The console on Rstudio didn't find a data file when loading rstan library

Interfaces RStan
1

When I loaded rstan library with necessary dependencies,
it was given an error as follows.

①fit <- stan(file=scr, model_name=scr, data=data, pars=par, verbose=F,seed=see, chains=cha, warmup=war,iter=ite)
Error in stan(file = scr, model_name = scr, data = data, pars = par, verbose = F, :
‘data’ must be a list, environment, or character vector

②Error in file(filename, “r”, encoding = encoding) :
cannot open the connection
In addition: Warning message:
In file(filename, “r”, encoding = encoding) :
cannot open file ‘data622.R’: No such file or directory

The code shows as follows

library(rstan) 
options(mc.cores = parallel::detectCores())
scr <- "model622.stan" 
source("data622.R") 
data <- list(N=N,x=x) 
par <-c("mu", "Sigma", "rho","delta","delta_over","delta_over2", "rho_over","rho_over05")
war <- 1000 
ite <- 110000 
see <- 1234 
dig <- 3 
cha <- 1 
fit <- stan(file=scr, model_name=scr, data=data, pars=par, verbose=F,seed=see, chains=cha, warmup=war,iter=ite)
print(fit,pars=par,digits_summary=dig) 
plot(fit, pars=par)
traceplot(fit,inc_warmup = T, pars=par)

Mac OS/X 10.13.6
R Version: 3.6.1
Rstan:2.19.2

2

The above seems to be a problem. You need to give the function the path to the file, if you’re not using the directory where the file is as a working directory. This is not a Stan problem. :)

3

Thank you very much for answering my question. I tried to run my file on a working directory, but I had the same error. When I tried to confirm path using Sys.getenv(), I got several environment variables including PATH /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin. Please tell me how to read my file on Rstudio by setting the path to the file with Sys.setenv().

4

Hey!

No, you literally just have to give the path to the file as a character string, like

scr <- "C:/My Files/Stan Models/model622.stan

Or

source("C:/My Files/Data/data622.R")

You can also run

scr <- file.choose() in an interactive session and find the file via the menu.

All these are R specific questions and this is a Stan forum. I don’t mean to sound harsh, but it seems to me like you need to go back to learning the basics of R (you should find plenty of resources online). For R questions you can usually just Google, like “how to source file in R” or something like that.

Cheers!

2 Likes
5

I also encountered such an error.
The following site is very helpful for me, and I think for you.

6

Thank for your help.
Of course, I have already investigated the site related to R such as Stack Overflow, and Google. In fact, this sample script, which read in the Bayes’ textbook, was run on this summer, but I haven’t recently run it. When I try to change the code on Mac as you said,I also have errors as follows. I could have a problem to set up on Rstudio or Stan. Could you tell me an explanation for the error?

Changed code:
scr <- "/Users/lina/Downloads/model622.stan"
source("/Users/lina/Downloads/data622.R")

Error:
in stan_model(file, model_name = model_name, model_code = model_code, :
model name must match (^[[:alnum:]]{2,}.*)|(^[A-E,G-S,U-Z,a-z].*)|(^[F,T].+).
In addition: Warning message:
In readLines(file, warn = TRUE) :
incomplete final line found on ‘/Users/lina/Downloads/model622.stan’.

7

Thank for your advise. Of course, I am going to use Stack Overflow from now, but I think the Stan discourse site is more active in discussion than Stack Overflow.