Merge pull request #10 from mrc-ide/feature/pass_checks

tweaks to pass checks and added github actions

.Rbuildignore

@@ -18,3 +18,5 @@ vignettes_src
 docs
 vignettes/introduction_cache
 vignettes_src/introduction_cache
+^\.github$
+^index.md$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/checks_develop.yaml

@@ -0,0 +1,47 @@
+# 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:
+      - develop
+  pull_request:
+    branches:
+      - develop
+
+name: checks_develop
+
+jobs:
+  R-CMD-check:
+
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - name: Install Dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - name: Build Package
+        uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--ignore-vignettes")'
+          build_args: 'c("--no-build-vignettes")'

.github/workflows/checks_master.yaml

@@ -0,0 +1,47 @@
+# 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:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: checks_master
+
+jobs:
+  R-CMD-check:
+
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - name: Install Dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - name: Build Package
+        uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--ignore-vignettes")'
+          build_args: 'c("--no-build-vignettes")'

DESCRIPTION

@@ -2,18 +2,17 @@ Package: MIPanalyzer
 Type: Package
 Title: Filtering and analysis of MIP data
 Version: 1.0.0
-Author: Bob Verity
-Maintainer: Bob Verity <r.verity@imperial.ac.uk>
+Authors@R: as.person(c(
+    "Bob Verity <r.verity@imperial.ac.uk> [aut, cre]"
+  ))
 Description: Filtering and analysis of MIP data.
 License: MIT + file LICENSE
 Encoding: UTF-8
-LazyData: true
 LinkingTo: 
     Rcpp
 Imports: 
     Rcpp,
     vcfR,
-    magrittr,
     dplyr,
     reshape2,
     RColorBrewer,
@@ -23,12 +22,16 @@ Imports:
     ape,
     stringr,
     methods,
-    rworldmap
-RoxygenNote: 7.0.2
+    rworldmap,
+    coda,
+    data.table
+RoxygenNote: 7.2.3
 SystemRequirements: C++11
 Suggests: 
     testthat,
-    covr,
     knitr,
-    rmarkdown
+    rmarkdown,
+    here,
+    kableExtra,
+    tidyverse
 VignetteBuilder: knitr

NAMESPACE

@@ -4,9 +4,8 @@ S3method(print,mipanalyzer_biallelic)
 S3method(print,mipanalyzer_multiallelic)
 S3method(summary,mipanalyzer_biallelic)
 S3method(summary,mipanalyzer_multiallelic)
-export("%>%")
-export(MIPanalyzerbi2vcfR)
 export(Pf_chrom_lengths)
+export(check_MIPanalyzer_loaded)
 export(explore_filter_coverage_loci)
 export(explore_filter_coverage_samples)
 export(filter_counts)
@@ -26,6 +25,7 @@ export(inbreeding_mle)
 export(is.mipanalyzer_biallelic)
 export(is.mipanalyzer_multiallelic)
 export(lonlat_to_bearing)
+export(mipanalyzer_biallelic_to_vcfR)
 export(mipanalyzer_file)
 export(pca_wsaf)
 export(pcoa_genomic_distance)
@@ -39,14 +39,17 @@ export(print_full)
 export(rbetabinom)
 export(rdirichlet)
 export(sim_biallelic)
-export(vcf2mipanalyzer_biallelic)
-export(vcf2mipanalyzer_multiallelic)
+export(vcf_to_mipanalyzer_biallelic)
+export(vcf_to_mipanalyzer_multiallelic)
 import(ggplot2)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(Rcpp,sourceCpp)
 importFrom(ape,pcoa)
+importFrom(coda,geweke.diag)
+importFrom(coda,mcmc)
+importFrom(data.table,fread)
 importFrom(grDevices,grey)
-importFrom(magrittr,"%>%")
+importFrom(methods,is)
 importFrom(methods,new)
 importFrom(plotly,layout)
 importFrom(plotly,plot_ly)

R/MIPanalyzer.R

@@ -0,0 +1,27 @@
+#------------------------------------------------
+#' @title MIPanalyzer
+#'
+#' @description This package can be used to read in raw molecular inversion
+#'   probe (MIP) data from vcf into a format that is convenient to work with.
+#'   Data can be filtered based on counts, frequencies, missingness or other
+#'   criteria. Filtered data can be analysed by common methods including PCA and
+#'   various pairwise genetic metrics, and can be visualised in multiple ways.
+#'   This package is intended to evolve as new MIP analyses are needed, thereby
+#'   making it easy to repeat common analyses as new data becomes available.
+#'
+#' @docType package
+#' @name MIPanalyzer
+NULL
+
+#------------------------------------------------
+# link to Rcpp
+#' @useDynLib MIPanalyzer, .registration = TRUE
+#' @importFrom Rcpp sourceCpp
+NULL
+
+#------------------------------------------------
+# unload dll when package is unloaded
+#' @noRd
+.onUnload <- function(libpath) {
+  library.dynam.unload("MIPanalyzer", libpath)
+}