R erasing objects without command line for this [closed] - r

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I have a this problem with my code: when I run all the script I get the error Error: object 'i' not found and Error: object 'scp.L50' not found. The data frame and de counter i are erased without order, and after that, (obviously) R cannot find scp.L50 and add information on it. But, I don't know why, when I run just a part of the code (without the #bla bla bla) it works ok.
A few days ago all code was working fine, but now I have this issue. I've tried to update R (smooth sidewalk to full of ingredients) but still not working. Can someone help me?
Thanks!
Here is the code:
library("minpack.lm", lib.loc="/Library/Frameworks/R.framework/Versions/3.1/Resources/library")
library("gdata", lib.loc="/Library/Frameworks/R.framework/Versions/3.1/Resources/library")
sex<-c("FEMALE","MALE","ALL")
files <- list.files(pattern = "txt")
scp.L50<-data.frame()
for (i in 1:length(files)){
dados<-read.table(files[i],header=TRUE,fill = TRUE)
dados<-na.exclude(dados)
dados<-dados[order(dados[,1]),]
rownames(dados)<-1:nrow(dados)
species<-gsub(".txt", "", files[i]);print(paste("Species: ",gsub("_", " ", species)))
if (ncol(dados)==3){
dadosF<-dados[(which(dados[,3]=="F",arr.ind=TRUE)),]; dadosM<-dados[(which(dados[,3]=="M",arr.ind=TRUE)),]; dados.total<-dados
if (length(dadosF[,1])!=0){
dadosF<-dadosF[order(dadosF[,1]),]
} else {
rm(dadosF)}
if (length(dadosM[,1])!=0){
dadosM<-dadosM[order(dadosM[,1]),]
} else {
rm(dadosM)}}
if(ncol(dados)==3){
for (gender in sex){
try({
if (gender=="FEMALE") {
dados<-dadosF
}},silent=TRUE)
try({
if (gender=="MALE"){
dados<-dadosM
}},silent=TRUE)
try({
if (gender=="ALL"){
dados<-dados.total
}},silent=TRUE)
dados<-dados[,-3]
par(mfrow=c(1,1))
if (dados[1,1]==0) {
dados<-dados[-1,]}
unifitted<-nlsLM(Weight~a*Length^b,
data=dados,
start=list(a=0.1,b=3),
weights=wfct(fitted),
control=nls.lm.control(maxiter=1024))
coeff.uni<-as.data.frame(coef(summary(unifitted))[,1:2])
dados<-cbind(dados,resid(unifitted)/dados[,2],predict(unifitted))
sd.dados<-sd(dados[,3])
rownames(dados)<-1:nrow(dados)
sd.dados<-sd(dados[,3])
for (j in nrow(dados):1){
if (dados[j,3]/sd.dados > 2.5){dados<-dados[-j,]
}else{
if (dados[j,3]/sd.dados < -2.5){dados<-dados[-j,]}
}}
interval.cons(25)
unifitted.aver<-(coeff.uni[1,1]*dataLC[,1]^coeff.uni[2,1])
unifitted.aver.resid<-(dataLC[,2]-(coeff.uni[1,1]*dataLC[,1]^coeff.uni[2,1]))/dataLC$AvWeight
dataLC<-cbind(dataLC,unifitted.aver.resid,unifitted.aver)
rownames(dados)<-1:nrow(dados)
dados.1.3<-dados[1:(round(nrow(dados)/3)),]
dados.3.3<-dados[(nrow(dados)-(round(nrow(dados)/3))):nrow(dados),]
assign("best.loop",.GlobalEnv)
sum.resid<-999999999999999999999999999999
polyfitted.1.3<-nlsLM(Weight ~ a * Length^b,
data=dados.1.3,
start=list(a=0.01,b=3),
control=nls.lm.control(maxiter=1024))
coeff.poly.1.3<-as.vector(coef(polyfitted.1.3))
polyfitted.3.3<-nlsLM(Weight ~ a * Length^b,
data=dados.3.3,
start=list(a=0.01,b=3),
control=nls.lm.control(maxiter=1024))
coeff.poly.3.3<-as.vector(coef(polyfitted.3.3))
scp.matrix<-seq(from=dados[30,1], to=dados[(nrow(dados)-30),1], by=1)
r.squared.test<-2
for (scp.loop in scp.matrix){
for (fit.rate in 1:10){
try({
polyfitted.total<-nlsLM(Weight ~ (a2 * Length^b2) * (1/(1 + exp(-fit.rate * (Length - scp.loop)))) +
(a1 * Length^b1) * (1-(1/(1 + exp(-fit.rate * (Length - scp.loop))))),
data=dados,
start=list(a1=coeff.poly.1.3[[1]],b1=coeff.poly.1.3[[2]],a2=coeff.poly.3.3[[1]],b2=coeff.poly.3.3[[2]]),
lower=c(a1=coeff.poly.1.3[[1]]-coeff.poly.1.3[[1]]*0.7,b1=coeff.poly.1.3[[2]]-coeff.poly.1.3[[2]]*0.7,a2=coeff.poly.3.3[[1]]-coeff.poly.3.3[[1]]*0.7,b2=coeff.poly.3.3[[2]]-coeff.poly.3.3[[2]]*0.7),
upper=c(a1=coeff.poly.1.3[[1]]+coeff.poly.1.3[[1]]*0.7,b1=coeff.poly.1.3[[2]]+coeff.poly.1.3[[2]]*0.7,a2=coeff.poly.3.3[[1]]+coeff.poly.3.3[[1]]*0.7,b2=coeff.poly.3.3[[2]]+coeff.poly.3.3[[2]]*0.7),
control=nls.lm.control(maxiter=1024))
coeff.poly<-as.vector(coef(polyfitted.total))
polyfitted.aver.resid<-(dataLC$AvWeight-((coeff.poly[[3]] * dataLC$LengthClass^coeff.poly[[4]]) * (1/(1 + exp(-fit.rate * (dataLC$LengthClass - scp.loop)))) +
(coeff.poly[[1]] * dataLC$LengthClass^coeff.poly[[2]]) * (1-(1/(1 + exp(-fit.rate * (dataLC$LengthClass - scp.loop)))))))/dataLC$AvWeight
polyfitted.aver<-((coeff.poly[[3]] * dataLC$LengthClass^coeff.poly[[4]]) * (1/(1 + exp(-fit.rate * (dataLC$LengthClass - scp.loop))))) +
((coeff.poly[[1]] * dataLC$LengthClass^coeff.poly[[2]]) * (1-(1/(1 + exp(-fit.rate * (dataLC$LengthClass - scp.loop))))))
polyfitted.resid<-(dados[,2]-((coeff.poly[[3]] * dados[,1]^coeff.poly[[4]]) * (1/(1 + exp(-fit.rate * (dados[,1] - scp.loop)))) +
(coeff.poly[[1]] * dados[,1]^coeff.poly[[2]]) * (1-(1/(1 + exp(-fit.rate * (dados[,1] - scp.loop)))))))/dados[,2]
polyfitted<-((coeff.poly[[3]] * dados[,1]^coeff.poly[[4]]) * (1/(1 + exp(-fit.rate * (dados[,1] - scp.loop))))) +
((coeff.poly[[1]] * dados[,1]^coeff.poly[[2]]) * (1-(1/(1 + exp(-fit.rate * (dados[,1] - scp.loop))))))
dados<-dados[,-5:-6]
dataLC<-dataLC[,-5:-6]
dados<<-cbind(dados,polyfitted.resid,polyfitted)
dataLC<<-cbind(dataLC,polyfitted.aver.resid,polyfitted.aver)
