generated from pharmaverse/admiraltemplate
-
Notifications
You must be signed in to change notification settings - Fork 4
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Browse files
Browse the repository at this point in the history
* (#23) Initial commit * (#23) Styled file * (#23) Small editorial changes * Moved to templates folder (#23) * Implemented review suggestions (#23) * Added `adsl_vars` as global object (#23) * (#23) Code review suggestions * (#23) Suggestions from code review * (#23) Height measurment set to baseline * Typo Co-authored-by: Andrii Yurovskyi <[email protected]> --------- Co-authored-by: Andrii Yurovskyi <[email protected]>
- Loading branch information
1 parent
e625fd8
commit 1502544
Showing
1 changed file
with
276 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,276 @@ | ||
# Name: ADVS | ||
# | ||
# Label: Vital Signs Analysis dataset | ||
# | ||
# Input: adsl, vs | ||
|
||
|
||
# Attach/load required packages ---- | ||
library(admiral) | ||
library(admiralmetabolic) | ||
library(tibble) | ||
library(dplyr) | ||
library(stringr) | ||
|
||
|
||
# Define project options/variables ---- | ||
# Use the admiral option functionality to store subject key variables in one | ||
# place (note: `subject_keys` defaults to STUDYID and USUBJID) | ||
set_admiral_options(subject_keys = exprs(STUDYID, USUBJID)) | ||
|
||
# Store ADSL variables required for derivations as an R object, enabling | ||
# simplified usage throughout the program | ||
adsl_vars <- exprs(TRTSDT, TRTEDT, TRT01P, TRT01A) | ||
|
||
|
||
# Read in data ---- | ||
# See the "Read in Data" vignette section for more information: | ||
# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#readdata) | ||
|
||
# Read data | ||
vs_metabolic <- admiralmetabolic::vs_metabolic | ||
adsl <- admiral::admiral_adsl | ||
|
||
# Convert SAS missing character values to NA | ||
advs <- vs_metabolic %>% | ||
convert_blanks_to_na() | ||
adsl <- adsl %>% | ||
convert_blanks_to_na() | ||
|
||
# Merge ADSL variables (stored in `adsl_vars`) needed for ADVS | ||
advs <- advs %>% | ||
derive_vars_merged( | ||
dataset_add = adsl, | ||
new_vars = adsl_vars, | ||
by_vars = get_admiral_option("subject_keys") | ||
) | ||
|
||
# Define parameter look-up table used for merging parameter codes to ADVS | ||
param_lookup <- tribble( | ||
~VSTESTCD, ~PARAMCD, ~PARAM, ~PARAMN, ~PARCAT1, ~PARCAT1N, | ||
"HEIGHT", "HEIGHT", "Height (cm)", 1, "Anthropometric measurement", 1, | ||
"WEIGHT", "WEIGHT", "Weight (kg)", 2, "Anthropometric measurement", 1, | ||
"BMI", "BMI", "Body Mass Index(kg/m2)", 3, "Anthropometric measurement", 1, | ||
"HIPCIR", "HIPCIR", "Hip Circumference (cm)", 4, "Anthropometric measurement", 1, | ||
"WSTCIR", "WSTCIR", "Waist Circumference (cm)", 5, "Anthropometric measurement", 1, | ||
"DIABP", "DIABP", "Diastolic Blood Pressure (mmHg)", 6, "Vital Sign", 2, | ||
"PULSE", "PULSE", "Pulse Rate (beats/min)", 7, "Vital Sign", 2, | ||
"SYSBP", "SYSBP", "Systolic Blood Pressure (mmHg)", 8, "Vital Sign", 2, | ||
"TEMP", "TEMP", "Temperature (C)", 9, "Vital Sign", 2 | ||
) | ||
|
||
# Add parameter (PARAMCD) info to enable later ADVS derivations. Additional | ||
# parameter information will be merged again, after all AVDS derivations are | ||
# completed. | ||
|
||
# See function documentation for `derive_vars_merged_lookup()`: | ||
# (https://pharmaverse.github.io/admiral/reference/derive_vars_merged_lookup.html) | ||
advs <- advs %>% | ||
derive_vars_merged_lookup( | ||
dataset_add = param_lookup, | ||
