@@ -24,7 +24,7 @@ Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,

 LinkingTo: Rcpp, RcppEigen

 License: MIT + file LICENSE

 Encoding: UTF-8

-LazyData: false

+LazyData: true

 RoxygenNote: 7.1.1

 BugReports: https://github.com/campbio/celda/issues

 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian

@@ -15,6 +15,7 @@

 #'  to use. Default "featureSubset".

 #' @param value Character vector of cell cluster labels for replacements. Works

 #'  only if \code{x} is a \linkS4class{SingleCellExperiment} object.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return One of

 #' \itemize{

 #'  \item Character vector if \code{x} is a

@@ -144,6 +145,7 @@ setReplaceMethod("celdaModules", signature(sce = "SingleCellExperiment"),

 #'  to use. Default "featureSubset".

 #' @param value Character vector of sample labels for replacements. Works

 #'  only is \code{x} is a \linkS4class{SingleCellExperiment} object.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return Character vector. Contains the sample labels provided at model

 #'  creation, or those automatically generated by celda.

 #' @export

@@ -201,7 +203,8 @@ setMethod("sampleLabel",

 #' @description Retrieves the K/L, model priors (e.g. alpha, beta),

 #'  and count matrix checksum parameters provided during the creation of the

 #'  provided celdaModel.

-#' @param celdaMod celdaModel. Options available in `celda::availableModels`.

+#' @param celdaMod celdaModel. Options available in

+#'  \code{celda::availableModels}.

 #' @return List. Contains the model-specific parameters for the provided celda

 #'  model object depending on its class.

 #' @export

@@ -262,6 +265,7 @@ setMethod("matrixNames",

 #'  \code{celdaList}.

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return Data Frame. Contains details on the various K/L parameters, chain

 #'  parameters, seed, and final log-likelihoods derived for each model in the

 #'  provided celdaList.

@@ -308,6 +312,7 @@ setMethod("runParams",

 #'  \code{celdaList}.

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return List. Contains one celdaModel object for each of the parameters

 #'  specified in \code{runParams(x)}.

 #' @export

@@ -354,6 +359,7 @@ setMethod("resList",

 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return Character. The celda model. Can be one of "celda_C", "celda_G", or

 #'  "celda_CG".

 #' @examples

@@ -46,6 +46,7 @@

 #' @return A \linkS4class{SingleCellExperiment} object. Function

 #'  parameter settings and celda model results are stored in the

 #'  \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @seealso \link{celda_G} for feature clustering, \link{celda_C} for

 #'  clustering of cells, and \link{celda_CG} for simultaneous clustering of

 #'  features and cells. \link{subsetCeldaList} can subset the \code{celdaList}

@@ -444,6 +445,7 @@ setMethod("celdaGridSearch",

 #'  \linkS4class{SingleCellExperiment} object. Default "counts".

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return One of

 #' \itemize{

 #'  \item A new \linkS4class{SingleCellExperiment} object containing

@@ -587,6 +589,7 @@ setMethod("subsetCeldaList",

 #'  \linkS4class{SingleCellExperiment} object. Default "counts".

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return One of

 #' \itemize{

 #'  \item A new \linkS4class{SingleCellExperiment} object containing

@@ -57,6 +57,7 @@

 #' @param logfile Character. Messages will be redirected to a file named

 #'  `logfile`. If NULL, messages will be printed to stdout.  Default NULL.

 #' @param verbose Logical. Whether to print log messages. Default TRUE.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object. Function

 #'  parameter settings are stored in the \link[S4Vectors]{metadata}

 #'  \code{"celda_parameters"} slot.

@@ -69,6 +69,7 @@

 #' @param logfile Character. Messages will be redirected to a file named

 #'  `logfile`. If NULL, messages will be printed to stdout.  Default NULL.

 #' @param verbose Logical. Whether to print log messages. Default TRUE.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return A \linkS4class{SingleCellExperiment} object. Function

 #'  parameter settings are stored in \link[S4Vectors]{metadata}

 #'  \code{"celda_parameters"} in \link[SingleCellExperiment]{altExp} slot.

@@ -51,6 +51,7 @@

 #' @param logfile Character. Messages will be redirected to a file named

 #'  `logfile`. If NULL, messages will be printed to stdout.  Default NULL.

 #' @param verbose Logical. Whether to print log messages. Default TRUE.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return A \linkS4class{SingleCellExperiment} object. Function

 #'  parameter settings are stored in the \link[S4Vectors]{metadata}

 #'  \code{"celda_parameters"} slot. Column \code{celda_feature_module} in

@@ -238,6 +238,7 @@ recodeClusterY <- function(sce, from, to, altExpName = "featureSubset") {

 #' @param celdaMod A \code{celdaModel} or \code{celdaList} object.

 #' @param errorOnMismatch Logical. Whether to throw an error in the event of

 #'  a mismatch. Default TRUE.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return Returns TRUE if provided count matrix matches the one used in the

 #'  celda object and/or \code{errorOnMismatch = FALSE}, FALSE otherwise.

 #' @export

@@ -45,6 +45,7 @@

 #' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility,

 #'  a default value of 12345 is used. If NULL, no calls to

 #'  \link[withr]{with_seed} are made.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return \code{sce} with t-SNE coordinates

 #'  (columns "celda_tSNE1" & "celda_tSNE2") added to

 #'  \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_tSNE")}.

@@ -14,6 +14,7 @@

 #'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return A \linkS4class{SingleCellExperiment} object. Function

 #'  parameter settings are stored in the \link[S4Vectors]{metadata}

 #'  \code{"celda_parameters"} slot.

@@ -15,6 +15,7 @@

 #' @param log Logical. If \code{FALSE}, then the normalized conditional

 #'  probabilities will be returned. If \code{TRUE}, then the unnormalized log

 #'  probabilities will be returned. Default \code{FALSE}.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @examples

 #' data(sceCeldaCG)

 #' clusterProb <- clusterProbability(sceCeldaCG, log = TRUE)

@@ -25,62 +25,61 @@ availableModels <- c("celda_C", "celda_G", "celda_CG")

 #' @description celda_CG model object generated from \code{celdaCGSim} using

 #'  old \code{celda_CG} function.

 #' @format A celda_CG object

-#' #@examples

-#' data(celdaCGSim)

-#' celdaCGMod <- celda_CG(celdaCGSim$counts,

-#'   K = celdaCGSim$K,

-#'   L = celdaCGSim$L,

-#'   nchains = 1)

+# @examples

+# data(celdaCGSim)

+# celdaCGMod <- celda_CG(celdaCGSim$counts,

+#   K = celdaCGSim$K,

+#   L = celdaCGSim$L,

+#   nchains = 1)

 "celdaCGMod"

 #' @title celdaCGGridSearchRes

 #' @description Example results of old celdaGridSearch on celdaCGSim

 #' @format An object as returned from old celdaGridSearch()

-#' #@examples

-#' data(celdaCGSim)

-#' celdaCGGridSearchRes <- celdaGridSearch(celdaCGSim$counts,

-#'   model = "celda_CG",

-#'   paramsTest = list(K = seq(4, 6), L = seq(9, 11)),

-#'   paramsFixed = list(sampleLabel = celdaCGSim$sampleLabel),

-#'   bestOnly = TRUE,

-#'   nchains = 1,

-#'   cores = 2

-#' )

+# @examples

+# data(celdaCGSim)

+# celdaCGGridSearchRes <- celdaGridSearch(celdaCGSim$counts,

+#   model = "celda_CG",

+#   paramsTest = list(K = seq(4, 6), L = seq(9, 11)),

+#   paramsFixed = list(sampleLabel = celdaCGSim$sampleLabel),

+#   bestOnly = TRUE,

+#   nchains = 1,

+#   cores = 2)

 "celdaCGGridSearchRes"

 #' @title celdaCSim

 #' @description An old example simulated count matrix from the celda_C model.

 #' @format A list of counts and properties as returned from old simulateCells().

