Dear all,
I have run the confint() function according to below and I get the
following error message:
> confint(stepAIC.glm.spe.var.konn2.abund, level=0.95)
Waiting for profiling to be done...
Error: missing value where logical needed
In addition: Warning message:
NaNs produced in: sqrt((fm$deviance - OriginalDeviance)/DispersionParameter)
or
> confint(stepAIC.glm.spe.var.konn2.abund, parm="DIA", level=0.95)
Waiting for profiling to be done...
Error in object[[pm]] : subscript out of bounds
if only one covariate is analysed.
Profiling seem to be the problem. I would too very much like to have know
what the warning and error messages mean.
All clues are welcome.
Thanks in advance!
Tord Sn?ll
Copy of the analysis:
standardiserat.data <- read.table("Inom_buffert
(standardiserat).txt",
header=TRUE)
library(mass)
glm.spe.var.konn2.abund<-
glm(OSPEINC~DIA+FICKAD+RINGB+TUNNB+UTANB+DYING+DEAD+QUAL+SPRUCEBR+SOILMOIST+
SHADE+BARKDEPTH+PPULABUN+SPEABART2+SPEABFER2, family=binomial,
data=standardiserat.data)
stepAIC.glm.spe.var.konn2.abund <- stepAIC(glm.spe.var.konn2.abund,
direction="both", trace=FALSE, test="Chisq")
> drop1(stepAIC.glm.spe.var.konn2.abund, test="Chisq")
Single term deletions
Model:
OSPEINC ~ DIA + RINGB + TUNNB + QUAL + SPRUCEBR + SHADE + SPEABFER2
Df Deviance AIC LRT Pr(Chi)
<none> 454.28 470.28
DIA 1 480.20 494.20 25.91 3.571e-07 ***
RINGB 1 460.01 474.01 5.73 0.0166762 *
TUNNB 1 458.47 472.47 4.19 0.0407075 *
QUAL 1 462.13 476.13 7.85 0.0050844 **
SPRUCEBR 1 457.07 471.07 2.78 0.0952700 .
SHADE 1 465.66 479.66 11.38 0.0007443 ***
SPEABFER2 1 460.00 474.00 5.72 0.0167640 *
---
Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1
` ' 1
> summary(stepAIC.glm.spe.var.konn2.abund, test="Chisq")
Call:
glm(formula = OSPEINC ~ DIA + RINGB + TUNNB + QUAL + SPRUCEBR +
SHADE + SPEABFER2, family = binomial, data = standardiserat.data)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.60196 -0.75333 -0.56346 -0.03123 2.45180
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.5160 0.2627 -5.770 7.93e-09 ***
DIA 0.6128 0.1221 5.018 5.23e-07 ***
RINGB -0.8115 1.1471 -0.707 0.47930
TUNNB -0.9344 1.1959 -0.781 0.43460
QUAL -0.3696 0.1421 -2.601 0.00930 **
SPRUCEBR -0.2059 0.1335 -1.543 0.12291
SHADE 0.4601 0.1417 3.247 0.00117 **
SPEABFER2 0.2711 0.1126 2.408 0.01602 *
---
Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1
` ' 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 512.21 on 466 degrees of freedom
Residual deviance: 454.28 on 459 degrees of freedom
AIC: 470.28
Number of Fisher Scoring iterations: 6
> confint(stepAIC.glm.spe.var.konn2.abund, level=0.95)
Waiting for profiling to be done...
Error: missing value where logical needed
In addition: Warning message:
NaNs produced in: sqrt((fm$deviance - OriginalDeviance)/DispersionParameter)
> profile.stepAIC.glm.spe.var.konn2.abund <-
profile(stepAIC.glm.spe.var.konn2.abund)
Error: missing value where logical needed
In addition: Warning message:
NaNs produced in: sqrt((fm$deviance - OriginalDeviance)/DispersionParameter)
> confint(stepAIC.glm.spe.var.konn2.abund, parm="DIA", level=0.95)
Waiting for profiling to be done...
Error in object[[pm]] : subscript out of bounds
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