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spatio-temporal/spatiotemporal_aic_comparison.R
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| ############ AIC comparison ############## | |
| setwd(getwd()) #specify working directory | |
| df <- read_csv("data.csv", col_types = "fifffiidf") #Read data and set correct data types into the columns | |
| #The following code fits every simplified version of the main model for each focal taxa and prints their Akaike information criterion. | |
| #This is solely for ensuring that there is no unjustified complexity (independent variables that increase AIC) involved in the main models. | |
| test <- filter(df, taxa == "E. nilssonii") | |
| fit <- glmmTMB(formula = cbind(succ, fail) ~ period+year+lat+lat*period+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| print(1) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+year+lat+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| print(2) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+lat+lat*period+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| print(3) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+lat+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| print(4) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+year+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| print(5) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ lat+year+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| print(6) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| print(7) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ lat+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| print(8) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ year+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| print(9) | |
| summary(fit)$AIC | |
| ### | |
| test <- filter(df, taxa == "Myotis sp.") | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+year+lat+lat*period+(1|station/place), | |
| data = test, family = binomial(link = "logit")) | |
| print(1) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+year+lat+(1|station/place), | |
| data = test, family = binomial(link = "logit")) | |
| print(2) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+lat+lat*period+(1|station/place), | |
| data = test, family = binomial(link = "logit")) | |
| print(3) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+lat+(1|station/place), | |
| data = test, family = binomial(link = "logit")) | |
| print(4) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+year+(1|station/place), | |
| data = test, family = binomial(link = "logit")) | |
| print(5) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ lat+year+(1|station/place), | |
| data = test, family = binomial(link = "logit")) | |
| print(6) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+(1|station/place), | |
| data = test, family = binomial(link = "logit")) | |
| print(7) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ lat+(1|station/place), | |
| data = test, family = binomial(link = "logit")) | |
| print(8) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ year+(1|station/place), | |
| data = test, family = binomial(link = "logit")) | |
| print(9) | |
| summary(fit)$AIC | |
| ### | |
| test <- filter(df, taxa == "P. nathusii", station == "Huso" | station == "Tvarminne" | station == "Seili") | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+year+period*year+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| fit <- update(fit, control=glmmTMBControl(optCtrl=list(iter.max=1e3,eval.max=1e3))) | |
| print(1) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+year+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| print(2) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ period+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| print(3) | |
| summary(fit)$AIC | |
| fit <- glmmTMB(formula = cbind(succ, fail)~ year+(1|station/place) + (1|mic), | |
| data = test, family = binomial(link = "logit")) | |
| print(4) | |
| summary(fit)$AIC |