updating everything for cran resubmission

NEWS.md

@@ -1,11 +1,13 @@
 # datelife 0.6.1
-  - functions:
+  - Functions:
     - `get_otol_chronograms` was updated and renamed to `get_opentree_chronograms`
-    - update `match_all_calibrations`
-  - documentation:
-    - added a "More" section describing return value attributes (will rename to "Attributes")
-    - eliminated unecessary examples
-  - vignettes: added case study vignette
+    - Update `match_all_calibrations`
+    - Added a `summary` method for `datelifeResult` objects
+  - Documentation:
+    - Added a "More" section describing return value attributes (will rename to "Attributes")
+    - Eliminated unnecessary examples
+  - Vignettes: added case study vignette
+  - Description: added `BiocManager` package to imports
 
 # datelife 0.6.0
 

R/data.R

@@ -256,7 +256,7 @@
 #' usethis::use_data(subset2_taxa)
 "subset2_taxa"
 
-#' A list with datelieQuery and datelifeResult objects from a search of taxon names from subset2_taxa
+#' A list with datelifeQuery and datelifeResult objects from a search of taxon names from subset2_taxa
 #'
 #' @name subset2_search
 #' @docType data

R/datelife_internal.R

@@ -110,7 +110,7 @@ patristic_matrix_array_subset_both <- function(patristic_matrix_array, taxa, phy
 
 #' Subset a patristic matrix array
 #' @inheritParams patristic_matrix_array_subset_both
-#' @return A list with a paristic maytrix array and a `$problem` if any.
+#' @return A list with a patristic matrix array and a `$problem` if any.
 patristic_matrix_array_subset <- function(patristic_matrix_array, taxa, phy4 = NULL) {
   # gets a subset of the patristic_matrix_array. If you give it a phylo4 object, it can check to see if taxa are a clade
   patristic_matrix_array <- patristic_matrix_array[rownames(patristic_matrix_array) %in% taxa, colnames(patristic_matrix_array) %in% taxa, ]
@@ -428,7 +428,7 @@ phylo_congruify <- function(reference_tree,
 }
 
 # Used inside: patristic_matrix_array_phylo_congruify and phylo_congruify.
-#' Congruify and check.
+#' Congruify and Check.
 #' @inheritParams geiger::congruify.phylo
 #' @inheritParams ape::is.ultrametric
 #' @param attempt_fix Default to `TRUE`. If congruification results in NA branch

R/groves.R

@@ -17,7 +17,7 @@ is_n_overlap <- function(names_1, names_2, n = 2) {
 
 #' Find the grove for a group of chronograms and build a matrix.
 #'
-#' @description This function implements theorem 1.1 of Anéet al. (2009) \doi{10.1007/s00026-009-0017-x}
+#' @description This function implements theorem 1.1 of Ané et al. (2009) \doi{10.1007/s00026-009-0017-x}
 #'   to find a grove for a given group of chronograms.
 #' @param datelife_result A `datelifeResult` object.
 #' @param n The degree of taxon name overlap among input chronograms. Defaults

R/opentree_chronograms.R

@@ -8,7 +8,7 @@
 #' \describe{
 #'   \item{authors}{A list of lists of author names of the original studies that
 #'     published chronograms in the Open Tree of Life database.}
-#'   \item{curators}{A list of lists of curator names that uplodaded chronograms
+#'   \item{curators}{A list of lists of curator names that uploaded chronograms
 #'     to the Open Tree of Life database.}
 #'   \item{studies}{A list of study identifiers.}
 #'   \item{trees}{A `multiPhylo` object storing the chronograms from Open Tree of
@@ -116,7 +116,7 @@ phylo_has_brlen <- function(phy) {
 #' \describe{
 #'   \item{authors}{A list of lists of author names of the original studies that
 #'     published chronograms currently stored in the Open Tree of Life database.}
-#'   \item{curators}{A list of lists of curator names that uplodaded chronograms
+#'   \item{curators}{A list of lists of curator names that uploaded chronograms
 #'     to the Open Tree of Life database.}
 #'   \item{studies}{A list of study identifiers from original studies that
 #'     published chronograms currently stored in the Open Tree of Life database.}

README.Rmd

@@ -15,6 +15,9 @@ knitr::opts_chunk$set(
 )
 IS_README <- TRUE
 library(datelife)
+if (!requireNamespace("versions")) {
+  install.packages("versions")
+}
 ```
 <img src='man/figures/datelife-hexsticker-ai.png' align='right' style='width:150px' />
 
@@ -52,13 +55,13 @@ You can also date a phylogenetic tree of your own making (or choosing one from t
 
 ## 1. Installation
 
-`datelife`s stable version is currently available for installation from CRAN with:
+`datelife`'s **stable version `r versions::available.versions("datelife")$datelife$version`** is available for installation from CRAN with:
 
