lsting <-as_listing( out,key_cols ="USUBJID",disp_cols =names(out),main_title =paste0("Listing of Anti-", drugcd, " Antibody Data for Treatment Emergent ADA Positive Patients, PK Population","\nProtocol: ", unique(adab$PARCAT1)[1] ),subtitles =paste("\nTreatment Group:", trt),main_footer ="Minimum reportable titer = 1.10 (example only)--- = No sample evaluatedADA = Anti-Drug Antibodies (is also referred to as ATA, or Anti-Therapeutic Antibodies)Number of patients positive for Treatment Emergent ADA = the number of post-baseline evaluable patients determined to have treatment-induced ADA or treatment-enhanced ADA during the study period.Treatment-induced ADA = a patient with negative or missing baseline ADA result(s) and at least one positive post-baseline ADA result.Treatment-enhanced ADA = a patient with positive ADA result at baseline who has one or more post-baseline titer results that are at least 0.60 t.u. greater than the baseline titer result.Transient ADA = ADA positive result detected (a) at only one post-baseline sampling timepoint (excluding last timepoint) OR (b) at 2 or more timepoints during treatment where the first and last ADA positive samples are separated by a period of < 16 weeks, irrespective of any negative samples in between.Persistent ADA = ADA positive result detected (a) at the last post-baseline sampling timepoint, OR (b) at 2 or more time points during treatment where the first and last ADA positive samples are separated by a period ≥ 16 weeks, irrespective of any negative samples in between.Asterisk denotes sample that tested positive for Neutralizing Antibodies.")head(lsting, 20)
Listing of Anti-R1800000 Antibody Data for Treatment Emergent ADA Positive Patients, PK Population
Protocol: A: Drug X Antibody
Treatment Group: A: Drug X
—————————————————————————————————————————————————————
Day 2 Patient Treatment
Subject ID (Day 1) Emergent ADA Status
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AB12345-BRA-1-id-105 --- Enhanced
AB12345-BRA-1-id-134 --- Enhanced
AB12345-BRA-1-id-42 --- Enhanced
AB12345-BRA-1-id-93 --- Enhanced
AB12345-BRA-11-id-217 --- Enhanced
AB12345-BRA-11-id-345 --- Enhanced
AB12345-BRA-11-id-397 --- Enhanced
AB12345-BRA-11-id-50 --- Enhanced
AB12345-BRA-13-id-177 --- Enhanced
AB12345-BRA-14-id-23 --- Enhanced
AB12345-BRA-15-id-36 --- Enhanced
AB12345-BRA-2-id-296 --- Enhanced
AB12345-BRA-6-id-369 --- Enhanced
AB12345-CAN-1-id-18 --- Enhanced
AB12345-CAN-11-id-139 --- Enhanced
AB12345-CAN-14-id-104 --- Enhanced
AB12345-CHN-1-id-119 --- Enhanced
AB12345-CHN-1-id-123 --- Enhanced
AB12345-CHN-1-id-133 --- Enhanced
AB12345-CHN-1-id-199 --- Enhanced
—————————————————————————————————————————————————————
Minimum reportable titer = 1.10 (example only)
--- = No sample evaluated
ADA = Anti-Drug Antibodies (is also referred to as ATA, or Anti-Therapeutic Antibodies)
Number of patients positive for Treatment Emergent ADA = the number of post-baseline evaluable patients determined to have treatment-induced ADA or treatment-enhanced ADA during the study period.
Treatment-induced ADA = a patient with negative or missing baseline ADA result(s) and at least one positive post-baseline ADA result.
Treatment-enhanced ADA = a patient with positive ADA result at baseline who has one or more post-baseline titer results that are at least 0.60 t.u. greater than the baseline titer result.
Transient ADA = ADA positive result detected (a) at only one post-baseline sampling timepoint (excluding last timepoint) OR (b) at 2 or more timepoints during treatment where the first and last ADA positive samples are separated by a period of < 16 weeks, irrespective of any negative samples in between.
Persistent ADA = ADA positive result detected (a) at the last post-baseline sampling timepoint, OR (b) at 2 or more time points during treatment where the first and last ADA positive samples are separated by a period ≥ 16 weeks, irrespective of any negative samples in between.
Asterisk denotes sample that tested positive for Neutralizing Antibodies.
Experimental use!
