Merge branch 'dev' into dev_bernd

.Rbuildignore

@@ -5,3 +5,7 @@
 README.md
 ^\.github$
 ^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^codemeta\.json$

.github/workflows/R-CMD-check-beta.yaml

@@ -62,8 +62,7 @@ jobs:
       - name: Install macos dependiencies
         if: runner.os == 'macOS'
         run: |
-          install.packages("rgdal", type="binary")
-        shell: Rscript {0}
+          brew install gdal proj geos
           
       - name: Install dependencies
         run: |

.github/workflows/R-CMD-check-dev.yaml

@@ -62,8 +62,7 @@ jobs:
       - name: Install macos dependiencies
         if: runner.os == 'macOS'
         run: |
-          install.packages("rgdal", type="binary")
-        shell: Rscript {0}
+          brew install gdal proj geos
           
       - name: Install dependencies
         run: |

.github/workflows/R-CMD-check-dev_Luis.yaml

@@ -62,8 +62,7 @@ jobs:
       - name: Install macos dependiencies
         if: runner.os == 'macOS'
         run: |
-          install.packages("rgdal", type="binary")
-        shell: Rscript {0}
+          brew install gdal proj geos
           
       - name: Install dependencies
         run: |

.github/workflows/R-CMD-check.yaml

@@ -60,15 +60,15 @@ jobs:
           do
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          sudo apt-get install libgdal-dev libproj-dev libgeos-dev libudunits2-dev netcdf-bin
+
       - name: Install macos dependiencies
         if: runner.os == 'macOS'
         run: |
-          install.packages("rgdal", type="binary")
-        shell: Rscript {0}
+          brew install gdal proj geos
           
       - name: Install dependencies
         run: |
-
           options(repos = c(CRAN = "https://cloud.r-project.org/"
           ))
           remotes::install_deps(dependencies = TRUE)

.github/workflows/pkgdown.yaml

@@ -0,0 +1,35 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: pkgdown
+          needs: website
+
+      - name: Deploy package
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.gitignore

@@ -9,3 +9,5 @@ dartR.Rproj
 dartR.Rproj
 /doc/
 /Meta/
+docs
+.RDataTmp

CONTRIBUTING.md

@@ -0,0 +1,93 @@
+# Contributing to dartR
+
+<!-- This CONTRIBUTING.md is adapted from https://gist.github.com/peterdesmet/e90a1b0dc17af6c12daf6e8b2f044e7c -->
+
+First of all, thanks for considering contributing to dartR! 👍 It's people like you that make it rewarding for us - the project maintainers - to work on dartR. 😊
+
+dartR is an open source project, maintained by people who care.
+
+[repo]: https://github.com/green-striped-gecko/dartR
+[issues]: https://github.com/green-striped-gecko/dartR/issues
+[new_issue]: https://github.com/green-striped-gecko/dartR/issues/new
+[website]: https://green-striped-gecko.github.io/dartR/
+[email]: mailto:Bernd.Gruber@canberra.edu.au
+[google]: https://groups.google.com/g/dartr?pli=1
+[developer]: http://georges.biomatix.org/storage/app/media/uploaded-files/Tutorial_0_dartR_for_the_Developer_2.0_19-Feb-22.pdf
+
+## Code of conduct
+
+Please note that this project is released with a [Contributor Code of Conduct](code_of_conduct.md). By participating in this project you agree to abide by its terms.
+
+## How you can contribute
+
+There are several ways you can contribute to this project. If you want to know more about why and how to contribute to open source projects like this one, see this [Open Source Guide](https://opensource.guide/how-to-contribute/).
+
+We have prepared a [document][developer] describing how independent developers can contribute to dartR. This document explains the structure of the functions in dartR, programming style, the data structure of the genlight object used in dartR, workflow and many other topics. 
+
+### Share the love ❤️
+
+Think dartR is useful? Let others discover it, by telling them in person, via Twitter or a blog post.
+
+If you use dartR in your research, please support us by citing dartR. You can find the citation information by typing in the R console:
+
+```{r}I
+citation("dartR”)
+```
+
+### Ask a question ⁉️
+
+Using dartR and got stuck? Browse the [documentation][website] to see if you can find a solution. Still stuck? Post your question in our [Google groups forum][new_issue] and we'll try to do our best to address it.
+
+Want to ask a question in private? Contact the package maintainer by [email][mailto:email].
+
+### Propose an idea 💡
+
+Have an idea for a new dartR feature? Take a look at the [documentation][website] and [issue list][issues] to see if it isn't included or suggested yet. If not, suggest your idea as an [issue on GitHub][new_issue]. While we can't promise to implement your idea, it helps to:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible.
+
+See below if you want to contribute code for your idea as well.
+
+### Report a bug 🐛
+
+Using dartR and discovered a bug? That's annoying! Don't let others have the same experience and report it as an [issue on GitHub][new_issue] so we can fix it. A good bug report makes it easier for us to do so, so please include:
+
+* Your operating system name and version (e.g. Mac OS 10.13.6).
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+### Improve the documentation 📖
+
+Noticed a typo on the website? Think a function could use a better example? Good documentation makes all the difference, so your help to improve it is very welcome!
+
+#### The website
+
+[This website][website] is generated with [`pkgdown`](http://pkgdown.r-lib.org/). That means we don't have to write any html: content is pulled together from documentation in the code, vignettes, [Markdown](https://guides.github.com/features/mastering-markdown/) files, the package `DESCRIPTION` and `_pkgdown.yml` settings. If you know your way around `pkgdown`, you can [propose a file change](https://help.github.com/articles/editing-files-in-another-user-s-repository/) to improve documentation. If not, [report an issue][new_issue] and we can point you in the right direction.
+
+#### Function documentation
+
+Functions are described as comments near their code and translated to documentation using [`roxygen2`](https://klutometis.github.io/roxygen/). If you want to improve a function description:
+
+1. Go to `R/` directory in the [code repository][repo].
+2. Look for the file with the name of the function.
+3. [Propose a file change](https://help.github.com/articles/editing-files-in-another-user-s-repository/) to update the function documentation in the roxygen comments (starting with `#'`).
+
+### Contribute code 📝
+
+Care to fix bugs or implement new functionality for dartR? Awesome! 👏 Have a look at the [issue list][issues] and leave a comment on the things you want to work on. See also the development guidelines below.
+
+## Development guidelines
+
+We try to follow the [GitHub flow](https://guides.github.com/introduction/flow/) for development.
+
+1. Fork [this repo][repo] and clone it to your computer. To learn more about this process, see [this guide](https://guides.github.com/activities/forking/).
+2. If you have forked and cloned the project before and it has been a while since you worked on it, [pull changes from the original repo](https://help.github.com/articles/merging-an-upstream-repository-into-your-fork/) to your clone by using `git pull upstream master`.
+3. Open the RStudio project file (`.Rproj`).
+4. Make your changes:
+    * Write your code.
+    * Test your code (bonus points for adding unit tests).
+    * Document your code (see function documentation above).
+    * Check your code with `devtools::check()` and aim for 0 errors and warnings.
+5. Commit and push your changes.
+6. Submit a [pull request](https://guides.github.com/activities/forking/#making-a-pull-request).

DESCRIPTION

@@ -54,6 +54,7 @@ Suggests:
     label.switching,
     leaflet,
     leaflet.minicharts,
+    maptools,
     markdown,
     mmod,
     networkD3,
@@ -83,10 +84,12 @@ Suggests:
     terra,
     tibble,
     tidyverse,
-    vcfR
+    vcfR,
+    zoo,
+    viridis
 License: GPL (>= 3)
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 NeedsCompilation: no
 Packaged: 2021-04-28 23:28:46 UTC; s425824
 Author: Bernd Gruber [aut, cre],
@@ -98,3 +101,6 @@ Author: Bernd Gruber [aut, cre],
   Lindsay V. Clark [ctb],
   Floriaan Devloo-Delva [ctb],
   Eric Archer [ctb]
+Config/testthat/edition: 3
+URL: https://green-striped-gecko.github.io/dartR/
+BugReports: https://groups.google.com/g/dartr?pli=1

NAMESPACE

@@ -8,6 +8,7 @@ export(gl.Ho)
 export(gl.LDNe)
 export(gl.alf)
 export(gl.amova)
+export(gl.assign.grm)
 export(gl.assign.mahalanobis)
 export(gl.assign.pa)
 export(gl.assign.pca)
@@ -34,6 +35,7 @@ export(gl.filter.callrate)
 export(gl.filter.hamming)
 export(gl.filter.heterozygosity)
 export(gl.filter.hwe)
+export(gl.filter.ld)
 export(gl.filter.locmetric)
 export(gl.filter.maf)
 export(gl.filter.monomorphs)
@@ -58,6 +60,8 @@ export(gl.join)
 export(gl.keep.ind)
 export(gl.keep.loc)
 export(gl.keep.pop)
+export(gl.ld.distance)
+export(gl.ld.haplotype)
 export(gl.list.reports)
 export(gl.load)
 export(gl.make.recode.ind)
@@ -119,6 +123,7 @@ export(gl.sim.ind)
 export(gl.sim.mutate)
 export(gl.sim.offspring)
 export(gl.smearplot)
+export(gl.spatial.autoCorr)
 export(gl.subsample.loci)
 export(gl.test.heterozygosity)
 export(gl.tree.nj)
@@ -146,6 +151,10 @@ export(gl2svdquartets)
 export(gl2treemix)
 export(gl2vcf)
 export(is.fixed)
+export(utils.assignment)
+export(utils.assignment_2)
+export(utils.assignment_3)
+export(utils.assignment_4)
 export(utils.basic.stats)
 export(utils.check.datatype)
 export(utils.dist.binary)
@@ -157,6 +166,7 @@ export(utils.n.var.invariant)
 export(utils.outflank)
 export(utils.outflank.MakeDiploidFSTMat)
 export(utils.outflank.plotter)
+export(utils.spautocor)
 export(utils.structure.evanno)
 export(utils.structure.genind2gtypes)
 export(utils.structure.run)
@@ -206,6 +216,7 @@ importFrom(dplyr,starts_with)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,vars)
 importFrom(grDevices,cm.colors)
+importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,hcl)
 importFrom(grDevices,hcl.pals)
@@ -268,6 +279,7 @@ importFrom(stats,variable.names)
 importFrom(stringr,str_pad)
 importFrom(stringr,str_trim)
 importFrom(tidyr,pivot_longer)
+importFrom(tidyr,pivot_wider)
 importFrom(utils,available.packages)
 importFrom(utils,combn)
 importFrom(utils,edit)