-#' #@examples

-#' celdaCSim <- simulateCells("celda_C")

+# @examples

+# celdaCSim <- simulateCells("celda_C")

 "celdaCSim"

 #' @title celdaCMod

 #' @description Old celda_C results generated from celdaCSim

 #' @format A celda_C object

-#' #@examples

-#' data(celdaCSim)

-#' celdaCMod <- celda_C(celdaCSim$counts, K = celdaCSim$K, nchains = 1)

+# @examples

+# data(celdaCSim)

+# celdaCMod <- celda_C(celdaCSim$counts, K = celdaCSim$K, nchains = 1)

 "celdaCMod"

 #' @title celdaGSim

 #' @description An old example simulated count matrix from the celda_G model.

 #' @format A list of counts and properties as returned from old simulateCells()

-#' #@examples

-#' celdaGSim <- simulateCells("celda_G")

+# @examples

+# celdaGSim <- simulateCells("celda_G")

 "celdaGSim"

 #' @title celdaGMod

 #' @description Old celda_G results generated from celdaGsim

 #' @format A celda_G object

-#' #@examples

-#' data(celdaGSim)

-#' celdaGMod <- celda_G(celdaGSim$counts, L = celdaGSim$L, nchains = 1)

+# @examples

+# data(celdaGSim)

+# celdaGMod <- celda_G(celdaGSim$counts, L = celdaGSim$L, nchains = 1)

 "celdaGMod"

@@ -27,6 +27,7 @@

 #' @param fdrThreshold Numeric. A number between 0 and 1 that specifies the

 #'  false discovery rate (FDR) threshold. Only features below this threshold

 #'  will be returned. Default 1.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return Data frame containing MAST results including statistics such as

 #'  p-value, log2 fold change, and FDR.

 #' @export

@@ -26,6 +26,7 @@

 #'  returns the posterior estimates which include the addition of the Dirichlet

 #'  concentration parameter (essentially as a pseudocount). Default

 #'  \code{"counts"}.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @export

 setGeneric("factorizeMatrix",

     function(x, celdaMod, ...) {

@@ -12,6 +12,7 @@

 #'  to use. Default "featureSubset".

 #' @param exactMatch Logical. Whether to look for exactMatch of the gene name

 #'  within counts matrix. Default \code{TRUE}.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return List. Each entry corresponds to the feature module determined for

 #' the provided features.

 #' @export

@@ -47,6 +47,7 @@

 #'  cluster that includes several clusters within it. Default is TRUE.

 #' @param seed Numeric. Seed used to enable reproducible UMAP results

 #'  for identifying metaclusters. Default is 12345.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return A named list with six elements:

 #' \itemize{

 #'   \item rules - A named list with one data frame for every label. Each

@@ -20,6 +20,7 @@

 #' @param fdr False discovery rate (FDR). Numeric. Cutoff value for adjusted

 #'  p-value, terms with FDR below this value are considered significantly

 #'  enriched.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return List of length 'L' where each member contains the significantly

 #'  enriched terms for the corresponding module.

 #' @importFrom enrichR enrichr

@@ -11,6 +11,7 @@

 #'  to use. Default "featureSubset".

 #' @param celdaMod celda model object. Ignored if \code{x} is a

 #'  \linkS4class{SingleCellExperiment} object.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return The log-likelihood of the cluster assignment for the

 #'  provided \linkS4class{SingleCellExperiment}.

 #' @seealso `celda_C()` for clustering cells

@@ -155,6 +156,7 @@ setMethod("logLikelihood", signature(x = "matrix", celdaMod = "celda_CG"),

 #'  model object.

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return Numeric. The log-likelihood at each step of Gibbs sampling used to

 #'  generate the model.

 #' @export

@@ -200,11 +202,12 @@ setMethod("logLikelihoodHistory",

 #'  sampling used to generate a celdaModel.

 #' @return Numeric. The log-likelihood at the final step of Gibbs sampling used

 #'  to generate the model.

-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

-#'  to use. Default "featureSubset".

 #' @param x A \linkS4class{SingleCellExperiment} object

 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}, or a celda

 #'  model object.

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @export

 setGeneric(

     "bestLogLikelihood",

@@ -15,8 +15,6 @@

 #'  \linkS4class{SingleCellExperiment} object. Default "counts".

