R/301.Find.RS.metric.R
In RajeswaranV/vcdPlus: Summary and inference of categorical data and contingency tables
Defines functions
Find.RS.metric
Find.sequence
pass2.In.Each.Row.new.cc.or
pass2.In.Each.Row.new.cc.rr
pass2.In.Each.Row.new.cc.rd
Documented in
Find.RS.metric
Find.sequence
pass2.In.Each.Row.new.cc.or
pass2.In.Each.Row.new.cc.rd
pass2.In.Each.Row.new.cc.rr
#' Find the point of reversal of OR/RR/RD
#' @param Figure.df - description
#' @return A dataframe with
#' \item{x1}{Sequence}
#' @family Internal methods
#' @keywords internal
Find.RS.metric<-function(Figure.df)
{
LHS.Flag.all.or=0
RHS.Flag.all.or=0
LHS.Flag.all.rr=0
RHS.Flag.all.rr=0
LHS.Flag.all.rd=0
RHS.Flag.all.rd=0
LHS.Flag.zero.or=0
RHS.Flag.zero.or=0
LHS.Flag.zero.rr=0
RHS.Flag.zero.rr=0
LHS.Flag.zero.rd=0
RHS.Flag.zero.rd=0
Figure.df$LHS.Flag.all.or=NULL
Figure.df$RHS.Flag.all.or=NULL
Figure.df$LHS.Flag.all.rr=NULL
Figure.df$RHS.Flag.all.rr=NULL
Figure.df$LHS.Flag.all.rd=NULL
Figure.df$RHS.Flag.all.rd=NULL
Figure.df$LHS.Flag.zero.or=NULL
Figure.df$RHS.Flag.zero.or=NULL
Figure.df$LHS.Flag.zero.rr=NULL
Figure.df$RHS.Flag.zero.rr=NULL
Figure.df$LHS.Flag.zero.rd=NULL
Figure.df$RHS.Flag.zero.rd=NULL
ibv.Rows=nrow(Figure.df)
for(i in 1:ibv.Rows){
if(is.between(1,Figure.df$or.cc.all.tpm8[i],Figure.df$or.cc.all.tpm4[i])){LHS.Flag.all.or=1/100000000;RHS.Flag.all.or=1/10000}
if(is.between(1,Figure.df$or.cc.all.tpm4[i],Figure.df$or.cc.all.001[i])){LHS.Flag.all.or=1/10000;RHS.Flag.all.or=0.0011}
if(is.between(1,Figure.df$or.cc.all.001[i],Figure.df$or.cc.all.01[i])){LHS.Flag.all.or=0.0011;RHS.Flag.all.or=0.011}
if(is.between(1,Figure.df$or.cc.all.01[i],Figure.df$or.cc.all.015[i])){LHS.Flag.all.or=0.011;RHS.Flag.all.or=0.0151}
if(is.between(1,Figure.df$or.cc.all.015[i],Figure.df$or.cc.all.1[i])){LHS.Flag.all.or=0.0151;RHS.Flag.all.or=0.11}
if(is.between(1,Figure.df$or.cc.all.1[i],Figure.df$or.cc.all.15[i])){LHS.Flag.all.or=0.11;RHS.Flag.all.or=0.151}
if(is.between(1,Figure.df$or.cc.all.15[i],Figure.df$or.cc.all.2[i])){LHS.Flag.all.or=0.151;RHS.Flag.all.or=0.21}
if(is.between(1,Figure.df$or.cc.all.2[i],Figure.df$or.cc.all.25[i])){LHS.Flag.all.or=0.21;RHS.Flag.all.or=0.251}
if(is.between(1,Figure.df$or.cc.all.25[i],Figure.df$or.cc.all.3[i])){LHS.Flag.all.or=0.251;RHS.Flag.all.or=0.31}
if(is.between(1,Figure.df$or.cc.all.3[i],Figure.df$or.cc.all.35[i])){LHS.Flag.all.or=0.31;RHS.Flag.all.or=0.351}
if(is.between(1,Figure.df$or.cc.all.35[i],Figure.df$or.cc.all.4[i])){LHS.Flag.all.or=0.351;RHS.Flag.all.or=0.41}
if(is.between(1,Figure.df$or.cc.all.4[i],Figure.df$or.cc.all.45[i])){LHS.Flag.all.or=0.41;RHS.Flag.all.or=0.451}
if(is.between(1,Figure.df$or.cc.all.45[i],Figure.df$or.cc.all.5[i])){LHS.Flag.all.or=0.451;RHS.Flag.all.or=0.5}
if(is.between(1,Figure.df$or.cc.zero.tpm8[i],Figure.df$or.cc.zero.tpm4[i])){LHS.Flag.zero.or=1/100000000;RHS.Flag.zero.or=1/10000}
if(is.between(1,Figure.df$or.cc.zero.tpm4[i],Figure.df$or.cc.zero.001[i])){LHS.Flag.zero.or=1/10000;RHS.Flag.zero.or=0.0011}
if(is.between(1,Figure.df$or.cc.zero.001[i],Figure.df$or.cc.zero.01[i])){LHS.Flag.zero.or=0.0011;RHS.Flag.zero.or=0.011}
if(is.between(1,Figure.df$or.cc.zero.01[i],Figure.df$or.cc.zero.015[i])){LHS.Flag.zero.or=0.011;RHS.Flag.zero.or=0.0151}
if(is.between(1,Figure.df$or.cc.zero.015[i],Figure.df$or.cc.zero.1[i])){LHS.Flag.zero.or=0.0151;RHS.Flag.zero.or=0.11}
if(is.between(1,Figure.df$or.cc.zero.1[i],Figure.df$or.cc.zero.15[i])){LHS.Flag.zero.or=0.11;RHS.Flag.zero.or=0.151}
if(is.between(1,Figure.df$or.cc.zero.15[i],Figure.df$or.cc.zero.2[i])){LHS.Flag.zero.or=0.151;RHS.Flag.zero.or=0.21}
if(is.between(1,Figure.df$or.cc.zero.2[i],Figure.df$or.cc.zero.25[i])){LHS.Flag.zero.or=0.21;RHS.Flag.zero.or=0.251}
if(is.between(1,Figure.df$or.cc.zero.25[i],Figure.df$or.cc.zero.3[i])){LHS.Flag.zero.or=0.251;RHS.Flag.zero.or=0.31}
if(is.between(1,Figure.df$or.cc.zero.3[i],Figure.df$or.cc.zero.35[i])){LHS.Flag.zero.or=0.31;RHS.Flag.zero.or=0.351}
if(is.between(1,Figure.df$or.cc.zero.35[i],Figure.df$or.cc.zero.4[i])){LHS.Flag.zero.or=0.351;RHS.Flag.zero.or=0.41}
if(is.between(1,Figure.df$or.cc.zero.4[i],Figure.df$or.cc.zero.45[i])){LHS.Flag.zero.or=0.41;RHS.Flag.zero.or=0.451}
if(is.between(1,Figure.df$or.cc.zero.45[i],Figure.df$or.cc.zero.5[i])){LHS.Flag.zero.or=0.451;RHS.Flag.zero.or=0.5}
Figure.df$LHS.Flag.all.or[i]=LHS.Flag.all.or
Figure.df$RHS.Flag.all.or[i]=RHS.Flag.all.or
