from the family (based on penalty parameter and/or goodness of it). See the documentation for getBestModel(), getModel() and plot() for the user-facing ones.

Super class

PLNmodels::PLNfamily -> Networkfamily

Active bindings

penalties

the sparsity level of the network in the successively fitted models

stability_path

the stability path of each edge as returned by the stars procedure

stability

mean edge stability along the penalty path

criteria

a data frame with the values of some criteria (variational log-likelihood, (E)BIC, ICL and R2, stability) for the collection of models / fits BIC, ICL and EBIC are defined so that they are on the same scale as the model log-likelihood, i.e. with the form, loglik - 0.5 penalty

Methods

Public methods

Inherited methods

Method new()

Initialize all models in the collection

Usage
Networkfamily$new(penalties, data, control)
Arguments
penalties

a vector of positive real number controlling the level of sparsity of the underlying network.

data

a named list used internally to carry the data matrices

control

a list for controlling the optimization.

Returns

Update all network fits in the family with smart starting values

Method optimize()

Call to the C++ optimizer on all models of the collection

Usage
Networkfamily$optimize(data, config)
Arguments
data

a named list used internally to carry the data matrices

config

a list for controlling the optimization.

Method coefficient_path()

Extract the regularization path of a Networkfamily

Usage
Networkfamily$coefficient_path(precision = TRUE, corr = TRUE)
Arguments
precision

Logical. Should the regularization path be extracted from the precision matrix Omega (TRUE, default) or from the variance matrix Sigma (FALSE)

corr

Logical. Should the matrix be transformed to (partial) correlation matrix before extraction? Defaults to TRUE

Method getBestModel()

Extract the best network in the family according to some criteria

Usage
Networkfamily$getBestModel(crit = c("BIC", "EBIC", "StARS"), stability = 0.9)
Arguments
crit

character. Criterion used to perform the selection. If "StARS" is chosen but ⁠$stability⁠ field is empty, will compute stability path.

stability

Only used for "StARS" criterion. A scalar indicating the target stability (= 1 - 2 beta) at which the network is selected. Default is 0.9.

Details

For BIC and EBIC criteria, higher is better.

Method plot()

Display various outputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of network fits (a Networkfamily)

Usage
Networkfamily$plot(
  criteria = c("loglik", "pen_loglik", "BIC", "EBIC"),
  reverse = FALSE,
  log.x = TRUE
)
Arguments
criteria

vector of characters. The criteria to plot in c("loglik", "pen_loglik", "BIC", "EBIC"). Defaults to all of them.

reverse

A logical indicating whether to plot the value of the criteria in the "natural" direction (loglik - 0.5 penalty) or in the "reverse" direction (-2 loglik + penalty). Default to FALSE, i.e use the natural direction, on the same scale as the log-likelihood.

log.x

logical: should the x-axis be represented in log-scale? Default is TRUE.

Returns

a ggplot2::ggplot graph

Method plot_stars()

Plot stability path

Usage
Networkfamily$plot_stars(stability = 0.9, log.x = TRUE)
Arguments
stability

scalar: the targeted level of stability using stability selection. Default is 0.9.

log.x

logical: should the x-axis be represented in log-scale? Default is TRUE.

Returns

a ggplot2::ggplot graph

Method plot_objective()

Plot objective value of the optimization problem along the penalty path

Usage
Networkfamily$plot_objective()
Returns

a ggplot2::ggplot graph

Method show()

User friendly print method

Usage
Networkfamily$show()

Method clone()

The objects of this class are cloneable with this method.

Usage
Networkfamily$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

The functions PLNnetwork(), ZIPLNnetwork() and the classes PLNnetworkfit, ZIPLNfit_sparse

Oaks amplicon data set

Description

This data set gives the abundance of 114 taxa (66 bacterial OTU, 48 fungal OTUs) in 116 samples. For each sample, 11 additional covariates are known.

Usage

oaks

Format

A data frame with 13 variables:

  • Abundance: A 114 taxa by 116 samples count matrix

  • Offset: A 114 taxa by 116 samples offset matrix

  • Sample: Unique sample id

  • tree: Tree status with respect to the pathogen (susceptible, intermediate or resistant)

  • branch: Unique branch id in each tree (4 branches were sampled in each tree, with 10 leaves per branch)

  • leafNO: Unique leaf id in each tree (40 leaves were sampled in each tree)

  • distTObase: Distance of the sampled leaf to the base of the branch

  • distTOtrunk: Distance of the sampled leaf to the base of the tree trunk

  • distTOground: Distance of the sampled leaf to the base of the ground

  • pmInfection: Powdery mildew infection, proportion of the upper leaf area displaying mildew symptoms

  • orientation: Orientation of the branch (South-West SW or North-East NE)

  • readsTOTfun: Total number of ITS1 reads for that leaf

  • readsTOTbac: Total number of 16S reads for that leaf

Source

Data from B. Jakuschkin and coauthors.

References

Jakuschkin, B., Fievet, V., Schwaller, L. et al. Deciphering the Pathobiome: Intra- and Interkingdom Interactions Involving the Pathogen Erysiphe alphitoides . Microb Ecol 72, 870–880 (2016). doi:10.1007/s00248-016-0777-x

See Also

prepare_data()

Examples

data(oaks)
## Not run: 
oaks_networks <- PLNnetwork(formula = Abundance ~ 1 + offset(log(Offset)), data = oaks)

## End(Not run)

Poisson lognormal model

Description

Fit the multivariate Poisson lognormal model with a variational algorithm. Use the (g)lm syntax for model specification (covariates, offsets, weights).

Usage

PLN(formula, data, subset, weights, control = PLN_param())

Arguments

formula

an object of class "formula": a symbolic description of the model to be fitted.
data

an optional data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model. If not found in data, the variables are taken from environment(formula), typically the environment from which PLN is called.
subset

an optional vector specifying a subset of observations to be used in the fitting process.
weights

an optional vector of observation weights to be used in the fitting process.
control

a list-like structure for controlling the optimization, with default generated by PLN_param(). See the associated documentation for details.

Value

an R6 object with class PLNfit

See Also

The class PLNfit and the configuration function PLN_param()

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLN(Abundance ~ 1, data = trichoptera)

Control of a PLN fit

Description

Helper to define list of parameters to control the PLN fit. All arguments have defaults.

Usage

PLN_param(
  backend = c("nlopt", "torch"),
  trace = 1,
  covariance = c("full", "diagonal", "spherical", "fixed"),
  Omega = NULL,
  config_post = list(),
  config_optim = list(),
  inception = NULL
)

Arguments

backend

optimization back used, either "nlopt" or "torch". Default is "nlopt"
trace

a integer for verbosity.
covariance

character setting the model for the covariance matrix. Either "full", "diagonal", "spherical" or "fixed". Default is "full".
Omega

precision matrix of the latent variables. Inverse of Sigma. Must be specified if covariance is "fixed"
config_post

a list for controlling the post-treatments (optional bootstrap, jackknife, R2, etc.). See details
config_optim

a list for controlling the optimizer (either "nlopt" or "torch" backend). See details
inception

Set up the parameters initialization: by default, the model is initialized with a multivariate linear model applied on log-transformed data, and with the same formula as the one provided by the user. However, the user can provide a PLNfit (typically obtained from a previous fit), which sometimes speeds up the inference.

Details

The list of parameters config_optim controls the optimizers. When "nlopt" is chosen the following entries are relevant

  • "algorithm" the optimization method used by NLOPT among LD type, e.g. "CCSAQ", "MMA", "LBFGS". See NLOPT documentation for further details. Default is "CCSAQ".

  • "maxeval" stop when the number of iteration exceeds maxeval. Default is 10000

  • "ftol_rel" stop when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 1e-8

  • "xtol_rel" stop when an optimization step changes every parameters by less than xtol multiplied by the absolute value of the parameter. Default is 1e-6

  • "ftol_abs" stop when an optimization step changes the objective function by less than ftol_abs. Default is 0.0 (disabled)

  • "xtol_abs" stop when an optimization step changes every parameters by less than xtol_abs. Default is 0.0 (disabled)

  • "maxtime" stop when the optimization time (in seconds) exceeds maxtime. Default is -1 (disabled)

When "torch" backend is used (only for PLN and PLNLDA for now), the following entries are relevant:

  • "algorithm" the optimizer used by torch among RPROP (default), RMSPROP, ADAM and ADAGRAD

  • "maxeval" stop when the number of iteration exceeds maxeval. Default is 10 000

  • "numepoch" stop training once this number of epochs exceeds numepoch. Set to -1 to enable infinite training. Default is 1 000

  • "num_batch" number of batches to use during training. Defaults to 1 (use full dataset at each epoch)

  • "ftol_rel" stop when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 1e-8

  • "xtol_rel" stop when an optimization step changes every parameters by less than xtol multiplied by the absolute value of the parameter. Default is 1e-6

  • "lr" learning rate. Default is 0.1.

  • "momentum" momentum factor. Default is 0 (no momentum). Only used in RMSPROP

  • "weight_decay" Weight decay penalty. Default is 0 (no decay). Not used in RPROP

  • "step_sizes" pair of minimal (default: 1e-6) and maximal (default: 50) allowed step sizes. Only used in RPROP

  • "etas" pair of multiplicative increase and decrease factors. Default is (0.5, 1.2). Only used in RPROP

  • "centered" if TRUE, compute the centered RMSProp where the gradient is normalized by an estimation of its variance weight_decay (L2 penalty). Default to FALSE. Only used in RMSPROP

The list of parameters config_post controls the post-treatment processing (for most ⁠PLN*()⁠ functions), with the following entries (defaults may vary depending on the specific function, check ⁠config_post_default_*⁠ for defaults values):

  • jackknife boolean indicating whether jackknife should be performed to evaluate bias and variance of the model parameters. Default is FALSE.

  • bootstrap integer indicating the number of bootstrap resamples generated to evaluate the variance of the model parameters. Default is 0 (inactivated).

  • variational_var boolean indicating whether variational Fisher information matrix should be computed to estimate the variance of the model parameters (highly underestimated). Default is FALSE.

  • sandwich_var boolean indicating whether sandwich estimation should be used to estimate the variance of the model parameters (highly underestimated). Default is FALSE.

  • rsquared boolean indicating whether approximation of R2 based on deviance should be computed. Default is TRUE

Value

list of parameters configuring the fit.

An R6 Class to represent a collection of PLNfit

Description

super class for PLNPCAfamily and PLNnetworkfamily.

Public fields

responses

the matrix of responses common to every models

covariates

the matrix of covariates common to every models

offsets

the matrix of offsets common to every models

weights

the vector of observation weights

inception

a PLNfit object, obtained when no sparsifying penalty is applied.

models

a list of PLNfit object, one per penalty.

Active bindings

criteria

a data frame with the values of some criteria (approximated log-likelihood, BIC, ICL, etc.) for the collection of models / fits BIC and ICL are defined so that they are on the same scale as the model log-likelihood, i.e. with the form, loglik - 0.5 penalty

convergence

sends back a data frame with some convergence diagnostics associated with the optimization process (method, optimal value, etc)

Methods

Public methods

Method new()

Create a new PLNfamily object.

Usage
PLNfamily$new(responses, covariates, offsets, weights, control)
Arguments
responses

the matrix of responses common to every models

covariates

the matrix of covariates common to every models

offsets

the matrix of offsets common to every models

weights

the vector of observation weights

control

list controlling the optimization and the model

Returns

A new PLNfamily object

Method postTreatment()

Update fields after optimization

Usage
PLNfamily$postTreatment(config_post, config_optim)
Arguments
config_post

a list for controlling the post-treatments (optional bootstrap, jackknife, R2, etc.).

config_optim

a list for controlling the optimization parameters used during post_treatments

Method getModel()

Extract a model from a collection of models

Usage
PLNfamily$getModel(var, index = NULL)
Arguments
var

value of the parameter (rank for PLNPCA, sparsity for PLNnetwork) that identifies the model to be extracted from the collection. If no exact match is found, the model with closest parameter value is returned with a warning.

index

Integer index of the model to be returned. Only the first value is taken into account.

Returns

A PLNfit object

Method plot()

Lineplot of selected criteria for all models in the collection

Usage
PLNfamily$plot(criteria, reverse)
Arguments
criteria

A valid model selection criteria for the collection of models. Includes loglik, BIC (all), ICL (PLNPCA) and pen_loglik, EBIC (PLNnetwork)

reverse

A logical indicating whether to plot the value of the criteria in the "natural" direction (loglik - penalty) or in the "reverse" direction (-2 loglik + penalty). Default to FALSE, i.e use the natural direction, on the same scale as the log-likelihood.

Returns

A ggplot2::ggplot object

Method show()

User friendly print method

Usage
PLNfamily$show()

Method print()

User friendly print method

Usage
PLNfamily$print()

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNfamily$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

getModel()

An R6 Class to represent a PLNfit in a standard, general framework

Description

The function PLN() fit a model which is an instance of a object with class PLNfit. Objects produced by the functions PLNnetwork(), PLNPCA(), PLNmixture() and PLNLDA() also enjoy the methods of PLNfit() by inheritance.

This class comes with a set of R6 methods, some of them being useful for the user and exported as S3 methods. See the documentation for coef(), sigma(), predict(), vcov() and standard_error().

Fields are accessed via active binding and cannot be changed by the user.

Active bindings

n

number of samples

q

number of dimensions of the latent space

p

number of species

d

number of covariates

nb_param

number of parameters in the current PLN model

model_par

a list with the matrices of the model parameters: B (covariates), Sigma (covariance), Omega (precision matrix), plus some others depending on the variant)

var_par

a list with the matrices of the variational parameters: M (means) and S2 (variances)

optim_par

a list with parameters useful for monitoring the optimization

latent

a matrix: values of the latent vector (Z in the model)

latent_pos

a matrix: values of the latent position vector (Z) without covariates effects or offset

fitted

a matrix: fitted values of the observations (A in the model)

vcov_coef

matrix of sandwich estimator of the variance-covariance of B (need fixed -ie known- covariance at the moment)

vcov_model

character: the model used for the residual covariance

weights

observational weights

loglik

(weighted) variational lower bound of the loglikelihood

loglik_vec

element-wise variational lower bound of the loglikelihood

AIC

variational lower bound of the AIC

BIC

variational lower bound of the BIC

entropy

Entropy of the variational distribution

ICL

variational lower bound of the ICL

R_squared

approximated goodness-of-fit criterion

criteria

a vector with loglik, BIC, ICL and number of parameters

Methods

Public methods

Method new()

Initialize a PLNfit model

Usage
PLNfit$new(responses, covariates, offsets, weights, formula, control)
Arguments
responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily-class

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

weights

an optional vector of observation weights to be used in the fitting process.

formula

model formula used for fitting, extracted from the formula in the upper-level call

control

a list-like structure for controlling the fit, see PLN_param().

Method update()

Update a PLNfit object

Usage
PLNfit$update(
  B = NA,
  Sigma = NA,
  Omega = NA,
  M = NA,
  S = NA,
  Ji = NA,
  R2 = NA,
  Z = NA,
  A = NA,
  monitoring = NA
)
Arguments
B

matrix of regression matrix

Sigma

variance-covariance matrix of the latent variables

Omega

precision matrix of the latent variables. Inverse of Sigma.

M

matrix of variational parameters for the mean

S

matrix of variational parameters for the variance

Ji

vector of variational lower bounds of the log-likelihoods (one value per sample)

R2

approximate R^2 goodness-of-fit criterion

Z

matrix of latent vectors (includes covariates and offset effects)

A

matrix of fitted values

monitoring

a list with optimization monitoring quantities

Returns

Update the current PLNfit object

Method optimize()

Call to the NLopt or TORCH optimizer and update of the relevant fields

Usage
PLNfit$optimize(responses, covariates, offsets, weights, config)
Arguments
responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily-class

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

weights

an optional vector of observation weights to be used in the fitting process.

config

part of the control argument which configures the optimizer

Method optimize_vestep()

Result of one call to the VE step of the optimization procedure: optimal variational parameters (M, S) and corresponding log likelihood values for fixed model parameters (Sigma, B). Intended to position new data in the latent space.

