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kieran (2) [Avatar] Offline
#1
I'm getting an error message 'Error: could not find function "parcor"' and 'Error: could not find function "pcor" when I use this command within the ggm package, as prescribed on page 162 of 'R in Action' (Kabacoff, Manning, 2011).

I'm puzzled as the components of the package list includes both pcor and parcor.

I should be appreciative if you can throw any light on the path to a resolution of the difficulty.
robert.kabacoff (170) [Avatar] Offline
#2
Re: Difficulty with partial correlation
It looks like package versions have gotten out of sink as development continues.

I ran the following commands:

source("http://bioconductor.org/biocLite.R")
biocLite(character(), ask=FALSE)

to update all out of date packages, and after much chugging along, ggm and the pcor() function in particular started working again.

Hope this helps.

Rob
kieran (2) [Avatar] Offline
#3
Re: Difficulty with partial correlation
Thank you: I've tried just as you proposed, Robert

The package you recommend downloaded its contents and I tried again, but still could not get ggm to yield the pcor function.When I input library(ggm), the response was
Loading required package: gRbase
Loading required package: graph
Error: package ‘graph’ could not be loaded
In addition: Warning messages:
1: package ‘ggm’ was built under R version 2.15.1
2: package ‘gRbase’ was built under R version 2.15.1
3: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
there is no package called ‘graph’
And then the error message to the pcor command was as before

On the R Progamming Group on LinkedIn,, there's a suggestion that ggm doesn't work on 2.15.1: 'it needs RBGL, which is no longer available'.

Any other way I can get the partial correlation ?