Hello R Users,
I am having difficulty deleting the last warning message in a loop so that the
only warning that is produced is that from the most recent line of code. I
have tried options(warn=1), rm(last.warning), and resetting the last.warning
using something like:
> warning("Resetting warning message")
This problem has been addressed in a previous listserve string, however I do
not follow the advice given. See the below web link. Any help would be
greatly appreciated.
Thanks!
Aaron Wells
https://stat.ethz.ch/pipermail/r-help/2008-October/176765.html
A general example is first, followed by an example with the loop.
---------------------------------------------------------------------------------------------------------------------------------------------
Example 1:
> demo.glm<-glm(test.data[,1]~c(1:38)+I(c(1:38)^2),family=binomial) ###
> Generalized linear model run on the first column of my example data
> warnings() ### no warnings reported
NULL
> demo.glm<-glm(test.data[,9]~c(1:38)+I(c(1:38)^2),family=binomial) ###
> Generalized linear model run on the 9th column of my example data
Warning messages:
1: In glm.fit(x = X, y = Y, weights = weights, start = start, etastart =
etastart, :
algorithm did not converge
2: In glm.fit(x = X, y = Y, weights = weights, start = start, etastart =
etastart, :
fitted probabilities numerically 0 or 1 occurred
> warnings() ### the model with column 9 as data produces warnings
Warning messages:
1: In glm.fit(x = X, y = Y, weights = weights, start = start, ... :
algorithm did not converge
2: In glm.fit(x = X, y = Y, weights = weights, start = start, ... :
fitted probabilities numerically 0 or 1 occurred
> demo.glm<-glm(test.data[,1]~c(1:38)+I(c(1:38)^2),family=binomial) ### Re-run
> the model with column 1 as data
> warnings() ### reports the same warnings from the column 9 model, ideally
> it would report the actual warning message for the column 1 model ("NULL") as
> above
Warning messages:
1: In glm.fit(x = X, y = Y, weights = weights, start = start, ... :
algorithm did not converge
2: In glm.fit(x = X, y = Y, weights = weights, start = start, ... :
fitted probabilities numerically 0 or 1 occurred
----------------------------------------------------------------------------------------------------------------------------------------------
Example 2: Loop
###In the below example I have reset warnings() before each iteration by using
warning("Resetting warning message"). I would like the warnings to somehow be
consolidated into a list that I could later examine to determine which model
iterations ran with and without warnings. The below code doesn't work because
the functions are
being run in the loop environment, and not the base environment.
> test.warn<-rep(0,ncol(test.data));test.warn<-as.list(test.warn)
>
>
> for (i in 1:ncol(test.data)) {warn.reset<-warning("Resetting warning message")
+ demo.glm<-glm(test.data[,i]~c(1:38)+I(c(1:38)^2),family=binomial)
+ warn.new<-warnings()
+ cbind.warn<-cbind(warn.reset,warn.new)
+ test.warn[[i]]<-cbind.warn
+ test.warn
+ }
There were 38 warnings (use warnings() to see them)
> test.warn
[[1]]
warn.reset warn.new
Resetting warning message "Resetting warning message" NULL
[[2]]
warn.reset warn.new
Resetting warning message "Resetting warning message" NULL
.
.
.
Aaron F. Wells, PhD
Senior Scientist
ABR, Inc.
2842 Goldstream Road
Fairbanks, AK 99709
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