CODEWITHSUNDEEP
rjags
user27115
user27115

Reputation: 13

How to write some R data into a .csv file?

I'm trying to export some sampled output values from JAGS into .csv format in order to perform further analysis in R, but got some troubles.

> 
> codaSamples
[[1]]
Markov Chain Monte Carlo (MCMC) output:
Start = 4001 
End = 14000 
Thinning interval = 1 
           pai     theta[1]     theta[2]   theta[3]   theta[4]
[1,] 0.9774972 0.0081192689 0.0101738296 0.06981109 0.10674466
[2,] 0.9527935 0.0076402088 0.0099482287 0.07593964 0.11060883
[3,] 0.9467507 0.0076402088 0.0099482287 0.07593964 0.11060883
[4,] 0.9514251 0.0076402088 0.0099482287 0.07593964 0.11060883
[5,] 0.9419245 0.0076402088 0.0099482287 0.07593964 0.11060883
[6,] 0.9914296 0.0076402088 0.0099482287 0.07593964 0.11060883
[7,] 0.9903451 0.0076402088 0.0099482287 0.07593964 0.11060883
[8,] 0.9917113 0.0064704730 0.0095551321 0.06748512 0.11033123
...
... 

[10000,] 0.9917113 0.0064704730 0.0095551321 0.06748512 0.11033123

> write.csv(codaSamples,"CODASAMPLES.csv",row.names=FALSE)
Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors =       stringsAsFactors) : 
cannot coerce class '"mcmc.list"' into a data.frame

Upvotes: 1

Views: 1913

Answers (2)

Adam Hyland
Adam Hyland

Reputation: 1057

write.table expects a data frame or a matrix (if you don't pass it one, it will try and coerce it). If you look at the structure of codaSamples with e.g. str(codaSamples) you'll see that it is a list object with elements which are lists or data frames or matrices (I don't know what it actually is). IF it is mixed like that, write.table has no idea how to turn it into a csv.

If you want to select only the matrix you can find the name of the element with names(codaSamples) or again from str(codaSamples) and then do something like sample.mcmc <- codaSamples[['Matrix']] or whatever the name is, then you should be able to save sample.mcmc to a file just like you have.

Upvotes: 2

Sam Mason
Sam Mason

Reputation: 16184

a mcmc.list can contain multiple chains, you'd want to select out the chain you want when writing to the CSV file:

write.csv(codaSamples[[1]], "CODASAMPLES.csv",row.names=FALSE)

Should do the "right thing", although I don't have a chain to test this with at the moment.

Upvotes: 3

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