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Closes #17 New anti-cancer start date vignette draft 1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,220 @@ | ||
| --- | ||
| title: "Creating and Using New Anti-Cancer Start Date" | ||
| output: | ||
| rmarkdown::html_vignette | ||
| vignette: > | ||
| %\VignetteIndexEntry{Creating and Using New Anti-Cancer Start Date} | ||
| %\VignetteEngine{knitr::rmarkdown} | ||
| %\VignetteEncoding{UTF-8} | ||
| --- | ||
|
|
||
| ```{r, include = FALSE} | ||
| knitr::opts_chunk$set( | ||
| collapse = TRUE, | ||
| comment = "#>" | ||
| ) | ||
| library(admiralonco) | ||
| link <- function(text, url) { | ||
| return( | ||
| paste0( | ||
| "[", text, "]", | ||
| "(", url, ")" | ||
| ) | ||
| ) | ||
| } | ||
| dyn_link <- function(text, | ||
| base_url, | ||
| relative_url = "", | ||
| # Change to TRUE when admiral adopts multiversion docs | ||
| is_multiversion = FALSE, | ||
| multiversion_default_ref = "main") { | ||
| url <- paste(base_url, relative_url, sep = "/") | ||
| if (is_multiversion) { | ||
| url <- paste( | ||
| base_url, | ||
| Sys.getenv("BRANCH_NAME", multiversion_default_ref), | ||
| relative_url, | ||
| sep = "/" | ||
| ) | ||
| } | ||
| return(link(text, url)) | ||
| } | ||
| # Other variables | ||
| admiral_homepage <- "https://pharmaverse.github.io/admiral/cran-release" | ||
| library(admiraldev) | ||
| ``` | ||
|
|
||
| # Introduction | ||
|
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| In Oncology trials, for censoring the patients for any time-to-event analysis (e.g., progression free survival analysis, duration of response, etc.), it is necessary to check if the patients have started any new anti-cancer therapy. Anti-cancer therapy generally includes radiation therapy, cancer related surgery and any systemic anti-cancer therapy such as chemotherapy, t-cell therapy, etc. | ||
| These therapies can be collected on a prior or on-treatment CRF pages, with radiation and surgery being mapped to the SDTM PR domain and systemic anti-cancer therapy being mapped to the SDTM CM domain. Collection and mapping may vary with each company and it is important that only on-treatment therapies are considered for the censoring of time-to-event. Generally, if the patients start a new anti-cancer therapy that were on-treatment, they should be discontinued from the study treatment and no further efficacy assessments should be performed. | ||
|
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| This article describes a process for creating a new anti-cancer start date from a single and multiple source SDTMs. | ||
|
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||
| # Programming Workflow | ||
|
|
||
| - [Read in Data and create test data](#readdata) | ||
| - [Single Source](#input) | ||
| - [Multiple Sources - Prerequisite Step](#multiinput) | ||
| - [Multiple Sources - Derive New Anti-Cancer Start Date and Merge with `ADSL`](#nactdt) | ||
| - [Using the New Anti-Cancer Therapy Date](#unactdt) | ||
| - [Derive Date Parameter](#par) | ||
|
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||
| ## Read in Data {#readdata} | ||
|
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| To start, all data frames needed for the creation of the new anti-cancer therapy start date (`NACTDT`) should be read into the environment. This will be a company specific process. Some of the data frames needed may be `CM` and `PR`. | ||
|
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| For example purpose, `CM` and `PR` has been generated (based on CDISC Pilot test data), with oncology specific test data. | ||
|
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||
| ```{r, warning=FALSE, message=FALSE} | ||
