[R] polr, lrm - ordinal data
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
[R] polr, lrm - ordinal data
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
