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ADLB

The document loads various packages and datasets. It merges a subject level dataset with a lab dataset, assigns identifier variables, and derives various timing variables. It then calculates analysis relative day, assigns parameter and parameter code variables, and derives flags for baseline, analysis, and change from baseline calculations.

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Vijaya Lakshmi

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0% found this document useful (0 votes)

42 views23 pages

ADLB

Uploaded by

Vijaya Lakshmi

We take content rights seriously. If you suspect this is your content, claim it here.

Available Formats

Download as PDF, TXT or read online on Scribd

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rm (list = ls(all.

names = TRUE))

# Loading required packages

#install.packages("hms")

pac <- c ("tidyverse","pharmaversesdtm", "sassy", "metacore", "readxl", "haven", "lubridate", "hms"

, "admiral")

lapply(pac, require, character.only = TRUE , warn.conflicts=TRUE)

# Assigning file path for log file

lfth <- "C:/Users/manimaranp/Desktop/RP/log"

log_open(file.path(lfth, "adlb.log"))

#######################################################################

sep ("Loading subject level dataset & lab dataset into workspace")

#######################################################################

admfth <- "C:/Users/manimaranp/Desktop/RP/ADAM"

load(file = file.path(admfth, "adsl.sas7bdat"))

put (adsl)

data("lb")

head(lb, n=10)

put (lb)

#####################################################################

sep ("merge subject level dataset & lab dataset")

###################################################################
adsl_lb <- inner_join(adsl,lb, by=c("STUDYID","USUBJID"), multiple="all")

put(adsl_lb)

colnames(adsl_lb)

##################################################################

sep ("Assigning indentifier variables")

#################################################################

lb1 <- adsl_lb %>% mutate(SRCDOM = DOMAIN, SRCSEQ = LBSEQ)

put (lb1)

colnames(lb1)

####################################################################

sep ("Timing variables")

##################################################################

lb2 <- lb1 %>% mutate(lst = str_length(LBDTC)) %>%

mutate(ADT = if_else(!is.na(LBDTC) & lst == 10, ymd(as.POSIXct(LBDTC)),

ymd (as.POSIXct(str_sub(LBDTC, 1, 10))))) %>%

mutate(ADTM = if_else(!is.na(LBDTC) & lst == 16 ,

as.POSIXct (LBDTC, format="%Y-%m-%dT%R"), NA)) %>%

mutate(ATM = if_else (!is.na(LBDTC) & lst == 16, as_hms(str_sub(ADTM,12,18)), NA))

put (lb2)

############################################################################

sep ("calculating analysis relative day")

###########################################################################

lb3 <- lb2 %>% mutate(ADY = if_else(!is.na(TRTSDT) & !is.na(ADT) & (ADT >= TRTSDT),
time_length(ADT - TRTSDT, "days") +1,

time_length(ADT- TRTSDT, "days"))) %>%

mutate(AVISIT = if_else (!is.na(lb2$VISIT) & ! str_detect(VISIT, "UNSCHEDULED") ,

VISIT, "UNSCHEDULED"))

put (lb3)

vsn <- function (invar) {case_when(invar == "SCREENING 1" ~ 1,

invar == "WEEK 2" ~ 2,

invar == "WEEK 4" ~ 3,

invar == "WEEK 6" ~ 4 ,

invar == "WEEK 8" ~ 5,

invar == "WEEK 12" ~ 6,

invar == "WEEK 16" ~ 7,

invar == "WEEK 20" ~ 8,

invar == "WEEK 24" ~ 9,

invar == "WEEK 26" ~ 10,

invar == "UNSCHEDULED" ~ 999) }

lb4 <- lb3 %>% mutate(AVISITN = vsn (AVISIT))

put (lb4)

##################################################################################

sep ("Assiging param and paramcd and PARAMN")

#################################################################################

lb5 <- lb4 %>% mutate(PARAM = if_else(!is.na(LBTEST) & !is.na(LBSTRESU),

paste0(LBTEST," ",LBSTRESU), LBTEST)) %>%

mutate (PARAMCD = if_else (!is.na(LBTESTCD) & !is.na(PARAM), LBTESTCD, NA))

put (lb5)
param_unq <- lb5 %>% distinct (PARAM) %>% arrange(PARAM) %>%

mutate(PARAMN = seq (1, 47))

lb6 <- left_join(lb5, param_unq, by="PARAM", multiple="all")

put (lb6)

lb7 <- derive_var_obs_number(lb6,

by_vars = exprs(STUDYID, USUBJID),

order = exprs(PARAM))

put(lb7)

#############################################################################

sep ("Assiging aval and avalc")

############################################################################

lb8 <- lb7 %>% mutate(AVAL = if_else (!is.na(LBSTRESN), LBSTRESN, NA),

AVALC = if_else(!is.na(LBSTRESC), LBSTRESC, NA))

put (lb8)

lb8_sas <- as_tibble (lb8) %>% write_sas("lb8_sas.sas7bdat")

#########################################################################

sep ("Baseline flag & Base & BaseC")

########################################################################

lb_abl <- lb8 %>%

restrict_derivation(
derivation = derive_var_extreme_flag,

args = params(

by_vars = exprs(USUBJID, PARAMN, PARAMCD),

order= exprs(ADT, AVISITN, SRCSEQ),

new_var=ABLFL,

mode="last"

filter=(!is.na(AVALC) & !is.na(ADT) & !is.na(TRTSDT) & ADT <= TRTSDT)

put (lb_abl)

lb_base<- lb_abl %>%

derive_var_base (

by_vars = exprs(USUBJID, PARAMCD),

source_var = AVAL,

new_var = BASE

put (lb_base)

lb_basec<- lb_base %>%

derive_var_base (

by_vars = exprs(USUBJID, PARAMCD),

source_var = AVALC,

new_var = BASEC

put (lb_basec)

lb_f1 <- lb_basec %>% mutate(AVISIT = replace(AVISIT, ABLFL == "Y", "Baseline"))

put (lb_f1)

lb_f2 <- derive_var_chg(lb_f1)

lb_f3 <- lb_f2 %>% mutate(PCHG = if_else (CHG != 0 , (CHG/BASE)*100, NA))

put (lb_f3)

##################################################################

sep ("Analysis Flag variable derivation")

##################################################################

adlb <- lb_f3 %>% restrict_derivation(

derivation = derive_var_extreme_flag,

args = params(

by_vars = exprs(USUBJID,PARAMN,AVISITN,AVISIT ),

order = exprs(ADT),

new_var= ANL01FL,

mode="last"

filter= !is.na(AVISIT) & !is.na(AVISITN)

put (adlb)
=========================================================================

Log Path: C:/Users/manimaranp/Desktop/RP/log/adlb.log

Program Path: C:/Users/manimaranp/Desktop/R1/data-adam/ADLB.R

Working Directory: C:/Users/manimaranp/Documents

User Name: manimaranp

R Version: 4.2.2 (2022-10-31 ucrt)

Machine: LP2245 x86-64

Operating System: Windows 10 x64 build 19045

Base Packages: stats graphics grDevices utils datasets methods base Other

Packages: admiral_0.12.2.9001 hms_1.1.3 haven_2.5.1 readxl_1.4.3 metacore_0.1.2

procs_1.0.3 reporter_1.4.2 libr_1.2.8 fmtr_1.6.0 logr_1.3.4 common_1.0.9

sassy_1.2.0 pharmaversesdtm_0.1.1 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0

dplyr_1.1.0 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.1.8 ggplot2_3.4.1

tidyverse_2.0.0

Log Start Time: 2024-01-03 13:08:12

=========================================================================

Loading subject level dataset & lab dataset into workspace

=========================================================================

# A tibble: 306 × 43

STUDYID USUBJID SUBJID SITEID RFSTDTC RFENDTC RFXST…¹ RFXEN…² RFICDTC RFPEN…³

1 CDISCP… 01-701… 1015 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

2 CDISCP… 01-701… 1023 701 2012-0… 2012-0… 2012-0… 2012-0… <NA> 2013-0…

3 CDISCP… 01-701… 1028 701 2013-0… 2014-0… 2013-0… 2014-0… <NA> 2014-0…

4 CDISCP… 01-701… 1033 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

5 CDISCP… 01-701… 1034 701 2014-0… 2014-1… 2014-0… 2014-1… <NA> 2014-1…

6 CDISCP… 01-701… 1047 701 2013-0… 2013-0… 2013-0… 2013-0… <NA> 2013-0…

7 CDISCP… 01-701… 1057 701 <NA> <NA> <NA> <NA> <NA> 2013-1…
8 CDISCP… 01-701… 1097 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

9 CDISCP… 01-701… 1111 701 2012-0… 2012-0… 2012-0… 2012-0… <NA> 2013-0…

10 CDISCP… 01-701… 1115 701 2012-1… 2013-0… 2012-1… 2013-0… <NA> 2013-0…

# … with 296 more rows, 33 more variables: DTHDTC <chr>, DTHFL <chr>,

# AGE <dbl>, AGEU <chr>, AGEGR1 <chr>, AGEGR1N <dbl>, SEX <chr>, RACE <chr>,

# ETHNIC <chr>, ARM <chr>, ARMCD <chr>, ACTARM <chr>, ACTARMCD <chr>,

# COUNTRY <chr>, REGION1 <chr>, REGION1N <dbl>, SAFFL <chr>, SAFFLN <dbl>,

# TRT01P <chr>, TRT01PN <dbl>, TRT01A <chr>, TRT01AN <dbl>, TRTSDT <date>,

# TRTEDT <date>, TRTDURD <dbl>, RANDDT <date>, EOSSTT <chr>, EOSDT <date>,

# DTHDT <date>, DTHCAUS <chr>, DCSREAS <chr>, DCSREASP <chr>, …

# ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names

NOTE: Data frame has 306 rows and 43 columns.