Usage
PLNfit$optimize_vestep(
  covariates,
  offsets,
  responses,
  weights,
  B = self$model_par$B,
  Omega = self$model_par$Omega,
  control = PLN_param(backend = "nlopt")
)
Arguments
covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily-class

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

weights

an optional vector of observation weights to be used in the fitting process.

B

Optional fixed value of the regression parameters

Omega

precision matrix of the latent variables. Inverse of Sigma.

control

a list-like structure for controlling the fit, see PLN_param().

Sigma

variance-covariance matrix of the latent variables

Returns

A list with three components:

  • the matrix M of variational means,

  • the matrix S2 of variational variances

  • the vector log.lik of (variational) log-likelihood of each new observation

Method postTreatment()

Update R2, fisher and std_err fields after optimization

Usage
PLNfit$postTreatment(
  responses,
  covariates,
  offsets,
  weights = rep(1, nrow(responses)),
  config_post,
  config_optim,
  nullModel = NULL
)
Arguments
responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily-class

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

weights

an optional vector of observation weights to be used in the fitting process.

config_post

a list for controlling the post-treatments (optional bootstrap, jackknife, R2, etc.). See details

config_optim

a list for controlling the optimization (optional bootstrap, jackknife, R2, etc.). See details

nullModel

null model used for approximate R2 computations. Defaults to a GLM model with same design matrix but not latent variable.

Details

The list of parameters config controls the post-treatment processing, with the following entries:

  • jackknife boolean indicating whether jackknife should be performed to evaluate bias and variance of the model parameters. Default is FALSE.

  • bootstrap integer indicating the number of bootstrap resamples generated to evaluate the variance of the model parameters. Default is 0 (inactivated).

  • variational_var boolean indicating whether variational Fisher information matrix should be computed to estimate the variance of the model parameters (highly underestimated). Default is FALSE.

  • sandwich_var boolean indicating whether sandwich estimator should be computed to estimate the variance of the model parameters (highly underestimated). Default is FALSE.

  • trace integer for verbosity. should be > 1 to see output in post-treatments

Method predict()

Predict position, scores or observations of new data.

Usage
PLNfit$predict(
  newdata,
  responses = NULL,
  type = c("link", "response"),
  level = 1,
  envir = parent.frame()
)
Arguments
newdata

A data frame in which to look for variables with which to predict. If omitted, the fitted values are used.

responses

Optional data frame containing the count of the observed variables (matching the names of the provided as data in the PLN function), assuming the interest is in testing the model.

type

Scale used for the prediction. Either link (default, predicted positions in the latent space) or response (predicted counts).

level

Optional integer value the level to be used in obtaining the predictions. Level zero corresponds to the population predictions (default if responses is not provided) while level one (default) corresponds to predictions after evaluating the variational parameters for the new data.

envir

Environment in which the prediction is evaluated

Details

Note that level = 1 can only be used if responses are provided, as the variational parameters can't be estimated otherwise. In the absence of responses, level is ignored and the fitted values are returned

Returns

A matrix with predictions scores or counts.

Method predict_cond()

Predict position, scores or observations of new data, conditionally on the observation of a (set of) variables

Usage
PLNfit$predict_cond(
  newdata,
  cond_responses,
  type = c("link", "response"),
  var_par = FALSE,
  envir = parent.frame()
)
Arguments
newdata

a data frame containing the covariates of the sites where to predict

cond_responses

a data frame containing the count of the observed variables (matching the names of the provided as data in the PLN function)

type

Scale used for the prediction. Either link (default, predicted positions in the latent space) or response (predicted counts).

var_par

Boolean. Should new estimations of the variational parameters of mean and variance be sent back, as attributes of the matrix of predictions. Default to FALSE.

envir

Environment in which the prediction is evaluated

Returns

A matrix with predictions scores or counts.

Method show()

User friendly print method

Usage
PLNfit$show(
  model = paste("A multivariate Poisson Lognormal fit with", self$vcov_model,
    "covariance model.\n")
)
Arguments
model

First line of the print output

Method print()

User friendly print method

Usage
PLNfit$print()

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNfit$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLN(Abundance ~ 1, data = trichoptera)
class(myPLN)
print(myPLN)

## End(Not run)

An R6 Class to represent a PLNfit in a standard, general framework, with diagonal residual covariance

Description

The function PLNLDA() produces an instance of an object with class PLNLDAfit.

This class comes with a set of methods, some of them being useful for the user: See the documentation for the methods inherited by PLNfit(), the plot() method for LDA visualization and predict() method for prediction

Super class

PLNmodels::PLNfit -> PLNfit_diagonal

Active bindings

nb_param

number of parameters in the current PLN model

vcov_model

character: the model used for the residual covariance

Methods

Public methods

Inherited methods

Method new()

Initialize a PLNfit model

Usage
PLNfit_diagonal$new(responses, covariates, offsets, weights, formula, control)
Arguments
responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily-class

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

weights

an optional vector of observation weights to be used in the fitting process.

formula

model formula used for fitting, extracted from the formula in the upper-level call

control

a list for controlling the optimization. See details.

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNfit_diagonal$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Super classes

PLNmodels::PLNfit -> PLNmodels::PLNLDAfit -> PLNLDAfit_spherical

Active bindings

vcov_model

character: the model used for the residual covariance

nb_param

number of parameters in the current PLN model

Methods

Public methods

Inherited methods

Method new()

Initialize a PLNfit model

Usage
PLNLDAfit_spherical$new(
  grouping,
  responses,
  covariates,
  offsets,
  weights,
  formula,
  control
)
Arguments
grouping

a factor specifying the class of each observation used for discriminant analysis.

responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily-class

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

weights

an optional vector of observation weights to be used in the fitting process.

formula

model formula used for fitting, extracted from the formula in the upper-level call

control

a list for controlling the optimization. See details.

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNLDAfit_spherical$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLN(Abundance ~ 1, data = trichoptera)
class(myPLN)
print(myPLN)

## End(Not run)
## Not run: 
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLNLDA <- PLNLDA(Abundance ~ 1, data = trichoptera, control = PLN_param(covariance = "spherical"))
class(myPLNLDA)
print(myPLNLDA)

## End(Not run)

An R6 Class to represent a PLNfit in a standard, general framework, with fixed (inverse) residual covariance

Description

An R6 Class to represent a PLNfit in a standard, general framework, with fixed (inverse) residual covariance

An R6 Class to represent a PLNfit in a standard, general framework, with fixed (inverse) residual covariance

Super class

PLNmodels::PLNfit -> PLNfit_fixedcov

Active bindings

nb_param

number of parameters in the current PLN model

vcov_model

character: the model used for the residual covariance

vcov_coef

matrix of sandwich estimator of the variance-covariance of B (needs known covariance at the moment)

Methods

Public methods

Inherited methods

Method new()

Initialize a PLNfit model

Usage
PLNfit_fixedcov$new(responses, covariates, offsets, weights, formula, control)
Arguments
responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily-class

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

weights

an optional vector of observation weights to be used in the fitting process.

formula

model formula used for fitting, extracted from the formula in the upper-level call

control

a list for controlling the optimization. See details.

Method optimize()

Call to the NLopt or TORCH optimizer and update of the relevant fields

Usage
PLNfit_fixedcov$optimize(responses, covariates, offsets, weights, config)
Arguments
responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily-class

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

weights

an optional vector of observation weights to be used in the fitting process.

config

part of the control argument which configures the optimizer

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNfit_fixedcov$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLN(Abundance ~ 1, data = trichoptera)
class(myPLN)
print(myPLN)

## End(Not run)

An R6 Class to represent a PLNfit in a standard, general framework, with spherical residual covariance

Description

An R6 Class to represent a PLNfit in a standard, general framework, with spherical residual covariance

An R6 Class to represent a PLNfit in a standard, general framework, with spherical residual covariance

Super class

PLNmodels::PLNfit -> PLNfit_spherical

Active bindings

nb_param

number of parameters in the current PLN model

vcov_model

character: the model used for the residual covariance

Methods

Public methods

Inherited methods

Method new()

Initialize a PLNfit model

Usage
PLNfit_spherical$new(responses, covariates, offsets, weights, formula, control)
Arguments
responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily-class

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

weights

an optional vector of observation weights to be used in the fitting process.

formula

model formula used for fitting, extracted from the formula in the upper-level call

control

a list for controlling the optimization. See details.

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNfit_spherical$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLN(Abundance ~ 1, data = trichoptera)
class(myPLN)
print(myPLN)

## End(Not run)

Poisson lognormal model towards Linear Discriminant Analysis

Description

Fit the Poisson lognormal for LDA with a variational algorithm. Use the (g)lm syntax for model specification (covariates, offsets).

Usage

PLNLDA(formula, data, subset, weights, grouping, control = PLN_param())

Arguments

formula

an object of class "formula": a symbolic description of the model to be fitted.
data

an optional data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model. If not found in data, the variables are taken from environment(formula), typically the environment from which lm is called.
subset

an optional vector specifying a subset of observations to be used in the fitting process.
weights

an optional vector of observation weights to be used in the fitting process.
grouping

a factor specifying the class of each observation used for discriminant analysis.
control

a list-like structure for controlling the optimization, with default generated by PLN_param(). See the associated documentation

Details

The parameter control is a list controlling the optimization with the following entries:

  • "covariance" character setting the model for the covariance matrix. Either "full" or "spherical". Default is "full".

  • "trace" integer for verbosity.

  • "inception" Set up the initialization. By default, the model is initialized with a multivariate linear model applied on log-transformed data. However, the user can provide a PLNfit (typically obtained from a previous fit), which often speed up the inference.

  • "ftol_rel" stop when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 1e-8

  • "ftol_abs" stop when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 0

  • "xtol_rel" stop when an optimization step changes every parameters by less than xtol multiplied by the absolute value of the parameter. Default is 1e-6

  • "xtol_abs" stop when an optimization step changes every parameters by less than xtol multiplied by the absolute value of the parameter. Default is 0

  • "maxeval" stop when the number of iteration exceeds maxeval. Default is 10000

  • "maxtime" stop when the optimization time (in seconds) exceeds maxtime. Default is -1 (no restriction)

  • "algorithm" the optimization method used by NLOPT among LD type, i.e. "CCSAQ", "MMA", "LBFGS", "VAR1", "VAR2". See NLOPT documentation for further details. Default is "CCSAQ".

Value

an R6 object with class PLNLDAfit()

See Also

The class PLNLDAfit

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLNLDA <- PLNLDA(Abundance ~ 1, grouping = Group, data = trichoptera)

Control of a PLNLDA fit

Description

Helper to define list of parameters to control the PLNLDA fit. All arguments have defaults.

Usage

PLNLDA_param(
  backend = c("nlopt", "torch"),
  trace = 1,
  covariance = c("full", "diagonal", "spherical"),
  config_post = list(),
  config_optim = list(),
  inception = NULL
)

Arguments

backend

optimization back used, either "nlopt" or "torch". Default is "nlopt"
trace

a integer for verbosity.
covariance

character setting the model for the covariance matrix. Either "full", "diagonal" or "spherical". Default is "full".
config_post

a list for controlling the post-treatments (optional bootstrap, jackknife, R2, etc.). See details
config_optim

a list for controlling the optimizer (either "nlopt" or "torch" backend). See details
inception

Set up the parameters initialization: by default, the model is initialized with a multivariate linear model applied on log-transformed data, and with the same formula as the one provided by the user. However, the user can provide a PLNfit (typically obtained from a previous fit), which sometimes speeds up the inference.

Details

The list of parameters config_optim controls the optimizers. When "nlopt" is chosen the following entries are relevant

  • "algorithm" the optimization method used by NLOPT among LD type, e.g. "CCSAQ", "MMA", "LBFGS". See NLOPT documentation for further details. Default is "CCSAQ".

  • "maxeval" stop when the number of iteration exceeds maxeval. Default is 10000

  • "ftol_rel" stop when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 1e-8

  • "xtol_rel" stop when an optimization step changes every parameters by less than xtol multiplied by the absolute value of the parameter. Default is 1e-6

  • "ftol_abs" stop when an optimization step changes the objective function by less than ftol_abs. Default is 0.0 (disabled)

  • "xtol_abs" stop when an optimization step changes every parameters by less than xtol_abs. Default is 0.0 (disabled)

  • "maxtime" stop when the optimization time (in seconds) exceeds maxtime. Default is -1 (disabled)

When "torch" backend is used (only for PLN and PLNLDA for now), the following entries are relevant:

  • "algorithm" the optimizer used by torch among RPROP (default), RMSPROP, ADAM and ADAGRAD

  • "maxeval" stop when the number of iteration exceeds maxeval. Default is 10 000

  • "numepoch" stop training once this number of epochs exceeds numepoch. Set to -1 to enable infinite training. Default is 1 000

  • "num_batch" number of batches to use during training. Defaults to 1 (use full dataset at each epoch)

  • "ftol_rel" stop when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 1e-8

  • "xtol_rel" stop when an optimization step changes every parameters by less than xtol multiplied by the absolute value of the parameter. Default is 1e-6

  • "lr" learning rate. Default is 0.1.

  • "momentum" momentum factor. Default is 0 (no momentum). Only used in RMSPROP

  • "weight_decay" Weight decay penalty. Default is 0 (no decay). Not used in RPROP

  • "step_sizes" pair of minimal (default: 1e-6) and maximal (default: 50) allowed step sizes. Only used in RPROP

  • "etas" pair of multiplicative increase and decrease factors. Default is (0.5, 1.2). Only used in RPROP

  • "centered" if TRUE, compute the centered RMSProp where the gradient is normalized by an estimation of its variance weight_decay (L2 penalty). Default to FALSE. Only used in RMSPROP

The list of parameters config_post controls the post-treatment processing (for most ⁠PLN*()⁠ functions), with the following entries (defaults may vary depending on the specific function, check ⁠config_post_default_*⁠ for defaults values):

  • jackknife boolean indicating whether jackknife should be performed to evaluate bias and variance of the model parameters. Default is FALSE.

  • bootstrap integer indicating the number of bootstrap resamples generated to evaluate the variance of the model parameters. Default is 0 (inactivated).

  • variational_var boolean indicating whether variational Fisher information matrix should be computed to estimate the variance of the model parameters (highly underestimated). Default is FALSE.

  • sandwich_var boolean indicating whether sandwich estimation should be used to estimate the variance of the model parameters (highly underestimated). Default is FALSE.

  • rsquared boolean indicating whether approximation of R2 based on deviance should be computed. Default is TRUE

Value

list of parameters configuring the fit.

An R6 Class to represent a PLNfit in a LDA framework

Description

The function PLNLDA() produces an instance of an object with class PLNLDAfit.

This class comes with a set of methods, some of them being useful for the user: See the documentation for the methods inherited by PLNfit(), the plot() method for LDA visualization and predict() method for prediction

Super class

PLNmodels::PLNfit -> PLNLDAfit

Active bindings

rank

the dimension of the current model

nb_param

number of parameters in the current PLN model

model_par

a list with the matrices associated with the estimated parameters of the PLN model: B (covariates), Sigma (latent covariance), C (latent loadings), P (latent position) and Mu (group means)

percent_var

the percent of variance explained by each axis

corr_map

a matrix of correlations to plot the correlation circles

scores

a matrix of scores to plot the individual factor maps

group_means

a matrix of group mean vectors in the latent space.