Figure.df$LHS.Flag.zero.or[i]=LHS.Flag.zero.or
Figure.df$RHS.Flag.zero.or[i]=RHS.Flag.zero.or
if(is.between(1,Figure.df$rr.cc.all.tpm8[i],Figure.df$rr.cc.all.tpm4[i])){LHS.Flag.all.rr=1/100000000;RHS.Flag.all.rr=1/10000}
if(is.between(1,Figure.df$rr.cc.all.tpm4[i],Figure.df$rr.cc.all.001[i])){LHS.Flag.all.rr=1/10000;RHS.Flag.all.rr=0.0011}
if(is.between(1,Figure.df$rr.cc.all.001[i],Figure.df$rr.cc.all.01[i])){LHS.Flag.all.rr=0.0011;RHS.Flag.all.rr=0.011}
if(is.between(1,Figure.df$rr.cc.all.01[i],Figure.df$rr.cc.all.015[i])){LHS.Flag.all.rr=0.011;RHS.Flag.all.rr=0.0151}
if(is.between(1,Figure.df$rr.cc.all.015[i],Figure.df$rr.cc.all.1[i])){LHS.Flag.all.rr=0.0151;RHS.Flag.all.rr=0.11}
if(is.between(1,Figure.df$rr.cc.all.1[i],Figure.df$rr.cc.all.15[i])){LHS.Flag.all.rr=0.11;RHS.Flag.all.rr=0.151}
if(is.between(1,Figure.df$rr.cc.all.15[i],Figure.df$rr.cc.all.2[i])){LHS.Flag.all.rr=0.151;RHS.Flag.all.rr=0.21}
if(is.between(1,Figure.df$rr.cc.all.2[i],Figure.df$rr.cc.all.25[i])){LHS.Flag.all.rr=0.21;RHS.Flag.all.rr=0.251}
if(is.between(1,Figure.df$rr.cc.all.25[i],Figure.df$rr.cc.all.3[i])){LHS.Flag.all.rr=0.251;RHS.Flag.all.rr=0.31}
if(is.between(1,Figure.df$rr.cc.all.3[i],Figure.df$rr.cc.all.35[i])){LHS.Flag.all.rr=0.31;RHS.Flag.all.rr=0.351}
if(is.between(1,Figure.df$rr.cc.all.35[i],Figure.df$rr.cc.all.4[i])){LHS.Flag.all.rr=0.351;RHS.Flag.all.rr=0.41}
if(is.between(1,Figure.df$rr.cc.all.4[i],Figure.df$rr.cc.all.45[i])){LHS.Flag.all.rr=0.41;RHS.Flag.all.rr=0.451}
if(is.between(1,Figure.df$rr.cc.all.45[i],Figure.df$rr.cc.all.5[i])){LHS.Flag.all.rr=0.451;RHS.Flag.all.rr=0.5}
if(is.between(1,Figure.df$rr.cc.zero.tpm8[i],Figure.df$rr.cc.zero.tpm4[i])){LHS.Flag.zero.rr=1/100000000;RHS.Flag.zero.rr=1/10000}
if(is.between(1,Figure.df$rr.cc.zero.tpm4[i],Figure.df$rr.cc.zero.001[i])){LHS.Flag.zero.rr=1/10000;RHS.Flag.zero.rr=0.0011}
if(is.between(1,Figure.df$rr.cc.zero.001[i],Figure.df$rr.cc.zero.01[i])){LHS.Flag.zero.rr=0.0011;RHS.Flag.zero.rr=0.011}
if(is.between(1,Figure.df$rr.cc.zero.01[i],Figure.df$rr.cc.zero.015[i])){LHS.Flag.zero.rr=0.011;RHS.Flag.zero.rr=0.0151}
if(is.between(1,Figure.df$rr.cc.zero.015[i],Figure.df$rr.cc.zero.1[i])){LHS.Flag.zero.rr=0.0151;RHS.Flag.zero.rr=0.11}
if(is.between(1,Figure.df$rr.cc.zero.1[i],Figure.df$rr.cc.zero.15[i])){LHS.Flag.zero.rr=0.11;RHS.Flag.zero.rr=0.151}
if(is.between(1,Figure.df$rr.cc.zero.15[i],Figure.df$rr.cc.zero.2[i])){LHS.Flag.zero.rr=0.151;RHS.Flag.zero.rr=0.21}
if(is.between(1,Figure.df$rr.cc.zero.2[i],Figure.df$rr.cc.zero.25[i])){LHS.Flag.zero.rr=0.21;RHS.Flag.zero.rr=0.251}
if(is.between(1,Figure.df$rr.cc.zero.25[i],Figure.df$rr.cc.zero.3[i])){LHS.Flag.zero.rr=0.251;RHS.Flag.zero.rr=0.31}
if(is.between(1,Figure.df$rr.cc.zero.3[i],Figure.df$rr.cc.zero.35[i])){LHS.Flag.zero.rr=0.31;RHS.Flag.zero.rr=0.351}
if(is.between(1,Figure.df$rr.cc.zero.35[i],Figure.df$rr.cc.zero.4[i])){LHS.Flag.zero.rr=0.351;RHS.Flag.zero.rr=0.41}
if(is.between(1,Figure.df$rr.cc.zero.4[i],Figure.df$rr.cc.zero.45[i])){LHS.Flag.zero.rr=0.41;RHS.Flag.zero.rr=0.451}
if(is.between(1,Figure.df$rr.cc.zero.45[i],Figure.df$rr.cc.zero.5[i])){LHS.Flag.zero.rr=0.451;RHS.Flag.zero.rr=0.5}
Figure.df$LHS.Flag.all.rr[i]=LHS.Flag.all.rr
Figure.df$RHS.Flag.all.rr[i]=RHS.Flag.all.rr
Figure.df$LHS.Flag.zero.rr[i]=LHS.Flag.zero.rr
Figure.df$RHS.Flag.zero.rr[i]=RHS.Flag.zero.rr
if(is.between(0,Figure.df$rd.cc.all.tpm8[i],Figure.df$rd.cc.all.tpm4[i])){LHS.Flag.all.rd=1/100000000;RHS.Flag.all.rd=1/10000}
if(is.between(0,Figure.df$rd.cc.all.tpm4[i],Figure.df$rd.cc.all.001[i])){LHS.Flag.all.rd=1/10000;RHS.Flag.all.rd=0.0011}
if(is.between(0,Figure.df$rd.cc.all.001[i],Figure.df$rd.cc.all.01[i])){LHS.Flag.all.rd=0.0011;RHS.Flag.all.rd=0.011}
if(is.between(0,Figure.df$rd.cc.all.01[i],Figure.df$rd.cc.all.015[i])){LHS.Flag.all.rd=0.011;RHS.Flag.all.rd=0.0151}
if(is.between(0,Figure.df$rd.cc.all.015[i],Figure.df$rd.cc.all.1[i])){LHS.Flag.all.rd=0.0151;RHS.Flag.all.rd=0.11}
if(is.between(0,Figure.df$rd.cc.all.1[i],Figure.df$rd.cc.all.15[i])){LHS.Flag.all.rd=0.11;RHS.Flag.all.rd=0.151}
if(is.between(0,Figure.df$rd.cc.all.15[i],Figure.df$rd.cc.all.2[i])){LHS.Flag.all.rd=0.151;RHS.Flag.all.rd=0.21}
if(is.between(0,Figure.df$rd.cc.all.2[i],Figure.df$rd.cc.all.25[i])){LHS.Flag.all.rd=0.21;RHS.Flag.all.rd=0.251}
if(is.between(0,Figure.df$rd.cc.all.25[i],Figure.df$rd.cc.all.3[i])){LHS.Flag.all.rd=0.251;RHS.Flag.all.rd=0.31}
if(is.between(0,Figure.df$rd.cc.all.3[i],Figure.df$rd.cc.all.35[i])){LHS.Flag.all.rd=0.31;RHS.Flag.all.rd=0.351}
if(is.between(0,Figure.df$rd.cc.all.35[i],Figure.df$rd.cc.all.4[i])){LHS.Flag.all.rd=0.351;RHS.Flag.all.rd=0.41}
if(is.between(0,Figure.df$rd.cc.all.4[i],Figure.df$rd.cc.all.45[i])){LHS.Flag.all.rd=0.41;RHS.Flag.all.rd=0.451}
if(is.between(0,Figure.df$rd.cc.all.45[i],Figure.df$rd.cc.all.5[i])){LHS.Flag.all.rd=0.451;RHS.Flag.all.rd=0.5}
if(is.between(0,Figure.df$rd.cc.zero.tpm8[i],Figure.df$rd.cc.zero.tpm4[i])){LHS.Flag.zero.rd=1/100000000;RHS.Flag.zero.rd=1/10000}
if(is.between(0,Figure.df$rd.cc.zero.tpm4[i],Figure.df$rd.cc.zero.001[i])){LHS.Flag.zero.rd=1/10000;RHS.Flag.zero.rd=0.0011}
if(is.between(0,Figure.df$rd.cc.zero.001[i],Figure.df$rd.cc.zero.01[i])){LHS.Flag.zero.rd=0.0011;RHS.Flag.zero.rd=0.011}
if(is.between(0,Figure.df$rd.cc.zero.01[i],Figure.df$rd.cc.zero.015[i])){LHS.Flag.zero.rd=0.011;RHS.Flag.zero.rd=0.0151}
if(is.between(0,Figure.df$rd.cc.zero.015[i],Figure.df$rd.cc.zero.1[i])){LHS.Flag.zero.rd=0.0151;RHS.Flag.zero.rd=0.11}
if(is.between(0,Figure.df$rd.cc.zero.1[i],Figure.df$rd.cc.zero.15[i])){LHS.Flag.zero.rd=0.11;RHS.Flag.zero.rd=0.151}
if(is.between(0,Figure.df$rd.cc.zero.15[i],Figure.df$rd.cc.zero.2[i])){LHS.Flag.zero.rd=0.151;RHS.Flag.zero.rd=0.21}
if(is.between(0,Figure.df$rd.cc.zero.2[i],Figure.df$rd.cc.zero.25[i])){LHS.Flag.zero.rd=0.21;RHS.Flag.zero.rd=0.251}
if(is.between(0,Figure.df$rd.cc.zero.25[i],Figure.df$rd.cc.zero.3[i])){LHS.Flag.zero.rd=0.251;RHS.Flag.zero.rd=0.31}
if(is.between(0,Figure.df$rd.cc.zero.3[i],Figure.df$rd.cc.zero.35[i])){LHS.Flag.zero.rd=0.31;RHS.Flag.zero.rd=0.351}
if(is.between(0,Figure.df$rd.cc.zero.35[i],Figure.df$rd.cc.zero.4[i])){LHS.Flag.zero.rd=0.351;RHS.Flag.zero.rd=0.41}
if(is.between(0,Figure.df$rd.cc.zero.4[i],Figure.df$rd.cc.zero.45[i])){LHS.Flag.zero.rd=0.41;RHS.Flag.zero.rd=0.451}
if(is.between(0,Figure.df$rd.cc.zero.45[i],Figure.df$rd.cc.zero.5[i])){LHS.Flag.zero.rd=0.451;RHS.Flag.zero.rd=0.5}
Figure.df$LHS.Flag.all.rd[i]=LHS.Flag.all.rd
Figure.df$RHS.Flag.all.rd[i]=RHS.Flag.all.rd
Figure.df$LHS.Flag.zero.rd[i]=LHS.Flag.zero.rd
Figure.df$RHS.Flag.zero.rd[i]=RHS.Flag.zero.rd
} # End of for loop extracting ibv range
ibv.ident.Rows=nrow(Figure.df)
for(kk in 1:ibv.ident.Rows){
Bet.all.or=Figure.df$RHS.Flag.all.or[kk]-Figure.df$LHS.Flag.all.or[kk]
if(Bet.all.or>0){
BAll.seq.or= Find.sequence(Figure.df$RHS.Flag.all.or[kk],Figure.df$LHS.Flag.all.or[kk])
BAll.values.or= pass2.In.Each.Row.new.cc.or(Figure.df[kk,],BAll.seq.or)
}
if(Bet.all.or==0){
BAll.values.or= data.frame( RS.all.or=0)
}
Bet.zero.or=Figure.df$RHS.Flag.zero.or[kk]-Figure.df$LHS.Flag.zero.or[kk]
if(Bet.zero.or>0){
BAll.seq.or= Find.sequence(Figure.df$RHS.Flag.zero.or[kk],Figure.df$LHS.Flag.zero.or[kk])
BAll.values.zor= pass2.In.Each.Row.new.cc.or(Figure.df[kk,],BAll.seq.or)
}
if(Bet.zero.or==0){
BAll.values.zor= data.frame( RS.zero.or=0)
}
##################### RR #################################################################################
Bet.all.rr=Figure.df$RHS.Flag.all.rr[kk]-Figure.df$LHS.Flag.all.rr[kk]
if(Bet.all.rr>0){
BAll.seq.rr= Find.sequence(Figure.df$RHS.Flag.all.rr[kk],Figure.df$LHS.Flag.all.rr[kk])
BAll.values.rr= pass2.In.Each.Row.new.cc.rr(Figure.df[kk,],BAll.seq.rr)
}
if(Bet.all.rr==0){
BAll.values.rr= data.frame( RS.all.rr=0)
}
Bet.zero.rr=Figure.df$RHS.Flag.zero.rr[kk]-Figure.df$LHS.Flag.zero.rr[kk]
if(Bet.zero.rr>0){
BAll.seq.rr= Find.sequence(Figure.df$RHS.Flag.zero.rr[kk],Figure.df$LHS.Flag.zero.rr[kk])
BAll.values.zrr= pass2.In.Each.Row.new.cc.rr(Figure.df[kk,],BAll.seq.rr)
}
if(Bet.zero.rr==0){
BAll.values.zrr= data.frame( RS.zero.rr=0)
}
#################### RD #################################################################################
Bet.all.rd=Figure.df$RHS.Flag.all.rd[kk]-Figure.df$LHS.Flag.all.rd[kk]
if(Bet.all.rd>0){
BAll.seq.rd= Find.sequence(Figure.df$RHS.Flag.all.rd[kk],Figure.df$LHS.Flag.all.rd[kk])
BAll.values.rd= pass2.In.Each.Row.new.cc.rd(Figure.df[kk,],BAll.seq.rd)
}
if(Bet.all.rd==0){
BAll.values.rd= data.frame(RS.all.rd=0)
}
Bet.zero.rd=Figure.df$RHS.Flag.zero.rd[kk]-Figure.df$LHS.Flag.zero.rd[kk]
if(Bet.zero.rd>0){
BAll.seq.rd= Find.sequence(Figure.df$RHS.Flag.zero.rd[kk],Figure.df$LHS.Flag.zero.rd[kk])
BAll.values.zrd= pass2.In.Each.Row.new.cc.rd(Figure.df[kk,],BAll.seq.rd)
}
if(Bet.zero.rd==0){
