XML: Reading transition matrices into R

Hello,
thanks a lot. This is a form which I can work with in R.

Another question, which I hope is not a bridge too far: Can I write
the R matrix which your code created back into the xml format (i.e.
with the same tags and structure) from which it came and hence feed it
back to the original software?

Best,
Stefan


On Thu, Nov 12, 2009 at 3:17 PM, Duncan Temple Lang
<duncan at wald.ucdavis.edu> wrote:

stefan.duke at gmail.com wrote:

Hello,
from a software I have the following output in xml (see below):
It is a series of matrices, for each age one. I have 3 categories
(might vary in the application), hence, 3x3 matrices where each
element gives the probability of transition from i to j. I would like
read this data into R (preferably in a list, where each list element
is one of the age specific matrices) and - after altering the values
in R - write it back into the file.  I know that there is an xml
package in R with which I have already struggled, but I have to admit
my understanding is too limited. Maybe somebody had a similar problem
or know the code of the top of his or her head.

Hi Stefan

 There are many approaches for handling this. I assume that the primary
obstacle you are facing is extracting the values from the XML.  The following
will do that for you.
We start with the content in transition.xml (or in a string in R).
Since the XML is very shallow, i.e. not very hierarchical, and all
the information is in the transition nodes under the root, we can
use xmlToList().
This returns a list with an element for each <transition>
element, and such elements are character vectors containing the
values from age, sex, from, to, and percent.
So I've put these into a matrix and you are now back entirely
within R and can group the values by age and arrange them into
the individual transition matrices.


  doc = xmlParse("transition.xml")
  matrix(as.numeric(unlist(xmlToList(doc))), , 5, byrow = TRUE,
         dimnames = list(NULL, names(xmlRoot(doc)[[1]])))


 D.

Any help appreciated.

Thanks and best,
Stefan





<?xml version="1.0" encoding="UTF-8" standalone="no"?><transitionmatrix>
<transition><age>0</age><sex>0</sex><from>1</from><to>1</to><percent>99.99999</percent></transition><transition><age>0</age><sex>0</sex><from>1</from><to>2</to><percent>0.0</percent></transition><transition><age>0</age><sex>0</sex><from>1</from><to>3</to><percent>0.0</percent></transition><transition><age>0</age><sex>0</sex><from>2</from><to>1</to><percent>0.0</percent></transition><transition><age>0</age><sex>0</sex><from>2</from><to>2</to><percent>99.999985</percent></transition><transition><age>0</age><sex>0</sex><from>2</from><to>3</to><percent>0.0</percent></transition><transition><age>0</age><sex>0</sex><from>3</from><to>1</to><percent>0.0</percent></transition><transition><age>0</age><sex>0</sex><from>3</from><to>2</to><percent>0.0</percent></transition><transition><age>0</age><sex>0</sex><from>3</from><to>3</to><percent>99.999985</percent></transition><transition><age>0</age><sex>1</sex><from>1</from><to>1</to><percent>100.0</percent></transition><transition><age>

/!

 age><sex>1</sex><from>1</from><to>2</to><percent>0.0</percent></transition><transition><age>0</age><sex>1</sex><from>1</from><to>3</to><percent>0.0</percent></transition><transition><age>0</age><sex>1</sex><from>2</from><to>1</to><percent>0.0</percent></transition><transition><age>0</age><sex>1</sex><from>2</from><to>2</to><percent>100.0</percent></transition><transition><age>0</age><sex>1</sex><from>2</from><to>3</to><percent>0.0</percent></transition><transition><age>0</age><sex>1</sex><from>3</from><to>1</to><percent>0.0</percent></transition><transition><age>0</age><sex>1</sex><from>3</from><to>2</to><percent>0.0</percent></transition><transition><age>0</age><sex>1</sex><from>3</from><to>3</to><percent>100.0</percent></transition><transition><age>1</age><sex>0</sex><from>1</from><to>1</to><percent>99.99999</percent></transition><transition><age>1</age><sex>0</sex><from>1</from><to>2</to><percent>0.0</percent></transition><transition><age>1</age><sex>0</sex><from>1</f

m!

