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added support for offset to glm en negbin, fix for issue #25 #60

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added support for offset to glm en negbin, fix for issue #25 #60

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7 changes: 4 additions & 3 deletions R/add_pi_glm.R
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Original file line number Diff line number Diff line change
Expand Up @@ -123,9 +123,10 @@ get_sim_response <- function(df, fit, nSims){
overdisp <- summary(fit)$dispersion
sims <- arm::sim(fit, n.sims = nSims)
sim_response <- matrix(NA, ncol = nSims, nrow = nPreds)
offset <- if (is.null(fit$offset)) 0 else fit$offset

for (i in 1:nSims){
yhat <- inverselink(modmat %*% sims@coef[i,])
yhat <- inverselink((modmat %*% sims@coef[i,]) + offset)
if(response_distr == "poisson"){
sim_response[,i] <- rpois(n = nPreds,
lambda = yhat)
Expand All @@ -142,13 +143,13 @@ get_sim_response <- function(df, fit, nSims){
rate = 1/(yhat *overdisp))
}
if(response_distr == "binomial"){
yhat <- inverselink(modmat %*% sims@coef[i,]) * fit$prior.weights
yhat <- inverselink((modmat %*% sims@coef[i,]) + offset) * fit$prior.weights
sim_response[,i] <- rbinom(n = nPreds,
size = fit$prior.weights,
prob = yhat / fit$prior.weights)
}
if(response_distr == "gaussian"){
yhat <- inverselink(modmat %*% sims@coef[i,])
yhat <- inverselink((modmat %*% sims@coef[i,]) + offset)
sim_response[,i] <- rnorm(n = nPreds,
mean = yhat,
sd = sqrt(overdisp))
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4 changes: 3 additions & 1 deletion R/add_pi_negbin.R
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Original file line number Diff line number Diff line change
Expand Up @@ -135,9 +135,11 @@ get_sim_response_nb <- function(df, fit, nSims){
inverselink <- fit$family$linkinv
sims <- get_negbin_sims(fit, nSims)
sim_response <- matrix(0, ncol = nSims, nrow = nPreds)

offset <- if (is.null(fit$offset)) 0 else fit$offset

for (i in 1:nSims){
yhat <- inverselink(modmat %*% sims@coef[i,])
yhat <- inverselink((modmat %*% sims@coef[i,]) + offset)
sim_response[,i] <- rnegbin(n = nPreds,
mu = yhat,
theta = fit$theta)
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