From df7497aff1eeb55f7c7b9d8ad542284818671676 Mon Sep 17 00:00:00 2001
From: dgkf <18220321+dgkf@users.noreply.github.com>
Date: Fri, 3 Feb 2023 16:49:50 -0500
Subject: [PATCH 1/6] initial pass at using roxy tools

---
 DESCRIPTION          | 11 +++++++++--
 R/generate_data.R    | 29 +++++++++++++++++------------
 R/hello.R            |  8 +++++---
 R/inc_prop.R         | 31 ++++++++++++++++++++-----------
 man/generate_data.Rd | 15 ++++++++-------
 man/hello.Rd         |  4 ++--
 man/inc_prop.Rd      | 21 +++++++++++++++------
 man/roxygen/meta.R   | 12 ++++++++++++
 man/roxylint/meta.R  | 13 +++++++++++++
 man/roxytypes/meta.R |  5 +++++
 10 files changed, 106 insertions(+), 43 deletions(-)
 create mode 100644 man/roxygen/meta.R
 create mode 100644 man/roxylint/meta.R
 create mode 100644 man/roxytypes/meta.R

diff --git a/DESCRIPTION b/DESCRIPTION
index f91f866..0d6ee4f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -21,12 +21,19 @@ Suggests:
     httr,
     knitr,
     shinytest,
-    testthat (>= 2.0)
+    testthat (>= 2.0),
+    roxytypes,
+    roxylint
+Remotes:
+    roxytypes=github::dgkf/roxytypes,
+    roxylint=github::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
diff --git a/R/generate_data.R b/R/generate_data.R
index 521637a..06a2ca7 100644
--- a/R/generate_data.R
+++ b/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)
diff --git a/R/hello.R b/R/hello.R
index 58efee5..51740fe 100644
--- a/R/hello.R
+++ b/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") {
diff --git a/R/inc_prop.R b/R/inc_prop.R
index ba2a95d..d630b8c 100644
--- a/R/inc_prop.R
+++ b/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,
diff --git a/man/generate_data.Rd b/man/generate_data.Rd
index 4094c4e..c4d8b64 100644
--- a/man/generate_data.Rd
+++ b/man/generate_data.Rd
@@ -7,22 +7,23 @@
 generate_data(n, cens, haz_ae, haz_death, haz_soft)
 }
 \arguments{
-\item{n}{(\code{count})\cr number of patients.}
+\item{n}{(`count`)\cr number of patients.}
 
-\item{cens}{(\code{numeric})\cr minimum and maximum censoring time.}
+\item{cens}{(`numeric`)\cr minimum and maximum censoring time.}
 
-\item{haz_ae}{(\code{number})\cr constant hazard for AE.}
+\item{haz_ae}{(`number`)\cr constant hazard for AE.}
 
-\item{haz_death}{(\code{number})\cr constant hazard for death.}
+\item{haz_death}{(`number`)\cr constant hazard for death.}
 
-\item{haz_soft}{(\code{number})\cr constant hazard for soft competing event.}
+\item{haz_soft}{(`number`)\cr constant hazard for soft competing event.}
 }
 \value{
-A \code{data.frame} with the following columns:
+(`data.frame`)\cr a \code{data.frame} with the following columns:
 \itemize{
 \item \code{id}: Patient ID.
 \item \code{time_to_event}: Time to the first AE, death or soft competing event.
-\item \code{type_of_event}: 0 for censored, 1 for AE, 2 for death, 3 for soft competing event.
+\item \code{type_of_event}: 0 for censored, 1 for AE, 2 for death, 3 for soft
+competing event.
 \item \code{cens}: Censoring time.
 }
 }
diff --git a/man/hello.Rd b/man/hello.Rd
index e7eb880..ca21811 100644
--- a/man/hello.Rd
+++ b/man/hello.Rd
@@ -7,10 +7,10 @@
 hello(name = "your name")
 }
 \arguments{
-\item{name}{Your name (character string; e.g. "john doe").}
+\item{name}{(`string`)\cr a name, such as "john doe".}
 }
 \value{
-A character string, capitalized to title case.
+(`string`)\cr capitalized to title case.
 }
 \description{
 Greet a person and appropriately capitalize their name.
diff --git a/man/inc_prop.Rd b/man/inc_prop.Rd
index d0967d0..e8e8707 100644
--- a/man/inc_prop.Rd
+++ b/man/inc_prop.Rd
@@ -7,16 +7,18 @@
 inc_prop(data, tau)
 }
 \arguments{
-\item{data}{(\code{data.frame})\cr with columns including
+\item{data}{(`data.frame`)\cr with columns including:
 \itemize{
-\item \code{time_to_event}: Time to the first AE, death or soft competing event.
-\item \code{type_of_event}: 0 for censored, 1 for AE, 2 for death, 3 for soft competing event.
+\item \code{time_to_event}: Time to the first AE, death or soft competing
+event.
+\item \code{type_of_event}: 0 for censored, 1 for AE, 2 for death, 3 for soft
+competing event.
 }}
 
