In bletcher/linkedModels: Link movement, growth, and survival models
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(cache = TRUE)
library(lme4)
library(tidyverse)
load(file = paste0('D:/projects/linkedModels/data/out/dG_bktbntats1997_forLmer.RData')) # made by running mainAnalysis.R with speciesGr = c("bkt", "bnt","ats") through ddG[[ii]] <- dddG[[ii]] %>% prepareDataForJags("growth")
d2 <- data.frame(
#sampleNumber=ddG[[1]][[2]]$sampleNumber,
ind=ddG[[1]][[1]]$ind,
river=ddG[[1]][[1]]$riverDATA,
season=ddG[[1]][[1]]$season,
species=ddG[[1]][[1]]$species,
isYOY=ddG[[1]][[1]]$isYOYDATA,
length=ddG[[1]][[1]]$lengthDATAStd,
lengthByYear=ddG[[1]][[1]]$lengthDATAStd_ByYOY_Year,
grLength=ddG[[1]][[1]]$grNotUse,
tempStd=ddG[[1]][[1]]$tempStd,
flowStd=ddG[[1]][[1]]$flowStd,
countPStd=ddG[[1]][[1]]$countPAllSppStd,
countPStdBKT=ddG[[1]][[1]]$countPStdBKT,
countPStdBNT=ddG[[1]][[1]]$countPStdBNT,
countPStdATS=ddG[[1]][[1]]$countPStdATS
)
d <- d2 %>% filter(
# species == as.numeric(speciesInGr),
!is.na(grLength)
)
d <- d %>% mutate( tempStd2 = tempStd^2, flowStd2 = flowStd^2, countPStd2 = countPStd^2, length2 = length^2,
countPStdBKT2 = countPStdBKT^2,
countPStdBNT2 = countPStdBNT^2,
countPStdATS2 = countPStdATS^2,
isYOY = as.factor(isYOY), season = as.factor(season), river = as.factor(river), species = as.factor(species)
)
d$grLength <- ifelse(d$species == 2 & d$river == 3,NA,d$grLength)
mod <- list(list())
dIn <- list()
bySpecies <- d %>% group_by(species) %>% nest()
Try new, more flexible model structure
2a is best for BKT
2 is best for BNT
#BKT
sppMod <- 1
dIn[[sppMod]] <- d %>% filter(species == sppMod)
mod[[sppMod]][[1]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * river * season * ( tempStd * flowStd * length ) +
isYOY * river * season * ( length * countPStdBKT ) +
isYOY * river * season * ( length * countPStdBNT ) +
isYOY * river * season * ( length * countPStdATS ) +
isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
isYOY * river * season * ( length2 * countPStdBKT2 ) +
isYOY * river * season * ( length2 * countPStdBNT2 ) +
isYOY * river * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[sppMod]] )
mod[[sppMod]][[2]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * river * season * ( tempStd * flowStd * length ) +
# isYOY * river * season * ( length * countPStdBKT ) +
# isYOY * river * season * ( length * countPStdBNT ) +
# isYOY * river * season * ( length * countPStdATS ) +
# isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
# isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
# isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * river * season * ( length2 * countPStdBKT2 ) +
# isYOY * river * season * ( length2 * countPStdBNT2 ) +
# isYOY * river * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[sppMod]] )
mod[[sppMod]][[3]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * river * season * ( tempStd * flowStd * length ) +
# isYOY * river * season * ( length * countPStdBKT ) +
# isYOY * river * season * ( length * countPStdBNT ) +
# isYOY * river * season * ( length * countPStdATS ) +
isYOY * river * season * ( tempStd2 * flowStd2 ) +
# isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
# isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * river * season * ( length2 * countPStdBKT2 ) +
# isYOY * river * season * ( length2 * countPStdBNT2 ) +
# isYOY * river * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[sppMod]] )
mod[[sppMod]][[4]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * river * season * ( tempStd * flowStd * length ) +
# isYOY * river * season * ( length * countPStdBKT ) +
# isYOY * river * season * ( length * countPStdBNT ) +
# isYOY * river * season * ( length * countPStdATS ) +
isYOY * river * season * ( tempStd2 * flowStd2 ) +
isYOY * river * season * ( countPStdBKT2 ) +
isYOY * river * season * ( countPStdBNT2 ) +
isYOY * river * season * ( countPStdATS2 ) +
# # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * river * season * ( length2 * countPStdBKT2 ) +
# isYOY * river * season * ( length2 * countPStdBNT2 ) +
# isYOY * river * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[sppMod]] )
mod[[sppMod]][[5]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * river * season * ( tempStd * flowStd * length ) +