Methods

Public methods

Inherited methods

Method new()

Initialize a PLNLDAfit object

Usage
PLNLDAfit$new(
  grouping,
  responses,
  covariates,
  offsets,
  weights,
  formula,
  control
)
Arguments
grouping

a factor specifying the class of each observation used for discriminant analysis.

responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily-class

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

weights

an optional vector of observation weights to be used in the fitting process.

formula

model formula used for fitting, extracted from the formula in the upper-level call

control

list controlling the optimization and the model

Method optimize()

Compute group means and axis of the LDA (noted B in the model) in the latent space, update corresponding fields

Usage
PLNLDAfit$optimize(grouping, responses, covariates, offsets, weights, config)
Arguments
grouping

a factor specifying the class of each observation used for discriminant analysis.

responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

covariates

design matrix. Automatically built from the covariates and the formula from the call

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

weights

an optional vector of observation weights to be used in the fitting process.

config

list controlling the optimization

X

Abundance matrix.

Method postTreatment()

Update R2, fisher and std_err fields and visualization

Usage
PLNLDAfit$postTreatment(
  grouping,
  responses,
  covariates,
  offsets,
  config_post,
  config_optim
)
Arguments
grouping

a factor specifying the class of each observation used for discriminant analysis.

responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily-class

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

config_post

a list for controlling the post-treatments (optional bootstrap, jackknife, R2, etc.).

config_optim

list controlling the optimization parameters

Method setVisualization()

Compute LDA scores in the latent space and update corresponding fields.

Usage
PLNLDAfit$setVisualization(scale.unit = FALSE)
Arguments
scale.unit

Logical. Should LDA scores be rescaled to have unit variance

Method plot_individual_map()

Plot the factorial map of the LDA

Usage
PLNLDAfit$plot_individual_map(
  axes = 1:min(2, self$rank),
  main = "Individual Factor Map",
  plot = TRUE
)
Arguments
axes

numeric, the axes to use for the plot when map = "individual" or "variable". Default it c(1,min(rank))

main

character. A title for the single plot (individual or variable factor map). If NULL (the default), an hopefully appropriate title will be used.

plot

logical. Should the plot be displayed or sent back as ggplot object

Returns

a ggplot2::ggplot graphic

Method plot_correlation_map()

Plot the correlation circle of a specified axis for a PLNLDAfit object

Usage
PLNLDAfit$plot_correlation_map(
  axes = 1:min(2, self$rank),
  main = "Variable Factor Map",
  cols = "default",
  plot = TRUE
)
Arguments
axes

numeric, the axes to use for the plot when map = "individual" or "variable". Default it c(1,min(rank))

main

character. A title for the single plot (individual or variable factor map). If NULL (the default), an hopefully appropriate title will be used.

cols

a character, factor or numeric to define the color associated with the variables. By default, all variables receive the default color of the current palette.

plot

logical. Should the plot be displayed or sent back as ggplot object

Returns

a ggplot2::ggplot graphic

Method plot_LDA()

Plot a summary of the PLNLDAfit object

Usage
PLNLDAfit$plot_LDA(
  nb_axes = min(3, self$rank),
  var_cols = "default",
  plot = TRUE
)
Arguments
nb_axes

scalar: the number of axes to be considered when map = "both". The default is min(3,rank).

var_cols

a character, factor or numeric to define the color associated with the variables. By default, all variables receive the default color of the current palette.

plot

logical. Should the plot be displayed or sent back as ggplot object

Returns

a grob object

Method predict()

Predict group of new samples

Usage
PLNLDAfit$predict(
  newdata,
  type = c("posterior", "response", "scores"),
  scale = c("log", "prob"),
  prior = NULL,
  control = PLN_param(backend = "nlopt"),
  envir = parent.frame()
)
Arguments
newdata

A data frame in which to look for variables, offsets and counts with which to predict.

type

The type of prediction required. The default are posterior probabilities for each group (in either unnormalized log-scale or natural probabilities, see "scale" for details), "response" is the group with maximal posterior probability and "scores" is the average score along each separation axis in the latent space, with weights equal to the posterior probabilities.

scale

The scale used for the posterior probability. Either log-scale ("log", default) or natural probabilities summing up to 1 ("prob").

prior

User-specified prior group probabilities in the new data. If NULL (default), prior probabilities are computed from the learning set.

control

a list for controlling the optimization. See PLN() for details.

envir

Environment in which the prediction is evaluated

Method show()

User friendly print method

Usage
PLNLDAfit$show()

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNLDAfit$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

The function PLNLDA.

Examples

## Not run: 
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLNLDA <- PLNLDA(Abundance ~ 1, grouping = Group, data = trichoptera)
class(myPLNLDA)
print(myPLNLDA)

## End(Not run)

An R6 Class to represent a PLNfit in a LDA framework with diagonal covariance

Description

The function PLNLDA() produces an instance of an object with class PLNLDAfit.

This class comes with a set of methods, some of them being useful for the user: See the documentation for the methods inherited by PLNfit(), the plot() method for LDA visualization and predict() method for prediction

Super classes

PLNmodels::PLNfit -> PLNmodels::PLNLDAfit -> PLNLDAfit_diagonal

Active bindings

vcov_model

character: the model used for the residual covariance

nb_param

number of parameters in the current PLN model

Methods

Public methods

Inherited methods

Method new()

Initialize a PLNfit model

Usage
PLNLDAfit_diagonal$new(
  grouping,
  responses,
  covariates,
  offsets,
  weights,
  formula,
  control
)
Arguments
grouping

a factor specifying the class of each observation used for discriminant analysis.

responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily-class

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily-class

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily-class

weights

an optional vector of observation weights to be used in the fitting process.

formula

model formula used for fitting, extracted from the formula in the upper-level call

control

a list for controlling the optimization. See details.

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNLDAfit_diagonal$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLNLDA <- PLNLDA(Abundance ~ 1, data = trichoptera, control = PLN_param(covariance = "diagonal"))
class(myPLNLDA)
print(myPLNLDA)

## End(Not run)

Poisson lognormal mixture model

Description

Fit the mixture variants of the Poisson lognormal with a variational algorithm. Use the (g)lm syntax for model specification (covariates, offsets).

Usage

PLNmixture(formula, data, subset, clusters = 1:5, control = PLNmixture_param())

Arguments

formula

an object of class "formula": a symbolic description of the model to be fitted.
data

an optional data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model. If not found in data, the variables are taken from environment(formula), typically the environment from which lm is called.
subset

an optional vector specifying a subset of observations to be used in the fitting process.
clusters

a vector of integer containing the successive number of clusters (or components) to be considered
control

a list-like structure for controlling the optimization, with default generated by PLNmixture_param(). See the associated documentation for details.

Value

an R6 object with class PLNmixturefamily, which contains a collection of models with class PLNmixturefit

See Also

The classes PLNmixturefamily, PLNmixturefit and PLNmixture_param()

Examples

## Use future to dispatch the computations on 2 workers
## Not run: 
future::plan("multisession", workers = 2)

## End(Not run)

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myMixtures <- PLNmixture(Abundance ~ 1 + offset(log(Offset)), clusters = 1:4, data = trichoptera,
                         control = PLNmixture_param(smoothing = 'none'))

# Shut down parallel workers
## Not run: 
future::plan("sequential")

## End(Not run)

Control of a PLNmixture fit

Description

Helper to define list of parameters to control the PLNmixture fit. All arguments have defaults.

Usage

PLNmixture_param(
  backend = "nlopt",
  trace = 1,
  covariance = "spherical",
  init_cl = "kmeans",
  smoothing = "both",
  config_optim = list(),
  config_post = list(),
  inception = NULL
)

Arguments

backend

optimization back used, either "nlopt" or "torch". Default is "nlopt"
trace

a integer for verbosity.
covariance

character setting the model for the covariance matrices of the mixture components. Either "full", "diagonal" or "spherical". Default is "spherical".
init_cl

The initial clustering to apply. Either, 'kmeans', CAH' or a user defined clustering given as a list of clusterings, the size of which is equal to the number of clusters considered. Default is 'kmeans'.
smoothing

The smoothing to apply. Either, 'none', forward', 'backward' or 'both'. Default is 'both'.
config_optim

a list for controlling the optimizer (either "nlopt" or "torch" backend). See details
config_post

a list for controlling the post-treatments (optional bootstrap, jackknife, R2, etc.).
inception

Set up the parameters initialization: by default, the model is initialized with a multivariate linear model applied on log-transformed data, and with the same formula as the one provided by the user. However, the user can provide a PLNfit (typically obtained from a previous fit), which sometimes speeds up the inference.

Details

See PLN_param() for a full description of the generic optimization parameters. PLNmixture_param() also has additional parameters controlling the optimization due the inner-outer loop structure of the optimizer:

  • "ftol_out" outer solver stops when an optimization step changes the objective function by less than xtol multiplied by the absolute value of the parameter. Default is 1e-6

  • "maxit_out" outer solver stops when the number of iteration exceeds maxit_out. Default is 50

  • "it_smoothing" number of the iterations of the smoothing procedure. Default is 1.

Value

list of parameters configuring the fit.

See Also

PLN_param()

An R6 Class to represent a collection of PLNmixturefit

Description

The function PLNmixture() produces an instance of this class.

This class comes with a set of methods, some of them being useful for the user: See the documentation for getBestModel(), getModel() and plot().

Super class

PLNmodels::PLNfamily -> PLNmixturefamily

Active bindings

clusters

vector indicating the number of clusters considered is the successively fitted models

Methods

Public methods

Inherited methods

Method new()

helper function for forward smoothing: split a group

Initialize all models in the collection.

Usage
PLNmixturefamily$new(
  clusters,
  responses,
  covariates,
  offsets,
  formula,
  control
)
Arguments
clusters

the dimensions of the successively fitted models

responses

the matrix of responses common to every models

covariates

the matrix of covariates common to every models

offsets

the matrix of offsets common to every models

formula

model formula used for fitting, extracted from the formula in the upper-level call

control

a list for controlling the optimization. See details.

control

a list for controlling the optimization. See details.

Method optimize()

Call to the optimizer on all models of the collection

Usage
PLNmixturefamily$optimize(config)
Arguments
config

a list for controlling the optimization

Method smooth()

function to restart clustering to avoid local minima by smoothing the loglikelihood values as a function of the number of clusters

Usage
PLNmixturefamily$smooth(control)
Arguments
control

a list to control the smoothing process

Method plot()

Lineplot of selected criteria for all models in the collection

Usage
PLNmixturefamily$plot(criteria = c("loglik", "BIC", "ICL"), reverse = FALSE)
Arguments
criteria

A valid model selection criteria for the collection of models. Any of "loglik", "BIC" or "ICL" (all).

reverse

A logical indicating whether to plot the value of the criteria in the "natural" direction (loglik - 0.5 penalty) or in the "reverse" direction (-2 loglik + penalty). Default to FALSE, i.e use the natural direction, on the same scale as the log-likelihood..

Returns

A ggplot2::ggplot object

Method plot_objective()

Plot objective value of the optimization problem along the penalty path

Usage
PLNmixturefamily$plot_objective()
Returns

a ggplot2::ggplot graph

Method getBestModel()

Extract best model in the collection

Usage
PLNmixturefamily$getBestModel(crit = c("BIC", "ICL", "loglik"))
Arguments
crit

a character for the criterion used to performed the selection. Either "BIC", "ICL" or "loglik". Default is ICL

Returns

a PLNmixturefit object

Method show()

User friendly print method

Usage
PLNmixturefamily$show()

Method print()

User friendly print method

Usage
PLNmixturefamily$print()

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNmixturefamily$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

The function PLNmixture, the class PLNmixturefit

An R6 Class to represent a PLNfit in a mixture framework

Description

The function PLNmixture produces a collection of models which are instances of object with class PLNmixturefit. A PLNmixturefit (say, with k components) is itself a collection of k PLNfit.

This class comes with a set of methods, some of them being useful for the user: See the documentation for ...

Active bindings

n

number of samples

p

number of dimensions of the latent space

k

number of components

d

number of covariates

components

components of the mixture (PLNfits)

latent

a matrix: values of the latent vector (Z in the model)

latent_pos

a matrix: values of the latent position vector (Z) without covariates effects or offset

posteriorProb

matrix ofposterior probability for cluster belonging

memberships

vector for cluster index

mixtureParam

vector of cluster proportions

optim_par

a list with parameters useful for monitoring the optimization

nb_param

number of parameters in the current PLN model

entropy_clustering

Entropy of the variational distribution of the cluster (multinomial)

entropy_latent

Entropy of the variational distribution of the latent vector (Gaussian)

entropy

Full entropy of the variational distribution (latent vector + clustering)

loglik

variational lower bound of the loglikelihood

loglik_vec

element-wise variational lower bound of the loglikelihood

BIC

variational lower bound of the BIC

ICL

variational lower bound of the ICL (include entropy of both the clustering and latent distributions)

R_squared

approximated goodness-of-fit criterion

criteria

a vector with loglik, BIC, ICL, and number of parameters

model_par

a list with the matrices of parameters found in the model (Theta, Sigma, Mu and Pi)

vcov_model

character: the model used for the covariance (either "spherical", "diagonal" or "full")

fitted

a matrix: fitted values of the observations (A in the model)

group_means

a matrix of group mean vectors in the latent space.

Methods

Public methods

Method new()

Optimize a the

Initialize a PLNmixturefit model

Usage
PLNmixturefit$new(
  responses,
  covariates,
  offsets,
  posteriorProb,
  formula,
  control
)
Arguments
responses

the matrix of responses common to every models

covariates

the matrix of covariates common to every models

offsets

the matrix of offsets common to every models

posteriorProb

matrix ofposterior probability for cluster belonging

formula

model formula used for fitting, extracted from the formula in the upper-level call

control

a list for controlling the optimization.

Method optimize()

Optimize a PLNmixturefit model

Usage
PLNmixturefit$optimize(responses, covariates, offsets, config)
Arguments
responses

the matrix of responses common to every models

covariates

the matrix of covariates common to every models

offsets

the matrix of offsets common to every models

config

a list for controlling the optimization

Method predict()

Predict group of new samples

Usage
PLNmixturefit$predict(
  newdata,
  type = c("posterior", "response", "position"),
  prior = matrix(rep(1/self$k, self$k), nrow(newdata), self$k, byrow = TRUE),
  control = PLNmixture_param(),
  envir = parent.frame()
)
Arguments
newdata

A data frame in which to look for variables, offsets and counts with which to predict.

type

The type of prediction required. The default posterior are posterior probabilities for each group , response is the group with maximal posterior probability and latent is the averaged latent coordinate (without offset and nor covariate effects), with weights equal to the posterior probabilities.

prior

User-specified prior group probabilities in the new data. The default uses a uniform prior.

control

a list-like structure for controlling the fit. See PLNmixture_param() for details.

envir

Environment in which the prediction is evaluated

Method plot_clustering_data()

Plot the matrix of expected mean counts (without offsets, without covariate effects) reordered according the inferred clustering

Usage
PLNmixturefit$plot_clustering_data(
  main = "Expected counts reorder by clustering",
  plot = TRUE,
  log_scale = TRUE
)
Arguments
main

character. A title for the plot. An hopefully appropriate title will be used by default.

plot

logical. Should the plot be displayed or sent back as ggplot2::ggplot object

log_scale

logical. Should the color scale values be log-transform before plotting? Default is TRUE.

Returns

a ggplot2::ggplot graphic

Method plot_clustering_pca()

Plot the individual map of a PCA performed on the latent coordinates, where individuals are colored according to the memberships

Usage
PLNmixturefit$plot_clustering_pca(
  main = "Clustering labels in Individual Factor Map",
  plot = TRUE
)
Arguments
main

character. A title for the plot. An hopefully appropriate title will be used by default.

plot

logical. Should the plot be displayed or sent back as ggplot2::ggplot object

Returns

a ggplot2::ggplot graphic

Method postTreatment()

Update fields after optimization

Usage
PLNmixturefit$postTreatment(
  responses,
  covariates,
  offsets,
  weights,
  config_post,
  config_optim,
  nullModel
)
Arguments
responses

the matrix of responses common to every models

covariates

the matrix of covariates common to every models

offsets

the matrix of offsets common to every models

weights

an optional vector of observation weights to be used in the fitting process.

config_post

a list for controlling the post-treatment

config_optim

a list for controlling the optimization during the post-treatment computations

nullModel

null model used for approximate R2 computations. Defaults to a GLM model with same design matrix but not latent variable.

Method show()

User friendly print method

Usage
PLNmixturefit$show()

Method print()

User friendly print method

Usage
PLNmixturefit$print()

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNmixturefit$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

The function PLNmixture, the class PLNmixturefamily

Sparse Poisson lognormal model for network inference

Description

Perform sparse inverse covariance estimation for the Zero Inflated Poisson lognormal model using a variational algorithm. Iterate over a range of logarithmically spaced sparsity parameter values. Use the (g)lm syntax to specify the model (including covariates and offsets).

Usage

PLNnetwork(
  formula,
  data,
  subset,
  weights,
  penalties = NULL,
  control = PLNnetwork_param()
)

Arguments

formula

an object of class "formula": a symbolic description of the model to be fitted.
data

an optional data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model. If not found in data, the variables are taken from environment(formula), typically the environment from which lm is called.
subset

an optional vector specifying a subset of observations to be used in the fitting process.
weights

an optional vector of observation weights to be used in the fitting process.
penalties

an optional vector of positive real number controlling the level of sparsity of the underlying network. if NULL (the default), will be set internally. See PLNnetwork_param() for additional tuning of the penalty.
control

a list-like structure for controlling the optimization, with default generated by PLNnetwork_param(). See the corresponding documentation for details;

Value

an R6 object with class PLNnetworkfamily, which contains a collection of models with class PLNnetworkfit

See Also

The classes PLNnetworkfamily and PLNnetworkfit, and the and the configuration function PLNnetwork_param().

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)

Control of PLNnetwork fit

Description

Helper to define list of parameters to control the PLN fit. All arguments have defaults.

Usage

PLNnetwork_param(
  backend = c("nlopt", "torch"),
  inception_cov = c("full", "spherical", "diagonal"),
  trace = 1,
  n_penalties = 30,
  min_ratio = 0.1,
  penalize_diagonal = TRUE,
  penalty_weights = NULL,
  config_post = list(),
  config_optim = list(),
  inception = NULL
)

Arguments

backend

optimization back used, either "nlopt" or "torch". Default is "nlopt"
inception_cov

Covariance structure used for the inception model used to initialize the PLNfamily. Defaults to "full" and can be constrained to "diagonal" and "spherical".
trace

a integer for verbosity.
n_penalties

an integer that specifies the number of values for the penalty grid when internally generated. Ignored when penalties is non NULL
min_ratio

the penalty grid ranges from the minimal value that produces a sparse to this value multiplied by min_ratio. Default is 0.1.
penalize_diagonal

boolean: should the diagonal terms be penalized in the graphical-Lasso? Default is TRUE
penalty_weights

either a single or a list of p x p matrix of weights (default: all weights equal to 1) to adapt the amount of shrinkage to each pairs of node. Must be symmetric with positive values.
config_post

a list for controlling the post-treatment (optional bootstrap, jackknife, R2, etc).
config_optim

a list for controlling the optimizer (either "nlopt" or "torch" backend). See details
inception

Set up the parameters initialization: by default, the model is initialized with a multivariate linear model applied on log-transformed data, and with the same formula as the one provided by the user. However, the user can provide a PLNfit (typically obtained from a previous fit), which sometimes speeds up the inference.

Details

See PLN_param() for a full description of the generic optimization parameters. PLNnetwork_param() also has two additional parameters controlling the optimization due the inner-outer loop structure of the optimizer:

  • "ftol_out" outer solver stops when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 1e-6

  • "maxit_out" outer solver stops when the number of iteration exceeds maxit_out. Default is 50

Value

list of parameters configuring the fit.

See Also

PLN_param()

An R6 Class to represent a collection of PLNnetworkfits

Description

The function PLNnetwork() produces an instance of this class.

This class comes with a set of methods mostly used to compare network fits (in terms of goodness of fit) or extract one from the family (based on penalty parameter and/or goodness of it). See the documentation for getBestModel(), getModel() and plot() for the user-facing ones.

Super classes

PLNmodels::PLNfamily -> PLNmodels::Networkfamily -> PLNnetworkfamily

Methods

Public methods

Inherited methods

Method new()

Initialize all models in the collection

Usage
PLNnetworkfamily$new(penalties, data, control)
Arguments
penalties

a vector of positive real number controlling the level of sparsity of the underlying network.

data

a named list used internally to carry the data matrices

control

a list for controlling the optimization.

Returns

Update current PLNnetworkfit with smart starting values

Method stability_selection()

Compute the stability path by stability selection

Usage
PLNnetworkfamily$stability_selection(
  subsamples = NULL,
  control = PLNnetwork_param()
)
Arguments
subsamples

a list of vectors describing the subsamples. The number of vectors (or list length) determines the number of subsamples used in the stability selection. Automatically set to 20 subsamples with size 10*sqrt(n) if n >= 144 and 0.8*n otherwise following Liu et al. (2010) recommendations.

control

a list controlling the main optimization process in each call to PLNnetwork(). See PLNnetwork() and PLN_param() for details.

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNnetworkfamily$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

The function PLNnetwork(), the class PLNnetworkfit

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
class(fits)

An R6 Class to represent a PLNfit in a sparse inverse covariance framework

Description

The function PLNnetwork() produces a collection of models which are instances of object with class PLNnetworkfit. This class comes with a set of methods, some of them being useful for the user: See the documentation for plot() and methods inherited from PLNfit.

Super classes

PLNmodels::PLNfit -> PLNmodels::PLNfit_fixedcov -> PLNnetworkfit

Active bindings

vcov_model

character: the model used for the residual covariance

penalty

the global level of sparsity in the current model

penalty_weights

a matrix of weights controlling the amount of penalty element-wise.

n_edges

number of edges if the network (non null coefficient of the sparse precision matrix)

nb_param

number of parameters in the current PLN model

pen_loglik

variational lower bound of the l1-penalized loglikelihood

EBIC

variational lower bound of the EBIC

density

proportion of non-null edges in the network

criteria

a vector with loglik, penalized loglik, BIC, EBIC, ICL, R_squared, number of parameters, number of edges and graph density

Methods

Public methods

Inherited methods

Method new()

Initialize a PLNnetworkfit object

Usage
PLNnetworkfit$new(data, control)
Arguments
data

a named list used internally to carry the data matrices

control

a list for controlling the optimization.

Method optimize()

Call to the C++ optimizer and update of the relevant fields

Usage
PLNnetworkfit$optimize(data, config)
Arguments
data

a named list used internally to carry the data matrices

config

a list for controlling the optimization

Method latent_network()

Extract interaction network in the latent space

Usage
PLNnetworkfit$latent_network(type = c("partial_cor", "support", "precision"))
Arguments
type

edge value in the network. Can be "support" (binary edges), "precision" (coefficient of the precision matrix) or "partial_cor" (partial correlation between species)

Returns

a square matrix of size PLNnetworkfit$n

Method plot_network()

plot the latent network.

Usage
PLNnetworkfit$plot_network(
  type = c("partial_cor", "support"),
  output = c("igraph", "corrplot"),
  edge.color = c("#F8766D", "#00BFC4"),
  remove.isolated = FALSE,
  node.labels = NULL,
  layout = layout_in_circle,
  plot = TRUE
)
Arguments
type

edge value in the network. Either "precision" (coefficient of the precision matrix) or "partial_cor" (partial correlation between species).

output

Output type. Either igraph (for the network) or corrplot (for the adjacency matrix)

edge.color

Length 2 color vector. Color for positive/negative edges. Default is c("#F8766D", "#00BFC4"). Only relevant for igraph output.

remove.isolated

if TRUE, isolated node are remove before plotting. Only relevant for igraph output.

node.labels

vector of character. The labels of the nodes. The default will use the column names ot the response matrix.

layout

an optional igraph layout. Only relevant for igraph output.

plot

logical. Should the final network be displayed or only sent back to the user. Default is TRUE.

Method show()

User friendly print method

Usage
PLNnetworkfit$show()

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNnetworkfit$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

The function PLNnetwork(), the class PLNnetworkfamily

Examples

## Not run: 
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
nets <- PLNnetwork(Abundance ~ 1, data = trichoptera)
myPLNnet <- getBestModel(nets)
class(myPLNnet)
print(myPLNnet)

## End(Not run)

Poisson lognormal model towards Principal Component Analysis

Description

Fit the PCA variants of the Poisson lognormal with a variational algorithm. Use the (g)lm syntax for model specification (covariates, offsets).

Usage

PLNPCA(formula, data, subset, weights, ranks = 1:5, control = PLNPCA_param())

Arguments

formula

an object of class "formula": a symbolic description of the model to be fitted.
data

an optional data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model. If not found in data, the variables are taken from environment(formula), typically the environment from which lm is called.
subset

an optional vector specifying a subset of observations to be used in the fitting process.
weights

an optional vector of observation weights to be used in the fitting process.
ranks

a vector of integer containing the successive ranks (or number of axes to be considered)
control

a list-like structure for controlling the optimization, with default generated by PLNPCA_param(). See the associated documentation. for details.

Value

an R6 object with class PLNPCAfamily, which contains a collection of models with class PLNPCAfit

See Also

The classes PLNPCAfamily and PLNPCAfit, and the configuration function PLNPCA_param().

Examples

#' ## Use future to dispatch the computations on 2 workers
## Not run: 
future::plan("multisession", workers = 2)

## End(Not run)

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPCA <- PLNPCA(Abundance ~ 1 + offset(log(Offset)), data = trichoptera, ranks = 1:5)

# Shut down parallel workers
## Not run: 
future::plan("sequential")

## End(Not run)

Control of PLNPCA fit

Description

Helper to define list of parameters to control the PLNPCA fit. All arguments have defaults.

Usage

PLNPCA_param(
  backend = c("nlopt", "torch"),
  trace = 1,
  config_optim = list(),
  config_post = list(),
  inception = NULL
)

Arguments

backend

optimization back used, either "nlopt" or "torch". Default is "nlopt"
trace

a integer for verbosity.
config_optim

a list for controlling the optimizer (either "nlopt" or "torch" backend). See details
config_post

a list for controlling the post-treatments (optional bootstrap, jackknife, R2, etc.). See details
inception

Set up the parameters initialization: by default, the model is initialized with a multivariate linear model applied on log-transformed data, and with the same formula as the one provided by the user. However, the user can provide a PLNfit (typically obtained from a previous fit), which sometimes speeds up the inference.

Details

The list of parameters config_optim controls the optimizers. When "nlopt" is chosen the following entries are relevant

  • "algorithm" the optimization method used by NLOPT among LD type, e.g. "CCSAQ", "MMA", "LBFGS". See NLOPT documentation for further details. Default is "CCSAQ".

  • "maxeval" stop when the number of iteration exceeds maxeval. Default is 10000

  • "ftol_rel" stop when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 1e-8

  • "xtol_rel" stop when an optimization step changes every parameters by less than xtol multiplied by the absolute value of the parameter. Default is 1e-6

  • "ftol_abs" stop when an optimization step changes the objective function by less than ftol_abs. Default is 0.0 (disabled)

  • "xtol_abs" stop when an optimization step changes every parameters by less than xtol_abs. Default is 0.0 (disabled)

  • "maxtime" stop when the optimization time (in seconds) exceeds maxtime. Default is -1 (disabled)

When "torch" backend is used (only for PLN and PLNLDA for now), the following entries are relevant:

  • "algorithm" the optimizer used by torch among RPROP (default), RMSPROP, ADAM and ADAGRAD

  • "maxeval" stop when the number of iteration exceeds maxeval. Default is 10 000

  • "numepoch" stop training once this number of epochs exceeds numepoch. Set to -1 to enable infinite training. Default is 1 000

  • "num_batch" number of batches to use during training. Defaults to 1 (use full dataset at each epoch)

  • "ftol_rel" stop when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 1e-8

  • "xtol_rel" stop when an optimization step changes every parameters by less than xtol multiplied by the absolute value of the parameter. Default is 1e-6

  • "lr" learning rate. Default is 0.1.

  • "momentum" momentum factor. Default is 0 (no momentum). Only used in RMSPROP

  • "weight_decay" Weight decay penalty. Default is 0 (no decay). Not used in RPROP

  • "step_sizes" pair of minimal (default: 1e-6) and maximal (default: 50) allowed step sizes. Only used in RPROP

  • "etas" pair of multiplicative increase and decrease factors. Default is (0.5, 1.2). Only used in RPROP

  • "centered" if TRUE, compute the centered RMSProp where the gradient is normalized by an estimation of its variance weight_decay (L2 penalty). Default to FALSE. Only used in RMSPROP

The list of parameters config_post controls the post-treatment processing (for most ⁠PLN*()⁠ functions), with the following entries (defaults may vary depending on the specific function, check ⁠config_post_default_*⁠ for defaults values):

  • jackknife boolean indicating whether jackknife should be performed to evaluate bias and variance of the model parameters. Default is FALSE.

  • bootstrap integer indicating the number of bootstrap resamples generated to evaluate the variance of the model parameters. Default is 0 (inactivated).

  • variational_var boolean indicating whether variational Fisher information matrix should be computed to estimate the variance of the model parameters (highly underestimated). Default is FALSE.

  • sandwich_var boolean indicating whether sandwich estimation should be used to estimate the variance of the model parameters (highly underestimated). Default is FALSE.

  • rsquared boolean indicating whether approximation of R2 based on deviance should be computed. Default is TRUE

Value

list of parameters configuring the fit.

An R6 Class to represent a collection of PLNPCAfit

Description

The function PLNPCA() produces an instance of this class.

This class comes with a set of methods, some of them being useful for the user: See the documentation for getBestModel(), getModel() and plot().

Super class

PLNmodels::PLNfamily -> PLNPCAfamily

Active bindings

ranks

the dimensions of the successively fitted models

Methods

Public methods

Inherited methods

Method new()

Initialize all models in the collection.

Usage
PLNPCAfamily$new(
  ranks,
  responses,
  covariates,
  offsets,
  weights,
  formula,
  control
)
Arguments
ranks

the dimensions of the successively fitted models

responses

the matrix of responses common to every models

covariates

the matrix of covariates common to every models

offsets

the matrix of offsets common to every models

weights

the vector of observation weights

formula

model formula used for fitting, extracted from the formula in the upper-level call

control

list controlling the optimization and the model

Method optimize()

Call to the C++ optimizer on all models of the collection

Usage
PLNPCAfamily$optimize(config)
Arguments
config

list controlling the optimization.

Method getModel()

Extract model from collection and add "PCA" class for compatibility with factoextra::fviz()

Usage
PLNPCAfamily$getModel(var, index = NULL)
Arguments
var

value of the parameter (rank for PLNPCA, sparsity for PLNnetwork) that identifies the model to be extracted from the collection. If no exact match is found, the model with closest parameter value is returned with a warning.

index

Integer index of the model to be returned. Only the first value is taken into account.

Returns

a PLNPCAfit object

Method getBestModel()

Extract best model in the collection

Usage
PLNPCAfamily$getBestModel(crit = c("ICL", "BIC"))
Arguments
crit

a character for the criterion used to performed the selection. Either "ICL", "BIC". Default is ICL

Returns

a PLNPCAfit object

Method plot()

Lineplot of selected criteria for all models in the collection

Usage
PLNPCAfamily$plot(criteria = c("loglik", "BIC", "ICL"), reverse = FALSE)
Arguments
criteria

A valid model selection criteria for the collection of models. Any of "loglik", "BIC" or "ICL" (all).

reverse

A logical indicating whether to plot the value of the criteria in the "natural" direction (loglik - penalty) or in the "reverse" direction (-2 loglik + penalty). Default to FALSE, i.e use the natural direction, on the same scale as the log-likelihood.

