Thanks ! Ths switch excaped my attention, probably because it is buried
in a "literal example" section, which I didn't connect to noweb care
and feeding...
Maybe the "noweb" section might benefit of a discrete recall of
relevant switches ?
Thanks again !
--
Emmanuel Charpentier
Le mardi 09 avril 2019 à 16:19 +0000, Berry, Charles a écrit :
> > 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
