Nothing
cat(crayon::yellow("test aug_ZXy:\n"))
data("blackcap")
chk <- fitme(migStatus ~ 1+ Matern(1|latitude+longitude), fixed=list(lambda=2), data=blackcap)
if (how(chk, verbose=FALSE)$switches[["augZXy_cond"]]) stop("y-augmented method used with fixed lambda.")
#cat("\ntest no fixef, pw & REMLformula, by augZXy:\n")
if (FALSE) { # old tests of functionality. May be useful for later devels
if(requireNamespace("lme4", quietly = TRUE)) { # but it's faster than that.)
data("sleepstudy",package = "lme4")
oldopt <- spaMM.options(allow_augZXy=FALSE)
(fit <- fitme(Reaction ~ 0 + (1|Subject), data = sleepstudy))
set.seed(123)
sleepstudy$pw <- 1 + runif(180)
(fit <- fitme(Reaction ~ 0 + (1|Subject), data = sleepstudy, prior.weights=pw))
spaMM.options(allow_augZXy=2) # no longer quite effective ?
(fit <- fitme(Reaction ~ 0 + (1|Subject), data = sleepstudy, prior.weights=pw))
(fit <- fitme(Reaction ~ 0 + (1|Subject), data = sleepstudy, prior.weights=pw, REMLformula=Reaction ~ 1 + (1|Subject), method="REML"))
spaMM.options(allow_augZXy=FALSE)
(fit <- fitme(Reaction ~ 0 + (1|Subject), data = sleepstudy, prior.weights=pw, REMLformula=Reaction ~ 1 + (1|Subject), method="REML"))
spaMM.options(oldopt) # spaMM.options(allow_augZXy=NULL)
# works also with .HLfit_body_augZXy_W()
}
}
if (file.exists((privdata <- "D:/home/francois/travail/stats/spaMMplus/spaMM/package/tests_private/all_fitness.txt"))) {
my.data <- read.table(privdata, header = TRUE, sep = "\t",dec = ".")
my.data$line <- factor(as.character(my.data$line))
my.data <- na.omit(my.data)
# Minimal example (small matrices) for testing ranCoefs code in general:
set.seed(666)
perm <- sample(nrow(my.data))
if (exists(".HLfit_body_augZXy_invL",envir = asNamespace("spaMM"))) { # actually spprec case...
oldopt <- spaMM.options(augZXy_fitfn=".HLfit_body_augZXy_invL", check_alt_augZXy=FALSE) # F I X_invL no check_alt_augZXy bc it fails. But the final logLik is checked
(mini_rC <- fitme(total_red ~ 1 + (sex|env), data = my.data[perm[1:20],], method="ML"))
spaMM.options(oldopt)
} else message(".HLfit_body_augZXy_invL() not included in build => test not performed on pckage istalled from build")
# Plus an augZXy test (not ranCoefs):
(vanilla <- fitme(total_red ~ sex*env + (1|rep) + (1|line), data = my.data, method="ML"))
if (exists(".HLfit_body_augZXy_W",envir = asNamespace("spaMM"))) {
oldopt <- spaMM.options(augZXy_fitfn=".HLfit_body_augZXy_W", check_alt_augZXy=TRUE)
essainola <- fitme(total_red ~ sex*env + (1|rep) + (1|line), data = my.data, method="ML")
spaMM.options(oldopt)
testthat::test_that("private .HLfit_body_augZXy_W() returns a correct result.",
testthat::expect_true((diff(range(logLik(vanilla),logLik(essainola)))<1e-8)) )
} else message(".HLfit_body_augZXy_W() not included in build => test not performed on pckage istalled from build")
if (exists(".HLfit_body_augZXy_invL",envir = asNamespace("spaMM"))) {
oldopt <- spaMM.options(augZXy_fitfn=".HLfit_body_augZXy_invL", check_alt_augZXy=TRUE)
essainola <- fitme(total_red ~ sex*env + (1|rep) + (1|line), data = my.data, method="ML")
spaMM.options(oldopt)
testthat::expect_true((diff(range(logLik(vanilla),logLik(essainola)))<1e-8))
} else message(".HLfit_body_augZXy_invL() not included in build => test not performed on pckage istalled from build") # and it no longer exists...
}
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