[R] polr, lrm - ordinal data

[Chris Mcowen]

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