diff --git a/NEWS.md b/NEWS.md index 338a98e0..3582013d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,8 @@ # random.cdisc.data 0.3.13.9062 ### Enhancements +* Refactor `adpc` and `adab` following the new CDISC standard. + * Refactor `abab` parameters and visits to align with `adpc`. ### Breaking changes diff --git a/R/package.R b/R/package.R index 74f14bcb..b432c8cb 100644 --- a/R/package.R +++ b/R/package.R @@ -29,5 +29,6 @@ utils::globalVariables(c( "VSSTRESC", "WEIGHT", "WORS01FL", "ada_bl", "any_pos_postbl", "any_pos_postbl_nab", "changeind", "comp_count", "first_date", "inc_postbl", "inc_postbl_nab", "ka", "ke", "last_ada", "n_pos", "nab_bl", "onset_ada", "pos_bl", "pos_bl_nab", "pos_last_postbl", - "publication_name", "row_check" + "publication_name", "row_check", "AFRLT", "ARRLT", "NFRLT", "NRRLT", + "eortc_qlq_c30", "expect", "gdsr_param_adqlqc" )) diff --git a/R/radab.R b/R/radab.R index 211adf44..e06bd5a6 100644 --- a/R/radab.R +++ b/R/radab.R @@ -127,10 +127,10 @@ radab <- function(adsl, ARM, ACTARM, VISITDY, - ARELTM1, - NRELTM1, - ARELTM2, - NRELTM2, + AFRLT, + NFRLT, + ARRLT, + NRRLT, RELTMU ) %>% unique(), @@ -139,7 +139,7 @@ radab <- function(adsl, rename(ISTPT = PCTPT) # mutate time from dose variables from adpc to convert into Days - adab_visit <- adab_visit %>% dplyr::mutate_at(c("ARELTM1", "NRELTM1", "ARELTM2", "NRELTM2"), ~ . / 24) + adab_visit <- adab_visit %>% dplyr::mutate_at(c("AFRLT", "NFRLT", "ARRLT", "NRRLT"), ~ . / 24) @@ -230,12 +230,12 @@ radab <- function(adsl, adab <- adab %>% dplyr::mutate( RELTMU = "day", - ABLFL = ifelse(!is.na(NRELTM1) & NRELTM1 == 0, "Y", NA) # Baseline Record Flag + ABLFL = ifelse(!is.na(NFRLT) & NFRLT == 0, "Y", NA) # Baseline Record Flag , - ADABLPFL = ifelse(PARAMCD == "RESULT1" & !is.na(NRELTM1) & NRELTM1 == 0, "Y", NA) + ADABLPFL = ifelse(PARAMCD == "RESULT1" & !is.na(NFRLT) & NFRLT == 0, "Y", NA) # Baseline ADA Eval. Param-Level Flag, only populate for ADA, not for NAB , - ADPBLPFL = ifelse(PARAMCD == "RESULT1" & !is.na(NRELTM1) & NRELTM1 > 0 & !is.na(AVAL), "Y", NA) + ADPBLPFL = ifelse(PARAMCD == "RESULT1" & !is.na(NFRLT) & NFRLT > 0 & !is.na(AVAL), "Y", NA) # Post-Baseline ADA Eval. Param-Level Flag, only populate for ADA, not for NAB ) %>% dplyr::group_by(USUBJID) %>% @@ -254,7 +254,7 @@ radab <- function(adsl, any_pos_postbl_nab = any(PARAM == "NAB interpreted per sample result" & is.na(ABLFL) & AVALC == "POSITIVE"), pos_last_postbl = any(PARAM == "ADA interpreted per sample result" & - NRELTM1 == max(NRELTM1) & AVALC == "POSITIVE"), + NFRLT == max(NFRLT) & AVALC == "POSITIVE"), ada_bl = AVAL[PARAM == "Antibody titer units" & !is.na(ABLFL)], nab_bl = AVAL[PARAM == "Neutralizing Antibody titer units" & !is.na(ABLFL)] ) @@ -267,13 +267,13 @@ radab <- function(adsl, is.na(ABLFL) & (AVAL - nab_bl) > 0.60), onset_ada = if (any(PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE")) { - min(NRELTM1[PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE"]) + min(NFRLT[PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE"]) } else { NA }, last_ada = if (any(PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE")) { - max(NRELTM1[PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE"]) + max(NFRLT[PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE"]) } else { NA } @@ -282,7 +282,7 @@ radab <- function(adsl, dplyr::left_join(pos_tots, by = "USUBJID") %>% dplyr::select( USUBJID, - NRELTM1, + NFRLT, pos_bl, pos_bl_nab, any_pos_postbl, @@ -298,7 +298,7 @@ radab <- function(adsl, # add flags to ADAB dataset adab <- adab %>% - dplyr::left_join(adab_subj, by = c("USUBJID", "NRELTM1")) + dplyr::left_join(adab_subj, by = c("USUBJID", "NFRLT")) # derive subject-level variables adab[!(adab$PARAM %in% visit_lvl_params), ] <- adab %>% diff --git a/R/radpc.R b/R/radpc.R index d409e65c..b0c209c5 100644 --- a/R/radpc.R +++ b/R/radpc.R @@ -124,5 +124,15 @@ radpc <- function(adsl, adpc <- mutate_na(ds = adpc, na_vars = na_vars, na_percentage = na_percentage) } + adpc <- adpc %>% + rename( + AVALCAT1 = AVALC, + NFRLT = NRELTM1, + AFRLT = ARELTM1, + NRRLT = NRELTM2, + ARRLT = ARELTM2 + ) %>% + mutate(ANL02FL = "Y") + adpc <- apply_metadata(adpc, "metadata/ADPC.yml") } diff --git a/R/radqlqc.R b/R/radqlqc.R index c3964809..93350e15 100644 --- a/R/radqlqc.R +++ b/R/radqlqc.R @@ -290,6 +290,7 @@ get_qs_data <- function(adsl, QSORRES = c(1234, 0.2), QSSTRESC = c(1234, 0.2) )) { + load(system.file("sysdata.rda", package = "random.cdisc.data")) checkmate::assert_string(visit_format) checkmate::assert_integer(n_assessments, len = 1, any.missing = FALSE) checkmate::assert_integer(n_days, len = 1, any.missing = FALSE) @@ -656,6 +657,7 @@ prep_adqlqc <- function(df) { TRUE ~ QSTESTCD ) ) + load(system.file("sysdata.rda", package = "random.cdisc.data")) adqlqc1 <- dplyr::left_join( adqlqc, gdsr_param_adqlqc, @@ -679,7 +681,7 @@ calc_scales <- function(adqlqc1) { # parcat2 = scales or global health status # global health status/scales data # QSTESTCD: EOR0131 to EOR0145 (global health status and scales) - + load(system.file("sysdata.rda", package = "random.cdisc.data")) eortc_qlq_c30_sub <- filter( eortc_qlq_c30, !(as.numeric(str_extract(QSTESTCD, "\\d+$")) >= 101 & diff --git a/data/cadab.RData b/data/cadab.RData index f4529a92..060bb8da 100644 Binary files a/data/cadab.RData and b/data/cadab.RData differ diff --git a/data/cadae.RData b/data/cadae.RData index 3eaeeee1..8d10ad5f 100644 Binary files a/data/cadae.RData and b/data/cadae.RData differ diff --git a/data/cadaette.RData b/data/cadaette.RData index b7e9b395..d2704f3e 100644 Binary files a/data/cadaette.RData and b/data/cadaette.RData differ diff --git a/data/cadcm.RData b/data/cadcm.RData index 040dd63d..72d0973a 100644 Binary files a/data/cadcm.RData and b/data/cadcm.RData differ diff --git a/data/caddv.RData b/data/caddv.RData index 9666a05e..e1e1d210 100644 Binary files a/data/caddv.RData and b/data/caddv.RData differ diff --git a/data/cadeg.RData b/data/cadeg.RData index e97d84df..e602d566 100644 Binary files a/data/cadeg.RData and b/data/cadeg.RData differ diff --git a/data/cadex.RData b/data/cadex.RData index f2a5fd46..9a0937c7 100644 Binary files a/data/cadex.RData and b/data/cadex.RData differ diff --git a/data/cadhy.RData b/data/cadhy.RData index e6aebdba..3beb0456 100644 Binary files a/data/cadhy.RData and b/data/cadhy.RData differ diff --git a/data/cadlb.RData b/data/cadlb.RData index 989200ff..03a662d4 100644 Binary files a/data/cadlb.RData and b/data/cadlb.RData differ diff --git a/data/cadmh.RData b/data/cadmh.RData index 92bffe5d..a614a46d 100644 Binary files a/data/cadmh.RData and b/data/cadmh.RData differ diff --git a/data/cadpc.RData b/data/cadpc.RData index 22a69193..8c974ae8 100644 Binary files a/data/cadpc.RData and b/data/cadpc.RData differ diff --git a/data/cadpp.RData b/data/cadpp.RData index 9985d073..efc84fa1 100644 Binary files a/data/cadpp.RData and b/data/cadpp.RData differ diff --git a/data/cadqlqc.RData b/data/cadqlqc.RData index 9e7ed69c..edc0febb 100644 Binary files a/data/cadqlqc.RData and b/data/cadqlqc.RData differ diff --git a/data/cadqs.RData b/data/cadqs.RData index fe43620d..fdcdcd09 100644 Binary files a/data/cadqs.RData and b/data/cadqs.RData differ diff --git a/data/cadrs.RData b/data/cadrs.RData index 92b7c8f2..0b89e503 100644 Binary files a/data/cadrs.RData and b/data/cadrs.RData differ diff --git a/data/cadsl.RData b/data/cadsl.RData index eb6d5929..8f767851 100644 Binary files a/data/cadsl.RData and b/data/cadsl.RData differ diff --git a/data/cadsub.RData b/data/cadsub.RData index 16bd24c9..ba271340 100644 Binary files a/data/cadsub.RData and b/data/cadsub.RData differ diff --git a/data/cadtr.RData b/data/cadtr.RData index aa392054..126f6e27 100644 Binary files a/data/cadtr.RData and b/data/cadtr.RData differ diff --git a/data/cadtte.RData b/data/cadtte.RData index 763a4c81..2965c344 100644 Binary files