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

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

[Emmanuel Charpentier]

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

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

[Berry, Charles]

> 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

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

[Emmanuel Charpentier]

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