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

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

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:

#+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

#+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:

===================================================================
The structure of a probablity proble can be represented by a `JAGS'
code
snippet:
,----
| 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]
|   }
| }
`----

The same code snippet can be used for simulation:

,----
| 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 {
|        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]
| 	 }
|        }
| }"
| ## Compilation
| JM <- jags.model(textConnection(M), data=Params, n.adapt=1,
n.chains=1)
| ## Forward sampling
| JS <- coda.samples(JM, "Z", n.iter=1)
`----

and for inference, after adding priors of parameters:

,----
| ## Priors
| alpha ~ dt(0, 1e-2, 3)
| for (j in 1:nZ) {
|   beta[j] ~ dt(0,1e-2, 3)
| }
`----

,----
| 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 {
|        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]
| 	 }
|        }
|        ## Priors
|        alpha ~ dt(0, 1e-2, 3)
|        for (j in 1:nZ) {
| 	 beta[j] ~ dt(0,1e-2, 3)
|        }
| }"
| ## Compilation
| JMI <- jags.model(textConnection(MI), Data, n.chains=4)
| ## Inference sampling
| JMS <- coda.samples(JMI, c("alpha", "beta"), n.iter=1000)
`----
===================================================================

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 ?

--
Emmanuel Charpentier