BAll.values.zrd= data.frame(RS.zero.rd=0)
}
tvar=cbind(
BAll.values.or$RS.all.or,
BAll.values.rr$RS.all.rr,
BAll.values.rd$RS.all.rd,
BAll.values.zor$RS.zero.or,
BAll.values.zrr$RS.zero.rr,
BAll.values.zrd$RS.zero.rd)
tvar.df=as.data.frame(tvar)
names(tvar.df)= c( "RS.all.or",
"RS.all.rr",
"RS.all.rd",
"RS.zero.zor" ,
"RS.zero.zrr",
"RS.zero.zrd" )
rcc=cbind(Figure.df[kk,],RS.all.or=tvar.df$RS.all.or, RS.all.rr=tvar.df$RS.all.rr, RS.all.rd=tvar.df$RS.all.rd,
RS.zero.zor=tvar.df$RS.zero.zor,RS.zero.zrr=tvar.df$RS.zero.zrr,RS.zero.zrd=tvar.df$RS.zero.zrd )
}
return(rcc)
} # End of function Find.RS.Metric
######################################################################################################
#' Find the sequence for the given range
#' @param RHS/value - description
#' @param LHS.value - description
#' @return A dataframe with
#' \item{x1}{Sequence}
#' @family Internal methods
#' @keywords internal
Find.sequence <- function(RHS.value,LHS.value){
small=min(LHS.value, RHS.value)
#if(small>0.01){small=small+0.001}
big=max(LHS.value, RHS.value)
Ret.seq=seq(small, big, length.out = 10)
return(Ret.seq)
}
######################################################################################################
#' Find the OR,RR and RD for each row with new CC range
#' @param odf.row - description
#' @param cc.vals - description
#' @return A dataframe with
#' \item{x1}{Sequence}
#' @family Internal methods
#' @keywords internal
pass2.In.Each.Row.new.cc.or <-function(odf.row,cc.vals)
{
iterations = length(cc.vals)
previous.ora=data.frame(ora=0,orz=0)
previous.cc = 0
RS.all.or=0
RS.zero.or=0
for(i in 1:iterations){
cc.value = cc.vals[i]
ora.results=Calculate.cc.OR(odf.row, cc.value )
if(i>1){
if(previous.ora$ora==1){RS.all.or=previous.cc}
if(is.between(1,previous.ora$ora,ora.results$ora)){RS.all.or=previous.cc}
if(previous.ora$orz==1){RS.zero.or=previous.cc}
if(is.between(1,previous.ora$orz,ora.results$orz)){RS.zero.or=previous.cc}
}
previous.ora=ora.results
previous.cc = cc.value
}
RS.metric.or.df = data.frame(
RS.all.or=RS.all.or,
RS.zero.or=RS.zero.or)
return(RS.metric.or.df)
}
######################################################################################################
#' Find the OR,RR and RD for each row with new CC range
#' @param odf.row - description
#' @param cc.vals - description
#' @return A dataframe with
#' \item{x1}{Sequence}
#' @family Internal methods
#' @keywords internal
pass2.In.Each.Row.new.cc.rr <-function(odf.row,cc.vals)
{
iterations = length(cc.vals)
previous.rra=data.frame(rra=0,rrz=0)
previous.cc=0
RS.all.rr=0
RS.zero.rr=0
for(i in 1:iterations){
cc.value = cc.vals[i]
rra.results=Calculate.cc.RR(odf.row, cc.value )
if(i>1){
if(previous.rra$rra==1){RS.all.rr=previous.cc}
if(previous.rra$rrz==1){RS.zero.rr=previous.cc}
if(is.between(1,previous.rra$rra,rra.results$rra)){RS.all.rr=previous.cc}
if(is.between(1,previous.rra$rrz,rra.results$rrz)){RS.zero.rr=previous.cc}
}
previous.rra=rra.results
previous.cc=cc.value
}
RS.metric.rr.df = data.frame(
RS.all.rr=RS.all.rr,
RS.zero.rr=RS.zero.rr)
return(RS.metric.rr.df)
}
############################################################################################
######################################################################################################
#' Find the OR,RR and RD for each row with new CC range
#' @param odf.row - description
#' @param cc.vals - description
#' @return A dataframe with
#' \item{x1}{Sequence}
#' @family Internal methods
#' @keywords internal
pass2.In.Each.Row.new.cc.rd <-function(odf.row,cc.vals)
{
iterations = length(cc.vals)
previous.rda=data.frame(rda=0,rdz=0)
previous.cc=0
RS.all.rd=0
RS.zero.rd=0
for(i in 1:iterations){
cc.value = cc.vals[i]
rda.results=Calculate.cc.RD(odf.row, cc.value )
if(i>1){
if(previous.rda$rda==0){RS.all.rd=previous.cc}
if(previous.rda$rdz==0){RS.zero.rd=previous.cc}
if(is.between(0,previous.rda$rda,rda.results$rda)){RS.all.rd=previous.cc}
if(is.between(0,previous.rda$rdz,rda.results$rdz)){RS.zero.rd=previous.cc}
}
previous.rda=rda.results
previous.cc=cc.value
}
RS.metric.rd.df = data.frame(
RS.all.rd=RS.all.rd,
RS.zero.rd=RS.zero.rd)
return(RS.metric.rd.df)
}
############################################################################################
RajeswaranV/vcdPlus documentation built on May 27, 2019, 7:28 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.