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

-#' @param celdaMod Celda object of class \link{celda_G} or \link{celda_CG}. Used

-#'  only if \code{x} is a matrix object.

 #' @param featureModule Integer Vector. The featureModule(s) to display.

 #'  Multiple modules can be included in a vector. Default \code{NULL} which

 #'  plots all module heatmaps.

@@ -20,6 +20,7 @@

 #' @param newCounts A new counts matrix used to calculate perplexity. If NULL,

 #'  perplexity will be calculated for the matrix in \code{useAssay} slot in

 #'  \code{x}. Default NULL.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return Numeric. The perplexity for the provided \code{x} (and

 #'  \code{celdaModel}).

 #' @export

@@ -358,6 +359,7 @@ setMethod(

 #' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility,

 #'  a default value of 12345 is used. If NULL, no calls to

 #'  \link[withr]{with_seed} are made.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return A \linkS4class{SingleCellExperiment} object or

 #'  \code{celdaList} object with a \code{perplexity}

 #'  property, detailing the perplexity of all K/L combinations that appeared in

@@ -484,6 +486,7 @@ setMethod("resamplePerplexity",

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param sep Numeric. Breaks in the x axis of the resulting plot.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return A ggplot plot object showing perplexity as a function of clustering

 #'  parameters.

 #' @export

@@ -744,6 +747,7 @@ setMethod("plotGridSearchPerplexity",

 #'  to use. Default "featureSubset".

 #' @param sep Numeric. Breaks in the x axis of the resulting plot.

 #' @param n Integer. Width of the rolling window. Default 10.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return A ggplot plot object showing perplexity diferences as a function of

 #'  clustering parameters.

 #' @export

@@ -39,6 +39,7 @@

 #'  number of columns for facet wrap.

 #' @param headers Character vector. If `NULL`, the corresponding rownames are

 #'  used as labels. Otherwise, these headers are used to label the genes.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @param decreasing logical. Specifies the order of plotting the points.

 #'  If \code{FALSE}, the points will be plotted in increasing order where

 #'  the points with largest values will be on top. \code{TRUE} otherwise.

@@ -329,6 +330,7 @@ setMethod("plotDimReduceGrid",

 #'  the points with largest values will be on top. \code{TRUE} otherwise.

 #'  If \code{NULL}, no sorting is performed. Points will be plotted in their

 #'  current order in \code{x}. Default \code{FALSE}.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return The plot as a ggplot object

 #' @export

 setGeneric("plotDimReduceFeature", function(x, ...) {

@@ -601,6 +603,7 @@ setMethod("plotDimReduceFeature",

 #'  the points with largest values will be on top. \code{TRUE} otherwise.

 #'  If \code{NULL}, no sorting is performed. Points will be plotted in their

 #'  current order in \code{x}. Default \code{FALSE}.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return The plot as a ggplot object

 #' @export

 setGeneric("plotDimReduceModule", function(x, ...) {

@@ -1035,6 +1038,7 @@ setMethod("plotDimReduceCluster",

 #'  curve. Default \code{TRUE}.

 #' @param dotSize Numeric. Size of points if \code{plotDots = TRUE}.

 #' Default \code{0.1}.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return Violin plot for each feature, grouped by celda cluster

 #' @export

 setGeneric("plotCeldaViolin", function(x, ...) {

@@ -75,16 +75,16 @@

 #' @title Recursive cell splitting

-#' @description Uses the `celda_C` model to cluster cells into population for

-#'  range of possible K's. The cell population labels of the previous "K-1"

-#'  model are used as the initial values in the current model with K cell

-#'  populations. The best split of an existing cell population is found to

-#'  create the K-th cluster. This procedure is much faster than randomly

-#'  initializing each model with a different K. If module labels for each

-#'  feature are given in 'yInit', the `celda_CG` model will be used to split

-#'  cell populations based on those modules instead of individual features.

-#'  Module labels will also be updated during sampling and thus may end up

-#'  slightly different than `yInit`.

+#' @description Uses the \link{celda_C} model to cluster cells into

+#'  population for range of possible K's. The cell population labels of the

+#'  previous "K-1" model are used as the initial values in the current model

+#'  with K cell populations. The best split of an existing cell population is

+#'  found to create the K-th cluster. This procedure is much faster than

+#'  randomly initializing each model with a different K. If module labels for

+#'  each feature are given in 'yInit', the \link{celda_CG} model will be used to

+#'  split cell populations based on those modules instead of individual

+#'  features. Module labels will also be updated during sampling and thus

+#'  may end up slightly different than \code{yInit}.

 #' @param x A numeric \link{matrix} of counts or a

 #'  \linkS4class{SingleCellExperiment}

 #'  with the matrix located in the assay slot under \code{useAssay}.

@@ -99,24 +99,24 @@

 #' @param initialK Integer. Minimum number of cell populations to try.

 #' @param maxK Integer. Maximum number of cell populations to try.

 #' @param tempL Integer. Number of temporary modules to identify and use in cell

-#'  splitting. Only used if `yInit = NULL`. Collapsing features to a relatively

-#'  smaller number of modules will increase the speed of clustering and tend to

-#'  produce better cell populations. This number should be larger than the

-#'  number of true modules expected in the dataset. Default NULL.

+#'  splitting. Only used if \code{yInit = NULL}. Collapsing features to a

+#'  relatively smaller number of modules will increase the speed of clustering

+#'  and tend to produce better cell populations. This number should be larger

+#'  than the number of true modules expected in the dataset. Default NULL.

 #' @param yInit Integer vector. Module labels for features. Cells will be

-#'  clustered using the `celda_CG` model based on the modules specified in

-#'  `yInit` rather than the counts of individual features. While the features

-#'  will be initialized to the module labels in `yInit`, the labels will be

-#'  allowed to move within each new model with a different K.

+#'  clustered using the \link{celda_CG} model based on the modules specified in

+#'  \code{yInit} rather than the counts of individual features. While the

+#'  features will be initialized to the module labels in \code{yInit}, the

+#'  labels will be allowed to move within each new model with a different K.

 #' @param alpha Numeric. Concentration parameter for Theta. Adds a pseudocount

 #'  to each cell population in each sample. Default 1.

 #' @param beta Numeric. Concentration parameter for Phi. Adds a pseudocount to

-#'  each feature in each cell (if `yInit` is NULL) or to each module in each

-#'  cell population (if `yInit` is set). Default 1.

+#'  each feature in each cell (if \code{yInit} is NULL) or to each module in

+#'  each cell population (if \code{yInit} is set). Default 1.

 #' @param delta Numeric. Concentration parameter for Psi. Adds a pseudocount

-#'  to each feature in each module. Only used if `yInit` is set. Default 1.

+#'  to each feature in each module. Only used if \code{yInit} is set. Default 1.

 #' @param gamma Numeric. Concentration parameter for Eta. Adds a pseudocount

-#'  to the number of features in each module. Only used if `yInit` is set.

+#'  to the number of features in each module. Only used if \code{yInit} is set.

 #'  Default 1.

 #' @param minCell Integer. Only attempt to split cell populations with at

 #'  least this many cells.

@@ -130,10 +130,11 @@

 #'  \link[withr]{with_seed} are made.

 #' @param perplexity Logical. Whether to calculate perplexity for each model.

 #'  If FALSE, then perplexity can be calculated later with

-#'  `resamplePerplexity()`. Default TRUE.

+#'  \link{resamplePerplexity}. Default TRUE.

 #' @param verbose Logical. Whether to print log messages. Default TRUE.

 #' @param logfile Character. Messages will be redirected to a file named

-#'  `logfile`. If NULL, messages will be printed to stdout.  Default NULL.

+#'  "logfile". If NULL, messages will be printed to stdout.  Default NULL.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return A \linkS4class{SingleCellExperiment} object. Function

 #'  parameter settings and celda model results are stored in the

 #'  \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. The models in

@@ -872,12 +873,13 @@ setMethod("recursiveSplitCell",

 #'  should be larger than the number of true cell populations expected in the

 #'  dataset. Default 100.