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---title: ADAL02subtitle: Listing of Anti-Drug Antibody Data for Treatment Emergent ADA Positive Patients---------------------------------------------------------------------------{{< include ../../_utils/envir_hook.qmd >}}```{r setup, echo = FALSE, warning = FALSE, message = FALSE}library(dplyr)library(rlistings)adab <- random.cdisc.data::cadab %>% filter(NFRLT %% 1 == 0 & NFRLT > 0)trt <- "A: Drug X"drug_a <- "A: Drug X Antibody"drugcd <- unique(adab$PARAMCD[adab$PARAM == "Antibody titer units"])[1]min_titer <- 1.10adab_x <- adab %>% filter( ARM == trt, PARCAT1 == drug_a, ADPBLPFL == "Y" ) %>% select(-PARAMCD, -AVALC, -AVALU, -ARRLT, -NRRLT) %>% unique() %>% tidyr::pivot_wider( names_from = PARAM, values_from = AVAL ) %>% filter(if_any(matches("Treatment Emergent - Positive"), ~ .x == 1)) %>% # filter(`Treatment Emergent - Positive` == 1) %>% mutate( VISN = factor(paste0( VISIT, "\n(Day ", ifelse( NFRLT %% 1 == 0, NFRLT, as.character(format(round(NFRLT, 2), nsmall = 2)) ), ")" )), PTES = ifelse( ifelse("Treatment induced ADA" %in% names(.), `Treatment induced ADA` == 1, FALSE), ifelse( "Transient ADA" %in% names(.) & `Transient ADA` == 1, "Induced (Transient)", "Induced (Persistent)" ), "Enhanced" ) ) %>% mutate( AVAL = paste0( ifelse( ifelse("ADA interpreted per sample result" %in% names(.), `ADA interpreted per sample result` == 0, FALSE), "NEGATIVE", ifelse( ifelse("Antibody titer units" %in% names(.), !is.na(`Antibody titer units`), FALSE), ifelse( `Antibody titer units` < min_titer, paste0("<", format(min_titer, nsmall = 2)), as.character(format(round(`Antibody titer units`, 2), nsmall = 2)) ), "---" ) ), ifelse( ifelse("NAB interpreted per sample result" %in% names(.), `NAB interpreted per sample result` == 1, FALSE), "*", "" ) ) )out <- adab_x %>% select(USUBJID, VISN, AVAL, PTES) %>% tidyr::pivot_wider( names_from = VISN, values_from = AVAL ) %>% select(USUBJID, unique(adab_x$VISN[order(adab_x$NFRLT)]), PTES)var_labels(out) <- names(out)out <- out %>% var_relabel( USUBJID = "Subject ID", PTES = "Patient Treatment\nEmergent ADA Status" )``````{r include = FALSE}webr_code_labels <- c("setup")```{{< include ../../_utils/webr_no_include.qmd >}}## Output:::: panel-tabset## Standard Listing::: {.panel-tabset .nav-justified group="webr"}## {{< fa regular file-lines sm fw >}} Preview```{r lsting, test = list(lsting = "lsting")}lsting <- as_listing( out, key_cols = "USUBJID", disp_cols = names(out), main_title = paste0( "Listing of Anti-", drugcd, " Antibody Data for Treatment Emergent ADA Positive Patients, PK Population", "\nProtocol: ", unique(adab$PARCAT1)[1] ), subtitles = paste("\nTreatment Group:", trt), # nolint start: line_length. main_footer = "Minimum reportable titer = 1.10 (example only)--- = No sample evaluatedADA = Anti-Drug Antibodies (is also referred to as ATA, or Anti-Therapeutic Antibodies)Number of patients positive for Treatment Emergent ADA = the number of post-baseline evaluable patients determined to have treatment-induced ADA or treatment-enhanced ADA during the study period.Treatment-induced ADA = a patient with negative or missing baseline ADA result(s) and at least one positive post-baseline ADA result.Treatment-enhanced ADA = a patient with positive ADA result at baseline who has one or more post-baseline titer results that are at least 0.60 t.u. greater than the baseline titer result.Transient ADA = ADA positive result detected (a) at only one post-baseline sampling timepoint (excluding last timepoint) OR (b) at 2 or more timepoints during treatment where the first and last ADA positive samples are separated by a period of < 16 weeks, irrespective of any negative samples in between.Persistent ADA = ADA positive result detected (a) at the last post-baseline sampling timepoint, OR (b) at 2 or more time points during treatment where the first and last ADA positive samples are separated by a period ≥ 16 weeks, irrespective of any negative samples in between.Asterisk denotes sample that tested positive for Neutralizing Antibodies." # nolint end: line_length.)head(lsting, 20)``````{r include = FALSE}webr_code_labels <- c("lsting")```{{< include ../../_utils/webr.qmd >}}:::## Data Setup```{r setup}#| code-fold: show```::::{{< include ../../_utils/save_results.qmd >}}{{< include ../../repro.qmd >}}