Defines functions Find.RS.metric Find.sequence pass2.In.Each.Row.new.cc.or pass2.In.Each.Row.new.cc.rr pass2.In.Each.Row.new.cc.rd
Documented in Find.RS.metric Find.sequence pass2.In.Each.Row.new.cc.or pass2.In.Each.Row.new.cc.rd pass2.In.Each.Row.new.cc.rr
#' Find the point of reversal of OR/RR/RD
#' @param Figure.df - description
#' @return A dataframe with
#' \item{x1}{Sequence}
#' @family Internal methods
#' @keywords internal
Find.RS.metric<-function(Figure.df)
{
LHS.Flag.all.or=0
RHS.Flag.all.or=0
LHS.Flag.all.rr=0
RHS.Flag.all.rr=0
LHS.Flag.all.rd=0
RHS.Flag.all.rd=0
LHS.Flag.zero.or=0
RHS.Flag.zero.or=0
LHS.Flag.zero.rr=0
RHS.Flag.zero.rr=0
LHS.Flag.zero.rd=0
RHS.Flag.zero.rd=0
Figure.df$LHS.Flag.all.or=NULL
Figure.df$RHS.Flag.all.or=NULL
Figure.df$LHS.Flag.all.rr=NULL
Figure.df$RHS.Flag.all.rr=NULL
Figure.df$LHS.Flag.all.rd=NULL
Figure.df$RHS.Flag.all.rd=NULL
Figure.df$LHS.Flag.zero.or=NULL
Figure.df$RHS.Flag.zero.or=NULL
Figure.df$LHS.Flag.zero.rr=NULL
Figure.df$RHS.Flag.zero.rr=NULL
Figure.df$LHS.Flag.zero.rd=NULL
Figure.df$RHS.Flag.zero.rd=NULL
ibv.Rows=nrow(Figure.df)
for(i in 1:ibv.Rows){
if(is.between(1,Figure.df$or.cc.all.tpm8[i],Figure.df$or.cc.all.tpm4[i])){LHS.Flag.all.or=1/100000000;RHS.Flag.all.or=1/10000}
if(is.between(1,Figure.df$or.cc.all.tpm4[i],Figure.df$or.cc.all.001[i])){LHS.Flag.all.or=1/10000;RHS.Flag.all.or=0.0011}
if(is.between(1,Figure.df$or.cc.all.001[i],Figure.df$or.cc.all.01[i])){LHS.Flag.all.or=0.0011;RHS.Flag.all.or=0.011}
if(is.between(1,Figure.df$or.cc.all.01[i],Figure.df$or.cc.all.015[i])){LHS.Flag.all.or=0.011;RHS.Flag.all.or=0.0151}
if(is.between(1,Figure.df$or.cc.all.015[i],Figure.df$or.cc.all.1[i])){LHS.Flag.all.or=0.0151;RHS.Flag.all.or=0.11}
if(is.between(1,Figure.df$or.cc.all.1[i],Figure.df$or.cc.all.15[i])){LHS.Flag.all.or=0.11;RHS.Flag.all.or=0.151}
if(is.between(1,Figure.df$or.cc.all.15[i],Figure.df$or.cc.all.2[i])){LHS.Flag.all.or=0.151;RHS.Flag.all.or=0.21}
if(is.between(1,Figure.df$or.cc.all.2[i],Figure.df$or.cc.all.25[i])){LHS.Flag.all.or=0.21;RHS.Flag.all.or=0.251}
if(is.between(1,Figure.df$or.cc.all.25[i],Figure.df$or.cc.all.3[i])){LHS.Flag.all.or=0.251;RHS.Flag.all.or=0.31}
if(is.between(1,Figure.df$or.cc.all.3[i],Figure.df$or.cc.all.35[i])){LHS.Flag.all.or=0.31;RHS.Flag.all.or=0.351}
if(is.between(1,Figure.df$or.cc.all.35[i],Figure.df$or.cc.all.4[i])){LHS.Flag.all.or=0.351;RHS.Flag.all.or=0.41}
if(is.between(1,Figure.df$or.cc.all.4[i],Figure.df$or.cc.all.45[i])){LHS.Flag.all.or=0.41;RHS.Flag.all.or=0.451}
if(is.between(1,Figure.df$or.cc.all.45[i],Figure.df$or.cc.all.5[i])){LHS.Flag.all.or=0.451;RHS.Flag.all.or=0.5}
if(is.between(1,Figure.df$or.cc.zero.tpm8[i],Figure.df$or.cc.zero.tpm4[i])){LHS.Flag.zero.or=1/100000000;RHS.Flag.zero.or=1/10000}
if(is.between(1,Figure.df$or.cc.zero.tpm4[i],Figure.df$or.cc.zero.001[i])){LHS.Flag.zero.or=1/10000;RHS.Flag.zero.or=0.0011}
if(is.between(1,Figure.df$or.cc.zero.001[i],Figure.df$or.cc.zero.01[i])){LHS.Flag.zero.or=0.0011;RHS.Flag.zero.or=0.011}
if(is.between(1,Figure.df$or.cc.zero.01[i],Figure.df$or.cc.zero.015[i])){LHS.Flag.zero.or=0.011;RHS.Flag.zero.or=0.0151}
if(is.between(1,Figure.df$or.cc.zero.015[i],Figure.df$or.cc.zero.1[i])){LHS.Flag.zero.or=0.0151;RHS.Flag.zero.or=0.11}
if(is.between(1,Figure.df$or.cc.zero.1[i],Figure.df$or.cc.zero.15[i])){LHS.Flag.zero.or=0.11;RHS.Flag.zero.or=0.151}
if(is.between(1,Figure.df$or.cc.zero.15[i],Figure.df$or.cc.zero.2[i])){LHS.Flag.zero.or=0.151;RHS.Flag.zero.or=0.21}
if(is.between(1,Figure.df$or.cc.zero.2[i],Figure.df$or.cc.zero.25[i])){LHS.Flag.zero.or=0.21;RHS.Flag.zero.or=0.251}
if(is.between(1,Figure.df$or.cc.zero.25[i],Figure.df$or.cc.zero.3[i])){LHS.Flag.zero.or=0.251;RHS.Flag.zero.or=0.31}
if(is.between(1,Figure.df$or.cc.zero.3[i],Figure.df$or.cc.zero.35[i])){LHS.Flag.zero.or=0.31;RHS.Flag.zero.or=0.351}
if(is.between(1,Figure.df$or.cc.zero.35[i],Figure.df$or.cc.zero.4[i])){LHS.Flag.zero.or=0.351;RHS.Flag.zero.or=0.41}
if(is.between(1,Figure.df$or.cc.zero.4[i],Figure.df$or.cc.zero.45[i])){LHS.Flag.zero.or=0.41;RHS.Flag.zero.or=0.451}
if(is.between(1,Figure.df$or.cc.zero.45[i],Figure.df$or.cc.zero.5[i])){LHS.Flag.zero.or=0.451;RHS.Flag.zero.or=0.5}
Figure.df$LHS.Flag.all.or[i]=LHS.Flag.all.or
Figure.df$RHS.Flag.all.or[i]=RHS.Flag.all.or
Figure.df$LHS.Flag.zero.or[i]=LHS.Flag.zero.or
