More tests

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: unmarked
-Version: 1.4.1.9001
-Date: 2024-01-23
+Version: 1.4.1.9002
+Date: 2024-01-30
 Type: Package
 Title: Models for Data from Unmarked Animals
 Authors@R: c(

R/mixedModelTools.R

@@ -1,6 +1,6 @@
 # Generate required random effects info----------------------------------------
 # Sort-of drop-in replacement for lme4::mkReTrms
-get_reTrms <- function(formula, data, newdata=NULL){
+get_reTrms <- function(formula, data){
   if(!has_random(formula)){
     stop("No random effect terms in formula", call.=FALSE)
   }

tests/testthat/test_mixed_models.R

@@ -1,4 +1,5 @@
 context("mixed model tools")
+skip_on_cran()
 
 test_that("get_reTrms matches lme4::mkReTrms", {
 
@@ -65,11 +66,35 @@ test_that("get_reTrms matches lme4::mkReTrms", {
   expect_identical(r7$cnms, l7$cnms)
   attributes(l7$flist)$assign <- NULL
   expect_identical(r7$flist, l7$flist)
+
+  # Check that unused factor levels aren't dropped
+  dat2 <- data.frame(x = c(0.1, 0.2, -0.1),
+                    group = factor(c("a","b","c"), levels=c("a","b","c","d")))
+  form8 <- ~x + (1|group)
+  #l8 <- lme4::mkReTrms(lme4::findbars(form8), dat2, drop.unused.levels=FALSE)
+  r8 <- get_reTrms(form8, dat2)
+  expect_identical(r8$Z, Matrix::t(l8$Zt))
+
+  # Check that get_Z handles newdata
+  form9 <- ~x + (x||group) + (1|id)
+  nd <- data.frame(x=c(0.5,1), group=c("e","d"), id=c("i","i"))
+  Z <- get_Z(form9, dat, newdata=nd)
+  expect_equivalent(as.matrix(Z), matrix(c(0,1,0,0,0.5,0,0,0,1,
+                                      1,0,0,1,0,0,0,0,1), nrow=2, byrow=T))
+
+  # New level
+  nd <- data.frame(x=c(0.5,1), group=c("a","d"), id=c("i","i"))
+  expect_error(get_Z(form9, dat, newdata=nd))
 
-  #save(l1,l2,l3,l4,l5,l6,l7, file='lme4_output.Rdata')
+  #save(l1,l2,l3,l4,l5,l6,l7,l8, file='lme4_output.Rdata')
 })
 
 test_that("get_reTrms errors correctly", {
+  set.seed(123) 
+  dat <- data.frame(x = rnorm(20), y = rnorm(20), z = factor(sample(letters[1:3], 20, replace=T)),
+                    group = factor(sample(letters[4:6], 20, replace=T)),
+                    id = factor(sample(letters[7:9], 20, replace=T)))
+
   form1 <- ~x + (x+z||group) + (y||id)
   expect_error(get_reTrms(form1, dat))