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@StefanThoma
StefanThoma committed Sep 26, 2024
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16 changes: 9 additions & 7 deletions R/derive_vars_cat.R
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Original file line number Diff line number Diff line change
Expand Up @@ -183,13 +183,15 @@ derive_vars_cat <- function(dataset,
error = function(e) {
# Catch the error and append your own message
cli_abort(
paste(
"Failed to convert {.arg definition} to {.cls tibble}.",
"{.arg definition} should be specified similarly to how you would",
"specify a {.cls tibble} using the {.fun tibble::tribble}` function so it",
"can be converted to {.cls tibble}` using {.fun tibble::tribble}`."
),
e$message
c(
paste(
"Failed to convert {.arg definition} to {.cls tibble}.",
"{.arg definition} should be specified similarly to how you would",
"specify a {.cls tibble} using the {.fun tibble::tribble} function so it",
"can be converted to {.cls tibble} using {.fun tibble::tribble}."
),
e$message
)
)
}
)
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8 changes: 2 additions & 6 deletions tests/testthat/_snaps/derive_vars_cat.md
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Expand Up @@ -4,12 +4,8 @@
Did you forget to specify `by_vars`,
or are you rerunning your code?

# derive_vars_cat Test 5: Error when definition is not an exprs object

Argument `definition` must be a list of expressions but is a tibble.
i To create a list of expressions use `exprs()`.

# derive_vars_cat Test 13: definition has wrong shape

Failed to convert `definition` to `tibble`. `definition` should be specified similarly to how you would specify a `tibble` using the `tribble()` function so it can be converted to `tibble` using `tribble()`.
Failed to convert `definition` to <tibble>. `definition` should be specified similarly to how you would specify a <tibble> using the `tibble::tribble()` function so it can be converted to <tibble> using `tibble::tribble()`.
Data must be rectangular.

38 changes: 9 additions & 29 deletions tests/testthat/test-derive_vars_cat.R
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Original file line number Diff line number Diff line change
@@ -1,28 +1,3 @@
# Load the advs dataset
advs <- tibble::tribble(
~USUBJID, ~VSTEST, ~AVAL,
"01-701-1015", "Height", 147.32,
"01-701-1015", "Weight", 53.98,
"01-701-1023", "Height", 162.56,
"01-701-1023", "Weight", 78.47,
"01-701-1028", "Height", 177.8,
"01-701-1028", "Weight", 98.88,
"01-701-1033", "Height", 175.26,
"01-701-1033", "Weight", 88.45,
"01-701-1034", "Height", NA,
"01-701-1034", "Weight", NA,
"01-701-1047", "Height", NA,
"01-701-1047", "Weight", NA,
"01-701-1097", "Height", 168.91,
"01-701-1097", "Weight", 78.02,
"01-701-1111", "Height", 158.24,
"01-701-1111", "Weight", 60.33,
"01-701-1115", "Height", 181.61,
"01-701-1115", "Weight", 78.7,
"01-701-1118", "Height", 180.34,
"01-701-1118", "Weight", 71.67
) %>% arrange(VSTEST)

expected_result <- tibble::tribble(
~USUBJID, ~VSTEST, ~AVAL, ~AVALCAT1, ~AVALCA1N,
"01-701-1015", "Height", 147.32, "<160", 2,
Expand All @@ -46,6 +21,10 @@ expected_result <- tibble::tribble(
"01-701-1115", "Weight", 78.7, NA, NA,
"01-701-1118", "Weight", 71.67, NA, NA
)

advs <- expected_result %>% select(
USUBJID, VSTEST, AVAL
)
## Test 1: Basic functionality without by_vars ----
test_that("derive_vars_cat Test 1: Basic functionality without by_vars", {
# Define the condition and categories
Expand Down Expand Up @@ -124,8 +103,9 @@ test_that("derive_vars_cat Test 5: Error when definition is not an exprs object"
"AVAL < 160", "<160", 2
)
# Snapshot the error message
expect_snapshot_error(
derive_vars_cat(advs, definition)
expect_error(
derive_vars_cat(advs, definition),
class = "assert_expr_list"
)
})

Expand All @@ -152,8 +132,8 @@ test_that("derive_vars_cat Test 6: Error when required columns are missing from
test_that("derive_vars_cat Test 7: Correct behavior when no conditions are met", {
# Define conditions that do not match any rows
definition <- exprs(
~condition, ~AVALCAT1, ~AVALCA1N,
VSTEST == "Height" & AVAL < 0, "<0", 1
~condition, ~AVALCAT1, ~AVALCA1N,
VSTEST == "Height" & AVAL < 0, "<0", 1
)

expected_result <- tibble::tribble(
Expand Down
41 changes: 20 additions & 21 deletions vignettes/bds_exposure.Rmd
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Expand Up @@ -41,7 +41,7 @@ otherwise specified.*
* [Create 1:1 Mapping Records](#onetoone)
* [Create Summary Records](#summaryrec)
* [Assign `PARAMCD`, `PARAMN`, etc. from Reference Tables](#paramcd)
* [Derive Categorization Variables (`AVALCATx`)](#cat)
* [Derive Categorization Variables (`AVALCATy`)](#cat)
* [Assign `ASEQ`](#aseq)
* [Add ADSL variables `ASEQ`](#adsl_vars)
* [Add Labels and Attributes](#attributes)
Expand Down Expand Up @@ -514,18 +514,18 @@ TNDOSINT | Overall dose intensity (%) | 12

```{r eval=TRUE, include=FALSE, echo=FALSE}
param_lookup <- tribble(
~PARAMCD, ~PARAM, ~PARAMN,
"DURD", "Study drug duration during constant dosing interval (days)", 1,
"DOSE", "Dose administered during constant dosing interval (mg)", 2,
"PLDOSE", "Planned dose during constant dosing interval (mg)", 3,
"ADJ", "Dose adjusted during constant dosing interval", 4,
"ADJAE", "Dose adjusted due to AE during constant dosing interval", 5,
"TDURD", "Overall duration (days)", 6,
"TDOSE", "Total dose administered (mg)", 7,
"TPDOSE", "Total planned dose (mg)", 9,
"TADJ", "Dose adjusted during study", 10,
"TADJAE", "Dose adjusted during study due to AE", 11,
"TNDOSINT", "Overall dose intensity (%)", 12
~PARAMCD, ~PARAM, ~PARAMN,
"DURD", "Study drug duration during constant dosing interval (days)", 1,
"DOSE", "Dose administered during constant dosing interval (mg)", 2,
"PLDOSE", "Planned dose during constant dosing interval (mg)", 3,
"ADJ", "Dose adjusted during constant dosing interval", 4,
"ADJAE", "Dose adjusted due to AE during constant dosing interval", 5,
"TDURD", "Overall duration (days)", 6,
"TDOSE", "Total dose administered (mg)", 7,
"TPDOSE", "Total planned dose (mg)", 9,
"TADJ", "Dose adjusted during study", 10,
"TADJAE", "Dose adjusted during study due to AE", 11,
"TNDOSINT", "Overall dose intensity (%)", 12
)
```

Expand All @@ -549,17 +549,16 @@ We can use the `derive_vars_cat()` function to derive the categorization variabl

```{r eval=TRUE, echo=TRUE}
avalcax_lookup <- exprs(
~PARAMCD, ~condition, ~AVALCAT1,
"TDURD", AVAL >= 90, ">= 90 days",
~PARAMCD, ~condition, ~AVALCAT1,
"TDURD", AVAL >= 90, ">= 90 days",
"TDURD", AVAL >= 30 & AVAL < 90, ">= 30 and < 90 days",
"TDURD", AVAL < 30, "< 30 days",
"TDOSE", AVAL < 1000, "< 1000 mg",
"TDOSE", AVAL >= 1000, ">= 1000 mg",
"TPDOSE", AVAL < 1000, "< 1000 mg",
"TPDOSE", AVAL >= 1000, ">= 1000 mg"
"TDURD", AVAL < 30, "< 30 days",
"TDOSE", AVAL < 1000, "< 1000 mg",
"TDOSE", AVAL >= 1000, ">= 1000 mg",
"TPDOSE", AVAL < 1000, "< 1000 mg",
"TPDOSE", AVAL >= 1000, ">= 1000 mg"
)
adex <- adex %>%
derive_vars_cat(
definition = avalcax_lookup,
Expand Down
52 changes: 26 additions & 26 deletions vignettes/bds_finding.Rmd
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Expand Up @@ -44,7 +44,7 @@ otherwise specified.*
* [Derive Analysis Flags (e.g. `ANL01FL`)](#analysisrec)
* [Assign Treatment (`TRTA`, `TRTP`)](#treatment)
* [Assign `ASEQ`](#aseq)
* [Derive Categorization Variables (`AVALCATx`)](#cat)
* [Derive Categorization Variables (`AVALCATy`)](#cat)
* [Derive Criterion Variables (`CRITy`, `CRITyFL`, `CRITyFLN`)](#crit_vars)
* [Add ADSL variables](#adsl_vars)
* [Derive New Rows](#additional)
Expand Down Expand Up @@ -214,16 +214,16 @@ TEMP | TEMP | Temperature (C) | 7 | Vital Sign | 2
This lookup may now be joined to the source data:

