devel/NMctlBlocks.R
In philipdelff/NMdata: Preparation, Checking and Post-Processing Data for PK/PD Modeling
library(devtools)
load_all("~/wdirs/NMdata")
if(F){
library(data.table)
text <- c("
; matches format
$OMEGA BLOCK(3)
0.126303 ; IIV.CL ; 1 ;IIV ;Between-subject variability on CL;-
0.024 ; IIV.CL.V2.cov ; 1-2 ;IIV ;Covariance of BSV on CL and V2;-
0.127 ; IIV.V2 ; 2 ;IIV ;Between-subject variability on V2;-
0.2 ; IIV.CL.V3.cov ; 1-3 ;IIV ;Covariance of BSV on CL and V3;-
0.2 ; IIV.V2.V3.cov ; 2-3 ;IIV ;Covariance of BSV on V2 and V3;-
(0,0.38,9) ; IIV.V3 ; 3 ;IIV ;Between-subject variability on V3;-
$OMEGA 0 FIX ; IIV.KA ; 4 ;IIV ;Between-subject variability on KA;-
")
lines <- strsplit(text,split="\n")[[1]]
lines
om <- NMreadSection(lines=lines,section="OMEGA",keep.comments=T,as.one=T,keep.empty=T,keep.name=F)
dt.lines <- data.table(text=om)[,row:=.I]
## remove comments
dt.lines[,code:=sub(";.*","",text)]
## make "0 . 3" into "0.3"
dt.lines[,code:=gsub(" *\\. *",".",code)]
dt.lines[,code:=gsub("\\( *","(",code)]
dt.lines[,code:=gsub(" *)",")",code)]
dt.lines[,code:=gsub(" *, *",",",code)]
### not needed: derive (lower,init,upper)
## remove SAME - this should rather remover everything that is not either BLOCK(), a numeric or (numerics,)
dt.lines[,code:=gsub("SAME","",code)]
dt.lines[,code:=gsub("FIX","",code)]
## remove extra spaces
dt.lines[,code:=cleanSpaces(code)]
all.elements <- paste(dt.lines[,code], collapse=" ")
dt.lines[,code.blocks:=list(regmatches(code, gregexpr("BLOCK *\\( *([1-9][0-9]*) *\\)",code,perl=T)))]
dt.lines[,gsub("BLOCK *\\( *([1-9][0-9]*) *\\)","\\1",code)]
## a dt with a column containing lists of i and j. Or i and j are
## columns wit vectors - I dont know if that's possible.
## identify number of parameters in each line
## assign te indexes
######## approach 2
library(stringr)
# Updated regex pattern to include FIX and FIXED
pattern <- "BLOCK\\(\\d+\\)|\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)|\\bFIX\\b|\\bFIXED\\b"
pattern <- paste(
"BLOCK\\(\\d+\\)", # BLOCK(N)
"\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)", # (ll,init,ul)
"\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)", # (ll,init)
"\\(-?\\d+(\\.\\d+)?\\)", # (init)
"\\b-?\\d+(\\.\\d+)?\\b", # init (standalone number)
"\\bFIX\\b", # FIX
"\\bFIXED\\b", # FIXED
sep = "|"
)
lines2 <- str_replace(lines, ";.*", "")
# Extract matches
matches <- str_extract_all(lines2, pattern)
# Print results
for (i in seq_along(lines2)) {
cat("Line:", lines2[i], "\n")
cat("Matches:", paste(matches[[i]], collapse = ", "), "\n\n")
}
for (i in seq_along(lines2)) {
cat("Original Line:", lines[i], "\n")
cat("Cleaned Line:", lines2[i], "\n")
cat("Matches:", paste(matches[[i]], collapse = ", "), "\n\n")
}
########### approach 3
library(stringr)
# Comprehensive regex pattern
pattern <- paste(
"BLOCK\\(\\d+\\)", # BLOCK(N)
"\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)", # (ll,init,ul)
"\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)", # (ll,init)
"\\(-?\\d+(\\.\\d+)?\\)", # (init)
"\\b-?\\d+(\\.\\d+)?\\b", # init (standalone number)
"\\bFIX\\b", # FIX
"\\bFIXED\\b", # FIXED
sep = "|"
)
# Example input lines
lines <- c(
"BLOCK(3) and (1.0,2.0,3.0) FIX this ; ignore this comment",
