1
I would like to generate the confidence interval values for some explanatory variables of the HUNTED response variable. The data is distributed in 3 distinct time periods. However, when I use the code: library (MASS) confint (allspecies4) I only get error messages (see below). Would anyone know how to improve my script so I can access the confidence interval? Note: My data set is very large, so I only put a part of it here.
allspecies4<-read.csv(file= "dadosGLMM.csv", header= TRUE, sep= ";" )
attach(allspecies4)
library(lme4)
allspecies4<- glmer(HUNTED~ eco+TrophicLevel+age+ log(body_mass)+
habitat+ABUND + PERIOD + tabu +(1|Specie),
data=dadosGLMM, family=binomial)
library(MASS)
confint(allspecies4)library(MASS)
> confint(allspecies4)
Computing profile confidence intervals ...
Error in zeta(shiftpar, start = opt[seqpar1][-w]) :
profiling detected new, lower deviance
In addition: Warning messages:
1: In nextpar(mat, cc, i, delta, lowcut, upcut) :
unexpected decrease in profile: using minstep
2: In nextpar(mat, cc, i, delta, lowcut, upcut) :
unexpected decrease in profile: using minstep
3: In nextpar(mat, cc, i, delta, lowcut, upcut) :
unexpected decrease in profile: using minstep
4: In nextpar(mat, cc, i, delta, lowcut, upcut) :
unexpected decrease in profile: using minstep
5: In (function (fn, par, lower = rep.int(-Inf, n), upper = rep.int(Inf, :
failure to converge in 10000 evaluations
6: In nextpar(mat, cc, i, delta, lowcut, upcut) :
unexpected decrease in profile: using minstep
7: In nextpar(mat, cc, i, delta, lowcut, upcut) :
unexpected decrease in profile: using minstep
8: In nextpar(mat, cc, i, delta, lowcut, upcut) :
unexpected decrease in profile: using minstep
9: In FUN(X[[i]], ...) : non-monotonic profile for (Intercept)Specie body_mass TrophicLevel age eco habitat PERIOD HUNTED ABUND tabu
Cerc_mit 3.70 2 57 2 F DURING 0 2 1
Cerc_mit 3.70 2 57 2 F AFTER 0 3 1
Cerc_mit 3.70 2 57 2 F BEFORE 0 4 1
Cerc_mit 3.70 2 67 2 F DURING 1 2 1
Cerc_mit 3.70 2 67 2 F AFTER 0 2 1
Chlor_cyn 3.70 2 53 2 S DURING 0 3 0
Chlor_cyn 3.70 2 74 2 S DURING 0 3 0
Chlor_cyn 3.70 2 30 2 S DURING 0 4 0
Chlor_cyn 3.70 2 63 2 S DURING 0 4 0
Chlor_cyn 3.70 2 54 2 S DURING 0 3 0
Chlor_cyn 3.70 2 30 2 S DURING 0 4 0
Chlor_cyn 3.70 2 30 2 S DURING 0 3 0
Phil_mont 3.69 2 24 3 F DURING 0 3 0
Phil_mont 3.69 2 24 3 F BEFORE 0 4 0
Phil_mont 3.69 2 33 3 F AFTER 1 4 0
Phil_mont 3.69 2 33 3 F BEFORE 0 4 0
Phil_mont 3.69 2 33 3 F DURING 0 4 0
Phil_mont 3.69 2 43 3 F BEFORE 0 4 0
Phil_mont 3.69 2 43 3 F DURING 0 4 0
allspecies4<-read.csv(...)but thenallspecies4<- glmer(..., data=dadosGLMM)when the data name is not the file name, isallspecies4. And you should use another name for the model, never the name of the date.frame. 3) Never useattach, does nothing useful and can be dangerous. Delete that line quickly and don’t think about it anymore.– Rui Barradas