Fix bug in cAIC code #387

And increase precision on unit test

Author: seananderson

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: sdmTMB
 Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
-Version: 0.6.0.9016
+Version: 0.6.0.9017
 Authors@R: c(
     person(c("Sean", "C."), "Anderson", , "[email protected]",
            role = c("aut", "cre"),

R/caic.R

@@ -100,7 +100,7 @@ cAIC.sdmTMB <- function(object, what = c("cAIC", "EDF"), ...) {
   par <- obj$env$parList()
   parDataMode <- obj$env$last.par
   indx <- obj$env$lrandom()
-  q <- length(indx)
+  q <- sum(indx)
   p <- length(object$model$par)
 
   ## use '-' for Hess because model returns negative loglikelihood
@@ -115,8 +115,8 @@ cAIC.sdmTMB <- function(object, what = c("cAIC", "EDF"), ...) {
   if (what == "caic") {
     jnll <- obj$env$f(parDataMode)
     cnll <- jnll - obj_new$env$f(parDataMode)
-    cAIC <- 2 * cnll + 2 * (p + q) - 2 * sum(negEDF)
-    return(cAIC)
+    cAIC_out <- 2 * cnll + 2 * (p + q) - 2 * sum(negEDF)
+    return(cAIC_out)
   } else if (what == "edf") {
     ## Figure out group for each random-effect coefficient
     group <- factor(names(object$last.par.best[obj$env$random]))

tests/testthat/test-cAIC.R

@@ -14,8 +14,8 @@ test_that("cAIC and EDF work", {
       offset = log(dogfish$area_swept)
     )
   )
-  expect_equal(AIC(fit), 12192.9613, tolerance = 1e-1)
-  expect_equal(cAIC(fit), 12089.4289, tolerance = 1e-1)
+  expect_equal(AIC(fit), 12192.9613, tolerance = 1e-4)
+  expect_equal(cAIC(fit), 12071.4289, tolerance = 1e-4)
   edf <- cAIC(fit, what = "EDF")
-  expect_equal(sum(edf), 54.3870, tolerance = 1e-2)
+  expect_equal(sum(edf), 54.3870623, tolerance = 1e-4)
 })