Clean up example data modification

R/tm_g_barchart_simple.R

@@ -14,18 +14,11 @@
 #' @export
 #'
 #' @examples
-#' library(dplyr)
 #' library(nestcolor)
 #'
-#' adsl <- tmc_ex_adsl %>%
-#'   dplyr::mutate(ITTFL = factor("Y"))
-#' adae <- tmc_ex_adae
-#'
-#' adae_labels <- formatters::var_labels(adae, fill = FALSE)
-#' adae <- adae %>% dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
-#'
-#' # reinstate labels
-#' formatters::var_labels(adae) <- adae_labels
+#' adsl <- tmc_ex_adsl %>% dplyr::mutate(ITTFL = factor("Y") %>%
+#'   formatters::with_label("Intent-To-Treat Population Flag"))
+#' adae <- tmc_ex_adae %>% dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
 #'
 #' app <- init(
 #'   data = cdisc_data(

R/tm_g_forest_rsp.R

@@ -215,13 +215,13 @@ template_forest_rsp <- function(dataname = "ANL",
 #' @template author_song24
 #'
 #' @examples
-#' library(dplyr)
 #' library(nestcolor)
 #'
 #' adsl <- tmc_ex_adsl
 #' adrs <- tmc_ex_adrs %>%
-#'   mutate(AVALC = tern::d_onco_rsp_label(AVALC)) %>%
-#'   filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
+#'   dplyr::mutate(AVALC = tern::d_onco_rsp_label(AVALC) %>%
+#'     formatters::with_label("Character Result/Finding")) %>%
+#'   dplyr::filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
 #'
 #' arm_ref_comp <- list(
 #'   ARM = list(

R/tm_g_forest_tte.R

@@ -228,8 +228,7 @@ template_forest_tte <- function(dataname = "ANL",
 #'
 #' adsl <- tmc_ex_adsl
 #' adtte <- tmc_ex_adtte
-#'
-#' adsl$RACE <- droplevels(adsl$RACE)
+#' adsl$RACE <- droplevels(adsl$RACE) %>% formatters::with_label("Race")
 #'
 #' arm_ref_comp <- list(
 #'   ARM = list(

R/tm_g_ipp.R

@@ -186,27 +186,18 @@ template_g_ipp <- function(dataname = "ANL",
 #' @export
 #'
 #' @examples
-#' library(dplyr)
 #' library(nestcolor)
 #'
-#' adsl <- tmc_ex_adsl %>% slice(1:20)
-#' adlb <- tmc_ex_adlb
-#' adlb <- adlb %>% filter(USUBJID %in% adsl$USUBJID)
+#' adsl <- tmc_ex_adsl %>% dplyr::slice(1:20)
+#' adlb <- tmc_ex_adlb %>% dplyr::filter(USUBJID %in% adsl$USUBJID)
 #'
 #' adsl <- df_explicit_na(adsl)
-#' adlb <- df_explicit_na(adlb) %>%
-#'   dplyr::filter(AVISIT != "SCREENING")
+#' adlb <- df_explicit_na(adlb) %>% dplyr::filter(AVISIT != "SCREENING")
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset(
-#'       "ADSL",
-#'       adsl
-#'     ),
-#'     cdisc_dataset(
-#'       "ADLB",
-#'       adlb
-#'     )
+#'     cdisc_dataset("ADSL", adsl),
+#'     cdisc_dataset("ADLB", adlb)
 #'   ),
 #'   modules = modules(
 #'     tm_g_ipp(

R/tm_g_km.R

@@ -262,7 +262,7 @@ template_g_km <- function(dataname = "ANL",
 #'   ),
 #'   modules = modules(
 #'     tm_g_km(
-#'       label = "KM PLOT",
+#'       label = "Kaplan-Meier Plot",
 #'       dataname = "ADTTE",
 #'       arm_var = choices_selected(
 #'         variable_choices(adsl, c("ARM", "ARMCD", "ACTARMCD")),

R/tm_g_pp_adverse_events.R

@@ -182,8 +182,8 @@ template_adverse_events <- function(dataname = "ANL",
 #' @examples
 #' library(nestcolor)
 #'
-#' adsl <- tmc_ex_adsl
 #' adae <- tmc_ex_adae
+#' adsl <- tmc_ex_adsl %>% dplyr::filter(USUBJID %in% adae$USUBJID)
 #'
 #' app <- init(
 #'   data = cdisc_data(
@@ -192,7 +192,7 @@ template_adverse_events <- function(dataname = "ANL",
 #'   ),
 #'   modules = modules(
 #'     tm_g_pp_adverse_events(
-#'       label = "Adverse events",
+#'       label = "Adverse Events",
 #'       dataname = "ADAE",
 #'       parentname = "ADSL",
 #'       patient_col = "USUBJID",

R/tm_g_pp_patient_timeline.R

@@ -356,28 +356,21 @@ template_patient_timeline <- function(dataname = "ANL",
 #' @examples
 #' library(nestcolor)
 #'
-#' adsl <- tmc_ex_adsl
 #' adae <- tmc_ex_adae
-#' adcm <- tmc_ex_adcm
-#'
-#' # Modify ADCM
-#' adcm$CMDOSE <- 1
-#' adcm$CMDOSU <- "U"
-#' adcm$CMROUTE <- "CMROUTE"
-#' adcm$CMDOSFRQ <- "CMDOSFRQ"
-#' adcm$CMSTDY <- 1
-#' adcm[adcm$CMCAT == "medcl B", ]$CMSTDY <- 20
-#' adcm[adcm$CMCAT == "medcl C", ]$CMSTDY <- 150
-#' adcm$CMENDY <- 500
-#' 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"
+#' adsl <- tmc_ex_adsl %>% dplyr::filter(USUBJID %in% adae$USUBJID)
+#' adcm <- tmc_ex_adcm %>% dplyr::mutate(
+#'   CMSTDY = dplyr::case_when(
+#'     CMCAT == "medcl B" ~ 20,
+#'     CMCAT == "medcl C" ~ 150,
+#'     TRUE ~ 1
+#'   ) %>% formatters::with_label("Study Day of Start of Medication"),
+#'   CMENDY = dplyr::case_when(
+#'     CMCAT == "medcl B" ~ 700,
+#'     CMCAT == "medcl C" ~ 1000,
+#'     TRUE ~ 500
+#'   ) %>% formatters::with_label("Study Day of End of Medication"),
+#'   CMASTDTM = ASTDTM,
+#'   CMAENDTM = AENDTM
 #' )
 #' adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
 #'
@@ -389,7 +382,7 @@ template_patient_timeline <- function(dataname = "ANL",
 #'   ),
 #'   modules = modules(
 #'     tm_g_pp_patient_timeline(
-#'       label = "Patient timeline",
+#'       label = "Patient Timeline",
 #'       dataname_adae = "ADAE",
 #'       dataname_adcm = "ADCM",
 #'       parentname = "ADSL",

R/tm_g_pp_therapy.R

@@ -255,26 +255,10 @@ template_therapy <- function(dataname = "ANL",
 #' @examples
 #' library(nestcolor)
 #'
-#' adsl <- tmc_ex_adsl
 #' adcm <- tmc_ex_adcm
-#'
-#' # Modify 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"
+#' adsl <- tmc_ex_adsl %>% dplyr::filter(USUBJID %in% adcm$USUBJID)
 #' adcm$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_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
 #'
 #' app <- init(

R/tm_t_abnormality.R

@@ -232,19 +232,15 @@ template_abnormality <- function(parentname,
 #'
 #' @export
 #' @examples
-#' library(dplyr)
-#'
 #' adsl <- tmc_ex_adsl
 #' adlb <- tmc_ex_adlb %>%
-#'   mutate(
-#'     ONTRTFL = case_when(
+#'   dplyr::mutate(
+#'     ONTRTFL = dplyr::case_when(
 #'       AVISIT %in% c("SCREENING", "BASELINE") ~ "",
 #'       TRUE ~ "Y"
-#'     )
+#'     ) %>% formatters::with_label("On Treatment Record Flag")
 #'   )
 #'
-#' attr(adlb[["ONTRTFL"]], "label") <- "On Treatment Record Flag"
-#'
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset("ADSL", adsl),

R/tm_t_abnormality_by_worst_grade.R

@@ -226,11 +226,9 @@ template_abnormality_by_worst_grade <- function(parentname, # nolint
 #' @export
 #'
 #' @examples
-#' library(dplyr)
-#'
 #' adsl <- tmc_ex_adsl
 #' adlb <- tmc_ex_adlb %>%
-#'   filter(!AVISIT %in% c("SCREENING", "BASELINE"))
+#'   dplyr::filter(!AVISIT %in% c("SCREENING", "BASELINE"))
 #'
 #' app <- init(
 #'   data = cdisc_data(
@@ -239,7 +237,7 @@ template_abnormality_by_worst_grade <- function(parentname, # nolint
 #'   ),
 #'   modules = modules(
 #'     tm_t_abnormality_by_worst_grade(
-#'       label = "Laboratory test results with highest grade post-baseline",
+#'       label = "Laboratory Test Results with Highest Grade Post-Baseline",
 #'       dataname = "ADLB",
 #'       arm_var = choices_selected(
 #'         choices = variable_choices(adsl, subset = c("ARM", "ARMCD")),

R/tm_t_ancova.R

@@ -450,7 +450,7 @@ template_ancova <- function(dataname = "ANL",
 #'   ),
 #'   modules = modules(
 #'     tm_t_ancova(
-#'       label = "ANCOVA table",
+#'       label = "ANCOVA Table",
 #'       dataname = "ADQS",
 #'       avisit = choices_selected(
 #'         choices = value_choices(adqs, "AVISIT"),