 ```{r eval = FALSE}
 install.packages("datelife")
 ```
 
-You can install the development version from the GitHub repository:
+You can install `datelife`'s **development versions** from the GitHub repository with:
 
 ```{r eval = FALSE}
 devtools::install_github("phylotastic/datelife")
@@ -78,7 +81,7 @@ citation("datelife")
 toBibtex(citation("datelife"))
 ```
 
-.bibtex files are available
+".bibtex" files are also available.
 
 ## 3. Feedback and Information for Developers
 

README.md

@@ -4,7 +4,6 @@
 <img src='man/figures/datelife-hexsticker-ai.png' align='right' style='width:150px' />
 
 <!-- badges: start -->
-
 <!-- [![R build status](https://github.com/phylotastic/datelife/workflows/R-CMD-check/badge.svg)](https://github.com/phylotastic/datelife/actions) -->
 
 [![CRAN
@@ -23,7 +22,7 @@ Issues](https://img.shields.io/github/issues-closed-raw/phylotastic/datelife.svg
 [![NSF-1458572](https://img.shields.io/badge/NSF-1458572-white.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=1458572)
 <!-- badges: end -->
 
-# Welcome to DateLife’s R package GitHub repository\!
+# Welcome to DateLife’s R package GitHub repository!
 
 Get a phylogenetic tree with branch lengths proportional to geologic
 time (aka a ***chronogram***) of any two or more lineages of interest to
@@ -47,43 +46,39 @@ still under development.
 3.  [Feedback and info for developers](#feedback)
 4.  [License](#license)
 
-## 1\. Installation
+## 1. Installation
 
-`datelife`s stable version is currently available for installation from
+`datelife`’s **stable version 0.6.0** is available for installation from
 CRAN with:
 
 ``` r
 install.packages("datelife")
 ```
 
-You can install the development version from the GitHub repository:
+You can install `datelife`’s **development versions** from the GitHub
+repository with:
 
 ``` r
 devtools::install_github("phylotastic/datelife")
 ```
 
-## 2\. Citation
+## 2. Citation
 
 If you use `datelife` for a publication, please cite the R package and
 the accompanying paper:
 
 <p>
-
 O’Meara B, Sanchez-Reyes L, Eastman J, Heath T, Wright A, Schliep K,
 Chamberlain S, Midford P, Harmon L, Brown J, Pennell M, Alfaro M (2022).
 <em>datelife: Scientific Data on Time of Lineage Divergence for Your
-Taxa</em>. R package version 0.6.0,
+Taxa</em>. R package version 0.6.1,
 <a href="https://doi.org/10.5281/zenodo.593938">https://doi.org/10.5281/zenodo.593938</a>.
-
 </p>
-
 <p>
-
 Sanchez-Reyes L, O’Meara B (2019). “datelife: Leveraging databases and
 analytical tools to reveal the dated Tree of Life.” <em>bioRxiv</em>,
 <b>782094</b>.
 <a href="https://doi.org/10.1101/782094">https://doi.org/10.1101/782094</a>.
-
 </p>
 
 You can get these citations and the bibtex entry with:
@@ -93,9 +88,9 @@ citation("datelife")
 toBibtex(citation("datelife"))
 ```
 
-.bibtex files are available
+“.bibtex” files are also available.
 
-## 3\. Feedback and Information for Developers
+## 3. Feedback and Information for Developers
 
 We welcome and encourage to post a [GitHub
 issue](https://github.com/phylotastic/datelife/issues/new) with any
@@ -182,8 +177,8 @@ working clone of the `datelife` repo:
 cd ../
 ```
 
-Generate a tar ball for your package by running `R CMD build
-package-name`:
+Generate a tar ball for your package by running
+`R CMD build package-name`:
 
 ``` bash
 R CMD build datelife
@@ -210,6 +205,6 @@ To submit to CRAN call `devtools::release()` and answer the prompted
 questions. If the answer to all of these is *yes*, the package will be
 submitted to CRAN :rocket:
 
-## 4\. License
+## 4. License
 
 This package is free and open source software, licensed under GPL.

cran-comments.md

@@ -1,7 +1,8 @@
-## New submission
+## New submission v 0.6.1
 This is a new submission where I have:
 
-* Fixed examples with functions that use Internet resources that were not failing gracefully.
+* Fixed examples with functions from dependent packages that use Internet resources that were not failing properly.
+* Fixed note: "undeclared package ‘BiocManager’ in Rd xrefs" for r-devel-linux-x86_64-fedora-clang
 
 ### Test environments: