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styler updates
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@rammprasad
rammprasad committed Dec 6, 2023
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354 changes: 199 additions & 155 deletions inst/create_cm_template.R
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Original file line number Diff line number Diff line change
Expand Up @@ -14,173 +14,217 @@ library(dplyr)

# Read Specification

#sdtm_spec <- read_sdtm_spec(filename = "~/study/study_sdtm_spec.csv")
# sdtm_spec <- read_sdtm_spec(filename = "~/study/study_sdtm_spec.csv")

study_ct <- read_study_ct(filename = "~/study/study_sdtm_ct.csv")

# Read in raw data

MD1 <- read_raw_data_csv(filename = "~/study/MD1.csv") |>
# Derive oak_id_vars
# Derive oak_id_vars
derive_oak_id_vars()

# Create CM domain. The first step in creating CM domain is to create the topic variable

cm <- MD1 |>
#Derive topic variable
assign_no_ct(raw_dataset = MD1, #This is added for pseudocode. Not required as pipe will send it
raw_variable = MDRAW,
target_sdtm_var = CMTRT) |>
#Derive qualifier CMDOSU
#Use merge and add the qualifier to the topic variable
assign_ct(raw_dataset = MD1,
raw_variable = DOSU,
target_sdtm_var = CMDOSU,
study_ct = study_ct,
target_sdtm_variable_codelist_code = "C71620",
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>
#Derive qualifier CMDOSFRM and merge it with the target dataset
assign_ct(raw_dataset = MD1,
raw_variable = MDFORM,
target_sdtm_var = CMDOSFRM,
target_sdtm_variable_codelist_code = "C66726",
study_ct = study_ct,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>
# Derive topic variable
assign_no_ct(
raw_dataset = MD1, # This is added for pseudocode. Not required as pipe will send it
raw_variable = MDRAW,
target_sdtm_var = CMTRT
) |>
# Derive qualifier CMDOSU
# Use merge and add the qualifier to the topic variable
assign_ct(
raw_dataset = MD1,
raw_variable = DOSU,
target_sdtm_var = CMDOSU,
study_ct = study_ct,
target_sdtm_variable_codelist_code = "C71620",
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
# Derive qualifier CMDOSFRM and merge it with the target dataset
assign_ct(
raw_dataset = MD1,
raw_variable = MDFORM,
target_sdtm_var = CMDOSFRM,
target_sdtm_variable_codelist_code = "C66726",
study_ct = study_ct,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
# DERIVE CMROUTE
assign_ct(raw_dataset = MD1,
raw_variable = MDFORM,
target_sdtm_var = MDRTE,
target_sdtm_variable_codelist_code = "C66729",
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>
assign_ct(
raw_dataset = MD1,
raw_variable = MDFORM,
target_sdtm_var = MDRTE,
target_sdtm_variable_codelist_code = "C66729",
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
# DERIVE CMDOSFRQ
assign_ct(raw_dataset = MD1,
raw_variable = MDFRQ,
target_sdtm_var = CMDOSFRQ,
target_sdtm_variable_codelist_code = "C71113",
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>
# DERIVE CMINDC
assign_no_ct(raw_dataset = MD1,
raw_variable = MDIND,
target_sdtm_var = CMINDC,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>
#Derive qualifier CMDOS. Annotation text = If numeric then CM.CMDOSE
if_then_else(raw_dataset = MD1,
raw_variable = DOS,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = DOS,
condition_operator = "is_numeric",
sub_algorithm = assign_no_ct, #pass the function as the argument
target_sdtm_var = CMDOSE,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>
#Derive qualifier CMDOSTXT. Annotation text = If character then CM.CMDOSTXT
if_then_else(raw_dataset = MD1,
raw_variable = DOS,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = DOS,
condition_operator = "is_character",
sub_algorithm = assign_no_ct,
target_sdtm_var = CMDOSETXT,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>
#Derive qualifier CMMODIFY Annotation text = If different to CM.CMTRT then CM.CMMODIFY
if_then_else(raw_dataset = MD1,
raw_variable = CMMODIFY,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = CMMODIFY,
condition_operator = "diffferent_to",
condition_right_sdtm_variable_domain = CM,
condition_right_sdtm_variable = CMTRT,
sub_algorithm = assign_no_ct,
target_sdtm_var = CMDOSETXT,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>
#Derive CMDECOD
assign_no_ct(raw_dataset = MD1,
raw_variable = CMDECOD,
target_sdtm_var = CMDECOD) |>
#Derive CMSTDTC. This function calls create_iso8601
assign_no_ct(raw_dataset = MD1,
raw_variable = c("MDBD","MDBTM"),
target_sdtm_var = CMSTDTC,
.format = c("ddmmmyyyy", "HHMM")) |>
#Derive CMENDTC. This function calls create_iso8601
assign_no_ct(raw_dataset = MD1,
raw_variable = c("MDED","MDETM"),
target_sdtm_var = CMENDTC,
.format = c("ddmmmyyyy", "HHMM")) |>
#Derive qualifier CMSTRTPT Annotation text = If checked then CM.CMSTRTPT = 'BEFORE'
if_then_else(raw_dataset = MD1,
raw_variable = MDPRIOR,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = MDPRIOR,
condition_operator = "if_checked",
sub_algorithm = assign_ct,
target_sdtm_variable_codelist_code = "C66728",
target_sdtm_var = CMSTRTPT,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>
#Derive qualifier CMSTRTPT Annotation text = If checked then CM.CMSTTPT = 'SCREENING'
if_then_else(raw_dataset = MD1,
raw_variable = MDPRIOR,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = MDPRIOR,
condition_operator = "if_checked",
sub_algorithm = hardcode_no_ct,
target_hardcoded_value = "SCREENING",
target_sdtm_var = CM.CMSTTPT,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>
#Derive qualifier CMSTRTPT Annotation text = If checked then CM.CMENRTPT = 'ONGOING'
if_then_else(raw_dataset = MD1,
raw_variable = MDONG,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = MDONG,
condition_operator = "if_checked",
sub_algorithm = hardcode_ct,
target_hardcoded_value = "ONGOING",
target_sdtm_variable_codelist_code = "C66728",
target_sdtm_var = CMENRTPT,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>
#Derive qualifier CMSTRTPT Annotation text = If checked then CM.CMENTPT = 'DATE OF LAST ASSESSMENT'
if_then_else(raw_dataset = MD1,
raw_variable = MDONG,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = MDONG,
condition_operator = "if_checked",
sub_algorithm = hardcode_no_ct,
target_hardcoded_value = "DATE OF LAST ASSESSMENT",
target_sdtm_var = CMENTPT,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>
#Derive CMGRPID
assign_no_ct(raw_dataset = MD1,
raw_variable = MDNUM,
target_sdtm_var = CMGRPID,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW)) |>

