nonmem_txtmsgs <- read.csv("data-raw/nonmem_txtmsgs.csv", stringsAsFactors = FALSE)
#
nm_data_reserved_names <- c("ID", "L2", "DV", "MDV")
predpp_reserved_names <- c("TIME", "EVID", "AMT", "RATE", "SS", "II", "ADDL", "CMT", "PCMT", "CALL", "CONT")
nmtran_data_reserved_names <- c("DATE", "DAT1", "DAT2", "DAT3", "L1")
#
nm_reserved_names <- c(
nm_data_reserved_names, predpp_reserved_names, nmtran_data_reserved_names,
"PRED", "RES", "WRES"
)
# Predictions names
nm_predictions <- c(
"PRED", "PREDI",
"IPRED", "IPREDI", "IPRD",
"CPRED", "CPREDI",
"CIPRED", "CIPREDI",
"NPRED", "NIPRED",
"EPRED", "EIPRED"
)
# Residuals names
nm_residuals <- c(
"CWRES", "CWRESI",
"NPDE", "NPD",
"WRES", "WRESI",
"IWRES", "IWRESI", "IWRS",
"RES", "RESI",
"CRES", "CRESI",
"IRES", "IRESI", "IRS",
"CIRES", "CIWRES",
"CIRESI", "CIWRESI",
"NRES", "NWRES",
"NIRES", "NIWRES",
"ERES", "EWRES", "ECWRES",
"EIRES", "EIWRES"
)
# NONMEM run object example
EXAMPLERUN <- load_nm_run("data-raw/TMDD_Djebli_al") %>%
recode_categorical_covariates(
covariates_levels =
list(
DISST = list("Healthy volunteer" = 0, "Patient" = 1),
ISC = list("IV administration" = 0, "SC administration" = 1),
SEX = list("Male" = 0, "Female" = 1),
STATIN = list("Without statin" = 0, "With statin" = 1)
)
) %>%
rename_covariates(covariates = c(
"Disease status" = "DISST",
"Administration route" = "ISC",
"Gender" = "SEX",
"Statin co-administration" = "STATIN",
"Study" = "STUD",
"Age (y)" = "AGE",
"BMI (kg/m²)" = "BMI",
"Baseline LDLC (mg/dL)" = "BSLDLC",
"Creatinine clearance (mL/min)" = "CLCR",
"Baseline free PCSK9 (nM)" = "FBSPCSK",
"Glomerular filtration rate (mL/min)" = "GFR",
"Baseline total PCSK9 (nM)" = "TBSPCSK",
"Weight (kg)" = "WT"
)) %>%
rename_compartments(compartments = c("Total Alirocumab" = 2,
"Total PCSK9" = 3))
EXAMPLERUN$info$path <- "~/pmxploit/example.tar.gz"
usethis::use_data(nm_reserved_names, nonmem_txtmsgs, nm_predictions, nm_residuals, EXAMPLERUN, internal = TRUE, overwrite = TRUE)
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