Figure.df$RHS.Flag.zero.or[i]=RHS.Flag.zero.or
if(is.between(1,Figure.df$rr.cc.all.tpm8[i],Figure.df$rr.cc.all.tpm4[i])){LHS.Flag.all.rr=1/100000000;RHS.Flag.all.rr=1/10000}
if(is.between(1,Figure.df$rr.cc.all.tpm4[i],Figure.df$rr.cc.all.001[i])){LHS.Flag.all.rr=1/10000;RHS.Flag.all.rr=0.0011}
if(is.between(1,Figure.df$rr.cc.all.001[i],Figure.df$rr.cc.all.01[i])){LHS.Flag.all.rr=0.0011;RHS.Flag.all.rr=0.011}
if(is.between(1,Figure.df$rr.cc.all.01[i],Figure.df$rr.cc.all.015[i])){LHS.Flag.all.rr=0.011;RHS.Flag.all.rr=0.0151}
if(is.between(1,Figure.df$rr.cc.all.015[i],Figure.df$rr.cc.all.1[i])){LHS.Flag.all.rr=0.0151;RHS.Flag.all.rr=0.11}
if(is.between(1,Figure.df$rr.cc.all.1[i],Figure.df$rr.cc.all.15[i])){LHS.Flag.all.rr=0.11;RHS.Flag.all.rr=0.151}
if(is.between(1,Figure.df$rr.cc.all.15[i],Figure.df$rr.cc.all.2[i])){LHS.Flag.all.rr=0.151;RHS.Flag.all.rr=0.21}
if(is.between(1,Figure.df$rr.cc.all.2[i],Figure.df$rr.cc.all.25[i])){LHS.Flag.all.rr=0.21;RHS.Flag.all.rr=0.251}
if(is.between(1,Figure.df$rr.cc.all.25[i],Figure.df$rr.cc.all.3[i])){LHS.Flag.all.rr=0.251;RHS.Flag.all.rr=0.31}
if(is.between(1,Figure.df$rr.cc.all.3[i],Figure.df$rr.cc.all.35[i])){LHS.Flag.all.rr=0.31;RHS.Flag.all.rr=0.351}
if(is.between(1,Figure.df$rr.cc.all.35[i],Figure.df$rr.cc.all.4[i])){LHS.Flag.all.rr=0.351;RHS.Flag.all.rr=0.41}
if(is.between(1,Figure.df$rr.cc.all.4[i],Figure.df$rr.cc.all.45[i])){LHS.Flag.all.rr=0.41;RHS.Flag.all.rr=0.451}
if(is.between(1,Figure.df$rr.cc.all.45[i],Figure.df$rr.cc.all.5[i])){LHS.Flag.all.rr=0.451;RHS.Flag.all.rr=0.5}
if(is.between(1,Figure.df$rr.cc.zero.tpm8[i],Figure.df$rr.cc.zero.tpm4[i])){LHS.Flag.zero.rr=1/100000000;RHS.Flag.zero.rr=1/10000}
if(is.between(1,Figure.df$rr.cc.zero.tpm4[i],Figure.df$rr.cc.zero.001[i])){LHS.Flag.zero.rr=1/10000;RHS.Flag.zero.rr=0.0011}
if(is.between(1,Figure.df$rr.cc.zero.001[i],Figure.df$rr.cc.zero.01[i])){LHS.Flag.zero.rr=0.0011;RHS.Flag.zero.rr=0.011}
if(is.between(1,Figure.df$rr.cc.zero.01[i],Figure.df$rr.cc.zero.015[i])){LHS.Flag.zero.rr=0.011;RHS.Flag.zero.rr=0.0151}
if(is.between(1,Figure.df$rr.cc.zero.015[i],Figure.df$rr.cc.zero.1[i])){LHS.Flag.zero.rr=0.0151;RHS.Flag.zero.rr=0.11}
if(is.between(1,Figure.df$rr.cc.zero.1[i],Figure.df$rr.cc.zero.15[i])){LHS.Flag.zero.rr=0.11;RHS.Flag.zero.rr=0.151}
if(is.between(1,Figure.df$rr.cc.zero.15[i],Figure.df$rr.cc.zero.2[i])){LHS.Flag.zero.rr=0.151;RHS.Flag.zero.rr=0.21}
if(is.between(1,Figure.df$rr.cc.zero.2[i],Figure.df$rr.cc.zero.25[i])){LHS.Flag.zero.rr=0.21;RHS.Flag.zero.rr=0.251}
if(is.between(1,Figure.df$rr.cc.zero.25[i],Figure.df$rr.cc.zero.3[i])){LHS.Flag.zero.rr=0.251;RHS.Flag.zero.rr=0.31}
if(is.between(1,Figure.df$rr.cc.zero.3[i],Figure.df$rr.cc.zero.35[i])){LHS.Flag.zero.rr=0.31;RHS.Flag.zero.rr=0.351}
if(is.between(1,Figure.df$rr.cc.zero.35[i],Figure.df$rr.cc.zero.4[i])){LHS.Flag.zero.rr=0.351;RHS.Flag.zero.rr=0.41}
if(is.between(1,Figure.df$rr.cc.zero.4[i],Figure.df$rr.cc.zero.45[i])){LHS.Flag.zero.rr=0.41;RHS.Flag.zero.rr=0.451}
if(is.between(1,Figure.df$rr.cc.zero.45[i],Figure.df$rr.cc.zero.5[i])){LHS.Flag.zero.rr=0.451;RHS.Flag.zero.rr=0.5}
Figure.df$LHS.Flag.all.rr[i]=LHS.Flag.all.rr
Figure.df$RHS.Flag.all.rr[i]=RHS.Flag.all.rr
Figure.df$LHS.Flag.zero.rr[i]=LHS.Flag.zero.rr
Figure.df$RHS.Flag.zero.rr[i]=RHS.Flag.zero.rr
if(is.between(0,Figure.df$rd.cc.all.tpm8[i],Figure.df$rd.cc.all.tpm4[i])){LHS.Flag.all.rd=1/100000000;RHS.Flag.all.rd=1/10000}
if(is.between(0,Figure.df$rd.cc.all.tpm4[i],Figure.df$rd.cc.all.001[i])){LHS.Flag.all.rd=1/10000;RHS.Flag.all.rd=0.0011}
if(is.between(0,Figure.df$rd.cc.all.001[i],Figure.df$rd.cc.all.01[i])){LHS.Flag.all.rd=0.0011;RHS.Flag.all.rd=0.011}
if(is.between(0,Figure.df$rd.cc.all.01[i],Figure.df$rd.cc.all.015[i])){LHS.Flag.all.rd=0.011;RHS.Flag.all.rd=0.0151}
if(is.between(0,Figure.df$rd.cc.all.015[i],Figure.df$rd.cc.all.1[i])){LHS.Flag.all.rd=0.0151;RHS.Flag.all.rd=0.11}
if(is.between(0,Figure.df$rd.cc.all.1[i],Figure.df$rd.cc.all.15[i])){LHS.Flag.all.rd=0.11;RHS.Flag.all.rd=0.151}
if(is.between(0,Figure.df$rd.cc.all.15[i],Figure.df$rd.cc.all.2[i])){LHS.Flag.all.rd=0.151;RHS.Flag.all.rd=0.21}
if(is.between(0,Figure.df$rd.cc.all.2[i],Figure.df$rd.cc.all.25[i])){LHS.Flag.all.rd=0.21;RHS.Flag.all.rd=0.251}
if(is.between(0,Figure.df$rd.cc.all.25[i],Figure.df$rd.cc.all.3[i])){LHS.Flag.all.rd=0.251;RHS.Flag.all.rd=0.31}