Returns

A ggplot2::ggplot object

Method show()

User friendly print method

Usage
PLNPCAfamily$show()

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNPCAfamily$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

The function PLNPCA(), the class PLNPCAfit()

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPCAs <- PLNPCA(Abundance ~ 1 + offset(log(Offset)), data = trichoptera, ranks = 1:5)
class(myPCAs)

An R6 Class to represent a PLNfit in a PCA framework

Description

The function PLNPCA() produces a collection of models which are instances of object with class PLNPCAfit. This class comes with a set of methods, some of them being useful for the user: See the documentation for the methods inherited by PLNfit and the plot() methods for PCA visualization

Super class

PLNmodels::PLNfit -> PLNPCAfit

Active bindings

rank

the dimension of the current model

vcov_model

character: the model used for the residual covariance

nb_param

number of parameters in the current PLN model

entropy

entropy of the variational distribution

latent_pos

a matrix: values of the latent position vector (Z) without covariates effects or offset

model_par

a list with the matrices associated with the estimated parameters of the pPCA model: B (covariates), Sigma (covariance), Omega (precision) and C (loadings)

percent_var

the percent of variance explained by each axis

corr_circle

a matrix of correlations to plot the correlation circles

scores

a matrix of scores to plot the individual factor maps (a.k.a. principal components)

rotation

a matrix of rotation of the latent space

eig

description of the eigenvalues, similar to percent_var but for use with external methods

var

a list of data frames with PCA results for the variables: coord (coordinates of the variables), cor (correlation between variables and dimensions), cos2 (Cosine of the variables) and contrib (contributions of the variable to the axes)

ind

a list of data frames with PCA results for the individuals: coord (coordinates of the individuals), cos2 (Cosine of the individuals), contrib (contributions of individuals to an axis inertia) and dist (distance of individuals to the origin).

call

Hacky binding for compatibility with factoextra functions

Methods

Public methods

Inherited methods

Method new()

Initialize a PLNPCAfit object

Usage
PLNPCAfit$new(rank, responses, covariates, offsets, weights, formula, control)
Arguments
rank

rank of the PCA (or equivalently, dimension of the latent space)

responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily

weights

an optional vector of observation weights to be used in the fitting process.

formula

model formula used for fitting, extracted from the formula in the upper-level call

control

a list for controlling the optimization. See details.

Method update()

Update a PLNPCAfit object

Usage
PLNPCAfit$update(
  B = NA,
  Sigma = NA,
  Omega = NA,
  C = NA,
  M = NA,
  S = NA,
  Z = NA,
  A = NA,
  Ji = NA,
  R2 = NA,
  monitoring = NA
)
Arguments
B

matrix of regression matrix

Sigma

variance-covariance matrix of the latent variables

Omega

precision matrix of the latent variables. Inverse of Sigma.

C

matrix of PCA loadings (in the latent space)

M

matrix of mean vectors for the variational approximation

S

matrix of variance vectors for the variational approximation

Z

matrix of latent vectors (includes covariates and offset effects)

A

matrix of fitted values

Ji

vector of variational lower bounds of the log-likelihoods (one value per sample)

R2

approximate R^2 goodness-of-fit criterion

monitoring

a list with optimization monitoring quantities

Returns

Update the current PLNPCAfit object

Method optimize()

Call to the C++ optimizer and update of the relevant fields

Usage
PLNPCAfit$optimize(responses, covariates, offsets, weights, config)
Arguments
responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily

weights

an optional vector of observation weights to be used in the fitting process.

config

part of the control argument which configures the optimizer

Method optimize_vestep()

Result of one call to the VE step of the optimization procedure: optimal variational parameters (M, S) and corresponding log likelihood values for fixed model parameters (C, B). Intended to position new data in the latent space for further use with PCA.

Usage
PLNPCAfit$optimize_vestep(
  covariates,
  offsets,
  responses,
  weights = rep(1, self$n),
  control = PLNPCA_param(backend = "nlopt")
)
Arguments
covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily

responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily

weights

an optional vector of observation weights to be used in the fitting process.

control

a list for controlling the optimization. See details.

Returns

A list with three components:

  • the matrix M of variational means,

  • the matrix S2 of variational variances

  • the vector log.lik of (variational) log-likelihood of each new observation

Method project()

Project new samples into the PCA space using one VE step

Usage
PLNPCAfit$project(newdata, control = PLNPCA_param(), envir = parent.frame())
Arguments
newdata

A data frame in which to look for variables, offsets and counts with which to predict.

control

a list for controlling the optimization. See PLN() for details.

envir

Environment in which the projection is evaluated

Returns

  • the named matrix of scores for the newdata, expressed in the same coordinate system as self$scores

Method setVisualization()

Compute PCA scores in the latent space and update corresponding fields.

Usage
PLNPCAfit$setVisualization(scale.unit = FALSE)
Arguments
scale.unit

Logical. Should PCA scores be rescaled to have unit variance

Method postTreatment()

Update R2, fisher, std_err fields and set up visualization

Usage
PLNPCAfit$postTreatment(
  responses,
  covariates,
  offsets,
  weights,
  config_post,
  config_optim,
  nullModel
)
Arguments
responses

the matrix of responses (called Y in the model). Will usually be extracted from the corresponding field in PLNfamily

covariates

design matrix (called X in the model). Will usually be extracted from the corresponding field in PLNfamily

offsets

offset matrix (called O in the model). Will usually be extracted from the corresponding field in PLNfamily

weights

an optional vector of observation weights to be used in the fitting process.

config_post

a list for controlling the post-treatments (optional bootstrap, jackknife, R2, etc.). See details

config_optim

a list for controlling the optimizer (either "nlopt" or "torch" backend). See details

nullModel

null model used for approximate R2 computations. Defaults to a GLM model with same design matrix but not latent variable.

Details

The list of parameters config_post controls the post-treatment processing, with the following entries:

  • jackknife boolean indicating whether jackknife should be performed to evaluate bias and variance of the model parameters. Default is FALSE.

  • bootstrap integer indicating the number of bootstrap resamples generated to evaluate the variance of the model parameters. Default is 0 (inactivated).

  • variational_var boolean indicating whether variational Fisher information matrix should be computed to estimate the variance of the model parameters (highly underestimated). Default is FALSE.

  • rsquared boolean indicating whether approximation of R2 based on deviance should be computed. Default is TRUE

  • trace integer for verbosity. should be > 1 to see output in post-treatments

Method plot_individual_map()

Plot the factorial map of the PCA

Usage
PLNPCAfit$plot_individual_map(
  axes = 1:min(2, self$rank),
  main = "Individual Factor Map",
  plot = TRUE,
  cols = "default"
)
Arguments
axes

numeric, the axes to use for the plot when map = "individual" or "variable". Default it c(1,min(rank))

main

character. A title for the single plot (individual or variable factor map). If NULL (the default), an hopefully appropriate title will be used.

plot

logical. Should the plot be displayed or sent back as ggplot object

cols

a character, factor or numeric to define the color associated with the individuals. By default, all individuals receive the default color of the current palette.

Returns

a ggplot2::ggplot graphic

Method plot_correlation_circle()

Plot the correlation circle of a specified axis for a PLNLDAfit object

Usage
PLNPCAfit$plot_correlation_circle(
  axes = 1:min(2, self$rank),
  main = "Variable Factor Map",
  cols = "default",
  plot = TRUE
)
Arguments
axes

numeric, the axes to use for the plot when map = "individual" or "variable". Default it c(1,min(rank))

main

character. A title for the single plot (individual or variable factor map). If NULL (the default), an hopefully appropriate title will be used.

cols

a character, factor or numeric to define the color associated with the variables. By default, all variables receive the default color of the current palette.

plot

logical. Should the plot be displayed or sent back as ggplot object

Returns

a ggplot2::ggplot graphic

Method plot_PCA()

Plot a summary of the PLNPCAfit object

Usage
PLNPCAfit$plot_PCA(
  nb_axes = min(3, self$rank),
  ind_cols = "ind_cols",
  var_cols = "var_cols",
  plot = TRUE
)
Arguments
nb_axes

scalar: the number of axes to be considered when map = "both". The default is min(3,rank).

ind_cols

a character, factor or numeric to define the color associated with the individuals. By default, all variables receive the default color of the current palette.

var_cols

a character, factor or numeric to define the color associated with the variables. By default, all variables receive the default color of the current palette.

plot

logical. Should the plot be displayed or sent back as ggplot object

Returns

a grob object

Method show()

User friendly print method

Usage
PLNPCAfit$show()

Method clone()

The objects of this class are cloneable with this method.

Usage
PLNPCAfit$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

The function PLNPCA, the class PLNPCAfamily

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPCAs <- PLNPCA(Abundance ~ 1 + offset(log(Offset)), data = trichoptera, ranks = 1:5)
myPCA <- getBestModel(myPCAs)
class(myPCA)
print(myPCA)

Display various outputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of network fits (either PLNnetworkfamily or ZIPLNnetworkfamily)

Description

Display various outputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of network fits (either PLNnetworkfamily or ZIPLNnetworkfamily)

Usage

## S3 method for class 'Networkfamily'
plot(
  x,
  type = c("criteria", "stability", "diagnostic"),
  criteria = c("loglik", "pen_loglik", "BIC", "EBIC"),
  reverse = FALSE,
  log.x = TRUE,
  stability = 0.9,
  ...
)

## S3 method for class 'PLNnetworkfamily'
plot(
  x,
  type = c("criteria", "stability", "diagnostic"),
  criteria = c("loglik", "pen_loglik", "BIC", "EBIC"),
  reverse = FALSE,
  log.x = TRUE,
  stability = 0.9,
  ...
)

## S3 method for class 'ZIPLNnetworkfamily'
plot(
  x,
  type = c("criteria", "stability", "diagnostic"),
  criteria = c("loglik", "pen_loglik", "BIC", "EBIC"),
  reverse = FALSE,
  log.x = TRUE,
  stability = 0.9,
  ...
)

Arguments

x

an R6 object with class PLNnetworkfamily or ZIPLNnetworkfamily
type

a character, either "criteria", "stability" or "diagnostic" for the type of plot.
criteria

Vector of criteria to plot, to be selected among "loglik" (log-likelihood), "BIC", "ICL", "R_squared", "EBIC" and "pen_loglik" (penalized log-likelihood). Default is c("loglik", "pen_loglik", "BIC", "EBIC"). Only used when type = "criteria".
reverse

A logical indicating whether to plot the value of the criteria in the "natural" direction (loglik - 0.5 penalty) or in the "reverse" direction (-2 loglik + penalty). Default to FALSE, i.e use the natural direction, on the same scale as the log-likelihood.
log.x

logical: should the x-axis be represented in log-scale? Default is TRUE.
stability

scalar: the targeted level of stability in stability plot. Default is .9.
...

additional parameters for S3 compatibility. Not used

Details

The BIC and ICL criteria have the form 'loglik - 1/2 * penalty' so that they are on the same scale as the model log-likelihood. You can change this direction and use the alternate form '-2*loglik + penalty', as some authors do, by setting reverse = TRUE.

Value

Produces either a diagnostic plot (with type = 'diagnostic'), a stability plot (with type = 'stability') or the evolution of the criteria of the different models considered (with type = 'criteria', the default).

Functions

  • plot(PLNnetworkfamily): Display various outputs associated with a collection of network fits

  • plot(ZIPLNnetworkfamily): Display various outputs associated with a collection of network fits

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
## Not run: 
plot(fits)

## End(Not run)

Display the criteria associated with a collection of PLN fits (a PLNfamily)

Description

Display the criteria associated with a collection of PLN fits (a PLNfamily)

Usage

## S3 method for class 'PLNfamily'
plot(x, criteria = c("loglik", "BIC", "ICL"), reverse = FALSE, ...)

Arguments

x

an R6 object with class PLNfamily
criteria

vector of characters. The criteria to plot in c("loglik", "BIC", "ICL"). Default is c("loglik", "BIC", "ICL").
reverse

A logical indicating whether to plot the value of the criteria in the "natural" direction (loglik - 0.5 penalty) or in the "reverse" direction (-2 loglik + penalty). Default to FALSE, i.e use the natural direction, on the same scale as the log-likelihood.
...

additional parameters for S3 compatibility. Not used

Details

The BIC and ICL criteria have the form 'loglik - 1/2 * penalty' so that they are on the same scale as the model log-likelihood. You can change this direction and use the alternate form '-2*loglik + penalty', as some authors do, by setting reverse = TRUE.

Value

Produces a plot representing the evolution of the criteria of the different models considered, highlighting the best model in terms of BIC and ICL (see details).

See Also

plot.PLNPCAfamily() and plot.PLNnetworkfamily()

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPCAs <- PLNPCA(Abundance ~ 1 + offset(log(Offset)), data = trichoptera, ranks = 1:5)
## Not run: 
plot(myPCAs)

## End(Not run)

LDA visualization (individual and/or variable factor map(s)) for a PLNPCAfit object

Description

LDA visualization (individual and/or variable factor map(s)) for a PLNPCAfit object

Usage

## S3 method for class 'PLNLDAfit'
plot(
  x,
  map = c("both", "individual", "variable"),
  nb_axes = min(3, x$rank),
  axes = seq.int(min(2, x$rank)),
  var_cols = "var_colors",
  plot = TRUE,
  main = NULL,
  ...
)

Arguments

x

an R6 object with class PLNPCAfit
map

the type of output for the PCA visualization: either "individual", "variable" or "both". Default is "both".
nb_axes

scalar: the number of axes to be considered when map = "both". The default is min(3,rank).
axes

numeric, the axes to use for the plot when map = "individual" or "variable". Default it c(1,min(rank))
var_cols

a character or factor to define the color associated with the variables. By default, all variables receive the default color of the current palette.
plot

logical. Should the plot be displayed or sent back as ggplot2::ggplot object
main

character. A title for the single plot (individual or variable factor map). If NULL (the default), an hopefully appropriate title will be used.
...

Not used (S3 compatibility).

Value

displays an individual and/or variable factor maps for the corresponding axes, and/or sends back a ggplot2::ggplot or gtable object

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLNLDA <- PLNLDA(Abundance ~ 1, grouping = Group, data = trichoptera)
## Not run: 
plot(myPLNLDA, map = "individual", nb_axes = 2)

## End(Not run)

Display the criteria associated with a collection of PLNmixture fits (a PLNmixturefamily)

Description

Display the criteria associated with a collection of PLNmixture fits (a PLNmixturefamily)

Usage

## S3 method for class 'PLNmixturefamily'
plot(
  x,
  type = c("criteria", "diagnostic"),
  criteria = c("loglik", "BIC", "ICL"),
  reverse = FALSE,
  ...
)

Arguments

x

an R6 object with class PLNmixturefamily
type

a character, either "criteria" or "diagnostic" for the type of plot.
criteria

vector of characters. The criteria to plot in c("loglik", "BIC", "ICL"). Default is c("loglik", "BIC", "ICL").
reverse

A logical indicating whether to plot the value of the criteria in the "natural" direction (loglik - 0.5 penalty) or in the "reverse" direction (-2 loglik + penalty). Default to FALSE, i.e use the natural direction, on the same scale as the log-likelihood.
...

additional parameters for S3 compatibility. Not used

Details

The BIC and ICL criteria have the form 'loglik - 1/2 * penalty' so that they are on the same scale as the model log-likelihood. You can change this direction and use the alternate form '-2*loglik + penalty', as some authors do, by setting reverse = TRUE.

Value

Produces either a diagnostic plot (with type = 'diagnostic') or the evolution of the criteria of the different models considered (with type = 'criteria', the default).

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myMixtures <- PLNmixture(Abundance ~ 1 + offset(log(Offset)),
           data = trichoptera, control = PLNmixture_param(smoothing = "none"))
plot(myMixtures, reverse = TRUE)

Mixture visualization of a PLNmixturefit object

Description

Represent the result of the clustering either by coloring the individual in a two-dimension PCA factor map, or by representing the expected matrix of count reorder according to the clustering.

Usage

## S3 method for class 'PLNmixturefit'
plot(x, type = c("pca", "matrix"), main = NULL, plot = TRUE, ...)

Arguments

x

an R6 object with class PLNmixturefit
type

character for the type of plot, either "pca", for or "matrix". Default is "pca".
main

character. A title for the plot. If NULL (the default), an hopefully appropriate title will be used.
plot

logical. Should the plot be displayed or sent back as ggplot2::ggplot object
...

