linting package

poissonconsulting · Oct 11, 2023 · dceed5e · dceed5e
1 parent 4818c3c
commit dceed5e
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Showing 7 changed files with 13 additions and 9 deletions.
diff --git a/R/ggproto.R b/R/ggproto.R
@@ -62,7 +62,7 @@ GeomHcintersect <- ggproto(
   default_aes = aes(colour = "black", linewidth = 0.5, linetype = "dotted", alpha = NA),
   draw_key = draw_key_path,
   draw_panel = function(data, panel_params, coord) {
-    data$group <- 1:nrow(data)
+    data$group <- seq_len(nrow(data))
     data$x <- data$xintercept
     data$y <- data$yintercept
     start <- data

diff --git a/R/gompertz.R b/R/gompertz.R
@@ -98,8 +98,8 @@ sgompertz <- function(data, pars = NULL) {
   if (!is.null(pars)) {
     pars <- rev(unlist(pars))
   }
-
-  fit <- suppressWarnings(vglm(x ~ 1, gompertz, coefstart = pars))
+  data <- data.frame(x = x)
+  fit <- suppressWarnings(vglm(x ~ 1, gompertz, coefstart = pars, data = data))
   list(
     log_location = unname(coef(fit)[2]),
     log_shape = unname(coef(fit)[1])

diff --git a/R/test-helpers.R b/R/test-helpers.R
@@ -44,10 +44,10 @@ expect_snapshot_plot <- function(x, name) {
 }
 
 expect_snapshot_boot_data <- function(x, name, digits = 6, min_pboot = 0.9, max_pboot = 1) {
-  if (!is.na(min_pboot) & min_pboot > 0) {
+  if (!is.na(min_pboot) && min_pboot > 0) {
     testthat::expect_true(all(x$pboot >= min_pboot))
   }
-  if (!is.na(min_pboot) & max_pboot < 1) {
+  if (!is.na(min_pboot) && max_pboot < 1) {
     testthat::expect_true(all(x$pboot <= max_pboot))
   }
   x$pboot <- NULL

diff --git a/scripts/build.R b/scripts/build.R
@@ -17,6 +17,10 @@ styler::style_pkg(
   scope = "line_breaks",
   filetype = c("R", "Rmd")
 )
+
+lintr::lint_package(linters = linters_with_defaults(
+  line_length_linter = line_length_linter(1000))
+)
 lintr::lint_package()
 
 devtools::test()

diff --git a/tests/testthat/test-print.R b/tests/testthat/test-print.R
@@ -10,7 +10,7 @@ test_that("print fitdists", {
 
 test_that("summary fitdists with left censored, rescaled, weighted data", {
   data <- ssddata::ccme_boron
-  data$Mass <- 1:nrow(data)
+  data$Mass <- seq_len(nrow(data))
   data$Other <- data$Conc
   data$Conc[2] <- NA
   fits <- ssd_fit_dists(data, right = "Other", weight = "Mass", rescale = TRUE, dists = "lnorm")
@@ -28,7 +28,7 @@ test_that("summary fitdists with inconsistently censored data", {
 
 test_that("summary fitdists with right censored, rescaled, weighted data", {
   data <- ssddata::ccme_boron
-  data$Mass <- 1:nrow(data)
+  data$Mass <- seq_len(nrow(data))
   data$Other <- data$Conc
   data$Other[1] <- Inf
   expect_error(fits <- ssd_fit_dists(data, right = "Other", weight = "Mass", rescale = TRUE, dists = "lnorm"))

diff --git a/tests/testthat/test-summary.R b/tests/testthat/test-summary.R
@@ -40,7 +40,7 @@ test_that("summary fitdists with multiple dists", {
 
 test_that("summary fitdists with censored, rescaled, unequally weighted data", {
   data <- ssddata::ccme_boron
-  data$Mass <- 1:nrow(data)
+  data$Mass <- seq_len(nrow(data))
   data$Other <- data$Conc
   data$Conc[2] <- NA
   fits <- ssd_fit_dists(data, right = "Other", weight = "Mass", rescale = TRUE, dists = "lnorm")

diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
@@ -60,7 +60,7 @@ test_that("ssd_sort_data works censored data", {
   data <- ssddata::ccme_boron
   data$Other <- data$Conc * 2
   data$Conc[1] <- NA
-  data$ID <- 1:nrow(data)
+  data$ID <- seq_len(nrow(data))
   expect_identical(
     ssd_sort_data(data, right = "Other")$ID[1:5],
     c(1L, 19L, 20L, 21L, 2L)