Dear List,
I have developed a model and am looking to predict a response for 1-6 ( it is
ordered i.e the difference between level 1 and 2 is the same as between level 2
and 3 etc.
I have used the predict function for a polr model (below) and a lrm model, and
both give similar results, however for some reason the outcome are all 1 or 6
i.e no level 2,3,4,5.
This is not correct, i am unsure if it is because my model is not good enough to
predict to this accuracy or if it is something i am doing wrong?
Thanks
Chris
> test <- polr(extinction ~
FR*HAB+WO+ALT+BIO+REG,method="logistic")
> > test
> Call:
> polr(formula = extinction ~ FR * HAB + WO + ALT + BIO + REG,
> method = "logistic")
>
> Coefficients:
> FRNon_fleshy HABSemi-aquatic
HABTerrestrial WOWoody ALTHigh
> 0.09758543 -0.05988101
-0.29744997 0.32746840 -0.39191606
> ALTLow ALTMid
BIOBoreal BIOMediterranean BIOSubtropical/Tropical
> -0.56523156 -0.18979562
-0.22743656 -0.31344233 1.77031824
> BIOTemperate REGTwo_plus
FRNon_fleshy:HABSemi-aquatic FRNon_fleshy:HABTerrestrial
> 1.45071627 -0.67654880
-2.06919408 -0.31706541
>
> Intercepts:
> 1|2 2|3 3|4 4|5 5|6
> 0.4874828 0.8340901 1.3994091 1.8091463 2.1295630
>
> Residual Deviance: 2471.053
> AIC: 2509.053
> > predict(test)
> [1] 1 1 1 1 1 1 1 1 1 1 6 1 6 1 1 6 1 1 1 6 1 1 1 6 1 1 1 1 6 1 6 6 1 1 6
1 1 1 1 6 1 1 1 1 6 6 1 1 6 1 1 1 1 1 6 1 1 1 1 6 1 1 6 1 6 1 6 1 1 1 1 1 1 1
> [75] 1 1 1 1 1 1 1 6 6 1 1 1 6 6 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1 1 6 1 6 6 1
1 1 1 1 1 6 1 1 1 1 1 6 1 1 1 1 1 6 6 1 6 1 1 1 1 1 1 6 1 1 1 1 1 6 1 1 1 1 6
> [149] 1 1 1 1 1 1 1 1 1 1 1 6 1 1 1 6 1 1 1 1 1 1 6 1 6 1 1 1 1 1 6 1 1 6 1
1 1 1 1 6 1 1 1 1 1 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 6 1 1 6 1 1 1 1 1 1 6 1 1
> [223] 1 1 1 1 1 1 1 1 1 1 1 6 1 1 6 6 6 1 1 6 6 1 1 1 1 1 1 1 1 1 1 1 1 1 6
1 1 6 1 1 1 1 1 1 6 1 1 1 1 6 1 1 6 6 1 6 1 1 1 1 1 1 1 1 1 1 1 1 6 1 6 6 1 1
> [297] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 6 1 1 1 1 1 1 1 1 6 1 1 6 1 1
6 1 6 1 1 6 1 1 1 1 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 6 1 1 1 6 1 1
> [371] 1 1 1 1 1 1 1 6 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 6 6 6 1 1 1 1 6 1 1 1
1 1 1 1 1 6 1 1 1 6 1 1 1 1 1 1 1 6 1 1 1 1 6 1 6 1 1 6 1 1 1 1 1 1 1 1 1 1 1
> [445] 1 6 1 1 1 1 1 1 6 1 1 1 1 1 6 1 1 1 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1
6 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 6
> [519] 1 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 6 1 1 1 1 1 6 1 1 1 1 1 1 1 6 1 1 6