"FIXED BLOCK(10) some text (0.1,-1.5) ; another comment here",
"Just a standalone number 42 and (3.14) ; comment again",
"Nothing to match here ; no matches"
)
# Preprocess to remove comments (everything after ";")
lines_cleaned <- str_replace(lines, ";.*", "")
# Extract matches
matches <- str_extract_all(lines_cleaned, pattern)
# Function to classify matches and insert NA where applicable
classify_matches <- function(matches) {
categorized <- list(
BLOCK = NA,
FIX = NA,
ll = NA,
init = NA,
ul = NA
)
for (match in matches) {
if (str_detect(match, "^BLOCK\\(\\d+\\)$")) {
categorized$BLOCK <- match
} else if (str_detect(match, "^FIX|FIXED$")) {
categorized$FIX <- match
} else if (str_detect(match, "^\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)$")) {
# Split ll, init, ul
nums <- as.numeric(str_match_all(match, "-?\\d+(\\.\\d+)?")[[1]][, 1])
categorized$ll <- nums[1]
categorized$init <- nums[2]
categorized$ul <- nums[3]
} else if (str_detect(match, "^\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)$")) {
# Split ll, init
nums <- as.numeric(str_match_all(match, "-?\\d+(\\.\\d+)?")[[1]][, 1])
categorized$ll <- nums[1]
categorized$init <- nums[2]
} else if (str_detect(match, "^\\(-?\\d+(\\.\\d+)?\\)$")) {
# Extract init
nums <- as.numeric(str_match(match, "-?\\d+(\\.\\d+)?")[1, 1])
categorized$init <- nums
} else if (str_detect(match, "^-?\\d+(\\.\\d+)?$")) {
# Standalone init
nums <- as.numeric(match)
categorized$init <- nums
}
}
# Return categorized matches
return(categorized)
}
# Process and classify matches for each line
results <- lapply(matches, classify_matches)
# Display results
for (i in seq_along(lines)) {
cat("Original Line:", lines[i], "\n")
cat("Cleaned Line:", lines_cleaned[i], "\n")
cat("Categorized Matches:\n")
print(results[[i]])
cat("\n")
}
do.call(rbind,results)
### approach 4 - wrapped up
library(stringr)
processLines <- function(lines) {
# Comprehensive regex pattern
pattern <- paste(
"BLOCK\\(\\d+\\)", # BLOCK(N)
"\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)", # (ll,init,ul)
"\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)", # (ll,init)
"\\(-?\\d+(\\.\\d+)?\\)", # (init)
"\\b-?\\d+(\\.\\d+)?\\b", # init (standalone number)
"\\bFIX\\b", # FIX
"\\bFIXED\\b", # FIXED
sep = "|"
)
# Preprocess to remove comments (everything after ";")
lines_cleaned <- str_replace(lines, ";.*", "")
# Extract matches
matches <- str_extract_all(lines_cleaned, pattern)
# Function to classify matches and insert NA where applicable
classify_matches <- function(matches) {
categorized <- list(
BLOCK = NA,
FIX = NA,
ll = NA,
init = NA,
ul = NA
)
for (match in matches) {
if (str_detect(match, "^BLOCK\\(\\d+\\)$")) {
categorized$BLOCK <- match
} else if (str_detect(match, "^FIX|FIXED$")) {
categorized$FIX <- match
} else if (str_detect(match, "^\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)$")) {
# Split ll, init, ul
nums <- as.numeric(str_match_all(match, "-?\\d+(\\.\\d+)?")[[1]][, 1])
categorized$ll <- nums[1]
categorized$init <- nums[2]
categorized$ul <- nums[3]
} else if (str_detect(match, "^\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)$")) {
# Split ll, init
nums <- as.numeric(str_match_all(match, "-?\\d+(\\.\\d+)?")[[1]][, 1])
categorized$ll <- nums[1]
categorized$init <- nums[2]
} else if (str_detect(match, "^\\(-?\\d+(\\.\\d+)?\\)$")) {
# Extract init
nums <- as.numeric(str_match(match, "-?\\d+(\\.\\d+)?")[1, 1])
categorized$init <- nums
} else if (str_detect(match, "^-?\\d+(\\.\\d+)?$")) {
# Standalone init
nums <- as.numeric(match)
categorized$init <- nums
}
}
# Return categorized matches
return(categorized)
}
# Process and classify matches for each line
results <- lapply(matches, classify_matches)
return(results)
}
# Example usage:
lines.gen <- c(
"BLOCK(3) and (1.0,2.0,3.0) FIX this ; ignore this comment",
"FIXED BLOCK(10) some text (0.1,-1.5) ; another comment here",
"Just a standalone number 42 and (3.14) ; comment again",
"Nothing to match here ; no matches"
)
# Call the function
results <- processLines(lines.gen)
# Display results
for (i in seq_along(lines)) {
cat("Original Line:", lines[i], "\n")
cat("Cleaned Line:", str_replace(lines[i], ";.*", ""), "\n")
cat("Categorized Matches:\n")
print(results[[i]])
cat("\n")
}
text <- c("
; matches format
$OMEGA BLOCK(3)
0.126303 ; IIV.CL ; 1 ;IIV ;Between-subject variability on CL;-
0.024 ; IIV.CL.V2.cov ; 1-2 ;IIV ;Covariance of BSV on CL and V2;-
0.127 ; IIV.V2 ; 2 ;IIV ;Between-subject variability on V2;-
0.2 ; IIV.CL.V3.cov ; 1-3 ;IIV ;Covariance of BSV on CL and V3;-
0.2 ; IIV.V2.V3.cov ; 2-3 ;IIV ;Covariance of BSV on V2 and V3;-
(0,0.38,9) ; IIV.V3 ; 3 ;IIV ;Between-subject variability on V3;-
$OMEGA 0 FIX ; IIV.KA ; 4 ;IIV ;Between-subject variability on KA;-
")
lines <- strsplit(text,split="\n")[[1]]
lines
results <- processLines(lines)
# Display results
for (i in seq_along(lines)) {
cat("Original Line:", lines[i], "\n")
cat("Cleaned Line:", str_replace(lines[i], ";.*", ""), "\n")
cat("Categorized Matches:\n")
print(results[[i]])
cat("\n")
}
do.call(rbind,results)
}
###### approach 2024-12-22 07:16
library(stringr)
library(data.table)
text <- c("
; matches format
$OMEGA BLOCK(2) 0.126303 ; IIV.CL ; 1 ;IIV ;Between-subject variability on CL;-
0.024 ; IIV.CL.V2.cov ; 1-2 ;IIV ;Covariance of BSV on CL and V2;-
0.127 ; IIV.V2 ; 2 ;IIV ;Between-subject variability on V2;-
0.2 ; IIV.CL.V3.cov ; 1-3 ;IIV ;Covariance of BSV on CL and V3;-
0.2 ; IIV.V2.V3.cov ; 2-3 ;IIV ;Covariance of BSV on V2 and V3;-
(0,0.38,9) ; IIV.V3 ; 3 ;IIV ;Between-subject variability on V3;-
$OMEGA 0 FIX ; IIV.KA ; 4 ;IIV ;Between-subject variability on KA;-
")
lines <- strsplit(text,split="\n")[[1]]
lines
if(F){
res1 <- processLines(lines)
res1
}
##### get info back on lines. First priority is i and j on the
##### lines. Look at result of NMreadParsText to see
##### how. NMreadParsText() should call this function.
if(F){
file.mod <- "~/wdirs/NMdata/tests/testthat/testData/nonmem/xgxr033.mod"
file.mod <- "/home/philip/wdirs/NMsim/devel/example_nonmem_models/lorlatinib_sim_est/mod_lorlatinib_estimate.mod"
load_all("~/wdirs/NMdata")
NMreadSection(file=file.mod,section="OMEGA")
NMreadParsText(file=file.mod,format="%init;%par")
lines.theta <- NMreadSection(file=file.mod,section="THETA")
processLines(lines.theta)
lines.theta <- NMreadSection(file=file.mod,section="THETA")
lines.omega <- NMreadSection(file=file.mod,section="OMEGA")
lines.sigma <- NMreadSection(file=file.mod,section="SIGMA")
lines.omega
processLines(lines.theta)
processLines(lines.omega)
processLines(lines.sigma)
