Merge pull request #46 from Spatiotemporal-Exposures-and-Toxicology/m…

…ain-sciome

Fix tests. Fix linting issues. Added release action.

.Rbuildignore

@@ -5,4 +5,5 @@
 ^\.Rproj\.user$
 ^doc$
 ^Meta$
-^\.github/
+^\.lintr
+^\.github

.github/workflows/lint.yaml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, build-workflow]
   pull_request:
     branches: [main, master]
 
@@ -12,6 +12,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     env:
+      R_LINTR_LINTER_FILE: .lintr
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v3
@@ -26,8 +27,7 @@ jobs:
           needs: lint
 
       - name: Lint
-        run: lintr::lint_package(linters = lintr::linters_with_defaults(object_name_linter = NULL,
-              commented_code_linter = NULL, cyclocomp_linter = NULL))
+        run: lintr::lint_package()
         shell: Rscript {0}
         env:
           LINTR_ERROR_ON_LINT: true

.github/workflows/release.yaml

@@ -0,0 +1,109 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+#
+# See https://github.com/r-lib/actions/tree/master/examples#readme for
+# additional example workflows available for the R community.
+
+name: Release New version
+
+on:
+  push: 
+    tags: 
+    - '*'
+    branches: ["build-workflow"]
+  workflow_dispatch: 
+
+jobs:
+  create_release:
+    name: Create release
+    runs-on: ubuntu-latest
+    outputs:
+        upload_url: ${{ steps.create_release.outputs.upload_url }}
+    steps:
+        - name: Create release
+          id: create_release
+          uses: ncipollo/release-action@v1
+          with:
+            allowUpdates: true
+  build_upload_artefacts:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    strategy: 
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: macos-latest, r: 'release'}
+        #   - {os: windows-latest, r: '4.2'}
+        #   - {os: ubuntu-latest, r: '4.2'}
+        #   - {os: macos-latest, r: '4.2'}
+    env: 
+        R_KEEP_PKG_SOURCE: yes
+    steps:
+      # see this for details: https://msmith.de/2020/03/12/r-cmd-check-github-actions.html
+      - name: Configure git
+        run: git config --global core.autocrlf false
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-tinytex@v2
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 2
+          extra-packages: |
+            any::ggplot2
+            any::rcmdcheck
+            any::roxygen2
+          needs: |
+            check
+            roxygen2
+      - name: Read VERSION file
+        if: runner.os != 'macOs'
+        id: getversion
+        shell: bash
+        run: |
+          echo "VERSION=$(cat DESCRIPTION | grep -Po '(?<=Version\:\s).*')" >> $GITHUB_OUTPUT
+      - name: Read VERSION file (macOS)
+        if: runner.os == 'macOs'
+        id: getversion_mac
+        run: |
+          echo "VERSION=$(sed -n 's/Version:[[:space:]]*//p' DESCRIPTION | tr -d '[:space:]')" >> $GITHUB_OUTPUT
+      - name: Build package (Windows)
+        if: runner.os == 'Windows'
+        shell: cmd
+        run: R CMD build --no-build-vignettes .
+      - name: Build package
+        if: runner.os == 'Linux' || runner.os == 'macOs' 
+        run: R CMD build --no-build-vignettes .
+      - name: Test Install (Windows)
+        if: runner.os == 'Windows'
+        shell: cmd
+        run: R CMD INSTALL --build PrestoGP_${{ steps.getversion.outputs.VERSION }}.tar.gz
+      - name: Test Install (Linux)
+        if: runner.os == 'Linux'
+        run: R CMD INSTALL --build PrestoGP_${{ steps.getversion.outputs.VERSION }}.tar.gz
+      - name: Test Install (macOs)
+        if: runner.os == 'macOs'
+        run: R CMD INSTALL --build PrestoGP_${{ steps.getversion_mac.outputs.VERSION }}.tar.gz
+      - uses: svenstaro/upload-release-action@v2
+        if: runner.os == 'macOs'
+        with:
+            tag: ${{ github.ref }}
+            file: PrestoGP_${{ steps.getversion_mac.outputs.VERSION }}.tgz
+            asset_name: "PrestoGP_${{ steps.getversion_mac.outputs.VERSION }}-x86_64-macOs-R.${{ matrix.config.r }}.tgz"
+      - uses: svenstaro/upload-release-action@v2
+        if: runner.os == 'Linux'
+        with:
+            tag: ${{ github.ref }}
+            file: "PrestoGP_${{ steps.getversion.outputs.VERSION }}_R_x86_64-pc-linux-gnu.tar.gz"
+            asset_name: PrestoGP_${{ steps.getversion.outputs.VERSION }}-x86_64-linux-R.${{ matrix.config.r }}.zip
+      - uses: svenstaro/upload-release-action@v2
+        if: runner.os == 'Windows'
+        with:
+            tag: ${{ github.ref }}
+            file: PrestoGP_${{ steps.getversion.outputs.VERSION }}.zip
+            asset_name: PrestoGP_${{ steps.getversion.outputs.VERSION }}-windows-R.${{ matrix.config.r }}.zip
+

.github/workflows/sanitizers.yaml

@@ -84,12 +84,12 @@ jobs:
         run: rcmdcheck::rcmdcheck(build_args = "--no-build-vignettes", args = c("--no-codoc", "--no-examples", "--no-manual", "--ignore-vignettes"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@v3
-        with:
-          name: ${{ runner.os }}-asan-rrelease-results
-          path: check
+      # - name: Upload check results
+      #   if: failure()
+      #   uses: actions/upload-artifact@v3
+      #   with:
+      #     name: ${{ runner.os }}-asan-rrelease-results
+      #     path: check
   sanitizer-check-usan:
     runs-on: ubuntu-latest
     env:
@@ -162,9 +162,9 @@ jobs:
         run: rcmdcheck::rcmdcheck(build_args = "--no-build-vignettes", args = c("--no-codoc", "--no-examples", "--no-manual", "--ignore-vignettes"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@v3
-        with:
-          name: ${{ runner.os }}-ubsan-rrelease-results
-          path: check
+      # - name: Upload check results
+      #   if: failure()
+      #   uses: actions/upload-artifact@v3
+      #   with:
+      #     name: ${{ runner.os }}-ubsan-rrelease-results
+      #     path: check

.lintr

@@ -0,0 +1,13 @@
+linters: linters_with_defaults(
+    line_length_linter(160L),
+    commented_code_linter = NULL,
+    object_name_linter = NULL,
+    cyclocomp_linter = NULL,
+    object_length_linter = NULL,
+    indentation_linter(
+      indent = 2L,
+      hanging_indent_style = "never",
+      assignment_as_infix = FALSE
+    )
+  )
+encoding: "UTF-8"

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: PrestoGP
 Type: Package
 Title: Penalized Regression for Spatio-Temporal Outcomes via Gaussian Processes 
-Version: 0.2.0.9021
+Version: 0.2.0.9023
 Authors@R: c(
     person(given = "Eric",
            family = "Bair",
@@ -47,7 +47,8 @@ Imports:
     spam,
     psych,
     doParallel,
-    covr
+    covr,
+    mvtnorm
 License: GPL-3
 Encoding: UTF-8
 VignetteBuilder: knitr 

NAMESPACE

@@ -29,7 +29,6 @@ import(glmnet)
 import(ncvreg)
 import(readxl)
 import(scoringRules)
-import(covr)
 importFrom(aod,wald.test)
 importFrom(dplyr,"%>%")
 importFrom(foreach,"%dopar%")

R/Log_Likelihood.R

@@ -12,18 +12,21 @@
 #'
 #' @examples
 #' @noRd
-negloglik_vecchia_ST <- function(logparms, res, vecchia.approx, param.seq,
-                                 scaling, nscale) {
+negloglik_vecchia_ST <- function(logparms, res, vecchia.approx, param.seq, scaling, nscale) {
   parms <- unlog.params(logparms, param.seq, 1)
   locs.scaled <- vecchia.approx$locsord
   for (j in 1:nscale) {
     locs.scaled[, scaling == j] <- locs.scaled[, scaling == j] /
       parms[param.seq[2, 1] + j - 1]
   }
   vecchia.approx$locsord <- locs.scaled
-  -vecchia_likelihood(res, vecchia.approx, c(parms[1], 1,
-                                             parms[param.seq[3, 1]]),
-                      parms[param.seq[4, 1]])
+  -vecchia_likelihood(
+    res, vecchia.approx, c(
+      parms[1], 1,
+      parms[param.seq[3, 1]]
+    ),
+    parms[param.seq[4, 1]]
+  )
 }
 
 #' negloglik_vecchia
@@ -42,8 +45,10 @@ negloglik_vecchia_ST <- function(logparms, res, vecchia.approx, param.seq,
 #' @noRd
 negloglik_vecchia <- function(logparms, res, vecchia.approx, param.seq) {
   parms <- unlog.params(logparms, param.seq, 1)
-  -vecchia_likelihood(res, vecchia.approx, c(parms[1], parms[2], parms[3]),
-                      parms[4])
+  -vecchia_likelihood(
+    res, vecchia.approx, c(parms[1], parms[2], parms[3]),
+    parms[4]
+  )
 }
 
 #' negloglik_full_ST
@@ -95,8 +100,10 @@ negloglik.full <- function(logparams, d, y, param.seq) {
   params <- unlog.params(logparams, param.seq, 1)
   #    d <- fields::rdist(locs)
   N <- nrow(d)
-  cov.mat <- params[1] * fields::Matern(d, range = params[2],
-                                        smoothness = params[3]) +
+  cov.mat <- params[1] * fields::Matern(d,
+    range = params[2],
+    smoothness = params[3]
+  ) +
     params[4] * diag(N)
   return(-1 * mvtnorm::dmvnorm(y, rep(0, N), cov.mat, log = TRUE))
 }
@@ -133,8 +140,7 @@ mvnegloglik <- function(logparams, vecchia.approx, y, param.seq, P) {
 ##############################################################################
 ### Flexible Spatiotemporal Multivariate Matern Negative Loglikelihood Function ###########
 
-mvnegloglik_ST <- function(logparams, vecchia.approx, y, param.seq, P, scaling,
-                           nscale) {
+mvnegloglik_ST <- function(logparams, vecchia.approx, y, param.seq, P, scaling, nscale) {
   #  Input-
   #  logparams: A numeric vector of length (4*P)+(4*choose(P,2)).
   #             To construct these parameters we unlist a list of the 7 covariance
@@ -227,8 +233,7 @@ mvnegloglik.full <- function(logparams, locs, y, param.seq) {
 }
 
 ##############################################################################
-create.cov.upper.flex <- function(P, marg.var, marg.range, marg.smooth,
-                                  nugget, R.corr) {
+create.cov.upper.flex <- function(P, marg.var, marg.range, marg.smooth, nugget, R.corr) {
   # Create the symmetrical marginal+cross-covariance flexible matern from the
   # given parameters. Output is a list of the 4 Matern parameters as matrices
   sig2.mat <- diag(marg.var, P, P)
@@ -237,20 +242,17 @@ create.cov.upper.flex <- function(P, marg.var, marg.range, marg.smooth,
   nugget.mat <- diag(nugget, P, P)
   if (P > 1) {
     combs <- gtools::combinations(P, 2)
-    for (iter in 1:nrow(combs)) {
+    for (iter in seq_len(nrow(combs))) {
       i <- combs[iter, 1]
       j <- combs[iter, 2]
 
       smoothness.mat[i, j] <- (marg.smooth[i] + marg.smooth[j]) / 2
-      range.mat[i, j] <- 1 / sqrt(((1 / marg.range[i])^2 +
-                                     (1 / marg.range[j])^2) / 2)
+      range.mat[i, j] <- 1 / sqrt(((1 / marg.range[i])^2 + (1 / marg.range[j])^2) / 2)
 
       s1 <- sqrt(marg.var[i] * marg.var[j])
-      s2 <- ((1 / marg.range[i])^marg.smooth[i] *
-               (1 / marg.range[j])^marg.smooth[j]) /
+      s2 <- ((1 / marg.range[i])^marg.smooth[i] * (1 / marg.range[j])^marg.smooth[j]) /
         ((1 / range.mat[i, j])^(2 * smoothness.mat[i, j]))
-      s3 <- gamma(smoothness.mat[i, j]) / (sqrt(gamma(marg.smooth[i])) *
-                                             sqrt(gamma(marg.smooth[j])))
+      s3 <- gamma(smoothness.mat[i, j]) / (sqrt(gamma(marg.smooth[i])) * sqrt(gamma(marg.smooth[j])))
       s4 <- R.corr[iter]
       sig2.mat[i, j] <- s1 * s2 * s3 * s4
     }
@@ -284,20 +286,24 @@ cat.covariances <- function(locs.list, sig2, range, smoothness, nugget) {
 
   l <- length(locs.list)
   combs <- gtools::combinations(l, 2, repeats.allowed = TRUE)
-  for (iter in 1:nrow(combs)) {
+  for (iter in seq_len(nrow(combs))) {
     i <- combs[iter, 1]
     j <- combs[iter, 2]
     # d <- fields::rdist.earth(locs.list[[i]],locs.list[[j]],miles = FALSE)
     d <- fields::rdist(locs.list[[i]], locs.list[[j]])
     # Calculate the covariance matrix - if/then based on its location in the super-matrix
     N <- nrow(d)
     if (i == j) { # To accomodate varying size outcomes- the nugget is not included on cross-covariances
-      cov.mat.ij <- sig2[i, j] * geoR::matern(d, phi = range[i, j], kappa =
-                                                smoothness[i, j]) +
+      cov.mat.ij <- sig2[i, j] * geoR::matern(d,
+        phi = range[i, j], kappa =
+          smoothness[i, j]
+      ) +
         nugget[i, j] * diag(N)
     } else {
-      cov.mat.ij <- sig2[i, j] * geoR::matern(d, phi = range[i, j], kappa =
-                                                smoothness[i, j])
+      cov.mat.ij <- sig2[i, j] * geoR::matern(d,
+        phi = range[i, j], kappa =
+          smoothness[i, j]
+      )
     }
 
 
@@ -328,8 +334,7 @@ cat.covariances <- function(locs.list, sig2, range, smoothness, nugget) {
 ##############################################################################
 ### Create the likelihood initial values                    #########
 
-create.initial.values.flex <- function(marg.var, marg.range, marg.smooth,
-                                       nugget, R.corr, P) {
+create.initial.values.flex <- function(marg.var, marg.range, marg.smooth, nugget, R.corr, P) {
   # Log-transform the covariance parameters and arrange in the proper order
   # for the likelihood function
   logparams.init <- c(