Merge branch 'release/v0.2.0'

.Rbuildignore

@@ -11,3 +11,7 @@
 ^vignettes/precompile\.R$
 ^vignettes/children/*$
 ^cran-comments\.md$
+^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/.gitignore

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

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

@@ -0,0 +1,102 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on: [push, pull_request]
+
+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: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      CI: true
+      CXX_OLEVEL: 2
+      CXX: g++
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        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 system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Setup makevars
+        run: |
+          Sys.chmod("configure", mode = "0777")
+          dir.create("~/.R/")
+          if (Sys.info()[["sysname"]] == "Windows") {
+            mv <- "~/.R/Makevars.win"
+          } else {
+            mv <- "~/.R/Makevars"
+          }
+          file.create(mv)
+          CXX <- Sys.getenv("CXX")
+          cCXX <- system("R CMD config CXX", intern = TRUE)
+          if (CXX == "clang++") {
+            cCXX <- gsub(" g++", " clang++ -Qunused-arguments -fcolor-diagnostics", cCXX, fixed = TRUE)
+          }
+          cat("CXX =", cCXX, "\n", file = mv, append = TRUE)
+          cCXXFLAGS <- system("R CMD config CXXFLAGS", intern = TRUE)
+          cCXXFLAGS <- gsub("O[0-3]", paste0("O", Sys.getenv("CXX_OLEVEL")), cCXXFLAGS)
+          cat("CXXFLAGS =", cCXXFLAGS, "-pedantic -g0 -flto", "\n", file = mv, append = TRUE)
+          cat("LDFLAGS += -flto", "\n", file = mv, append = TRUE)
+          cat(readLines(mv), sep = "\n")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_DONTTEST_EXAMPLES_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-multiarch"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/pkgdown.yaml

@@ -0,0 +1,73 @@
+on:
+  push:
+    branches:
+      - develop
+      - master
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CXX_OLEVEL: 2
+      CXX: g++
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        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: |
+          remotes::install_deps(dependencies = TRUE)
+          install.packages("pkgdown", type = "binary")
+        shell: Rscript {0}
+
+      - name: Setup makevars
+        run: |
+          Sys.chmod("configure", mode = "0777")
+          dir.create("~/.R/")
+          if (Sys.info()[["sysname"]] == "Windows") {
+            mv <- "~/.R/Makevars.win"
+          } else {
+            mv <- "~/.R/Makevars"
+          }
+          file.create(mv)
+          CXX <- Sys.getenv("CXX")
+          cCXX <- system("R CMD config CXX", intern = TRUE)
+          if (CXX == "clang++") {
+            cCXX <- gsub(" g++", " clang++ -Qunused-arguments -fcolor-diagnostics", cCXX, fixed = TRUE)
+          }
+          cat("CXX =", cCXX, "\n", file = mv, append = TRUE)
+          cCXXFLAGS <- system("R CMD config CXXFLAGS", intern = TRUE)
+          cCXXFLAGS <- gsub("O[0-3]", paste0("O", Sys.getenv("CXX_OLEVEL")), cCXXFLAGS)
+          cat("CXXFLAGS =", cCXXFLAGS, "-pedantic -g0 -flto", "\n", file = mv, append = TRUE)
+          cat("LDFLAGS += -flto", "\n", file = mv, append = TRUE)
+          cat(readLines(mv), sep = "\n")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'options(width = 100, mc.cores = parallel::detectCores(), rmarkdown.html_vignette.check_title = FALSE); pkgdown::deploy_to_branch(new_process = FALSE)'

.gitignore

@@ -15,3 +15,4 @@ vignettes/*_files
 inst/*.bib.bak
 inst/*.bib.sav
 inst/doc
+docs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: multinma
 Title: Bayesian Network Meta-Analysis of Individual and Aggregate Data
-Version: 0.1.3
+Version: 0.2.0
 Authors@R: 
     person(given = c("David", "M."),
            family = "Phillippo",
@@ -23,18 +23,19 @@ Imports:
     stats,
     graphics,
     Rcpp (>= 0.12.0),
+    RcppParallel (>= 5.0.1),
     rstan (>= 2.19.2),
     rstantools (>= 2.0.0),
     Rdpack (>= 0.7),
-    tibble,
-    dplyr (>= 0.8.1),
+    tibble (>= 2.1.3),
+    dplyr (>= 0.8.3),
     rlang,
     purrr,
     forcats,
     glue,
     randtoolbox,
     copula,
-    tidyr (>= 0.8.3),
+    tidyr (>= 1.0.0),
     stringr,
     Matrix,
     igraph,
@@ -47,10 +48,11 @@ LinkingTo:
     BH (>= 1.66.0),
     Rcpp (>= 0.12.0),
     RcppEigen (>= 0.3.3.3.0),
+    RcppParallel (>= 5.0.1),
     rstan (>= 2.18.1),
     StanHeaders (>= 2.18.0)
 SystemRequirements: GNU make
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)
 Suggests: 
     testthat (>= 2.1.0),
@@ -62,10 +64,11 @@ Suggests:
     loo (>= 2.0.0),
     logitnorm,
     crayon,
-    tidygraph
+    tidygraph,
+    pkgdown
 RdMacros: Rdpack
-URL: http://github.com/dmphillippo/multinma
-BugReports: http://github.com/dmphillippo/multinma/issues
+URL: https://dmphillippo.github.io/multinma/, https://github.com/dmphillippo/multinma
+BugReports: https://github.com/dmphillippo/multinma/issues
 VignetteBuilder: 
     knitr,
     R.rsp

NAMESPACE

@@ -50,11 +50,13 @@ export(dic)
 export(distr)
 export(dlogitnorm)
 export(exponential)
+export(flat)
 export(half_cauchy)
 export(half_normal)
 export(half_student_t)
 export(is_network_connected)
 export(log_normal)
+export(multi)
 export(nma)
 export(normal)
 export(pbern)
@@ -95,6 +97,7 @@ importFrom(rstan,sampling)
 importFrom(stats,as.formula)
 importFrom(stats,complete.cases)
 importFrom(stats,dbinom)
+importFrom(stats,dunif)
 importFrom(stats,median)
 importFrom(stats,model.frame)
 importFrom(stats,model.matrix)

NEWS.md

@@ -1,10 +1,34 @@
+# multinma 0.2.0
+
+* Feature: The `set_*()` functions now accept `dplyr::mutate()` style semantics,
+allowing inline variable transformations.
+* Feature: Added ordered multinomial models, with helper function `multi()` for
+specifying the outcomes. Accompanied by a new data set `hta_psoriasis` and
+vignette.
+* Feature: Implicit flat priors can now be specified, on any parameter, using
+`flat()`.
+* Improvement: `as.array.stan_nma()` is now much more efficient, meaning that
+many post-estimation functions are also now much more efficient.
+* Improvement: `plot.nma_dic()` is now more efficient, particularly with large
+numbers of data points.
+* Improvement: The layering of points when producing "dev-dev" plots using
+`plot.nma_dic()` with multiple data types has been reversed for improved clarity
+(now AgD over the top of IPD).
+* Improvement: Aggregate-level predictions with `predict()` from ML-NMR / IPD
+regression models are now calculated in a much more memory-efficient manner.
+* Improvement: Added an overview of examples given in the vignettes.
+* Improvement: Network plots with `weight_edges = TRUE` no longer produce
+legends with non-integer values for the number of studies.
+* Fix: `plot.nma_dic()` no longer gives an error when attempting to specify
+`.width` argument when producing "dev-dev" plots.
+
 # multinma 0.1.3
 
 * Format DESCRIPTION to CRAN requirements
 
 # multinma 0.1.2
 
-* Wrapped long-running examples in \donttest{} instead of \dontrun{}
+* Wrapped long-running examples in `\donttest{}` instead of `\dontrun{}`
 
 # multinma 0.1.1
 

R/adapt_delta.R

@@ -13,7 +13,7 @@
 #'   divergent transitions.
 #'
 #'   For more details see the Stan documentation available from
-#'   https://mc-stan.org/users/documentation/.
+#'   \url{https://mc-stan.org/users/documentation/}.
 #'
 #' @name adapt_delta
 #'

R/data.R

@@ -304,3 +304,42 @@
 
 "bcg_vaccine"
 
+#' HTA Plaque Psoriasis
+#'
+#' Data frame containing the results of 16 trials comparing 8 treatments for
+#' moderate-to-severe plaque psoriasis from an HTA report
+#' \insertCite{Woolacott2006}{multinma}, analysed in TSD2
+#' \insertCite{TSD2}{multinma}. Outcomes are success/failure to achieve 50%,
+#' 75%, or 90% reduction in symptoms on the Psoriasis Area and Severity Index
+#' (PASI) scale. Some studies report all three ordered outcomes, others only one
+#' or two. The latter are coded as missing values (see details).
+#'
+#' @format A data frame with 39 rows and 9 variables:
+#' \describe{
+#'   \item{studyn}{numeric study ID}
+#'   \item{studyc}{study name}
+#'   \item{year}{year of publication}
+#'   \item{trtn}{numeric treatment code}
+#'   \item{trtc}{treatment name}
+#'   \item{sample_size}{sample size in each arm}
+#'   \item{PASI50, PASI75, PASI90}{ordered multinomial outcome counts (exclusive, see details)}
+#' }
+#'
+#' @details Outcome counts are "exclusive"; that is, for a study reporting all
+#'   outcomes, the counts represent the categories 50 < PASI < 75, 75 < PASI <
+#'   90, and 90 < PASI < 100, and are named by the lower end of the interval.
+#'   (As opposed to "inclusive" counts, which would represent the overlapping
+#'   categories PASI > 50, PASI > 70, and PASI > 90.) The count for the fourth
+#'   category (the lowest), 0 < PASI < 50, is equal to `sample_size - PASI50 -
+#'   PASI75 - PASI90`.
+#'
+#'   Missing values are used where studies only report a subset of the outcomes.
+#'   For a study reporting only two outcomes, say 50 and 75, the counts
+#'   represent 50 < PASI < 75 and 75 < PASI < 100. For a study reporting only
+#'   one outcome, say PASI 75, the count represents 75 < PASI < 100.
+#'
+#' @references
+#'   \insertAllCited{}
+#'
+
+"hta_psoriasis"