revisit decouple scda

.Rbuildignore

@@ -42,3 +42,4 @@ SECURITY.md
 ^LICENSE\.md$
 coverage.*
 ^\.pre-commit-config\.yaml$
+data-raw/data.R

R/data.R

@@ -3,7 +3,7 @@
 #' @description Random adverse events
 #' @docType data
 #'
-#' @usage data(rADAE)
+#' @usage rADAE
 #'
 #' @keywords datasets internal
 #'
@@ -16,7 +16,7 @@
 #' @description Random Concomitant Medications
 #' @docType data
 #'
-#' @usage data(rADCM)
+#' @usage rADCM
 #'
 #' @keywords datasets internal
 #'
@@ -29,7 +29,7 @@
 #' @description Random Exposure
 #' @docType data
 #'
-#' @usage data(rADEX)
+#' @usage rADEX
 #'
 #' @keywords datasets internal
 #'
@@ -42,7 +42,7 @@
 #' @description Random lab analysis
 #' @docType data
 #'
-#' @usage data(rADLB)
+#' @usage rADLB
 #'
 #' @keywords datasets internal
 #'
@@ -55,7 +55,7 @@
 #' @description Random response
 #' @docType data
 #'
-#' @usage data(rADRS)
+#' @usage rADRS
 #'
 #' @keywords datasets internal
 #'
@@ -70,7 +70,7 @@
 #'
 #' @keywords datasets internal
 #'
-#' @usage data(rADSL)
+#' @usage rADSL
 #'
 #' @source internal
 #' @name rADSL
@@ -83,7 +83,7 @@
 #'
 #' @keywords datasets internal
 #'
-#' @usage data(rADTR)
+#' @usage rADTR
 #'
 #' @source internal
 #' @name rADTR
@@ -96,7 +96,7 @@
 #'
 #' @keywords datasets internal
 #'
-#' @usage data(rADTTE)
+#' @usage rADTTE
 #'
 #' @source internal
 #' @name rADTTE

R/g_ae_sub.R

@@ -32,8 +32,8 @@
 #'
 #' @examples
 #' library(grid)
-#' ADAE <- rADAE
-#' ADSL <- rADSL
+#' ADAE <- osprey::rADAE
+#' ADSL <- osprey::rADSL
 #'
 #' id <- ADAE$USUBJID
 #' arm <- ADAE$ACTARMCD
@@ -89,8 +89,8 @@
 #' # Example 3: preprocess data to only include treatment and control arm patients
 #' trt <- "ARM A"
 #' ref <- "ARM C"
-#' ADAE <- rADAE
-#' ADSL <- rADSL %>% filter(ACTARMCD %in% c(trt, ref))
+#' ADAE <- osprey::rADAE
+#' ADSL <- osprey::rADSL %>% filter(ACTARMCD %in% c(trt, ref))
 #' id <- ADAE$USUBJID
 #' arm <- ADAE$ACTARMCD
 #' arm_sl <- as.character(ADSL$ACTARMCD)

R/g_butterfly.R

@@ -44,10 +44,10 @@
 #' library(dplyr)
 #' library(nestcolor)
 #'
-#' ADSL <- rADSL %>%
+#' ADSL <- osprey::rADSL %>%
 #'   select(USUBJID, STUDYID, SEX, ARM, RACE) %>%
 #'   dplyr::filter(SEX %in% c("F", "M"))
-#' ADAE <- rADAE %>% select(USUBJID, STUDYID, AEBODSYS, AETOXGR)
+#' ADAE <- osprey::rADAE %>% select(USUBJID, STUDYID, AEBODSYS, AETOXGR)
 #'
 #' ANL <- left_join(ADAE, ADSL, by = c("STUDYID", "USUBJID"))
 #' ANL <- ANL %>%