# isYOY * river * season * ( length * countPStdBKT ) +
# isYOY * river * season * ( length * countPStdBNT ) +
# isYOY * river * season * ( length * countPStdATS ) +
isYOY * river * season * ( tempStd2 * flowStd2 ) +
isYOY * river * season * ( countPStdBNT2 ) +
# isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * river * season * ( length2 * countPStdBKT2 ) +
# isYOY * river * season * ( length2 * countPStdBNT2 ) +
# isYOY * river * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[sppMod]] )
mod[[sppMod]][[6]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * river * season * ( tempStd * flowStd * length ) +
isYOY * river * season * ( length * countPStdBKT ) +
isYOY * river * season * ( length * countPStdBNT ) +
isYOY * river * season * ( length * countPStdATS ) +
# isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
# isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
# isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * river * season * ( length2 * countPStdBKT2 ) +
# isYOY * river * season * ( length2 * countPStdBNT2 ) +
# isYOY * river * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[sppMod]] )
mod[[sppMod]][[7]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * river * season * ( tempStd * flowStd * length ) +
isYOY * river * season * ( length * countPStdBKT ) +
isYOY * river * season * ( length * countPStdBNT ) +
isYOY * river * season * ( length * countPStdATS ) +
isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * river * season * ( length2 * countPStdBKT2 ) +
# isYOY * river * season * ( length2 * countPStdBNT2 ) +
# isYOY * river * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[sppMod]] )
mod[[sppMod]][[8]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * river * season * ( tempStd * flowStd * length ) +
isYOY * river * season * ( length * countPStdBKT ) +
isYOY * river * season * ( length * countPStdBNT ) +
isYOY * river * season * ( length * countPStdATS ) +
isYOY * river * season * ( tempStd2 * flowStd2 ) +
isYOY * river * season * ( tempStd2 * flowStd2 ) +
isYOY * river * season * ( tempStd2 * flowStd2 ) +
# # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * river * season * ( length2 * countPStdBKT2 ) +
# isYOY * river * season * ( length2 * countPStdBNT2 ) +
# isYOY * river * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[sppMod]] )
mod[[sppMod]][[9]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * river * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * river * season * ( tempStd * flowStd * length ) +
# isYOY * river * season * ( length * countPStdBKT ) +
# isYOY * river * season * ( length * countPStdBNT ) +
# isYOY * river * season * ( length * countPStdATS ) +
isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * river * season * ( length2 * countPStdBKT2 ) +
# isYOY * river * season * ( length2 * countPStdBNT2 ) +
# isYOY * river * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[sppMod]] )
mod[[sppMod]][[10]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
# isYOY * season * ( length * countPStdBKT ) +
# isYOY * season * ( length * countPStdBNT ) +
# isYOY * season * ( length * countPStdATS ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[sppMod]] )
mod[[sppMod]][[11]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
# isYOY * season * ( length * countPStdBKT ) +
# isYOY * season * ( length * countPStdBNT ) +
# isYOY * season * ( length * countPStdATS ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[sppMod]] )
mod[[sppMod]][[12]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
# isYOY * season * ( length * countPStdBKT ) +
# isYOY * season * ( length * countPStdBNT ) +
# isYOY * season * ( length * countPStdATS ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[sppMod]] )
(aic[[sppMod]] <- AIC(mod1,mod2,mod2a,mod2b,mod2c,mod3,mod4,mod4a,mod5,mod5a,mod5b,mod5c) %>% rownames_to_column() %>% arrange(AIC))
For salmon - need to get rid of 'river'
mod5 is best
#ATS
sppMod <- 3
dIn[[3]] <- d %>% filter(species == sppMod)
mod[[3]][[1]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
isYOY * season * ( length * countPStdBKT ) +
isYOY * season * ( length * countPStdBNT ) +