R/tm_t_binary_outcome.R

@@ -391,12 +391,14 @@ template_binary_outcome <- function(dataname,
 #' @export
 #'
 #' @examples
-#' library(dplyr)
-#'
 #' adsl <- tmc_ex_adsl
 #' adrs <- tmc_ex_adrs %>%
-#'   mutate(AVALC = d_onco_rsp_label(AVALC)) %>%
-#'   filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
+#'   dplyr::mutate(
+#'     AVALC = tern::d_onco_rsp_label(AVALC) %>%
+#'       formatters::with_label("Character Result/Finding")
+#'   ) %>%
+#'   dplyr::filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
+#'
 #' arm_ref_comp <- list(
 #'   ARMCD = list(ref = "ARM B", comp = c("ARM A", "ARM C")),
 #'   ARM = list(ref = "B: Placebo", comp = c("A: Drug X", "C: Combination"))

R/tm_t_coxreg.R

@@ -398,7 +398,7 @@ template_coxreg_m <- function(dataname,
 #' }
 #'
 #' The arm variables, stratification and covariate variables are taken from the
-#' `ADSL` data.
+#' ADSL data.
 #'
 #' @section Note:
 #' - The likelihood ratio test is not supported for model including strata,

R/tm_t_events.R

@@ -445,8 +445,6 @@ template_events <- function(dataname,
 #' @export
 #'
 #' @examples
-#' library(dplyr)
-#'
 #' adsl <- tmc_ex_adsl
 #' adae <- tmc_ex_adae
 #'

R/tm_t_events_by_grade.R

@@ -777,12 +777,11 @@ template_events_col_by_grade <- function(dataname,
 #'
 #' @export
 #' @examples
-#' library(dplyr)
-#' library(tern)
-#'
 #' adsl <- tmc_ex_adsl
+#' lbls_adae <- formatters::var_labels(tmc_ex_adae)
 #' adae <- tmc_ex_adae %>%
-#'   mutate_if(is.character, as.factor) # be certain of having factors
+#'   dplyr::mutate_if(is.character, as.factor) # be certain of having factors
+#' formatters::var_labels(adae) <- lbls_adae
 #'
 #' app <- init(
 #'   data = cdisc_data(

R/tm_t_events_summary.R

@@ -491,17 +491,13 @@ template_events_summary <- function(anl_name,
 #'
 #' @export
 #' @examples
-#' library(dplyr)
-#'
 #' adsl <- tmc_ex_adsl %>%
-#'   mutate(
-#'     DTHFL = case_when( # nolint
+#'   dplyr::mutate(
+#'     DTHFL = dplyr::case_when( # nolint
 #'       !is.na(DTHDT) ~ "Y",
 #'       TRUE ~ ""
-#'     )
+#'     ) %>% formatters::with_label("Subject Death Flag")
 #'   )
-#' attr(adsl[["DTHFL"]], "label") <- "Subject Death Flag"
-#'
 #' adae <- tmc_ex_adae
 #'
 #' add_event_flags <- function(dat) {

R/tm_t_logistic.R

@@ -229,11 +229,9 @@ template_logistic <- function(dataname,
 #'
 #' @export
 #' @examples
-#' library(dplyr)
-#'
 #' adsl <- tmc_ex_adsl
 #' adrs <- tmc_ex_adrs %>%
-#'   filter(PARAMCD %in% c("BESRSPI", "INVET"))
+#'   dplyr::filter(PARAMCD %in% c("BESRSPI", "INVET"))
 #'
 #' arm_ref_comp <- list(
 #'   ACTARMCD = list(

R/tm_t_mult_events.R

@@ -279,8 +279,6 @@ template_mult_events <- function(dataname,
 #' @export
 #'
 #' @examples
-#' library(dplyr)
-#'
 #' adsl <- tmc_ex_adsl
 #' adcm <- tmc_ex_adcm
 #' adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")

R/tm_t_pp_basic_info.R

@@ -63,7 +63,7 @@ template_basic_info <- function(dataname = "ANL",
 #'   ),
 #'   modules = modules(
 #'     tm_t_pp_basic_info(
-#'       label = "Basic info",
+#'       label = "Basic Info",
 #'       dataname = "ADSL",
 #'       patient_col = "USUBJID",
 #'       vars = choices_selected(

R/tm_t_pp_laboratory.R

@@ -108,8 +108,6 @@ template_laboratory <- function(dataname = "ANL",
 #' @export
 #'
 #' @examples
-#'
-#' # Reduced data for tests
 #' adsl <- tmc_ex_adsl
 #' adlb <- tmc_ex_adlb
 #'

R/tm_t_pp_medical_history.R

@@ -94,7 +94,7 @@ template_medical_history <- function(dataname = "ANL",
 #'   ),
 #'   modules = modules(
 #'     tm_t_pp_medical_history(
-#'       label = "Medical history",
+#'       label = "Medical History",
 #'       dataname = "ADMH",
 #'       parentname = "ADSL",
 #'       patient_col = "USUBJID",