}
###### write lines ctl style
parsToCtl <- function(res1){
}
## Ellis is a fun girl! I am proud to be her dad.
## brody
## yujjklmmmmmmmmmmmbzzxcvbnmasdfghjklqweertyuioooop12345678900`1234567890qwert890-sxcvhjkl <- 'fgnhmj,k.l
#### combine NMreadParsText with
philipdelff/NMdata documentation built on March 5, 2025, 12:20 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(devtools)
load_all("~/wdirs/NMdata")
if(F){
library(data.table)
text <- c("
; matches format
$OMEGA BLOCK(3)
0.126303 ; IIV.CL ; 1 ;IIV ;Between-subject variability on CL;-
0.024 ; IIV.CL.V2.cov ; 1-2 ;IIV ;Covariance of BSV on CL and V2;-
0.127 ; IIV.V2 ; 2 ;IIV ;Between-subject variability on V2;-
0.2 ; IIV.CL.V3.cov ; 1-3 ;IIV ;Covariance of BSV on CL and V3;-
0.2 ; IIV.V2.V3.cov ; 2-3 ;IIV ;Covariance of BSV on V2 and V3;-
(0,0.38,9) ; IIV.V3 ; 3 ;IIV ;Between-subject variability on V3;-
$OMEGA 0 FIX ; IIV.KA ; 4 ;IIV ;Between-subject variability on KA;-
")
lines <- strsplit(text,split="\n")[[1]]
lines
om <- NMreadSection(lines=lines,section="OMEGA",keep.comments=T,as.one=T,keep.empty=T,keep.name=F)
dt.lines <- data.table(text=om)[,row:=.I]
## remove comments
dt.lines[,code:=sub(";.*","",text)]
## make "0 . 3" into "0.3"
dt.lines[,code:=gsub(" *\\. *",".",code)]
dt.lines[,code:=gsub("\\( *","(",code)]
dt.lines[,code:=gsub(" *)",")",code)]
dt.lines[,code:=gsub(" *, *",",",code)]
### not needed: derive (lower,init,upper)
## remove SAME - this should rather remover everything that is not either BLOCK(), a numeric or (numerics,)
dt.lines[,code:=gsub("SAME","",code)]
dt.lines[,code:=gsub("FIX","",code)]
## remove extra spaces
dt.lines[,code:=cleanSpaces(code)]
all.elements <- paste(dt.lines[,code], collapse=" ")
dt.lines[,code.blocks:=list(regmatches(code, gregexpr("BLOCK *\\( *([1-9][0-9]*) *\\)",code,perl=T)))]
dt.lines[,gsub("BLOCK *\\( *([1-9][0-9]*) *\\)","\\1",code)]
## a dt with a column containing lists of i and j. Or i and j are
## columns wit vectors - I dont know if that's possible.
## identify number of parameters in each line
## assign te indexes
######## approach 2
library(stringr)
# Updated regex pattern to include FIX and FIXED
pattern <- "BLOCK\\(\\d+\\)|\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)|\\bFIX\\b|\\bFIXED\\b"
pattern <- paste(
"BLOCK\\(\\d+\\)", # BLOCK(N)
"\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)", # (ll,init,ul)
"\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)", # (ll,init)
"\\(-?\\d+(\\.\\d+)?\\)", # (init)
"\\b-?\\d+(\\.\\d+)?\\b", # init (standalone number)
"\\bFIX\\b", # FIX
"\\bFIXED\\b", # FIXED
sep = "|"
)
lines2 <- str_replace(lines, ";.*", "")
# Extract matches
matches <- str_extract_all(lines2, pattern)
# Print results
for (i in seq_along(lines2)) {
cat("Line:", lines2[i], "\n")
cat("Matches:", paste(matches[[i]], collapse = ", "), "\n\n")
}
for (i in seq_along(lines2)) {
cat("Original Line:", lines[i], "\n")
cat("Cleaned Line:", lines2[i], "\n")
cat("Matches:", paste(matches[[i]], collapse = ", "), "\n\n")
}
########### approach 3
library(stringr)
# Comprehensive regex pattern
pattern <- paste(
"BLOCK\\(\\d+\\)", # BLOCK(N)
"\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)", # (ll,init,ul)
"\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)", # (ll,init)
"\\(-?\\d+(\\.\\d+)?\\)", # (init)
"\\b-?\\d+(\\.\\d+)?\\b", # init (standalone number)
"\\bFIX\\b", # FIX
"\\bFIXED\\b", # FIXED
sep = "|"
)
# Example input lines
lines <- c(