dplyr::mutate(STUDYID = "test_study",
DOMAIN = "CM",
CMCAT = "GENERAL CONMED") |>
assign_ct(
raw_dataset = MD1,
raw_variable = MDFRQ,
target_sdtm_var = CMDOSFRQ,
target_sdtm_variable_codelist_code = "C71113",
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
# DERIVE CMINDC
assign_no_ct(
raw_dataset = MD1,
raw_variable = MDIND,
target_sdtm_var = CMINDC,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
# Derive qualifier CMDOS. Annotation text = If numeric then CM.CMDOSE
if_then_else(
raw_dataset = MD1,
raw_variable = DOS,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = DOS,
condition_operator = "is_numeric",
sub_algorithm = assign_no_ct, # pass the function as the argument
target_sdtm_var = CMDOSE,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
# Derive qualifier CMDOSTXT. Annotation text = If character then CM.CMDOSTXT
if_then_else(
raw_dataset = MD1,
raw_variable = DOS,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = DOS,
condition_operator = "is_character",
sub_algorithm = assign_no_ct,
target_sdtm_var = CMDOSETXT,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
# Derive qualifier CMMODIFY Annotation text = If different to CM.CMTRT then CM.CMMODIFY
if_then_else(
raw_dataset = MD1,
raw_variable = CMMODIFY,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = CMMODIFY,
condition_operator = "diffferent_to",
condition_right_sdtm_variable_domain = CM,
condition_right_sdtm_variable = CMTRT,
sub_algorithm = assign_no_ct,
target_sdtm_var = CMDOSETXT,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
# Derive CMDECOD
assign_no_ct(
raw_dataset = MD1,
raw_variable = CMDECOD,
target_sdtm_var = CMDECOD
) |>
# Derive CMSTDTC. This function calls create_iso8601
assign_no_ct(
raw_dataset = MD1,
raw_variable = c("MDBD", "MDBTM"),
target_sdtm_var = CMSTDTC,
.format = c("ddmmmyyyy", "HHMM")
) |>
# Derive CMENDTC. This function calls create_iso8601
assign_no_ct(
raw_dataset = MD1,
raw_variable = c("MDED", "MDETM"),
target_sdtm_var = CMENDTC,
.format = c("ddmmmyyyy", "HHMM")
) |>
# Derive qualifier CMSTRTPT Annotation text = If checked then CM.CMSTRTPT = 'BEFORE'
if_then_else(
raw_dataset = MD1,
raw_variable = MDPRIOR,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = MDPRIOR,
condition_operator = "if_checked",
sub_algorithm = assign_ct,
target_sdtm_variable_codelist_code = "C66728",
target_sdtm_var = CMSTRTPT,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
# Derive qualifier CMSTRTPT Annotation text = If checked then CM.CMSTTPT = 'SCREENING'
if_then_else(
raw_dataset = MD1,
raw_variable = MDPRIOR,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = MDPRIOR,
condition_operator = "if_checked",
sub_algorithm = hardcode_no_ct,
target_hardcoded_value = "SCREENING",
target_sdtm_var = CM.CMSTTPT,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
# Derive qualifier CMSTRTPT Annotation text = If checked then CM.CMENRTPT = 'ONGOING'
if_then_else(
raw_dataset = MD1,
raw_variable = MDONG,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = MDONG,
condition_operator = "if_checked",
sub_algorithm = hardcode_ct,
target_hardcoded_value = "ONGOING",
target_sdtm_variable_codelist_code = "C66728",
target_sdtm_var = CMENRTPT,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
# Derive qualifier CMSTRTPT Annotation text = If checked then CM.CMENTPT = 'DATE OF LAST ASSESSMENT'
if_then_else(
raw_dataset = MD1,
raw_variable = MDONG,
condition_left_raw_dataset = MD1,
condition_left_raw_variable = MDONG,
condition_operator = "if_checked",
sub_algorithm = hardcode_no_ct,
target_hardcoded_value = "DATE OF LAST ASSESSMENT",
target_sdtm_var = CMENTPT,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
# Derive CMGRPID
assign_no_ct(
raw_dataset = MD1,
raw_variable = MDNUM,
target_sdtm_var = CMGRPID,
merge_to_topic_by = c(oak_id_vars,
topic_var_source = MDRAW
)
) |>
dplyr::mutate(
STUDYID = "test_study",
DOMAIN = "CM",
CMCAT = "GENERAL CONMED"
) |>
derive_usubjid() |>
derive_sequence(keys = c(USUBJID,CMTRT)) |>
derive_sequence(keys = c(USUBJID, CMTRT)) |>
derive_visit_visitnum() |>
derive_study_day(var_in=CMSTDTC,
target_var=CMSTDY) |>
derive_study_day(var_in=CMENDTC,
target_var=CMENDY)








derive_study_day(
var_in = CMSTDTC,
target_var = CMSTDY
) |>
derive_study_day(
var_in = CMENDTC,
target_var = CMENDY
)
6 changes: 4 additions & 2 deletions vignettes/articles/algorithms.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -152,8 +152,10 @@ algorithms <- data.frame(
"VS.VSTEST = 'Systolic Blood Pressure'<br>",
"VS.VSORRESU = 'mmHg'<br>"
),
paste("FA.FASCAT = 'COVID-19 PROBABLE CASE'<br>",
"CM.CMTRT = 'FLUIDS'"),
paste(
"FA.FASCAT = 'COVID-19 PROBABLE CASE'<br>",
"CM.CMTRT = 'FLUIDS'"
),
paste(
"VS = 'Vital Signs'<br>",
"MH.MHCAT = 'PROSTATE CANCER HISTORY'<br>"
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