Merge pull request #248 from pharmaverse/247_update_adtr@33_recist@devel

Closes #247 update adtr

DESCRIPTION

@@ -44,7 +44,7 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Depends: R (>= 3.5)
 Imports:
-    admiral (>= 0.11.0),
+    admiral (>= 0.12.0),
     admiraldev (>= 0.4.0),
     dplyr (>= 0.8.4),
     lifecycle (>= 0.1.0),
@@ -54,7 +54,6 @@ Imports:
     tidyselect (>= 1.0.0)
 Suggests:
     pharmaversesdtm,
-    admiral.test,
     devtools,
     diffdf,
     lintr,

NEWS.md

@@ -17,6 +17,12 @@
     RECIST 1.1, e.g., iRECIST or International Myeloma Working Group (IMWG)
     criteria for the diagnosis of multiple myeloma.
 
+- The `ADRS` vignette and template were updated such that test data from
+`{pharmaversesdtm}` instead of `{admiral.test}` is used. (#226)
+
+- The "Create `ADTR`" vignette and the `ADTR` template were updated such that
+test data from `{pharmaversesdtm}` instead of `{admiral.test}` is used. (#247)
+
 - The confirmed response derivation was fixed in the basic `ADRS` vignette and
 template. When calling `derive_param_confirmed_resp()` the `filter_source`
 argument has to be set to `PARAMCD == "OVR" & ANL01FL == "Y"` instead of

inst/templates/ad_adtr.R

@@ -5,7 +5,7 @@
 # Input: adsl, rs, tr, tu
 library(admiral)
 library(admiralonco)
-library(admiral.test) # Contains example datasets from the CDISC pilot project
+library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project
 library(dplyr)
 library(lubridate)
 library(stringr)
@@ -14,16 +14,15 @@ library(stringr)
 
 # Use e.g. haven::read_sas to read in .sas7bdat, or other suitable functions
 # as needed and assign to the variables below.
-# For illustration purposes read in admiral test data
+# For illustration purposes read in pharmaverse test data
 data("admiral_adsl")
-data("admiral_rs")
-data("admiral_tu")
-data("admiral_tr")
+data("rs_onco_recist")
+data("tu_onco_recist")
+data("tr_onco_recist")
 adsl <- admiral_adsl
-adrs <- admiral_adrs
-tu <- admiral_tu
-tr <- admiral_tr
-rs <- admiral_rs
+tu <- tu_onco_recist
+tr <- tr_onco_recist
+rs <- rs_onco_recist
 
 tu <- convert_blanks_to_na(tu) %>%
   filter(TUEVAL == "INVESTIGATOR")
@@ -77,8 +76,16 @@ tr <- derive_vars_dt(
     source_vars = exprs(ADT)
   ) %>%
   mutate(
-    AVISIT = VISIT,
-    AVISITN = VISITNUM
+    AVISIT = if_else(
+      VISIT == "SCREENING",
+      "BASELINE",
+      VISIT
+    ),
+    AVISITN = if_else(
+      AVISIT == "BASELINE",
+      0,
+      VISITNUM
+    )
   )
 
 # Derive parameters for lesion diameters (LDIAMn & NLDIAMn) ----

inst/templates/ad_adtte.R

@@ -5,7 +5,6 @@
 # Input: adsl, adrs, tte_source objects
 library(admiral)
 library(admiralonco)
-library(admiral.test) # Contains example datasets from the CDISC pilot project
 library(dplyr)
 library(lubridate)
 

staged_dependencies.yaml

@@ -2,8 +2,6 @@
 upstream_repos:
   - repo: pharmaverse/admiral
     host: https://github.com
-  - repo: pharmaverse/admiral.test
-    host: https://github.com
   - repo: pharmaverse/pharmaversesdtm
     host: https://github.com
   - repo: pharmaverse/admiraldev

vignettes/adrs.Rmd

@@ -95,7 +95,7 @@ read into the environment. This will be a company specific process. Some
 of the data frames needed may be `ADSL`, `RS` and `TU`.
 
 For example purpose, the SDTM and ADaM datasets (based on CDISC Pilot
-test data)---which are included in `{admiral.test}`---are used.
+test data)---which are included in `{pharmaversesdtm}`---are used.
 
 ```{r message=FALSE}
 library(admiral)

vignettes/adrs_basic.Rmd

@@ -94,7 +94,7 @@ read into the environment. This will be a company specific process. Some
 of the data frames needed may be `ADSL`, `RS` and `TU`.
 
 For example purpose, the SDTM and ADaM datasets (based on CDISC Pilot
-test data)---which are included in `{admiral.test}`---are used.
+test data)---which are included in `{pharmaversesdtm}`---are used.
 