"BLOCK(3) and (1.0,2.0,3.0) FIX this ; ignore this comment",
"FIXED BLOCK(10) some text (0.1,-1.5) ; another comment here",
"Just a standalone number 42 and (3.14) ; comment again",
"Nothing to match here ; no matches"
)
# Preprocess to remove comments (everything after ";")
lines_cleaned <- str_replace(lines, ";.*", "")
# Extract matches
matches <- str_extract_all(lines_cleaned, pattern)
# Function to classify matches and insert NA where applicable
classify_matches <- function(matches) {
categorized <- list(
BLOCK = NA,
FIX = NA,
ll = NA,
init = NA,
ul = NA
)
for (match in matches) {
if (str_detect(match, "^BLOCK\\(\\d+\\)$")) {
categorized$BLOCK <- match
} else if (str_detect(match, "^FIX|FIXED$")) {
categorized$FIX <- match
} else if (str_detect(match, "^\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)$")) {
# Split ll, init, ul
nums <- as.numeric(str_match_all(match, "-?\\d+(\\.\\d+)?")[[1]][, 1])
categorized$ll <- nums[1]
categorized$init <- nums[2]
categorized$ul <- nums[3]
} else if (str_detect(match, "^\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)$")) {
# Split ll, init
nums <- as.numeric(str_match_all(match, "-?\\d+(\\.\\d+)?")[[1]][, 1])
categorized$ll <- nums[1]
categorized$init <- nums[2]
} else if (str_detect(match, "^\\(-?\\d+(\\.\\d+)?\\)$")) {
# Extract init
nums <- as.numeric(str_match(match, "-?\\d+(\\.\\d+)?")[1, 1])
categorized$init <- nums
} else if (str_detect(match, "^-?\\d+(\\.\\d+)?$")) {
# Standalone init
nums <- as.numeric(match)
categorized$init <- nums
}
}
# Return categorized matches
return(categorized)
}
# Process and classify matches for each line
results <- lapply(matches, classify_matches)
# Display results
for (i in seq_along(lines)) {
cat("Original Line:", lines[i], "\n")
cat("Cleaned Line:", lines_cleaned[i], "\n")
cat("Categorized Matches:\n")
print(results[[i]])
cat("\n")
}
do.call(rbind,results)
### approach 4 - wrapped up
library(stringr)
processLines <- function(lines) {
# Comprehensive regex pattern
pattern <- paste(
"BLOCK\\(\\d+\\)", # BLOCK(N)
"\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)", # (ll,init,ul)
"\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)", # (ll,init)
"\\(-?\\d+(\\.\\d+)?\\)", # (init)
"\\b-?\\d+(\\.\\d+)?\\b", # init (standalone number)
"\\bFIX\\b", # FIX
"\\bFIXED\\b", # FIXED
sep = "|"
)
# Preprocess to remove comments (everything after ";")
lines_cleaned <- str_replace(lines, ";.*", "")
# Extract matches
matches <- str_extract_all(lines_cleaned, pattern)
# Function to classify matches and insert NA where applicable
classify_matches <- function(matches) {
categorized <- list(
BLOCK = NA,
FIX = NA,
ll = NA,
init = NA,
ul = NA
)
for (match in matches) {
if (str_detect(match, "^BLOCK\\(\\d+\\)$")) {
categorized$BLOCK <- match
} else if (str_detect(match, "^FIX|FIXED$")) {
categorized$FIX <- match
} else if (str_detect(match, "^\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)$")) {
# Split ll, init, ul
nums <- as.numeric(str_match_all(match, "-?\\d+(\\.\\d+)?")[[1]][, 1])
categorized$ll <- nums[1]
categorized$init <- nums[2]
categorized$ul <- nums[3]
} else if (str_detect(match, "^\\(-?\\d+(\\.\\d+)?,-?\\d+(\\.\\d+)?\\)$")) {
# Split ll, init
nums <- as.numeric(str_match_all(match, "-?\\d+(\\.\\d+)?")[[1]][, 1])
categorized$ll <- nums[1]
categorized$init <- nums[2]
} else if (str_detect(match, "^\\(-?\\d+(\\.\\d+)?\\)$")) {
# Extract init
nums <- as.numeric(str_match(match, "-?\\d+(\\.\\d+)?")[1, 1])
categorized$init <- nums
} else if (str_detect(match, "^-?\\d+(\\.\\d+)?$")) {
# Standalone init
nums <- as.numeric(match)
categorized$init <- nums
}
}
# Return categorized matches
return(categorized)
}
# Process and classify matches for each line
results <- lapply(matches, classify_matches)
return(results)
}
# Example usage:
lines.gen <- c(
"BLOCK(3) and (1.0,2.0,3.0) FIX this ; ignore this comment",
"FIXED BLOCK(10) some text (0.1,-1.5) ; another comment here",
"Just a standalone number 42 and (3.14) ; comment again",
"Nothing to match here ; no matches"
)
# Call the function
results <- processLines(lines.gen)
# Display results
for (i in seq_along(lines)) {
cat("Original Line:", lines[i], "\n")
cat("Cleaned Line:", str_replace(lines[i], ";.*", ""), "\n")
cat("Categorized Matches:\n")
print(results[[i]])
cat("\n")
}
text <- c("
; matches format
$OMEGA BLOCK(3)
0.126303 ; IIV.CL ; 1 ;IIV ;Between-subject variability on CL;-
0.024 ; IIV.CL.V2.cov ; 1-2 ;IIV ;Covariance of BSV on CL and V2;-
0.127 ; IIV.V2 ; 2 ;IIV ;Between-subject variability on V2;-
0.2 ; IIV.CL.V3.cov ; 1-3 ;IIV ;Covariance of BSV on CL and V3;-
0.2 ; IIV.V2.V3.cov ; 2-3 ;IIV ;Covariance of BSV on V2 and V3;-
(0,0.38,9) ; IIV.V3 ; 3 ;IIV ;Between-subject variability on V3;-
$OMEGA 0 FIX ; IIV.KA ; 4 ;IIV ;Between-subject variability on KA;-
")
lines <- strsplit(text,split="\n")[[1]]
lines
results <- processLines(lines)
# Display results
for (i in seq_along(lines)) {
cat("Original Line:", lines[i], "\n")
cat("Cleaned Line:", str_replace(lines[i], ";.*", ""), "\n")
cat("Categorized Matches:\n")
print(results[[i]])
cat("\n")
}
do.call(rbind,results)
}
###### approach 2024-12-22 07:16
library(stringr)
library(data.table)
text <- c("
; matches format
$OMEGA BLOCK(2) 0.126303 ; IIV.CL ; 1 ;IIV ;Between-subject variability on CL;-
0.024 ; IIV.CL.V2.cov ; 1-2 ;IIV ;Covariance of BSV on CL and V2;-
0.127 ; IIV.V2 ; 2 ;IIV ;Between-subject variability on V2;-
0.2 ; IIV.CL.V3.cov ; 1-3 ;IIV ;Covariance of BSV on CL and V3;-
0.2 ; IIV.V2.V3.cov ; 2-3 ;IIV ;Covariance of BSV on V2 and V3;-
(0,0.38,9) ; IIV.V3 ; 3 ;IIV ;Between-subject variability on V3;-
$OMEGA 0 FIX ; IIV.KA ; 4 ;IIV ;Between-subject variability on KA;-
")
lines <- strsplit(text,split="\n")[[1]]
lines
if(F){
res1 <- processLines(lines)
res1
}
##### get info back on lines. First priority is i and j on the
##### lines. Look at result of NMreadParsText to see
##### how. NMreadParsText() should call this function.
if(F){
file.mod <- "~/wdirs/NMdata/tests/testthat/testData/nonmem/xgxr033.mod"
file.mod <- "/home/philip/wdirs/NMsim/devel/example_nonmem_models/lorlatinib_sim_est/mod_lorlatinib_estimate.mod"
load_all("~/wdirs/NMdata")
NMreadSection(file=file.mod,section="OMEGA")
NMreadParsText(file=file.mod,format="%init;%par")
lines.theta <- NMreadSection(file=file.mod,section="THETA")
processLines(lines.theta)
lines.theta <- NMreadSection(file=file.mod,section="THETA")
lines.omega <- NMreadSection(file=file.mod,section="OMEGA")
lines.sigma <- NMreadSection(file=file.mod,section="SIGMA")
lines.omega
processLines(lines.theta)
processLines(lines.omega)
processLines(lines.sigma)
}
###### write lines ctl style
parsToCtl <- function(res1){
}
## Ellis is a fun girl! I am proud to be her dad.
## brody
## yujjklmmmmmmmmmmmbzzxcvbnmasdfghjklqweertyuioooop12345678900`1234567890qwert890-sxcvhjkl <- 'fgnhmj,k.l
#### combine NMreadParsText with
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