 #' @param zInit Integer vector. Collapse cells to cell populations based on

-#'  labels in `zInit` and then perform module splitting. If NULL, no

-#'  collapasing will be performed unless `tempK` is specified. Default NULL.

+#'  labels in \code{zInit} and then perform module splitting. If NULL, no

+#'  collapasing will be performed unless \code{tempK} is specified.

+#'  Default NULL.

 #' @param sampleLabel Vector or factor. Denotes the sample label for each cell

-#'  (column) in the count matrix. Only used if `zInit` is set.

+#'  (column) in the count matrix. Only used if \code{zInit} is set.

 #' @param alpha Numeric. Concentration parameter for Theta. Adds a pseudocount

-#'  to each cell population in each sample. Only used if `zInit` is set.

+#'  to each cell population in each sample. Only used if \code{zInit} is set.

 #'  Default 1.

 #' @param beta Numeric. Concentration parameter for Phi. Adds a pseudocount

 #'  to each feature module in each cell. Default 1.

@@ -896,10 +898,11 @@ setMethod("recursiveSplitCell",

 #'  \link[withr]{with_seed} are made.

 #' @param perplexity Logical. Whether to calculate perplexity for each model.

 #'  If FALSE, then perplexity can be calculated later with

-#'  `resamplePerplexity()`. Default TRUE.

+#'  \link{resamplePerplexity}. Default TRUE.

 #' @param verbose Logical. Whether to print log messages. Default TRUE.

 #' @param logfile Character. Messages will be redirected to a file named

-#'  `logfile`. If NULL, messages will be printed to stdout.  Default NULL.

+#'  "logfile". If NULL, messages will be printed to stdout.  Default NULL.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return A \linkS4class{SingleCellExperiment} object. Function

 #'  parameter settings and celda model results are stored in the

 #'  \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. The models in

@@ -16,6 +16,7 @@

 #'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return A \linkS4class{SingleCellExperiment} object with a

 #'  \code{altExpName} \link[SingleCellExperiment]{altExp} slot. Function

 #'  parameter settings are stored in the \link[S4Vectors]{metadata}

@@ -15,6 +15,7 @@

 #' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility,

 #'  a default value of 12345 is used. If NULL, no calls to

 #'  \link[withr]{with_seed} are made.

+#' @param ... Ignored. Placeholder to prevent check warning.

 #' @return A updated \linkS4class{SingleCellExperiment} object with new

 #'  feature modules stored in column \code{celda_feature_module} in

 #'  \code{\link[SummarizedExperiment]{rowData}(x)}.

@@ -17,6 +17,8 @@ bestLogLikelihood(x, ...)

 returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}, or a celda

 model object.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot

 to use. Default "featureSubset".}

 }

@@ -6,16 +6,6 @@

 \title{celdaCGGridSearchRes}

 \format{

 An object as returned from old celdaGridSearch()

-#@examples

-data(celdaCGSim)

-celdaCGGridSearchRes <- celdaGridSearch(celdaCGSim$counts,

-  model = "celda_CG",

-  paramsTest = list(K = seq(4, 6), L = seq(9, 11)),

-  paramsFixed = list(sampleLabel = celdaCGSim$sampleLabel),

-  bestOnly = TRUE,

-  nchains = 1,

-  cores = 2

-)

 }

 \usage{

 celdaCGGridSearchRes

@@ -6,12 +6,6 @@

 \title{celdaCGmod}

 \format{

 A celda_CG object

-#@examples

-data(celdaCGSim)

-celdaCGMod <- celda_CG(celdaCGSim$counts,

-  K = celdaCGSim$K,

-  L = celdaCGSim$L,

-  nchains = 1)

 }

 \usage{

 celdaCGMod

@@ -6,9 +6,6 @@

 \title{celdaCMod}

 \format{

 A celda_C object

-#@examples

-data(celdaCSim)

-celdaCMod <- celda_C(celdaCSim$counts, K = celdaCSim$K, nchains = 1)

 }

 \usage{

 celdaCMod

@@ -6,8 +6,6 @@

 \title{celdaCSim}

 \format{

 A list of counts and properties as returned from old simulateCells().