 ```{r message=FALSE}
 library(admiral)

vignettes/adtr.Rmd

@@ -77,7 +77,7 @@ The examples of this vignette require the following packages.
 ```{r, warning=FALSE, message=FALSE}
 library(admiral)
 library(dplyr)
-library(admiral.test)
+library(pharmaversesdtm)
 library(lubridate)
 library(stringr)
 library(admiralonco)
@@ -104,14 +104,11 @@ To start, all data frames needed for the creation of `ADTR` should be read into
 Some of the data frames needed may be `ADSL`, `ADRS` ,`RS`, `TU`, `TR`, `SUPPTU` `SUPPTR`.
 
 For example purposes, the SDTM and ADaM datasets (based on CDISC Pilot test
-data)---which are included in `{admiral.test}`---are used [^1]. Also, see
+data)---which are included in `{pharmaversesdtm}`---are used. Also, see
 [Handling of Missing
 Values](https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values)
 explains why we need to use the `convert_blanks_to_na()` function.
 
-[^1]: In this vignette we use only data for subjects "01-701-1015",
-"01-701-1023", "01-701-1440". This avoids that the vignette takes a long time to load. 
-
 On the `TR` domain we filter on where tumor assessment short name `TRTESTCD` is
 `"LDIAM"` or `"LPERP"`. Depending on your data collection standards you may need
 to update the code to filter on `TRTESTCD == "DIAMETER"`. If this is the case
@@ -121,14 +118,14 @@ be updated accordingly.
 ```{r}
 data("admiral_adsl")
 data("admiral_adrs")
-data("admiral_rs")
-data("admiral_tu")
-data("admiral_tr")
+data("rs_onco_recist")
+data("tu_onco_recist")
+data("tr_onco_recist")
 adsl <- admiral_adsl
 adrs <- admiral_adrs
-tu <- admiral_tu
-tr <- admiral_tr
-rs <- admiral_rs
+tu <- tu_onco_recist
+tr <- tr_onco_recist
+rs <- rs_onco_recist
 
 tu <- convert_blanks_to_na(tu) %>%
   filter(TUEVAL == "INVESTIGATOR")
@@ -139,16 +136,6 @@ tr <- convert_blanks_to_na(tr) %>%
 rs <- convert_blanks_to_na(rs)
 ```
 
-```{r echo=FALSE}
-subjects <- c("01-701-1015", "01-701-1023", "01-701-1440")
-# exclude assessments after PD
-tr <- filter(tr, USUBJID %in% subjects & (USUBJID != "01-701-1440" | VISITNUM <= 7))
-tu <- filter(tu, USUBJID %in% subjects)
-rs <- filter(rs, USUBJID %in% subjects)
-adsl <- filter(adsl, USUBJID %in% subjects)
-adrs <- filter(adrs, USUBJID %in% subjects)
-```
-
 At this step, it may be useful to join `ADSL` to your `TR` domain.  For efficiency, only the `ADSL` variables (in this example, Randomization date (`RANDDT`) used for derivations are selected at this step.  The rest of the relevant `ADSL` variables would be added later.
 
 ```{r eval=TRUE}
@@ -243,8 +230,16 @@ uniquely in your SDTM.  However, if this is not the case and your grouping lesio
 ```{r}
 tr <- mutate(
   tr,
-  AVISIT = VISIT,
-  AVISITN = VISITNUM
+  AVISIT = if_else(
+    VISIT == "SCREENING",
+    "BASELINE",
+    VISIT
+  ),
+  AVISITN = if_else(
+    AVISIT == "BASELINE",
+    0,
+    VISITNUM
+  )
 )
 ```
 

vignettes/adtte.Rmd

@@ -71,7 +71,6 @@ The examples of this vignette require the following packages.
 library(admiral)
 library(admiralonco)
 library(dplyr)
-library(admiral.test)
 library(lubridate)
 ```
 

vignettes/nactdt.Rmd

@@ -70,7 +70,6 @@ For example purpose, `CM` and `PR` has been generated (based on CDISC Pilot test
 ```{r, warning=FALSE, message=FALSE}
 library(admiral)
 library(dplyr)
-library(admiral.test)
 
 adsl <- admiral_adsl