if(is.between(0,Figure.df$rd.cc.all.3[i],Figure.df$rd.cc.all.35[i])){LHS.Flag.all.rd=0.31;RHS.Flag.all.rd=0.351}
if(is.between(0,Figure.df$rd.cc.all.35[i],Figure.df$rd.cc.all.4[i])){LHS.Flag.all.rd=0.351;RHS.Flag.all.rd=0.41}
if(is.between(0,Figure.df$rd.cc.all.4[i],Figure.df$rd.cc.all.45[i])){LHS.Flag.all.rd=0.41;RHS.Flag.all.rd=0.451}
if(is.between(0,Figure.df$rd.cc.all.45[i],Figure.df$rd.cc.all.5[i])){LHS.Flag.all.rd=0.451;RHS.Flag.all.rd=0.5}
if(is.between(0,Figure.df$rd.cc.zero.tpm8[i],Figure.df$rd.cc.zero.tpm4[i])){LHS.Flag.zero.rd=1/100000000;RHS.Flag.zero.rd=1/10000}
if(is.between(0,Figure.df$rd.cc.zero.tpm4[i],Figure.df$rd.cc.zero.001[i])){LHS.Flag.zero.rd=1/10000;RHS.Flag.zero.rd=0.0011}
if(is.between(0,Figure.df$rd.cc.zero.001[i],Figure.df$rd.cc.zero.01[i])){LHS.Flag.zero.rd=0.0011;RHS.Flag.zero.rd=0.011}
if(is.between(0,Figure.df$rd.cc.zero.01[i],Figure.df$rd.cc.zero.015[i])){LHS.Flag.zero.rd=0.011;RHS.Flag.zero.rd=0.0151}
if(is.between(0,Figure.df$rd.cc.zero.015[i],Figure.df$rd.cc.zero.1[i])){LHS.Flag.zero.rd=0.0151;RHS.Flag.zero.rd=0.11}
if(is.between(0,Figure.df$rd.cc.zero.1[i],Figure.df$rd.cc.zero.15[i])){LHS.Flag.zero.rd=0.11;RHS.Flag.zero.rd=0.151}
if(is.between(0,Figure.df$rd.cc.zero.15[i],Figure.df$rd.cc.zero.2[i])){LHS.Flag.zero.rd=0.151;RHS.Flag.zero.rd=0.21}
if(is.between(0,Figure.df$rd.cc.zero.2[i],Figure.df$rd.cc.zero.25[i])){LHS.Flag.zero.rd=0.21;RHS.Flag.zero.rd=0.251}
if(is.between(0,Figure.df$rd.cc.zero.25[i],Figure.df$rd.cc.zero.3[i])){LHS.Flag.zero.rd=0.251;RHS.Flag.zero.rd=0.31}
if(is.between(0,Figure.df$rd.cc.zero.3[i],Figure.df$rd.cc.zero.35[i])){LHS.Flag.zero.rd=0.31;RHS.Flag.zero.rd=0.351}
if(is.between(0,Figure.df$rd.cc.zero.35[i],Figure.df$rd.cc.zero.4[i])){LHS.Flag.zero.rd=0.351;RHS.Flag.zero.rd=0.41}
if(is.between(0,Figure.df$rd.cc.zero.4[i],Figure.df$rd.cc.zero.45[i])){LHS.Flag.zero.rd=0.41;RHS.Flag.zero.rd=0.451}
if(is.between(0,Figure.df$rd.cc.zero.45[i],Figure.df$rd.cc.zero.5[i])){LHS.Flag.zero.rd=0.451;RHS.Flag.zero.rd=0.5}
Figure.df$LHS.Flag.all.rd[i]=LHS.Flag.all.rd
Figure.df$RHS.Flag.all.rd[i]=RHS.Flag.all.rd
Figure.df$LHS.Flag.zero.rd[i]=LHS.Flag.zero.rd
Figure.df$RHS.Flag.zero.rd[i]=RHS.Flag.zero.rd
} # End of for loop extracting ibv range
ibv.ident.Rows=nrow(Figure.df)
for(kk in 1:ibv.ident.Rows){
Bet.all.or=Figure.df$RHS.Flag.all.or[kk]-Figure.df$LHS.Flag.all.or[kk]
if(Bet.all.or>0){
BAll.seq.or= Find.sequence(Figure.df$RHS.Flag.all.or[kk],Figure.df$LHS.Flag.all.or[kk])
BAll.values.or= pass2.In.Each.Row.new.cc.or(Figure.df[kk,],BAll.seq.or)
}
if(Bet.all.or==0){
BAll.values.or= data.frame( RS.all.or=0)
}
Bet.zero.or=Figure.df$RHS.Flag.zero.or[kk]-Figure.df$LHS.Flag.zero.or[kk]
if(Bet.zero.or>0){
BAll.seq.or= Find.sequence(Figure.df$RHS.Flag.zero.or[kk],Figure.df$LHS.Flag.zero.or[kk])
BAll.values.zor= pass2.In.Each.Row.new.cc.or(Figure.df[kk,],BAll.seq.or)
}
if(Bet.zero.or==0){
BAll.values.zor= data.frame( RS.zero.or=0)
}
##################### RR #################################################################################
Bet.all.rr=Figure.df$RHS.Flag.all.rr[kk]-Figure.df$LHS.Flag.all.rr[kk]
if(Bet.all.rr>0){
BAll.seq.rr= Find.sequence(Figure.df$RHS.Flag.all.rr[kk],Figure.df$LHS.Flag.all.rr[kk])
BAll.values.rr= pass2.In.Each.Row.new.cc.rr(Figure.df[kk,],BAll.seq.rr)
}
if(Bet.all.rr==0){
BAll.values.rr= data.frame( RS.all.rr=0)
}
Bet.zero.rr=Figure.df$RHS.Flag.zero.rr[kk]-Figure.df$LHS.Flag.zero.rr[kk]
if(Bet.zero.rr>0){
BAll.seq.rr= Find.sequence(Figure.df$RHS.Flag.zero.rr[kk],Figure.df$LHS.Flag.zero.rr[kk])
BAll.values.zrr= pass2.In.Each.Row.new.cc.rr(Figure.df[kk,],BAll.seq.rr)
}
if(Bet.zero.rr==0){
BAll.values.zrr= data.frame( RS.zero.rr=0)
}
#################### RD #################################################################################
Bet.all.rd=Figure.df$RHS.Flag.all.rd[kk]-Figure.df$LHS.Flag.all.rd[kk]
if(Bet.all.rd>0){
BAll.seq.rd= Find.sequence(Figure.df$RHS.Flag.all.rd[kk],Figure.df$LHS.Flag.all.rd[kk])
BAll.values.rd= pass2.In.Each.Row.new.cc.rd(Figure.df[kk,],BAll.seq.rd)
}
if(Bet.all.rd==0){
BAll.values.rd= data.frame(RS.all.rd=0)
}
Bet.zero.rd=Figure.df$RHS.Flag.zero.rd[kk]-Figure.df$LHS.Flag.zero.rd[kk]
if(Bet.zero.rd>0){
BAll.seq.rd= Find.sequence(Figure.df$RHS.Flag.zero.rd[kk],Figure.df$LHS.Flag.zero.rd[kk])
BAll.values.zrd= pass2.In.Each.Row.new.cc.rd(Figure.df[kk,],BAll.seq.rd)
}
if(Bet.zero.rd==0){
