Release 1.0.3 (#53)

* fix invisible dkde1d and clean-up

* prepare release

* use github actions (#52)

* try actions

* try fix

* try to add token

.Rbuildignore

@@ -9,3 +9,4 @@ docs
 ^cran-comments\.md$
 ^revdep$
 ^.vscode$
+^\.github$

.github/.gitignore

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

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

@@ -0,0 +1,100 @@
+# NOTE: This workflow is overkill for most R packages
+# check-standard.yaml is likely a better choice
+# usethis::use_github_action("check-standard") will install it.
+#
+# 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: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-16.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        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", "16.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+
+      - name: Test coverage
+        if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'release'
+        run: |
+          Rscript -e 'remotes::install_github("r-lib/covr@gh-actions")'
+          Rscript -e 'covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: kde1d
 Type: Package
 Title: Univariate Kernel Density Estimation
-Version: 1.0.2
+Version: 1.0.3
 Authors@R: c(
         person("Thomas", "Nagler",, "mail@tnagler.com", role = c("aut", "cre")),
         person("Thibault", "Vatter",, "thibault.vatter@gmail.com", role = c("aut"))
@@ -25,7 +25,7 @@ Imports:
     randtoolbox,
     stats,
     utils
-RoxygenNote: 7.0.0
+RoxygenNote: 7.1.1
 Suggests: 
     testthat
 URL: https://github.com/tnagler/kde1d

NEWS.md

@@ -1,3 +1,10 @@
+# kde1d 1.0.3
+
+BUG FIXES
+
+  * fix invisible output in `dkde1d()`.
+
+
 # kde1d 1.0.2
 
 BUG FIXES

R/kde1d-methods.R

@@ -32,38 +32,15 @@
 #' @export
 dkde1d <- function(x, obj) {
   x <- prep_eval_arg(x, obj)
-  if (length(obj$jitter_info$i_disc) == 1) {
-    # for backwards compatibility with rvinecopulib
-    # TODO: remove next version
-    if (!is.ordered(x))
-      x <- ordered(x, obj$jitter_info$levels$x)
-    fhat <- dkde1d_cpp(as.numeric(x) - 1, obj)
-    f_all <- dkde1d_cpp(seq_along(obj$jitter_info$levels$x) - 1, obj)
-    fhat <- fhat / sum(f_all)
-  } else {
-    fhat <- dkde1d_cpp(x, obj)
-  }
+  dkde1d_cpp(x, obj)
 }
 
 #' @param q vector of quantiles.
 #' @rdname dkde1d
 #' @export
 pkde1d <- function(q, obj) {
   q <- prep_eval_arg(q, obj)
-  if (length(obj$jitter_info$i_disc) == 1) {
-    # for backwards compatibility with rvinecopulib
-    # TODO: remove next version
-    if (!is.ordered(q))
-      q <- ordered(q, obj$jitter_info$levels$x)
-    x_all <- as.ordered(obj$jitter_info$levels$x)
-    p_all <- dkde1d(x_all, obj)
-    p_total <- sum(p_all)
-    p <- sapply(q, function(y) sum(p_all[x_all <= y] / p_total))
-    p <- pmin(pmax(p, 0), 1)
-  } else {
-    p <- pkde1d_cpp(q, obj)
-  }
-  p
+  pkde1d_cpp(q, obj)
 }
 
 #' @param p vector of probabilities.
@@ -74,14 +51,7 @@ qkde1d <- function(p, obj) {
   if (is.ordered(obj$x)) {
     ## for discrete variables, add factor levels
     q <- ordered(levels(obj$x)[q + 1], levels(obj$x))
-  } else if (length(obj$jitter_info$i_disc) == 1) {
-    # for backwards compatibility with rvinecopulib
-    # TODO: remove next version
-    x_all <- as.ordered(obj$jitter_info$levels$x)
-    pp <- pkde1d(x_all, obj)
-    q <- x_all[vapply(p, function(y) which(y <= pp)[1], integer(1))]
   }
-
   q
 }
 

R/tools.R

@@ -71,11 +71,6 @@ prep_eval_arg <- function(x, obj) {
     return(x)
 
   stopifnot(is.ordered(x))
-  if (length(obj$jitter_info$i_disc) == 1) {
-    # for backwards compatibility with rvinecopulib
-    # TODO: remove next version
-    return(x)
-  }
 
   if (!all(levels(x) %in% levels(obj$x)))
     stop("'x' contains levels that weren't present when fitting.")

README.md

@@ -1,9 +1,10 @@
 # kde1d
 
-[![Build status Linux](https://travis-ci.org/tnagler/kde1d.svg?branch=master)](https://travis-ci.org/tnagler/kde1d)
-[![Windows Build status](http://ci.appveyor.com/api/projects/status/github/tnagler/kde1d?svg=true)](https://ci.appveyor.com/project/tnagler/kde1d)
+<!-- badges: start -->
+[![R build status](https://github.com/tnagler/kde1d/workflows/R-CMD-check/badge.svg)](https://github.com/tnagler/kde1d/actions)
 [![CRAN version](http://www.r-pkg.org/badges/version/kde1d)](https://cran.r-project.org/package=kde1d) 
 [![Coverage Status](https://img.shields.io/codecov/c/github/tnagler/kde1d/master.svg)](https://codecov.io/github/tnagler/kde1d?branch=master)
+<!-- badges: end -->
 
 
 ### Summary