bump version

Author: ShixiangWang

.github/workflows/r-release-check.yml

@@ -1,54 +1,31 @@
-# 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
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    runs-on: macOS-latest
-    #env:
-    #  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: actions/checkout@v3
 
-      - 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
+      - uses: r-lib/actions/setup-r@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: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          use-public-rspm: true
 
-      - name: Check
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+              any::rcmdcheck
+              any::XML
+          needs: check
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v2

DESCRIPTION

@@ -2,12 +2,9 @@ Type: Package
 Package: ezcox
 Title: Easily Process a Batch of Cox Models
 Version: 1.0.4
-Date: 2022-8-16
+Date: 2023-5-8
 Authors@R: 
-    person(given = "Shixiang",
-           family = "Wang",
-           role = c("aut", "cre"),
-           email = "[email protected]",
+    person("Shixiang", "Wang", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9855-7357"))
 Maintainer: Shixiang Wang <[email protected]>
 Description: A tool to operate a batch of univariate or multivariate Cox
@@ -22,26 +19,27 @@ Imports:
     forestmodel,
     ggplot2,
     magrittr (>= 1.5),
+    methods,
     purrr (>= 0.3.2),
     rlang (>= 0.1.2),
     scales,
     survival,
     tibble,
-    utils,
-    utf8
+    utf8,
+    utils
 Suggests: 
     covr (>= 3.2.1),
     furrr,
     future,
     knitr,
+    prettydoc,
     rmarkdown,
     roxygen2 (>= 6.1.1),
-    testthat (>= 2.1.0),
-    prettydoc
+    testthat (>= 2.1.0)
 VignetteBuilder: 
     knitr
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace", "rd",
     "roxytest::testthat_roclet"))
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3

NAMESPACE

@@ -27,6 +27,7 @@ importFrom(dplyr,if_else)
 importFrom(dplyr,tibble)
 importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")
+importFrom(methods,is)
 importFrom(purrr,map2_df)
 importFrom(rlang,":=")
 importFrom(rlang,.data)
@@ -38,4 +39,5 @@ importFrom(rlang,expr)
 importFrom(rlang,sym)
 importFrom(rlang,syms)
 importFrom(stats,as.formula)
+importFrom(utf8,output_utf8)
 importFrom(utils,packageVersion)

NEWS.md

@@ -1,5 +1,6 @@
 # ezcox 1.0.4
 
+* Refined the handle of `isValidAndUnreserved()`.
 * Enhanced the `forester()` to render labels better.
 
 # ezcox 1.0.3

R/ezcox.R

@@ -25,6 +25,8 @@
 #' @importFrom stats as.formula
 #' @importFrom dplyr tibble
 #' @importFrom purrr map2_df
+#' @importFrom methods is
+#' @importFrom utf8 output_utf8
 #' @return a `ezcox` object
 #' @author Shixiang Wang <[email protected]>
 #' @export
@@ -176,12 +178,12 @@ ezcox <- function(data, covariates, controls = NULL,
       model_df <- dplyr::tibble(
         Variable = y,
         model = list(cox),
-        status = ifelse(class(cox) == "coxph", TRUE, FALSE)
+        status = ifelse(is(cox, "coxph"), TRUE, FALSE)
       )
       saveRDS(model_df, file = model_file)
     }
 
-    if (any(grepl("[*:|()]", controls)) & class(cox) == "coxph") {
+    if (any(grepl("[*:|()]", controls)) & is(cox, "coxph")) {
       out <- as.data.frame(summary(cox)$coef)
       cox_sum <- summary(cox)
       glob.pval <- signif(cox_sum[[test]]["pvalue"], digits = 3)
@@ -206,7 +208,7 @@ ezcox <- function(data, covariates, controls = NULL,
         model_file = ifelse(exists("model_file"), model_file, NA_character_)
       )
     } else {
-      if (class(cox) != "coxph" | all(is.na(tbl[["ref_level"]]))) {
+      if (is(cox, "coxph") | all(is.na(tbl[["ref_level"]]))) {
         glob.pval <- p.value <- beta <- HR <- lower_95 <- upper_95 <- NA
       } else {
         cox <- summary(cox)

