fix package --as-cran (#602)

* update link and examples * [skip actions] Restyle files * update examples * [skip actions] Restyle files * update example as pointed out by lint * [skip actions] Roxygen Man Pages Auto Update * update per lint findings * update more modules * [skip actions] Restyle files * [skip actions] Roxygen Man Pages Auto Update * lintr * capitalize time Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> Co-authored-by: Mahmoud Hallal <86970066+mhallal1@users.noreply.github.com> Co-authored-by: Mahmoud Hallal <mahmoud.hallal@roche.com>
insightsengineering · Sep 28, 2022 · e3ecbf9 · e3ecbf9
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diff --git a/R/arm_ref_comp.R b/R/arm_ref_comp.R
@@ -24,11 +24,11 @@
 #' @keywords internal
 #'
 #' @examples
+#' \dontrun{
 #' ds <- teal:::get_dummy_datasets()
 #'
 #' arm_ref_comp <- list(ARMCD = list(ref = "ARM A", comp = c("ARM B")))
 #' arm_var <- choices_selected(c("ARM", "ARMCD"), "ARM")
-#' \dontrun{
 #' shinyApp(
 #'   ui = fluidPage(
 #'     teal.widgets::optionalSelectInput(

diff --git a/R/tm_a_mmrm.R b/R/tm_a_mmrm.R
@@ -454,8 +454,9 @@ template_mmrm_plots <- function(fit_name,
 #'
 #' library(scda)
 #'
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' ADQS <- synthetic_cdisc_data("latest")$adqs %>%
+#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
+#' ADSL <- synthetic_cdisc_data_latest$adsl
+#' ADQS <- synthetic_cdisc_data_latest$adqs %>%
 #'   dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
 #'   dplyr::filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>%
 #'   dplyr::mutate(
@@ -475,9 +476,13 @@ template_mmrm_plots <- function(fit_name,
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"),
+#'     cdisc_dataset("ADSL", ADSL,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'               ADSL <- synthetic_cdisc_data_latest$adsl"
+#'     ),
 #'     cdisc_dataset("ADQS", ADQS,
-#'       code = 'ADQS <- synthetic_cdisc_data("latest")$adqs %>%
+#'       code = 'synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
+#'               ADQS <- synthetic_cdisc_data("latest")$adqs %>%
 #'               dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
 #'               dplyr::filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>%
 #'               dplyr::mutate(
@@ -487,8 +492,7 @@ template_mmrm_plots <- function(fit_name,
 #'                   as.numeric() %>%
 #'                   as.factor() # making consecutive numeric factor
 #'               )'
-#'     ),
-#'     check = TRUE
+#'     )
 #'   ),
 #'   modules = modules(
 #'     tm_a_mmrm(

diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R
@@ -38,8 +38,7 @@
 #'                 dplyr::filter(!((AETOXGR == 1) & (AESEV == 'MILD') & (ARM == 'A: Drug X')))
 #'               formatters::var_labels(ADAE) <- adae_labels
 #'               ADAE"
-#'     ),
-#'     check = TRUE
+#'     )
 #'   ),
 #'   modules = modules(
 #'     tm_g_barchart_simple(

diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R
@@ -220,8 +220,9 @@ template_forest_rsp <- function(dataname = "ANL",
 #' library(dplyr)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' ADRS <- synthetic_cdisc_data("latest")$adrs %>%
+#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
+#' ADSL <- synthetic_cdisc_data_latest$adsl
+#' ADRS <- synthetic_cdisc_data_latest$adrs %>%
 #'   mutate(AVALC = d_onco_rsp_label(AVALC)) %>%
 #'   filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
 #'
@@ -241,11 +242,11 @@ template_forest_rsp <- function(dataname = "ANL",
 #'     cdisc_dataset("ADSL", ADSL),
 #'     cdisc_dataset("ADRS", ADRS),
 #'     code =
-#'       "ADSL <- synthetic_cdisc_data('latest')$adsl
-#'        ADRS <- synthetic_cdisc_data('latest')$adrs %>%
+#'       "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'        ADSL <- synthetic_cdisc_data_latest$adsl
+#'        ADRS <- synthetic_cdisc_data_latest$adrs %>%
 #'        mutate(AVALC = d_onco_rsp_label(AVALC)) %>%
-#'        filter(PARAMCD != 'OVRINV' | AVISIT == 'FOLLOW UP')",
-#'     check = TRUE
+#'        filter(PARAMCD != 'OVRINV' | AVISIT == 'FOLLOW UP')"
 #'   ),
 #'   modules = modules(
 #'     tm_g_forest_rsp(

diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R
@@ -227,8 +227,10 @@ template_forest_tte <- function(dataname = "ANL",
 #' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' ADTTE <- synthetic_cdisc_data("latest")$adtte
+#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
+#'
+#' ADSL <- synthetic_cdisc_data_latest$adsl
+#' ADTTE <- synthetic_cdisc_data_latest$adtte
 #'
 #' ADSL$RACE <- droplevels(ADSL$RACE)
 #'
@@ -246,13 +248,16 @@ template_forest_tte <- function(dataname = "ANL",
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset(
-#'       "ADSL",
-#'       ADSL,
-#'       code = "ADSL <- synthetic_cdisc_data('latest')$adsl
+#'       "ADSL", ADSL,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADSL <- synthetic_cdisc_data_latest$adsl
 #'         ADSL$RACE <- droplevels(ADSL$RACE)"
 #'     ),
-#'     cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_data("latest")$adtte'),
-#'     check = TRUE
+#'     cdisc_dataset(
+#'       "ADTTE", ADTTE,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADTTE <- synthetic_cdisc_data_latest$adtte"
+#'     )
 #'   ),
 #'   modules = modules(
 #'     tm_g_forest_tte(

diff --git a/R/tm_g_km.R b/R/tm_g_km.R
@@ -287,8 +287,7 @@ template_g_km <- function(dataname = "ANL",
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'),
-#'     cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_data("latest")$adtte'),
-#'     check = TRUE
+#'     cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_data("latest")$adtte')
 #'   ),
 #'   modules = modules(
 #'     tm_g_km(

diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R
@@ -207,17 +207,23 @@ template_g_lineplot <- function(dataname = "ANL",
 #' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' ADLB <- synthetic_cdisc_data("latest")$adlb
+#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
+#' ADSL <- synthetic_cdisc_data_latest$adsl
+#' ADLB <- synthetic_cdisc_data_latest$adlb
 #'
 #' ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'),
-#'     cdisc_dataset("ADLB", ADLB, code = 'ADLB <- synthetic_cdisc_data("latest")$adlb
-#'                    ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))'),
-#'     check = TRUE
+#'     cdisc_dataset("ADSL", ADSL,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADSL <- synthetic_cdisc_data_latest$adsl"
+#'     ),
+#'     cdisc_dataset("ADLB", ADLB,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADLB <- synthetic_cdisc_data_latest$adlb
+#'         ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))"
+#'     )
 #'   ),
 #'   modules = modules(
 #'     tm_g_lineplot(

diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R
@@ -182,14 +182,21 @@ template_adverse_events <- function(dataname = "ANL",
 #' @examples
 #' library(scda)
 #' library(nestcolor)
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' ADAE <- synthetic_cdisc_data("latest")$adae
+#'
+#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
+#' ADSL <- synthetic_cdisc_data_latest$adsl
+#' ADAE <- synthetic_cdisc_data_latest$adae
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"),
-#'     cdisc_dataset("ADAE", ADAE, code = "ADAE <- synthetic_cdisc_data('latest')$adae"),
-#'     check = TRUE
+#'     cdisc_dataset("ADSL", ADSL,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADSL <- synthetic_cdisc_data_latest$adsl"
+#'     ),
+#'     cdisc_dataset("ADAE", ADAE,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADAE <- synthetic_cdisc_data_latest$adae"
+#'     )
 #'   ),
 #'   modules = modules(
 #'     tm_g_pp_adverse_events(

diff --git a/R/tm_g_pp_patient_timeline.R b/R/tm_g_pp_patient_timeline.R
@@ -356,9 +356,12 @@ template_patient_timeline <- function(dataname = "ANL",
 #' @examples
 #' library(scda)
 #' library(nestcolor)
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' ADAE <- synthetic_cdisc_data("latest")$adae
-#' ADCM <- synthetic_cdisc_data("latest")$adcm
+#'
+#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
+#'
+#' ADSL <- synthetic_cdisc_data_latest$adsl
+#' ADAE <- synthetic_cdisc_data_latest$adae
+#' ADCM <- synthetic_cdisc_data_latest$adcm
 #'
 #' #' Modify ADCM
 #' ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
@@ -386,32 +389,38 @@ template_patient_timeline <- function(dataname = "ANL",
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'),
-#'     cdisc_dataset("ADAE", ADAE, code = 'ADAE <- synthetic_cdisc_data("latest")$adae'),
+#'     cdisc_dataset("ADSL", ADSL,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADSL <- synthetic_cdisc_data_latest$adsl"
+#'     ),
+#'     cdisc_dataset("ADAE", ADAE,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADAE <- synthetic_cdisc_data_latest$adae"
+#'     ),
 #'     cdisc_dataset("ADCM", ADCM,
-#'       code = 'ADCM <- synthetic_cdisc_data("latest")$adcm
-#'         ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADCM <- synthetic_cdisc_data_latest$adcm
+#'         ADCM$CMINDC <- paste0('Indication_', as.numeric(ADCM$CMDECOD))
 #'         ADCM$CMDOSE <- 1
-#'         ADCM$CMDOSU <- "U"
-#'         ADCM$CMROUTE <- "CMROUTE"
-#'         ADCM$CMDOSFRQ <- "CMDOSFRQ"
+#'         ADCM$CMDOSU <- 'U'
+#'         ADCM$CMROUTE <- 'CMROUTE'
+#'         ADCM$CMDOSFRQ <- 'CMDOSFRQ'
 #'         ADCM$CMSTDY <- 1
-#'         ADCM[ADCM$CMCAT == "medcl B", ]$CMSTDY <- 20
-#'         ADCM[ADCM$CMCAT == "medcl C", ]$CMSTDY <- 150
+#'         ADCM[ADCM$CMCAT == 'medcl B', ]$CMSTDY <- 20
+#'         ADCM[ADCM$CMCAT == 'medcl C', ]$CMSTDY <- 150
 #'         ADCM$CMENDY <- 500
-#'         ADCM[ADCM$CMCAT == "medcl B", ]$CMENDY <- 700
-#'         ADCM[ADCM$CMCAT == "medcl C", ]$CMENDY <- 1000
+#'         ADCM[ADCM$CMCAT == 'medcl B', ]$CMENDY <- 700
+#'         ADCM[ADCM$CMCAT == 'medcl C', ]$CMENDY <- 1000
 #'         ADCM$CMASTDTM <- ADCM$ASTDTM
 #'         ADCM$CMAENDTM <- ADCM$AENDTM
 #'         formatters::var_labels(
-#'           ADCM[c("CMINDC", "CMDECOD", "CMSTDY", "CMENDY")]) <- c(
-#'             "Indication",
-#'             "Reported Name of Drug, Med, or Therapy",
-#'             "Study Day of Start of Medication",
-#'             "Study Day of End of Medication")',
+#'           ADCM[c('CMINDC', 'CMDECOD', 'CMSTDY', 'CMENDY')]) <- c(
+#'             'Indication',
+#'             'Reported Name of Drug, Med, or Therapy',
+#'             'Study Day of Start of Medication',
+#'             'Study Day of End of Medication')",
 #'       keys = adcm_keys
-#'     ),
-#'     check = TRUE
+#'     )
 #'   ),
 #'   modules = modules(
 #'     tm_g_pp_patient_timeline(

diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R
@@ -256,8 +256,9 @@ template_therapy <- function(dataname = "ANL",
 #' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' ADCM <- synthetic_cdisc_data("latest")$adcm
+#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
+#' ADSL <- synthetic_cdisc_data_latest$adsl
+#' ADCM <- synthetic_cdisc_data_latest$adcm
 #'
 #' #' Modify ADCM
 #' ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
@@ -280,27 +281,29 @@ template_therapy <- function(dataname = "ANL",
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'),
+#'     cdisc_dataset("ADSL", ADSL,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADSL <- synthetic_cdisc_data_latest$adsl"
+#'     ),
 #'     cdisc_dataset("ADCM", ADCM,
-#'       code = 'ADCM <- synthetic_cdisc_data("latest")$adcm
-#'         ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
+#'       code = "ADCM <- synthetic_cdisc_data('latest')$adcm
+#'         ADCM$CMINDC <- paste0('Indication_', as.numeric(ADCM$CMDECOD))
 #'         ADCM$CMDOSE <- 1
 #'         ADCM$CMTRT <- ADCM$CMCAT
-#'         ADCM$CMDOSU <- "U"
-#'         ADCM$CMROUTE <- "CMROUTE"
-#'         ADCM$CMDOSFRQ <- "CMDOSFRQ"
+#'         ADCM$CMDOSU <- 'U'
+#'         ADCM$CMROUTE <- 'CMROUTE'
+#'         ADCM$CMDOSFRQ <- 'CMDOSFRQ'
 #'         ADCM$CMASTDTM <- ADCM$ASTDTM
 #'         ADCM$CMAENDTM <- ADCM$AENDTM
 #'         formatters::var_labels(
-#'           ADCM[c("CMINDC", "CMTRT", "ASTDY", "AENDY")]) <- c(
-#'             "Indication",
-#'             "Reported Name of Drug, Med, or Therapy",
-#'             "Study Day of Start of Medication",
-#'             "Study Day of End of Medication")
-#'         ADCM',
+#'           ADCM[c('CMINDC', 'CMTRT', 'ASTDY', 'AENDY')]) <- c(
+#'             'Indication',
+#'             'Reported Name of Drug, Med, or Therapy',
+#'             'Study Day of Start of Medication',
+#'             'Study Day of End of Medication')
+#'         ADCM",
 #'       keys = adcm_keys
-#'     ),
-#'     check = TRUE
+#'     )
 #'   ),
 #'   modules = modules(
 #'     tm_g_pp_therapy(

diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R
@@ -194,14 +194,20 @@ template_vitals <- function(dataname = "ANL",
 #' @examples
 #' library(scda)
 #' library(nestcolor)
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' ADVS <- synthetic_cdisc_data("latest")$advs
+#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
+#' ADSL <- synthetic_cdisc_data_latest$adsl
+#' ADVS <- synthetic_cdisc_data_latest$advs
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'),
-#'     cdisc_dataset("ADVS", ADVS, code = 'ADVS <- synthetic_cdisc_data("latest")$advs'),
-#'     check = TRUE
+#'     cdisc_dataset("ADSL", ADSL,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADSL <- synthetic_cdisc_data_latest$adsl"
+#'     ),
+#'     cdisc_dataset("ADVS", ADVS,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADVS <- synthetic_cdisc_data_latest$advs"
+#'     )
 #'   ),
 #'   modules = modules(
 #'     tm_g_pp_vitals(

diff --git a/R/tm_t_abnormality.R b/R/tm_t_abnormality.R
@@ -235,8 +235,9 @@ template_abnormality <- function(parentname,
 #' library(scda)
 #' library(dplyr)
 #'
-#' adsl <- synthetic_cdisc_data("latest")$adsl
-#' adlb <- synthetic_cdisc_data("latest")$adlb %>%
+#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
+#' adsl <- synthetic_cdisc_data_latest$adsl
+#' adlb <- synthetic_cdisc_data_latest$adlb %>%
 #'   mutate(
 #'     ONTRTFL = case_when(
 #'       AVISIT %in% c("SCREENING", "BASELINE") ~ "",
@@ -247,9 +248,13 @@ template_abnormality <- function(parentname,
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", adsl, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"),
+#'     cdisc_dataset("ADSL", adsl,
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'         ADSL <- synthetic_cdisc_data_latest$adsl"
+#'     ),
 #'     cdisc_dataset("ADLB", adlb,
-#'       code = "ADLB <- synthetic_cdisc_data('latest')$adlb %>%
+#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
+#'               ADLB <- synthetic_cdisc_data_latest$adlb %>%
 #'                 mutate(
 #'                   ONTRTFL = case_when(
 #'                     AVISIT %in% c('SCREENING', 'BASELINE') ~ '',
@@ -258,8 +263,7 @@ template_abnormality <- function(parentname,
 #'                 )
 #'               attr(ADLB[['ONTRTFL']], 'label') <- 'On Treatment Record Flag'
 #'               ADLB"
-#'     ),
-#'     check = TRUE
+#'     )
 #'   ),
 #'   modules = modules(
 #'     tm_t_abnormality(