> On Apr 8, 2019, at 4:01 PM, Emmanuel Charpentier <emm.charpent...@free.fr>
> wrote:
>
> Compare this org source:
>
> ===================================================================
> # A small :noweb mystery: indentation
>
> #+property: header-args:R :session
> #+options: toc:nil
> #+author:
> #+date:
>
> The structure of a probablity proble can be represented by a ~JAGS~
> code snippet:
> #+name: Struct
> #+begin_src R :eval never :exports code
> for (i in 1:nObs) {
> for (j in 1:nZ) {
> Z[i,j] ~ dbern(P[i,j])
> logit(P[i,j]) <- alpha + beta[j]*X[i]
> }
> }
> #+end_src
>
> The same code snippet can be used for simulation:
>
See Org Manual (org) Literal Examples for information about the -i switch
Try:
#+begin_src R -i :exports code :results none :noweb yes
instead of this:
> #+begin_src R :exports code :results none :noweb yes
> library(rjags)
> library(coda)
> ## Reproducibility ?
> set.seed(813)
> Params <- local({
> nObs <- 500
> nZ <- 5
> X <- rnorm(nObs)
> alpha <- rnorm(1,0,3)
> beta <- rnorm(nZ,-1,2)
> list(
> nObs=nObs,
> nZ=nZ,
> X=X,
> alpha=alpha,
> beta=beta)
> })
> ## Wrap model code
> M <-
> "model {
> <<Struct>>
> }"
> ## Compilation
> JM <- jags.model(textConnection(M), data=Params, n.adapt=1,
> n.chains=1)
> ## Forward sampling
> JS <- coda.samples(JM, "Z", n.iter=1)
> #+end_src
>
> and for inference, after adding priors of parameters:
>
> #+name: Priors
> #+begin_src R :eval never :exports code
> ## Priors
> alpha ~ dt(0, 1e-2, 3)
> for (j in 1:nZ) {
> beta[j] ~ dt(0,1e-2, 3)
> }
> #+end_src
>
And again here:
> #+name: Inference
> #+begin_src R :noweb yes :exports code
> Data <- list(
> nObs=Params$nObs,
> nZ=Params$nZ,
> X=Params$X,
> Z=matrix(as.matrix(JS), ncol=Params$nZ, byrow=FALSE))
> ## Wrap inference model
> MI <-
> "model {
> <<Struct>>
> <<Priors>>
> }"
> ## Compilation
> JMI <- jags.model(textConnection(MI), Data, n.chains=4)
> ## Inference sampling
> JMS <- coda.samples(JMI, c("alpha", "beta"), n.iter=1000)
> #+end_src
>
> #+RESULTS: Inference
> ===================================================================
>
> With the result of its export to Ascii:
>
[snip]
> The indentation is not respected in the included JAGS snippets. Further
> attempts with exporting to PDF (both the built-in exporter and ox-
> pandoc) and DOCX (ox-pandoc) show that the problem remains the same,
> but, IIRC, with slight variations in whitespace.
>
> That's not serious (just ugly) for R/JAGS ; but it might be serious for
> Python/Sage, where whitespace is syntaxic.
>
> Thoughts ?
>
Try the switch.
HTH,
Chuck