phases<-apply(dados,2,function(x) length(x[x<=scp.loop]));phases<-phases[-2:-6]
polyfitted.phase1.res<-dados[1:phases,5]
polyfitted.phase2.res<-dados[(phases+1):nrow(dados),5]
polyfitted.phase1.lr<<-lm(polyfitted.phase1.res~dados[1:phases,1])
polyfitted.phase2.lr<<-lm(polyfitted.phase2.res~dados[(phases+1):nrow(dados),1])
r.squared.lr<-(summary(polyfitted.phase1.lr)$r.squared)+(summary(polyfitted.phase2.lr)$r.squared)
if(sum(resid(polyfitted.total)^2)<sum.resid){
if(r.squared.test>r.squared.lr){
print(">> Best combination found <<")
best.loop<<-polyfitted.total
sum.resid<-sum(resid(polyfitted.total)^2)
rate<<-fit.rate
scp<<-scp.loop
r.squared.test<-r.squared.lr
coeff.poly<<-as.vector(coef(polyfitted.total))
}}else{coeff.poly.only.res<<-coef(polyfitted.total)}
},silent=FALSE)}}
sd.dados<-sd(dados[,5])
rownames(dados)<-1:nrow(dados)
for (j in nrow(dados):1){
if (dados[j,5]/sd.dados > 1.96){dados<-dados[-j,]
}else{
if (dados[j,5]/sd.dados < -1.96){dados<-dados[-j,]}
}}
rownames(dados)<-1:nrow(dados)
rm(j,sd.dados)
keep(dados,dadosF,dadosM,dados.total,interval.cons,files,sex,gender,sure=T)
if (nrow(dados)<150){next}
cut.point<-round((nrow(dados)*0.025),digits=0)
dados<-dados[-1:-cut.point,]
dados<-dados[(nrow(dados)-cut.point:nrow(dados)),]
dados<-dados[order(dados[,1]),]
rownames(dados)<-1:nrow(dados)
print(paste("Calculating ", gender, " data: ",length(dados[,1])," points"))
interval.cons(25)
dados<-dados[,-3:-6]
unifitted<-nlsLM(Weight~a*Length^b,
data=dados,
start=list(a=0.1,b=3),
weights=wfct(fitted),
control=nls.lm.control(maxiter=1024))
coeff.uni<-as.data.frame(coef(summary(unifitted))[,1:2])
unifitted.aver.resid<-(dataLC[,2]-(coeff.uni[1,1]*dataLC[,1]^coeff.uni[2,1]))/dataLC$AvWeight
unifitted.aver<-(coeff.uni[1,1]*dataLC[,1]^coeff.uni[2,1])
dados<-cbind(dados,resid(unifitted)/dados[,2],predict(unifitted))
dataLC<-cbind(dataLC,unifitted.aver.resid,unifitted.aver)
Linf<-exp(0.044 + 0.9841*log(max(dados[,1])))
if (gender=="FEMALE"){
L50<-exp(0.9469*log(Linf) - 0.1162)
}
if (gender=="MALE"){
L50<-exp(0.8915*log(Linf) - 0.1032)
}
if(gender=="ALL"){
L50<-exp(0.8979*log(Linf) - 0.0782)
}
dados.1.3<-dados[1:(round(nrow(dados)/3)),]
dados.3.3<-dados[(nrow(dados)-(round(nrow(dados)/3))):nrow(dados),]
assign("best.loop",.GlobalEnv)
sum.resid<-999999999999999999999999999999
polyfitted.1.3<-nlsLM(Weight ~ a * Length^b,
data=dados.1.3,
start=list(a=0.01,b=3),
control=nls.lm.control(maxiter=1024))
coeff.poly.1.3<-as.vector(coef(polyfitted.1.3))
polyfitted.3.3<-nlsLM(Weight ~ a * Length^b,
data=dados.3.3,
start=list(a=0.01,b=3),