new_vars = exprs(PARAMCD), | ||
by_vars = exprs(VSTESTCD) | ||
) | ||
|
||
|
||
# Derive Date/Time and Analysis Day ---- | ||
# See the "Derive/Impute Numeric Date/Time and Analysis Day" vignette section | ||
# for more information: | ||
# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#datetime) | ||
|
||
# Add vital sign analysis date (ADT) and treatment start date (TRTSDT) | ||
advs <- advs %>% | ||
derive_vars_dt(new_vars_prefix = "A", dtc = VSDTC) %>% | ||
derive_vars_dy(reference_date = TRTSDT, source_vars = exprs(ADT)) | ||
|
||
|
||
# Derive visit info ---- | ||
# See the "Visit and Period Variables" vignette for more information: | ||
# (https://pharmaverse.github.io/admiral/articles/visits_periods.html) | ||
|
||
# Derive analysis time point (ATPT, ATPTN) and analysis visit (AVISIT, AVISITN) | ||
advs <- advs %>% | ||
mutate( | ||
ATPT = VSTPT, | ||
ATPTN = VSTPTNUM, | ||
AVISIT = case_when( | ||
is.na(VISIT) ~ NA_character_, | ||
VSTESTCD == "HEIGHT" & VISIT == "SCREENING 1" ~ "Baseline", | ||
str_detect(VISIT, "SCREEN|UNSCHED|RETRIEVAL|AMBUL") ~ NA_character_, | ||
TRUE ~ str_to_title(VISIT) | ||
), | ||
AVISITN = case_when( | ||
VISIT == "BASELINE" | (VSTESTCD == "HEIGHT" & VISIT == "SCREENING 1") ~ 0, | ||
str_detect(VISIT, "WEEK") ~ as.integer(str_extract(VISIT, "\\d+")), | ||
TRUE ~ NA_integer_ | ||
) | ||
) | ||
|
||
|
||
# Derive results ---- | ||
# See the "Derive Results (AVAL, AVALC)" vignette section for more information: | ||
# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#aval) | ||
|
||
# Derive analysis result (AVAL) | ||
advs <- advs %>% | ||
mutate(AVAL = VSSTRESN) | ||
|
||
|
||
# Derive domain specific variables ---- | ||
# See the "Derive Additional Parameters" vignette section for more information: | ||
# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#derive_param) | ||
|
||
# Derive BMI | ||
advs <- advs %>% | ||
filter(VSTESTCD != "BMI") %>% | ||
derive_param_bmi( | ||
by_vars = exprs( | ||
!!!get_admiral_option("subject_keys"), !!!adsl_vars, | ||
AVISIT, AVISITN, ADT, ADY, ATPT, ATPTN | ||
), | ||
set_values_to = exprs( | ||
PARAMCD = "BMI" | ||
), | ||
get_unit_expr = VSSTRESU, | ||
constant_by_vars = get_admiral_option("subject_keys") | ||
) | ||
|
||
|
||
# Derive categorization variables ---- | ||
# See the "Derive Categorization Variables" vignette section for more | ||
# information: | ||
# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#cat) | ||
|
||
# Create analysis categories look-up (conditional look-up) table | ||
avalcat_lookup <- exprs( | ||
~PARAMCD, ~condition, ~AVALCAT1, ~AVALCA1N, | ||
"BMI", AVAL < 18.5, "Underweight", 1, | ||
"BMI", AVAL >= 18.5 & AVAL < 25, "Normal weight", 2, | ||
"BMI", AVAL >= 25 & AVAL < 30, "Overweight", 3, | ||
"BMI", AVAL >= 30 & AVAL < 35, "Obesity class I", 4, | ||
"BMI", AVAL >= 35 & AVAL < 40, "Obesity class II", 5, | ||
"BMI", AVAL >= 40, "Obesity class III", 6, | ||
"BMI", is.na(AVAL), NA_character_, NA_integer_ | ||
) | ||
|
||
# Derive BMI class (AVALCAT1, AVALCA1N) | ||
advs <- advs %>% | ||
derive_vars_cat( | ||
definition = avalcat_lookup, | ||
by_vars = exprs(PARAMCD) | ||
) | ||
|
||
|
||
# Derive Baseline variables ---- | ||
# See the "Derive Baseline" and "Derive Change from Baseline " vignette sections | ||
# for more information: | ||
# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#baseline) | ||
# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#bchange) | ||
|
||
# Add baseline flag (ABLFL) | ||
advs <- advs %>% | ||
restrict_derivation( | ||