-#@examples

-celdaCSim <- simulateCells("celda_C")

 }

 \usage{

 celdaCSim

@@ -30,6 +30,8 @@ a \link[SingleCellExperiment]{altExp} slot with name \code{altExpName} will

 be used. Rows represent features and columns represent cells.

 \item Celda model object.}}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot

 to use. Default "featureSubset".}

@@ -6,9 +6,6 @@

 \title{celdaGMod}

 \format{

 A celda_G object

-#@examples

-data(celdaGSim)

-celdaGMod <- celda_G(celdaGSim$counts, L = celdaGSim$L, nchains = 1)

 }

 \usage{

 celdaGMod

@@ -6,8 +6,6 @@

 \title{celdaGSim}

 \format{

 A list of counts and properties as returned from old simulateCells()

-#@examples

-celdaGSim <- simulateCells("celda_G")

 }

 \usage{

 celdaGSim

@@ -48,6 +48,8 @@ celdaGridSearch(x, ...)

 with the matrix located in the assay slot under \code{useAssay}.

 Rows represent features and columns represent cells.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying the name of the

 \link[SummarizedExperiment]{assay} slot to use. Default "counts".}

@@ -14,6 +14,8 @@ celdaModel(sce, ...)

 \item{sce}{A \link[SingleCellExperiment]{SingleCellExperiment} object

 returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot

 to use. Default "featureSubset".}

 }

@@ -23,7 +23,7 @@ celdaProbabilityMap(sce, ...)

   clusterRows = FALSE,

   clusterColumns = FALSE,

   showHeatmapLegend = TRUE,

-  heatmapLegendParam = list(title = NULL, legend_height = unit(6, "cm"))

+  heatmapLegendParam = list(title = NULL, legend_height = grid::unit(6, "cm"))

 )

 }

 \arguments{

@@ -28,6 +28,8 @@ celdaTsne(sce, ...)

 \item{sce}{A \linkS4class{SingleCellExperiment} object

 returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}

 slot to use. Default "counts".}

@@ -59,6 +59,8 @@ with the matrix located in the assay slot under \code{useAssay} in

 \code{altExp(x, altExpName)}.

 Rows represent features and columns represent cells.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying the name of the

 \link[SummarizedExperiment]{assay} slot to use. Default "counts".}

@@ -69,6 +69,8 @@ with the matrix located in the \link[SummarizedExperiment]{assay}

 slot under \code{useAssay} in \code{altExp(x, altExpName)}.

 Rows represent features and columns represent cells.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying the name of the

 \link[SummarizedExperiment]{assay} slot to use. Default "counts".}

@@ -56,6 +56,8 @@ celda_G(x, ...)

 with the matrix located in the assay slot under \code{useAssay}.

 Rows represent features and columns represent cells.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying the name of the

 \link[SummarizedExperiment]{assay} slot to use. Default "counts".}

@@ -46,6 +46,8 @@ using older versions of \code{celda}.}

 \code{celdaModel}. Dimensions and MD5 checksum will be checked by

 \link{compareCountMatrix}.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying the name of the

 \link[SummarizedExperiment]{assay} slot to use. Default "counts".}

@@ -21,6 +21,8 @@ clusterProbability(sce, ...)

 located in the \code{useAssay} assay slot.

 Rows represent features and columns represent cells.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}

 slot to use. Default "counts".}

@@ -18,6 +18,8 @@ cells.}

 \item{celdaMod}{A \code{celdaModel} or \code{celdaList} object.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{errorOnMismatch}{Logical. Whether to throw an error in the event of

 a mismatch. Default TRUE.}

 }

@@ -37,6 +37,8 @@ Rows represent features and columns represent cells. Must contain cluster

 labels in \code{celdaClusters(x, altExpName = altExpName)} if \code{x} is a

 \linkS4class{SingleCellExperiment} object.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}

 slot to use if \code{x} is a

 \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".}

@@ -38,6 +38,8 @@ cells. This matrix should be the same as the one used to generate

 \item{celdaMod}{Celda model object. Only works if \code{x} is an integer

 counts matrix.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}

 slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object.

 Default "counts".}

@@ -20,6 +20,8 @@ featureModuleLookup(sce, ...)

 located in the \code{useAssay} assay slot.

 Rows represent features and columns represent cells.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{feature}{Character vector. Identify feature modules for the specified

 feature names. \code{feature} must match the rownames of \code{sce}.}

@@ -49,6 +49,8 @@ findMarkersTree(x, ...)

 with the matrix located in the assay slot under \code{useAssay}.

 Rows represent features and columns represent cells.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}

 slot to use if \code{x} is a

 \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".}

@@ -25,6 +25,8 @@ with the matrix located in the assay slot under \code{useAssay}.

 Rows represent features and columns represent cells. Rownames of the

 matrix or \linkS4class{SingleCellExperiment} object should be gene names.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}

 slot to use if \code{x} is a

 \linkS4class{SingleCellExperiment} object. Default "counts".}

@@ -27,6 +27,8 @@ Rows represent features and columns represent cells.}

 \item{celdaMod}{celda model object. Ignored if \code{x} is a

 \linkS4class{SingleCellExperiment} object.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}

 slot to use. Default "counts".}

@@ -17,6 +17,8 @@ logLikelihoodHistory(x, ...)

 returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}, or a celda

 model object.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot

 to use. Default "featureSubset".}

 }

@@ -156,9 +156,6 @@ vector of the same length as \code{length(unique(celdaModules(x)))} or

 \item{labelJust}{Passed to \link[multipanelfigure]{fill_panel}.

 Justification for the label within the interpanel spacing grob to the

 top-left of the panel content grob.}

-

-\item{celdaMod}{Celda object of class \link{celda_G} or \link{celda_CG}. Used

-only if \code{x} is a matrix object.}

 }

 \value{

 A \link[multipanelfigure]{multi_panel_figure} object.

@@ -10,7 +10,8 @@ params(celdaMod)

 \S4method{params}{celdaModel}(celdaMod)

 }

 \arguments{

-\item{celdaMod}{celdaModel. Options available in `celda::availableModels`.}

+\item{celdaMod}{celdaModel. Options available in

+\code{celda::availableModels}.}

 }

 \value{

 List. Contains the model-specific parameters for the provided celda

@@ -37,6 +37,8 @@ cells. This matrix should be the same as the one used to generate

 \item{celdaMod}{Celda model object. Only works if \code{x} is an integer

 counts matrix.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}

 slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object.

 Default "counts".}

@@ -32,6 +32,8 @@ plotCeldaViolin(x, ...)

 with the matrix located in the assay slot under \code{useAssay}. Rows

 represent features and columns represent cells.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{features}{Character vector. Uses these genes for plotting.}

 \item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}

@@ -60,6 +60,8 @@ plotDimReduceFeature(x, ...)

 with the matrix located in the assay slot under \code{useAssay}. Rows

 represent features and columns represent cells.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{reducedDimName}{The name of the dimension reduction slot in

 \code{reducedDimNames(x)} if \code{x} is a

 \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and

@@ -52,6 +52,8 @@ plotDimReduceGrid(x, ...)

 with the matrix located in the assay slot under \code{useAssay}. Each

 row of the matrix will be plotted as a separate facet.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{reducedDimName}{The name of the dimension reduction slot in

 \code{reducedDimNames(x)} if \code{x} is a

 \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and

@@ -50,6 +50,8 @@ plotDimReduceModule(x, ...)

 with the matrix located in the assay slot under \code{useAssay}. Rows

 represent features and columns represent cells.}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{reducedDimName}{The name of the dimension reduction slot in

 \code{reducedDimNames(x)} if \code{x} is a

 \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and

@@ -21,6 +21,8 @@ plotGridSearchPerplexity(x, ...)

  \code{"celda_grid_search"} in \code{metadata(x)}.

  \item celdaList object.}}

+\item{...}{Ignored. Placeholder to prevent check warning.}

+

 \item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot

 to use. Default "featureSubset".}

@@ -21,6 +21,8 @@ plotGridSearchPerplexityDiff(x, ...)

  \code{"celda_grid_search"} in \code{metadata(x)}.