1 6 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 6 1 1 6 1 6 1 1 6 6 1 1 1 1 1 1 1 1 1 1 1
> [593] 6 1 1 1 1 1 1 6 1 1 6 1 1 6 6 1 6 1 1 1 6 1 1 1 1 1 1 1 6 1 1 1 1 1 1
1 1 1 6 1 1 1 1 1 1 1 1 1 6 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> [667] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 6 1 6 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1 1
> [741] 1 1 1 6 6 1 1 1 6 1 1 1 1 1 6 1 1 1 1 1 1 1 6 1 1 6 1 1 6 1 1 1 6 1 6
1 6 6 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 6 1 1 1 1 1 1 6 1 1 1 1 1 6 1
> [815] 6 6 1 1 1 1 1 1 1 6 1 6 1 1 1 1 1 1 1 1
> Levels: 1 2 3 4 5 6
this is the "correct output"
> extinction
> [1] 3 1 6 4 2 1 6 1 2 6 6 1 5 1 1 1 1 6 2 4 1 4 1 3 6 3 5 1 4 3 3 5 3 3 3
5 1 6 6 3 6 6 1 1 5 1 5 3 3 6 1 1 6 2 6 1 3 1 2 6 1 1 3 4 6 3 3 1 1 3 6 3 1 6
> [75] 3 4 1 1 1 3 1 3 6 1 2 1 6 6 3 6 6 5 1 1 4 6 3 1 2 1 1 1 4 6 3 1 2 6 1
3 2 1 1 6 1 6 2 3 6 2 4 6 6 5 2 4 6 6 1 2 6 6 4 1 1 1 5 5 1 1 1 6 6 1 1 1 2 6
> [149] 4 5 6 6 6 1 3 1 4 3 1 3 6 1 3 6 1 2 1 3 4 1 3 1 6 3 6 1 6 2 1 3 4 6 6
1 1 1 1 5 1 2 1 6 3 1 6 6 1 1 6 6 1 1 2 2 4 1 4 3 5 4 1 4 3 6 1 2 6 1 1 5 6 1
> [223] 1 2 1 6 3 6 1 1 1 6 1 6 3 4 1 5 5 6 3 2 3 6 1 1 1 5 1 6 6 1 4 3 1 4 6
1 3 5 1 4 4 6 2 6 6 1 6 3 2 6 3 1 4 1 5 6 1 6 4 5 4 1 4 1 4 1 1 1 4 1 6 6 6 6
> [297] 1 1 1 1 6 1 3 2 1 6 6 6 1 1 3 3 1 4 1 6 2 2 6 3 1 1 6 6 2 6 1 1 6 6 1
2 1 6 4 1 4 1 1 5 1 3 6 6 1 1 3 6 6 6 1 6 1 1 6 3 4 6 1 6 1 3 1 2 1 1 6 6 1 1
> [371] 1 6 3 1 1 2 5 1 1 1 1 1 6 1 1 1 1 2 4 6 1 5 1 1 6 6 3 1 6 1 6 6 4 1 1
4 2 6 1 1 3 6 1 2 6 1 2 1 1 4 5 1 6 1 6 1 1 6 1 3 6 1 1 1 3 1 2 6 3 5 2 1 3 1
> [445] 3 2 4 1 6 6 1 4 5 2 1 6 1 3 4 3 1 1 1 6 1 3 5 6 1 1 1 6 1 1 2 1 1 1 1
2 4 1 1 1 1 3 1 1 1 1 1 1 6 6 4 1 1 2 1 6 6 6 6 6 6 6 1 3 4 3 1 1 1 1 2 1 5 1
> [519] 1 6 1 1 1 6 6 1 3 5 2 1 1 1 1 4 3 6 2 1 3 1 1 1 6 3 3 4 1 5 6 6 1 2 6
3 1 5 6 1 1 6 1 1 1 1 1 3 1 1 1 3 6 1 1 1 6 6 1 3 1 2 6 1 6 2 3 1 6 1 6 6 2 4
> [593] 1 1 5 3 1 1 1 6 3 1 6 6 4 4 1 6 6 6 1 1 6 1 6 3 1 1 2 1 6 1 1 1 6 1 3
6 6 1 3 3 2 2 6 1 1 1 1 6 1 3 1 2 1 6 1 4 1 1 1 6 1 4 4 1 6 3 1 6 1 3 1 1 2 6
> [667] 5 1 2 1 1 4 4 1 1 1 6 4 1 6 6 1 1 4 6 1 1 1 1 1 1 5 1 4 1 4 6 6 6 5 1
1 1 2 1 6 6 1 1 3 3 1 1 6 1 1 1 1 5 2 1 1 5 1 3 1 4 5 1 4 1 1 6 1 1 6 1 1 1 2
> [741] 3 6 1 4 2 1 2 1 1 1 1 1 4 6 2 4 1 4 3 4 1 4 5 3 1 3 1 6 4 1 3 1 5 6 3
3 3 1 1 1 1 2 5 1 4 6 5 3 1 6 5 1 5 1 6 6 3 6 1 5 1 6 1 1 5 4 3 2 4 1 2 1 3 3
> [815] 3 1 1 1 6 5 5 3 3 1 6 5 4 6 1 6 1 3 1 3
> Levels: 1 2 3 4 5 6