tests/test-publish-gls.R

In Publish: Format Output of Various Routines in a Suitable Way for Reports and Publication

### test-publish-gls.R --- 
#----------------------------------------------------------------------
## Author: Thomas Alexander Gerds
## Created: Aug 14 2017 (18:56) 
## Version: 
## Last-Updated: Dec  1 2020 (17:12) 
##           By: Thomas Alexander Gerds
##     Update #: 6
#----------------------------------------------------------------------
## 
### Commentary: 
## 
### Change Log:
#----------------------------------------------------------------------
## 
### Code:
if (requireNamespace("nlme",quietly=TRUE)){ 
    library(testthat)
    context("publish: gls regression")

    ## simulation
    library(nlme)
    library(Publish)
    library(lava)
    m <- lvm(Y ~ X1 + gender + group + Interaction)
    distribution(m, ~gender) <- binomial.lvm()
    distribution(m, ~group) <- binomial.lvm(size = 2)
    constrain(m, Interaction ~ gender + group) <- function(x){x[,1]*x[,2]}
    d <- sim(m, 1e2)
    d$gender <- factor(d$gender, labels = letters[1:2])
    d$group <- factor(d$group)

## model
test_that("publish matches gls", {
    e.gls <- gls(Y ~ X1 + gender+group, data = d,
                 weights = varIdent(form = ~1|group))
    res <- summary(regressionTable(e.gls))
    Sgls <- summary(e.gls)$tTable
    expect_equal(res$rawTable[c(1,3,5,6),"Coefficient"],
                 unname(Sgls[c("X1","genderb","group1","group2"),"Value"]))
    expect_equal(res$rawTable[c(1,3,5,6),"Pvalue"],
                 unname(Sgls[c("X1","genderb","group1","group2"),"p-value"]))
})

context("publish: lme regression")

data("Orthodont")
test_that("publish matches lme", {
    fm1 <- lme(distance ~ age+Sex, 
               random = ~1|Subject,
               data = Orthodont) 
    res <- publish(fm1)
    # main effects
    expect_equal(as.double(res$rawTable[c(1:2,4),"Coefficient"]),
                 as.double(fixef(fm1)[1:3]))
    expect_equal(as.double(res$rawTable[c(1:2,4),"Pvalue"]),
                 as.double(summary(fm1)$tTable[1:3,5]))
})

}

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### test-publish-gls.R ends here