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@jebyrnes
Last active April 22, 2019 21:20
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Take a glm and creates a deviance profile, as MASS::profile only returns a transformed version of the deviance.
library(ggplot2)
#A glm from the glm helpfile
counts <- c(18,17,15,20,10,20,25,13,12)
outcome <- gl(3,1,9)
treatment <- gl(3,3)
print(d.AD <- data.frame(treatment, outcome, counts))
glm.D93 <- glm(counts ~ outcome + treatment, family = poisson())
#The old way...
prof <- MASS:::profile.glm(glm.D93)
MASS:::plot.profile(prof)
#some info from https://stackoverflow.com/questions/11916139/plotting-profile-likelihood-curves-in-r
get_profile_glm <- function(aglm){
prof <- MASS:::profile.glm(aglm)
disp <- attr(prof,"summary")$dispersion
purrr::imap_dfr(prof, .f = ~data.frame(par = .y,
deviance=.x$z^2*disp+aglm$deviance,
values = as.data.frame(.x$par.vals)[[.y]],
stringsAsFactors = FALSE))
}
#make and plot a profile
ggplot(get_profile_glm(glm.D93), aes(x = values, y = deviance)) +
geom_point() +
geom_line() +
facet_wrap(~par, scale = "free_x")
#Or with another package
library(profileModel)
prof_mod <- profileModel(glm.D93, quantile = qchisq(0.95, 1) ,
objective = "ordinaryDeviance")
#nice
plot(prof_mod)
profConfint(prof_mod)
pairs(prof_mod)
#ggplot2?
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