Nothing
context("wqda")
test_that("wqda: misspecified arguments", {
data(iris)
# wrong variable names
expect_error(wqda(formula = Species ~ V1, data = iris))
# wrong class
expect_error(wqda(formula = iris, data = iris))
# target variable also in x
#expect_error(wqda(grouping = iris$Species, x = iris)) ## funktioniert, sollte aber nicht
# missing x
expect_error(wqda(grouping = iris$Species))
## wrong method argument
# missing quotes
expect_error(wqda(Species ~ ., data = iris, method = ML))
# method as vector
expect_error(wqda(Species ~ ., data = iris, method = c("ML","unbiased")))
})
test_that("wqda throws a warning if grouping variable is numeric", {
data(iris)
expect_warning(wqda(formula = Petal.Width ~ ., data = iris))
expect_warning(wqda(grouping = iris[,1], x = iris[,-1]))
expect_warning(wqda(grouping = iris$Petal.Width, x = iris[,-5]))
})
test_that("wqda works if only one predictor variable is given", {
data(iris)
fit <- wqda(Species ~ Petal.Width, data = iris, subset = 6:60)
expect_equal(ncol(fit$means), 1)
expect_equal(dim(fit$covs[[1]]), rep(1, 2))
})
test_that("wqda: training data from only one class", {
data(iris)
expect_that(wqda(Species ~ Petal.Width, data = iris, subset = 1:50), throws_error("training data from only one group given"))
expect_that(wqda(Species ~ ., data = iris, subset = 1), throws_error("training data from only one group given"))
})
test_that("wqda: weighting works correctly", {
data(iris)
## check if weighted solution with all weights = 1 equals unweighted solution
fit1 <- wqda(Species ~ ., data = iris)
fit2 <- wqda(Species ~ ., data = iris, weights = rep(1,150))
expect_equal(fit1[-9],fit2[-9])
## returned weights
a <- rep(1,150)
names(a) <- 1:150
expect_equal(fit1$weights, a)
expect_equal(fit2$weights, a)
## weights and subsetting
# formula, data
fit <- wqda(Species ~ ., data = iris, subset = 11:60)
a <- rep(1,50)
names(a) <- 11:60
expect_equal(fit$weights, a)
# formula, data, weights
fit <- wqda(Species ~ ., data = iris, weights = rep(1:3, 50), subset = 11:60)
b <- rep(1:3,50)[11:60]
names(b) <- 11:60
expect_equal(fit$weights, b)
# x, grouping
fit <- wqda(x = iris[,-5], grouping = iris$Species, subset = 11:60)
expect_equal(fit$weights, a)
# x, grouping, weights
fit <- wqda(x = iris[,-5], grouping = iris$Species, weights = rep(1:3, 50), subset = 11:60)
expect_equal(fit$weights, b)
## wrong specification of weights argument
# weights in a matrix
weight <- matrix(seq(1:150),nrow=50)
expect_error(wqda(Species ~ ., data = iris, weights = weight))
# weights < 0
expect_error(wqda(Species ~ ., data = iris, weights = rep(-5, 150)))
# weights true/false
expect_error(wqda(Species ~ ., data = iris, weights = TRUE))
})
test_that("wqda: subsetting works", {
data(iris)
# formula, data
fit1 <- wqda(Species ~ ., data = iris, subset = 1:80)
fit2 <- wqda(Species ~ ., data = iris[1:80,])
expect_equal(fit1[-9],fit2[-9])
# formula, data, weights
fit1 <- wqda(Species ~ ., data = iris, weights = rep(1:3, each = 50), subset = 1:80)
fit2 <- wqda(Species ~ ., data = iris[1:80,], weights = rep(1:3, each = 50)[1:80])
expect_equal(fit1[-9],fit2[-9])
expect_equal(length(fit1$weights), 80)
# x, grouping
fit1 <- wqda(grouping = iris$Species, x = iris[,-5], subset = 1:80)
fit2 <- wqda(grouping = iris$Species[1:80], x = iris[1:80,-5])
expect_equal(fit1[c(1:8)],fit2[c(1:8)])
# x, grouping, weights
fit1 <- wqda(grouping = iris$Species, x = iris[,-5], weights = rep(1:3, each = 50), subset = 1:80)
fit2 <- wqda(grouping = iris$Species[1:80], x = iris[1:80,-5], weights = rep(1:3, each = 50)[1:80])
expect_equal(fit1[c(1:8)],fit2[c(1:8)])
expect_equal(length(fit1$weights), 80)
# wrong specification of subset argument
expect_error(wqda(Species ~ ., data = iris, subset = iris[1:10,]))
expect_error(wqda(Species ~ ., data = iris, subset = FALSE))
expect_error(wqda(Species ~ ., data = iris, subset = 0))
