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Unnaming $penalty for bipartite, fixing broken CRAN badge #14

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Sep 9, 2024
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Unnaming $penalty for bipartite, fixing broken CRAN badge #14

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3acbd4e
BipartiteSBM_fit: unnaming penalty and modifying test accordingly
Polarolouis Sep 6, 2024
d494e8c
readme: fixing CRAN status badge
Polarolouis Sep 6, 2024
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87 changes: 47 additions & 40 deletions R/R6Class-BipartiteSBM_fit.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,14 +9,14 @@ BipartiteSBM_fit <-
classname = "BipartiteSBM_fit",
inherit = BipartiteSBM,
private = list(
J = NULL, # approximation of the log-likelihood
vICL = NULL, # approximation of the ICL
BMobject = NULL, # blockmodels output (used to stored the optimization results when blockmodels is used)
J = NULL, # approximation of the log-likelihood
vICL = NULL, # approximation of the ICL
BMobject = NULL, # blockmodels output (used to stored the optimization results when blockmodels is used)
import_from_BM = function(index = which.max(private$BMobject$ICL)) {
private$J <- private$BMobject$PL[index]
private$vICL <- private$BMobject$ICL[index]
parameters <- private$BMobject$model_parameters[[index]]
private$beta <- parameters$beta ## NULL if no covariates
private$J <- private$BMobject$PL[index]
private$vICL <- private$BMobject$ICL[index]
parameters <- private$BMobject$model_parameters[[index]]
private$beta <- parameters$beta ## NULL if no covariates
private$theta <- switch(private$BMobject$model_name,
"bernoulli" = list(mean = parameters$pi),
"bernoulli_covariates" = list(mean = .logistic(parameters$m)),
Expand All @@ -32,7 +32,6 @@ BipartiteSBM_fit <-
col = private$BMobject$memberships[[index]]$Z2
)
private$pi <- lapply(private$Z, colMeans)

}
),
public = list(
Expand All @@ -41,10 +40,9 @@ BipartiteSBM_fit <-
#' @param model character (\code{'bernoulli'}, \code{'poisson'}, \code{'gaussian'})
#' @param dimLabels labels of each dimension (in row, in columns)
#' @param covarList and optional list of covariates, each of whom must have the same dimension as \code{incidenceMatrix}
initialize = function(incidenceMatrix, model, dimLabels=c(row="row", col="col"), covarList=list()) {

initialize = function(incidenceMatrix, model, dimLabels = c(row = "row", col = "col"), covarList = list()) {
## SANITY CHECKS on data
stopifnot(is.matrix(incidenceMatrix)) # must be a matrix
stopifnot(is.matrix(incidenceMatrix)) # must be a matrix
stopifnot(all(sapply(covarList, nrow) == nrow(incidenceMatrix))) # consistency of the covariates
stopifnot(all(sapply(covarList, ncol) == ncol(incidenceMatrix))) # with the network data

Expand All @@ -57,37 +55,38 @@ BipartiteSBM_fit <-
)

## INITIALIZE THE SBM OBJECT ACCORDING TO THE DATA
super$initialize(model = model,
nbNodes = dim(incidenceMatrix),
blockProp = rep(list(vector("numeric", 0)), 2),
connectParam = connectParam,
dimLabels = dimLabels,
covarList = covarList)
super$initialize(
model = model,
nbNodes = dim(incidenceMatrix),
blockProp = rep(list(vector("numeric", 0)), 2),
connectParam = connectParam,
dimLabels = dimLabels,
covarList = covarList
)
private$Y <- incidenceMatrix
},
#' @description function to perform optimization
#' @param estimOptions a list of parameters controlling the inference algorithm and model selection. See details.
#' @inherit estimateSimpleSBM details
optimize = function(estimOptions = list()){

if(private$model == 'ZIgaussian') stop("Inference not yet implemented for Bipartite ZI gaussian network")
optimize = function(estimOptions = list()) {
if (private$model == "ZIgaussian") stop("Inference not yet implemented for Bipartite ZI gaussian network")

currentOptions <- list(
verbosity = 3,
plot = TRUE,
exploreFactor = 1.5,
exploreMin = 4,
exploreMax = Inf,
nbBlocksRange = c(4,Inf),
nbCores = 2,
fast = TRUE
verbosity = 3,
plot = TRUE,
exploreFactor = 1.5,
exploreMin = 4,
exploreMax = Inf,
nbBlocksRange = c(4, Inf),
nbCores = 2,
fast = TRUE
)
currentOptions[names(estimOptions)] <- estimOptions

## Transform estimOptions to a suited for blockmodels list of options
blockmodelsOptions <- list(
verbosity = currentOptions$verbosity,
plotting = if(currentOptions$plot) character(0) else "",
plotting = if (currentOptions$plot) character(0) else "",
explore_min = currentOptions$exploreMin,
explore_max = currentOptions$exploreMax,
ncores = currentOptions$nbCores,
Expand All @@ -103,8 +102,8 @@ BipartiteSBM_fit <-

