Yf post release fixes (#24)

- refactored a bunch
- added tests
- added documentation

.Rbuildignore

@@ -6,3 +6,4 @@
 ^LICENSE\.md$
 LD_LINK_TOKEN
 installation
+demo/

.github/workflows/check-release.yaml

@@ -17,12 +17,32 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
+
       - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: '4.0.3' 
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
       - name: Install dependencies
         run: |
-          install.packages(c("remotes", "rcmdcheck"))
+          install.packages(c("remotes", "rcmdcheck", "renv"))
           remotes::install_deps(dependencies = TRUE)
+          renv::restore()
         shell: Rscript {0}
+
       - name: Check
         run: |
           options(crayon.enabled = TRUE)

.github/workflows/test-coverage.yaml

@@ -19,6 +19,8 @@ jobs:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: '4.0.3'
 
       - uses: r-lib/actions/setup-pandoc@v1
 
@@ -38,9 +40,10 @@ jobs:
 
       - name: Install dependencies
         run: |
-          install.packages(c("remotes"))
+          install.packages(c("remotes","renv"))
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("covr")
+          renv::restore()
         shell: Rscript {0}
 
       - name: Test coverage

.gitignore

@@ -2,6 +2,7 @@
 .Rhistory
 .RData
 .Ruserdata
+.Renviron
 tests
 LD_LINK_TOKEN
 inst/doc

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: MRutils
-Version: 0.1.0.0
+Version: 0.2.0.0
 Date: 2021-05-14
 Title: Utility functions for preparing data for Two-Sample MR
 Authors@R: c(person("Yossi", "Farjoun", role = c("aut", "cre"),
@@ -33,7 +33,9 @@ Imports:
     validate,
     assertthat,
     methods,
-    curry,
     here,
-    readr
+    readr,
+    digest,
+    yaml,
+    ggplot2
 VignetteBuilder: knitr

NAMESPACE

@@ -2,18 +2,30 @@
 
 export("%>%")
 export("%vin%")
+export(assert_chr)
 export(assert_gwas)
 export(assert_probabilities)
 export(assert_rsids)
 export(assert_valid_data)
+export(choose_best_proxies)
 export(extract_snps_from_bgzip)
+export(fill_gwas_unknown_rsids)
 export(filter_and_write_exposure_data)
+export(fix_proxy_alleles)
 export(get_2smr_results)
+export(get_LD_pairs)
 export(get_cached_rsid_from_position)
+export(get_proxies)
+export(get_rsid)
 export(get_rsid_from_position)
 export(get_unknown_rsids_from_locus)
+export(merge_rsids_into_gwas)
+export(prune_snps)
+export(remove_linked_snps)
+export(replace_alleles)
 export(required_headers)
 export(valid_contigs)
 export(valid_contigs_with_chr)
+export(valid_references)
 importFrom(magrittr,"%>%")
 importFrom(validate,"%vin%")