isYOY * season * ( length * countPStdATS ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
isYOY * season * ( length2 * countPStdBKT2 ) +
isYOY * season * ( length2 * countPStdBNT2 ) +
isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[3]] )
mod[[3]][[2]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
# isYOY * season * ( length * countPStdBKT ) +
# isYOY * season * ( length * countPStdBNT ) +
# isYOY * season * ( length * countPStdATS ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[3]] )
mod[[3]][[3]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
# isYOY * season * ( length * countPStdBKT ) +
# isYOY * season * ( length * countPStdBNT ) +
# isYOY * season * ( length * countPStdATS ) +
isYOY * season * ( tempStd2 * flowStd2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[3]] )
mod[[3]][[4]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
# isYOY * season * ( length * countPStdBKT ) +
# isYOY * season * ( length * countPStdBNT ) +
# isYOY * season * ( length * countPStdATS ) +
isYOY * season * ( tempStd2 * flowStd2 ) +
isYOY * season * ( countPStdBKT2 ) +
isYOY * season * ( countPStdBNT2 ) +
isYOY * season * ( countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[3]] )
mod[[3]][[5]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
# isYOY * season * ( length * countPStdBKT ) +
# isYOY * season * ( length * countPStdBNT ) +
# isYOY * season * ( length * countPStdATS ) +
isYOY * season * ( tempStd2 * flowStd2 ) +
isYOY * season * ( countPStdBNT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[3]] )
mod[[3]][[6]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
isYOY * season * ( length * countPStdBKT ) +
isYOY * season * ( length * countPStdBNT ) +
isYOY * season * ( length * countPStdATS ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[3]] )
mod[[3]][[7]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
isYOY * season * ( length * countPStdBKT ) +
isYOY * season * ( length * countPStdBNT ) +
isYOY * season * ( length * countPStdATS ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[3]] )
mod[[3]][[8]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
isYOY * season * ( length * countPStdBKT ) +
isYOY * season * ( length * countPStdBNT ) +
isYOY * season * ( length * countPStdATS ) +
isYOY * season * ( tempStd2 * flowStd2 ) +
isYOY * season * ( tempStd2 * flowStd2 ) +
isYOY * season * ( tempStd2 * flowStd2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[3]] )
mod[[3]][[9]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
# isYOY * season * ( length * countPStdBKT ) +
# isYOY * season * ( length * countPStdBNT ) +
# isYOY * season * ( length * countPStdATS ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[3]] )
mod[[3]][[10]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
# isYOY * season * ( length * countPStdBKT ) +
# isYOY * season * ( length * countPStdBNT ) +
# isYOY * season * ( length * countPStdATS ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[3]] )
mod[[3]][[11]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
# isYOY * season * ( length * countPStdBKT ) +
# isYOY * season * ( length * countPStdBNT ) +
# isYOY * season * ( length * countPStdATS ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[3]] )
mod[[3]][[12]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) +
isYOY * season * ( tempStd * flowStd * countPStdBNT ) +
isYOY * season * ( tempStd * flowStd * countPStdATS ) +
isYOY * season * ( tempStd * flowStd * length ) +
# isYOY * season * ( length * countPStdBKT ) +
# isYOY * season * ( length * countPStdBNT ) +
# isYOY * season * ( length * countPStdATS ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) +
# isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) +
isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) +
# # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in
# isYOY * season * ( length2 * countPStdBKT2 ) +
# isYOY * season * ( length2 * countPStdBNT2 ) +
# isYOY * season * ( length2 * countPStdATS2 ) +
(1|ind), data = dIn[[3]] )
(aic[[sppMod]] <- AIC(mod1,mod2,mod2a,mod2b,mod2c,mod3,mod4,mod4a,mod5,mod5a,mod5b,mod5c) %>% rownames_to_column() %>% arrange(AIC))
bletcher/linkedModels documentation built on May 14, 2019, 5:24 p.m.
