#' @export
first_inclusion_step <- function(scm.log.file) {
log_input <- read.delim(scm.log.file,header=F)
log <- log_input
log$V1 <- as.character(log$V1)
i <- 0 #rows
start <- 0
end <- 0
n1 <- 0 #Number of covariate tested in first step
while(end==0) {
i <- i+1
text_part <- unlist(strsplit(log$V1[i], " "))[1]
if((start==1) && ((text_part=="Parameter-covariate") || (text_part=="--------------------"))) {
end <- 1
}
if(start==1 && end==0) {
n1 <- n1+1
}
if((text_part=="MODEL")) {
previous_first <- unlist(strsplit(log$V1[i-1], " "))[1] #an extra check
previous_second <- unlist(strsplit(log$V1[i-1], " "))[2]
if((previous_first=="Model") && (previous_second=="directory")) {
start <- 1
}
}
}
log <- log[(i-n1):(i-1),]
log1 <- strsplit(log, " ")
i <- 1
r <- c()
while(i <= length(log1)){
j <- 1
log2 <- unlist(log1[i])
while(j <= length(log2)){
if((log2[j]!="") & (j==1)) r <- log2[j]
if((log2[j]!="") & (j!=1)) r <- c(r, log2[j])
j <- j+1
}
if(i==1) out <- r
if(i!=1) out <- rbind(out,r)
i <- i+1
}
if(class(out)!="matrix") {
out <- matrix(out,1)
}
rownames(out) <- NULL
x <- c(1:n1)
y <- as.numeric(out[,4])
data <- data.frame(x,y)
alphaf <- as.numeric(out[1,7])
base <- as.numeric(out[1,3])
sign <- base - alphaf
name <- c(out[,1])
list_out <- list(log_input=log_input,
n1=n1,
log=log,
log1=log1,
out=out,
data=data,
alphaf=alphaf,
base=base,
sign=sign,
name=name)
return(list_out)
}
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