control=nls.lm.control(maxiter=1024))
coeff.poly.3.3<-as.vector(coef(polyfitted.3.3))
scp.matrix<-seq(from=dados[30,1], to=dados[(nrow(dados)-30),1], by=1)
r.squared.test<-2
for (scp.loop in scp.matrix){
for (fit.rate in 1:10){
try({
polyfitted.total<-nlsLM(Weight ~ (a2 * Length^b2) * (1/(1 + exp(-fit.rate * (Length - scp.loop)))) +
(a1 * Length^b1) * (1-(1/(1 + exp(-fit.rate * (Length - scp.loop))))),
data=dados,
start=list(a1=coeff.poly.1.3[[1]],b1=coeff.poly.1.3[[2]],a2=coeff.poly.3.3[[1]],b2=coeff.poly.3.3[[2]]),
lower=c(a1=coeff.poly.1.3[[1]]-coeff.poly.1.3[[1]]*0.7,b1=coeff.poly.1.3[[2]]-coeff.poly.1.3[[2]]*0.7,a2=coeff.poly.3.3[[1]]-coeff.poly.3.3[[1]]*0.7,b2=coeff.poly.3.3[[2]]-coeff.poly.3.3[[2]]*0.7),
upper=c(a1=coeff.poly.1.3[[1]]+coeff.poly.1.3[[1]]*0.7,b1=coeff.poly.1.3[[2]]+coeff.poly.1.3[[2]]*0.7,a2=coeff.poly.3.3[[1]]+coeff.poly.3.3[[1]]*0.7,b2=coeff.poly.3.3[[2]]+coeff.poly.3.3[[2]]*0.7),
control=nls.lm.control(maxiter=1024))
coeff.poly<-as.vector(coef(polyfitted.total))
polyfitted.aver.resid<-(dataLC$AvWeight-((coeff.poly[[3]] * dataLC$LengthClass^coeff.poly[[4]]) * (1/(1 + exp(-fit.rate * (dataLC$LengthClass - scp.loop)))) +
(coeff.poly[[1]] * dataLC$LengthClass^coeff.poly[[2]]) * (1-(1/(1 + exp(-fit.rate * (dataLC$LengthClass - scp.loop)))))))/dataLC$AvWeight
polyfitted.aver<-((coeff.poly[[3]] * dataLC$LengthClass^coeff.poly[[4]]) * (1/(1 + exp(-fit.rate * (dataLC$LengthClass - scp.loop))))) +
((coeff.poly[[1]] * dataLC$LengthClass^coeff.poly[[2]]) * (1-(1/(1 + exp(-fit.rate * (dataLC$LengthClass - scp.loop))))))
polyfitted.resid<-(dados[,2]-((coeff.poly[[3]] * dados[,1]^coeff.poly[[4]]) * (1/(1 + exp(-fit.rate * (dados[,1] - scp.loop)))) +
(coeff.poly[[1]] * dados[,1]^coeff.poly[[2]]) * (1-(1/(1 + exp(-fit.rate * (dados[,1] - scp.loop)))))))/dados[,2]
polyfitted<-((coeff.poly[[3]] * dados[,1]^coeff.poly[[4]]) * (1/(1 + exp(-fit.rate * (dados[,1] - scp.loop))))) +
((coeff.poly[[1]] * dados[,1]^coeff.poly[[2]]) * (1-(1/(1 + exp(-fit.rate * (dados[,1] - scp.loop))))))
dados<-dados[,-5:-6]
dataLC<-dataLC[,-5:-6]
dados<<-cbind(dados,polyfitted.resid,polyfitted)
dataLC<<-cbind(dataLC,polyfitted.aver.resid,polyfitted.aver)
phases<-apply(dados,2,function(x) length(x[x<=scp.loop]));phases<-phases[-2:-6]
polyfitted.phase1.res<-dados[1:phases,5]
polyfitted.phase2.res<-dados[(phases+1):nrow(dados),5]
polyfitted.phase1.lr<<-lm(polyfitted.phase1.res~dados[1:phases,1])
polyfitted.phase2.lr<<-lm(polyfitted.phase2.res~dados[(phases+1):nrow(dados),1])
r.squared.lr<-(summary(polyfitted.phase1.lr)$r.squared)+(summary(polyfitted.phase2.lr)$r.squared)
