R Under development (unstable) (2024-02-14 r85901 ucrt) -- "Unsuffered Consequences"
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> # Tests for extracting coefficients and vcov matrix from regression fits
> library(cpr)
> require(lme4)
Loading required package: lme4
Loading required package: Matrix
> 
> ################################################################################
> # There is one method of interest, and it is non exported.  There are several S3
> # methods to check.
> stopifnot(!grepl("loglikelihood", ls("package:cpr")))
> cpr_namespace <- ls( getNamespace("cpr"), all.names = TRUE)
> stopifnot(sum(cpr_namespace == "loglikelihood") == 1L)
> stopifnot(sum(cpr_namespace == "loglikelihood.default") == 1L)
> stopifnot(sum(cpr_namespace == "loglikelihood.geeglm") == 1L)
> stopifnot(sum(grepl("^loglikelihood", cpr_namespace)) == 3L)
> 
> ################################################################################
> e <- new.env()
> with(e, {
+   fit <- lm(mpg ~ wt, data = mtcars)
+   stopifnot("recover loglikelihood from lm" =
+             isTRUE(all.equal(cpr:::loglikelihood(fit), as.numeric(stats::logLik(fit)))))
+ })
> 
> ################################################################################
> e <- new.env()
> with(e, {
+   fit <- glm(I(mpg < 20) ~ wt, data = mtcars, family = quasibinomial())
+   stopifnot("recover quasiloglikelihood from glm" =
+             isTRUE(all.equal(cpr:::loglikelihood(fit), as.numeric(stats::logLik(fit)))))
+ })
> 
> ################################################################################
> e <- new.env()
> with(e, {
+   require(lme4)
+   fit <- lmer(mpg ~ wt + (1|cyl), data = mtcars)
+   stopifnot("recover loglikelihood from lme4" =
+             isTRUE(all.equal(cpr:::loglikelihood(fit), as.numeric(stats::logLik(fit)))))
+ })
> 
> ################################################################################
> e <- new.env()
> with(e, {
+   require(geepack)
+   fit <- geeglm(mpg ~ wt, id = cyl, data = mtcars, family = gaussian())
+   y <- fit$y
+   mu <- fit$fitted.values
+   stopifnot("recover loglikelihood from gaussian geeglm" =
+             isTRUE(all.equal(cpr:::loglikelihood(fit), -sum((y - mu)^2 / 2))))
+ })
Loading required package: geepack
> 
> ################################################################################
> e <- new.env()
> with(e, {
+   require(geepack)
+   fit <- geeglm(I(mpg < 20) ~ wt, id = cyl, data = mtcars, family = binomial())
+   y <- fit$y
+   mu <- fit$fitted.values
+   stopifnot("recover loglikelihood from binomial geeglm" =
+             isTRUE(all.equal(cpr:::loglikelihood(fit),
+                              sum(y * log(mu/(1 - mu)) + log(1 - mu)))))
+ })
> 
> ################################################################################
> e <- new.env()
> with(e, {
+   require(geepack)
+   fit <- geeglm(as.integer(mpg) ~ wt, id = cyl, data = mtcars, family = poisson())
+   y <- fit$y
+   mu <- fit$fitted.values
+   stopifnot("recover loglikelihood from poisson geeglm" =
+             isTRUE(all.equal(cpr:::loglikelihood(fit),
+                              sum(y * log(mu) - mu))))
+ })
> 
> ################################################################################
> e <- new.env()
> with(e, {
+   require(geepack)
+   fit <- geeglm(mpg ~ wt, id = cyl, data = mtcars, family = Gamma())
+   y <- fit$y
+   mu <- fit$fitted.values
+   stopifnot("recover loglikelihood from Gamma geeglm" =
+             isTRUE(all.equal(cpr:::loglikelihood(fit), -sum(y/mu + log(mu)))))
+ })
> 
> ################################################################################
> #                                 End of File                                  #
> ################################################################################
> 
> proc.time()
   user  system elapsed 
   2.65    0.28    2.93