Not used (S3 compatibility).

Value

a ggplot2::ggplot graphic

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLNmixture(Abundance ~ 1 + offset(log(Offset)),
           data = trichoptera, control = PLNmixture_param(smoothing = "none"))  %>% getBestModel()
## Not run: 
plot(myPLN, "pca")
plot(myPLN, "matrix")

## End(Not run)

Extract and plot the network (partial correlation, support or inverse covariance) from a PLNnetworkfit object

Description

Extract and plot the network (partial correlation, support or inverse covariance) from a PLNnetworkfit object

Usage

## S3 method for class 'PLNnetworkfit'
plot(
  x,
  type = c("partial_cor", "support"),
  output = c("igraph", "corrplot"),
  edge.color = c("#F8766D", "#00BFC4"),
  remove.isolated = FALSE,
  node.labels = NULL,
  layout = layout_in_circle,
  plot = TRUE,
  ...
)

Arguments

x

an R6 object with class PLNnetworkfit
type

character. Value of the weight of the edges in the network, either "partial_cor" (partial correlation) or "support" (binary). Default is "partial_cor".
output

the type of output used: either 'igraph' or 'corrplot'. Default is 'igraph'.
edge.color

Length 2 color vector. Color for positive/negative edges. Default is c("#F8766D", "#00BFC4"). Only relevant for igraph output.
remove.isolated

if TRUE, isolated node are remove before plotting. Only relevant for igraph output.
node.labels

vector of character. The labels of the nodes. The default will use the column names ot the response matrix.
layout

an optional igraph layout. Only relevant for igraph output.
plot

logical. Should the final network be displayed or only sent back to the user. Default is TRUE.
...

Not used (S3 compatibility).

Value

Send back an invisible object (igraph or Matrix, depending on the output chosen) and optionally displays a graph (via igraph or corrplot for large ones)

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
myNet <- getBestModel(fits)
## Not run: 
plot(myNet)

## End(Not run)

Display the criteria associated with a collection of PLNPCA fits (a PLNPCAfamily)

Description

Display the criteria associated with a collection of PLNPCA fits (a PLNPCAfamily)

Usage

## S3 method for class 'PLNPCAfamily'
plot(x, criteria = c("loglik", "BIC", "ICL"), reverse = FALSE, ...)

Arguments

x

an R6 object with class PLNPCAfamily
criteria

vector of characters. The criteria to plot in c("loglik", "BIC", "ICL"). Default is c("loglik", "BIC", "ICL").
reverse

A logical indicating whether to plot the value of the criteria in the "natural" direction (loglik - 0.5 penalty) or in the "reverse" direction (-2 loglik + penalty). Default to FALSE, i.e use the natural direction, on the same scale as the log-likelihood.
...

additional parameters for S3 compatibility. Not used

Details

The BIC and ICL criteria have the form 'loglik - 1/2 * penalty' so that they are on the same scale as the model log-likelihood. You can change this direction and use the alternate form '-2*loglik + penalty', as some authors do, by setting reverse = TRUE.

Value

Produces a plot representing the evolution of the criteria of the different models considered, highlighting the best model in terms of BIC and ICL (see details).

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPCAs <- PLNPCA(Abundance ~ 1 + offset(log(Offset)), data = trichoptera, ranks = 1:5)
## Not run: 
plot(myPCAs)

## End(Not run)

PCA visualization (individual and/or variable factor map(s)) for a PLNPCAfit object

Description

PCA visualization (individual and/or variable factor map(s)) for a PLNPCAfit object

Usage

## S3 method for class 'PLNPCAfit'
plot(
  x,
  map = c("both", "individual", "variable"),
  nb_axes = min(3, x$rank),
  axes = seq.int(min(2, x$rank)),
  ind_cols = "ind_colors",
  var_cols = "var_colors",
  plot = TRUE,
  main = NULL,
  ...
)

Arguments

x

an R6 object with class PLNPCAfit
map

the type of output for the PCA visualization: either "individual", "variable" or "both". Default is "both".
nb_axes

scalar: the number of axes to be considered when map = "both". The default is min(3,rank).
axes

numeric, the axes to use for the plot when map = "individual" or map = "variable". Default it c(1,min(rank))
ind_cols

a character, factor or numeric to define the color associated with the individuals. By default, all variables receive the default color of the current palette.
var_cols

a character, factor or numeric to define the color associated with the variables. By default, all variables receive the default color of the current palette.
plot

logical. Should the plot be displayed or sent back as ggplot2::ggplot object
main

character. A title for the single plot (individual or variable factor map). If NULL (the default), an hopefully appropriate title will be used.
...

Not used (S3 compatibility).

Value

displays an individual and/or variable factor maps for the corresponding axes, and/or sends back a ggplot2::ggplot or gtable object

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPCAs <- PLNPCA(Abundance ~ 1 + offset(log(Offset)), data = trichoptera, ranks = 1:5)
myPCA <- getBestModel(myPCAs)
## Not run: 
plot(myPCA, map = "individual", nb_axes=2, ind_cols = trichoptera$Group)
plot(myPCA, map = "variable", nb_axes=2)
plot(myPCA, map = "both", nb_axes=2, ind_cols = trichoptera$Group)

## End(Not run)

Extract and plot the network (partial correlation, support or inverse covariance) from a ZIPLNfit_sparse object

Description

Extract and plot the network (partial correlation, support or inverse covariance) from a ZIPLNfit_sparse object

Usage

## S3 method for class 'ZIPLNfit_sparse'
plot(
  x,
  type = c("partial_cor", "support"),
  output = c("igraph", "corrplot"),
  edge.color = c("#F8766D", "#00BFC4"),
  remove.isolated = FALSE,
  node.labels = NULL,
  layout = layout_in_circle,
  plot = TRUE,
  ...
)

Arguments

x

an R6 object with class ZIPLNfit_sparse
type

character. Value of the weight of the edges in the network, either "partial_cor" (partial correlation) or "support" (binary). Default is "partial_cor".
output

the type of output used: either 'igraph' or 'corrplot'. Default is 'igraph'.
edge.color

Length 2 color vector. Color for positive/negative edges. Default is c("#F8766D", "#00BFC4"). Only relevant for igraph output.
remove.isolated

if TRUE, isolated node are remove before plotting. Only relevant for igraph output.
node.labels

vector of character. The labels of the nodes. The default will use the column names ot the response matrix.
layout

an optional igraph layout. Only relevant for igraph output.
plot

logical. Should the final network be displayed or only sent back to the user. Default is TRUE.
...

Not used (S3 compatibility).

Value

Send back an invisible object (igraph or Matrix, depending on the output chosen) and optionally displays a graph (via igraph or corrplot for large ones)

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fit <- ZIPLN(Abundance ~ 1, data = trichoptera, control = ZIPLN_param(penalty = 0.1))
## Not run: 
plot(fit)

## End(Not run)

Predict counts conditionally

Description

Predict counts of a new sample conditionally on a (set of) observed variables

Usage

predict_cond(
  object,
  newdata,
  cond_responses,
  type = c("link", "response"),
  var_par = FALSE
)

## S3 method for class 'PLNfit'
predict_cond(
  object,
  newdata,
  cond_responses,
  type = c("link", "response"),
  var_par = FALSE
)

Arguments

object

an R6 object with class PLNfit
newdata

A data frame in which to look for variables and offsets with which to predict
cond_responses

a data frame containing the counts of the observed variables (matching the names provided as data in the PLN function)
type

The type of prediction required. The default is on the scale of the linear predictors (i.e. log average count)
var_par

Boolean. Should new estimations of the variational parameters of mean and variance be sent back, as attributes of the matrix of predictions. Default to FALSE.

Value

A list containing:

pred

A matrix of predicted log-counts (if type = "link") or predicted counts (if type = "response")
M

A matrix containing E(Z_uncond | Y_c) for each given site.
S

A matrix containing Var(Z_uncond | Y_c) for each given site (sites are the third dimension of the array)

Methods (by class)

  • predict_cond(PLNfit): Predict counts of a new sample conditionally on a (set of) observed variables for a PLNfit

Examples

data(trichoptera)
trichoptera_prep <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLN(Abundance ~ Temperature + Wind, trichoptera_prep)
#Condition on the set of the first two species in the dataset (Hym, Hys) at the ten first sites
Yc <- trichoptera$Abundance[1:10, c(1, 2), drop=FALSE]
newX <- cbind(1, trichoptera$Covariate[1:10, c("Temperature", "Wind")])
pred <- predict_cond(myPLN, newX, Yc, type = "response")

Predict counts of a new sample

Description

Predict counts of a new sample

Usage

## S3 method for class 'PLNfit'
predict(
  object,
  newdata,
  responses = NULL,
  level = 1,
  type = c("link", "response"),
  ...
)

Arguments

object

an R6 object with class PLNfit
newdata

A data frame in which to look for variables and offsets with which to predict
responses

Optional data frame containing the count of the observed variables (matching the names of the provided as data in the PLN function), assuming the interest in in testing the model.
level

Optional integer value the level to be used in obtaining the predictions. Level zero corresponds to the population predictions (default if responses is not provided) while level one (default) corresponds to predictions after evaluating the variational parameters for the new data.
type

The type of prediction required. The default is on the scale of the linear predictors (i.e. log average count)
...

additional parameters for S3 compatibility. Not used

Value

A matrix of predicted log-counts (if type = "link") or predicted counts (if type = "response").

Predict group of new samples

Description

Predict group of new samples

Usage

## S3 method for class 'PLNLDAfit'
predict(
  object,
  newdata,
  type = c("posterior", "response", "scores"),
  scale = c("log", "prob"),
  prior = NULL,
  control = PLN_param(backend = "nlopt"),
  ...
)

Arguments

object

an R6 object with class PLNLDAfit
newdata

A data frame in which to look for variables, offsets and counts with which to predict.
type

The type of prediction required. The default are posterior probabilities for each group (in either unnormalized log-scale or natural probabilities, see "scale" for details), "response" is the group with maximal posterior probability and "scores" is the average score along each separation axis in the latent space, with weights equal to the posterior probabilities.
scale

The scale used for the posterior probability. Either log-scale ("log", default) or natural probabilities summing up to 1 ("prob").
prior

User-specified prior group probabilities in the new data. If NULL (default), prior probabilities are computed from the learning set.
control

a list for controlling the optimization. See PLN() for details.
...

additional parameters for S3 compatibility. Not used

Value

A matrix of posterior probabilities for each group (if type = "posterior"), a matrix of (average) scores in the latent space (if type = "scores") or a vector of predicted groups (if type = "response").

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myLDA <- PLNLDA(Abundance ~ 0 + offset(log(Offset)),
                grouping = Group,
                data = trichoptera)
## Not run: 
post_probs <- predict(myLDA, newdata = trichoptera, type = "posterior", scale = "prob")
head(round(post_probs, digits = 3))
predicted_group <- predict(myLDA, newdata = trichoptera, type = "response")
table(predicted_group, trichoptera$Group, dnn = c("predicted", "true"))

## End(Not run)

Prediction for a PLNmixturefit object

Description

Predict either posterior probabilities for each group or latent positions based on new samples

Usage

## S3 method for class 'PLNmixturefit'
predict(
  object,
  newdata,
  type = c("posterior", "response", "position"),
  prior = matrix(rep(1/object$k, object$k), nrow(newdata), object$k, byrow = TRUE),
  control = PLNmixture_param(),
  ...
)

Arguments

object

an R6 object with class PLNmixturefit
newdata

A data frame in which to look for variables, offsets and counts with which to predict.
type

The type of prediction required. The default posterior are posterior probabilities for each group , response is the group with maximal posterior probability and latent is the averaged latent in the latent space, with weights equal to the posterior probabilities.
prior

User-specified prior group probabilities in the new data. The default uses a uniform prior.
control

a list-like structure for controlling the fit. See PLNmixture_param() for details.
...

additional parameters for S3 compatibility. Not used

Value

A matrix of posterior probabilities for each group (if type = "posterior"), a matrix of (average) position in the latent space (if type = "position") or a vector of predicted groups (if type = "response").

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLNmixture(Abundance ~ 1 + offset(log(Offset)),
           data = trichoptera, control = PLNmixture_param(smoothing = "none"))  %>% getBestModel()
predict(myPLN, trichoptera, "posterior")
predict(myPLN, trichoptera, "position")
predict(myPLN, trichoptera, "response")

Predict counts of a new sample

Description

Predict counts of a new sample

Usage

## S3 method for class 'ZIPLNfit'
predict(
  object,
  newdata,
  responses = NULL,
  level = 1,
  type = c("link", "response", "deflated"),
  ...
)

Arguments

object

an R6 object with class ZIPLNfit
newdata

A data frame in which to look for variables and offsets with which to predict
responses

Optional data frame containing the count of the observed variables (matching the names of the provided as data in the PLN function), assuming the interest in in testing the model.
level

Optional integer value the level to be used in obtaining the predictions. Level zero corresponds to the population predictions (default if responses is not provided) while level one (default) corresponds to predictions after evaluating the variational parameters for the new data.
type

Scale used for the prediction. Either "link" (default, predicted positions in the latent space), "response" (predicted average counts, accounting for zero-inflation) or "deflated" (predicted average counts, not accounting for zero-inflation and using only the PLN part of the model).
...

additional parameters for S3 compatibility. Not used

Details

Note that level = 1 can only be used if responses are provided, as the variational parameters can't be estimated otherwise. In the absence of responses, level is ignored and the fitted values are returned

Note also that when type = "response" corresponds to predicting values with (1−π)A(1 - \pi)A, where AA is the average count in the PLN part of the model and π\pi the probability of zero-inflation, whereas type = "deflated" corresponds to AA.

Prepare data for use in PLN models

Description

Prepare data in proper format for use in PLN model and its variants. The function (i) merges a count table and a covariate data frame in the most comprehensive way and (ii) computes offsets from the count table using one of several normalization schemes (TSS, CSS, RLE, GMPR, Wrench, etc). The function fails with informative messages when the heuristics used for sample matching fail.

Usage

prepare_data(
  counts,
  covariates,
  offset = "TSS",
  call = rlang::caller_env(),
  ...
)

Arguments

counts

Required. An abundance count table, preferably with dimensions names and species as columns.
covariates

Required. A covariates data frame, preferably with row names.
offset

Optional. Normalization scheme used to compute scaling factors used as offset during PLN inference. Available schemes are "TSS" (Total Sum Scaling, default), "CSS" (Cumulative Sum Scaling, used in metagenomeSeq), "RLE" (Relative Log Expression, used in DESeq2), "GMPR" (Geometric Mean of Pairwise Ratio, introduced in Chen et al., 2018), Wrench (introduced in Kumar et al., 2018) or "none". Alternatively the user can supply its own vector or matrix of offsets (see note for specification of the user-supplied offsets).
call

Optional. The execution environment in which to set the local error call.
...

Additional parameters passed on to compute_offset()

Value

A data.frame suited for use in PLN() and its variants with two specials components: an abundance count matrix (in component "Abundance") and an offset vector/matrix (in component "Offset", only if offset is not set to "none")

Note

User supplied offsets should be either vectors/column-matrices or have the same number of column as the original count matrix and either (i) dimension names or (ii) the same dimensions as the count matrix. Samples are trimmed in exactly the same way to remove empty samples.