expect_error(wqda(Species ~ ., data = iris, subset = -10:50))
})
test_that("wqda: NA handling works correctly", {
### NA in x
data(iris)
irisna <- iris
irisna[1:10, c(1,3)] <- NA
## formula, data
# na.fail
expect_error(wqda(Species ~ ., data = irisna, subset = 6:60, na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(Species ~ ., data = irisna, subset = 6:60, na.action = na.omit)
fit2 <- wqda(Species ~ ., data = irisna, subset = 11:60)
expect_equal(fit1[-c(9, 12)], fit2[-9])
expect_equal(length(fit1$weights), 50)
## formula, data, weights
# na.fail
expect_error(wqda(Species ~ ., data = irisna, subset = 6:60, weights = rep(1:3, 50), na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(Species ~ ., data = irisna, subset = 6:60, weights = rep(1:3, 50), na.action = na.omit)
fit2 <- wqda(Species ~ ., data = irisna, subset = 11:60, weights = rep(1:3, 50))
expect_equal(fit1[-c(9, 12)], fit2[-9])
expect_equal(length(fit1$weights), 50)
## x, grouping
# na.fail
expect_error(wqda(grouping = irisna$Species, x = irisna[,-5], subset = 6:60, na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(grouping = irisna$Species, x = irisna[,-5], subset = 6:60, na.action = na.omit)
fit2 <- wqda(grouping = irisna$Species, x = irisna[,-5], subset = 11:60)
expect_equal(fit1[1:8], fit2[1:8])
expect_equal(length(fit1$weights), 50)
## x, grouping, weights
# na.fail
expect_error(wqda(grouping = irisna$Species, x = irisna[,-5], subset = 6:60, weights = rep(1:3, 50), na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(grouping = irisna$Species, x = irisna[,-5], subset = 6:60, weights = rep(1:3, 50), na.action = na.omit)
fit2 <- wqda(grouping = irisna$Species, x = irisna[,-5], subset = 11:60, weights = rep(1:3, 50))
expect_equal(fit1[1:8], fit2[1:8])
expect_equal(length(fit1$weights), 50)
### NA in grouping
irisna <- iris
irisna$Species[1:10] <- NA
## formula, data
# na.fail
expect_error(wqda(Species ~ ., data = irisna, subset = 6:60, na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(Species ~ ., data = irisna, subset = 6:60, na.action = na.omit)
fit2 <- wqda(Species ~ ., data = irisna, subset = 11:60)
expect_equal(fit1[-c(9, 12)], fit2[-9])
expect_equal(length(fit1$weights), 50)
## formula, data, weights
# na.fail
expect_error(wqda(Species ~ ., data = irisna, subset = 6:60, weights = rep(1:3, 50), na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(Species ~ ., data = irisna, subset = 6:60, weights = rep(1:3, 50), na.action = na.omit)
fit2 <- wqda(Species ~ ., data = irisna, subset = 11:60, weights = rep(1:3, 50))
expect_equal(fit1[-c(9, 12)], fit2[-9])
expect_equal(length(fit1$weights), 50)
## x, grouping
# na.fail
expect_error(wqda(grouping = irisna$Species, x = irisna[,-5], subset = 6:60, na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(grouping = irisna$Species, x = irisna[,-5], subset = 6:60, na.action = na.omit)
fit2 <- wqda(grouping = irisna$Species, x = irisna[,-5], subset = 11:60)
expect_equal(fit1[1:8], fit2[1:8])
expect_equal(length(fit1$weights), 50)
## x, grouping, weights
# na.fail
expect_error(wqda(grouping = irisna$Species, x = irisna[,-5], subset = 6:60, weights = rep(1:3, 50), na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(grouping = irisna$Species, x = irisna[,-5], subset = 6:60, weights = rep(1:3, 50), na.action = na.omit)
fit2 <- wqda(grouping = irisna$Species, x = irisna[,-5], subset = 11:60, weights = rep(1:3, 50))
expect_equal(fit1[1:8], fit2[1:8])
expect_equal(length(fit1$weights), 50)
### NA in weights
weights <- rep(1:3,50)
weights[1:10] <- NA
## formula, data, weights
# na.fail
expect_error(wqda(Species ~ ., data = iris, subset = 6:60, weights = weights, na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(Species ~ ., data = iris, subset = 6:60, weights = weights, na.action = na.omit)