NOTE: Log Print Time: 2024-01-03 13:08:13

NOTE: Elapsed Time: 0.481739044189453 secs

# A tibble: 59,580 × 23

STUDYID DOMAIN USUBJID LBSEQ LBTES…¹ LBTEST LBCAT LBORRES LBORR…² LBORN…³

1 CDISCPILOT… LB 01-701… 1 ALB Album… CHEM… 3.8 g/dL 3.3

2 CDISCPILOT… LB 01-701… 39 ALB Album… CHEM… 3.9 g/dL 3.3

3 CDISCPILOT… LB 01-701… 74 ALB Album… CHEM… 3.8 g/dL 3.3

4 CDISCPILOT… LB 01-701… 104 ALB Album… CHEM… 3.7 g/dL 3.3

5 CDISCPILOT… LB 01-701… 134 ALB Album… CHEM… 3.8 g/dL 3.3

6 CDISCPILOT… LB 01-701… 164 ALB Album… CHEM… 3.8 g/dL 3.3

7 CDISCPILOT… LB 01-701… 199 ALB Album… CHEM… 3.7 g/dL 3.3

8 CDISCPILOT… LB 01-701… 229 ALB Album… CHEM… 3.7 g/dL 3.3

9 CDISCPILOT… LB 01-701… 259 ALB Album… CHEM… 3.8 g/dL 3.3

10 CDISCPILOT… LB 01-701… 294 ALB Album… CHEM… 3.8 g/dL 3.3

# … with 59,570 more rows, 13 more variables: LBORNRHI <chr>, LBSTRESC <chr>,
# LBSTRESN <dbl>, LBSTRESU <chr>, LBSTNRLO <dbl>, LBSTNRHI <dbl>,

# LBNRIND <chr>, LBBLFL <chr>, VISITNUM <dbl>, VISIT <chr>, VISITDY <dbl>,

# LBDTC <chr>, LBDY <dbl>, and abbreviated variable names ¹LBTESTCD,

# ²LBORRESU, ³LBORNRLO

# ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names

NOTE: Data frame has 59580 rows and 23 columns.

NOTE: Log Print Time: 2024-01-03 13:08:13

NOTE: Elapsed Time: 0.59731912612915 secs

=========================================================================

merge subject level dataset & lab dataset

=========================================================================

# A tibble: 59,580 × 64

STUDYID USUBJID SUBJID SITEID RFSTDTC RFENDTC RFXST…¹ RFXEN…² RFICDTC RFPEN…³

1 CDISCP… 01-701… 1015 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

2 CDISCP… 01-701… 1015 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

3 CDISCP… 01-701… 1015 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

4 CDISCP… 01-701… 1015 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

5 CDISCP… 01-701… 1015 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

6 CDISCP… 01-701… 1015 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

7 CDISCP… 01-701… 1015 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

8 CDISCP… 01-701… 1015 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

9 CDISCP… 01-701… 1015 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

10 CDISCP… 01-701… 1015 701 2014-0… 2014-0… 2014-0… 2014-0… <NA> 2014-0…

# … with 59,570 more rows, 54 more variables: DTHDTC <chr>, DTHFL <chr>,

# AGE <dbl>, AGEU <chr>, AGEGR1 <chr>, AGEGR1N <dbl>, SEX <chr>, RACE <chr>,

# ETHNIC <chr>, ARM <chr>, ARMCD <chr>, ACTARM <chr>, ACTARMCD <chr>,
# COUNTRY <chr>, REGION1 <chr>, REGION1N <dbl>, SAFFL <chr>, SAFFLN <dbl>,

# TRT01P <chr>, TRT01PN <dbl>, TRT01A <chr>, TRT01AN <dbl>, TRTSDT <date>,

# TRTEDT <date>, TRTDURD <dbl>, RANDDT <date>, EOSSTT <chr>, EOSDT <date>,

# DTHDT <date>, DTHCAUS <chr>, DCSREAS <chr>, DCSREASP <chr>, …

# ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names

NOTE: Data frame has 59580 rows and 64 columns.

NOTE: Log Print Time: 2024-01-03 13:08:14

NOTE: Elapsed Time: 0.472997903823853 secs

=========================================================================

Assigning indentifier variables

=========================================================================

# A tibble: 59,580 × 66