update roxygen to markdown syntax

Author: GuangchuangYu

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tidytree
 Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
-Version: 0.2.4
+Version: 0.2.5
 Authors@R: c(
            person("Guangchuang", "Yu",   email = "[email protected]", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
            person("Bradley", "Jones",    email = "[email protected]",             role = "ctb"),
@@ -32,3 +32,4 @@ BugReports: https://github.com/GuangchuangYu/tidytree/issues
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.1.1
+Roxygen: list(markdown = TRUE)

Makefile

@@ -12,20 +12,23 @@ readme:
 
 
 build:
-	cd ..;\
-	R CMD build $(PKGSRC)
+	Rscript -e 'devtools::build()'
+	# cd ..;\
+	# R CMD build $(PKGSRC)
 
 build2:
-	cd ..;\
-	R CMD build --no-build-vignettes $(PKGSRC)
+	Rscript -e 'devtools::build(vignettes = FALSE)'
+	# cd ..;\
+	# R CMD build --no-build-vignettes $(PKGSRC)
 
 install:
 	cd ..;\
 	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
 
-check: build
-	cd ..;\
-	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz", args="--as-cran")'
+check:
+	Rscript -e 'devtools::check()'
+	# cd ..;\
+	# Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz", args="--as-cran")'
 
 check2: build
 	cd ..;\

NEWS.md

@@ -1,3 +1,7 @@
+# tidytree 0.2.5
+
++ convert elements of roxygen documentation to markdown (2019-05-05, Thu)
+
 # tidytree 0.2.4
 
 + call `child.tbl_tree` instead of `child` in `offspring`, (2019-02-26, Tue)

R/AllClasses.R

@@ -26,7 +26,7 @@ setOldClass("DNAbin")
 ##' @importFrom methods representation
 ##' @importFrom ape as.DNAbin
 ##' @exportClass treedata
-##' @author guangchuang yu \url{https://guangchuangyu.github.io}
+##' @author Guangchuang Yu <https://guangchuangyu.github.io>
 ##' @keywords classes
 setClass("treedata",
          representation = representation(

R/AllGenerics.R

@@ -21,7 +21,7 @@ as.treedata <- function(tree, ...) {
 ##' @name get.fields
 ##' @rdname get.fields-methods
 ##' @title get.fields method
-##' @param object \code{treedata} object
+##' @param object `treedata` object
 ##' @param ... additional parameter
 ##' @return available annotation variables
 ##' @export
@@ -31,7 +31,7 @@ setGeneric("get.fields", function(object, ...) standardGeneric("get.fields"))
 ##' @name get.data
 ##' @rdname get.data-methods
 ##' @title get.data method
-##' @param object \code{treedata} object
+##' @param object `treedata` object
 ##' @param ... additional parameter
 ##' @return associated data of phylogeny
 ##' @export

R/as-tibble.R

@@ -74,7 +74,7 @@ as_tibble.treedata <- function(x, ...) {
 ##'
 ##'
 ##' @title get_tree_data
-##' @param tree_object a \code{treedata} object
+##' @param tree_object a `treedata` object
 ##' @return tbl_df
 ##' @export
 ##' @author guangchuang yu

R/show.R

@@ -1,17 +1,17 @@
-##' show method for \code{treedata} instance
+##' show method for `treedata` instance
 ##'
 ##'
 ##' @name show
 ##' @docType methods
 ##' @rdname show-methods
 ##'
 ##' @title show method
-##' @param object \code{treedata} object
+##' @param object `treedata` object
 ##' @return print info
 ##' @importFrom methods show
 ##' @exportMethod show
 ##' @usage show(object)
-##' @author Guangchuang Yu \url{https://guangchuangyu.github.io}
+##' @author Guangchuang Yu <https://guangchuangyu.github.io>
 setMethod("show", signature(object = "treedata"),
           function(object) {
               print.treedata(object)