R/utils.R

@@ -15,3 +15,8 @@ isValidAndUnreserved <- function(string) {
 split_vector <- function(x, batch_size) {
   split(x, ceiling(seq_along(x) / batch_size))
 }
+
+utils::globalVariables(
+  "estimate2"
+)
+.x = utf8::output_utf8

README.Rmd

@@ -19,7 +19,6 @@ knitr::opts_chunk$set(
 [![](https://cranlogs.r-pkg.org/badges/grand-total/ezcox?color=blue)](https://cran.r-project.org/package=ezcox)
 [![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fgithub.com%2FShixiangWang%2Fezcox&count_bg=%2379C83D&title_bg=%23555555&icon=fandom.svg&icon_color=%23E7E7E7&title=hits&edge_flat=false)](https://hits.seeyoufarm.com)
 ![R-CMD-check](https://github.com/ShixiangWang/ezcox/workflows/R-CMD-check/badge.svg)
-[![Codecov test coverage](https://app.codecov.io/gh/ShixiangWang/ezcox/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ShixiangWang/ezcox?branch=master)
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html)
 <!-- badges: end -->
 

README.md

@@ -10,16 +10,14 @@ status](https://www.r-pkg.org/badges/version/ezcox)](https://CRAN.R-project.org/
 [![](https://cranlogs.r-pkg.org/badges/grand-total/ezcox?color=blue)](https://cran.r-project.org/package=ezcox)
 [![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fgithub.com%2FShixiangWang%2Fezcox&count_bg=%2379C83D&title_bg=%23555555&icon=fandom.svg&icon_color=%23E7E7E7&title=hits&edge_flat=false)](https://hits.seeyoufarm.com)
 ![R-CMD-check](https://github.com/ShixiangWang/ezcox/workflows/R-CMD-check/badge.svg)
-[![Codecov test
-coverage](https://app.codecov.io/gh/ShixiangWang/ezcox/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ShixiangWang/ezcox?branch=master)
 [![Lifecycle:
 stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html)
 <!-- badges: end -->
 
 The goal of ezcox is to operate a batch of univariate or multivariate
 Cox models and return tidy result.
 
-## :arrow\_double\_down: Installation
+## :arrow_double_down: Installation
 
 You can install the released version of ezcox from
 [CRAN](https://CRAN.R-project.org) with:
@@ -57,12 +55,11 @@ of cox models.
 library(ezcox)
 #> Welcome to 'ezcox' package!
 #> =======================================================================
-#> You are using ezcox version 0.8.1
+#> You are using ezcox version 1.0.2
 #> 
-#> Github page  : https://github.com/ShixiangWang/ezcox
-#> Documentation: https://shixiangwang.github.io/ezcox/articles/ezcox.html
-#> 
-#> Run citation("ezcox") to see how to cite 'ezcox'.
+#> Project home : https://github.com/ShixiangWang/ezcox
+#> Documentation: https://shixiangwang.github.io/ezcox
+#> Cite as      : arXiv:2110.14232
 #> =======================================================================
 #> 
 library(survival)
@@ -82,13 +79,14 @@ ezcox(lung, covariates = c("age", "sex", "ph.ecog"))
 #> ==> Building Cox model...
 #> ==> Done.
 #> # A tibble: 3 × 12
-#>   Variable is_control contrast_level ref_level n_contrast n_ref    beta    HR
-#>   <chr>    <lgl>      <chr>          <chr>          <int> <int>   <dbl> <dbl>
-#> 1 age      FALSE      age            age              228   228  0.0187 1.02 
-#> 2 sex      FALSE      sex            sex              228   228 -0.531  0.588
-#> 3 ph.ecog  FALSE      ph.ecog        ph.ecog          227   227  0.476  1.61 
-#> # … with 4 more variables: lower_95 <dbl>, upper_95 <dbl>, p.value <dbl>,
-#> #   global.pval <dbl>
+#>   Variable is_cont…¹ contr…² ref_l…³ n_con…⁴ n_ref    beta    HR lower…⁵ upper…⁶
+#>   <chr>    <lgl>     <chr>   <chr>     <int> <int>   <dbl> <dbl>   <dbl>   <dbl>
+#> 1 age      FALSE     age     age         228   228  0.0187 1.02    1       1.04 
+#> 2 sex      FALSE     sex     sex         228   228 -0.531  0.588   0.424   0.816
+#> 3 ph.ecog  FALSE     ph.ecog ph.ecog     227   227  0.476  1.61    1.29    2.01 
+#> # … with 2 more variables: p.value <dbl>, global.pval <dbl>, and abbreviated
+#> #   variable names ¹​is_control, ²​contrast_level, ³​ref_level, ⁴​n_contrast,
+#> #   ⁵​lower_95, ⁶​upper_95
 