derivation = derive_var_extreme_flag, | ||
args = params( | ||
by_vars = exprs(!!!get_admiral_option("subject_keys"), PARAMCD), | ||
order = exprs(ADT, ATPTN, AVISITN), | ||
new_var = ABLFL, | ||
mode = "last" | ||
), | ||
filter = (!is.na(AVAL) & ADT <= TRTSDT) | ||
) | ||
|
||
# Derive baseline analysis value (BASE) | ||
advs <- advs %>% | ||
derive_var_base( | ||
by_vars = exprs(!!!get_admiral_option("subject_keys"), PARAMCD), | ||
source_var = AVAL, | ||
new_var = BASE | ||
) | ||
|
||
# Derive absolute (CHG) and relative (PCHG) change from baseline | ||
advs <- advs %>% | ||
restrict_derivation( | ||
derivation = derive_var_chg, | ||
filter = !(is.na(AVISIT) | toupper(AVISIT) %in% "BASELINE") | ||
) %>% | ||
restrict_derivation( | ||
derivation = derive_var_pchg, | ||
filter = !(is.na(AVISIT) | toupper(AVISIT) %in% "BASELINE") | ||
) | ||
|
||
|
||
# Derive criterion variables ---- | ||
# See the "Derive Criterion Variables" vignette section for more information: | ||
# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#crit_vars) | ||
|
||
# Set weight loss criterion flags (CRIT1, CRIT1FL) | ||
advs <- advs %>% | ||
restrict_derivation( | ||
derivation = derive_vars_crit_flag, | ||
args = params( | ||
condition = PCHG <= -5 & PARAMCD == "WEIGHT", | ||
description = "Achievement of ≥ 5% weight reduction from baseline", | ||
crit_nr = 1, | ||
values_yn = TRUE, | ||
create_numeric_flag = FALSE | ||
), | ||
filter = AVISITN > 0 & PARAMCD == "WEIGHT" | ||
) %>% | ||
restrict_derivation( | ||
derivation = derive_vars_crit_flag, | ||
args = params( | ||
condition = PCHG <= -10 & PARAMCD == "WEIGHT", | ||
description = "Achievement of ≥ 10% weight reduction from baseline", | ||
crit_nr = 2, | ||
values_yn = TRUE, | ||
create_numeric_flag = FALSE | ||
), | ||
filter = AVISITN > 0 & PARAMCD == "WEIGHT" | ||
) | ||
|
||
|
||
# Assign parameter variables ---- | ||
# See the "Assign PARAMCD, PARAM, PARAMN, PARCAT1" vignette section for more | ||
# information: | ||
# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#paramcd) | ||
|
||
# Add all parameter variables (PARAM, PARAMN, PARCAT1, PARCAT1N) | ||
advs <- advs %>% | ||
derive_vars_merged_lookup( | ||
dataset_add = param_lookup, | ||
new_vars = exprs(PARAMCD, PARAM, PARAMN, PARCAT1, PARCAT1N), | ||
by_vars = exprs(PARAMCD) | ||
) | ||
|
||
|
||
# Add ADSL variables ---- | ||
# See the "Add ADSL variables" vignette section for more information: | ||
# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#adsl_vars) | ||
|
||
# Add all ADSL variables besides TRTSDT, TRTEDT, TRT01P, TRT01A (stored in | ||
# `adsl_vars`) | ||
advs <- advs %>% | ||
derive_vars_merged( | ||
dataset_add = select(adsl, !!!negate_vars(adsl_vars)), | ||
by_vars = get_admiral_option("subject_keys") | ||
) | ||
|
||
|
||
# Add Labels and Attributes ---- | ||
# This process is usually based on one's metadata. As such, no specific example | ||
# will be given. See the "Add Labels and Attributes" vignette section for | ||
# description of several open source R packages which can be used to handle | ||
# metadata. | ||
# (https://pharmaverse.github.io/admiral/articles/bds_finding.html#attributes) | ||
|
||
|
||
# Save output ---- | ||
|
||
# Change to whichever directory you want to save the dataset in | ||
dir <- tools::R_user_dir("admiral_templates_data", which = "cache") # Cache | ||
if (!file.exists(dir)) { | ||
# Create the folder | ||
dir.create(dir, recursive = TRUE, showWarnings = FALSE) | ||
} | ||
save(advs, file = file.path(dir, "advs.rda"), compress = "bzip2") |