Merge pull request #232 from grunwaldlab/cran-patch-docs

poppr 2.8.7 (cran maintenance)

CRAN-RELEASE

@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2020-06-01.
-Once it is accepted, delete this file and tag the release (commit 9e5bef4ee8).
+This package was submitted to CRAN on 2021-01-04.
+Once it is accepted, delete this file and tag the release (commit 6150de2a).

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: poppr
 Type: Package
 Title: Genetic Analysis of Populations with Mixed Reproduction
-Version: 2.8.6.99-18
+Version: 2.8.7
 Authors@R: c(person(c("Zhian", "N."), "Kamvar", role = c("cre", "aut"),
     email = "zkamvar@gmail.com", comment = c(ORCID = "0000-0003-1458-7108")),
     person(c("Javier", "F."), "Tabima", role = "aut",
@@ -26,16 +26,16 @@ Authors@R: c(person(c("Zhian", "N."), "Kamvar", role = c("cre", "aut"),
     email = "grunwaln@science.oregonstate.edu", comment = c(ORCID = "0000-0003-1656-7602")))
 Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
 Encoding: UTF-8
-URL: https://grunwaldlab.github.io/poppr,
-    https://github.com/grunwaldlab/poppr,
+URL: https://grunwaldlab.github.io/poppr/,
+    https://github.com/grunwaldlab/poppr/,
     https://grunwaldlab.github.io/Population_Genetics_in_R/
 Description: Population genetic analyses for hierarchical analysis of partially
     clonal populations built upon the architecture of the 'adegenet' package. 
     Originally described in Kamvar, Tabima, and Grünwald (2014) 
     <doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and 
     Grünwald (2015) <doi:10.3389/fgene.2015.00208>.
-MailingList: https://groups.google.com/group/poppr
-BugReports: https://github.com/grunwaldlab/poppr/issues
+MailingList: https://groups.google.com/d/forum/poppr
+BugReports: https://github.com/grunwaldlab/poppr/issues/
 Depends:
     R (>= 2.15.1),
     adegenet (>= 2.0.0)

NEWS.md

@@ -1,5 +1,5 @@
-poppr 2.8.7
-==========
+poppr 2.9.0
+===========
 
 NEW FEATURES
 ------------
@@ -13,13 +13,20 @@ DEPRECATION
 * The argument `blacklist` has been deprecated in favor of `exclude` for the
   following functions: `bruvo.msn()`, `poppr.msn()`, `clonecorrect()`, `poppr()`, 
   `mlg.table()`, `mlg.crosspop()`, and `popsub()`. It will be removed in the
-  poppr version 2.9
+  poppr version 2.10 (@zkamvar, #218)
 
 GITHUB
 ------
 
-* The default branch for the repository is now "main", so development versions
-  will install `remotes::install_github("grunwaldlab/poppr@main")`
+* The default branch for the repository is now "main" (@zkamvar, #218)
+
+poppr 2.8.7
+===========
+
+CRAN MAINTENANCE
+----------------
+
+* Links to other packages are now formatted correctly.
 
 poppr 2.8.6
 ===========

R/bootstraping.R

@@ -137,7 +137,7 @@
 #' @references
 #' Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of 
 #' genome-wide population genetic data with emphasis on clonality. 
-#' Frontiers in Genetics 6:208. <http://dx.doi.org/10.3389/fgene.2015.00208> 
+#' Frontiers in Genetics 6:208. \doi{10.3389/fgene.2015.00208}
 #' @export
 #' @md
 #' @keywords bootstrap

