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148 changes: 148 additions & 0 deletions R/sim_glmms.R
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Original file line number Diff line number Diff line change
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# Replace NAs with 0
od_joined <- od_joined %>% mutate_all(~replace(., is.na(.), 0))

library(glmmTMB)

# Calculate row and column sums
origin_totals <- tapply(od_joined$origin_n_o, od_joined$O, mean, na.rm = TRUE)
destination_totals <- tapply(od_joined$destination_n_d, od_joined$D, mean, na.rm=TRUE)

# Function for plots and model predictions
model_assessment <- function(model, data, index_yvar){
data$predicted = predict(model,
newdata=data, type="response",
allow.new.levels=TRUE)
# data$predicted = fitted(model)
#cdatasubmat2 <- dcast(data, O ~ D, sum, value.var = "predicted", margins=c("O", "D"))

plot(data$n_observed, data$predicted)
r2_p = cor(data$predicted,data[,index_yvar])^2

origin_totals_o <- tapply(data[,index_yvar], data$O, sum, na.rm = TRUE)
destination_totals_o <- tapply(data[,index_yvar], data$D, sum, na.rm=TRUE)

origin_totals_p <- tapply(data$predicted, data$O, sum, na.rm = TRUE)
destination_totals_p <- tapply(data$predicted, data$D, sum, na.rm=TRUE)

plot(origin_totals_o, origin_totals_p)
r2_o = cor(origin_totals_o,origin_totals_p)^2

plot(destination_totals_o, destination_totals_p)
r2_d = cor(destination_totals_o, destination_totals_p)^2

cat("r2 predicted is ",r2_p, " r2 origin is ", r2_o, " r2 destination is ", r2_d )
}


# Unconstrained model

## ZINB
nb_model_unconstrained = glmmTMB(n_observed ~ log(origin_n_o) +
log(destination_n_d) +
log(distance_euclidean),
zi = ~.,
family=nbinom2, data=od_joined)

summary(nb_model_unconstrained)
model_assessment(nb_model_unconstrained, od_joined, 7)

## Poisson Model
poisson_model_unconstrained <- glmmTMB(n_observed ~ log(origin_n_o) +
log(destination_n_d) +
log(distance_euclidean),
family=poisson, data=od_joined)

summary(poisson_model_unconstrained)
model_assessment(poisson_model_unconstrained, od_joined,7)

## Poisson Model with random effects
poisson_model_unconstrained_r <- glmmTMB(n_observed ~ log(origin_n_o) +
log(destination_n_d) +
log(distance_euclidean)+(1|D),
family=poisson, data=od_joined)

summary(poisson_model_unconstrained_r)
model_assessment(poisson_model_unconstrained_r, od_joined,7)

## Hurdle Poisson model
hurdle_unconstrained <- glmmTMB(n_observed ~ log(origin_n_o) +
log(destination_n_d) +
(distance_euclidean),
zi = ~.,
family=truncated_poisson, data=od_joined)
summary(hurdle_unconstrained)
model_assessment(hurdle_unconstrained, od_joined,7)

## Hurdle Poisson model with random effects
hurdle_unconstrained_r <- glmmTMB(n_observed ~ log(origin_n_o) +
log(destination_n_d) +
log(distance_euclidean)+(1|O+D),
zi = ~log(origin_n_o) +
log(destination_n_d) +
log(distance_euclidean),
family=truncated_poisson, data=od_joined)
summary(hurdle_unconstrained_r)
model_assessment(hurdle_unconstrained_r, od_joined,7)

################## DOUBLY CONSTRAINT #####################
##########################################################

# Add offset terms to the data

od_joined$origin_offset <- (origin_totals[od_joined$O])
od_joined$destination_offset <- (destination_totals[od_joined$D])

# Fit the Poisson model with offsets
poisson_model_constrained = glmmTMB(n_observed ~
#log(origin_n_o) +
#log(destination_n_d) +
log(distance_euclidean)+
offset(log(origin_offset)) +
offset(log(destination_offset)),
family=poisson,
data=od_joined)
summary(poisson_model_constrained)
model_assessment(poisson_model_constrained, od_joined,7)

# Fit the Poisson model with offsets and random effects
poisson_model_constrained_r = glmmTMB(n_observed ~
#log(origin_n_o) +
#log(destination_n_d) +
log(distance_euclidean)+
offset(log(origin_offset)) +
offset(log(destination_offset))+
(log(origin_n_o)|O+D),
family=poisson,
data=od_joined)
summary(poisson_model_constrained_r)
model_assessment(poisson_model_constrained_r, od_joined,7)


###### YORK ####
######
names(od_res)
poisson_model_constrained_r = lme4::lmer(log(trips) ~
log(origin_f0_to_15) +
log(destination_n_pupils) +
log(distance_euclidean)+
(1|O)+(1|D),
data=od_res)
summary(poisson_model_constrained_r)
exp(predict(poisson_model_constrained_r, od_res))

plot(exp(predict(poisson_model_constrained_r, od_res)), od_res$trips)

model_assessment(poisson_model_constrained_r, od_res,22)

poisson_model_constrained_r = robustlmm::rlmer(log(trips) ~
log(origin_f0_to_15) +
log(destination_n_pupils) +
log(distance_euclidean)+
(1|O)+(1|D),
data=od_res)
summary(poisson_model_constrained_r)
exp(predict(poisson_model_constrained_r, od_res))

plot(exp(predict(poisson_model_constrained_r, od_res)), od_res$trips)

model_assessment(poisson_model_constrained_r, od_res,22)