Censored (#6)

* first working version
* update data handling
* Update zcurve.Rd
* updating plotting and summary functions
* updating documentation & removing travis
* adding unit tests and github actions
* update actions and documentation
* adding github pages (https://gist.github.com/ramnathv/2227408)

.github/.gitignore

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

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

@@ -0,0 +1,109 @@
+# 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:
+    branches:
+      - main
+      - master
+      - pre-release
+      - censored
+  pull_request:
+    branches:
+      - main
+      - master
+      - pre-release
+      - censored
+
+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", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+
+    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@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: 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 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: Check
+        if: runner.os != 'Windows'
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(
+            args        = c("--no-manual", "--as-cran", "--ignore-vignettes"),
+            build_args  = c("--no-build-vignettes"),
+            error_on    = "warning",
+            check_dir   = "check")
+        shell: Rscript {0}"
+
+      - name: Check
+        if: runner.os == 'Windows'
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          JAGS_ROOT: "/c/progra~1/JAGS/JAGS-4.2.0"
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(
+            args        = c("--no-manual", "--as-cran", "--ignore-vignettes"),
+            build_args  = c("--no-build-vignettes"),
+            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/R-CMD-tests.yaml

@@ -0,0 +1,83 @@
+# 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:
+    branches:
+      - main
+      - master
+      - pre-release
+      - censored
+  pull_request:
+    branches:
+      - main
+      - master
+      - pre-release
+      - censored
+
+name: R-CMD-tests
+
+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"}
+
+    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@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: 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 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 and test z-curve (non-Windows)
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+          install.packages("devtools")
+          install.packages("testhat")
+          install.packages("vdiffr")
+          devtools::install()
+          library(vdiffr)
+          library(testthat)
+          devtools::test()
+        shell: Rscript {0}"

.github/workflows/pkgdown.yaml

@@ -0,0 +1,50 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      -'*'
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: 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: |
+          remotes::install_deps(dependencies = TRUE)
+          install.packages("pkgdown", type = "binary")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

DESCRIPTION

@@ -1,17 +1,17 @@
 Package: zcurve
 Title: An Implementation of Z-Curves
-Version: 1.0.9
+Version: 2.0.0
 Authors@R: c(
     person("František", "Bartoš", email = "[email protected]", role = c("aut", "cre")),
     person("Ulrich", "Schimmack", email = "[email protected]", role = c("aut")))
 Maintainer: František Bartoš <[email protected]>
 Description: An implementation of z-curves - a method for estimating expected discovery 
     and replicability rates on the bases of test-statistics of published studies. The package 
     provides functions for fitting the new density and EM version 
-    (Bartoš & Schimmack, 2020, <doi:10.31234/osf.io/urgtn>) as well as the original density 
-    z-curve (Brunner & Schimmack, 2020, <doi:10.15626/MP.2018.874>). Furthermore, the package 
-    provides summarizing and plotting functions for the fitted z-curve objects. See the 
-    aforementioned articles for more information about the z-curves, expected discovery 
+    (Bartoš & Schimmack, 2020, <doi:10.31234/osf.io/urgtn>), censored observations,  
+    as well as the original density z-curve (Brunner & Schimmack, 2020, <doi:10.15626/MP.2018.874>). 
+    Furthermore, the package provides summarizing and plotting functions for the fitted z-curve objects. 
+    See the aforementioned articles for more information about the z-curves, expected discovery 
     and replicability rates, validation studies, and limitations.
 License: GPL-3
 Encoding: UTF-8
@@ -27,6 +27,8 @@ Imports:
     Rdpack
 LinkingTo: Rcpp
 Suggests:
-    spelling
+    spelling,
+    testthat,
+    vdiffr
 Language: en-US
 RdMacros: Rdpack

R/RcppExports.R

@@ -13,6 +13,10 @@
     .Call(`_zcurve_zdist_pdf`, x, mu, sigma, a, b)
 }
 
+.zdist_cens_lpdf <- function(lb, ub, mu, sigma, a, b) {
+    .Call(`_zcurve_zdist_cens_lpdf`, lb, ub, mu, sigma, a, b)
+}
+
 .tdist_pdf <- function(x, mu, df, a, b) {
     .Call(`_zcurve_tdist_pdf`, x, mu, df, a, b)
 }
@@ -29,6 +33,10 @@
     .Call(`_zcurve_zcurve_EM_fit_fast_RCpp`, x, mu, sigma, theta, a, b, sig_level, max_iter, criterion)
 }
 
+.zcurve_EMc_fit_fast_RCpp <- function(x, lb, ub, mu, sigma, theta, a, b, sig_level, max_iter, criterion) {
+    .Call(`_zcurve_zcurve_EMc_fit_fast_RCpp`, x, lb, ub, mu, sigma, theta, a, b, sig_level, max_iter, criterion)
+}
+
 .zcurve_EM_start_RCpp <- function(x, type, K, mu, sigma, mu_alpha, mu_max, theta_alpha, a, b, sig_level, fit_reps, max_iter, criterion) {
     .Call(`_zcurve_zcurve_EM_start_RCpp`, x, type, K, mu, sigma, mu_alpha, mu_max, theta_alpha, a, b, sig_level, fit_reps, max_iter, criterion)
 }
@@ -45,3 +53,11 @@
     .Call(`_zcurve_zcurve_EM_boot_fast_RCpp`, x, mu, sigma, theta, a, b, sig_level, bootstrap, max_iter, criterion)
 }
 
+.zcurve_EMc_start_fast_RCpp <- function(x, lb, ub, K, mu, sigma, mu_alpha, mu_max, theta_alpha, a, b, sig_level, fit_reps, max_iter, criterion) {
+    .Call(`_zcurve_zcurve_EMc_start_fast_RCpp`, x, lb, ub, K, mu, sigma, mu_alpha, mu_max, theta_alpha, a, b, sig_level, fit_reps, max_iter, criterion)
+}
+
+.zcurve_EMc_boot_fast_RCpp <- function(x, lb, ub, mu, sigma, theta, a, b, sig_level, bootstrap, max_iter, criterion) {
+    .Call(`_zcurve_zcurve_EMc_boot_fast_RCpp`, x, lb, ub, mu, sigma, theta, a, b, sig_level, bootstrap, max_iter, criterion)
+}
+