if(sum(resid(polyfitted.total)^2)<sum.resid){
if(r.squared.test>r.squared.lr){
print(">> Best combination found <<")
best.loop<<-polyfitted.total
sum.resid<-sum(resid(polyfitted.total)^2)
rate<<-fit.rate
scp<<-scp.loop
r.squared.test<-r.squared.lr
coeff.poly<<-as.vector(coef(polyfitted.total))
}}else{coeff.poly.only.res<<-coef(polyfitted.total)}
},silent=FALSE)}}
coeff.poly<-as.vector(coef(best.loop))
polyfitted.total.rate.scp<-nlsLM(Weight ~ (a2 * Length^b2) * (1/(1 + exp(-fit.rate * (Length - fit.scp)))) +
(a1 * Length^b1) * (1-(1/(1 + exp(-fit.rate * (Length - fit.scp))))),
data=dados,
start=list(a1=coeff.poly[[1]],b1=coeff.poly[[2]],a2=coeff.poly[[3]],b2=coeff.poly[[4]],fit.rate=rate,fit.scp=scp),
lower=c(a1=coeff.poly[[1]]-coeff.poly[[1]]*0.5,b1=coeff.poly[[2]]-coeff.poly[[2]]*0.5,a2=coeff.poly[[3]]-coeff.poly[[3]]*0.5,b2=coeff.poly[[4]]-coeff.poly[[4]]*0.5,fit.rate=rate-(rate*0.2),fit.scp=(scp-(scp*0.2))),
upper=c(a1=coeff.poly[[1]]+coeff.poly[[1]]*0.5,b1=coeff.poly[[2]]+coeff.poly[[2]]*0.5,a2=coeff.poly[[3]]+coeff.poly[[3]]*0.5,b2=coeff.poly[[4]]+coeff.poly[[4]]*0.5,fit.rate=rate+(rate*0.2),fit.scp=(scp+(scp*0.2))),
weights=wfct(fitted),
control=nls.lm.control(maxiter=1024))
coeff.poly.rate.scp<-as.vector(coef(polyfitted.total.rate.scp))
polyfitted.aver.resid<-(dataLC$AvWeight-((coeff.poly.rate.scp[[3]] * dataLC$LengthClass^coeff.poly.rate.scp[[4]]) * (1/(1 + exp(-coeff.poly.rate.scp[[5]] * (dataLC$LengthClass - coeff.poly.rate.scp[[6]])))) +
(coeff.poly.rate.scp[[1]] * dataLC$LengthClass^coeff.poly.rate.scp[[2]]) * (1-(1/(1 + exp(-coeff.poly.rate.scp[[5]] * (dataLC$LengthClass - coeff.poly.rate.scp[[6]])))))))/dataLC$AvWeight
polyfitted.aver<-((coeff.poly.rate.scp[[3]] * dataLC$LengthClass^coeff.poly.rate.scp[[4]]) * (1/(1 + exp(-coeff.poly.rate.scp[[5]] * (dataLC$LengthClass - coeff.poly.rate.scp[[6]]))))) +
((coeff.poly.rate.scp[[1]] * dataLC$LengthClass^coeff.poly.rate.scp[[2]]) * (1-(1/(1 + exp(-coeff.poly.rate.scp[[5]] * (dataLC$LengthClass - coeff.poly.rate.scp[[6]]))))))
polyfitted.resid<-(dados[,2]-((coeff.poly.rate.scp[[3]] * dados[,1]^coeff.poly.rate.scp[[4]]) * (1/(1 + exp(-coeff.poly.rate.scp[[5]] * (dados[,1] - coeff.poly.rate.scp[[6]])))) +
(coeff.poly.rate.scp[[1]] * dados[,1]^coeff.poly.rate.scp[[2]]) * (1-(1/(1 + exp(-coeff.poly.rate.scp[[5]] * (dados[,1] - coeff.poly.rate.scp[[6]])))))))/dados[,2]
polyfitted<-((coeff.poly.rate.scp[[3]] * dados[,1]^coeff.poly.rate.scp[[4]]) * (1/(1 + exp(-coeff.poly.rate.scp[[5]] * (dados[,1] - coeff.poly.rate.scp[[6]]))))) +
