From 6150de2a0b511499960954e5ca6ea861d8d39048 Mon Sep 17 00:00:00 2001 From: "Zhian N. Kamvar" Date: Mon, 4 Jan 2021 15:41:28 -0800 Subject: [PATCH] fix dois --- R/bootstraping.R | 2 +- R/bruvo.r | 8 ++++---- R/poppr.R | 7 +++---- man/Pram.Rd | 2 +- man/aboot.Rd | 2 +- man/fix_replen.Rd | 4 ++-- man/poppr-package.Rd | 5 ++--- man/test_replen.Rd | 4 ++-- 8 files changed, 16 insertions(+), 18 deletions(-) diff --git a/R/bootstraping.R b/R/bootstraping.R index 07bb107b..281959f0 100644 --- a/R/bootstraping.R +++ b/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. +#' Frontiers in Genetics 6:208. \doi{10.3389/fgene.2015.00208} #' @export #' @md #' @keywords bootstrap diff --git a/R/bruvo.r b/R/bruvo.r index 5961ac28..187d438d 100755 --- a/R/bruvo.r +++ b/R/bruvo.r @@ -618,12 +618,12 @@ 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 @@ -669,7 +669,7 @@ 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 @@ -690,7 +690,7 @@ 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 diff --git a/R/poppr.R b/R/poppr.R index 6db950e3..e7658658 100644 --- a/R/poppr.R +++ b/R/poppr.R @@ -238,12 +238,11 @@ #' #' 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 +#' 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 -#' +#' 6:208. \doi{10.3389/fgene.2015.00208} #' #' --------- Papers referencing data sets --------- #' @@ -360,7 +359,7 @@ NULL #' @docType data #' @usage data(Pram) #' @description This is the data set from -#' . 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 diff --git a/man/Pram.Rd b/man/Pram.Rd index 661a20c9..bae361d6 100644 --- a/man/Pram.Rd +++ b/man/Pram.Rd @@ -16,7 +16,7 @@ data(Pram) } \description{ This is the data set from - . 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 diff --git a/man/aboot.Rd b/man/aboot.Rd index 8052bee6..43256ea8 100644 --- a/man/aboot.Rd +++ b/man/aboot.Rd @@ -189,7 +189,7 @@ aboot(Aeut.pop, tree = myFastME, sample = 1000) \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. \url{http://dx.doi.org/10.3389/fgene.2015.00208} +Frontiers in Genetics 6:208. \doi{10.3389/fgene.2015.00208} } \seealso{ \code{\link[=nei.dist]{nei.dist()}} \code{\link[=edwards.dist]{edwards.dist()}} diff --git a/man/fix_replen.Rd b/man/fix_replen.Rd index b957043f..608ec0e4 100644 --- a/man/fix_replen.Rd +++ b/man/fix_replen.Rd @@ -26,7 +26,7 @@ Attempts to fix inconsistent repeat lengths found by \code{test_replen} } \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 @@ -72,7 +72,7 @@ diff(PxPcr) 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 diff --git a/man/poppr-package.Rd b/man/poppr-package.Rd index bb79d93e..ebf08899 100644 --- a/man/poppr-package.Rd +++ b/man/poppr-package.Rd @@ -226,12 +226,11 @@ Analysis of multilocus linkage disequilibrium. 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 \url{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 -\url{https://doi.org/10.3389/fgene.2015.00208} +6:208. \doi{10.3389/fgene.2015.00208} --------- Papers referencing data sets --------- diff --git a/man/test_replen.Rd b/man/test_replen.Rd index be8a09f1..35695097 100644 --- a/man/test_replen.Rd +++ b/man/test_replen.Rd @@ -21,7 +21,7 @@ able to be represented as discrete units after division and rounding. } \details{ This function is modified from the version used in - \url{https://doi.org/10.5281/zenodo.13007}. + \doi{10.5281/zenodo.13007}. } \examples{ data(Pram) @@ -32,7 +32,7 @@ test_replen(Pram, Pram_replen) 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