R help - Nov 2010 - predict.drm not generating confidence intervals

R-helpers,

I recently submitted a help request for the predict.drm function found in the
drc package.  I am still having issues with the function and I am submitting
reproducible code hoping that somebody can help me figure out what is going on.

--------
library(drc)

# Fit a 4 parameter logistic model to ryegrass dataset
fit <- drm(rootl ~ conc, data = ryegrass, fct = LL.4())
summary(fit)

# Generate a fake dataset for prediction
newdt <- data.frame( matrix(c(seq(0.2, 9, 0.01), rep(NA,881)), ncol=2))
	colnames(newdt) <- c('rootl', 'conc')

# Generate prediction intervals and confidence intervals
prd.p <- predict(fit, newdata=newdt, interval='prediction')
prd.c <- predict(fit, newdata=newdt, interval='confidence')

# Check output
> head(prd.p)
     Prediction Lower Upper
[1,]   7.790812    NA    NA
[2,]   7.790476    NA    NA
[3,]   7.790106    NA    NA
[4,]   7.789702    NA    NA
[5,]   7.789262    NA    NA
[6,]   7.788784    NA    NA  
> head(prd.c)
     Prediction Lower Upper
[1,]   7.790812    NA    NA
[2,]   7.790476    NA    NA
[3,]   7.790106    NA    NA
[4,]   7.789702    NA    NA
[5,]   7.789262    NA    NA
[6,]   7.788784    NA    NA

--------

There appears to be a problem with the predict.drc function.  This code previous
generated confidence and prediction intervals in columns 2 and 3 of the
prediction matrices but now fails for reasons unknown to me.  Anyone have an
idea of what is going on and how I can remedy the situation?

Brant Inman



	[[alternative HTML version deleted]]

Puzzled. Why are the data you offer to predict() for the independent  
variable, conc, all NA's? Is there something reversed or inverted  
about how drc functions handle formulas.

-- 
David.

On Nov 28, 2010, at 2:33 PM, Brant Inman wrote:
> R-helpers,
>
> I recently submitted a help request for the predict.drm function  
> found in the drc package.  I am still having issues with the  
> function and I am submitting reproducible code hoping that somebody  
> can help me figure out what is going on.
>
> --------
> library(drc)
>
> # Fit a 4 parameter logistic model to ryegrass dataset
> fit <- drm(rootl ~ conc, data = ryegrass, fct = LL.4())
> summary(fit)
>
> # Generate a fake dataset for prediction
> newdt <- data.frame( matrix(c(seq(0.2, 9, 0.01), rep(NA,881)),  
> ncol=2))
> 	colnames(newdt) <- c('rootl', 'conc')
>
> # Generate prediction intervals and confidence intervals
> prd.p <- predict(fit, newdata=newdt, interval='prediction')
> prd.c <- predict(fit, newdata=newdt, interval='confidence')
>
> # Check output
>> head(prd.p)
>     Prediction Lower Upper
> [1,]   7.790812    NA    NA
> [2,]   7.790476    NA    NA
> [3,]   7.790106    NA    NA
> [4,]   7.789702    NA    NA
> [5,]   7.789262    NA    NA
> [6,]   7.788784    NA    NA
>
>> head(prd.c)
>     Prediction Lower Upper
> [1,]   7.790812    NA    NA
> [2,]   7.790476    NA    NA
> [3,]   7.790106    NA    NA
> [4,]   7.789702    NA    NA
> [5,]   7.789262    NA    NA
> [6,]   7.788784    NA    NA
>
> --------
>
> There appears to be a problem with the predict.drc function.  This  
> code previous generated confidence and prediction intervals in  
> columns 2 and 3 of the prediction matrices but now fails for reasons  
> unknown to me.  Anyone have an idea of what is going on and how I  
> can remedy the situation?
>
> Brant Inman
>
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT