Merge pull request #205 from grunwaldlab/cran-release-2.8.3

Cran release 2.8.3

.Rbuildignore

@@ -13,7 +13,6 @@
 ^vignettes/figure
 ^tests/testthat/Rplots.pdf
 ^CODE_OF_CONDUCT\.md$
-^NEWS\.md$
 ^cran-comments\.md$
 ^docs/*$
 ^ISSUE_TEMPLATE\.md$

CRAN-RELEASE

@@ -0,0 +1,2 @@
+This package was submitted to CRAN on 2019-06-14.
+Once it is accepted, delete this file and tag the release (commit a2b31fd4d3).

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: poppr
 Type: Package
 Title: Genetic Analysis of Populations with Mixed Reproduction
-Version: 2.8.2.99-13
-Date: 2019-05-02
+Version: 2.8.3
+Date: 2019-06-13
 Authors@R: c(person(c("Zhian", "N."), "Kamvar", role = c("cre", "aut"),
     email = "[email protected]", comment = c(ORCID = "0000-0003-1458-7108")),
     person(c("Javier", "F."), "Tabima", role = "aut",
@@ -21,15 +21,18 @@ Authors@R: c(person(c("Zhian", "N."), "Kamvar", role = c("cre", "aut"),
     email = "[email protected]", comment = c(ORCID = "0000-0002-6395-8107")),
     person(c("Frédéric", "D."), "Chevalier", role = "ctb",
     email = "[email protected]", comment = c(ORCID = "0000-0003-2611-8106")),
-    person(c("Niklaus", "J."), "Grunwald", role = "ths",
+    person(c("Niklaus", "J."), "Grünwald", role = "ths",
     email = "[email protected]", comment = c(ORCID = "0000-0003-1656-7602")))
 Maintainer: Zhian N. Kamvar <[email protected]>
 Encoding: UTF-8
-URL: https://github.com/grunwaldlab/poppr,
-    https://grunwaldlab.github.io/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.
+    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
 Depends:

NAMESPACE

@@ -11,6 +11,7 @@ export("%>%")
 export("cutoff<-")
 export("distalgo<-")
 export("distargs<-")
+export("distenv<-")
 export("distname<-")
 export("mlg.filter<-")
 export("mll.custom<-")
@@ -35,6 +36,7 @@ export(cutoff_predictor)
 export(diss.dist)
 export(distalgo)
 export(distargs)
+export(distenv)
 export(distname)
 export(diversity_boot)
 export(diversity_ci)

NEWS.md

@@ -1,20 +1,35 @@
-poppr 2.8.2.99
+poppr 2.8.3
 ===========
 
 BUG FIX
-=======
+-------
 
 * `read.genalex()` now correctly parses strata when the user imports data that
   contains duplicated data AND has some individuals named as integers less than
   the number of samples in the data (prepended by zeroes) 
   (See https://github.com/grunwaldlab/poppr/pull/202).
 
-MISC
-====
+NEW FEATURES
+------------
 
 * MSN functions: nodes with single populations displayed as circles instead of 
   pies. (@fdchevalier, https://github.com/grunwaldlab/poppr/pull/203)
 
+MISC
+----
+
+* `mlg.vector()` is now safer as it now uses a for loop instead of a
+  function with the out-of-scope operator (`<<-`) (see #205)
+* `shufflepop()` is now safer as it now uses a for loop instead of a
+  function with the out-of-scope operator (`<<-`) (see #205)
+* The MLG class gains a new `distenv` slot, which will store the environment
+  where the distance function or matrix exists. This is accompanied by an 
+  accessor of the same name (see #206).
+* `"mlg.filter<-"()` replacement methods will no longer search the global
+  environment when evaluating the distance function or matrix (see #206).
+* Tests for `mlg.filter()` no longer assign objects to the global environment
+* DOIs for the publications have been added to the DESCRIPTION
+
 poppr 2.8.2
 ===========
 

R/Index_calculations.r

@@ -479,11 +479,8 @@ poppr <- function(dat, total = TRUE, sublist = "ALL", blacklist = NULL,
 #' # Obtain a list of fstat files from a directory.
 #' x <- getfile(multi=TRUE, pattern="^.+?dat$")
 #'
-#' # set the working directory to that directory.
-#' setwd(x$path)
-#'
 #' # run the analysis on each file.
-#' poppr.all(x$files)
+#' poppr.all(file.path(x$path, x$files))
 #' }
 #==============================================================================# 
 poppr.all <- function(filelist, ...){

R/aaaMLGclass.R

@@ -58,6 +58,7 @@ setClassUnion("charORLang", c("character", "language"))
 #'   accessed.
 #' @slot distname the name of the distance function or matrix used to collapse 
 #'   mlgs.
+#' @slot distenv the environment that contains the distance function or matrix
 #' @slot distargs the arguments provided to compute the distance function.
 #' @slot distalgo the algorithm used to contract multilocus genotypes.
 #' @slot cutoff Two numbers specifying the cutoff value for expanding and 
@@ -97,12 +98,14 @@ setClass("MLG",
          representation(visible = "character",
                         cutoff = "numeric",
                         distname = "charORLang",
+                        distenv  = "environment",
                         distargs = "list",
                         distalgo = "character",
                         mlg = "data.frame"),
          prototype(visible = character(0), 
                    cutoff = numeric(0), 
                    distname = character(0), 
+                   distenv = as.environment(.GlobalEnv),
                    distargs = list(),
                    distalgo = "farthest_neighbor", 
                    mlg = data.frame(expanded = numeric(0), 
@@ -111,4 +114,4 @@ setClass("MLG",
                                     custom = factor(character(0))
                                     )
                    )
-         )
+         )

R/aaaMLGmethods.R

@@ -91,6 +91,7 @@ setMethod(
     slot(.Object, "mlg")      <- mlg
     slot(.Object, "visible")  <- "original"
     slot(.Object, "distname") <- "diss.dist"
+    slot(.Object, "distenv")  <- .GlobalEnv
     slot(.Object, "distargs") <- list()
     slot(.Object, "distalgo") <- "farthest_neighbor"
     return(.Object)
@@ -444,6 +445,22 @@ setMethod(
     x@distname
   })
 
+#==============================================================================#
+#' @rdname MLG-accessors
+#' @aliases distenv,MLG-method
+#' @export
+#==============================================================================#
+setGeneric("distenv", function(x) {
+  standardGeneric("distenv")
+})
+
+setMethod(
+  f = "distenv", 
+  signature(x = "MLG"), 
+  definition = function(x) {
+    x@distenv
+  })
+
 #==============================================================================#
 #' @rdname MLG-accessors
 #' @aliases distname<-,MLG-method
@@ -461,6 +478,23 @@ setMethod(
     return(x)
   })
 
+#==============================================================================#
+#' @rdname MLG-accessors
+#' @aliases distenv<-,MLG-method
+#' @export
+#==============================================================================#
+setGeneric("distenv<-", function(x, value) {
+  standardGeneric("distenv<-")
+})
+
+setMethod(
+  f = "distenv<-", 
+  signature(x = "MLG"), 
+  definition = function(x, value) {
+    x@distenv <- value
+    return(x)
+  })
+
 #==============================================================================#
 #' @rdname MLG-accessors
 #' @aliases distargs,MLG-method
@@ -560,4 +594,4 @@ setMethod(
   definition = function(x, value) {
     x@cutoff <- value
     return(x)
-  })
+  })

R/file_handling.r

@@ -80,9 +80,6 @@
 #'
 #' yfiles <- poppr.all(y$files)
 #' 
-#' # Write results to a file in that directory.
-#' setwd(y$path)
-#' write.csv(yfiles)
 #' }  
 #' @export
 #==============================================================================#