```{r eval=TRUE, include=FALSE}
param_lookup <- tribble(
~VSTESTCD, ~PARAMCD, ~PARAM, ~PARAMN, ~PARCAT1, ~PARCAT1N,
"HEIGHT", "HEIGHT", "Height (cm)", 1, "Subject Characteristic", 1,
"WEIGHT", "WEIGHT", "Weight (kg)", 2, "Subject Characteristic", 1,
"DIABP", "DIABP", "Diastolic Blood Pressure (mmHg)", 3, "Vital Sign", 2,
"MAP", "MAP", "Mean Arterial Pressure (mmHg)", 4, "Vital Sign", 2,
"BSA", "BSA", "Body Surface Area (m^2)", 5, "Vital Sign", 2,
"PULSE", "PULSE", "Pulse Rate (beats/min)", 6, "Vital Sign", 2,
"SYSBP", "SYSBP", "Systolic Blood Pressure (mmHg)", 7, "Vital Sign", 2,
"TEMP", "TEMP", "Temperature (C)", 8, "Vital Sign", 2
param_lookup <- tibble::tribble(
~VSTESTCD, ~PARAMCD, ~PARAM, ~PARAMN, ~PARCAT1, ~PARCAT1N,
"HEIGHT", "HEIGHT", "Height (cm)", 1, "Subject Characteristic", 1,
"WEIGHT", "WEIGHT", "Weight (kg)", 2, "Subject Characteristic", 1,
"DIABP", "DIABP", "Diastolic Blood Pressure (mmHg)", 3, "Vital Sign", 2,
"MAP", "MAP", "Mean Arterial Pressure (mmHg)", 4, "Vital Sign", 2,
"BSA", "BSA", "Body Surface Area (m^2)", 5, "Vital Sign", 2,
"PULSE", "PULSE", "Pulse Rate (beats/min)", 6, "Vital Sign", 2,
"SYSBP", "SYSBP", "Systolic Blood Pressure (mmHg)", 7, "Vital Sign", 2,
"TEMP", "TEMP", "Temperature (C)", 8, "Vital Sign", 2
)
attr(param_lookup$VSTESTCD, "label") <- "Vital Signs Test Short Name"
```
Expand Down Expand Up @@ -345,11 +345,11 @@ created with a function call. See example below for `PARAMCD` = `QTCF`.

```{r eval=FALSE}
adeg <- tibble::tribble(
~USUBJID, ~EGSTRESU, ~PARAMCD, ~AVAL, ~VISIT,
"P01", "msec", "QT", 350, "CYCLE 1 DAY 1",
"P01", "msec", "QT", 370, "CYCLE 2 DAY 1",
"P01", "msec", "RR", 842, "CYCLE 1 DAY 1",
"P01", "msec", "RR", 710, "CYCLE 2 DAY 1"
~USUBJID, ~EGSTRESU, ~PARAMCD, ~AVAL, ~VISIT,
"P01", "msec", "QT", 350, "CYCLE 1 DAY 1",
"P01", "msec", "QT", 370, "CYCLE 2 DAY 1",
"P01", "msec", "RR", 842, "CYCLE 1 DAY 1",
"P01", "msec", "RR", 710, "CYCLE 2 DAY 1"
)
adeg <- derive_param_qtc(
Expand All @@ -366,11 +366,11 @@ for lab differentials converted to absolute values. See example below:

```{r eval=FALSE}
adlb <- tibble::tribble(
~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT,
"P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1",
"P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1",
"P01", "LYMLE", 0.90, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1",
"P01", "LYMLE", 0.70, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1"
~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT,
"P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1",
"P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1",
"P01", "LYMLE", 0.90, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1",
"P01", "LYMLE", 0.70, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1"
)
derive_param_wbc_abs(
Expand Down Expand Up @@ -515,10 +515,10 @@ and `ref_end_date = AP01EDT`.
advs_pre <- select(advs, -ONTRTFL)
advs <- tibble::tribble(
~USUBJID, ~ASTDT, ~AP01SDT, ~AP01EDT, ~AENDT,
~USUBJID, ~ASTDT, ~AP01SDT, ~AP01EDT, ~AENDT,
"P01", ymd("2020-03-15"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-12-01"),
"P02", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-03-15"),
"P03", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), NA,
"P03", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), NA,
)
```

Expand Down Expand Up @@ -852,9 +852,9 @@ We can use the `derive_vars_cat()` function to derive the categorization variabl

```{r eval=TRUE}
avalcat_lookup <- exprs(
~PARAMCD, ~condition, ~AVALCAT1, ~AVALCA1N,
"HEIGHT", AVAL > 140, ">140 cm", 1,
"HEIGHT", AVAL <= 140, "<= 140 cm", 2
~PARAMCD, ~condition, ~AVALCAT1, ~AVALCA1N,
"HEIGHT", AVAL > 140, ">140 cm", 1,
"HEIGHT", AVAL <= 140, "<= 140 cm", 2
)
advs <- advs %>%
derive_vars_cat(
Expand Down

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