R/datasets.r

@@ -33,8 +33,8 @@
 #' A simulated genlight object created to run a landscape genetic example
 #'
 #'This a test data set to run a landscape genetics example. It contains 10 
-#'populations of 30 individuals each and each individual has 300 loci. There are 
-#'no covariates for individuals or loci.
+#'populations of 30 individuals each and each individual has 300 loci. There 
+#'are no covariates for individuals or loci.
 #' @name possums.gl
 #' @format genlight object
 #' @docType data
@@ -127,8 +127,8 @@ NULL
 #' library(PopGenReport)
 #' read.csv( paste(.libPaths()[1],'/dartR/extdata/platy.csv',sep='' ))
 #' platy <- read.genetable( paste(.libPaths()[1],'/dartR/extdata/platy.csv',
-#' sep='' ), ind=1, pop=2, lat=3, long=4, other.min=5, other.max=6, oneColPerAll=FALSE,
-#' sep='/')
+#' sep='' ), ind=1, pop=2, lat=3, long=4, other.min=5, other.max=6, 
+#' oneColPerAll=FALSE, sep='/')
 #' platy.gl <- gi2gl(platy, parallel=FALSE)
 #' df.loc <- data.frame(RepAvg = runif(nLoc(platy.gl)), CallRate = 1)
 #' platy.gl@other$loc.metrics <- df.loc

R/gl.LDNe.r

@@ -151,7 +151,7 @@ gl.LDNe <- function(x,
   }
 
   #change into tempdir (run it there)
-  old.path = getwd()
+  old.path <-getwd()
   setwd(tempdir())
   system(cmd)
   res <- read.delim(outfile)

R/gl.amova.r

@@ -21,7 +21,8 @@
 #' degrees of freedom, and a vector of variance components.
 #' @importFrom StAMPP stamppNeisD
 #' @export
-#' @author Bernd Gruber (bugs? Post to \url{https://groups.google.com/d/forum/dartr})
+#' @author Bernd Gruber (bugs? Post to 
+#' \url{https://groups.google.com/d/forum/dartr})
 #' @examples
 #' #permutations should be higher, here set to 10 because of speed
 #' out <- gl.amova(bandicoot.gl, permutations=10)
@@ -64,21 +65,21 @@ gl.amova <- function(x,
         sample <- row.names(geno)
         pop.names <- pop(geno2)
         ploidy <- ploidy(geno2)
-        geno = geno * (1 / ploidy)
-        geno[is.na(geno)] = NaN
+        geno <-geno * (1 / ploidy)
+        geno[is.na(geno)] <- NaN
         format <- vector(length = length(geno[, 1]))
-        format[1:length(geno[, 1])] = "genlight"
+        format[1:length(geno[, 1])] <- "genlight"
         pops <- unique(pop.names)
         pop.num <- vector(length = length(geno[, 1]))
         for (i in 1:length(geno[, 1])) {
-            pop.num[i] = which(pop.names[i] == pops)
+            pop.num[i] <- which(pop.names[i] == pops)
         }
         genoLHS <-
             as.data.frame(cbind(sample, pop.names, pop.num, ploidy, format))
         geno <- cbind(genoLHS, geno)
-        geno[, 2] = as.character(pop.names)
-        geno[, 4] = as.numeric(as.character(geno[, 4]))
-        row.names(geno) = NULL
+        geno[, 2] <- as.character(pop.names)
+        geno[, 4] <- as.numeric(as.character(geno[, 4]))
+        row.names(geno) <- NULL
     }
     pop.names <- geno[, 2]
     pop.names <- factor(pop.names)