fix dois

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

@@ -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

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 <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 ---------
 #' 
@@ -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