Merge branch 'v1.0.2' into 'master'

V1.0.2

See merge request aduvermy/HTRfit!2

man/getSE_df.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/wrapperdeseq2.R
+% Please edit documentation in R/wrapper_dds.R
 \name{getSE_df}
 \alias{getSE_df}
 \title{Extract Standard Error Information from DESeq2 Results}

man/getSampleID.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulation2.R
+% Please edit documentation in R/simulation.R
 \name{getSampleID}
 \alias{getSampleID}
 \title{getSampleID}
@@ -15,3 +15,6 @@ A sorted vector of sample IDs
 \description{
 getSampleID
 }
+\examples{
+getSampleID(init_variable())
+}

man/getSampleMetadata.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulation2.R
+% Please edit documentation in R/simulation.R
 \name{getSampleMetadata}
 \alias{getSampleMetadata}
 \title{Get sample metadata}

man/getValidDispersion.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mock-rnaseq.R
+% Please edit documentation in R/mock_rnaseq.R
 \name{getValidDispersion}
 \alias{getValidDispersion}
 \title{Validate and Filter Dispersion Values}

man/get_inference.Rd → man/get_inference_dds.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/wrapperdeseq2.R
-\name{get_inference}
-\alias{get_inference}
+% Please edit documentation in R/wrapper_dds.R
+\name{get_inference_dds}
+\alias{get_inference_dds}
 \title{Calculate Inference for Differential Expression Analysis}
 \usage{
-get_inference(dds_full, lfcThreshold, altHypothesis, correction_method)
+get_inference_dds(dds_full, lfcThreshold, altHypothesis, correction_method)
 }
 \arguments{
 \item{dds_full}{A data frame containing DESeq2 results, including estimate and standard error information.}
@@ -24,7 +24,7 @@ This function calculates inference for differential expression analysis based on
 \examples{
 \dontrun{
 # Example usage of the function
-inference_result <- get_inference(dds_full, lfcThreshold = 0.5, 
+inference_result <- get_inference_dds(dds_full, lfcThreshold = 0.5, 
                                    altHypothesis = "greater", 
                                    correction_method = "BH")
 }

man/glance_tmb.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/glance_tmb.R
+% Please edit documentation in R/glance_glmmtmb.R
 \name{glance_tmb}
 \alias{glance_tmb}
 \title{Extracts the summary statistics from a list of glmmTMB models.}
 \usage{
-glance_tmb(l_tmb)
+glance_tmb(list_tmb)
 }
 \arguments{
-\item{l_tmb}{A list of glmmTMB models or a unique glmmTMB obj model}
+\item{list_tmb}{A list of glmmTMB models or a unique glmmTMB obj model}
 }
 \value{
 A DataFrame with the summary statistics for all the glmmTMB models in the list.

man/group_logQij_per_genes_and_labels.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/evaluationwithmixedeffect.R
+% Please edit documentation in R/evaluation_withmixedeffect.R
 \name{group_logQij_per_genes_and_labels}
 \alias{group_logQij_per_genes_and_labels}
 \title{Group log_qij values per genes and labels.}

man/handleAnovaError.Rd

@@ -4,10 +4,10 @@
 \alias{handleAnovaError}
 \title{Handle ANOVA Errors}
 \usage{
-handleAnovaError(l_TMB, group, ...)
+handleAnovaError(list_tmb, group, ...)
 }
 \arguments{
-\item{l_TMB}{A list of fitted glmmTMB models.}
+\item{list_tmb}{A list of fitted glmmTMB models.}
 
 \item{group}{A character string indicating the group for which ANOVA is calculated.}
 
@@ -20,8 +20,8 @@ A data frame containing ANOVA results for the specified group.
 This function handles ANOVA errors and warnings during the ANOVA calculation process.
 }
 \examples{
-l_tmb <- fitModelParallel(Sepal.Length ~ Sepal.Width + Petal.Length,
+list_tmb <- fitModelParallel(Sepal.Length ~ Sepal.Width + Petal.Length,
                           data = iris, group_by = "Species", n.cores = 1)
-anova_res <- handleAnovaError(l_tmb, "setosa", type = "III")
+anova_res <- handleAnovaError(list_tmb, "setosa", type = "III")
 
 }

man/identity_plot.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/identityplot.R
+% Please edit documentation in R/identity_plot.R
 \name{identity_plot}
 \alias{identity_plot}
 \title{Generate an identity plot}

man/inferenceToExpected_withMixedEff.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/evaluationwithmixedeffect.R
+% Please edit documentation in R/evaluation_withmixedeffect.R
 \name{inferenceToExpected_withMixedEff}
 \alias{inferenceToExpected_withMixedEff}
 \title{Compare the mixed-effects inference to expected values.}

man/isValidInput2fit.Rd

@@ -22,4 +22,3 @@ data(iris)
 formula <- Sepal.Length ~ Sepal.Width + Petal.Length
 isValidInput2fit(iris, formula) # Returns TRUE if all required variables are present
 }
-\keyword{internal}

man/dot-isDispersionMatrixValid.Rd → man/is_dispersionMatrixValid.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mock-rnaseq.R
-\name{.isDispersionMatrixValid}
-\alias{.isDispersionMatrixValid}
+% Please edit documentation in R/mock_rnaseq.R
+\name{is_dispersionMatrixValid}
+\alias{is_dispersionMatrixValid}
 \title{Check the validity of the dispersion matrix}
 \usage{
-.isDispersionMatrixValid(matx_dispersion, matx_bool_replication)
+is_dispersionMatrixValid(matx_dispersion, matx_bool_replication)
 }
 \arguments{
 \item{matx_dispersion}{Replication matrix}
@@ -20,5 +20,5 @@ Checks if the dispersion matrix has the correct dimensions.
 \examples{
 matx_dispersion <- matrix(1:12, nrow = 3, ncol = 4)
 matx_bool_replication <- matrix(TRUE, nrow = 3, ncol = 4)
-.isDispersionMatrixValid(matx_dispersion, matx_bool_replication)
+is_dispersionMatrixValid(matx_dispersion, matx_bool_replication)
 }

man/is_formula_mixedTypeI.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/evaluationwithmixedeffect.R
+% Please edit documentation in R/evaluation_withmixedeffect.R
 \name{is_formula_mixedTypeI}
 \alias{is_formula_mixedTypeI}
 \title{Check if the formula follows a specific type I mixed effect structure.}

man/is_mixedEffect_inFormula.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/evaluationwithmixedeffect.R
+% Please edit documentation in R/evaluation_withmixedeffect.R
 \name{is_mixedEffect_inFormula}
 \alias{is_mixedEffect_inFormula}
 \title{Check if the formula contains a mixed effect structure.}

man/is_positive_definite.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/datafrommvrnorm_manipulations.R
+% Please edit documentation in R/utils.R
 \name{is_positive_definite}
 \alias{is_positive_definite}
 \title{Check if a matrix is positive definite

man/launchUpdate.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/updatefitmodel.R
+% Please edit documentation in R/update_fittedmodel.R
 \name{launchUpdate}
 \alias{launchUpdate}
 \title{Launch the update process for a GLMNB model.}
 \usage{
-launchUpdate(glmnb_obj, formula, ...)
+launchUpdate(glmm_obj, formula, ...)
 }
 \arguments{
-\item{glmnb_obj}{A GLMNB object to be updated.}
+\item{glmm_obj}{A glmmTMB object to be updated.}
 
 \item{formula}{Formula for the updated GLMNB model.}
 

man/metrics_plot.Rd

@@ -4,10 +4,10 @@
 \alias{metrics_plot}
 \title{Plot Metrics for Generalized Linear Mixed Models (GLMM)}
 \usage{
-metrics_plot(l_tmb, focus = NULL)
+metrics_plot(list_tmb, focus = NULL)
 }
 \arguments{
-\item{l_tmb}{A list of GLMM objects to extract metrics from.}
+\item{list_tmb}{A list of GLMM objects to extract metrics from.}
 
 \item{focus}{A character vector specifying the metrics to focus on. Possible
 values include "AIC", "BIC", "logLik", "deviance", "df.resid", and

man/mock_rnaseq.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mock-rnaseq.R
+% Please edit documentation in R/mock_rnaseq.R
 \name{mock_rnaseq}
 \alias{mock_rnaseq}
 \title{Perform RNA-seq simulation}

man/dot-parallel_fit.Rd → man/parallel_fit.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/fitmodel.R
-\name{.parallel_fit}
-\alias{.parallel_fit}
+\name{parallel_fit}
+\alias{parallel_fit}
 \title{Fit models in parallel for each group using mclapply and handle logging.
 Uses parallel_fit to fit the models.}
 \usage{
-.parallel_fit(groups, group_by, formula, data, n.cores = NULL, log_file, ...)
+parallel_fit(
+  groups,
+  group_by,
+  formula,
+  data,
+  n.cores = NULL,
+  log_file = paste(tempdir(check = FALSE), "htrfit.log", sep = "/"),
+  ...
+)
 }
 \arguments{
 \item{groups}{Vector of unique group values}
@@ -19,7 +27,7 @@ Uses parallel_fit to fit the models.}
 \item{n.cores}{The number of CPU cores to use for parallel processing.
 If set to NULL (default), the number of available CPU cores will be automatically detected.}
 
-\item{log_file}{File to write log (default : log.txt)}
+\item{log_file}{File to write log (default : Rtmpdir/htrfit.log)}
 
 \item{...}{Additional arguments to be passed to the glmmTMB::glmmTMB function}
 }
@@ -31,7 +39,7 @@ Fit models in parallel for each group using mclapply and handle logging.
 Uses parallel_fit to fit the models.
 }
 \examples{
-.parallel_fit(group_by = "Species", "setosa", 
+parallel_fit(group_by = "Species", "setosa", 
                formula = Sepal.Length ~ Sepal.Width + Petal.Length, 
-               data = iris, n.cores = 1, log_file = "log.txt" )
+               data = iris, n.cores = 1 )
 }

man/dot-parallel_update.Rd → man/parallel_update.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/updatefitmodel.R
-\name{.parallel_update}
-\alias{.parallel_update}
-\title{Internal function to fit GLMNB models in parallel.}
+% Please edit documentation in R/update_fittedmodel.R
+\name{parallel_update}
+\alias{parallel_update}
+\title{Internal function to fit glmmTMB models in parallel.}
 \usage{
-.parallel_update(formula, l_tmb, n.cores = NULL, log_file = "log.txt", ...)
+parallel_update(
+  formula,
+  list_tmb,
+  n.cores = NULL,
+  log_file = paste(tempdir(check = FALSE), "htrfit.log", sep = "/"),
+  ...
+)
 }
 \arguments{
 \item{formula}{Formula for the GLMNB model.}
 
-\item{l_tmb}{List of GLMNB objects.}
+\item{list_tmb}{List of glmmTMB objects.}
 
 \item{n.cores}{Number of cores to use for parallel processing.}
 
-\item{log_file}{File path for the log output.}
+\item{log_file}{File path for the log output (default : Rtmpdir/htrfit.log).}
 
 \item{...}{Additional arguments to be passed to the glmmTMB::glmmTMB function.}
 }
@@ -21,7 +27,7 @@
 A list of updated GLMNB models.
 }
 \description{
-This function is used internally by \code{\link{updateParallel}} to fit GLMNB models in parallel.
+This function is used internally by \code{\link{updateParallel}} to fit glmmTMB models in parallel.
 }
 \examples{
 data(iris)
@@ -30,5 +36,5 @@ group_by <- "Species"
 formula <- Sepal.Length ~ Sepal.Width + Petal.Length
 fitted_models <- fitModelParallel(formula, iris, group_by, n.cores = 1)
 new_formula <- Sepal.Length ~ Sepal.Width 
-results <- .parallel_update(new_formula, fitted_models, n.cores = 1)
+results <- parallel_update(new_formula, fitted_models, n.cores = 1)
 }