Demo of roxy tools

DESCRIPTION

@@ -21,12 +21,19 @@ Suggests:
     httr,
     knitr,
     shinytest,
-    testthat (>= 2.0)
+    testthat (>= 2.0),
+    roxytypes,
+    roxylint
+Remotes:
+    dgkf/roxytypes,
+    dgkf/roxylint,
+Config/Needs/documentation:
+    roxytypes,
+    roxylint
 VignetteBuilder:
     knitr
 biocViews:
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3

R/generate_data.R

@@ -5,21 +5,26 @@
 #' hazard for the competing event of death, and the hazard for the "soft" competing events.
 #' Censoring is uniform in the given range.
 #'
-#' @param n (`count`)\cr number of patients.
-#' @param cens (`numeric`)\cr minimum and maximum censoring time.
-#' @param haz_ae (`number`)\cr constant hazard for AE.
-#' @param haz_death (`number`)\cr constant hazard for death.
-#' @param haz_soft (`number`)\cr constant hazard for soft competing event.
+#' @typed n: count
+#'   number of patients.
+#' @typed cens: numeric
+#'   minimum and maximum censoring time.
+#' @typed haz_ae: number
+#'   constant hazard for AE.
+#' @typed haz_death: number
+#'   constant hazard for death.
+#' @typed haz_soft: number
+#'   constant hazard for soft competing event.
 #'
-#' @return A `data.frame` with the following columns:
-#'
-#' - `id`: Patient ID.
-#' - `time_to_event`: Time to the first AE, death or soft competing event.
-#' - `type_of_event`: 0 for censored, 1 for AE, 2 for death, 3 for soft competing event.
-#' - `cens`: Censoring time.
+#' @typedreturn data.frame
+#'   a `data.frame` with the following columns:
+#'   - `id`: Patient ID.
+#'   - `time_to_event`: Time to the first AE, death or soft competing event.
+#'   - `type_of_event`: 0 for censored, 1 for AE, 2 for death, 3 for soft
+#'     competing event.
+#'   - `cens`: Censoring time.
 #'
 #' @export
-#'
 #' @examples
 #' set.seed(123)
 #' generate_data(n = 5, cens = c(2, 5), haz_ae = 2, haz_death = 3, haz_soft = 5)

R/hello.R

@@ -2,11 +2,13 @@
 #'
 #' @description Greet a person and appropriately capitalize their name.
 #'
-#' @param name Your name (character string; e.g. "john doe").
+#' @typed name: string
+#'   a name, such as "john doe".
 #'
-#' @return A character string, capitalized to title case.
-#' @export
+#' @typedreturn string
+#'   capitalized to title case.
 #'
+#' @export
 #' @examples
 #' hello("james bond")
 hello <- function(name = "your name") {

R/inc_prop.R

@@ -1,21 +1,30 @@
 #' Computing the Incidence Proportion
 #'
-#' @param data (`data.frame`)\cr with columns including
-#'  - `time_to_event`: Time to the first AE, death or soft competing event.
-#'  - `type_of_event`: 0 for censored, 1 for AE, 2 for death, 3 for soft competing event.
+#' @typed data: data.frame
+#'   with columns including:
+#'   - `time_to_event`: Time to the first AE, death or soft competing
+#'     event.
+#'   - `type_of_event`: 0 for censored, 1 for AE, 2 for death, 3 for soft
+#'     competing event.
+#' @typed tau: numeric
+#'   milestone at which incidence proportion is computed.
 #'
-#' @param tau (`numeric`)\cr milestone at which incidence proportion is computed.
-#'
-#' @return A `vector` with the following entries:
-#'
-#' - `ae_prob`: Estimated probability of AE.
-#' - `ae_prob_var`: Variance of that estimate.
+#' @typedreturn vector
+#'   a vector with the following entries:
+#'   - `ae_prob`: Estimated probability of AE.
+#'   - `ae_prob_var`: Variance of that estimate.
 #'
 #' @export
-#'
 #' @examples
 #' set.seed(123)
-#' dat <- generate_data(n = 5, cens = c(2, 5), haz_ae = 2, haz_death = 3, haz_soft = 5)
+#' dat <- generate_data(
+#'   n = 5,
+#'   cens = c(2, 5),
+#'   haz_ae = 2,
+#'   haz_death = 3,
+#'   haz_soft = 5
+#' )
+#'
 #' inc_prop(dat, tau = 4)
 #'
 inc_prop <- function(data,

man/roxygen/meta.R

@@ -0,0 +1,12 @@
+list(
+  markdown = TRUE,
+  packages = c(
+    "roxylint",
+    "roxytypes"
+    ),
+  roclets = c(
+    "namespace",
+    "rd",
+    "roxylint::roxylint"
+  )
+)

man/roxylint/meta.R

@@ -0,0 +1,13 @@
+list(
+  linters = list(
+    typed = list(
+      "descriptions should start lowercase" = "^[^[:upper:]]",
+      roxylint::lint_full_stop,
+      NULL  # disallow registration of package defaults
+    ),
+    param = list(
+      "descriptions should start lowercase" = "^[^[:upper:]]",
+      roxylint::lint_full_stop
+    )
+  )
+)

man/roxytypes/meta.R

@@ -0,0 +1,5 @@
+list(
+  format = function(x, name, type, default, description, ...) {
+    glue::glue("(`{type}`)\\cr {description}")
+  }
+)