References

Chen, L., Reeve, J., Zhang, L., Huang, S., Wang, X. and Chen, J. (2018) GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data. PeerJ, 6, e4600 doi:10.7717/peerj.4600

Paulson, J. N., Colin Stine, O., Bravo, H. C. and Pop, M. (2013) Differential abundance analysis for microbial marker-gene surveys. Nature Methods, 10, 1200-1202 doi:10.1038/nmeth.2658

Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biology, 11, R106 doi:10.1186/gb-2010-11-10-r106

Kumar, M., Slud, E., Okrah, K. et al. (2018) Analysis and correction of compositional bias in sparse sequencing count data. BMC Genomics 19, 799 doi:10.1186/s12864-018-5160-5

Robinson, M.D., Oshlack, A. (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11, R25 doi:10.1186/gb-2010-11-3-r25

See Also

compute_offset() for details on the different normalization schemes

Examples

data(trichoptera)
proper_data <- prepare_data(
 counts     = trichoptera$Abundance,
 covariates = trichoptera$Covariate,
 offset     = "GMPR",
 scale      = "count"
)
proper_data$Abundance
proper_data$Offset

PLN RNG

Description

Random generation for the PLN model with latent mean equal to mu, latent covariance matrix equal to Sigma and average depths (sum of counts in a sample) equal to depths

Usage

rPLN(
  n = 10,
  mu = rep(0, ncol(Sigma)),
  Sigma = diag(1, 5, 5),
  depths = rep(10000, n)
)

Arguments

n

the sample size
mu

vectors of means of the latent variable
Sigma

covariance matrix of the latent variable
depths

Numeric vector of target depths. The first is recycled if there are not n values

Details

The default value for mu and Sigma assume equal abundances and no correlation between the different species.

Value

a n * p count matrix, with row-sums close to depths, with an attribute "offsets" corresponding to the true generated offsets (in log-scale).

Examples

## 10 samples of 5 species with equal abundances, no covariance and target depths of 10,000
rPLN()
## 2 samples of 10 highly correlated species with target depths 1,000 and 100,000
## very different abundances
mu <- rep(c(1, -1), each = 5)
Sigma <- matrix(0.8, 10, 10); diag(Sigma) <- 1
rPLN(n=2, mu = mu, Sigma = Sigma, depths = c(1e3, 1e5))

Single cell RNA-seq data

Description

A dataset containing the counts of the 500 most varying transcripts in the mixtures of 5 cell lines in human liver (obtained with standard 10x scRNAseq Chromium protocol).

Usage

scRNA

Format

A data frame named 'scRNA' with 3918 rows (the cells) and 3 variables:

counts

a 500 trancript by 3918 count matrix

cell_line

factor, the cell line of the current row (among 5)

total_counts

Total number of reads for that cell

...

Source

https://github.com/LuyiTian/sc_mixology/

Extract variance-covariance of residuals 'Sigma'

Description

Extract the variance-covariance matrix of the residuals, usually noted

Σ\Sigma

in PLN models. This captures the correlation between the species in the latent space.

Usage

## S3 method for class 'PLNfit'
sigma(object, ...)

Arguments

object

an R6 object with class PLNfit
...

additional parameters for S3 compatibility. Not used

Value

A semi definite positive matrix of size p, assuming there are p species in the model.

See Also

coef.PLNfit(), standard_error.PLNfit() and vcov.PLNfit() for other ways to access

Σ\Sigma

.

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLN(Abundance ~ 1 + offset(log(Offset)), data = trichoptera)
sigma(myPLN) ## Sigma

Extract variance-covariance of residuals 'Sigma'

Description

Extract the variance-covariance matrix of the residuals, usually noted

Σ\Sigma

in PLN models. This captures the correlation between the species in the latent space. or PLNmixture, it is a weighted mean of the variance-covariance matrices of each component.

Usage

## S3 method for class 'PLNmixturefit'
sigma(object, ...)

Arguments

object

an R6 object with class PLNmixturefit
...

additional parameters for S3 compatibility. Not used

Value

A semi definite positive matrix of size p, assuming there are p species in the model.

See Also

coef.PLNmixturefit() for other ways to access

Σ\Sigma

.

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLNmixture(Abundance ~ 1 + offset(log(Offset)),
           data = trichoptera, control = PLNmixture_param(smoothing = "none"))  %>% getBestModel()
sigma(myPLN) ## Sigma

Extract variance-covariance of residuals 'Sigma'

Description

Extract the variance-covariance matrix of the residuals, usually noted Σ\Sigma in ZIPLN models.

Usage

## S3 method for class 'ZIPLNfit'
sigma(object, ...)

Arguments

object

an R6 object with class ZIPLNfit
...

additional parameters for S3 compatibility. Not used

Value

A semi definite positive matrix of size p, assuming there are p species in the model.

See Also

coef.ZIPLNfit()

Compute the stability path by stability selection

Description

This function computes the StARS stability criteria over a path of penalties. If a path has already been computed, the functions stops with a message unless force = TRUE has been specified.

Usage

stability_selection(
  Robject,
  subsamples = NULL,
  control = PLNnetwork_param(),
  force = FALSE
)

Arguments

Robject

an object with class PLNnetworkfamily or ZIPLNnetworkfamily, i.e. an output from PLNnetwork() or ZIPLNnetwork()
subsamples

a list of vectors describing the subsamples. The number of vectors (or list length) determines th number of subsamples used in the stability selection. Automatically set to 20 subsamples with size 10*sqrt(n) if n >= 144 and 0.8*n otherwise following Liu et al. (2010) recommendations.
control

a list controlling the main optimization process in each call to PLNnetwork() or ZIPLNnetwork(). See PLN_param() or ZIPLN_param() for details.
force

force computation of the stability path, even if a previous one has been detected.

Value

the list of subsamples. The estimated probabilities of selection of the edges are stored in the fields stability_path of the initial Robject with class Networkfamily

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
## Not run: 
n <- nrow(trichoptera)
subs <- replicate(10, sample.int(n, size = n/2), simplify = FALSE)
stability_selection(nets, subsamples = subs)

## End(Not run)

Component-wise standard errors of B

Description

Extracts univariate standard errors for the estimated coefficient of B. Standard errors are computed from the (approximate) Fisher information matrix.

Usage

## S3 method for class 'PLNPCAfit'
standard_error(
  object,
  type = c("variational", "jackknife", "sandwich"),
  parameter = c("B", "Omega")
)

standard_error(
  object,
  type = c("sandwich", "variational", "jackknife"),
  parameter = c("B", "Omega")
)

## S3 method for class 'PLNfit'
standard_error(
  object,
  type = c("sandwich", "variational", "jackknife", "bootstrap"),
  parameter = c("B", "Omega")
)

## S3 method for class 'PLNfit_fixedcov'
standard_error(
  object,
  type = c("sandwich", "variational", "jackknife", "bootstrap"),
  parameter = c("B", "Omega")
)

## S3 method for class 'PLNmixturefit'
standard_error(
  object,
  type = c("variational", "jackknife", "sandwich"),
  parameter = c("B", "Omega")
)

## S3 method for class 'PLNnetworkfit'
standard_error(
  object,
  type = c("variational", "jackknife", "sandwich"),
  parameter = c("B", "Omega")
)

Arguments

object

an R6 object with class PLNfit
type

string describing the type of variance approximation: "variational", "jackknife", "sandwich". Default is "sandwich".
parameter

string describing the target parameter: either B (regression coefficients) or Omega (inverse residual covariance)

Value

A p * d positive matrix (same size as BB) with standard errors for the coefficients of BB

Methods (by class)

  • standard_error(PLNPCAfit): Component-wise standard errors of B in PLNPCAfit (not implemented yet)

  • standard_error(PLNfit): Component-wise standard errors of B in PLNfit

  • standard_error(PLNfit_fixedcov): Component-wise standard errors of B in PLNfit_fixedcov

  • standard_error(PLNmixturefit): Component-wise standard errors of B in PLNmixturefit (not implemented yet)

  • standard_error(PLNnetworkfit): Component-wise standard errors of B in PLNnetworkfit (not implemented yet)

See Also

vcov.PLNfit() for the complete variance covariance estimation of the coefficient

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLN(Abundance ~ 1 + offset(log(Offset)), data = trichoptera,
              control = PLN_param(config_post = list(sandwich_var = TRUE)))
standard_error(myPLN)

Trichoptera data set

Description

Data gathered between 1959 and 1960 during 49 insect trapping nights. For each trapping night, the abundance of 17 Trichoptera species is recorded as well as 6 meteorological variables which may influence the abundance of each species. Finally, the observations (that is to say, the trapping nights), have been classified into 12 groups corresponding to contiguous nights between summer 1959 and summer 1960.

Usage

trichoptera

Format

A list with 2 two data frames:

Abundance

a 49 x 17 matrix of abundancies/counts (49 trapping nights and 17 trichoptera species)

Covariate

a 49 x 7 data frame of covariates:

Temperature

Evening Temperature in Celsius

Wind

Wind in m/s

Pressure

Pressure in mm Hg

Humidity

relative to evening humidity in percent

Cloudiness

proportion of sky coverage at 9pm

Precipitation

Nighttime precipitation in mm

Group

a factor of 12 levels for the definition of the consecutive night groups

In order to prepare the data for using formula in multivariate analysis (multiple outputs and inputs), use prepare_data(). We only kept a subset of the original meteorological covariates for illustration purposes.

Source

Data from P. Usseglio-Polatera.

References

Usseglio-Polatera, P. and Auda, Y. (1987) Influence des facteurs météorologiques sur les résultats de piégeage lumineux. Annales de Limnologie, 23, 65–79. (code des espèces p. 76) See a data description at http://pbil.univ-lyon1.fr/R/pdf/pps034.pdf (in French)

See Also

prepare_data()

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)

Calculate Variance-Covariance Matrix for a fitted PLN() model object

Description

Returns the variance-covariance matrix of the main parameters of a fitted PLN() model object. The main parameters of the model correspond to

BB

, as returned by coef.PLNfit(). The function can also be used to return the variance-covariance matrix of the residuals. The latter matrix can also be accessed via sigma.PLNfit()

Usage

## S3 method for class 'PLNfit'
vcov(object, type = c("main", "covariance"), ...)

Arguments

object

an R6 object with class PLNfit
type

type of parameter that should be extracted. Either "main" (default) for

BB

or "covariance" for

Σ\Sigma

...

additional parameters for S3 compatibility. Not used

Value

A matrix of variance/covariance extracted from the PLNfit model. If type="main" and BB is a matrix of size d * p, the result is a block-diagonal matrix with p (number of species) blocks of size d (number of covariates). if type="main", it is a symmetric matrix of size p. .

See Also

sigma.PLNfit(), coef.PLNfit(), standard_error.PLNfit()

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLN(Abundance ~ 1 + offset(log(Offset)), data = trichoptera)
vcov(myPLN, type = "covariance") ## Sigma

Zero Inflated Poisson lognormal model

Description

Fit the multivariate Zero Inflated Poisson lognormal model with a variational algorithm. Use the (g)lm syntax for model specification (covariates, offsets, subset).

Usage

ZIPLN(
  formula,
  data,
  subset,
  zi = c("single", "row", "col"),
  control = ZIPLN_param()
)

Arguments

formula

an object of class "formula": a symbolic description of the model to be fitted.
data

an optional data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model. If not found in data, the variables are taken from environment(formula), typically the environment from which PLN is called.
subset

an optional vector specifying a subset of observations to be used in the fitting process.
zi

a character describing the model used for zero inflation, either of

  • "single" (default, one parameter shared by all counts)

  • "col" (one parameter per variable / feature)

  • "row" (one parameter per sample / individual). If covariates are specified in the formula RHS (see details) this parameter is ignored.

control

a list-like structure for controlling the optimization, with default generated by ZIPLN_param(). See the associated documentation for details.

Details

Covariates for the Zero-Inflation parameter (using a logistic regression model) can be specified in the formula RHS using the pipe (⁠~ PLN effect | ZI effect⁠) to separate covariates for the PLN part of the model from those for the Zero-Inflation part. Note that different covariates can be used for each part.

Value

an R6 object with class ZIPLNfit

See Also

The class ZIPLNfit

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
## Use different models for zero-inflation...
myZIPLN_single <- ZIPLN(Abundance ~ 1, data = trichoptera, zi = "single")
## Not run: 
myZIPLN_row    <- ZIPLN(Abundance ~ 1, data = trichoptera, zi = "row")
myZIPLN_col    <- ZIPLN(Abundance ~ 1, data = trichoptera, zi = "col")
## ...including logistic regression on covariates
myZIPLN_covar  <- ZIPLN(Abundance ~ 1 | 1 + Wind, data = trichoptera)

## End(Not run)

Control of a ZIPLN fit

Description

Helper to define list of parameters to control the PLN fit. All arguments have defaults.

Usage

ZIPLN_param(
  backend = c("nlopt"),
  trace = 1,
  covariance = c("full", "diagonal", "spherical", "fixed", "sparse"),
  Omega = NULL,
  penalty = 0,
  penalize_diagonal = TRUE,
  penalty_weights = NULL,
  config_post = list(),
  config_optim = list(),
  inception = NULL
)

Arguments

backend

optimization back used, either "nlopt" or "torch". Default is "nlopt"
trace

a integer for verbosity.
covariance

character setting the model for the covariance matrix. Either "full", "diagonal", "spherical" or "fixed". Default is "full".
Omega

precision matrix of the latent variables. Inverse of Sigma. Must be specified if covariance is "fixed"
penalty

a user-defined penalty to sparsify the residual covariance. Defaults to 0 (no sparsity).
penalize_diagonal

boolean: should the diagonal terms be penalized in the graphical-Lasso? Default is TRUE
penalty_weights

either a single or a list of p x p matrix of weights (default: all weights equal to 1) to adapt the amount of shrinkage to each pairs of node. Must be symmetric with positive values.
config_post

a list for controlling the post-treatments (optional bootstrap, jackknife, R2, etc.). See details
config_optim

a list for controlling the optimizer (either "nlopt" or "torch" backend). See details
inception

Set up the parameters initialization: by default, the model is initialized with a multivariate linear model applied on log-transformed data, and with the same formula as the one provided by the user. However, the user can provide a PLNfit (typically obtained from a previous fit), which sometimes speeds up the inference.

Details

See PLN_param() and PLNnetwork_param() for a full description of the generic optimization parameters. Like PLNnetwork_param(), ZIPLN_param() has two parameters controlling the optimization due the inner-outer loop structure of the optimizer:

  • "ftol_out" outer solver stops when an optimization step changes the objective function by less than ftol_out multiplied by the absolute value of the parameter. Default is 1e-6

  • "maxit_out" outer solver stops when the number of iteration exceeds maxit_out. Default is 100 and one additional parameter controlling the form of the variational approximation of the zero inflation:

  • "approx_ZI" either uses an exact or approximated conditional distribution for the zero inflation. Default is FALSE

Value

list of parameters used during the fit and post-processing steps

An R6 Class to represent a ZIPLNfit

Description

The function ZIPLN() fits a model which is an instance of an object with class ZIPLNfit.

This class comes with a set of R6 methods, some of which are useful for the end-user and exported as S3 methods. See the documentation for coef(), sigma(), predict().

Fields are accessed via active binding and cannot be changed by the user.

Details

Covariates for the Zero-Inflation parameter (using a logistic regression model) can be specified in the formula RHS using the pipe (⁠~ PLN effect | ZI effect⁠) to separate covariates for the PLN part of the model from those for the Zero-Inflation part. Note that different covariates can be used for each part.

