Fixing docs

DESCRIPTION

@@ -23,7 +23,7 @@ Imports: Rcpp (>= 0.12.1), Matrix, methods, coda, fmcmc,
 Suggests: covr, knitr, tinytest, AUC, rmarkdown,
 VignetteBuilder: knitr
 LinkingTo: Rcpp
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 URL: https://github.com/USCbiostats/aphylo
 BugReports: https://github.com/USCbiostats/aphylo/issues

Makefile

@@ -48,3 +48,7 @@ docker-check-all:
 		APHYLO_ATLAS_TEST=true \
 		R CMD check --ignore-vignettes aphylo_*.tar.gz
 
+docker-interactive:
+	podman run --mount type=bind,source=$(PWD),target=/mnt -w /mnt -it \
+		rocker/geospatial:4.4.0 bash
+

NEWS.md

@@ -1,3 +1,8 @@
+# Changes in aphylo version 0.3-4
+
+* Fixing documentation (CRAN request).
+
+
 # Changes in aphylo version 0.3-3
 
 * Removing C++ requirement as requested by CRAN.

R/aphylo-package.R

@@ -72,10 +72,9 @@ release_questions <- function() {
 #' 
 #' Statistical Inference in Annotated Phylogenetic Trees
 #' 
-#' @docType package
 #' @name aphylo-package
 #' 
-NULL
+"_PACKAGE"
 
 .onLoad <- function(libname, pkgname) {
   options(

R/data-management.R

@@ -19,8 +19,8 @@
 #' \item{pseq}{Integer vector. The pruning sequence (postorder).}
 #' \item{reduced_pseq}{Integer vector. The reduced version of `pseq`.}
 #' \item{Ntips.annotated}{Integer. Number of tips with annotations.}
-#' \item{tip.type}{Binary of length [Ntip()]. 0 means duplication and 1 speciation.}
-#' \item{tip.type}{Binary of length [Nnode()]. 0 means duplication and 1 speciation.}
+#' \item{tip.type}{Binary of length [ape::Ntip()]. 0 means duplication and 1 speciation.}
+#' \item{tip.type}{Binary of length [ape::Nnode()]. 0 means duplication and 1 speciation.}
 #' 
 #' @examples 
 #' # A simple example ----------------------------------------------------------

R/simulation.R

@@ -1,8 +1,7 @@
 #' Random tree generation
-#' 
+#' @details
 #' An alternative to [ape::rtree]. This function was written in C++ and is 
 #' significantly faster than `rtree`. 
-#' 
 #' @param n Integer scalar. Number of leaf nodes.
 #' @param edge.length A Function. Used to set the length of the edges.
 #' 
@@ -60,8 +59,7 @@ sim_tree <- function(n, edge.length = stats::runif) {
 
 }
 
-#' Simulate functions on a ginven tree
-#' 
+#' @title Simulate functions on a ginven tree
 #' @param tree An object of class [phylo][ape::read.tree]
 #' @template parameters
 #' @templateVar .psi 1
@@ -243,7 +241,6 @@ sim_fun_on_tree <- function(
 }
 
 #' Simulation of Annotated Phylogenetic Trees
-#' 
 #' @param n Integer scalar. Number of leafs. If not specified, then 
 #' @param tree An object of class [phylo][ape::read.tree].
 #' @param P Integer scalar. Number of functions to generate.
@@ -370,11 +367,9 @@ rmultiAphylo <- function(R, ...) {
 #' 
 #' @param atree An object of class [aphylo].
 #' @template parameters
-#' @templateVar .psi
-#' 
+#' @templateVar .psi 1
 #' @return An object of class [aphylo] with modified labels.
 #' @examples 
-#' 
 #' set.seed(131)
 #' x <- raphylo(5, P=2, psi=c(0,0))
 #' x$tip.annotation

docker/Makefile

@@ -1,13 +1,17 @@
+ifndef CNTR
+	CNTR = docker
+endif
+
 build:
-	docker build -t uscbiostats/aphylo:release -f Dockerfile . && \
-		docker build -t uscbiostats/aphylo:devel -f Dockerfile.dev .
+	$(CNTR) build -t uscbiostats/aphylo:release -f Dockerfile . && \
+		$(CNTR) build -t uscbiostats/aphylo:devel -f Dockerfile.dev .
 
 clang:
-	docker build -t uscbiostats/aphylo:clang -f Dockerfile-clang .
+	$(CNTR) build -t uscbiostats/aphylo:clang -f Dockerfile-clang .
 
 flexiblas:
-	docker build -t uscbiostats/aphylo:flexiblas -f Dockerfile.flexiblas .
+	$(CNTR) build -t uscbiostats/aphylo:flexiblas -f Dockerfile.flexiblas .
 
 push: build
-	docker push uscbiostats/aphylo:release && \
-		docker push uscbiostats/aphylo:devel
+	$(CNTR) push uscbiostats/aphylo:release && \
+		$(CNTR) push uscbiostats/aphylo:devel

inst/NEWS

@@ -1,3 +1,7 @@
+Changes in aphylo version 0.3-4
+
+-   Fixing documentation (CRAN request).
+
 Changes in aphylo version 0.3-3
 
 -   Removing C++ requirement as requested by CRAN.

man-roxygen/edges.r

@@ -1,3 +1,2 @@
-#' \code{}
 #' @param edges Integer matrix with two columns. An edgelist where each row is in the form of \\code{(parent, offspring)}.
 #' 

man-roxygen/parameters.r

@@ -1,4 +1,3 @@
-#' \code{}
 #' <%=ifelse(exists(".annotationslab"), "@param annotations Matrix of size \\eqn{n\\times P + 1}{n*P + 1}. Annotation data, where the first column is the nodeid (should coincide with the coding of the tree), the following columns are function annotations coded as \\code{1} if the node has the function, \\code{0} if the node doesn't has the function and \\code{9} or \\code{NA} otherwise (no information).", "") %>
 #' <%=ifelse(exists(".annotations"),    "@param annotations Matrix of size \\eqn{n\\times P}{n*P}. Annotation data, each column is a functional annotation coded as \\code{1} if the node has the function, \\code{0} if the node doesn't has the function and \\code{9} or \\code{NA} otherwise (no information).", "") %>
 #' <%=ifelse(exists(".tip.annotation"), "@param tip.annotation,node.annotation Annotation data. See [aphylo-class].", "") %>
@@ -9,5 +8,5 @@
 #' <%=ifelse(exists(".offspring"),   "@param offspring List of length \\eqn{n}. Offspring of each node (see \\code{\\link{new_aphylo}}).", "") %>
 #' <%=ifelse(exists(".S"),           "@param S Integer matrix of size \\eqn{2^P\\times P}{2^P * P}. See \\code{\\link{states}}.", "") %>
 #' <%=ifelse(exists(".tree"),       "@param tree An object of class [phylo][ape::read.tree]", "") %>
-#' <%=ifelse(exists(".types"),       "@param tip.type,node.type Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in [LogLike].", "") %>
+#' <%=ifelse(exists(".types"),       "@param tip.type,node.type Integer vectors with values 0 or 1. 0 denotes duplication node and 1 speciation node. This is used in [LogLike].", "") %>
 NULL