Incorporated CRAN comments, resubmitted

Author: gvegayon

DESCRIPTION

@@ -1,18 +1,23 @@
 Package: aphylo
 Title: Statistical Inference and Prediction of Annotations in Phylogenetic Trees
-Authors@R: person("George", "Vega Yon", role=c("aut","cre"),
-         email="g.vegayon@gmail.com", comment = c(ORCID = "0000-0002-3171-0844"))
+Authors@R: c(person("George", "Vega Yon", role=c("aut","cre"),
+         email="g.vegayon@gmail.com", comment = c(ORCID = "0000-0002-3171-0844")),
+         person("National
+         Cancer Institute (NCI)", role = "fnd", comment = "Grant Number
+         5P01CA196569-02"),
+         person("USC Biostatistics", role = "cph")
+         )
 Version: 0.2-1
 Date: 2022-01-14
 Description: Implements a parsimonious evolutionary model to analyze and
   predict gene-functional annotations in phylogenetic trees as described in Vega
   Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. With a focus on
-  computational efficiency, aphylo makes it possible to estimate pooled
+  computational efficiency, 'aphylo' makes it possible to estimate pooled
   phylogenetic models, including thousands (hundreds) of annotations (trees) in
   the same run. The package also provides the tools for visualization of
   annotated phylogenies, calculation of posterior probabilities (prediction,)
   and goodness-of-fit assessment featured in Vega Yon et al. (2021).
-Depends: R (>= 3.1.1), ape (>= 5.0)
+Depends: R (>= 3.5.0), ape (>= 5.0)
 LazyData: true
 Imports: Rcpp (>= 0.12.1), Matrix, methods, coda, fmcmc,
          utils, MASS, xml2

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2017
-COPYRIGHT HOLDER: USC Biostats
+YEAR: 2022
+COPYRIGHT HOLDER: USC Biostatistics

R/accuracy_sifter.R

@@ -23,10 +23,16 @@
 #' excluded from the analysis.
 #' 
 #' When `highlight = ""`, no highlight is done.
+#' @returns 
+#' A data frame with `Ntip()` rows and four variables. The variables are:
+#' - Gene: Label of the gene
+#' - Predicted: The assigned gene function.
+#' - Observed: The true set of gene functions.
+#' - Accuracy: The measurement of accuracy according to Engelhardt et al. (2011).
 #' 
 #' @examples 
 #' set.seed(81231)
-#' atree <- raphylo(100, psi = c(0,0), P = 3)
+#' atree <- raphylo(50, psi = c(0,0), P = 3)
 #' ans <- aphylo_mcmc(atree ~ mu_d + mu_s + Pi)
 #' 
 #' accuracy_sifter(ans)

R/aphylo_mcmc.R

@@ -37,7 +37,7 @@ APHYLO_DEFAULT_MCMC_CONTROL <- list(
 #' @examples 
 #' # Using the MCMC ------------------------------------------------------------
 #' 
-#' \dontrun{
+#' \donttest{
 #' 
 #' set.seed(1233)
 #' # Simulating a tree

R/cv.R

@@ -20,7 +20,7 @@
 #' @export
 #' @examples 
 #' # It takes about two minutes to run this example
-#' \dontrun{
+#' \donttest{
 #' 
 #'   set.seed(123)
 #'   atrees <- rmultiAphylo(10, 10, P = 1)

R/indexing.R

@@ -8,12 +8,21 @@
 #' the [aphylo] object. Whenever `i` is specified, then aphylo returns the corresponding
 #' annotations.
 #' @name aphylo-index
+#' @returns 
+#' - When indexing with `i`: A data frame with the annotations of the
+#'   selected genes.
+#' - When only indexing with `j` (`drop = FALSE`): An `aphylo` object with the selected sets of
+#'   annotations.
+#' - When only indexing with `j` (`drop = TRUE`): A data.frame with the selected
+#'   annotations.
+#' - When indexing on both `i` and `j`: A data.frame with the selected genes and annotations.
 #' @examples 
 #' set.seed(12312)
 #' atree <- raphylo(50, P = 4)
 #' atree[1:10,]
 #' atree[,2:3]
 #' atree[, 2:3, drop = TRUE]
+#' atree[1:10, 2:3]
 #' 
 #' 
 NULL

R/multiaphylo.R

@@ -5,6 +5,9 @@
 #' @param ... One or several object of class `aphylo` or `multiAPhylo`. Ignored
 #' in the case of `print.multiAphylo`.
 #' @name multiAphylo
+#' @returns 
+#' A list of class `multiAphylo`. Each element corresponds to a single `aphylo`
+#' object.
 #' @examples 
 #' data(fakeexperiment)
 #' data(faketree)

R/plot_logLik.R

@@ -2,6 +2,8 @@
 #' @param x An object of class [aphylo()]
 #' @inheritParams plot_multivariate
 #' @param ... Aditional parameters to be passed to `plotfun`.
+#' @returns 
+#' NULL (invisible). Generates a plot of the loglikelihood of the model.
 #' @examples 
 #' # Loading data
 #' data(fakeexperiment)
@@ -192,6 +194,10 @@ plot_logLik.aphylo_estimates <- function(x, sets,...) {
 #' generate all possible combinations as `combn(names(params), 2)`.
 #' @param mfrow Passed to [graphics::par].
 #' @export
+#' @returns 
+#' A list of length `length(sets)`, each with the following:
+#' - x,y,z vectors of coordinates. 
+#' - xlab,ylab vectors with the corresponding labels.
 #' 
 #' @examples 
 #' # Example: A model with less parameters

R/prediction_score.R

@@ -8,7 +8,23 @@
 #' @export
 #' @details In the case of `prediction_score`, `...` are passed to
 #' `predict.aphylo_estimates`.
-#' 
+#' @returns 
+#' A list of class `aphylo_prediction_score`:
+#' -  obs       : Observed 1 - MAE.
+#' -  obs_raw   : Unnormalized (raw) scores.
+#' -  random_raw: Unnormalized (raw) scores.
+#' -  worse_raw : Unnormalized (raw) scores.
+#' -  pval      : Computed p-value.
+#' -  worse     : Reference of worse case.
+#' -  predicted : Numeric matrix with observed predictions.
+#' -  expected  : Integer matrix with expected annotations.
+#' -  random    : Random score (null).
+#' -  alpha0    : The passed alpha parameters.
+#' -  alpha1    : The passed alpha parameters.
+#' -  auc       : An object of class `aphylo_auc`.
+#' -  obs.ids   : Indices of the ids.
+#' -  leaf.ids  : IDs of the leafs (if present).
+#' -  tree      : Of class `phylo`.
 #' @examples 
 #' # Example with prediction_score ---------------------------------------------
 #' set.seed(11552)
@@ -350,6 +366,8 @@ blue <- function(x) {
 #' 
 #' If `include.labels = NULL` and `ncol(x$expected) > 40`,
 #' then `include.labels=FALSE` by default.
+#' @returns 
+#' NULL (invisible) Generates a plot of the predictions.
 #' @aliases plot-prediction
 #' @examples 
 #' set.seed(8783)

R/read_sifter.R

@@ -79,6 +79,8 @@ read_pli <- function(fn, dropNAs = TRUE) {
 #' @param family_id Character scalar. Name of the family
 #' @param file Character scalar passed to [cat].
 #' @export
+#' @returns 
+#' A string with the XML file.
 #' @examples 
 #' set.seed(882)
 #' atree <- raphylo(5)