Loading, listing, and using R Modules and Functions in PL/R
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
?
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 withapt-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. 开发者_开发技巧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?
- Loading an R module into PG.
- Writing a PG wrapper for the desired R function.
- 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!
Overview
These steps list how to call an R function from PostgreSQL using PL/R.
Prerequisties
You must already have PostgreSQL, R, and PL/R installed.
Steps
- Find R Module name (e.g.,
Kendall
) - Change to the database user:
sudo su - postgres
- Run R
R
- Install R Module (accept
$HOME/R/x86_64-pc-linux-gnu-library/2.9/
):install.packages("Kendall", dependencies = TRUE)
- Choose a CRAN Mirror, when prompted.
- Create the following table:
CREATE TABLE plr_modules ( modseq int4, modsrc text );
- Insert into that table the directive to load the R Module in question:
INSERT INTO plr_modules VALUES (0, 'library(Kendall)' );
- Restart the database (or
SELECT * FROM reload_plr_modules();
):sudo /etc/init.d/postgresql-8.4 restart
- Create a wrapper function in PostgreSQL:
CREATE OR REPLACE FUNCTION climate.plr_corr_kendall( double precision[], double precision[] ) RETURNS double precision AS $BODY$ Kendall(arg1, arg2) $BODY$ LANGUAGE 'plr' VOLATILE STRICT;
- Create a function that uses the wrapper function.
- Test the new function.
Wrapper Function
This function performs the work of gathering data from the database and creating two arrays. These arrays are passed into the plr_corr_kendall
wrapper function.
CREATE OR REPLACE FUNCTION climate.analysis_vector()
RETURNS double precision AS
$BODY$
DECLARE
v_year_taken double precision[];
v_amount double precision[];
i RECORD;
BEGIN
FOR i IN (
SELECT
extract(YEAR FROM m.taken) AS year_taken,
avg( m.amount ) AS amount
FROM
climate.city c,
climate.station s,
climate.station_category sc,
climate.measurement m
WHERE
c.id = 5148 AND
earth_distance(
ll_to_earth(c.latitude_decimal,c.longitude_decimal),
ll_to_earth(s.latitude_decimal,s.longitude_decimal)) <= 30 AND
s.elevation BETWEEN 0 AND 3000 AND
s.applicable AND
sc.station_id = s.id AND
sc.category_id = 1 AND
extract(YEAR FROM sc.taken_start) >= 1900 AND
extract(YEAR FROM sc.taken_end) <= 2009 AND
m.station_id = s.id AND
m.taken BETWEEN sc.taken_start AND sc.taken_end AND
m.category_id = sc.category_id
GROUP BY
extract(YEAR FROM m.taken)
ORDER BY
extract(YEAR FROM m.taken)
) LOOP
SELECT array_append( v_year_taken, i.year_taken ) INTO v_year_taken;
SELECT array_append( v_amount, i.amount::double precision ) INTO v_amount;
END LOOP;
RAISE NOTICE '%', v_year_taken;
RAISE NOTICE '%', v_amount;
RETURN climate.plr_corr_kendall( v_year_taken, v_amount );
END;
$BODY$
LANGUAGE 'plpgsql' VOLATILE
COST 100;
Test
Test the function as follows:
SELECT
*
FROM
climate.analysis_vector();
Result
A number: -0.0578900910913944
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