R/g_events_term_id.R

@@ -44,8 +44,8 @@
 #' library(grid)
 #' library(nestcolor)
 #'
-#' ADSL <- rADSL
-#' ADAE <- rADAE
+#' ADSL <- osprey::rADSL
+#' ADAE <- osprey::rADAE
 #'
 #' # add additional dummy causality flags
 #' ADAE <- ADAE %>%
@@ -409,7 +409,7 @@ g_events_term_id <- function(term,
 #' @examples
 #' library(dplyr)
 #'
-#' ADAE <- rADAE
+#' ADAE <- osprey::rADAE
 #'
 #' # add additional dummy causality flags
 #' ADAE <- ADAE %>%

R/g_heat_bygrade.R

@@ -33,10 +33,10 @@
 #' @examples
 #' library(dplyr)
 #'
-#' ADSL <- rADSL %>% slice(1:30)
-#' ADEX <- rADEX %>% filter(USUBJID %in% ADSL$USUBJID)
-#' ADAE <- rADAE %>% filter(USUBJID %in% ADSL$USUBJID)
-#' ADCM <- rADCM %>% filter(USUBJID %in% ADSL$USUBJID)
+#' ADSL <- osprey::rADSL %>% slice(1:30)
+#' ADEX <- osprey::rADEX %>% filter(USUBJID %in% ADSL$USUBJID)
+#' ADAE <- osprey::rADAE %>% filter(USUBJID %in% ADSL$USUBJID)
+#' ADCM <- osprey::rADCM %>% filter(USUBJID %in% ADSL$USUBJID)
 #' # function to derive AVISIT from ADEX
 #' add_visit <- function(data_need_visit) {
 #'   visit_dates <- ADEX %>%

R/g_hy_law.R

@@ -61,8 +61,8 @@
 #' library(nestcolor)
 #'
 #' # Note: CRP is being used in place of Bilirubin here because this is the only available data
-#' adsl <- rADSL
-#' adlb <- rADLB %>% mutate(ANRHI = 50)
+#' adsl <- osprey::rADSL
+#' adlb <- osprey::rADLB %>% mutate(ANRHI = 50)
 #'
 #' # Example 1, - Hy's law template (3 and 2 X ULN)
 #' g_hy_law(

R/g_patient_profile.R

@@ -70,7 +70,7 @@
 #' library(dplyr)
 #'
 #' # ADSL
-#' ADSL <- rADSL %>%
+#' ADSL <- osprey::rADSL %>%
 #'   filter(USUBJID == rADSL$USUBJID[1]) %>%
 #'   mutate(
 #'     TRTSDT = as.Date(TRTSDTM),
@@ -82,7 +82,7 @@
 #'
 #'
 #' # Example 1 Exposure "ADEX"
-#' ADEX <- rADEX %>%
+#' ADEX <- osprey::rADEX %>%
 #'   select(USUBJID, STUDYID, ASTDTM, PARCAT2, AVAL, AVALU, PARAMCD)
 #' ADEX <- left_join(ADSL, ADEX, by = c("USUBJID", "STUDYID"))
 #' ADEX <- ADEX %>%
@@ -136,7 +136,7 @@
 #' # If AENDY and ASTDY occur on the same day only AENDY will be shown.
 #'
 #' # Adverse Event ADAE
-#' ADAE <- rADAE %>%
+#' ADAE <- osprey::rADAE %>%
 #'   select(USUBJID, STUDYID, AESOC, AEDECOD, AESER, AETOXGR, AEREL, ASTDY, AENDY)
 #' ADAE <- left_join(ADSL, ADAE, by = c("USUBJID", "STUDYID"))
 #'
@@ -172,7 +172,7 @@
 #' p2
 #'
 #' # Example 3 Tumor Response "ADRS"
-#' ADRS <- rADRS %>%
+#' ADRS <- osprey::rADRS %>%
 #'   select(USUBJID, STUDYID, PARAMCD, PARAM, AVALC, AVAL, ADY, ADTM)
 #' ADRS <- left_join(ADSL, ADRS, by = c("USUBJID", "STUDYID"))
 #' p3 <- patient_domain_profile(
@@ -211,7 +211,7 @@
 #' p3
 #'
 #' # Example 4 Concomitant Med "ADCM"
-#' ADCM <- rADCM %>%
+#' ADCM <- osprey::rADCM %>%
 #'   select(USUBJID, STUDYID, ASTDTM, AENDTM, CMDECOD, ASTDY, AENDY)
 #' ADCM <- left_join(ADSL, ADCM, by = c("USUBJID", "STUDYID"))
 #' p4 <- patient_domain_profile(
@@ -234,7 +234,7 @@
 #' p4
 #'
 #' # Example 5 Laboratory "ADLB"
-#' ADLB <- rADLB %>%
+#' ADLB <- osprey::rADLB %>%
 #'   select(
 #'     USUBJID, STUDYID, LBSEQ, PARAMCD, BASETYPE,
 #'     ADTM, ADY, ATPTN, AVISITN, LBTESTCD, ANRIND
@@ -612,7 +612,7 @@ patient_domain_profile <- function(domain = NULL,
 #' library(dplyr)
 #' library(nestcolor)
 #' # ADSL
-#' ADSL <- rADSL %>%
+#' ADSL <- osprey::rADSL %>%
 #'   filter(USUBJID == rADSL$USUBJID[1]) %>%
 #'   mutate(
 #'     TRTSDT = as.Date(TRTSDTM),
@@ -623,7 +623,7 @@ patient_domain_profile <- function(domain = NULL,
 #'
 #'
 #' # ADEX
-#' ADEX <- rADEX %>%
+#' ADEX <- osprey::rADEX %>%
 #'   select(USUBJID, STUDYID, ASTDTM, PARCAT2, AVAL, AVALU, PARAMCD)
 #' ADEX <- left_join(ADSL, ADEX, by = c("USUBJID", "STUDYID"))
 #'
@@ -642,22 +642,22 @@ patient_domain_profile <- function(domain = NULL,
 #'   ))
 #'
 #' # ADAE
-#' ADAE <- rADAE %>%
+#' ADAE <- osprey::rADAE %>%
 #'   select(USUBJID, STUDYID, AESOC, AEDECOD, AESER, AETOXGR, AEREL, ASTDY, AENDY)
 #' ADAE <- left_join(ADSL, ADAE, by = c("USUBJID", "STUDYID"))
 #'
 #' # ADRS
-#' ADRS <- rADRS %>%
+#' ADRS <- osprey::rADRS %>%
 #'   select(USUBJID, STUDYID, PARAMCD, PARAM, AVALC, AVAL, ADY, ADTM)
 #' ADRS <- left_join(ADSL, ADRS, by = c("USUBJID", "STUDYID"))
 #'
 #' # ADCM
-#' ADCM <- rADCM %>%
+#' ADCM <- osprey::rADCM %>%
 #'   select(USUBJID, STUDYID, ASTDTM, AENDTM, CMDECOD, ASTDY, AENDY)
 #' ADCM <- left_join(ADSL, ADCM, by = c("USUBJID", "STUDYID"))
 #'
 #' # ADLB
-#' ADLB <- rADLB %>%
+#' ADLB <- osprey::rADLB %>%
 #'   select(
 #'     USUBJID, STUDYID, LBSEQ, PARAMCD, BASETYPE, ADTM,
 #'     ADY, ATPTN, AVISITN, LBTESTCD, ANRIND

R/g_spiderplot.R

@@ -46,8 +46,8 @@
 #' library(dplyr)
 #' library(nestcolor)
 #'
-#' ADTR <- rADTR %>% select(STUDYID, USUBJID, ADY, AVISIT, CHG, PCHG, PARAMCD)
-#' ADSL <- rADSL %>% select(STUDYID, USUBJID, RACE, SEX, ARM)
+#' ADTR <- osprey::rADTR %>% select(STUDYID, USUBJID, ADY, AVISIT, CHG, PCHG, PARAMCD)
+#' ADSL <- osprey::rADSL %>% select(STUDYID, USUBJID, RACE, SEX, ARM)
 #' ANL <- left_join(ADTR, ADSL, by = c("STUDYID", "USUBJID"))
 #' ANL <- ANL %>%
 #'   dplyr::filter(PARAMCD == "SLDINV" & AVISIT != "POST-BASELINE MINIMUM") %>%