 # Build multi-variable models
 # Control variable 'age'
@@ -102,14 +100,15 @@ ezcox(lung, covariates = c("sex", "ph.ecog"), controls = "age")
 #> ==> Building Cox model...
 #> ==> Done.
 #> # A tibble: 4 × 12
-#>   Variable is_control contrast_level ref_level n_contrast n_ref    beta    HR
-#>   <chr>    <lgl>      <chr>          <chr>          <int> <int>   <dbl> <dbl>
-#> 1 sex      FALSE      sex            sex              228   228 -0.513  0.599
-#> 2 sex      TRUE       age            age              228   228  0.017  1.02 
-#> 3 ph.ecog  FALSE      ph.ecog        ph.ecog          227   227  0.443  1.56 
-#> 4 ph.ecog  TRUE       age            age              228   228  0.0113 1.01 
-#> # … with 4 more variables: lower_95 <dbl>, upper_95 <dbl>, p.value <dbl>,
-#> #   global.pval <dbl>
+#>   Variable is_cont…¹ contr…² ref_l…³ n_con…⁴ n_ref    beta    HR lower…⁵ upper…⁶
+#>   <chr>    <lgl>     <chr>   <chr>     <int> <int>   <dbl> <dbl>   <dbl>   <dbl>
+#> 1 sex      FALSE     sex     sex         228   228 -0.513  0.599   0.431   0.831
+#> 2 sex      TRUE      age     age         228   228  0.017  1.02    0.999   1.04 
+#> 3 ph.ecog  FALSE     ph.ecog ph.ecog     227   227  0.443  1.56    1.24    1.96 
+#> 4 ph.ecog  TRUE      age     age         228   228  0.0113 1.01    0.993   1.03 
+#> # … with 2 more variables: p.value <dbl>, global.pval <dbl>, and abbreviated
+#> #   variable names ¹​is_control, ²​contrast_level, ³​ref_level, ⁴​n_contrast,
+#> #   ⁵​lower_95, ⁶​upper_95
 ```
 
 ``` r
@@ -142,17 +141,17 @@ show_models(mds)
 
 ## :star2: Vignettes
 
--   [ezcox: Easily Process a Batch of Cox
-    Models](https://CRAN.R-project.org/package=ezcox/vignettes/ezcox.html)
--   [ezcox: Easily Show Cox Forestplot in One
-    Command](https://CRAN.R-project.org/package=ezcox/vignettes/ezforest.html)
--   [ezcox: Easy Group Cox Analysis and
-    Visualization](https://CRAN.R-project.org/package=ezcox/vignettes/ezgroup.html)
--   [ezcox: an R Package for Cox Model Batch Processing and
-    Visualization - An Use
-    Case](https://shixiangwang.github.io/ezcox-adv-usage/)
-
-## :page\_with\_curl: Citation
+- [ezcox: Easily Process a Batch of Cox
+  Models](https://CRAN.R-project.org/package=ezcox/vignettes/ezcox.html)
+- [ezcox: Easily Show Cox Forestplot in One
+  Command](https://CRAN.R-project.org/package=ezcox/vignettes/ezforest.html)
+- [ezcox: Easy Group Cox Analysis and
+  Visualization](https://CRAN.R-project.org/package=ezcox/vignettes/ezgroup.html)
+- [ezcox: an R Package for Cox Model Batch Processing and
+  Visualization - An Use
+  Case](https://shixiangwang.github.io/ezcox-adv-usage/)
+
+## :page_with_curl: Citation
 
 If you are using it in academic research, please cite the preprint
 [arXiv:2110.14232](https://arxiv.org/abs/2110.14232) along with URL of