BAll.values.zrd= data.frame(RS.zero.rd=0)
}
tvar=cbind(
BAll.values.or$RS.all.or,
BAll.values.rr$RS.all.rr,
BAll.values.rd$RS.all.rd,
BAll.values.zor$RS.zero.or,
BAll.values.zrr$RS.zero.rr,
BAll.values.zrd$RS.zero.rd)
tvar.df=as.data.frame(tvar)
names(tvar.df)= c( "RS.all.or",
"RS.all.rr",
"RS.all.rd",
"RS.zero.zor" ,
"RS.zero.zrr",
"RS.zero.zrd" )
rcc=cbind(Figure.df[kk,],RS.all.or=tvar.df$RS.all.or, RS.all.rr=tvar.df$RS.all.rr, RS.all.rd=tvar.df$RS.all.rd,
RS.zero.zor=tvar.df$RS.zero.zor,RS.zero.zrr=tvar.df$RS.zero.zrr,RS.zero.zrd=tvar.df$RS.zero.zrd )
}
return(rcc)
} # End of function Find.RS.Metric
######################################################################################################
#' Find the sequence for the given range
#' @param RHS/value - description
#' @param LHS.value - description
#' @return A dataframe with
#' \item{x1}{Sequence}
#' @family Internal methods
#' @keywords internal
Find.sequence <- function(RHS.value,LHS.value){
small=min(LHS.value, RHS.value)
#if(small>0.01){small=small+0.001}
big=max(LHS.value, RHS.value)
Ret.seq=seq(small, big, length.out = 10)
return(Ret.seq)
}
######################################################################################################
#' Find the OR,RR and RD for each row with new CC range
#' @param odf.row - description
#' @param cc.vals - description
#' @return A dataframe with
#' \item{x1}{Sequence}
#' @family Internal methods
#' @keywords internal
pass2.In.Each.Row.new.cc.or <-function(odf.row,cc.vals)
{
iterations = length(cc.vals)
previous.ora=data.frame(ora=0,orz=0)
previous.cc = 0
RS.all.or=0
RS.zero.or=0
for(i in 1:iterations){
cc.value = cc.vals[i]
ora.results=Calculate.cc.OR(odf.row, cc.value )
if(i>1){
if(previous.ora$ora==1){RS.all.or=previous.cc}
if(is.between(1,previous.ora$ora,ora.results$ora)){RS.all.or=previous.cc}
if(previous.ora$orz==1){RS.zero.or=previous.cc}
if(is.between(1,previous.ora$orz,ora.results$orz)){RS.zero.or=previous.cc}
}
previous.ora=ora.results
previous.cc = cc.value
}
RS.metric.or.df = data.frame(
RS.all.or=RS.all.or,
RS.zero.or=RS.zero.or)
return(RS.metric.or.df)
}
######################################################################################################
#' Find the OR,RR and RD for each row with new CC range
#' @param odf.row - description
#' @param cc.vals - description
#' @return A dataframe with
#' \item{x1}{Sequence}
#' @family Internal methods
#' @keywords internal
pass2.In.Each.Row.new.cc.rr <-function(odf.row,cc.vals)
{
iterations = length(cc.vals)
previous.rra=data.frame(rra=0,rrz=0)
previous.cc=0
RS.all.rr=0
RS.zero.rr=0
for(i in 1:iterations){
cc.value = cc.vals[i]
rra.results=Calculate.cc.RR(odf.row, cc.value )
if(i>1){
if(previous.rra$rra==1){RS.all.rr=previous.cc}
if(previous.rra$rrz==1){RS.zero.rr=previous.cc}
if(is.between(1,previous.rra$rra,rra.results$rra)){RS.all.rr=previous.cc}
if(is.between(1,previous.rra$rrz,rra.results$rrz)){RS.zero.rr=previous.cc}
}
previous.rra=rra.results
previous.cc=cc.value
}
RS.metric.rr.df = data.frame(
RS.all.rr=RS.all.rr,
RS.zero.rr=RS.zero.rr)
return(RS.metric.rr.df)
}
############################################################################################
######################################################################################################
#' Find the OR,RR and RD for each row with new CC range
#' @param odf.row - description
#' @param cc.vals - description
#' @return A dataframe with
#' \item{x1}{Sequence}
#' @family Internal methods
#' @keywords internal
pass2.In.Each.Row.new.cc.rd <-function(odf.row,cc.vals)
{
iterations = length(cc.vals)
previous.rda=data.frame(rda=0,rdz=0)
previous.cc=0
RS.all.rd=0
RS.zero.rd=0
for(i in 1:iterations){
cc.value = cc.vals[i]
rda.results=Calculate.cc.RD(odf.row, cc.value )
if(i>1){
if(previous.rda$rda==0){RS.all.rd=previous.cc}
if(previous.rda$rdz==0){RS.zero.rd=previous.cc}
if(is.between(0,previous.rda$rda,rda.results$rda)){RS.all.rd=previous.cc}
if(is.between(0,previous.rda$rdz,rda.results$rdz)){RS.zero.rd=previous.cc}
}
previous.rda=rda.results
previous.cc=cc.value
}
RS.metric.rd.df = data.frame(
RS.all.rd=RS.all.rd,
RS.zero.rd=RS.zero.rd)
return(RS.metric.rd.df)
}
############################################################################################
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