Re: Possible bug (?): :noweb doesn't respect indentations (at least i R/BUGS/JAGS).

[Emmanuel Charpentier <emm.charpentier@free.fr>]

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.charpentier@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