[R-sig-ME] Predict in glmer using method from Owl data ( Ben Bolker)

[Chris Mcowen]

Dear List and Ben,

I am having some trouble replicating the method used by Ben for getting predicted values from glmer. 

I had heard that as long as the model is selected taking into account the random effects then it should be fine to use a lm and the predict function to get the predicted values. I have done this and the model performs OK with binomial data C value - 0.77 and Bieber score - 0.199. However when i try and do this for a ordinal response then the model performs badly in predicting. I am wondering if this is because it makes no account for random effects so i have decided to revisit mixed models.

> > g1
> Generalized linear mixed model fit by the Laplace approximation 
> Formula: THREAT ~ 1 + (1 | order/fam) + BS * FR + HAB + SEA + PD + WO +      ALT + REG + BIO + LIF 

Where i am trying to predict if a species is threatened or not based on a series of life history traits. I have a list of species where i know their life history but not threat level.


I am using the method Ben used in his example to get the predicted values , however i am having trouble. The output contains a large number of outputs (7000+), where as my data frame only has 993, i feel the problem may arise from setting up the data frame (see below) the output makes no sense in relation to my data for example only 6 species are Arctic where as the data frame has loads?

> >  pframe0 <- with(traits,expand.grid(BS=levels(BS),FR=levels(FR),WO=levels(WO),PD=levels(PD),HAB=levels(HAB),SEA=levels(SEA),ALT=levels(ALT),BIO=levels(BIO),REG=levels(REG),LIF=levels(LIF)))


> pframe0

>                      BS         FR        WO      PD          HAB       SEA  ALT                  BIO      REG     LIF
> 1       Bisexual_flower     Fleshy Non_woody Abiotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 2     Unisexual_flowers     Fleshy Non_woody Abiotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 3       Unisexual_plant     Fleshy Non_woody Abiotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 4       Bisexual_flower Non_fleshy Non_woody Abiotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 5     Unisexual_flowers Non_fleshy Non_woody Abiotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 6       Unisexual_plant Non_fleshy Non_woody Abiotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 7       Bisexual_flower     Fleshy     Woody Abiotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 8     Unisexual_flowers     Fleshy     Woody Abiotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 9       Unisexual_plant     Fleshy     Woody Abiotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 10      Bisexual_flower Non_fleshy     Woody Abiotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 11    Unisexual_flowers Non_fleshy     Woody Abiotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 12      Unisexual_plant Non_fleshy     Woody Abiotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 13      Bisexual_flower     Fleshy Non_woody  Biotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 14    Unisexual_flowers     Fleshy Non_woody  Biotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 15      Unisexual_plant     Fleshy Non_woody  Biotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 16      Bisexual_flower Non_fleshy Non_woody  Biotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 17    Unisexual_flowers Non_fleshy Non_woody  Biotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 18      Unisexual_plant Non_fleshy Non_woody  Biotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 19      Bisexual_flower     Fleshy     Woody  Biotic     Epiphyte    Annual  All               Arctic      One  Bamboo
> 20    Unisexual_flowers     Fleshy     Woody  Biotic     Epiphyte    Annual  All               Arctic      One  Bamboo

I then tried to attach the fixed effects predictions, i got values but as there are a huge number of enterys in the data frame i am unsure what they correspond to (see below)

> pframe1 <- data.frame(pframe0,eta=mm%*%fixef(g1))

I am sorry if this is hard to follow, i can supply more data or clarify further if required

Chris