((coeff.poly.rate.scp[[1]] * dados[,1]^coeff.poly.rate.scp[[2]]) * (1-(1/(1 + exp(-coeff.poly.rate.scp[[5]] * (dados[,1] - coeff.poly.rate.scp[[6]]))))))
dados<-dados[,-5:-6]
dataLC<-dataLC[,-5:-6]
dados<-cbind(dados,polyfitted.resid,polyfitted)
dataLC<-cbind(dataLC,polyfitted.aver.resid,polyfitted.aver)
coeff.poly<-as.data.frame(coef(summary(polyfitted.total.rate.scp))[,1:2])
phases<-apply(dataLC,2,function(x) length(x[x<=coeff.poly[6,1]]));phases<-phases[-2:-6]
unifitted.phase1.res<-dataLC[,3]; unifitted.phase1.res<-unifitted.phase1.res[1:phases];
unifitted.phase2.res<-dataLC[,3]; unifitted.phase2.res<-unifitted.phase2.res[(phases+1):nrow(dataLC)]
unifitted.phase1.lr<-lm(unifitted.phase1.res~dataLC[1:phases,1]); unifitted.phase2.lr<-lm(unifitted.phase2.res~dataLC[(phases+1):nrow(dataLC),1])
polyfitted.phase1.res<-dataLC[1:phases,5]
polyfitted.phase2.res<-dataLC[(phases+1):nrow(dataLC),5]
polyfitted.phase1.lr<-lm(polyfitted.phase1.res~dataLC[1:phases,1])
polyfitted.phase2.lr<-lm(polyfitted.phase2.res~dataLC[(phases+1):nrow(dataLC),1])
graph.name<-paste(files[i],gender,sep=" ");graph.name<-gsub(".txt", "", graph.name);graph.name<-gsub("_", " ", graph.name)
a.values<-paste("a = ",round(coeff.uni[1,1],digits=4)," (se: ",round(coeff.uni[1,2],digits=4),")",sep="")
b.values<-paste("b = ",round(coeff.uni[2,1],digits=4)," (se: ",round(coeff.uni[2,2],digits=4),")",sep="")
a1.values<-paste("a = ",round(coeff.poly[1,1],digits=4)," (se: ",round(coeff.poly[3,2],digits=4),")",sep="")
b1.values<-paste("b = ",round(coeff.poly[2,1],digits=4)," (se: ",round(coeff.poly[4,2],digits=4),")",sep="")
a2.values<-paste("a = ",round(coeff.poly[3,1],digits=4)," (se: ",round(coeff.poly[1,2],digits=4),")",sep="")
b2.values<-paste("b = ",round(coeff.poly[4,1],digits=4)," (se: ",round(coeff.poly[2,2],digits=4),")",sep="")
scp.values<-paste("SCP = ",round(coeff.poly[6,1],digits=2)," (se: ",round(coeff.poly[6,2],digits=2),")",sep="")
rate.values<-paste("rate = ",round(coeff.poly[5,1],digits=3)," (se: ",round(coeff.poly[5,2],digits=3),")",sep="")
L50.values<-paste("L = ",round(L50,digits=2),sep="")
par(mfrow=c(2,2))
plot(dados[,1],dados[,3],pch=21,col="gray65",bg="white",xlab="Length (cm)",ylab="Residuals",main="Huxley")
points(dataLC[,1],dataLC[,3],pch=21,col="black",bg="black")
try({
lines(dataLC[1:phases,1],predict(unifitted.phase1.lr),lwd=3,col="gray35"); lines(dataLC[(phases+1):nrow(dataLC),1],predict(unifitted.phase2.lr),lwd=3,col="gray35")
},silent=TRUE)
abline(h=0,lty=2:2)
plot(dados[,1],dados[,2],pch=21,col="gray65",bg="white", main="Huxley",xlab="Length (cm)",ylab="Weight (g)")
lines(dados[,1],dados[,4],lwd=3)
mtext(a.values,line=-1.5,adj=0.05,cex=.6)
mtext(b.values,line=-2.4,adj=0.05,cex=.6)
plot(dados[,1],dados[,5],pch=21,col="gray65",bg="white", main="Polyphasic",xlab="Length (cm)",ylab="Residuals")
points(dataLC[,1],dataLC[,5],pch=21,col="black",bg="black")
abline(v=coeff.poly[6,1],lty=2:2)
try({
lines(dataLC[1:phases,1],predict(polyfitted.phase1.lr),lwd=3,col="gray35"); lines(dataLC[(phases+1):nrow(dataLC),1],predict(polyfitted.phase2.lr),lwd=3,col="gray35")
},silent=TRUE)
abline(h=0,lty=2:2)
abline(v=L50,lty=3)
plot(dados[,1],dados[,2],pch=21,col="gray65",bg="white", main="Polyphasic",xlab="Length (cm)",ylab="Weight (g)")
lines(dados[,1],dados[,6],lwd=3)
abline(v=coeff.poly[6,1],lty=2:2)
abline(v=L50,lty=3)
mtext(a1.values,line=-1.5,adj=0.05,cex=.6)
mtext("1",line=-1.6,adj=0.05,cex=.35)
mtext(b1.values,line=-2.4,adj=0.05,cex=.6)
mtext("1",line=-2.5,adj=0.05,cex=.35)
mtext(a2.values,line=-3.3,adj=0.05,cex=.6)
mtext("2",line=-3.4,adj=0.05,cex=.35)
mtext(b2.values,line=-4.2,adj=0.05,cex=.6)
mtext("2",line=-4.3,adj=0.05,cex=.35)
mtext(scp.values,line=-5.1,adj=0.05,cex=.6)
mtext(rate.values,line=-6,adj=0.05,cex=.6)
mtext(L50.values,line=-6.9,adj=0.04,cex=.6)
mtext("50",line=-7,adj=0.06,cex=.35)
par(mfrow=c(2,2),oma = c(0, 0, 1.5, 0))
mtext(graph.name, outer = TRUE, cex = 1.5)
mypath <- file.path("~/Documents/Doutorado/Dados R/Gráficos",paste(graph.name, ".pdf", sep = ""))
mypath.rdata <- file.path("~/Documents/Doutorado/Dados R/Resultados novos",paste(graph.name, ".Rdata", sep = ""))
save(list=ls(all=TRUE),file=mypath.rdata)
pdf(file=mypath)
par(mfrow=c(2,2))
plot(dados[,1],dados[,3],pch=21,col="gray65",bg="white",xlab="Length (cm)",ylab="Residuals",main="Huxley")
points(dataLC[,1],dataLC[,3],pch=21,col="black",bg="black")
try({
lines(dataLC[1:phases,1],predict(unifitted.phase1.lr),lwd=3,col="gray35"); lines(dataLC[(phases+1):nrow(dataLC),1],predict(unifitted.phase2.lr),lwd=3,col="gray35")
},silent=TRUE)
abline(h=0,lty=2:2)
plot(dados[,1],dados[,2],pch=21,col="gray65",bg="white", main="Huxley",xlab="Length (cm)",ylab="Weight (g)")
lines(dados[,1],dados[,4],lwd=3)
mtext(a.values,line=-1.5,adj=0.05,cex=.6)
mtext(b.values,line=-2.4,adj=0.05,cex=.6)
plot(dados[,1],dados[,5],pch=21,col="gray65",bg="white", main="Polyphasic",xlab="Length (cm)",ylab="Residuals")
points(dataLC[,1],dataLC[,5],pch=21,col="black",bg="black")
abline(v=coeff.poly[6,1],lty=2:2)
try({
lines(dataLC[1:phases,1],predict(polyfitted.phase1.lr),lwd=3,col="gray35"); lines(dataLC[(phases+1):nrow(dataLC),1],predict(polyfitted.phase2.lr),lwd=3,col="gray35")
},silent=TRUE)
abline(h=0,lty=2:2)
abline(v=L50,lty=3)
