Loading, listing, and using R Modules and Functions in PL/R

Posted by Dave Jarvis on Stack Overflow See other posts from Stack Overflow or by Dave Jarvis
Published on 2010-05-28T19:50:45Z Indexed on 2010/05/29 2:22 UTC
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I am having difficulty with:

  • Listing the R packages and functions available to PostgreSQL.
  • Installing a package (such as Kendall) for use with PL/R
  • Calling an R function within PostgreSQL

Listing Available R Packages

Q.1. How do you find out what R modules have been loaded?

SELECT * FROM r_typenames();

That shows the types that are available, but what about checking if Kendall( X, Y ) is loaded? For example, the documentation shows:

CREATE TABLE plr_modules (
  modseq int4,
  modsrc text
);

That seems to allow inserting records to dictate that Kendall is to be loaded, but the following code doesn't explain, syntactically, how to ensure that it gets loaded:

INSERT INTO plr_modules
  VALUES (0, 'pg.test.module.load <-function(msg) {print(msg)}');

Q.2. What would the above line look like if you were trying to load Kendall?
Q.3. Is it applicable?

Installing R Packages

Using the "synaptic" package manager the following packages have been installed:

r-base
r-base-core
r-base-dev
r-base-html
r-base-latex
r-cran-acepack
r-cran-boot
r-cran-car
r-cran-chron
r-cran-cluster
r-cran-codetools
r-cran-design
r-cran-foreign
r-cran-hmisc
r-cran-kernsmooth
r-cran-lattice
r-cran-matrix
r-cran-mgcv
r-cran-nlme
r-cran-quadprog
r-cran-robustbase
r-cran-rpart
r-cran-survival
r-cran-vr
r-recommended

Q.4. How do I know if Kendall is in there?
Q.5. If it isn't, how do I find out what package it is in?
Q.6. If it isn't in a package suitable for installing with apt-get (aptitude, synaptic, dpkg, what have you), how do I go about installing it on Ubuntu?
Q.7. Where are the installation steps documented?

Calling R Functions

I have the following code:

EXECUTE 'SELECT '
  'regr_slope( amount, year_taken ),'
  'regr_intercept( amount, year_taken ),'
  'corr( amount, year_taken ),'
  'sum( measurements ) AS total_measurements '
'FROM temp_regression'
INTO STRICT slope, intercept, correlation, total_measurements;

This code calls the PostgreSQL function corr to calculate Pearson's correlation over the data. Ideally, I'd like to do the following (by switching corr for plr_kendall):

EXECUTE 'SELECT '
  'regr_slope( amount, year_taken ),'
  'regr_intercept( amount, year_taken ),'
  'plr_kendall( amount, year_taken ),'
  'sum( measurements ) AS total_measurements '
'FROM temp_regression'
INTO STRICT slope, intercept, correlation, total_measurements;

Q.8. Do I have to write plr_kendall myself?
Q.9. Where can I find a simple example that walks through:

  1. Loading an R module into PG.
  2. Writing a PG wrapper for the desired R function.
  3. Calling the PG wrapper from a SELECT.

For example, would the last two steps look like:

create or replace function plr_kendall( _float8, _float8 ) returns float as '
  agg_kendall(arg1, arg2)
' language 'plr';

CREATE AGGREGATE agg_kendall (
  sfunc = plr_array_accum,
  basetype = float8, -- ???
  stype = _float8, -- ???
  finalfunc = plr_kendall
);

And then the SELECT as above?

Thank you!

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