R/bruvo.r

@@ -670,17 +670,17 @@ bruvo.msn <- function (gid, replen = 1, add = TRUE, loss = TRUE,
 #'   consistent.
 #'   
 #' @details This function is modified from the version used in 
-#'   \url{https://doi.org/10.5281/zenodo.13007}.
+#'   \doi{10.5281/zenodo.13007}.
 #'   
 #' @references Zhian N. Kamvar, Meg M. Larsen, Alan M. Kanaskie, Everett M. 
 #'   Hansen, & Niklaus J. Grünwald. Sudden_Oak_Death_in_Oregon_Forests: Spatial
 #'   and temporal population dynamics of the sudden oak death epidemic in Oregon
-#'   Forests. ZENODO, https://doi.org/10.5281/zenodo.13007, 2014.
+#'   Forests. ZENODO, \doi{10.5281/zenodo.13007}, 2014.
 #'   
 #'   Kamvar, Z. N., Larsen, M. M., Kanaskie, A. M., Hansen, E. M., & Grünwald,
 #'   N. J. (2015). Spatial and temporal analysis of populations of the sudden
 #'   oak death pathogen in Oregon forests. Phytopathology 105:982-989.
-#'   doi: \href{https://doi.org/10.1094/PHYTO-12-14-0350-FI}{10.1094/PHYTO-12-14-0350-FI}
+#'   doi: \doi{10.1094/PHYTO-12-14-0350-FI}
 #'   
 #'   Ruzica Bruvo, Nicolaas K. Michiels, Thomas G. D'Souza, and Hinrich 
 #'   Schulenburg. A simple method for the calculation of microsatellite genotype
@@ -721,7 +721,7 @@ consistent_replen <- function(index, alleles, replen){
 #'   fixed will. If \code{FALSE}, the original repeat lengths will not be fixed.
 #' @return a numeric vector of corrected repeat motif lengths.
 #' @details This function is modified from the version used in 
-#'   \url{https://doi.org/10.5281/zenodo.13007}.\cr Before being fed into the
+#'   \doi{10.5281/zenodo.13007}.\cr Before being fed into the
 #'   algorithm to calculate Bruvo's distance, the amplicon length is divided by
 #'   the repeat unit length. Because of the amplified primer sequence attached
 #'   to sequence repeat, this division does not always result in an integer and
@@ -742,12 +742,12 @@ consistent_replen <- function(index, alleles, replen){
 #' @references Zhian N. Kamvar, Meg M. Larsen, Alan M. Kanaskie, Everett M. 
 #'   Hansen, & Niklaus J. Grünwald. Sudden_Oak_Death_in_Oregon_Forests: Spatial
 #'   and temporal population dynamics of the sudden oak death epidemic in Oregon
-#'   Forests. ZENODO, https://doi.org/10.5281/zenodo.13007, 2014.
+#'   Forests. ZENODO, \doi{10.5281/zenodo.13007}, 2014.
 #'   
 #'   Kamvar, Z. N., Larsen, M. M., Kanaskie, A. M., Hansen, E. M., & Grünwald,
 #'   N. J. (2015). Spatial and temporal analysis of populations of the sudden
 #'   oak death pathogen in Oregon forests. Phytopathology 105:982-989.
-#'   doi: \href{https://doi.org/10.1094/PHYTO-12-14-0350-FI}{10.1094/PHYTO-12-14-0350-FI}
+#'   doi: \doi{10.1094/PHYTO-12-14-0350-FI}
 #'   
 #'   Ruzica Bruvo, Nicolaas K. Michiels, Thomas G. D'Souza, and Hinrich 
 #'   Schulenburg. A simple method for the calculation of microsatellite genotype

R/filter_stats.R

@@ -75,17 +75,17 @@
 #' @seealso \code{\link{mlg.filter}} \code{\link{cutoff_predictor}} 
 #'   \code{\link{bitwise.dist}} \code{\link{diss.dist}}
 #' @note This function originally appeared in 
-#'   \href{https://doi.org/10.5281/zenodo.17424}{DOI: 10.5281/zenodo.17424}
+#'   \doi{10.5281/zenodo.17424}{DOI: 10.5281/zenodo.17424}
 #' @references ZN Kamvar, JC Brooks, and NJ Grünwald. 2015. Supplementary 
 #'   Material for Frontiers Plant Genetics and Genomics 'Novel R tools for 
 #'   analysis of genome-wide population genetic data with emphasis on
 #'   clonality'. DOI:
-#'   \href{https://doi.org/10.5281/zenodo.17424}{10.5281/zenodo.17424}
+#'   \doi{10.5281/zenodo.17424}
 #'   
 #'   Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of 
 #'   genome-wide population genetic data with emphasis on clonality. Front.
 #'   Genet. 6:208. doi: 
-#'   \href{https://doi.org/10.3389/fgene.2015.00208}{10.3389/fgene.2015.00208}
+#'   \doi{10.3389/fgene.2015.00208}
 #'   
 #' @author Zhian N. Kamvar, Jonah C. Brooks
 #' @examples
@@ -153,18 +153,18 @@ filter_stats <- function(x, distance = bitwise.dist,
 #'   lineages should be defined.
 #' @seealso \code{\link{filter_stats}} \code{\link{mlg.filter}}
 #' @note This function originally appeared in 
-#'   \href{https://doi.org/10.5281/zenodo.17424}{DOI: 10.5281/zenodo.17424}. 
+#'   \doi{10.5281/zenodo.17424}{DOI: 10.5281/zenodo.17424}. 
 #'   This is a bit of a blunt instrument.
 #' @export
 #' @references ZN Kamvar, JC Brooks, and NJ Grünwald. 2015. Supplementary
 #' Material for Frontiers Plant Genetics and Genomics 'Novel R tools for
 #' analysis of genome-wide population genetic data with emphasis on clonality'.
-#' DOI: \href{https://doi.org/10.5281/zenodo.17424}{10.5281/zenodo.17424}
+#' DOI: \doi{10.5281/zenodo.17424}
 #' 
 #' Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of 
 #' genome-wide population genetic data with emphasis on clonality. Front. Genet.
 #' 6:208. doi:
-#' \href{https://doi.org/10.3389/fgene.2015.00208}{10.3389/fgene.2015.00208}
+#' \doi{10.3389/fgene.2015.00208}
 #' 
 #' @author Zhian N. Kamvar
 #' @examples
@@ -203,17 +203,17 @@ cutoff_predictor <- function(thresholds, fraction = 0.5){
 #' @export
 #' @seealso \code{\link{filter_stats}}
 #' @note This function originally appeared in 
-#'   \href{https://doi.org/10.5281/zenodo.17424}{DOI: 10.5281/zenodo.17424}
+#'   \doi{10.5281/zenodo.17424}{DOI: 10.5281/zenodo.17424}
 #' @author Zhian N. Kamvar
 #' @references ZN Kamvar, JC Brooks, and NJ Grünwald. 2015. Supplementary
 #' Material for Frontiers Plant Genetics and Genomics 'Novel R tools for
 #' analysis of genome-wide population genetic data with emphasis on clonality'.
-#' DOI: \href{https://doi.org/10.5281/zenodo.17424}{10.5281/zenodo.17424}
+#' DOI: \doi{10.5281/zenodo.17424}
 #' 
 #' Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of 
 #' genome-wide population genetic data with emphasis on clonality. Front. Genet.
 #' 6:208. doi:
-#' \href{https://doi.org/10.3389/fgene.2015.00208}{10.3389/fgene.2015.00208}
+#' \doi{10.3389/fgene.2015.00208}
 #' 
 #' @keywords internal
 #==============================================================================#

R/poppr.R

@@ -84,11 +84,11 @@
 #'
 #'   Examples of analyses are available in a primer written by Niklaus J.
 #'   Grünwald, Zhian N. Kamvar, and Sydney E.  Everhart at
-#'   <http://grunwaldlab.github.io/Population_Genetics_in_R>.}
+#'   <http://grunwaldlab.github.io/Population_Genetics_in_R/>.}
 #'   
 #'   \subsection{Getting help}{ If you have a specific question or issue with 
 #'   \pkg{poppr}, feel free to contribute to the google group at 
-#'   <https://groups.google.com/group/poppr>. If you find a bug and 
+#'   <https://groups.google.com/d/forum/poppr>. If you find a bug and 
 #'   are a github user, you can submit bug reports at 
 #'   <https://github.com/grunwaldlab/poppr/issues>. Otherwise, leave a
 #'   message on the groups. Personal emails are highly discouraged as they do 
@@ -238,24 +238,23 @@
 #' 
 #' Kamvar ZN, Tabima JF, Grünwald NJ. (2014) Poppr: an R package for genetic
 #' analysis of populations with clonal, partially clonal, and/or sexual
-#' reproduction. PeerJ 2:e281 <https://doi.org/10.7717/peerj.281>
+#' reproduction. PeerJ 2:e281 \doi{10.7717/peerj.281}
 #' 
 #' Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of 
 #' genome-wide population genetic data with emphasis on clonality. Front. Genet.
-#' 6:208. doi: 10.3389/fgene.2015.00208 
-#' <https://doi.org/10.3389/fgene.2015.00208>
+#' 6:208. \doi{10.3389/fgene.2015.00208}
 #' 
 #' --------- Papers referencing data sets ---------
 #' 
 #' Grünwald, NJ and Hoheisel, G.A. 2006. Hierarchical Analysis of Diversity, 
 #' Selfing, and Genetic Differentiation in Populations of the Oomycete 
 #' *Aphanomyces euteiches*. Phytopathology 96:1134-1141 doi: 
-#' \href{https://doi.org/10.1094/PHYTO-96-1134}{10.1094/PHYTO-96-1134}
+#' \doi{10.1094/PHYTO-96-1134}
 #' 
 #' SE Everhart, H Scherm, (2015) Fine-scale genetic structure of *Monilinia
 #' fructicola* during brown rot epidemics within individual peach tree canopies.
 #' Phytopathology 105:542-549 doi: 
-#' \href{https://doi.org/10.1094/PHYTO-03-14-0088-R}{10.1094/PHYTO-03-14-0088-R}
+#' \doi{10.1094/PHYTO-03-14-0088-R}
 #' 
 #' Bo Peng and Christopher Amos (2008) Forward-time simulations of nonrandom 
 #' mating populations using simuPOP. *bioinformatics*, 24 (11): 1408-1409.
@@ -265,18 +264,18 @@
 #' Grünwald. (2014) "The Irish potato famine pathogen *Phytophthora 
 #' infestans* originated in central Mexico rather than the Andes." Proceedings 
 #' of the National Academy of Sciences 111:8791-8796. doi: 
-#' \href{https://doi.org/10.1073/pnas.1401884111}{10.1073/pnas.1401884111}
+#' \doi{10.1073/pnas.1401884111}
 #' 
 #' Kamvar, Z. N., Larsen, M. M., Kanaskie, A. M., Hansen, E. M., & Grünwald, N.
 #' J. (2015). Spatial and temporal analysis of populations of the sudden oak
 #' death pathogen in Oregon forests. Phytopathology 105:982-989. doi: 
-#' \href{https://doi.org/10.1094/PHYTO-12-14-0350-FI}{10.1094/PHYTO-12-14-0350-FI}
+#' \doi{10.1094/PHYTO-12-14-0350-FI}
 #' 
 #' 
 #' Goss, E. M., Larsen, M., Chastagner, G. A., Givens, D. R., and Grünwald, N. 
 #' J. 2009. Population genetic analysis infers migration pathways of 
 #' *Phytophthora ramorum* in US nurseries. PLoS Pathog. 5:e1000583. doi: 
-#' \href{https://doi.org/10.1371/journal.ppat.1000583}{10.1371/journal.ppat.1000583}
+#' \doi{10.1371/journal.ppat.1000583}
 #'   
 #' 
 #' @name poppr-package
@@ -299,7 +298,7 @@ NULL
 #' @references Grunwald, NJ and Hoheisel, G.A. 2006. Hierarchical Analysis of
 #'   Diversity, Selfing, and Genetic Differentiation in Populations of the 
 #'   Oomycete *Aphanomyces euteiches*. Phytopathology 96:1134-1141
-#'   doi: \href{https://doi.org/10.1094/PHYTO-96-1134}{10.1094/PHYTO-96-1134}
+#'   doi: \doi{10.1094/PHYTO-96-1134}
 #==============================================================================#
 NULL
 #==============================================================================#
@@ -344,7 +343,7 @@ NULL
 #'   Cardenas, and Niklaus J. Grünwald. "The Irish potato famine pathogen 
 #'   *Phytophthora infestans* originated in central Mexico rather than the 
 #'   Andes." Proceedings of the National Academy of Sciences 111:8791-8796. doi:
-#'   \href{https://doi.org/10.1073/pnas.1401884111}{10.1073/pnas.1401884111}
+#'   \doi{10.1073/pnas.1401884111}
 #==============================================================================#
 NULL
 #==============================================================================#
@@ -360,7 +359,7 @@ NULL
 #' @docType data
 #' @usage data(Pram)
 #' @description This is the data set from 
-#'   <https://doi.org/10.5281/zenodo.13007>. It has been converted to the 
+#'   \doi{10.5281/zenodo.13007}. It has been converted to the 
 #'   genclone object as of poppr version 2.0. It contains 729 samples of the 
 #'   Sudden Oak Death pathogen *Phytophthora ramorum* genotyped over five 
 #'   microsatellite loci (Kamvar et. al., 2015). 513 samples were collected from
@@ -378,19 +377,19 @@ NULL
 #'   Grünwald, N. J. (2015). Spatial and temporal analysis of populations of the
 #'   sudden oak death pathogen in Oregon forests. Phytopathology 105:982-989. 
 #'   doi:
-#'   \href{https://doi.org/10.1094/PHYTO-12-14-0350-FI}{10.1094/PHYTO-12-14-0350-FI}
+#'   \doi{10.1094/PHYTO-12-14-0350-FI}
 #'   
 #'   
 #'   Zhian N. Kamvar, Meg M. Larsen, Alan M. Kanaskie, Everett M. Hansen, & 
 #'   Niklaus J. Grünwald. 2014. Sudden_Oak_Death_in_Oregon_Forests: Spatial and 
 #'   temporal population dynamics of the sudden oak death epidemic in Oregon 
 #'   Forests. ZENODO, doi:
-#'   \href{https://doi.org/10.5281/zenodo.13007}{10.5281/zenodo.13007}
+#'   \doi{10.5281/zenodo.13007}
 #'   
 #'   Goss, E. M., Larsen, M., Chastagner, G. A., Givens, D. R., and Grünwald, N.
 #'   J. 2009. Population genetic analysis infers migration pathways of 
 #'   *Phytophthora ramorum* in US nurseries. PLoS Pathog. 5:e1000583. doi:
-#'   \href{https://doi.org/10.1371/journal.ppat.1000583}{10.1371/journal.ppat.1000583}
+#'   \doi{10.1371/journal.ppat.1000583}
 #'   
 #' @examples
 #' data(Pram)
@@ -424,7 +423,7 @@ NULL
 #' @references SE Everhart, H Scherm, (2015) Fine-scale genetic structure of 
 #'   *Monilinia fructicola* during brown rot epidemics within individual
 #'   peach tree canopies. Phytopathology 105:542-549 doi:
-#'   \href{https://doi.org/10.1094/PHYTO-03-14-0088-R}{10.1094/PHYTO-03-14-0088-R}
+#'   \doi{10.1094/PHYTO-03-14-0088-R}
 #'   
 #' @examples
 #' data(monpop)

R/zzz.r

@@ -57,7 +57,7 @@
   if (!interactive() || stats::runif(1) > 0.1) return()
 
   tips <- c(
-    "\nNeed help? Try the poppr mailing list: http://groups.google.com/group/poppr.\n",
+    "\nNeed help? Try the poppr mailing list: http://groups.google.com/d/forum/poppr.\n",
     "\nUse suppressPackageStartupMessages(library(\"poppr\")) to eliminate package startup messages.\n"
   )
 

README.md

@@ -1,13 +1,6 @@
 # Poppr version 2 <img src="man/figures/small_logo.png" align="right" height="98"/>
 
 <!-- badges: start -->
-
-[![Build Status](https://travis-ci.org/grunwaldlab/poppr.svg?branch=main)](https://travis-ci.org/grunwaldlab/poppr)
-[![Coverage Status](https://coveralls.io/repos/grunwaldlab/poppr/badge.svg?branch=main)](https://coveralls.io/r/grunwaldlab/poppr?branch=main)
-[![CRAN version](https://www.r-pkg.org/badges/version-ago/poppr)](https://cran.r-project.org/package=poppr)
-[![CRAN check status](https://cranchecks.info/badges/worst/poppr)](https://cran.r-project.org/web/checks/check_results_poppr.html)
-[![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/poppr)](https://www.r-pkg.org/pkg/poppr)
-
 [![R build status](https://github.com/grunwaldlab/poppr/workflows/R-CMD-check/badge.svg)](https://github.com/grunwaldlab/poppr/actions)
 <!-- badges: end -->
 
@@ -73,7 +66,7 @@ Please also cite:
 > Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of
 > genome-wide population genetic data with emphasis on clonality. Front. Genet.
 > 6:208. doi:
-> [10.3389/fgene.2015.00208](https://journal.frontiersin.org/article/10.3389/fgene.2015.00208/abstract)
+> [10.3389/fgene.2015.00208](https://www.frontiersin.org/articles/10.3389/fgene.2015.00208/abstract)
   
 You can obtain citation information in R by typing:
 
@@ -103,7 +96,7 @@ github below.
 
 To install this package from github, make sure you have the following:
 
-- [Xcode](https://developer.apple.com/xcode) (OSX)
+- [Xcode](https://developer.apple.com/xcode/) (OSX)
     OR [Rtools](https://cran.r-project.org/bin/windows/Rtools/) (Windows)
 - [{remotes}](https://github.com/r-lib/remotes) (to install, use: `install.packages("remotes")`)
 
@@ -166,7 +159,7 @@ A few vignettes have been written for poppr:
 
 Users who have any questions/comments/suggestions regarding any version of poppr
 (stable or development) should direct their comments to the [Poppr google
-group](https://groups.google.com/group/poppr)
+group](https://groups.google.com/d/forum/poppr)
 
 ### Book/Primer