| library(admiral) | ||
| library(dplyr) | ||
| library(admiral.test) | ||
| adsl <- admiral_adsl | ||
| cm <- tribble( | ||
| ~STUDYID, ~USUBJID, ~CMCAT, ~CMSCAT, ~CMTRT, ~CMSTDTC, | ||
| "CDISCPILOT01", "01-701-1015", "PRIOR TREATMENT", "CHEMOTHERAPY", "DEXRAZOXANE", NA, | ||
| "CDISCPILOT01", "01-701-1015", "ON TREATMENT", "CHEMOTHERAPY", "DEXROZOXANE", "2014-07-02", | ||
| "CDISCPILOT01", "01-701-1015", "ON TREATMENT", "CHEMOTHERAPY", "DEXROZOXANE", "2014-06-19", | ||
| "CDISCPILOT01", "01-701-1028", "PRIOR TREATMENT", "CHEMOTHERAPY", "METHOTREXATE", NA, | ||
| "CDISCPILOT01", "01-701-1028", "ON TREATMENT", "CHEMOTHERAPY", "METHOTREXATE", "2014-01-14", | ||
| "CDISCPILOT01", "01-701-1034", "PRIOR TREATMENT", "CHEMOTHERAPY", "OLAPARIB", NA, | ||
| "CDISCPILOT01", "01-701-1034", "ON TREATMENT", "CHEMOTHERAPY", "OLAPARIB", "2014-12-30", | ||
| "CDISCPILOT01", "01-701-1097", "PRIOR TREATMENT", "CHEMOTHERAPY", "TEMODAL", NA, | ||
| "CDISCPILOT01", "01-701-1097", "ON TREATMENT", "CHEMOTHERAPY", "TEMODAL", "2013-12-31", | ||
| ) | ||
| pr <- tribble( | ||
| ~STUDYID, ~USUBJID, ~PRCAT, ~PRSCAT, ~PRTRT, ~PRSTDTC, | ||
| "CDISCPILOT01", "01-701-1015", "CANCER RELATED", "ON TREATMENT", "SURGERY", "2014-06-18", | ||
| "CDISCPILOT01", "01-701-1034", "CANCER RELATED", "ON TREATMENT", "SURGERY", "2014-12-16", | ||
| "CDISCPILOT01", "01-701-1028", "CANCER RELATED", "PRIOR TREATMENT", "SURGERY", NA, | ||
| ) | ||
| ``` | ||
|
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| ## Single Source{#input} | ||
|
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| To derive the New Anti-Cancer Therapy start date with data from a single source, the function `admiral::derive_vars_merged()` can be used. If numeric date is required, `admiral::convert_dtc_to_dt` , or if time part is needed, `admiral::convert_dtc_to_dtm()` can be used as part of an expression for the `new_vars` argument. | ||
|
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||
| ```{r message=FALSE} | ||
| adsl <- derive_vars_merged( | ||
| admiral_adsl, | ||
| dataset_add = cm, | ||
| by_vars = exprs(STUDYID, USUBJID), | ||
| order = exprs(NACTDT), | ||
| mode = "first", | ||
| new_vars = exprs(NACTDT = convert_dtc_to_dt(CMSTDTC)), | ||
| filter_add = CMSCAT == "CHEMOTHERAPY" & CMCAT == "ON TREATMENT" | ||
| ) | ||
| ``` | ||
|
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| ```{r, eval=TRUE, echo=FALSE} | ||
| dataset_vignette( | ||
| adsl, | ||
| display_vars = exprs(USUBJID, NACTDT), | ||
| filter = !is.na(NACTDT) | ||
| ) | ||
| ``` | ||
|
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| ## Multiple Sources - Prerequisite Steps {#multiinput} | ||
|
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| To derive the New Anti-Cancer Therapy start date with data from multiple sources, the function `admiral::derive_var_extreme_dt()` can be used, or if time part is needed, `admiral::derive_var_extreme_dtm()` can be used. | ||
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|
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| ### Prerequisite | ||
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| Prior to calling the function, an input `date_source` object must be created for each source dataset using `admiral::date_source()`. Within this function, any company-specific subsetting can be passed to the `filter` argument. If numeric version of the dates will be needed, `admiral::convert_dtc_to_dt()`, or if time part is needed, `admiral::convert_dtc_to_dtm()` can be used as part of an expression for the `new_vars` argument. | ||
|
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| ```{r message=FALSE} | ||
| cm_date <- date_source( | ||
| dataset_name = "cm", | ||