 ><to>3</to><percent>0.0</percent></transition><transition><age>1</age>

<sex>0</sex><from>2</from><to>1</to><percent>0.0</percent></transition><transition><age>1</age><sex>0</sex><from>2</from><to>2</to><percent>99.999985</percent></transition><transition><age>1</age><sex>0</sex><from>2</from><to>3</to><percent>0.0</percent></transition><transition><age>1</age><sex>0</sex><from>3</from><to>1</to><percent>0.0</percent></transition><transition><age>1</age><sex>0</sex><from>3</from><to>2</to><percent>0.0</percent></transition><transition><age>1</age><sex>0</sex><from>3</from><to>3</to><percent>99.999985</percent></transition><transition><age>1</age><sex>1</sex><from>1</from><to>1</to><percent>100.0</percent></transition><transition><age>1</age><sex>1</sex><from>1</from><to>2</to><percent>0.0</percent></transition><transition><age>1</age><sex>1</sex><from>1</from><to>3</to><percent>0.0</percent></transition><transition><age>1</age><sex>1</sex><from>2</from><to>1</to><percent>0.0</percent></transition><transition><age>1</age><sex>1</sex><from>2</f

m!

 ><to>2</to><percent>100.0</percent></transition><transition><age>1</age><sex>1</sex><from>2</from><to>3</to><percent>0.0</percent></transition><transition><age>1</age><sex>1</sex><from>3</from><to>1</to><percent>0.0</percent></transition><transition><age>1</age><sex>1</sex><from>3</from><to>2</to><percent>0.0</percent></transition><transition><age>1</age><sex>1</sex><from>3</from><to>3</to><percent>100.0</percent></transition><transition><age>2</age><sex>0</sex><from>1</from><to>1</to><percent>99.35205</percent></transition><transition><age>2</age><sex>0</sex><from>1</from><to>2</to><percent>0.6479474</percent></transition><transition><age>2</age><sex>0</sex><from>1</from><to>3</to><percent>0.0</percent></transition><transition><age>2</age><sex>0</sex><from>2</from><to>1</to><percent>0.0</percent></transition><transition><age>2</age><sex>0</sex><from>2</from><to>2</to><percent>97.101456</percent></transition><transition><age>2</age><sex>0</sex><from>2</from><to>3</to><pe

e!

 nt>2.8985496</percent></transition><transition><age>2</age><sex>0</sex

<from>3</from><to>1</to><percent>0.0</percent></transition><transition><age>2</age><sex>0</sex><from>3</from><to>2</to><percent>0.0</percent></transition><transition><age>2</age><sex>0</sex><from>3</from><to>3</to><percent>100.0</percent></transition><transition><age>2</age><sex>1</sex><from>1</from><to>1</to><percent>97.82136</percent></transition><transition><age>2</age><sex>1</sex><from>1</from><to>2</to><percent>2.1786473</percent></transition><transition><age>2</age><sex>1</sex><from>1</from><to>3</to><percent>0.0</percent></transition><transition><age>2</age><sex>1</sex><from>2</from><to>1</to><percent>0.0</percent></transition><transition><age>2</age><sex>1</sex><from>2</from><to>2</to><percent>93.33336</percent></transition><transition><age>2</age><sex>1</sex><from>2</from><to>3</to><percent>6.6666408</percent></transition><transition><age>2</age><sex>1</sex><from>3</from><to>1</to><percent>0.0</percent></transition><transition><age>2</age><sex>1</sex><from>3</fr

!
 <to>2</to><percent>0.0</percent></transition><transition><age>2</age><sex>1</sex><from>3</from><to>3</to><percent>100.0</percent></transition>
</transitionmatrix>