a/data/cadtte.RData and b/data/cadtte.RData differ diff --git a/data/cadvs.RData b/data/cadvs.RData index 460dbb8d..8cd05632 100644 Binary files a/data/cadvs.RData and b/data/cadvs.RData differ diff --git a/inst/metadata/ADAB.yml b/inst/metadata/ADAB.yml index 46f0eb3b..6b1ab93d 100644 --- a/inst/metadata/ADAB.yml +++ b/inst/metadata/ADAB.yml @@ -42,15 +42,15 @@ variables: RELTMU: label: Relative Actual/Nominal Time Units type: factor - NRELTM1: - label: Nominal Relative Time from First Dose + NFRLT: + label: Nom. Rel. Time from Analyte First Dose type: numeric - ARELTM1: - label: Analysis Rel. Actual Time from First Dose + AFRLT: + label: Act. Rel. Time from Analyte First Dose type: numeric - NRELTM2: - label: Nominal Relative Time from Most Recent Dose + NRRLT: + label: Nominal Rel. Time from Ref. Dose type: numeric - ARELTM2: - label: Analysis Rel. Actual Time from Most Recent Dose + ARRLT: + label: Actual Rel. Time from Ref. Dose type: numeric diff --git a/inst/metadata/ADPC.yml b/inst/metadata/ADPC.yml index 881bab35..6763da97 100644 --- a/inst/metadata/ADPC.yml +++ b/inst/metadata/ADPC.yml @@ -3,17 +3,17 @@ domain: label: Pharmacokinetic Analysis Dataset variables: - NRELTM1: - label: Nominal Relative Time from First Dose + NFRLT: + label: Nom. Rel. Time from Analyte First Dose type: numeric - ARELTM1: - label: Analysis Rel. Actual Time from First Dose + AFRLT: + label: Act. Rel. Time from Analyte First Dose type: numeric - NRELTM2: - label: Nominal Relative Time from Most Recent Dose + NRRLT: + label: Nominal Rel. Time from Ref. Dose type: numeric - ARELTM2: - label: Analysis Rel. Actual Time from Most Recent Dose + ARRLT: + label: Actual Rel. Time from Ref. Dose type: numeric PCTPTNUM: label: Planned Time Point Number @@ -30,8 +30,8 @@ variables: AVAL: label: Analysis Value type: numeric - AVALC: - label: Analysis Value (C) + AVALCAT1: + label: Analysis Value Category 1 type: character AVALU: label: Analysis Value Unit @@ -51,3 +51,6 @@ variables: VISITDY: label: Visit (N) type: integer + ANL02FL: + label: Analysis Flag 02 + type: character diff --git a/R/sysdata.rda b/inst/sysdata.rda similarity index 100% rename from R/sysdata.rda rename to inst/sysdata.rda diff --git a/man/cadab.Rd b/man/cadab.Rd index 5009990b..1dab4e05 100644 --- a/man/cadab.Rd +++ b/man/cadab.Rd @@ -5,7 +5,7 @@ \alias{cadab} \title{Cached ADAB} \format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 58520 rows and 22 columns. +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 6916 rows and 21 columns. } \usage{ data(cadab) diff --git a/man/cadpc.Rd b/man/cadpc.Rd index 4a2712a5..ce410178 100644 --- a/man/cadpc.Rd +++ b/man/cadpc.Rd @@ -5,7 +5,7 @@ \alias{cadpc} \title{Cached ADPC} \format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 6640 rows and 71 columns. +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 6640 rows and 72 columns. } \usage{ data(cadpc) diff --git a/tests/testthat/_snaps/row_values.md b/tests/testthat/_snaps/row_values.md index 706c5a37..8a6c6de9 100644 --- a/tests/testthat/_snaps/row_values.md +++ b/tests/testthat/_snaps/row_values.md @@ -4145,7 +4145,7 @@ Code first_pt_rows Output - # A tibble: 30 x 71 + # A tibble: 30 x 72 STUDYID USUBJID SUBJID SITEID AGE AGEU SEX 1 AB12345 AB12345-BRA-1-id-9 id-9 BRA-1 35 YEARS F @@ -4434,77 +4434,109 @@ 28 COMPLETED 2024-01-18 1096 NA NA 29 COMPLETED 2024-01-18 1096 NA NA 30 COMPLETED 2024-01-18 1096 NA NA - LSTALVDT DTHADY ADTHAUT NRELTM1 ARELTM1 NRELTM2 ARELTM2 PCTPTNUM PCTPT - - 1 2024-02-10 NA 0 0 0 0 0 Predose - 2 2024-02-10 NA 0.5 0.5 0.5 0.5 0.5 0.5H - 3 2024-02-10 NA 1 1 1 1 1 1H - 4 2024-02-10 NA 1.5 1.5 1.5 1.5 1.5 1.5H - 5 2024-02-10 NA 2 2 2 2 2 2H - 6 2024-02-10 NA 3 3 3 3 3 3H - 7 2024-02-10 NA 4 4 4 4 4 4H - 8 2024-02-10 NA 8 8 8 8 8 8H - 9 2024-02-10 NA 12 12 12 12 12 12H - 10 2024-02-10 NA 0 0 0 0 0 Predose - 11 2024-02-10 NA 0.5 0.5 0.5 0.5 0.5 0.5H - 12 2024-02-10 NA 1 1 1 1 1 1H - 13 2024-02-10 NA 1.5 