R help - Nov 2004 - scan or source a text file into a list

I've ported somebody else's rather cumbersome Matlab model to R for
colleagues that want a free build of the model with the same type of I/O.

The Matlab model reads a text file with the initial parameters specified as:

C:\Data\Carluc\Rport>more Params.R
# Number of years to simulate
nYears = 50;
# Initial year for graphing purposes
year0 = 1970;
# NPP/GPP ratio (cpp0 unitless)
fnr = 0.30;
# Quantum efficency
qe  = 0.040;

That is, there are four input variables (for this run - there can be many
more) written in a way that R can understand them. In R, I can have the
model source the parameter text file easily enough and have the objects in
the workspace. The model function in R takes a list at runtime. How can I
have R read that file and put the contents into the list I need?

E.g.,
> rm(list = ls())
> source("Params.R")
> ls()
[1] "fnr"    "nYears" "qe"    
"year0"
> fnr
[1] 0.3
> nYears
[1] 50
> foo.list <- list(fnr = fnr, nYears = nYears)
>
> foo.list
$fnr
[1] 0.3

$nYears
[1] 50


The model is then run with
> CarlucR(inputParamList = foo.list, ...)
I can't build inputParamList "by hand" as above because the number
of
initial parameters changes with the model run and this runs in a wrapper.

Any thoughts? Some combination of paste with scan or parse?
-Andy

> version
         _
platform i386-pc-mingw32
arch     i386
os       mingw32
system   i386, mingw32
status
major    2
minor    0.0
year     2004
month    10
day      04
language R
>

use an 'environment' to read in the values; e.g.,
> with(e1 <- new.env(),source('/tempxx.txt', local=T)) # read in
the file
to a new environment
> myList <- list()  # define empty list
> for (i in ls(e1)){  # process each element
+ myList[i] <- get(i, e1)
+ }
>
> ls(e1)  # show objects in the list
[1] "fnr"    "nYears" "qe"    
"year0"
> myList  # output my list
$fnr
[1] 0.3

$nYears
[1] 50

$qe
[1] 0.04

$year0
[1] 1970
>
__________________________________________________________
James Holtman        "What is the problem you are trying to solve?"
Executive Technical Consultant  --  Office of Technology, Convergys
james.holtman at convergys.com
+1 (513) 723-2929



                      "Andy Bunn"
                      <abunn at whrc.org>             To:      
"R-Help" <r-help at stat.math.ethz.ch>
                      Sent by:                     cc:
                      r-help-bounces at stat.m        Subject:  [R] scan or
source a text file into a list
                      ath.ethz.ch


                      11/11/2004 10:57






I've ported somebody else's rather cumbersome Matlab model to R for
colleagues that want a free build of the model with the same type of I/O.

The Matlab model reads a text file with the initial parameters specified
as:

C:\Data\Carluc\Rport>more Params.R
# Number of years to simulate
nYears = 50;
# Initial year for graphing purposes
year0 = 1970;
# NPP/GPP ratio (cpp0 unitless)
fnr = 0.30;
# Quantum efficency
qe  = 0.040;

That is, there are four input variables (for this run - there can be many
more) written in a way that R can understand them. In R, I can have the
model source the parameter text file easily enough and have the objects in
the workspace. The model function in R takes a list at runtime. How can I
have R read that file and put the contents into the list I need?

E.g.,
> rm(list = ls())
> source("Params.R")
> ls()
[1] "fnr"    "nYears" "qe"    
"year0"
> fnr
[1] 0.3
> nYears
[1] 50
> foo.list <- list(fnr = fnr, nYears = nYears)
>
> foo.list
$fnr
[1] 0.3

$nYears
[1] 50


The model is then run with
> CarlucR(inputParamList = foo.list, ...)
I can't build inputParamList "by hand" as above because the number
of
initial parameters changes with the model run and this runs in a wrapper.

Any thoughts? Some combination of paste with scan or parse?
-Andy

> version
         _
platform i386-pc-mingw32
arch     i386
os       mingw32
system   i386, mingw32
status
major    2
minor    0.0
year     2004
month    10
day      04
language R
>
______________________________________________
R-help at stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

Here's one way:
> myList <- mget(ls(), .GlobalEnv)
> myList
$fnr
[1] 0.3

$nYears
[1] 50

$qe
[1] 0.04

$year0
[1] 1970

HTH,
Andy
> From: Andy Bunn
> 
> I've ported somebody else's rather cumbersome Matlab model to R for
> colleagues that want a free build of the model with the same 
> type of I/O.
> 
> The Matlab model reads a text file with the initial 
> parameters specified as:
> 
> C:\Data\Carluc\Rport>more Params.R
> # Number of years to simulate
> nYears = 50;
> # Initial year for graphing purposes
> year0 = 1970;
> # NPP/GPP ratio (cpp0 unitless)
> fnr = 0.30;
> # Quantum efficency
> qe  = 0.040;
> 
> That is, there are four input variables (for this run - there 
> can be many
> more) written in a way that R can understand them. In R, I 
> can have the
> model source the parameter text file easily enough and have 
> the objects in
> the workspace. The model function in R takes a list at 
> runtime. How can I
> have R read that file and put the contents into the list I need?
> 
> E.g.,
> > rm(list = ls())
> > source("Params.R")
> > ls()
> [1] "fnr"    "nYears" "qe"    
"year0"
> > fnr
> [1] 0.3
> > nYears
> [1] 50
> > foo.list <- list(fnr = fnr, nYears = nYears)
> >
> > foo.list
> $fnr
> [1] 0.3
> 
> $nYears
> [1] 50
> 
> 
> The model is then run with
> > CarlucR(inputParamList = foo.list, ...)
> 
> I can't build inputParamList "by hand" as above because the
number of
> initial parameters changes with the model run and this runs 
> in a wrapper.
> 
> Any thoughts? Some combination of paste with scan or parse?
> -Andy
> 
> 
> > version
>          _
> platform i386-pc-mingw32
> arch     i386
> os       mingw32
> system   i386, mingw32
> status
> major    2
> minor    0.0
> year     2004
> month    10
> day      04
> language R
> >
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
> 
>

Not sure if I understand your question.

If you know the complete list of all possible variable names, then you
can grep for each occurrence and split on the "=". Otherwise, I hope
you
have some sort of markers (like main()) to seperate the input and actual
commands. I think perl and bash are probably more suitable for this kind
of job.

Then you can try commandArgs() to feed into R.



On Thu, 2004-11-11 at 15:57, Andy Bunn wrote:
> I've ported somebody else's rather cumbersome Matlab model to R for
> colleagues that want a free build of the model with the same type of I/O.
> 
> The Matlab model reads a text file with the initial parameters specified
as:
> 
> C:\Data\Carluc\Rport>more Params.R
> # Number of years to simulate
> nYears = 50;
> # Initial year for graphing purposes
> year0 = 1970;
> # NPP/GPP ratio (cpp0 unitless)
> fnr = 0.30;
> # Quantum efficency
> qe  = 0.040;
> 
> That is, there are four input variables (for this run - there can be many
> more) written in a way that R can understand them. In R, I can have the
> model source the parameter text file easily enough and have the objects in
> the workspace. The model function in R takes a list at runtime. How can I
> have R read that file and put the contents into the list I need?
> 
> E.g.,
> > rm(list = ls())
> > source("Params.R")
> > ls()
> [1] "fnr"    "nYears" "qe"    
"year0"
> > fnr
> [1] 0.3
> > nYears
> [1] 50
> > foo.list <- list(fnr = fnr, nYears = nYears)
> >
> > foo.list
> $fnr
> [1] 0.3
> 
> $nYears
> [1] 50
> 
> 
> The model is then run with
> > CarlucR(inputParamList = foo.list, ...)
> 
> I can't build inputParamList "by hand" as above because the
number of
> initial parameters changes with the model run and this runs in a wrapper.
> 
> Any thoughts? Some combination of paste with scan or parse?
> -Andy
> 
> 
> > version
>          _
> platform i386-pc-mingw32
> arch     i386
> os       mingw32
> system   i386, mingw32
> status
> major    2
> minor    0.0
> year     2004
> month    10
> day      04
> language R
> >
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

On Thursday 11 November 2004 09:57, Andy Bunn wrote:
> I've ported somebody else's rather cumbersome Matlab model to R for
> colleagues that want a free build of the model with the same type of
> I/O.
>
> The Matlab model reads a text file with the initial parameters
> specified as:
>
> C:\Data\Carluc\Rport>more Params.R
> # Number of years to simulate
> nYears = 50;
> # Initial year for graphing purposes
> year0 = 1970;
> # NPP/GPP ratio (cpp0 unitless)
> fnr = 0.30;
> # Quantum efficency
> qe  = 0.040;
>
> That is, there are four input variables (for this run - there can be
> many more) written in a way that R can understand them. In R, I can
> have the model source the parameter text file easily enough and have
> the objects in the workspace. The model function in R takes a list at
> runtime. How can I have R read that file and put the contents into
> the list I need?
>
> E.g.,
>
> > rm(list = ls())
> > source("Params.R")
> > ls()
>
> [1] "fnr"    "nYears" "qe"    
"year0"
>
> > fnr
>
> [1] 0.3
>
> > nYears
>
> [1] 50
>
> > foo.list <- list(fnr = fnr, nYears = nYears)
> >
> > foo.list
>
> $fnr
> [1] 0.3
>
> $nYears
> [1] 50
>
>
> The model is then run with
>
> > CarlucR(inputParamList = foo.list, ...)
>
> I can't build inputParamList "by hand" as above because the
number of
> initial parameters changes with the model run and this runs in a
> wrapper.
>
> Any thoughts? Some combination of paste with scan or parse?
Approaching this slightly differently, how about 

read.pars <- function(file)
{
    foo <- read.table(file, as.is = TRUE)
    ans <- lapply(strsplit(foo[[3]], ";"), as.numeric)
    names(ans) <- foo[[1]]
    ans
}