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knitr::opts_chunk$set(echo = TRUE) knitr::opts_chunk$set(cache = TRUE) library(lme4) library(tidyverse)
load(file = paste0('D:/projects/linkedModels/data/out/dG_bktbntats1997_forLmer.RData')) # made by running mainAnalysis.R with speciesGr = c("bkt", "bnt","ats") through ddG[[ii]] <- dddG[[ii]] %>% prepareDataForJags("growth") d2 <- data.frame( #sampleNumber=ddG[[1]][[2]]$sampleNumber, ind=ddG[[1]][[1]]$ind, river=ddG[[1]][[1]]$riverDATA, season=ddG[[1]][[1]]$season, species=ddG[[1]][[1]]$species, isYOY=ddG[[1]][[1]]$isYOYDATA, length=ddG[[1]][[1]]$lengthDATAStd, lengthByYear=ddG[[1]][[1]]$lengthDATAStd_ByYOY_Year, grLength=ddG[[1]][[1]]$grNotUse, tempStd=ddG[[1]][[1]]$tempStd, flowStd=ddG[[1]][[1]]$flowStd, countPStd=ddG[[1]][[1]]$countPAllSppStd, countPStdBKT=ddG[[1]][[1]]$countPStdBKT, countPStdBNT=ddG[[1]][[1]]$countPStdBNT, countPStdATS=ddG[[1]][[1]]$countPStdATS ) d <- d2 %>% filter( # species == as.numeric(speciesInGr), !is.na(grLength) ) d <- d %>% mutate( tempStd2 = tempStd^2, flowStd2 = flowStd^2, countPStd2 = countPStd^2, length2 = length^2, countPStdBKT2 = countPStdBKT^2, countPStdBNT2 = countPStdBNT^2, countPStdATS2 = countPStdATS^2, isYOY = as.factor(isYOY), season = as.factor(season), river = as.factor(river), species = as.factor(species) ) d$grLength <- ifelse(d$species == 2 & d$river == 3,NA,d$grLength) mod <- list(list()) dIn <- list() bySpecies <- d %>% group_by(species) %>% nest()
Try new, more flexible model structure
2a is best for BKT 2 is best for BNT
#BKT sppMod <- 1 dIn[[sppMod]] <- d %>% filter(species == sppMod) mod[[sppMod]][[1]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * river * season * ( tempStd * flowStd * countPStdATS ) + isYOY * river * season * ( tempStd * flowStd * length ) + isYOY * river * season * ( length * countPStdBKT ) + isYOY * river * season * ( length * countPStdBNT ) + isYOY * river * season * ( length * countPStdATS ) + isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in isYOY * river * season * ( length2 * countPStdBKT2 ) + isYOY * river * season * ( length2 * countPStdBNT2 ) + isYOY * river * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[sppMod]] ) mod[[sppMod]][[2]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * river * season * ( tempStd * flowStd * countPStdATS ) + isYOY * river * season * ( tempStd * flowStd * length ) + # isYOY * river * season * ( length * countPStdBKT ) + # isYOY * river * season * ( length * countPStdBNT ) + # isYOY * river * season * ( length * countPStdATS ) + # isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + # isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + # isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * river * season * ( length2 * countPStdBKT2 ) + # isYOY * river * season * ( length2 * countPStdBNT2 ) + # isYOY * river * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[sppMod]] ) mod[[sppMod]][[3]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * river * season * ( tempStd * flowStd * countPStdATS ) + isYOY * river * season * ( tempStd * flowStd * length ) + # isYOY * river * season * ( length * countPStdBKT ) + # isYOY * river * season * ( length * countPStdBNT ) + # isYOY * river * season * ( length * countPStdATS ) + isYOY * river * season * ( tempStd2 * flowStd2 ) + # isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + # isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * river * season * ( length2 * countPStdBKT2 ) + # isYOY * river * season * ( length2 * countPStdBNT2 ) + # isYOY * river * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[sppMod]] ) mod[[sppMod]][[4]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * river * season * ( tempStd * flowStd * countPStdATS ) + isYOY * river * season * ( tempStd * flowStd * length ) + # isYOY * river * season * ( length * countPStdBKT ) + # isYOY * river * season * ( length * countPStdBNT ) + # isYOY * river * season * ( length * countPStdATS ) + isYOY * river * season * ( tempStd2 * flowStd2 ) + isYOY * river * season * ( countPStdBKT2 ) + isYOY * river * season * ( countPStdBNT2 ) + isYOY * river * season * ( countPStdATS2 ) + # # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * river * season * ( length2 * countPStdBKT2 ) + # isYOY * river * season * ( length2 * countPStdBNT2 ) + # isYOY * river * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[sppMod]] ) mod[[sppMod]][[5]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * river * season * ( tempStd * flowStd * countPStdATS ) + isYOY * river * season * ( tempStd * flowStd * length ) + # isYOY * river * season * ( length * countPStdBKT ) + # isYOY * river * season * ( length * countPStdBNT ) + # isYOY * river * season * ( length * countPStdATS ) + isYOY * river * season * ( tempStd2 * flowStd2 ) + isYOY * river * season * ( countPStdBNT2 ) + # isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * river * season * ( length2 * countPStdBKT2 ) + # isYOY * river * season * ( length2 * countPStdBNT2 ) + # isYOY * river * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[sppMod]] ) mod[[sppMod]][[6]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * river * season * ( tempStd * flowStd * countPStdATS ) + isYOY * river * season * ( tempStd * flowStd * length ) + isYOY * river * season * ( length * countPStdBKT ) + isYOY * river * season * ( length * countPStdBNT ) + isYOY * river * season * ( length * countPStdATS ) + # isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + # isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + # isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * river * season * ( length2 * countPStdBKT2 ) + # isYOY * river * season * ( length2 * countPStdBNT2 ) + # isYOY * river * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[sppMod]] ) mod[[sppMod]][[7]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * river * season * ( tempStd * flowStd * countPStdATS ) + isYOY * river * season * ( tempStd * flowStd * length ) + isYOY * river * season * ( length * countPStdBKT ) + isYOY * river * season * ( length * countPStdBNT ) + isYOY * river * season * ( length * countPStdATS ) + isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * river * season * ( length2 * countPStdBKT2 ) + # isYOY * river * season * ( length2 * countPStdBNT2 ) + # isYOY * river * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[sppMod]] ) mod[[sppMod]][[8]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * river * season * ( tempStd * flowStd * countPStdATS ) + isYOY * river * season * ( tempStd * flowStd * length ) + isYOY * river * season * ( length * countPStdBKT ) + isYOY * river * season * ( length * countPStdBNT ) + isYOY * river * season * ( length * countPStdATS ) + isYOY * river * season * ( tempStd2 * flowStd2 ) + isYOY * river * season * ( tempStd2 * flowStd2 ) + isYOY * river * season * ( tempStd2 * flowStd2 ) + # # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * river * season * ( length2 * countPStdBKT2 ) + # isYOY * river * season * ( length2 * countPStdBNT2 ) + # isYOY * river * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[sppMod]] ) mod[[sppMod]][[9]] <- lmer( grLength ~ isYOY * river * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * river * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * river * season * ( tempStd * flowStd * countPStdATS ) + isYOY * river * season * ( tempStd * flowStd * length ) + # isYOY * river * season * ( length * countPStdBKT ) + # isYOY * river * season * ( length * countPStdBNT ) + # isYOY * river * season * ( length * countPStdATS ) + isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + isYOY * river * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + isYOY * river * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * river * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * river * season * ( length2 * countPStdBKT2 ) + # isYOY * river * season * ( length2 * countPStdBNT2 ) + # isYOY * river * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[sppMod]] ) mod[[sppMod]][[10]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + # isYOY * season * ( length * countPStdBKT ) + # isYOY * season * ( length * countPStdBNT ) + # isYOY * season * ( length * countPStdATS ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[sppMod]] ) mod[[sppMod]][[11]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + # isYOY * season * ( length * countPStdBKT ) + # isYOY * season * ( length * countPStdBNT ) + # isYOY * season * ( length * countPStdATS ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[sppMod]] ) mod[[sppMod]][[12]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + # isYOY * season * ( length * countPStdBKT ) + # isYOY * season * ( length * countPStdBNT ) + # isYOY * season * ( length * countPStdATS ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[sppMod]] ) (aic[[sppMod]] <- AIC(mod1,mod2,mod2a,mod2b,mod2c,mod3,mod4,mod4a,mod5,mod5a,mod5b,mod5c) %>% rownames_to_column() %>% arrange(AIC))
For salmon - need to get rid of 'river' mod5 is best
