Adding tests

DESCRIPTION

@@ -2,7 +2,7 @@ Package: HydeNet
 Type: Package
 Title: Hybrid Bayesian Networks Using R and JAGS
 Version: 0.9.1
-Date: 2015-07-06
+Date: 2015-08-27
 Author: Jarrod E. Dalton <daltonj@ccf.org> and Benjamin Nutter <benjamin.nutter@gmail.com>
 Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>
 Description: Facilities for easy implementation of hybrid Bayesian networks
@@ -38,7 +38,9 @@ Imports:
     utils
 Suggests:
     knitr,
+    survival,
     testthat
+VignetteBuilder: knitr
 SystemRequirements: JAGS (http://mcmc-jags.sourceforge.net)
 LazyLoad: yes
 LazyData: true

R/rToJags.R

@@ -73,7 +73,7 @@ rToJags <- function(f){
     x <- gsub(" ", "", x)
     if (grepl("logit[(]", x)){
       if (grepl("inverse[=]T", x)){
-        x <- gsub("(logit[(]|qlogis[(]", "ilogit(", x)
+        x <- gsub("(logit[(]|qlogis[(])", "ilogit(", x)
       }
       x <- gsub(",[[:print:]]+[)]", ")", x)
       return(x)

tests/testthat/test-cpt.R

@@ -0,0 +1,24 @@
+context("cpt")
+
+test_that("cpt.list",
+{
+  n <- 50000
+  data <- data.frame(
+    di1 = as.factor(1:6 %*% rmultinom(n,1,prob=c(.4,.3,.15,.10,.03,.02))),
+    di2 = as.factor(1:6 %*% rmultinom(n,1,prob=rev(c(.4,.3,.15,.10,.03,.02)))),
+    di3 = as.factor(1:6 %*% rmultinom(n,1,prob=c(.15,.10,.02,.3,.4,.03)))
+  )
+
+  expect_that(cpt(list(y = "di3", x = c("di1", "di2")), data= data),
+              not(throws_error()))
+})
+
+test_that("cpt with weights",
+{
+  echodata <- cbind(expand.grid(list(echo = c("Negative", "Positive"),
+                                     cad = c("No","Yes"))),
+                    data.frame(pr=c(0.83,0.17,0.12,0.88)))
+  expect_that(cpt(echo ~ cad, data=echodata, wt=echodata$pr),
+              not(throws_error()))
+})
+

tests/testthat/test-modelToNode.R

@@ -0,0 +1,19 @@
+context("modelToNode")
+
+test_that("modelToNode: coxph should return an error",
+{
+  library(survival)
+  test2 <- list(start=c(1,2,5,2,1,7,3,4,8,8), 
+                stop=c(2,3,6,7,8,9,9,9,14,17), 
+                event=c(1,1,1,1,1,1,1,0,0,0), 
+                x=c(1,0,0,1,0,1,1,1,0,0)) 
+  fit <- coxph(Surv(start, stop, event) ~ x, test2)
+  expect_error(modelToNode(fit))
+})
+
+test_that("modelToNode: multinom",
+{
+  fit.gear <- multinom(gear ~ mpg + factor(am), data=mtcars)
+  expect_that(modelToNode(fit.gear), not(throws_error()))
+})
+

tests/testthat/test-rToJags.R

@@ -0,0 +1,13 @@
+context("rToJags")
+
+test_that("rToJags: exponents",
+{
+  expect_equal(rToJags(y ~ x^2),
+               "y ~ pow(x,2)")
+})
+
+test_that("rToJags: logit (from VGAM package)",
+{
+  expect_equal(rToJags(y ~ logit(x, inverse=TRUE)),
+               "y ~ ilogit(x)")
+})

tests/testthat/test-writeJagsFormula.R

@@ -0,0 +1,14 @@
+context("writeJagsFormula")
+
+test_that("writeJagsFormula: Poisson Regression",
+{
+  fit <- glm(gear ~ mpg + am, data = mtcars, family = poisson)
+  expect_that(writeJagsFormula(fit, c("gear", "mpg", "am")),
+              not(throws_error()))
+})
+
+test_that("writeJagsFormula: Multinomial Regression",
+{
+  fit.gear <- multinom(gear ~ mpg + factor(am), data=mtcars)
+  expect_that(writeJagsFormula(fit.gear), not(throws_error()))
+})