Merge pull request #5 from jackwasey/test-update

Update testing from travis and appveyor to GitHub actions

.Rbuildignore

@@ -19,3 +19,5 @@ man-roxygen
 .*\.ods$
 physiology\.Rcheck
 physiology_.*\.tar\.gz
+^\.github$
+^\.lintr$

.github/.gitignore

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

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

@@ -0,0 +1,49 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+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-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/lint.yaml

@@ -0,0 +1,30 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}

.github/workflows/test-coverage.yaml

@@ -0,0 +1,31 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: covr::codecov(quiet = FALSE)
+        shell: Rscript {0}

.lintr

@@ -1 +1,2 @@
-inst/.lintr
+linters: linters_with_defaults(object_name_linter = NULL, line_length_linter(80)) # see vignette("lintr")
+encoding: "UTF-8"

DESCRIPTION

@@ -37,7 +37,8 @@ Suggests:
     knitr,
     spelling,
     tidyr,
-    utils
+    utils,
+    covr
 LinkingTo: 
     Rcpp
 VignetteBuilder: 

R/bmi.R

@@ -27,13 +27,15 @@ ideal_weight <- function(height_m, ..., age_y = NULL, male = NULL) {
 
 #' @describeIn ideal_weight Ideal weight of an adult
 #' @export
-ideal_weight_adult <- function(height_m, male, ...)
+ideal_weight_adult <- function(height_m, male, ...) {
   ideal_weight_Devine(height_m, male, ...)
+}
 
 #' @describeIn ideal_weight Ideal weight of a child, age >= 1 and age < 18 years
 #' @export
-ideal_weight_child <- function(height_m, age_y = NULL, ...)
+ideal_weight_child <- function(height_m, age_y = NULL, ...) {
   ideal_weight_Traub(height_m, age_y, ...)
+}
 
 #' ideal weight for child per Traub
 #'
@@ -76,8 +78,9 @@ ideal_weight_Traub <- function(height_m, age_y = NULL, ...) {
 #'   ref.)
 #' @rdname ideal_weight
 #' @export
-ideal_weight_Devine <- function(height_m, male, ...)
+ideal_weight_Devine <- function(height_m, male, ...) {
   ideal_weight_linear(height_m, male, 60, 50, 45.5, 2.3, 2.3, ...)
+}
 
 #' @title ideal weight by Robinson method
 #' @rdname ideal_weight
@@ -86,8 +89,9 @@ ideal_weight_Devine <- function(height_m, male, ...)
 #'   relationship. (Robinson JD, Lupkiewicz SM, Palenik L et al. Determination
 #'   of ideal body weight for drug dosage calculations. Am J Hosp Pharm 1983;
 #'   40: 1016-9.)
-ideal_weight_Robinson <- function(height_m, male, ...)
+ideal_weight_Robinson <- function(height_m, male, ...) {
   ideal_weight_linear(height_m, male, 60, 52, 49, 1.9, 1.7, ...)
+}
 
 
 #' @title ideal weight by Miller
@@ -96,17 +100,19 @@ ideal_weight_Robinson <- function(height_m, male, ...)
 #' @description Miller's method for ideal weight: different linear relationship.
 #'   (Miller DR, Carlson JD, Loyd BJ et al. Determining ideal body weight.
 #'   (Letter). Am J Hosp Pharm 1983; 40: 1622.)
-ideal_weight_Miller <- function(height_m, male, ...)
+ideal_weight_Miller <- function(height_m, male, ...) {
   ideal_weight_linear(height_m, male, 60, 56.2, 53.1, 1.41, 1.36, ...)
+}
 
 #' @title ideal weight by Broca
 #' @description Calculate ideal weight based on Broca (1871) Height in cm -100
 #'   for women, -105 for men Broca PP. Memoires d'anthropologie. Paris 1871 /
 #'   1877.
 #' @rdname ideal_weight
 #' @export
-ideal_weight_Broca <- function(height_m, male, ...)
+ideal_weight_Broca <- function(height_m, male, ...) {
   ideal_weight_linear(height_m, male, 0, -100, -105, 2.54, 2.54, ...)
+}
 
 #' @title ideal weight by Lemmens
 #' @description Lemmens method assumes BMI 22 as ideal (Obesity Surgery 2005)

R/deadspace.R

@@ -84,8 +84,9 @@ deadspace_anatomic_child <- function(ideal_weight_kg, age_y = NULL) {
 #'   independent
 #' @details 'Mean intrathoracic anatomic dead space was 1.03 ml/kg and was not
 #'   related to age.' Numa, 1985
-deadspace_intrathoracic_ml <- function(ideal_weight_kg)
+deadspace_intrathoracic_ml <- function(ideal_weight_kg) {
   1.03 * ideal_weight_kg
+}
 