1.5 1.5 1.5 1.5 1.5H - 14 2024-02-10 NA 2 2 2 2 2 2H - 15 2024-02-10 NA 3 3 3 3 3 3H - 16 2024-02-10 NA 4 4 4 4 4 4H - 17 2024-02-10 NA 8 8 8 8 8 8H - 18 2024-02-10 NA 12 12 12 12 12 12H - 19 2024-02-10 NA 0 0 0 0 0 Predose - 20 2024-02-10 NA 4 4 4 4 4 0H - 4H - 21 2024-02-10 NA 8 8 8 8 8 4H - 8H - 22 2024-02-10 NA 12 12 12 12 12 8H - 12H - 23 2024-02-10 NA 0 0 0 0 0 Predose - 24 2024-02-10 NA 4 4 4 4 4 0H - 4H - 25 2024-02-10 NA 8 8 8 8 8 4H - 8H - 26 2024-02-10 NA 12 12 12 12 12 8H - 12H - 27 2024-02-10 NA 24 24 0 0 24 24H - 28 2024-02-10 NA 24 24 0 0 24 24H - 29 2024-02-10 NA 24 24 0 0 24 0H - 24H - 30 2024-02-10 NA 24 24 0 0 24 0H - 24H - PCVOL PCVOLU AVAL AVALC AVALU RELTMU PARAM ASMED VISIT VISITDY - - 1 NA "" 0 BLQ ug/mL hr Plasma Drug X PLASMA Day 1 1 - 2 NA "" 15.3 15.3 ug/mL hr Plasma Drug X PLASMA Day 1 1 - 3 NA "" 19.2 19.205 ug/mL hr Plasma Drug X PLASMA Day 1 1 - 4 NA "" 18.1 18.082 ug/mL hr Plasma Drug X PLASMA Day 1 1 - 5 NA "" 15.1 15.136 ug/mL hr Plasma Drug X PLASMA Day 1 1 - 6 NA "" 8.95 8.953 ug/mL hr Plasma Drug X PLASMA Day 1 1 - 7 NA "" 4.71 4.71 ug/mL hr Plasma Drug X PLASMA Day 1 1 - 8 NA "" 0.23 0.23 ug/mL hr Plasma Drug X PLASMA Day 1 1 - 9 NA "" 0.008 0.008 ug/mL hr Plasma Drug X PLASMA Day 1 1 - 10 NA "" 0 BLQ ug/mL hr Plasma Drug Y PLASMA Day 1 1 - 11 NA "" 30.6 30.6 ug/mL hr Plasma Drug Y PLASMA Day 1 1 - 12 NA "" 38.4 38.409 ug/mL hr Plasma Drug Y PLASMA Day 1 1 - 13 NA "" 36.2 36.164 ug/mL hr Plasma Drug Y PLASMA Day 1 1 - 14 NA "" 30.3 30.272 ug/mL hr Plasma Drug Y PLASMA Day 1 1 - 15 NA "" 17.9 17.905 ug/mL hr Plasma Drug Y PLASMA Day 1 1 - 16 NA "" 9.42 9.419 ug/mL hr Plasma Drug Y PLASMA Day 1 1 - 17 NA "" 0.459 0.459 ug/mL hr Plasma Drug Y PLASMA Day 1 1 - 18 NA "" 0.017 0.017 ug/mL hr Plasma Drug Y PLASMA Day 1 1 - 19 1122. "mL" 0 BLQ ug/mL hr Urine Drug X URINE Day 1 1 - 20 152. "mL" 4.71 4.71 ug/mL hr Urine Drug X URINE Day 1 1 - 21 370. "mL" 0.23 0.23 ug/mL hr Urine Drug X URINE Day 1 1 - 22 605. "mL" 0.008 0.008 ug/mL hr Urine Drug X URINE Day 1 1 - 23 1122. "mL" 0 BLQ ug/mL hr Urine Drug Y URINE Day 1 1 - 24 152. "mL" 4.71 4.71 ug/mL hr Urine Drug Y URINE Day 1 1 - 25 370. "mL" 0.23 0.23 ug/mL hr Urine Drug Y URINE Day 1 1 - 26 605. "mL" 0.008 0.008 ug/mL hr Urine Drug Y URINE Day 1 1 - 27 NA "" 0 BLQ ug/mL hr Plasma Drug X PLASMA Day 2 2 - 28 NA "" 0 BLQ ug/mL hr Plasma Drug Y PLASMA Day 2 2 - 29 1055. "mL" 0 BLQ ug/mL hr Urine Drug X URINE Day 2 2 - 30 1055. "mL" 0 BLQ ug/mL hr Urine Drug Y URINE Day 2 2 + LSTALVDT DTHADY ADTHAUT NFRLT AFRLT NRRLT ARRLT PCTPTNUM PCTPT PCVOL + + 1 2024-02-10 NA 0 0 0 0 0 Predose NA + 2 2024-02-10 NA 0.5 0.5 0.5 0.5 0.5 0.5H NA + 3 2024-02-10 NA 1 1 1 1 1 1H NA + 4 2024-02-10 NA 1.5 1.5 1.5 1.5 1.5 1.5H NA + 5 2024-02-10 NA 2 2 2 2 2 2H NA + 6 2024-02-10 NA 3 3 3 3 3 3H NA + 7 2024-02-10 NA 4 4 4 4 4 4H NA + 8 2024-02-10 NA 8 8 8 8 8 8H NA + 9 2024-02-10 NA 12 12 12 12 12 12H NA + 10 2024-02-10 NA 0 0 0 0 0 Predose NA + 11 2024-02-10 NA 0.5 0.5 0.5 0.5 0.5 0.5H NA + 12 2024-02-10 NA 1 1 1 1 1 1H NA + 13 2024-02-10 NA 1.5 1.5 1.5 1.5 1.5 1.5H NA + 14 2024-02-10 NA 2 2 2 2 2 2H NA + 15 2024-02-10 NA 3 3 3 3 3 3H NA + 16 2024-02-10 NA 4 4 4 4 4 4H NA + 17 2024-02-10 NA 8 8 8 8 8 8H NA + 18 2024-02-10 NA 12 12 12 12 12 12H NA + 19 2024-02-10 NA 0 0 0 0 0 Predose 1122. + 20 2024-02-10 NA 4 4 4 4 4 0H - 4H 152. + 21 2024-02-10 NA 8 8 8 8 8 4H - 8H 370. + 22 2024-02-10 NA 12 12 12 12 12 8H - 12H 605. + 23 2024-02-10 NA 0 0 0 0 0 Predose 1122. + 24 2024-02-10 NA 4 4 4 4 4 0H - 4H 152. + 25 2024-02-10 NA 8 8 8 8 8 4H - 8H 370. + 26 2024-02-10 NA 12 12 12 12 12 8H - 12H 605. + 27 2024-02-10 NA 24 24 0 0 24 24H NA + 28 2024-02-10 NA 24 24 0 0 24 24H NA + 29 2024-02-10 NA 24 24 0 0 24 0H - 24H 1055. + 30 2024-02-10 NA 24 24 0 0 24 0H - 24H 1055. + PCVOLU AVAL AVALCAT1 AVALU RELTMU PARAM ASMED VISIT VISITDY + + 1 "" 0 BLQ ug/mL hr Plasma Drug X PLASMA Day 1 1 + 2 "" 15.3 15.3 ug/mL hr Plasma Drug X PLASMA Day 1 1 + 3 "" 19.2 19.205 ug/mL hr Plasma Drug X PLASMA Day 1 1 + 4 "" 18.1 18.082 ug/mL hr Plasma Drug X PLASMA Day 1 1 + 5 "" 15.1 15.136 ug/mL hr Plasma Drug X PLASMA Day 1 1 + 6 "" 8.95 8.953 ug/mL hr Plasma Drug X PLASMA Day 1 1 + 7 "" 4.71 4.71 ug/mL hr Plasma Drug X PLASMA Day 1 1 + 8 "" 0.23 0.23 ug/mL hr Plasma Drug X PLASMA Day 1 1 + 9 "" 0.008 0.008 ug/mL hr Plasma Drug X PLASMA Day 1 1 + 10 "" 0 BLQ ug/mL hr Plasma Drug Y PLASMA Day 1 1 + 11 "" 30.6 30.6 ug/mL hr Plasma Drug Y PLASMA Day 1 1 + 12 "" 38.4 38.409 ug/mL hr Plasma Drug Y PLASMA Day 1 1 + 13 "" 36.2 36.164 ug/mL hr Plasma Drug Y PLASMA Day 1 1 + 14 "" 30.3 30.272 ug/mL hr Plasma Drug Y PLASMA Day 1 1 + 15 "" 17.9 17.905 ug/mL hr Plasma Drug Y PLASMA Day 1 1 + 16 "" 9.42 9.419 ug/mL hr Plasma Drug Y PLASMA Day 1 1 + 17 "" 0.459 0.459 ug/mL hr Plasma Drug Y PLASMA Day 1 1 + 18 "" 0.017 0.017 ug/mL hr Plasma Drug Y PLASMA Day 1 1 + 19 "mL" 0 BLQ ug/mL hr Urine Drug X URINE Day 1 1 + 20 "mL" 4.71 4.71 ug/mL hr Urine Drug X URINE Day 1 1 + 21 "mL" 0.23 0.23 ug/mL hr Urine Drug X URINE Day 1 1 + 22 "mL" 0.008 0.008 ug/mL hr Urine Drug X URINE Day 1 1 + 23 "mL" 0 BLQ ug/mL hr Urine Drug Y URINE Day 1 1 + 24 "mL" 4.71 4.71 ug/mL hr Urine Drug Y URINE Day 1 1 + 25 "mL" 0.23 0.23 ug/mL hr Urine Drug Y URINE Day 1 1 + 26 "mL" 0.008 0.008 ug/mL hr Urine Drug Y URINE Day 1 1 + 27 "" 0 BLQ ug/mL hr Plasma Drug X PLASMA Day 2 2 + 28 "" 0 BLQ ug/mL hr Plasma Drug Y PLASMA Day 2 2 + 29 "mL" 0 BLQ ug/mL hr Urine Drug X URINE Day 2 2 + 30 "mL" 0 BLQ ug/mL hr Urine Drug Y URINE Day 2 2 + ANL02FL + + 1 Y + 2 Y + 3 Y + 4 Y + 5 Y + 6 Y + 7 Y + 8 Y + 9 Y + 10 Y + 11 Y + 12 Y + 13 Y + 14 Y + 15 Y + 16 Y + 17 Y + 18 Y + 19 Y + 20 Y + 21 Y + 22 Y + 23 Y + 24 Y + 25 Y + 26 Y + 27 Y + 28 Y + 29 Y + 30 Y --- Code rand_rows Output - # A tibble: 10 x 71 + # A tibble: 10 x 72 STUDYID USUBJID SUBJID SITEID AGE AGEU SEX 1 AB12345 AB12345-USA-13-id-3 id-3 USA-13 35 YEARS F @@ -4613,42 +4645,42 @@ 8 2022-09-21 20:25:18 COMPLETED COMPLETED 2022-09-21 1096 NA 9 2023-10-27 16:16:26 COMPLETED COMPLETED 2023-10-27 1096 NA 10 2022-09-21 20:25:18 COMPLETED COMPLETED 2022-09-21 1096 NA - DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT NRELTM1 ARELTM1 - - 1 NA 2022-10-30 NA 24 24 - 2 NA 2022-10-30 NA 4 4 - 3 NA 2023-07-10 NA 8 8 - 4 NA 2023-07-10 NA 4 4 - 5 NA 2023-07-10 NA 4 4 - 6 NA NA NA 3 3 - 7 NA 2024-02-10 NA 0.5 0.5 - 8 NA 2022-10-09 NA 12 12 - 9 NA 2023-11-13 NA 4 4 - 10 NA 2022-10-09 NA 8 8 - NRELTM2 ARELTM2 PCTPTNUM PCTPT PCVOL PCVOLU AVAL AVALC AVALU RELTMU - - 1 0 0 24 24H NA "" 0 BLQ ug/mL hr - 2 4 4 4 0H - 4H 120. "mL" 5.27 5.269 ug/mL hr - 3 8 8 8 4H - 8H 236. "mL" 0.665 0.665 ug/mL hr - 4 4 4 4 0H - 4H 97.1 "mL" 6.11 6.106 ug/mL hr - 5 4 4 4 4H NA "" 6.11 6.106 ug/mL hr - 6 3 3 3 3H NA "" 9.11 9.113 ug/mL hr - 7 0.5 0.5 0.5 0.5H NA "" 15.3 15.3 ug/mL hr - 8 12 12 12 8H - 12H 528. "mL" 0.005 0.005 ug/mL hr - 9 4 4 4 0H - 4H 117. "mL" 4.37 4.371 ug/mL hr - 10 8 8 8 8H NA "" 0.151 0.151 ug/mL hr - PARAM ASMED VISIT VISITDY - - 1 Plasma Drug X PLASMA Day 2 2 - 2 Urine Drug X URINE Day 1 1 - 3 Urine Drug X URINE Day 1 1 - 4 Urine Drug Y URINE Day 1 1 - 5 Plasma Drug X PLASMA Day 1 1 - 6 Plasma Drug X PLASMA Day 1 1 - 7 Plasma Drug X PLASMA Day 1 1 - 8 Urine Drug X URINE Day 1 1 - 9 Urine Drug X URINE Day 1 1 - 10 Plasma Drug X PLASMA Day 1 1 + DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT NFRLT AFRLT NRRLT + + 1 NA 2022-10-30 NA 24 24 0 + 2 NA 2022-10-30 NA 4 4 4 + 3 NA 2023-07-10 NA 8 8 8 + 4 NA 2023-07-10 NA 4 4 4 + 5 NA 2023-07-10 NA 4 4 4 + 6 NA NA NA 3 3 3 + 7 NA 2024-02-10 NA 0.5 0.5 0.5 + 8 NA 2022-10-09 NA 12 12 12 + 9 NA 2023-11-13 NA 4 4 4 + 10 NA 2022-10-09 NA 8 8 8 + ARRLT PCTPTNUM PCTPT PCVOL PCVOLU AVAL AVALCAT1 AVALU RELTMU + + 1 0 24 24H NA "" 0 BLQ ug/mL hr + 2 4 4 0H - 4H 120. "mL" 5.27 5.269 ug/mL hr + 3 8 8 4H - 8H 236. "mL" 0.665 0.665 ug/mL hr + 4 4 4 0H - 4H 97.1 "mL" 6.11 6.106 ug/mL hr + 5 4 4 4H NA "" 6.11 6.106 ug/mL hr + 6 3 3 3H NA "" 9.11 9.113 ug/mL hr + 7 0.5 0.5 0.5H NA "" 15.3 15.3 ug/mL hr + 8 12 12 8H - 12H 528. "mL" 0.005 0.005 ug/mL hr + 9 4 4 0H - 4H 117. "mL" 4.37 4.371 ug/mL hr + 10 8 8 8H NA "" 0.151 0.151 ug/mL hr + PARAM ASMED VISIT VISITDY ANL02FL + + 1 Plasma Drug X PLASMA Day 2 2 Y + 2 Urine Drug X URINE Day 1 1 Y + 3 Urine Drug X URINE Day 1 1 Y + 4 Urine Drug Y URINE Day 1 1 Y + 5 Plasma Drug X PLASMA Day 1 1 Y + 6 Plasma Drug X PLASMA Day 1 1 Y + 7 Plasma Drug X PLASMA Day 1 1 Y + 8 Urine Drug X URINE Day 1 1 Y + 9 Urine Drug X URINE Day 1 1 Y + 10 Plasma Drug X PLASMA Day 1 1 Y # radab produces expected values @@ -4740,62 +4772,62 @@ 24 Treatment unaffected, Neutralizing Antibody EMERPOS2 NA 25 Time to onset of ADA BFLAG2 NA 26 ADA Duration TRUNAFF2 NA - PARCAT1 ADABLPFL ADPBLPFL ABLFL RELTMU NRELTM1 - - 1 A: Drug X Antibody Y day 0 - 2 A: Drug X Antibody day 1 - 3 A: Drug X Antibody Y Y day 0 - 4 A: Drug X Antibody Y day 1 - 5 A: Drug X Antibody Y day 0 - 6 A: Drug X Antibody day 1 - 7 A: Drug X Antibody Y day 0 - 8 A: Drug X Antibody day 1 - 9 A: Drug X Antibody day NA - 10 A: Drug X Antibody day NA - 11 A: Drug X Antibody day NA - 12 A: Drug X Antibody day NA - 13 A: Drug X Antibody day NA - 14 A: Drug X Antibody day NA - 15 A: Drug X Antibody day NA - 16 A: Drug X Antibody day NA - 17 A: Drug X Antibody day NA - 18 A: Drug X Neutralizing Antibody day NA - 19 A: Drug X Neutralizing Antibody day NA - 20 A: Drug X Neutralizing Antibody day NA - 21 A: Drug X Neutralizing Antibody day NA - 22 A: Drug X Neutralizing Antibody day NA - 23 A: Drug X Antibody day NA - 24 A: Drug X Neutralizing Antibody day NA - 25 A: Drug X Antibody day NA - 26 A: Drug X Antibody day NA - ARELTM1 NRELTM2 ARELTM2 - - 1 0 0 0 - 2 1 0 0 - 3 0 0 0 - 4 1 0 0 - 5 0 0 0 - 6 1 0 0 - 7 0 0 0 - 8 1 0 0 - 9 NA NA NA - 10 NA NA NA - 11 NA NA NA - 12 NA NA NA - 13 NA NA NA - 14 NA NA NA - 15 NA NA NA - 16 NA NA NA - 17 NA NA NA - 18 NA NA NA - 19 NA NA NA - 20 NA NA NA - 21 NA NA NA - 22 NA NA NA - 23 NA NA NA - 24 NA NA NA - 25 NA NA NA - 26 NA NA NA + PARCAT1 ADABLPFL ADPBLPFL ABLFL RELTMU NFRLT AFRLT + + 1 A: Drug X Antibody Y day 0 0 + 2 A: Drug X Antibody day 1 1 + 3 A: Drug X Antibody Y Y day 0 0 + 4 A: Drug X Antibody Y day 1 1 + 5 A: Drug X Antibody Y day 0 0 + 6 A: Drug X Antibody day 1 1 + 7 A: Drug X Antibody Y day 0 0 + 8 A: Drug X Antibody day 1 1 + 9 A: Drug X Antibody day NA NA + 10 A: Drug X Antibody day NA NA + 11 A: Drug X Antibody day NA NA + 12 A: Drug X Antibody day NA NA + 13 A: Drug X Antibody day NA NA + 14 A: Drug X Antibody day NA NA + 15 A: Drug X Antibody day NA NA + 16 A: Drug X Antibody day NA NA + 17 A: Drug X Antibody day NA NA + 18 A: Drug X Neutralizing Antibody day NA NA + 19 A: Drug X Neutralizing Antibody day NA NA + 20 A: Drug X Neutralizing Antibody day NA NA + 21 A: Drug X Neutralizing Antibody day NA NA + 22 A: Drug X Neutralizing Antibody day NA NA + 23 A: Drug X Antibody day NA NA + 24 A: Drug X Neutralizing Antibody day NA NA + 25 A: Drug X Antibody day NA NA + 26 A: Drug X Antibody day NA NA + NRRLT ARRLT + + 1 0 0 + 2 0 0 + 3 0 0 + 4 0 0 + 5 0 0 + 6 0 0 + 7 0 0 + 8 0 0 + 9 NA NA + 10 NA NA + 11 NA NA + 12 NA NA + 13 NA NA + 14 NA NA + 15 NA NA + 16 NA NA + 17 NA NA + 18 NA NA + 19 NA NA + 20 NA NA + 21 NA NA + 22 NA NA + 23 NA NA + 24 NA NA + 25 NA NA + 26 NA NA --- @@ -4839,18 +4871,18 @@ 8 PERSADA1 NA A: Drug X Antibody 9 EMERNEG1 NA A: Drug X Antibody 10 ADASTAT1 NA A: Drug X Antibody - ABLFL RELTMU NRELTM1 ARELTM1 NRELTM2 ARELTM2 - - 1 day NA NA NA NA - 2 day 1 1 0 0 - 3 day NA NA NA NA - 4 day 1 1 0 0 - 5 day NA NA NA NA - 6 Y day 0 0 0 0 - 7 day NA NA NA NA - 8 day NA NA NA NA - 9 day NA NA NA NA - 10 day NA NA NA NA + ABLFL RELTMU NFRLT AFRLT NRRLT ARRLT + + 1 day NA NA NA NA + 2 day 1 1 0 0 + 3 day NA NA NA NA + 4 day 1 1 0 0 + 5 day NA NA NA NA + 6 Y day 0 0 0 0 + 7 day NA NA NA NA + 8 day NA NA NA NA + 9 day NA NA NA NA + 10 day NA NA NA NA # radpp produces expected values @@ -9207,14 +9239,14 @@ 8 Overall Response by Investigator - by visit OVRINV 3 SD ADTM ADY AVISIT AVISITN - 1 2021-10-12 20:00:00 269 CYCLE 2 DAY 1 2 - 2 2021-11-10 19:00:00 298 END OF INDUCTION 999 - 3 2020-10-08 20:00:00 -100 SCREENING -1 - 4 2021-01-16 19:00:00 0 BASELINE 0 - 5 2021-10-12 20:00:00 269 CYCLE 2 DAY 1 2 - 6 2021-12-11 19:00:00 329 CYCLE 4 DAY 1 4 - 7 2021-11-10 19:00:00 298 END OF INDUCTION 999 - 8 2022-05-01 20:00:00 470 FOLLOW UP 999 + 1 2021-10-13 00:00:00 269 CYCLE 2 DAY 1 2 + 2 2021-11-11 00:00:00 298 END OF INDUCTION 999 + 3 2020-10-09 00:00:00 -100 SCREENING -1 + 4 2021-01-17 00:00:00 0 BASELINE 0 + 5 2021-10-13 00:00:00 269 CYCLE 2 DAY 1 2 + 6 2021-12-12 00:00:00 329 CYCLE 4 DAY 1 4 + 7 2021-11-11 00:00:00 298 END OF INDUCTION 999 + 8 2022-05-02 00:00:00 470 FOLLOW UP 999 --- @@ -9368,16 +9400,16 @@ 10 Overall Response by Investigator - by visit OVRINV 3 SD ADTM ADY AVISIT AVISITN - 1 2021-04-27 20:00:00 361 CYCLE 2 DAY 1 2 - 2 2021-06-20 20:00:00 613 CYCLE 2 DAY 1 2 - 3 2021-07-08 20:00:00 377 END OF INDUCTION 999 - 4 2021-12-31 19:00:00 491 END OF INDUCTION 999 - 5 2020-08-27 20:00:00 0 BASELINE 0 - 6 2019-06-13 20:00:00 -100 SCREENING -1 - 7 2021-08-31 20:00:00 888 END OF INDUCTION 999 - 8 2020-12-14 19:00:00 329 END OF INDUCTION 999 - 9 2021-10-12 20:00:00 269 CYCLE 2 DAY 1 2 - 10 2020-03-18 20:00:00 -100 SCREENING -1 + 1 2021-04-28 00:00:00 361 CYCLE 2 DAY 1 2 + 2 2021-06-21 00:00:00 613 CYCLE 2 DAY 1 2 + 3 2021-07-09 00:00:00 377 END OF INDUCTION 999 + 4 2022-01-01 00:00:00 491 END OF INDUCTION 999 + 5 2020-08-28 00:00:00 0 BASELINE 0 + 6 2019-06-14 00:00:00 -100 SCREENING -1 + 7 2021-09-01 00:00:00 888 END OF INDUCTION 999 + 8 2020-12-15 00:00:00 329 END OF INDUCTION 999 + 9 2021-10-13 00:00:00 269 CYCLE 2 DAY 1 2 + 10 2020-03-19 00:00:00 -100 SCREENING -1 # radsaftte produces expected values @@ -9782,11 +9814,11 @@ 5 2024-02-10 NA Baseline Biomarker Mutation BBMRKR1 1 WILD TYPE AVALU AVALCAT1 ADTM AVISIT AVISITN SRCSEQ - 1 "kg" "" 2021-01-07 19:00:00 BASELINE 0 1 - 2 "m" "" 2021-01-07 19:00:00 BASELINE 0 1 - 3 "kg/m2" ">30" 2021-01-07 19:00:00 BASELINE 0 1 - 4 "" "4-5" 2021-01-07 19:00:00 BASELINE 0 1 - 5 "" "" 2021-01-07 19:00:00 BASELINE 0 1 + 1 "kg" "" 2021-01-08 00:00:00 BASELINE 0 1 + 2 "m" "" 2021-01-08 00:00:00 BASELINE 0 1 + 3 "kg/m2" ">30" 2021-01-08 00:00:00 BASELINE 0 1 + 4 "" "4-5" 2021-01-08 00:00:00 BASELINE 0 1 + 5 "" "" 2021-01-08 00:00:00 BASELINE 0 1 --- @@ -9928,16 +9960,16 @@ 10 Baseline ECOG BECOG 0 0 "" "0-1" ADTM AVISIT AVISITN SRCSEQ - 1 2019-09-19 20:00:00 BASELINE 0 1 - 2 2020-10-24 20:00:00 BASELINE 0 1 - 3 2019-03-25 20:00:00 BASELINE 0 1 - 4 2019-09-19 20:00:00 BASELINE 0 1 - 5 2020-08-24 20:00:00 BASELINE 0 1 - 6 2020-02-24 19:00:00 BASELINE 0 1 - 7 2020-01-16 19:00:00 BASELINE 0 1 - 8 2020-08-24 20:00:00 BASELINE 0 1 - 9 2019-03-25 20:00:00 BASELINE 0 1 - 10 2020-02-24 19:00:00 BASELINE 0 1 + 1 2019-09-20 00:00:00 BASELINE 0 1 + 2 2020-10-25 00:00:00 BASELINE 0 1 + 3 2019-03-26 00:00:00 BASELINE 0 1 + 4 2019-09-20 00:00:00 BASELINE 0 1 + 5 2020-08-25 00:00:00 BASELINE 0 1 + 6 2020-02-25 00:00:00 BASELINE 0 1 + 7 2020-01-17 00:00:00 BASELINE 0 1 + 8 2020-08-25 00:00:00 BASELINE 0 1 + 9 2019-03-26 00:00:00 BASELINE 0 1 + 10 2020-02-25 00:00:00 BASELINE 0 1 # radtr produces expected values @@ -10032,22 +10064,22 @@ 5 Sum of Longest Diameter by Investigator SLDINV CYCLE 2 DAY 1 2 6 Sum of Longest Diameter by Investigator SLDINV CYCLE 4 DAY 1 4 7 Sum of Longest Diameter by Investigator SLDINV END OF INDUCTION 999 - ADTM ADY DTYPE AVAL AVALC AVALU BASE - 1 2022-05-01 20:00:00 470 145.9484 145.948361883575 mm 209.412 - 2 2021-12-11 19:00:00 329 MINIMUM 118.6760 118.675961210504 mm 209.412 - 3 2020-10-08 20:00:00 -100 192.9907 192.990711051031 mm 209.412 - 4 2021-01-16 19:00:00 0 NA mm 209.412 - 5 2021-10-12 20:00:00 269 138.9834 138.983355706005 mm 209.412 - 6 2021-12-11 19:00:00 329 118.6760 118.675961210504 mm 209.412 - 7 2021-11-10 19:00:00 298 167.0916 167.091588823272 mm 209.412 - ABLFL CHG PCHG ONTRTFL ANL01FL ANL02FL ANL03FL - 1 -63.46364 -30.30563 Y Y - 2 -90.73604 -43.32896 Y Y - 3 NA NA - 4 Y NA NA Y Y - 5 -70.42864 -33.63162 Y Y - 6 -90.73604 -43.32896 Y Y - 7 -42.32041 -20.20916 Y Y + ADTM ADY DTYPE AVAL AVALC AVALU BASE ABLFL + 1 2022-05-02 470 145.9484 145.948361883575 mm 209.412 + 2 2021-12-12 329 MINIMUM 118.6760 118.675961210504 mm 209.412 + 3 2020-10-09 -100 192.9907 192.990711051031 mm 209.412 + 4 2021-01-17 0 NA mm 209.412 Y + 5 2021-10-13 269 138.9834 138.983355706005 mm 209.412 + 6 2021-12-12 329 118.6760 118.675961210504 mm 209.412 + 7 2021-11-11 298 167.0916 167.091588823272 mm 209.412 + CHG PCHG ONTRTFL ANL01FL ANL02FL ANL03FL + 1 -63.46364 -30.30563 Y Y + 2 -90.73604 -43.32896 Y Y + 3 NA NA + 4 NA NA Y Y + 5 -70.42864 -33.63162 Y Y + 6 -90.73604 -43.32896 Y Y + 7 -42.32041 -20.20916 Y Y --- @@ -10186,28 +10218,28 @@ 2 Sum of Longest Diameter by Investigator SLDINV POST-BASELINE MINIMUM 1 Sum of Longest Diameter by Investigator SLDINV FOLLOW UP 3 Sum of Longest Diameter by Investigator SLDINV SCREENING - AVISITN ADTM ADY DTYPE AVAL AVALC AVALU - 32 999 2021-08-31 20:00:00 888 104.2930 104.292995987107 mm - 39 0 2020-06-26 20:00:00 0 NA mm - 37 999 2021-07-08 20:00:00 377 158.0130 158.012963723167 mm - 12 0 2020-01-20 19:00:00 0 NA mm - 14 -1 2019-10-12 20:00:00 -100 222.0485 222.048532815143 mm - 16 999 2021-02-14 19:00:00 289 MINIMUM 128.7016 128.701607072346 mm - 15 4 2021-06-26 20:00:00 421 215.1784 215.178350110865 mm - 2 4 2021-12-11 19:00:00 329 MINIMUM 118.6760 118.675961210504 mm - 1 999 2022-05-01 20:00:00 470 145.9484 145.948361883575 mm - 3 -1 2020-10-08 20:00:00 -100 192.9907 192.990711051031 mm - BASE ABLFL CHG PCHG ONTRTFL ANL01FL ANL02FL ANL03FL - 32 132.3144 -28.021376 -21.177878 Y Y Y - 39 159.9885 Y NA NA Y Y - 37 159.9885 -1.975547 -1.234806 Y Y Y - 12 148.8228 Y NA NA Y Y - 14 148.8228 NA NA - 16 193.9666 -65.265039 -33.647558 Y Y - 15 193.9666 21.211704 10.935748 Y Y Y - 2 209.4120 -90.736036 -43.328958 Y Y - 1 209.4120 -63.463635 -30.305635 Y Y - 3 209.4120 NA NA + AVISITN ADTM ADY DTYPE AVAL AVALC AVALU BASE + 32 999 2021-09-01 888 104.2930 104.292995987107 mm 132.3144 + 39 0 2020-06-27 0 NA mm 159.9885 + 37 999 2021-07-09 377 158.0130 158.012963723167 mm 159.9885 + 12 0 2020-01-21 0 NA mm 148.8228 + 14 -1 2019-10-13 -100 222.0485 222.048532815143 mm 148.8228 + 16 999 2021-02-15 289 MINIMUM 128.7016 128.701607072346 mm 193.9666 + 15 4 2021-06-27 421 215.1784 215.178350110865 mm 193.9666 + 2 4 2021-12-12 329 MINIMUM 118.6760 118.675961210504 mm 209.4120 + 1 999 2022-05-02 470 145.9484 145.948361883575 mm 209.4120 + 3 -1 2020-10-09 -100 192.9907 192.990711051031 mm 209.4120 + ABLFL CHG PCHG ONTRTFL ANL01FL ANL02FL ANL03FL + 32 -28.021376 -21.177878 Y Y Y + 39 Y NA NA Y Y + 37 -1.975547 -1.234806 Y Y Y + 12 Y NA NA Y Y + 14 NA NA + 16 -65.265039 -33.647558 Y Y + 15 21.211704 10.935748 Y Y Y + 2 -90.736036 -43.328958 Y Y + 1 -63.463635 -30.305635 Y Y + 3 NA NA # radtte produces expected values diff --git a/vignettes/rebuild_cached_data.Rmd b/vignettes/rebuild_cached_data.Rmd index 9653f2ae..0f8ebb4c 100644 --- a/vignettes/rebuild_cached_data.Rmd +++ b/vignettes/rebuild_cached_data.Rmd @@ -58,8 +58,6 @@ cadtr_new <- radtr(cadsl_new, seed = 1, na_vars = list()) %>% `attr<-`("creation caddv_new <- raddv(cadsl_new, seed = 1, na_vars = list()) %>% `attr<-`("creation date", Sys.Date()) cadsub_new <- radsub(cadsl_new, seed = 1, na_vars = list()) %>% `attr<-`("creation date", Sys.Date()) cadhy_new <- radhy(cadsl_new, seed = 1) %>% `attr<-`("creation date", Sys.Date()) - -load(system.file("R", "sysdata.rda", package = "random.cdisc.data")) cadqlqc_new <- radqlqc(cadsl_new, percent = 80, number = 2, seed = 1) %>% `attr<-`("creation date", Sys.Date()) # use diffdf package: diffdf() to compare cached vs new and review/verify differences