| filter = CMSCAT == "CHEMOTHERAPY" & CMCAT == "ON TREATMENT" & !is.na(CMSTDTC), | ||
| date = convert_dtc_to_dt(CMSTDTC) | ||
| ) | ||
| pr_date <- date_source( | ||
| dataset_name = "pr", | ||
| filter = PRCAT == "CANCER RELATED" & PRSCAT == "ON TREATMENT" & !is.na(PRSTDTC), | ||
| date = convert_dtc_to_dt(PRSTDTC) | ||
| ) | ||
| ``` | ||
|
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| ## Multiple Sources - Derive New Anti-Cancer Start Date and Merge with `ADSL` {#nactdt} | ||
|
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| After completion of the prerequisite step, the new anti-cancer date can be derived while simultaneously adding it to `ADSL`. | ||
|
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| ```{r message=FALSE} | ||
| adsl <- admiral_adsl %>% | ||
| derive_var_extreme_dt( | ||
| new_var = NACTDT, | ||
| cm_date, pr_date, | ||
| source_datasets = list( | ||
| cm = cm, | ||
| pr = pr | ||
| ), | ||
| mode = "first" | ||
| ) | ||
| ``` | ||
|
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||
| ```{r, eval=TRUE, echo=FALSE} | ||
| dataset_vignette( | ||
| adsl, | ||
| display_vars = exprs(USUBJID, NACTDT), | ||
| filter = !is.na(NACTDT) | ||
| ) | ||
| ``` | ||
|
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| ## Using the New Anti-Cancer Therapy Date {#unactdt} | ||
|
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| Please refer to `{admiralonco}` [Derive `ANL01FL`](adrs.html#anl01fl) for an example on the usage of `NACTDT`. Additionally, `{admiralonco}` [Creating Your Own Time-to-Event Source Objects](adtte.html#tteobj) may be referenced for case usage. | ||
|
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| ## Derive Date Parameter {#par} | ||
|
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| As of `{admiral}` version 0.11.0, `admiral::derive_param_extreme_record()` is recommended to be used for deriving parameter based on the first or last observation from single and multiple sources. | ||
|
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| Based on individual company standards, this parameter may be added to an event or date dataset such as `ADEVENT` or `ADDATES`, which are generally intermediate datasets to `ADTTE`. For demonstration purpose, a new anti-cancer date parameter will be merged into `ADRS`. A list of `record_source()` objects is expected and this will contain the sources of the dates and any company specific filtering. | ||
|
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||
| ```{r, eval=TRUE, echo=TRUE} | ||
| library(admiralonco) | ||
| adrs <- derive_param_extreme_record( | ||
| dataset = admiral_adrs, | ||
| sources = list( | ||
| records_source( | ||
| dataset_name = "cm", | ||
| filter = CMSCAT == "CHEMOTHERAPY" & CMCAT == "ON TREATMENT" & !is.na(CMSTDTC), | ||
| new_vars = exprs( | ||
| ADT = convert_dtc_to_dt(CMSTDTC), | ||
| AVALC = CMTRT | ||
| ) | ||
| ), | ||
| records_source( | ||
| dataset_name = "pr", | ||
| filter = PRCAT == "CANCER RELATED" & PRSCAT == "ON TREATMENT" & !is.na(PRSTDTC), | ||
| new_vars = exprs( | ||
| ADT = convert_dtc_to_dt(PRSTDTC), | ||
| AVALC = PRTRT | ||
| ) | ||
| ) | ||
| ), | ||
| source_datasets = list(cm = cm, pr = pr), | ||
| by_vars = exprs(STUDYID, USUBJID), | ||
| order = exprs(ADT), | ||
| mode = "first", | ||
| set_values_to = exprs( | ||
| PARAMCD = "NACTDT", | ||
| PARAM = "New Anti-Cancer Therapy Start Date" | ||
| ) | ||
| ) | ||
| ``` | ||
|
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| ```{r, eval=TRUE, echo=FALSE} | ||
| dataset_vignette( | ||
| adrs, | ||
| display_vars = exprs(USUBJID, PARAMCD, PARAM, ADT, AVALC), | ||
| filter = !is.na(ADT) & PARAMCD == "NACTDT" | ||
| ) | ||
| ``` |