 # nocov start
 deadspace_extrathoracic <- function(ideal_weight_kg = NULL, age_y = NULL) {

R/eGFR.R

@@ -205,7 +205,7 @@ egfr_mdrd <- function(scr_uM, age_y, male, black, idms_assay = TRUE,
     (age_y ^ (-0.203)) *
     (0.742 + 0.258 * male) *
     (1 + 0.212 * black)
-  if (any(ret > 60) & warn_ckdepi_preferred)
+  if (any(ret > 60) && warn_ckdepi_preferred)
     warning("The MDRD equation for eGFR is not recommended for values above ",
             "60 mL/min/1.73m^2 (CKD-EPI is recommended). ",
             "Use results above 60 with caution.")
@@ -245,7 +245,7 @@ egfr_ckdepi <- function(scr_uM, age_y, male, black, idms_assay = TRUE,
     0.993 ^ age_y *
     (1.018 - 0.018 * male) *
     (1 + 0.159 * black)
-  if (any(ret < 60) & warn_mdrd_preferred) {
+  if (any(ret < 60) && warn_mdrd_preferred) {
     warning("The CKD-EPI equation for eGFR is not recommended for values below",
             " 60 mL/min/1.73m^2 (MDRD is recommended). Use with caution.")
   }

R/physics.R

@@ -2,17 +2,19 @@
 #' @param temp_c Temperature in Celsius
 #' @family physics
 #' @export
-temp_c_to_k <- function(temp_c)
+temp_c_to_k <- function(temp_c) {
   273.15 + temp_c
+}
 
 #' Saturation vapor pressure of water at sea level
 #' @param temp_k Temperature in Kelvin
 #' @family physics
 #' @export
-svp_sea_level <- function(temp_k)
+svp_sea_level <- function(temp_k) {
   0.00750061683 *
-  exp(77.345 + 0.0057 * temp_k - 7235 / temp_k) /
-  temp_k ^ 8.2
+    exp(77.345 + 0.0057 * temp_k - 7235 / temp_k) /
+    temp_k ^ 8.2
+}
 
 #' Conversion factor from Pa to torr (mmHg)
 #'

R/valid.R

@@ -86,10 +86,11 @@ valid_age <- function(age_y, age_min = 0, age_max = 150,
 valid_age_adult <- function(age_y, age_min = 18, age_max = 150,
                             age_min_hard = 17, age_max_hard = 150,
                             extra_msg = "", do_warn = TRUE, do_stop = FALSE,
-                            equal_ok = FALSE)
+                            equal_ok = FALSE) {
   valid(age_y, "age", "yr",
         age_min, age_max, age_min_hard, age_max_hard,
         extra_msg, do_warn, do_stop, equal_ok = equal_ok)
+}
 
 #' @rdname valid_height
 #' @param scr_uM numeric serum creatinine (umol/L)
@@ -103,7 +104,7 @@ valid_age_adult <- function(age_y, age_min = 18, age_max = 150,
 #'   \code{warn}
 #' @export
 valid_creatinine <- function(scr_uM, scr_min = 8, scr_max = 1000,
-                             scr_min_hard=0, scr_max_hard = 4000,
+                             scr_min_hard = 0, scr_max_hard = 4000,
                              extra_msg = "", do_warn = TRUE, do_stop = FALSE,
                              equal_ok = FALSE) {
   # Note that scr_min was selected to help ensure that unit conversion errors

README.Rmd

@@ -17,12 +17,13 @@ knitr::opts_chunk$set(
 
 # physiology
 
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/jackwasey/physiology/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jackwasey/physiology/actions/workflows/R-CMD-check.yaml)
 [![CRAN status](https://www.r-pkg.org/badges/version/physiology)](https://cran.r-project.org/package=physiology)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
-[![Travis build Status](https://travis-ci.org/jackwasey/physiology.svg?branch=master)](https://travis-ci.org/jackwasey/physiology)
-[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/jackwasey/physiology?branch=master&svg=true)](https://ci.appveyor.com/project/jackwasey/physiology)
-[![Coverage status](https://codecov.io/gh/jackwasey/physiology/branch/master/graph/badge.svg)](https://codecov.io/github/jackwasey/physiology?branch=master)
+[![Codecov test coverage](https://codecov.io/gh/jackwasey/physiology/branch/master/graph/badge.svg)](https://app.codecov.io/gh/jackwasey/physiology?branch=master)
 [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
+<!-- badges: end -->
 
 ## Calculate physiologic characteristics of awake and anesthetized adults, children and infants