#ATS sppMod <- 3 dIn[[3]] <- d %>% filter(species == sppMod) mod[[3]][[1]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + isYOY * season * ( length * countPStdBKT ) + isYOY * season * ( length * countPStdBNT ) + isYOY * season * ( length * countPStdATS ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in isYOY * season * ( length2 * countPStdBKT2 ) + isYOY * season * ( length2 * countPStdBNT2 ) + isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[3]] ) mod[[3]][[2]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + # isYOY * season * ( length * countPStdBKT ) + # isYOY * season * ( length * countPStdBNT ) + # isYOY * season * ( length * countPStdATS ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[3]] ) mod[[3]][[3]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + # isYOY * season * ( length * countPStdBKT ) + # isYOY * season * ( length * countPStdBNT ) + # isYOY * season * ( length * countPStdATS ) + isYOY * season * ( tempStd2 * flowStd2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[3]] ) mod[[3]][[4]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + # isYOY * season * ( length * countPStdBKT ) + # isYOY * season * ( length * countPStdBNT ) + # isYOY * season * ( length * countPStdATS ) + isYOY * season * ( tempStd2 * flowStd2 ) + isYOY * season * ( countPStdBKT2 ) + isYOY * season * ( countPStdBNT2 ) + isYOY * season * ( countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[3]] ) mod[[3]][[5]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + # isYOY * season * ( length * countPStdBKT ) + # isYOY * season * ( length * countPStdBNT ) + # isYOY * season * ( length * countPStdATS ) + isYOY * season * ( tempStd2 * flowStd2 ) + isYOY * season * ( countPStdBNT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[3]] ) mod[[3]][[6]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + isYOY * season * ( length * countPStdBKT ) + isYOY * season * ( length * countPStdBNT ) + isYOY * season * ( length * countPStdATS ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[3]] ) mod[[3]][[7]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + isYOY * season * ( length * countPStdBKT ) + isYOY * season * ( length * countPStdBNT ) + isYOY * season * ( length * countPStdATS ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[3]] ) mod[[3]][[8]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + isYOY * season * ( length * countPStdBKT ) + isYOY * season * ( length * countPStdBNT ) + isYOY * season * ( length * countPStdATS ) + isYOY * season * ( tempStd2 * flowStd2 ) + isYOY * season * ( tempStd2 * flowStd2 ) + isYOY * season * ( tempStd2 * flowStd2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[3]] ) mod[[3]][[9]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + # isYOY * season * ( length * countPStdBKT ) + # isYOY * season * ( length * countPStdBNT ) + # isYOY * season * ( length * countPStdATS ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[3]] ) mod[[3]][[10]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + # isYOY * season * ( length * countPStdBKT ) + # isYOY * season * ( length * countPStdBNT ) + # isYOY * season * ( length * countPStdATS ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[3]] ) mod[[3]][[11]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + # isYOY * season * ( length * countPStdBKT ) + # isYOY * season * ( length * countPStdBNT ) + # isYOY * season * ( length * countPStdATS ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[3]] ) mod[[3]][[12]] <- lmer( grLength ~ isYOY * season * ( tempStd * flowStd * countPStdBKT ) + isYOY * season * ( tempStd * flowStd * countPStdBNT ) + isYOY * season * ( tempStd * flowStd * countPStdATS ) + isYOY * season * ( tempStd * flowStd * length ) + # isYOY * season * ( length * countPStdBKT ) + # isYOY * season * ( length * countPStdBNT ) + # isYOY * season * ( length * countPStdATS ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBKT2 ) + # isYOY * season * ( tempStd2 * flowStd2 * countPStdBNT2 ) + isYOY * season * ( tempStd2 * flowStd2 * countPStdATS2 ) + # # isYOY * season * ( tempStd2 * flowStd2 * length2 ) + # model error with this line in # isYOY * season * ( length2 * countPStdBKT2 ) + # isYOY * season * ( length2 * countPStdBNT2 ) + # isYOY * season * ( length2 * countPStdATS2 ) + (1|ind), data = dIn[[3]] ) (aic[[sppMod]] <- AIC(mod1,mod2,mod2a,mod2b,mod2c,mod3,mod4,mod4a,mod5,mod5a,mod5b,mod5c) %>% rownames_to_column() %>% arrange(AIC))
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