Merge pull request #40 from mrc-ide/gh-actions

Migrate to github actions, qualify package names

.Rbuildignore

@@ -1,5 +1,11 @@
 ^README\.Rmd$
+^README\.md$
+^\.idea$
 ^data-raw$
 ^LICENSE\.md$
 ^dev$
-^.travis.yml$
+^.*\.Rproj$
+^\.Rproj\.user$
+^.github$
+^.ProgramDataGuidance\.md$
+^.SurveyDataGuidance\.md$

.github/.gitignore

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

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

@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: actions/checkout@master
+        with:
+          repository: mrc-ide/shiny90_sample_files
+          ## ${{ github.token }} is scoped to the current repository, so we
+          ## need to provide our own PAT
+          token: ${{ secrets.SAMPLE_FILES_GH_PAT }}
+          path: tests/testthat/sample_files
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          error-on: '"error"'

.gitignore

@@ -7,7 +7,8 @@
 .DS_Store
 .idea
 tests/testthat/sample_files
+tests/testthat/Rplots.pdf
 *.tar.gz
 *.Rcheck
 
-README.html
+README.html

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: first90
-Version: 1.6.9
+Version: 1.6.10
 Title: The first90 model
 Description: Implements the Shiny90 model for estimating progress towards the UNAIDS "first 90" target for HIV awareness of status in sub-Saharan Africa.
 Authors@R:
@@ -25,7 +25,7 @@ Encoding: UTF-8
 LazyData: true
 ByteCompile: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends:
     R (>= 2.10)
 Imports:

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export()
 export(add_ss_indices)
 export(artcov15to49)
 export(combine_inputs)

NEWS.md

@@ -1,3 +1,7 @@
+# first90 1.6.10
+
+* Qualify package names, fix some R CMD warnings and notes
+
 # first90 1.6.9
 
 * Bug fix: account for end-year net migration in the ART population in the first year of ART start (implemented in v1.6.0).

R/create_hts_param.R

@@ -60,32 +60,32 @@ create_hts_param <- function(theta, fp) {
   n_k1 <- length(knots) - 1 # we remove 1995
   n_k2 <- n_k1 + length(knots_rr_dxunt)
   rate_f <- exp(theta[1:n_k1])
-  rr_dxunt <- plogis(theta[(n_k1 + 1):n_k2]) * 8 # Range is 0-8
-  rr_m <- plogis(theta[(n_k2 + 1):(n_k2 + 2)]) * 1.1
-  rr_test <- 0.95 + plogis(theta[(n_k2 + 3):(n_k2 + 4)]) * 7.05 # Range is 1-8
-  rr_plhiv <- 0.05 + plogis(theta[n_k2 + 5]) * (1.95 - 0.05)
-  rr_dxart <- plogis(theta[n_k2 + 6]) 
-  rr_25m <- 0.1 + plogis(theta[n_k2 + 7]) * (6 - 0.1)
-  rr_35m <- 0.1 + plogis(theta[n_k2 + 8]) * (6 - 0.1)
-  rr_25f <- 0.1 + plogis(theta[n_k2 + 9]) * (6 - 0.1)
-  rr_35f <- 0.1 + plogis(theta[n_k2 + 10]) * (6 - 0.1)
-  pr_oidx <- 0.25 + (plogis(theta[n_k2 + 11]) * (1.75 - 0.25))
+  rr_dxunt <- stats::plogis(theta[(n_k1 + 1):n_k2]) * 8 # Range is 0-8
+  rr_m <- stats::plogis(theta[(n_k2 + 1):(n_k2 + 2)]) * 1.1
+  rr_test <- 0.95 + stats::plogis(theta[(n_k2 + 3):(n_k2 + 4)]) * 7.05 # Range is 1-8
+  rr_plhiv <- 0.05 + stats::plogis(theta[n_k2 + 5]) * (1.95 - 0.05)
+  rr_dxart <- stats::plogis(theta[n_k2 + 6])
+  rr_25m <- 0.1 + stats::plogis(theta[n_k2 + 7]) * (6 - 0.1)
+  rr_35m <- 0.1 + stats::plogis(theta[n_k2 + 8]) * (6 - 0.1)
+  rr_25f <- 0.1 + stats::plogis(theta[n_k2 + 9]) * (6 - 0.1)
+  rr_35f <- 0.1 + stats::plogis(theta[n_k2 + 10]) * (6 - 0.1)
+  pr_oidx <- 0.25 + (stats::plogis(theta[n_k2 + 11]) * (1.75 - 0.25))
 
   # Age function for males and females
   agefn_m <- c(rep(1, 3), rep(rr_25m, 2), rep(rr_35m, 3), rr_35m * 0.8112) # last age group is 50+
   agefn_f <- c(rep(1, 3), rep(rr_25f, 2), rep(rr_35f, 3), rr_35f * 0.8183) # last age group is 50+
 
   # Time trends in testing rates
   fp$t_hts_start <- as.integer(1995 - fp$ss$proj_start + 1L)
-  base_rate_f <- approx(knots, c(0, rate_f), seq_len(fp$ss$PROJ_YEARS), rule = 2)$y
+  base_rate_f <- stats::approx(knots, c(0, rate_f), seq_len(fp$ss$PROJ_YEARS), rule = 2)$y
 
   knots_rr_m <- c(2005, 2012) - fp$ss$proj_start + 1L
-  rr_m <- approx(knots_rr_m, rr_m, seq_len(fp$ss$PROJ_YEARS), rule = 2)$y
+  rr_m <- stats::approx(knots_rr_m, rr_m, seq_len(fp$ss$PROJ_YEARS), rule = 2)$y
   base_rate_m <- base_rate_f * rr_m
 
   # Retest with time 
   knots_rr_test <- c(2005, 2010, 2015) - fp$ss$proj_start + 1L
-  rate_rr_test <- exp(approx(knots_rr_test, log(c(1, rr_test)), seq_len(fp$ss$PROJ_YEARS), rule = 2)$y)
+  rate_rr_test <- exp(stats::approx(knots_rr_test, log(c(1, rr_test)), seq_len(fp$ss$PROJ_YEARS), rule = 2)$y)
 
   ## Testing rate for HIV negative population:
   ## 1: never tested
@@ -147,7 +147,7 @@ create_hts_param <- function(theta, fp) {
 
   ## Relative testing among aware
   # Re-testing rate among PLHIV aware (not on ART)
-  rate_dxunt <- approx(knots_rr_dxunt, rr_dxunt, seq_len(fp$ss$PROJ_YEARS), rule = 2)$y
+  rate_dxunt <- stats::approx(knots_rr_dxunt, rr_dxunt, seq_len(fp$ss$PROJ_YEARS), rule = 2)$y
 
   diagn_rate_dxunt <- sweep(diagn_rate[,,,3,, drop = FALSE], 5, rate_dxunt, "*")
   diagn_rate[,,,3,] <- diagn_rate_dxunt 
@@ -162,4 +162,3 @@ create_hts_param <- function(theta, fp) {
 
   fp
 }
-

R/extract-pjnz.R

@@ -134,9 +134,9 @@ extract_pjnz <- function(pjnz = NULL, dp_file= NULL, pjn_file = NULL){
     v$art15plus_num <- v$art15plus_num * adult_artadj_factor
   }
 
-  v$art15plus_eligthresh <- setNames(as.numeric(dpsub(dp, "<CD4ThreshHoldAdults MV>", 2, col_idx)), proj_years)
+  v$art15plus_eligthresh <- stats::setNames(as.numeric(dpsub(dp, "<CD4ThreshHoldAdults MV>", 2, col_idx)), proj_years)
 
-  artelig_specpop <- setNames(dpsub(dp, "<PopsEligTreat MV>", 3:9, 2:6),
+  artelig_specpop <- stats::setNames(dpsub(dp, "<PopsEligTreat MV>", 3:9, 2:6),
                               c("description", "pop", "elig", "percent", "year"))
   artelig_specpop$pop <- c("PW", "TBHIV", "DC", "FSW", "MSM", "IDU", "OTHER")
   artelig_specpop$elig <- as.logical(as.integer(artelig_specpop$elig))
@@ -146,8 +146,8 @@ extract_pjnz <- function(pjnz = NULL, dp_file= NULL, pjn_file = NULL){
   rownames(artelig_specpop) <- artelig_specpop$pop
   v$artelig_specpop <- artelig_specpop
 
-  v$median_cd4init <- setNames(as.numeric(dpsub(dp, "<MedCD4CountInit MV>", 2, col_idx)), proj_years)
-  v$art_dropout <- setNames(as.numeric(dpsub(dp, "<PercLostFollowup MV>", 2, col_idx)), proj_years)
+  v$median_cd4init <- stats::setNames(as.numeric(dpsub(dp, "<MedCD4CountInit MV>", 2, col_idx)), proj_years)
+  v$art_dropout <- stats::setNames(as.numeric(dpsub(dp, "<PercLostFollowup MV>", 2, col_idx)), proj_years)
 
   v$art_alloc_method <- get_dp_art_alloc_method(dp)
   v$art_prop_alloc <- get_dp_art_prop_alloc(dp)
@@ -763,7 +763,7 @@ get_pjn_iso3 <- function(pjn){
 
 #' @export
 file_in_zip <- function(zfile, ext){
-  ff <- grep(ext, unzip(zfile, list = TRUE)$Name, value = TRUE)
+  ff <- grep(ext, utils::unzip(zfile, list = TRUE)$Name, value = TRUE)
   unz(zfile, ff)
 }
 

R/first90-package.R

@@ -5,3 +5,13 @@ NULL
 #' @importFrom Rcpp sourceCpp
 ## usethis namespace: end
 NULL
+
+## Suppress R CMD check NOTEs about "no visible binding for
+## global variable". These NOTEs aren't that important as we're using
+## but the thousands of lines of NOTE they print does obscure real issues.
+utils::globalVariables(c(
+  "DT", "PROJ_YEARS", "ag.idx", "agegr", "aglast.idx", "country", "f.idx",
+  "h.ag.span", "h.age15plus.idx", "h.fert.idx", "hAG", "hDS", "hTS",
+  "hiv_steps_per_year", "hivn.idx", "hivp.idx", "hivstatus", "logit", "m.idx",
+  "nearPD", "outcome", "p.age15plus.idx", "p.age15to49.idx", "p.fert.idx",
+  "pAG", "pDS", "quantile", "sex", "tot", "totpos", "year"))