plot(dados[,1],dados[,2],pch=21,col="gray65",bg="white", main="Polyphasic",xlab="Length (cm)",ylab="Weight (g)")
lines(dados[,1],dados[,6],lwd=3)
abline(v=coeff.poly[6,1],lty=2:2)
abline(v=L50,lty=3)
mtext(a1.values,line=-1.5,adj=0.05,cex=.6)
mtext("1",line=-1.6,adj=0.05,cex=.35)
mtext(b1.values,line=-2.4,adj=0.05,cex=.6)
mtext("1",line=-2.5,adj=0.05,cex=.35)
mtext(a2.values,line=-3.3,adj=0.05,cex=.6)
mtext("2",line=-3.4,adj=0.05,cex=.35)
mtext(b2.values,line=-4.2,adj=0.05,cex=.6)
mtext("2",line=-4.3,adj=0.05,cex=.35)
mtext(scp.values,line=-5.1,adj=0.05,cex=.6)
mtext(rate.values,line=-6,adj=0.05,cex=.6)
mtext(L50.values,line=-6.9,adj=0.04,cex=.6)
mtext("50",line=-7,adj=0.05,cex=.35)
par(mfrow=c(2,2),oma = c(0, 0, 1.5, 0))
mtext(graph.name, outer = TRUE, cex = 1.5)
dev.off()
scp.L50.paste<-cbind(species,gender,round(coeff.poly[6,1],digits=1),round(L50,digits=1),round(AIC(unifitted),digits=2),round(AIC(polyfitted.total.rate.scp),digits=2))
scp.L50<-rbind(scp.L50,scp.L50.paste)
}}
names(scp.L50)<-c("Species","Gender","SCP","L50","AIC Huxley","AIC Polyphasic")
write.csv(scp.L50,file="Summary.csv")

Answer 1

I went through your code and there is indeed a missing bracket. Assuming that the indentation of your code is correct and that you only want to write the summary one time, this is where I think the problem is. Note that I already added the closing bracket on the line where I put my comment:
for (i in 1:length(files)){ # !! I believe you forgot to close this bracket !!
# Some code here..
species<-gsub(".txt", "", files[i]);print(paste("Species: ",gsub("_", " ", species)))
if (ncol(dados)==3){
# Some more code here..
}
if(ncol(dados)==3){
for (gender in sex){
# Wall of code
scp.L50.paste<-cbind(species,gender,round(coeff.poly[6,1],digits=1),round(L50,digits=1),round(AIC(unifitted),digits=2),round(AIC(polyfitted.total.rate.scp),digits=2))
scp.L50<-rbind(scp.L50,scp.L50.paste)
}}
} # !! I believe your closing bracket should be added here !!
names(scp.L50)<-c("Species","Gender","SCP","L50","AIC Huxley","AIC Polyphasic")
write.csv(scp.L50,file="Summary.csv")
EDIT: In other words, it is most likely the most outer for loop that is not closed properly.

Answer 2

The code has 43 opening brackets and 42 closing brackets, so if you're executing it as a script, you can't expect that to run correctly. I don't know for sure where your missing bracket should be, because it depends on what you want to do, but you should take a closer look and attempt to find it. Take a look at your recent changes, have you forgotten to close a loop or something similar?