Deepayan

On Thu, 11 Nov 2004, Andy Bunn wrote:
> I've ported somebody else's rather cumbersome Matlab model to R for
> colleagues that want a free build of the model with the same type of I/O.
> 
> The Matlab model reads a text file with the initial parameters specified
as:
I think I would be tempted to try out read.dcf() for this, which returns a 
character matrix of field values in named columns, from which values cast 
to numeric:
> system("cat tmp/Params.dcf")
nYears: 50
year0: 1970
fnr: 0.30
qe: 0.040
> x <- read.dcf("tmp/Params.dcf")
> x
     nYears year0  fnr    qe     
[1,] "50"   "1970" "0.30"
"0.040"
> str(x)
 chr [1, 1:4] "50" "1970" "0.30" "0.040"
 - attr(*, "dimnames")=List of 2
  ..$ : NULL
  ..$ : chr [1:4] "nYears" "year0" "fnr"
"qe"


Since you will know the mode you need, you could read the same-mode fields 
together and cast them:
> x <- read.dcf("tmp/Params.dcf", fields=c("nYears",
"year0"))
> mode(x) <- "integer"
> x
     nYears year0
[1,]     50  1970

and make x a data frame if say x$nYears is needed, which gets to list:
> as.list(data.frame(x))
$nYears
[1] 50

$year0
[1] 1970

and c() of the different mode lists to make inputParamList. I think 
treating everything as numeric may be enough, and the DCF format is 
flexible.

Roger
> 
> C:\Data\Carluc\Rport>more Params.R
> # Number of years to simulate
> nYears = 50;
> # Initial year for graphing purposes
> year0 = 1970;
> # NPP/GPP ratio (cpp0 unitless)
> fnr = 0.30;
> # Quantum efficency
> qe  = 0.040;
> 
> That is, there are four input variables (for this run - there can be many
> more) written in a way that R can understand them. In R, I can have the
> model source the parameter text file easily enough and have the objects in
> the workspace. The model function in R takes a list at runtime. How can I
> have R read that file and put the contents into the list I need?
> 
> E.g.,
> > rm(list = ls())
> > source("Params.R")
> > ls()
> [1] "fnr"    "nYears" "qe"    
"year0"
> > fnr
> [1] 0.3
> > nYears
> [1] 50
> > foo.list <- list(fnr = fnr, nYears = nYears)
> >
> > foo.list
> $fnr
> [1] 0.3
> 
> $nYears
> [1] 50
> 
> 
> The model is then run with
> > CarlucR(inputParamList = foo.list, ...)
> 
> I can't build inputParamList "by hand" as above because the
number of
> initial parameters changes with the model run and this runs in a wrapper.
> 
> Any thoughts? Some combination of paste with scan or parse?
> -Andy
> 
> 
> > version
>          _
> platform i386-pc-mingw32
> arch     i386
> os       mingw32
> system   i386, mingw32
> status
> major    2
> minor    0.0
> year     2004
> month    10
> day      04
> language R
> >
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
> 
-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Breiviksveien 40, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93
e-mail: Roger.Bivand at nhh.no

Andy Bunn <abunn <at> whrc.org> writes:

: 
: I've ported somebody else's rather cumbersome Matlab model to R for
: colleagues that want a free build of the model with the same type of I/O.
: 
: The Matlab model reads a text file with the initial parameters specified as:
: 
: C:\Data\Carluc\Rport>more Params.R
: # Number of years to simulate
: nYears = 50;
: # Initial year for graphing purposes
: year0 = 1970;
: # NPP/GPP ratio (cpp0 unitless)
: fnr = 0.30;
: # Quantum efficency
: qe  = 0.040;
: 
: That is, there are four input variables (for this run - there can be many
: more) written in a way that R can understand them. In R, I can have the
: model source the parameter text file easily enough and have the objects in
: the workspace. The model function in R takes a list at runtime. How can I
: have R read that file and put the contents into the list I need?
: 
: E.g.,
: > rm(list = ls())
: > source("Params.R")
: > ls()
: [1] "fnr"    "nYears" "qe"     "year0"
: > fnr
: [1] 0.3
: > nYears
: [1] 50
: > foo.list <- list(fnr = fnr, nYears = nYears)
: >
: > foo.list
: $fnr
: [1] 0.3
: 
: $nYears
: [1] 50
: 
: 
: The model is then run with
: > CarlucR(inputParamList = foo.list, ...)
: 
: I can't build inputParamList "by hand" as above because the
number of
: initial parameters changes with the model run and this runs in a wrapper.
: 


The following sources the file in the environment that
exists within function f returning a list of all variables in
that environment except those variables that begin with a dot. 
You could alternately replace the source(...) statement with 
eval(parse(.file)) .

R> f <- function(.file) { source(.file, local = TRUE);
as.list(environment()) }
R> f("clipboard")
$qe
[1] 0.04

$fnr
[1] 0.3

$year0
[1] 1970

$nYears
[1] 50

: