Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----load, warning=FALSE, message=FALSE---------------------------------------
library(NHSRdatasets)
library(dplyr)
library(ggplot2)
data("LOS_model")
head(LOS_model)
summary(LOS_model)
# 82.3% survived
prop.table(table(LOS_model$Death))
## ----VisageLOS----------------------------------------------------------------
ggplot(LOS_model, aes(x=Age)) +
geom_histogram(alpha=0.5, col=1, fill=12, bins=20)+
ggtitle("Distribution of Age")
ggplot(LOS_model, aes(x=LOS)) +
geom_histogram(alpha=0.5, col=1, fill=13, bins=20)+
ggtitle("Distribution of Length-of-Stay")
## ----glm1, collapse=TRUE------------------------------------------------------
glm_binomial <- glm(Death ~ Age + LOS, data=LOS_model, family="binomial")
summary(glm_binomial)
ModelMetrics::auc(glm_binomial)
## ----glm2---------------------------------------------------------------------
glm_binomial2<- glm(Death ~ Age + LOS + Age*LOS, data=LOS_model, family="binomial")
summary(glm_binomial2)
ModelMetrics::auc(glm_binomial2)
## ----glm5---------------------------------------------------------------------
LOS_model$preds <- predict(glm_binomial2, type="response")
head(LOS_model,5)
## ----glm3---------------------------------------------------------------------
glm_poisson <- glm(LOS ~ Age * Death, data=LOS_model, family="poisson" )
summary(glm_poisson)
## ----glm4---------------------------------------------------------------------
glm_poisson2 <- glm(LOS ~ Age + Death, data=LOS_model, family="poisson" )
AIC(glm_poisson)
AIC(glm_poisson2)
# anova(glm_poisson2, glm_poisson, test="Chisq") will do the same thing without using the lmtest package
lmtest::lrtest(glm_poisson, glm_poisson2)
## ----od-----------------------------------------------------------------------
sum(residuals(glm_poisson,type="pearson") ^2)/ df.residual(glm_poisson)
## ----quasi--------------------------------------------------------------------
quasi<-glm(LOS ~ Age * Death, data=LOS_model, family="quasipoisson" )
summary(quasi)
## ----nb, warning=FALSE, message=FALSE-----------------------------------------
library(MASS)
nb <- glm.nb(LOS ~ Age * Death, data=LOS_model,)
summary(nb)
## ----glmm, warning=FALSE------------------------------------------------------
library(lme4)
glmm <- glmer(LOS ~ scale(Age) * Death + (1|Organisation), data=LOS_model, family="poisson")
summary(glmm)
## ----confint------------------------------------------------------------------
confint(glmm)
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