I am currently trying to run some code (if you need to know the purpose to help me, ask me, but I'm trying to keep this question short). This is the code:
par<-c(a=.5,b=rep(1.3,4))
est<-rep(TRUE,length(par))
ncat<-5
Theta<-matrix(c(-6,-5.8,-5.6,-5.4,-5.2,-5,-4.8,-4.6,-4.4,-4.2,-4,-3.8,-3.6,-3.4,-3.2,-3,-2.8,-2.6,-2.4,-2.2,-2,-1.8,-1.6,-1.4,-1.2,-1,-0.8,-0.6,-0.4,-0.2,0,0.2,0.4,0.6,0.8,1,1.2,1.4,1.6,1.8,2,2.2,2.4,2.6,2.8,3,3.2,3.4,3.6,3.8,4,4.2,4.4,4.6,4.8,5,5.2,5.4,5.6,5.8,6))
p.grm<-function(par,Theta,ncat){
a<-par[1]
b<-par[2:length(par)]
z<-matrix(0,nrow(Theta),ncat)
y<-matrix(0,nrow(Theta),ncat)
y[,1]<-1
for(i in 1:ncat-1){
y[,i+1]<-(exp(a*(Theta-b[i])))/(1+exp(a*(Theta-b[i])))
}
for(i in 1:ncat-1){
z[,i]<-y[,i]-y[,i+1]
}
z[,ncat]<-y[,ncat]
z
}
However, when I try to run the code:
p.grm(par=par,Theta=Theta,ncat=ncat)
I get the following error:
Error: dims [product 61] do not match the length of object [0]
Traceback tells me that the error is occurring in the first for loop in the line:
y[,i+1]<-(exp(a*(Theta-b[i])))/(1+exp(a*(Theta-b[i])))
Could someone point me to what I'm doing wrong? When I try to run this code step by step outside of the custom p.grm function, everything seems to work fine.
It is a common mistake. When you write the for loop and you want it from 1 to ncat -1 remember to write it as for (i in 1:(ncat-1)) instead of for(i in 1:ncat-1) they are completly different.
You may also add to the function something to return return(z). Here it is the corrected code:
par<-c(a=.5,b=rep(1.3,4))
est<-rep(TRUE,length(par))
ncat<-5
Theta<-matrix(c(-6,-5.8,-5.6,-5.4,-5.2,-5,-4.8,-4.6,-4.4,-4.2,-4,-3.8,-3.6,-3.4,-3.2,-3,-2.8,-2.6,-2.4,-2.2,-2,-1.8,-1.6,-1.4,-1.2,-1,-0.8,-0.6,-0.4,-0.2,0,0.2,0.4,0.6,0.8,1,1.2,1.4,1.6,1.8,2,2.2,2.4,2.6,2.8,3,3.2,3.4,3.6,3.8,4,4.2,4.4,4.6,4.8,5,5.2,5.4,5.6,5.8,6))
p.grm<-function(par,Theta,ncat){
a<-par[1]
b<-par[2:length(par)]
z<-matrix(0,nrow(Theta),ncat)
y<-matrix(0,nrow(Theta),ncat)
y[,1]<-1
for(i in 1:(ncat-1)){
y[,i+1]<-(exp(a*(Theta-b[i])))/(1+exp(a*(Theta-b[i])))
}
for(i in 1:(ncat-1)){
z[,i]<-y[,i]-y[,i+1]
}
z[,ncat]<-y[,ncat]
return(z)
}
p.grm(par=par,Theta=Theta,ncat=ncat)
Related
I have create a small script that passes a vector through a loop. In this loop I am using an if else statement to check if folder exists and if not to create the folder. However, I am getting error: Error in file.exists(i) : invalid 'file' argument. This has to due with file.exist(). I dont understand why this isnt ok. I check the man using help. Seems like this should be working.
folders<- c("RawData", "Output", "BCV", "DEplots", "DEtables", "PathwayOuts", "VolcanoPLots")
for(i in 1:length(folders)){
if (file.exists(i)){
cat(paste0(i, "already exists"))
} else {
cat(paste0(i, "does not exists"))
dir.create(i)
}
}
You are looping over an index (that is, 1:length(folders) is just the vector 1:7, not the values of the folders vector itself. The easiest solution is to loop over the vector itself:
for (i in folders) {
Or, if you still want to loop over the index:
for (i in 1:length(folders)) {
if (file.exists(folders[i])){
cat(paste0(folders[i], "already exists"))
}
else {
cat(paste0(folders[i], "does not exists"))
dir.create(folders[i])
}
}
A quick tip: if you are debugging a for-loop, the place to start is to add print(i) at the start of the loop. You would have immediately seen the problem: i was an integer, not the first value of the vector.
I have a small testing program that uses testthat
library(testthat)
source("src/MyFile.r")
results <- test_dir("tests", reporter="summary")
So, I am running this via Rscript. The problem is that the exit code is always 0 even when there were test failures. So, I want to call stop if there are any failures. But I can't seem to get the right bit of code to do that. Is there a method or field in results that I should be looking at to determine if there were any errors?
You could also tweak jamesatha's answer to retrieve the number of test failures.
failed.tests <- sapply(results, function(r) {
!is(r$result[[1]], "expectation_success")
})
You then allows you to fail, as before:
if (any(failed.tests)) {
stop("There were test failures")
}
or do something more bespoke like
if (any(failed.tests)) {
failed.test.count <- length(which(failed.tests))
stop(paste(failed.test.count,"failed tests is",failed.test.count,"too many!")
}
Currently, my solution is iterating through the results like this:
for (i in 1:length(results)) {
if (!is(results[[i]]$result[[1]], "expectation_success")) {
stop("There were test failures")
}
}
You can simply pass stop_on_failure=TRUE in as a parameter to test_dir. If you get any test failures it will raise an error and exit non zero.
e.g:
results <- test_dir("mypath", stop_on_failure=TRUE)
This is documented here
I get an Argument is of length zero error when I run the below code
The code is from this blog -http://giventhedata.blogspot.in/2012/08/r-and-web-for-beginners-part-iii.html.
library(XML)
url<- "http://news.bbc.co.uk/2/hi/uk_politics/8044207.stm"
first<-"Abbott, Ms Diane"
url.tab <- readHTMLTable(url)
for (i in 1:length(url.tab)){
if (as.character(url.tab[[i]][1,1]) == first ) {print(first)}
}
I know that the url.tab[[5]][1,1]) does contain the string "Abbott, Ms Diane", and when I run IF statement in isolation replacing the i with 5, it runs fine. Any help would be appreciated. I also tried declaring i<-1 upfront. DInt change anything.
Some of your tables are in fact NULL.
So you have to test for is.null before trying to subset the table:
for (i in 1:length(url.tab)){
this.tab <- url.tab[[i]]
if(!is.null(this.tab)) if(as.character(this.tab[1,1]) == first ) {print(first)}
}
[1] "Abbott, Ms Diane"
I got warnings when running this code.
For example, when I put
tm1<- summary(tmfit)[c(4,8,9)],
I can get the result, but I need to run this code for each $i$.
Why do I get this error?
Is there any way to do this instead of via a for loop?
Specifically, I have many regressants ($y$) with the same two regressors ($x$'s).
How I can get these results of regression analysis(to make some comparisons)?
dreg=read.csv("dayreg.csv")
fundr=read.csv("fundreturnday.csv")
num=ncol(fundr)
exr=dreg[,2]
tm=dreg[,4]
for(i in 2:num)
{
tmfit=lm(fundr[,i]~exr+tm)
tm1[i]<- summary(tmfit)[c(4,8,9)]
}
Any help is highly appreciated
Try storing your result into a list instead of a vector.
dreg=read.csv("dayreg.csv")
fundr=read.csv("fundreturnday.csv")
num=ncol(fundr)
exr=dreg[,2]
tm = list()
for(i in 2:num)
{
tmfit=lm(fundr[,i]~exr+tm)
tm1[[i]]<- summary(tmfit)[c(4,8,9)]
}
You can look at an element in the list like so
tm1[[2]]
I am having a very hard time trying to subtract two vectors in my OpenBUGS model. The last line of the code below keeps giving the error "expected right parenthesis error":
model {
for ( i in 1:N) {
for(j in 1:q) {
vv[i,j] ~ dnorm(vz[i,j],tau.eta[j])
}
vz[i,1:q] ~ dmnorm(media.z[i,], K.delta[,])
for(j in 1:q) {
mean.z[i,j] <- inprod(K[i,] , vbeta[j,])
}
K[i,1] <- 1.0
for(j in 1:N) {
K[i,j+1] <- sum(ve[,i] - ve[,j])
}
}
If I change that line to K[i,j+1] <- sum(ve[,i]) - sum(ve[,j]), then the model works fine, but that is not what I want to do. I would like to subtract element-wise.
I searched SO for OpenBUGS, but there are only a few unrelated topics:
OpenBUGS - Variable is not defined
OpenBUGS: missing value in Bernoulli distribution
In Stats Stack Exchange there is this post which is close, but I still could not make how to implement this in my model:
https://stats.stackexchange.com/questions/20653/vector-multiplication-in-bugs-and-jags/20739#20739
I understand I have to write a for loop, but this thing is sure giving me a big headache. :)
I tried changing that line to:
for(k in 1:p) { temp [k] <- ve[k,i] - ve[k,j] }
K[i,j+1] <- sum(temp[])
where 'p' is the number of rows in each 've'. Now I keep getting the error "multiple definitions of node temp[1]".
I could definitely use some help. It will be much appreciated.
Best regards to all and thanks in advance!
PS: I wanted to add the tag "OpenBUGS" to this question but unfortunately I couldn't because it would be a new tag and I do not have enough reputation. I added "winbugs" instead.
The "multiple definitions" error is because temp[k] is redefined over and over again within a loop over i and another loop over j - you can only define it once. To get around that, use i and j subscripts like
for(k in 1:p) { temp[k,i,j] <- ve[k,i] - ve[k,j] }
K[i,j+1] <- sum(temp[,i,j])
Though if that compiles and runs, I'd check the results to make sure that's exactly what you want mathematically.