tests/testthat/test-oglm.R

In linogaliana/oglm: Estimation of Ordered Generalized Linear Models

testthat::context("oglm implements ordered and interval regression models")


# I - CREATE DATA -------------------------

set.seed(242)
n<-250
x1<-sample(c(0,1),n,replace=TRUE,prob=c(0.75,0.25))
x2<-vector("numeric",n)
x2[x1==0]<-sample(c(0,1),n-sum(x1==1),replace=TRUE,prob=c(2/3,1/3))
z<-rnorm(n,0.5)
# create latent outcome variable
latenty<-0.5+1.5*x1-0.5*x2+0.5*z+rnorm(n,sd=exp(0.5*x1-0.5*x2))
# observed y has four possible values: -1,0,1,2
# threshold values are: -0.5, 0.5, 1.5.
y<-vector("numeric",n)
y[latenty< -0.5]<--1
y[latenty>= -0.5 & latenty<0.5]<- 0
y[latenty>= 0.5 & latenty<1.5]<- 1
y[latenty>= 1.5]<- 2
dataset<-data.frame(y,x1,x2)


# POSSIBILITY TO CHANGE OPTIMIZATION METHOD -------------


testthat::test_that("Default method to Newton-Raphson", {
  mod1 <- oglm::oglmx(y ~ x1 + x2 + z,
                      data=dataset,link="probit",constantMEAN=FALSE,
                      constantSD=FALSE,delta=0,threshparam=NULL)
  mod2 <- oglm::oglmx(y ~ x1 + x2 + z,
                      data=dataset,link="probit",constantMEAN=FALSE,
                      constantSD=FALSE,delta=0,threshparam=NULL,
                      optmeth = "NR")
  mod1$call <- NULL
  mod2$call <- NULL

  testthat::expect_identical(
    mod1, mod2
  )

})


testthat::test_that("Raise error when argument not matched", {

  testthat::expect_error(
    oglm::oglmx(y ~ x1 + x2 + z,
                data=dataset,link="probit",constantMEAN=FALSE,
                constantSD=FALSE,delta=0,threshparam=NULL,
                optmeth = "nr")
  )
  testthat::expect_error(
    oglm::oglmx(y ~ x1 + x2 + z,
                data=dataset,link="probit",constantMEAN=FALSE,
                constantSD=FALSE,delta=0,threshparam=NULL,
                optmeth = "anything")
  )


})



# II - TEST OPTIONS -------------------

# II-1- FORMULA =====

testthat::test_that(
  "Excepting call and formula, elements are the same", {

    formulastr <- oglm::oglmx("y ~ x1 + x2",
                              data=dataset,link="probit",constantMEAN=FALSE,
                              constantSD=FALSE,delta=0,threshparam=NULL)
    formulaformal <- oglm::oglmx(y ~ x1 + x2,
                                 data=dataset,link="probit",constantMEAN=FALSE,
                                 constantSD=FALSE,delta=0,threshparam=NULL)

    formulastr$formula <- NULL
    formulastr$call <- NULL
    formulaformal$formula <- NULL
    formulaformal$call <- NULL

    testthat::expect_equal(
      formulastr,
      formulaformal
    )

  })


testthat::test_that(
  "Same call produces an error with oglmx package", {
    oglm::oglmx("y ~ x1 + x2",
                data=dataset,link="probit",constantMEAN=FALSE,
                constantSD=FALSE,delta=0,threshparam=NULL)
    testthat::expect_error(
      oglmx::oglmx("y ~ x1 + x2",
                   data=dataset,link="probit",constantMEAN=FALSE,
                   constantSD=FALSE,delta=0,threshparam=NULL)
    )
  })



# User-defined bounds can be provided ------

mod1 <- oglm::oglmx(y ~ x1 + x2 + z,
                    data=dataset,link="probit",
                    threshparam=c(-.5, .5,1.5))

testthat::test_that("When providing bounds, thresholds are not estimated but std is",{
  testthat::expect_identical(
    length(mod1$coefficients),
    1L + 3L + 1L #intercept + 3 variables + std
  )
  testthat::expect_identical(
    names(mod1$coefficients),
    c("(Intercept)","x1","x2","z","ln(sigma)")
  )
  testthat::expect_identical(
    attr(mod1$coefficients, "coefftypes"),
    list(
      c(rep(TRUE, 4), FALSE),
      c(rep(FALSE, 4), TRUE),
      rep(FALSE, 5)
    )
  )
})




# MODELS WITH SELECTION ----------------------