Active bindings

n

number of samples/sites

q

number of dimensions of the latent space

p

number of variables/species

d

number of covariates in the PLN part

d0

number of covariates in the ZI part

nb_param_zi

number of parameters in the ZI part of the model

nb_param_pln

number of parameters in the PLN part of the model

nb_param

number of parameters in the ZIPLN model

model_par

a list with the matrices of parameters found in the model (B, Sigma, plus some others depending on the variant)

var_par

a list with two matrices, M and S2, which are the estimated parameters in the variational approximation

optim_par

a list with parameters useful for monitoring the optimization

latent

a matrix: values of the latent vector (Z in the model)

latent_pos

a matrix: values of the latent position vector (Z) without covariates effects or offset

fitted

a matrix: fitted values of the observations (A in the model)

vcov_model

character: the model used for the covariance (either "spherical", "diagonal", "full" or "sparse")

zi_model

character: the model used for the zero inflation (either "single", "row", "col" or "covar")

loglik

(weighted) variational lower bound of the loglikelihood

loglik_vec

element-wise variational lower bound of the loglikelihood

AIC

variational lower bound of the AIC

BIC

variational lower bound of the BIC

entropy

Entropy of the variational distribution

entropy_ZI

Entropy of the variational distribution

entropy_PLN

Entropy of the Gaussian variational distribution in the PLN component

ICL

variational lower bound of the ICL

criteria

a vector with loglik, BIC, ICL and number of parameters

Methods

Public methods

Method update()

Update a ZIPLNfit object

Usage
ZIPLNfit$update(
  B = NA,
  B0 = NA,
  Pi = NA,
  Omega = NA,
  Sigma = NA,
  M = NA,
  S = NA,
  R = NA,
  Ji = NA,
  Z = NA,
  A = NA,
  monitoring = NA
)
Arguments
B

matrix of regression parameters in the Poisson lognormal component

B0

matrix of regression parameters in the zero inflated component

Pi

Zero inflated probability parameter (either scalar, row-vector, col-vector or matrix)

Omega

precision matrix of the latent variables

Sigma

covariance matrix of the latent variables

M

matrix of mean vectors for the variational approximation

S

matrix of standard deviation parameters for the variational approximation

R

matrix of probabilities for the variational approximation

Ji

vector of variational lower bounds of the log-likelihoods (one value per sample)

Z

matrix of latent vectors (includes covariates and offset effects)

A

matrix of fitted values

monitoring

a list with optimization monitoring quantities

Returns

Update the current ZIPLNfit object

Method new()

Initialize a ZIPLNfit model

Usage
ZIPLNfit$new(data, control)
Arguments
data

a named list used internally to carry the data matrices

control

a list for controlling the optimization. See details.

Method optimize()

Call to the Cpp optimizer and update of the relevant fields

Usage
ZIPLNfit$optimize(data, control)
Arguments
data

a named list used internally to carry the data matrices

control

a list for controlling the optimization. See details.

Method optimize_vestep()

Result of one call to the VE step of the optimization procedure: optimal variational parameters (M, S, R) and corresponding log likelihood values for fixed model parameters (Sigma, B, B0). Intended to position new data in the latent space.

Usage
ZIPLNfit$optimize_vestep(
  data,
  B = self$model_par$B,
  B0 = self$model_par$B0,
  Omega = self$model_par$Omega,
  control = ZIPLN_param(backend = "nlopt")$config_optim
)
Arguments
data

a named list used internally to carry the data matrices

B

Optional fixed value of the regression parameters in the PLN component

B0

Optional fixed value of the regression parameters in the ZI component

Omega

inverse variance-covariance matrix of the latent variables

control

a list for controlling the optimization. See details.

Returns

A list with three components:

  • the matrix M of variational means,

  • the matrix S of variational standard deviations

  • the matrix R of variational ZI probabilities

  • the vector Ji of (variational) log-likelihood of each new observation

  • a list monitoring with information about convergence status

Method predict()

Predict position, scores or observations of new data. See predict.ZIPLNfit() for the S3 method and additional details

Usage
ZIPLNfit$predict(
  newdata,
  responses = NULL,
  type = c("link", "response", "deflated"),
  level = 1,
  envir = parent.frame()
)
Arguments
newdata

A data frame in which to look for variables with which to predict. If omitted, the fitted values are used.

responses

Optional data frame containing the count of the observed variables (matching the names of the provided as data in the PLN function), assuming the interest in in testing the model.

type

Scale used for the prediction. Either "link" (default, predicted positions in the latent space), "response" (predicted average counts, accounting for zero-inflation) or "deflated" (predicted average counts, not accounting for zero-inflation and using only the PLN part of the model).

level

Optional integer value the level to be used in obtaining the predictions. Level zero corresponds to the population predictions (default if responses is not provided) while level one (default) corresponds to predictions after evaluating the variational parameters for the new data.

envir

Environment in which the prediction is evaluated

Returns

A matrix with predictions scores or counts.

Method show()

User friendly print method

Usage
ZIPLNfit$show(
  model = paste("A multivariate Zero Inflated Poisson Lognormal fit with",
    self$vcov_model, "covariance model.\n")
)
Arguments
model

First line of the print output

Method print()

User friendly print method

Usage
ZIPLNfit$print()

Method clone()

The objects of this class are cloneable with this method.

Usage
ZIPLNfit$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
# See other examples in function ZIPLN
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- ZIPLN(Abundance ~ 1, data = trichoptera)
class(myPLN)
print(myPLN)

## End(Not run)

An R6 Class to represent a ZIPLNfit in a standard, general framework, with diagonal residual covariance

Description

An R6 Class to represent a ZIPLNfit in a standard, general framework, with diagonal residual covariance

An R6 Class to represent a ZIPLNfit in a standard, general framework, with diagonal residual covariance

Super class

PLNmodels::ZIPLNfit -> ZIPLNfit_diagonal

Active bindings

nb_param_pln

number of parameters in the PLN part of the current model

vcov_model

character: the model used for the residual covariance

Methods

Public methods

Inherited methods

Method new()

Initialize a ZIPLNfit_diagonal model

Usage
ZIPLNfit_diagonal$new(data, control)
Arguments
data

a named list used internally to carry the data matrices

control

a list for controlling the optimization. See details.

Method clone()

The objects of this class are cloneable with this method.

Usage
ZIPLNfit_diagonal$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
# See other examples in function ZIPLN
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- ZIPLN(Abundance ~ 1, data = trichoptera, control = ZIPLN_param(covariance = "diagonal"))
class(myPLN)
print(myPLN)

## End(Not run)

An R6 Class to represent a ZIPLNfit in a standard, general framework, with fixed (inverse) residual covariance

Description

An R6 Class to represent a ZIPLNfit in a standard, general framework, with fixed (inverse) residual covariance

An R6 Class to represent a ZIPLNfit in a standard, general framework, with fixed (inverse) residual covariance

Super class

PLNmodels::ZIPLNfit -> ZIPLNfit_fixed

Active bindings

nb_param_pln

number of parameters in the PLN part of the current model

vcov_model

character: the model used for the residual covariance

Methods

Public methods

Inherited methods

Method new()

Initialize a ZIPLNfit_fixed model

Usage
ZIPLNfit_fixed$new(data, control)
Arguments
data

a named list used internally to carry the data matrices

control

a list for controlling the optimization. See details.

Method clone()

The objects of this class are cloneable with this method.

Usage
ZIPLNfit_fixed$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
# See other examples in function ZIPLN
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- ZIPLN(Abundance ~ 1, data = trichoptera,
    control = ZIPLN_param(Omega = diag(ncol(trichoptera$Abundance))))
class(myPLN)
print(myPLN)

## End(Not run)

An R6 Class to represent a ZIPLNfit in a standard, general framework, with sparse inverse residual covariance

Description

An R6 Class to represent a ZIPLNfit in a standard, general framework, with sparse inverse residual covariance

An R6 Class to represent a ZIPLNfit in a standard, general framework, with sparse inverse residual covariance

Super class

PLNmodels::ZIPLNfit -> ZIPLNfit_sparse

Active bindings

penalty

the global level of sparsity in the current model

penalty_weights

a matrix of weights controlling the amount of penalty element-wise.

n_edges

number of edges if the network (non null coefficient of the sparse precision matrix)

nb_param_pln

number of parameters in the PLN part of the current model

vcov_model

character: the model used for the residual covariance

pen_loglik

variational lower bound of the l1-penalized loglikelihood

EBIC

variational lower bound of the EBIC

density

proportion of non-null edges in the network

criteria

a vector with loglik, penalized loglik, BIC, EBIC, ICL, R_squared, number of parameters, number of edges and graph density

Methods

Public methods

Inherited methods

Method new()

Initialize a ZIPLNfit_fixed model

Usage
ZIPLNfit_sparse$new(data, control)
Arguments
data

a named list used internally to carry the data matrices

control

a list for controlling the optimization. See details.

Method latent_network()

Extract interaction network in the latent space

Usage
ZIPLNfit_sparse$latent_network(type = c("partial_cor", "support", "precision"))
Arguments
type

edge value in the network. Can be "support" (binary edges), "precision" (coefficient of the precision matrix) or "partial_cor" (partial correlation between species)

Returns

a square matrix of size ZIPLNfit_sparse$n

Method plot_network()

plot the latent network.

Usage
ZIPLNfit_sparse$plot_network(
  type = c("partial_cor", "support"),
  output = c("igraph", "corrplot"),
  edge.color = c("#F8766D", "#00BFC4"),
  remove.isolated = FALSE,
  node.labels = NULL,
  layout = layout_in_circle,
  plot = TRUE
)
Arguments
type

edge value in the network. Either "precision" (coefficient of the precision matrix) or "partial_cor" (partial correlation between species).

output

Output type. Either igraph (for the network) or corrplot (for the adjacency matrix)

edge.color

Length 2 color vector. Color for positive/negative edges. Default is c("#F8766D", "#00BFC4"). Only relevant for igraph output.

remove.isolated

if TRUE, isolated node are remove before plotting. Only relevant for igraph output.

node.labels

vector of character. The labels of the nodes. The default will use the column names ot the response matrix.

layout

an optional igraph layout. Only relevant for igraph output.

plot

logical. Should the final network be displayed or only sent back to the user. Default is TRUE.

Method clone()

The objects of this class are cloneable with this method.

Usage
ZIPLNfit_sparse$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
# See other examples in function ZIPLN
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- ZIPLN(Abundance ~ 1, data = trichoptera, control=  ZIPLN_param(penalty = 1))
class(myPLN)
print(myPLN)
plot(myPLN)

## End(Not run)

An R6 Class to represent a ZIPLNfit in a standard, general framework, with spherical residual covariance

Description

An R6 Class to represent a ZIPLNfit in a standard, general framework, with spherical residual covariance

An R6 Class to represent a ZIPLNfit in a standard, general framework, with spherical residual covariance

Super class

PLNmodels::ZIPLNfit -> ZIPLNfit_spherical

Active bindings

nb_param_pln

number of parameters in the PLN part of the current model

vcov_model

character: the model used for the residual covariance

Methods

Public methods

Inherited methods

Method new()

Initialize a ZIPLNfit_spherical model

Usage
ZIPLNfit_spherical$new(data, control)
Arguments
data

a named list used internally to carry the data matrices

control

a list for controlling the optimization. See details.

Method clone()

The objects of this class are cloneable with this method.

Usage
ZIPLNfit_spherical$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
# See other examples in function ZIPLN
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- ZIPLN(Abundance ~ 1, data = trichoptera, control = ZIPLN_param(covariance = "spherical"))
class(myPLN)
print(myPLN)

## End(Not run)

Zero Inflated Sparse Poisson lognormal model for network inference

Description

Perform sparse inverse covariance estimation for the Zero Inflated Poisson lognormal model using a variational algorithm. Iterate over a range of logarithmically spaced sparsity parameter values. Use the (g)lm syntax to specify the model (including covariates and offsets).

Usage

ZIPLNnetwork(
  formula,
  data,
  subset,
  weights,
  zi = c("single", "row", "col"),
  penalties = NULL,
  control = ZIPLNnetwork_param()
)

Arguments

formula

an object of class "formula": a symbolic description of the model to be fitted.
data

an optional data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model. If not found in data, the variables are taken from environment(formula), typically the environment from which lm is called.
subset

an optional vector specifying a subset of observations to be used in the fitting process.
weights

an optional vector of observation weights to be used in the fitting process.
zi

a character describing the model used for zero inflation, either of

  • "single" (default, one parameter shared by all counts)

  • "col" (one parameter per variable / feature)

  • "row" (one parameter per sample / individual). If covariates are specified in the formula RHS (see details) this parameter is ignored.

penalties

an optional vector of positive real number controlling the level of sparsity of the underlying network. if NULL (the default), will be set internally. See PLNnetwork_param() for additional tuning of the penalty.
control

a list-like structure for controlling the optimization, with default generated by ZIPLNnetwork_param(). See the associated documentation for details.

Details

Covariates for the Zero-Inflation parameter (using a logistic regression model) can be specified in the formula RHS using the pipe (⁠~ PLN effect | ZI effect⁠) to separate covariates for the PLN part of the model from those for the Zero-Inflation part. Note that different covariates can be used for each part.

Value

an R6 object with class ZIPLNnetworkfamily

See Also

The classes ZIPLNfit and ZIPLNnetworkfamily

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myZIPLNs <- ZIPLNnetwork(Abundance ~ 1, data = trichoptera, zi = "single")

Control of ZIPLNnetwork fit

Description

Helper to define list of parameters to control the ZIPLNnetwork fit. All arguments have defaults.

Usage

ZIPLNnetwork_param(
  backend = c("nlopt"),
  inception_cov = c("full", "spherical", "diagonal"),
  trace = 1,
  n_penalties = 30,
  min_ratio = 0.1,
  penalize_diagonal = TRUE,
  penalty_weights = NULL,
  config_post = list(),
  config_optim = list(),
  inception = NULL
)

Arguments

backend

optimization back used, either "nlopt" or "torch". Default is "nlopt"
inception_cov

Covariance structure used for the inception model used to initialize the PLNfamily. Defaults to "full" and can be constrained to "diagonal" and "spherical".
trace

a integer for verbosity.
n_penalties

an integer that specifies the number of values for the penalty grid when internally generated. Ignored when penalties is non NULL
min_ratio

the penalty grid ranges from the minimal value that produces a sparse to this value multiplied by min_ratio. Default is 0.1.
penalize_diagonal

boolean: should the diagonal terms be penalized in the graphical-Lasso? Default is TRUE
penalty_weights

either a single or a list of p x p matrix of weights (default: all weights equal to 1) to adapt the amount of shrinkage to each pairs of node. Must be symmetric with positive values.
config_post

a list for controlling the post-treatment (optional bootstrap, jackknife, R2, etc).
config_optim

a list for controlling the optimizer (either "nlopt" or "torch" backend). See details
inception

Set up the parameters initialization: by default, the model is initialized with a multivariate linear model applied on log-transformed data, and with the same formula as the one provided by the user. However, the user can provide a PLNfit (typically obtained from a previous fit), which sometimes speeds up the inference.

Details

See PLNnetwork_param() for a full description of the optimization parameters. Note that some defaults values are different than those used in PLNnetwork_param():

  • "ftol_out" (outer loop convergence tolerance the objective function) is set by default to 1e-6

  • "maxit_out" (max number of iterations for the outer loop) is set by default to 100

Value

list of parameters configuring the fit.

See Also

PLNnetwork_param() and PLN_param()

An R6 Class to represent a collection of ZIPLNnetwork

Description

The function ZIPLNnetwork() produces an instance of this class.

This class comes with a set of methods, some of them being useful for the user: See the documentation for getBestModel(), getModel() and plot()

Super classes

PLNmodels::PLNfamily -> PLNmodels::Networkfamily -> ZIPLNnetworkfamily

Public fields

covariates0

the matrix of covariates included in the ZI component

Methods

Public methods

Inherited methods

Method new()

Initialize all models in the collection

Usage
ZIPLNnetworkfamily$new(penalties, data, control)
Arguments
penalties

a vector of positive real number controlling the level of sparsity of the underlying network.

data

a named list used internally to carry the data matrices

control

a list for controlling the optimization.

Returns

Update current PLNnetworkfit with smart starting values

Method stability_selection()

Compute the stability path by stability selection

Usage
ZIPLNnetworkfamily$stability_selection(
  subsamples = NULL,
  control = ZIPLNnetwork_param()
)
Arguments
subsamples

a list of vectors describing the subsamples. The number of vectors (or list length) determines the number of subsamples used in the stability selection. Automatically set to 20 subsamples with size 10*sqrt(n) if n >= 144 and 0.8*n otherwise following Liu et al. (2010) recommendations.

control

a list controlling the main optimization process in each call to PLNnetwork(). See ZIPLNnetwork() and ZIPLN_param() for details.

Method clone()

The objects of this class are cloneable with this method.

Usage
ZIPLNnetworkfamily$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

The function ZIPLNnetwork(), the class ZIPLNfit_sparse

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
class(fits)