-\item{tau}{(\code{numeric})\cr milestone at which incidence proportion is computed.}
+\item{tau}{(`numeric`)\cr milestone at which incidence proportion is computed.}
 }
 \value{
-A \code{vector} with the following entries:
+(`vector`)\cr a vector with the following entries:
 \itemize{
 \item \code{ae_prob}: Estimated probability of AE.
 \item \code{ae_prob_var}: Variance of that estimate.
@@ -27,7 +29,14 @@ Computing the Incidence Proportion
 }
 \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)
 
 }
diff --git a/man/roxygen/meta.R b/man/roxygen/meta.R
new file mode 100644
index 0000000..8c6a99c
--- /dev/null
+++ b/man/roxygen/meta.R
@@ -0,0 +1,12 @@
+list(
+  markdown = TRUE,
+  packages = c(
+    "roxylint",
+    "roxytypes"
+    ),
+  roclets = c(
+    "namespace",
+    "rd",
+    "roxylint::roxylint"
+  )
+)
diff --git a/man/roxylint/meta.R b/man/roxylint/meta.R
new file mode 100644
index 0000000..88eef4a
--- /dev/null
+++ b/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
+    )
+  )
+)
diff --git a/man/roxytypes/meta.R b/man/roxytypes/meta.R
new file mode 100644
index 0000000..fd767f6
--- /dev/null
+++ b/man/roxytypes/meta.R
@@ -0,0 +1,5 @@
+list(
+  format = function(x, name, type, default, description, ...) {
+    glue::glue("(`{type}`)\\cr {description}")
+  }
+)

From 40cdc40765fa743a499b389dcfb12dbd3b3c1fc9 Mon Sep 17 00:00:00 2001
From: dgkf <18220321+dgkf@users.noreply.github.com>
Date: Fri, 3 Feb 2023 17:45:12 -0500
Subject: [PATCH 2/6] using markdown update to regenerate docs

---
 DESCRIPTION          |  4 ++--
 man/generate_data.Rd | 12 ++++++------
 man/hello.Rd         |  4 ++--
 man/inc_prop.Rd      |  6 +++---
 4 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0d6ee4f..ae58129 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -25,8 +25,8 @@ Suggests:
     roxytypes,
     roxylint
 Remotes:
-    roxytypes=github::dgkf/roxytypes,
-    roxylint=github::dgkf/roxylint,
+    dgkf/roxytypes,
+    dgkf/roxylint,
 Config/Needs/documentation:
     roxytypes,
     roxylint
diff --git a/man/generate_data.Rd b/man/generate_data.Rd
index c4d8b64..18af5d9 100644
--- a/man/generate_data.Rd
+++ b/man/generate_data.Rd
@@ -7,18 +7,18 @@
 generate_data(n, cens, haz_ae, haz_death, haz_soft)
 }
 \arguments{
-\item{n}{(`count`)\cr number of patients.}
+\item{n}{(\code{count})\cr number of patients.}
 
-\item{cens}{(`numeric`)\cr minimum and maximum censoring time.}
+\item{cens}{(\code{numeric})\cr minimum and maximum censoring time.}
 
-\item{haz_ae}{(`number`)\cr constant hazard for AE.}
+\item{haz_ae}{(\code{number})\cr constant hazard for AE.}
 
-\item{haz_death}{(`number`)\cr constant hazard for death.}
+\item{haz_death}{(\code{number})\cr constant hazard for death.}
 
-\item{haz_soft}{(`number`)\cr constant hazard for soft competing event.}
+\item{haz_soft}{(\code{number})\cr constant hazard for soft competing event.}
 }
 \value{
-(`data.frame`)\cr a \code{data.frame} with the following columns:
+(\code{data.frame})\cr a \code{data.frame} with the following columns:
 \itemize{
 \item \code{id}: Patient ID.
 \item \code{time_to_event}: Time to the first AE, death or soft competing event.
diff --git a/man/hello.Rd b/man/hello.Rd
index ca21811..c1e57d0 100644
--- a/man/hello.Rd
+++ b/man/hello.Rd
@@ -7,10 +7,10 @@
 hello(name = "your name")
 }
 \arguments{
-\item{name}{(`string`)\cr a name, such as "john doe".}
+\item{name}{(\code{string})\cr a name, such as "john doe".}
 }
 \value{
-(`string`)\cr capitalized to title case.
+(\code{string})\cr capitalized to title case.
 }
 \description{
 Greet a person and appropriately capitalize their name.
diff --git a/man/inc_prop.Rd b/man/inc_prop.Rd
index e8e8707..c2d7236 100644
--- a/man/inc_prop.Rd
+++ b/man/inc_prop.Rd
@@ -7,7 +7,7 @@
 inc_prop(data, tau)
 }
 \arguments{
-\item{data}{(`data.frame`)\cr with columns including:
+\item{data}{(\code{data.frame})\cr with columns including:
 \itemize{
 \item \code{time_to_event}: Time to the first AE, death or soft competing
 event.
@@ -15,10 +15,10 @@ event.
 competing event.
 }}
 
-\item{tau}{(`numeric`)\cr milestone at which incidence proportion is computed.}
+\item{tau}{(\code{numeric})\cr milestone at which incidence proportion is computed.}
 }
 \value{
-(`vector`)\cr a vector with the following entries:
+(\code{vector})\cr a vector with the following entries:
 \itemize{
 \item \code{ae_prob}: Estimated probability of AE.
 \item \code{ae_prob_var}: Variance of that estimate.

From e9a2d7548937ca24793d6fe37576e2b94a5f4cb7 Mon Sep 17 00:00:00 2001
From: dgkf <18220321+dgkf@users.noreply.github.com>
Date: Mon, 13 Feb 2023 11:17:27 -0500
Subject: [PATCH 3/6] moving roxy remote urls to openpharma org

---
 DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ae58129..fdfc051 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -25,8 +25,8 @@ Suggests:
     roxytypes,
     roxylint
 Remotes:
-    dgkf/roxytypes,
-    dgkf/roxylint,
+    openpharma/roxytypes,
+    openpharma/roxylint,
 Config/Needs/documentation:
     roxytypes,
     roxylint

From 6c4ed72ce28979a7144c0e45499672975c03978c Mon Sep 17 00:00:00 2001
From: dgkf <18220321+dgkf@users.noreply.github.com>
Date: Mon, 13 Feb 2023 15:38:05 -0500
Subject: [PATCH 4/6] linting meta files

---
 man/roxygen/meta.R  | 2 +-
 man/roxylint/meta.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/man/roxygen/meta.R b/man/roxygen/meta.R
index 8c6a99c..133fb01 100644
--- a/man/roxygen/meta.R
+++ b/man/roxygen/meta.R
@@ -3,7 +3,7 @@ list(
   packages = c(
     "roxylint",
     "roxytypes"
-    ),
+  ),
   roclets = c(
     "namespace",
     "rd",
diff --git a/man/roxylint/meta.R b/man/roxylint/meta.R
index 88eef4a..6cf39e4 100644
--- a/man/roxylint/meta.R
+++ b/man/roxylint/meta.R
@@ -3,7 +3,7 @@ list(
     typed = list(
       "descriptions should start lowercase" = "^[^[:upper:]]",
       roxylint::lint_full_stop,
-      NULL  # disallow registration of package defaults
+      NULL # disallow registration of package defaults
     ),
     param = list(
       "descriptions should start lowercase" = "^[^[:upper:]]",

From 41b3ada01c9ebe33ad3b803feedb5733d1c0b0dc Mon Sep 17 00:00:00 2001
From: Doug Kelkhoff <18220321+dgkf@users.noreply.github.com>
Date: Mon, 13 Feb 2023 15:44:05 -0500
Subject: [PATCH 5/6] Apply suggestions from code review

Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>
---
 R/inc_prop.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/inc_prop.R b/R/inc_prop.R
index d630b8c..7b4c0fe 100644
--- a/R/inc_prop.R
+++ b/R/inc_prop.R
@@ -10,7 +10,7 @@
 #'   milestone at which incidence proportion is computed.
 #'
 #' @typedreturn vector
-#'   a vector with the following entries:
+#'   with the following entries:
 #'   - `ae_prob`: Estimated probability of AE.
 #'   - `ae_prob_var`: Variance of that estimate.
 #'

From ff43913b6f9ec4dc984bf83db2390e24744f3659 Mon Sep 17 00:00:00 2001
From: dgkf <18220321+dgkf@users.noreply.github.com>
Date: Mon, 13 Feb 2023 15:48:11 -0500
Subject: [PATCH 6/6] rebuilding docs

---
 R/hello.R          | 2 +-
 man/inc_prop.Rd    | 2 +-
 man/plumber_api.Rd | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/hello.R b/R/hello.R
index 51740fe..e485612 100644
--- a/R/hello.R
+++ b/R/hello.R
@@ -48,7 +48,7 @@ shiny_app <- function() {
 #' @description Greet a person and appropriately capitalize their name
 #'              as a Plumber API.
 #'
-#' @param ... Additional arguments to plumber::pr_run()
+#' @param ... Additional arguments to plumber::pr_run().
 #'
 #' @return Plumber API showcasing the personal greeting feature.
 #' @export
diff --git a/man/inc_prop.Rd b/man/inc_prop.Rd
index c2d7236..62d954b 100644
--- a/man/inc_prop.Rd
+++ b/man/inc_prop.Rd
@@ -18,7 +18,7 @@ competing event.
 \item{tau}{(\code{numeric})\cr milestone at which incidence proportion is computed.}
 }
 \value{
-(\code{vector})\cr a vector with the following entries:
+(\code{vector})\cr with the following entries:
 \itemize{
 \item \code{ae_prob}: Estimated probability of AE.
 \item \code{ae_prob_var}: Variance of that estimate.
diff --git a/man/plumber_api.Rd b/man/plumber_api.Rd
index 84ef92b..ab96741 100644
--- a/man/plumber_api.Rd
+++ b/man/plumber_api.Rd
@@ -7,7 +7,7 @@
 plumber_api(...)
 }
 \arguments{
-\item{...}{Additional arguments to plumber::pr_run()}
+\item{...}{Additional arguments to plumber::pr_run().}
 }
 \value{
 Plumber API showcasing the personal greeting feature.