R/g_spiderplot_simple.R

@@ -20,8 +20,8 @@
 #' library(dplyr)
 #' library(nestcolor)
 #'
-#' ADSL <- rADSL[1:15, ]
-#' ADTR <- rADTR
+#' ADSL <- osprey::rADSL[1:15, ]
+#' ADTR <- osprey::rADTR
 #' ANL <- left_join(ADSL, ADTR)
 #'
 #' ANL %>%

R/g_swimlane.R

@@ -29,7 +29,7 @@
 #' library(dplyr)
 #' library(nestcolor)
 #'
-#' ADSL <- rADSL[1:20, ]
+#' ADSL <- osprey::rADSL[1:20, ]
 #' ADRS <- filter(rADRS, PARAMCD == "OVRINV")
 #' ANL <- left_join(ADSL, ADRS, by = c("STUDYID", "USUBJID"), multiple = "all")
 #' anno_txt <- ADSL[, c("ARMCD", "SEX")]
@@ -56,8 +56,8 @@
 #' library(dplyr)
 #' library(nestcolor)
 #'
-#' ADSL <- rADSL[1:20, ]
-#' ADRS <- rADRS
+#' ADSL <- osprey::rADSL[1:20, ]
+#' ADRS <- osprey::rADRS
 #'
 #' anno_txt_vars <- c("ARMCD", "SEX", "COUNTRY")
 #' anno_txt <- ADSL[, anno_txt_vars]

R/g_waterfall.R

@@ -46,10 +46,10 @@
 #' )
 #'
 #' # Example 1
-#' ADSL <- rADSL[1:15, ]
-#' ADRS <- rADRS %>%
+#' ADSL <- osprey::rADSL[1:15, ]
+#' ADRS <- osprey::rADRS %>%
 #'   filter(USUBJID %in% ADSL$USUBJID)
-#' ADTR <- rADTR %>%
+#' ADTR <- osprey::rADTR %>%
 #'   filter(USUBJID %in% ADSL$USUBJID) %>%
 #'   select(USUBJID, PCHG) %>%
 #'   group_by(USUBJID) %>%

R/stream_filter.R

@@ -14,8 +14,8 @@
 #' @author Iain Bennett
 #' @export
 #' @examples
-#' ADSL <- rADSL
-#' ADTTE <- rADTTE
+#' ADSL <- osprey::rADSL
+#' ADTTE <- osprey::rADTTE
 #' filters <- as.data.frame(rbind(
 #'   c(ID = "IT", FLTTARGET = "SLREF", FLTWHERE = "where 1 eq 1"),
 #'   c(ID = "BIO", FLTTARGET = "SLREF", FLTWHERE = "where BMRKR1 ge 4.3"),

data-raw/data.R

@@ -0,0 +1,25 @@
+## code to prepare `data` for testing examples
+library(scda)
+rADAE <- synthetic_cdisc_data("latest")$adae # nolint
+usethis::use_data(rADAE)
+
+rADCM <- synthetic_cdisc_data("latest")$adcm # nolint
+usethis::use_data(rADCM)
+
+rADEX <- synthetic_cdisc_data("latest")$adex # nolint
+usethis::use_data(rADEX)
+
+rADLB <- synthetic_cdisc_data("latest")$adlb # nolint
+usethis::use_data(rADLB)
+
+rADRS <- synthetic_cdisc_data("latest")$adrs # nolint
+usethis::use_data(rADRS)
+
+rADSL <- synthetic_cdisc_data("latest")$adsl # nolint
+usethis::use_data(rADSL)
+
+rADTR <- synthetic_cdisc_data("latest")$adtr # nolint
+usethis::use_data(rADTR)
+
+rADTTE <- synthetic_cdisc_data("latest")$adtte # nolint
+usethis::use_data(rADTTE)