## model construction

model_type <- ifelse(self$nbCovariates > 0, paste0(private$model,"_covariates"), private$model)
if (model_type == 'bernoulli_covariates' & fast == TRUE) model_type <- 'bernoulli_covariates_fast'
model_type <- ifelse(self$nbCovariates > 0, paste0(private$model, "_covariates"), private$model)
if (model_type == "bernoulli_covariates" & fast == TRUE) model_type <- "bernoulli_covariates_fast"
private$BMobject <- do.call(paste0("BM_", model_type), args)

## performing estimation
Expand Down Expand Up @@ -137,7 +136,7 @@ BipartiteSBM_fit <-
},
#' @description show method
#' @param type character used to specify the type of SBM
show = function(type = "Fit of a Bipartite Stochastic Block Model"){
show = function(type = "Fit of a Bipartite Stochastic Block Model") {
super$show(type)
cat("* Additional fields\n")
cat(" $probMemberships, $loglik, $ICL, $storedModels, \n")
Expand All @@ -147,26 +146,34 @@ BipartiteSBM_fit <-
),
active = list(
#' @field loglik double: approximation of the log-likelihood (variational lower bound) reached
loglik = function(value) {private$J},
loglik = function(value) {
private$J
},
#' @field ICL double: value of the integrated classification log-likelihood
ICL = function(value) {private$vICL},
ICL = function(value) {
private$vICL
},
#' @field penalty double, value of the penalty term in ICL
penalty = function(value) {(self$nbConnectParam + self$nbCovariates) * log(self$nbDyads) + (self$nbBlocks[1]-1) * log(private$dim[1]) + (self$nbBlocks[2]-1) * log(private$dim[2])},
penalty = function(value) {
unname((self$nbConnectParam + self$nbCovariates) * log(self$nbDyads) + (self$nbBlocks[1] - 1) * log(private$dim[1]) + (self$nbBlocks[2] - 1) * log(private$dim[2]))
},
#' @field entropy double, value of the entropy due to the clustering distribution
entropy = function(value) {-sum(.xlogx(private$Z[[1]]))-sum(.xlogx(private$Z[[2]]))},
entropy = function(value) {
-sum(.xlogx(private$Z[[1]])) - sum(.xlogx(private$Z[[2]]))
},
#' @field storedModels data.frame of all models fitted (and stored) during the optimization
storedModels = function(value) {
rowBlocks <- c(0, unlist(sapply(private$BMobject$memberships, function(m) ncol(m$Z1))))
colBlocks <- c(0, unlist(sapply(private$BMobject$memberships, function(m) ncol(m$Z2))))
nbConnectParam <- c(NA, unlist(sapply(private$BMobject$model_parameters, function(param) param$n_parameters)))
U <- data.frame(
indexModel = rowBlocks + colBlocks,
nbParams = nbConnectParam + rowBlocks + colBlocks - 2,
nbParams = nbConnectParam + rowBlocks + colBlocks - 2,
rowBlocks = rowBlocks,
colBlocks = colBlocks,
nbBlocks = rowBlocks + colBlocks,
ICL = private$BMobject$ICL,
loglik = private$BMobject$PL
nbBlocks = rowBlocks + colBlocks,
ICL = private$BMobject$ICL,
loglik = private$BMobject$PL
)
U[!is.na(U$nbParams), , drop = FALSE]
}
Expand Down
2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -18,7 +18,7 @@ knitr::opts_chunk$set(
<!-- badges: start -->
[![website](https://github.com/GrossSBM/sbm/workflows/pkgdown/badge.svg)](https://grosssbm.github.io/sbm/)
![R-CMD-check](https://github.com/GrossSBM/sbm/workflows/R-CMD-check/badge.svg?branch=master)
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/sbm)](https://cran.r-project.org/package=sbm)
[![CRAN status](https://www.r-pkg.org/badges/version/sbm)](https://CRAN.R-project.org/package=sbm)
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![](https://img.shields.io/github/last-commit/grossSBM/sbm.svg)](https://github.com/GrossSBM/sbm/commits/master)
[![Codecov test coverage](https://codecov.io/gh/GrossSBM/sbm/branch/master/graph/badge.svg)](
Expand Down
3 changes: 2 additions & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,8 @@

[![website](https://github.com/GrossSBM/sbm/workflows/pkgdown/badge.svg)](https://grosssbm.github.io/sbm/)
![R-CMD-check](https://github.com/GrossSBM/sbm/workflows/R-CMD-check/badge.svg?branch=master)
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/sbm)](https://cran.r-project.org/package=sbm)
[![CRAN
status](https://www.r-pkg.org/badges/version/sbm)](https://CRAN.R-project.org/package=sbm)
[![Lifecycle:
experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![](https://img.shields.io/github/last-commit/grossSBM/sbm.svg)](https://github.com/GrossSBM/sbm/commits/master)
Expand Down
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