fit2 <- wqda(Species ~ ., data = iris, subset = 11:60, weights = weights)
expect_equal(fit1[-c(9, 12)], fit2[-9])
expect_equal(length(fit1$weights), 50)
## x, grouping, weights
# na.fail
expect_error(wqda(grouping = iris$Species, x = iris[,-5], subset = 6:60, weights = weights, na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(grouping = iris$Species, x = iris[,-5], subset = 6:60, weights = weights, na.action = na.omit)
fit2 <- wqda(grouping = iris$Species, x = iris[,-5], subset = 11:60, weights = weights)
expect_equal(fit1[1:8], fit2[1:8])
expect_equal(length(fit1$weights), 50)
### NA in subset
subset <- 6:60
subset[1:5] <- NA
## formula, data
# na.fail
expect_error(wqda(Species ~ ., data = iris, subset = subset, na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(Species ~ ., data = iris, subset = subset, na.action = na.omit)
fit2 <- wqda(Species ~ ., data = iris, subset = 11:60)
expect_equal(fit1[-c(9, 12)], fit2[-9])
expect_equal(length(fit1$weights), 50)
## formula, data, weights
# na.fail
expect_error(wqda(Species ~ ., data = iris, subset = subset, weights = rep(1:3, 50), na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(Species ~ ., data = iris, subset = subset, weights = rep(1:3, 50), na.action = na.omit)
fit2 <- wqda(Species ~ ., data = iris, subset = 11:60, weights = rep(1:3, 50))
expect_equal(fit1[-c(9, 12)], fit2[-9])
expect_equal(length(fit1$weights), 50)
## x, grouping
# na.fail
expect_error(wqda(grouping = iris$Species, x = iris[,-5], subset = subset, na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(grouping = iris$Species, x = iris[,-5], subset = subset, na.action = na.omit)
fit2 <- wqda(grouping = iris$Species, x = iris[,-5], subset = 11:60)
expect_equal(fit1[1:8], fit2[1:8])
expect_equal(length(fit1$weights), 50)
## x, grouping, weights
# na.fail
expect_error(wqda(grouping = iris$Species, x = iris[,-5], subset = subset, weights = rep(1:3, 50), na.action = na.fail))
# check if na.omit works correctly
fit1 <- wqda(grouping = iris$Species, x = iris[,-5], subset = subset, weights = rep(1:3, 50), na.action = na.omit)
fit2 <- wqda(grouping = iris$Species, x = iris[,-5], subset = 11:60, weights = rep(1:3, 50))
expect_equal(fit1[1:8], fit2[1:8])
expect_equal(length(fit1$weights), 50)
})
#=================================================================================================================
context("predict.wqda")
test_that("predict.wqda works correctly with formula and data.frame interface and with missing newdata", {
data(iris)
ran <- sample(1:150,100)
## formula, data
fit <- wqda(formula = Species ~ ., data = iris, subset = ran)
pred <- predict(fit)
expect_equal(rownames(pred$posterior), rownames(iris)[ran])
## formula, data, newdata
fit <- wqda(formula = Species ~ ., data = iris, subset = ran)
predict(fit, newdata = iris[-ran,])
## grouping, x
fit <- wqda(x = iris[,-5], grouping = iris$Species, subset = ran)
pred <- predict(fit)
expect_equal(rownames(pred$posterior), rownames(iris)[ran])
## grouping, x, newdata
fit <- wqda(x = iris[,-5], grouping = iris$Species, subset = ran)
predict(fit, newdata = iris[-ran,-5])
})
test_that("predict.wqda works with missing classes in the training data", {
data(iris)
ran <- sample(1:150,100)
expect_warning(fit <- wqda(Species ~ ., data = iris, subset = 1:100))
pred <- predict(fit, newdata = iris[-ran,])
expect_equal(nlevels(pred$class), 3)
expect_equal(ncol(pred$posterior), 2)
# a <- rep(0,50)
# names(a) <- rownames(pred$posterior)
# expect_equal(pred$posterior[,3], a)
})
test_that("predict.wqda: retrieving training data works", {
data(iris)
## no subset
# formula, data
fit <- wqda(formula = Species ~ ., data = iris)
pred1 <- predict(fit)
pred2 <- predict(fit, newdata = iris)
expect_equal(pred1, pred2)
# y, x
fit <- wqda(x = iris[,-5], grouping = iris$Species)
pred1 <- predict(fit)
pred2 <- predict(fit, newdata = iris[,-5])
expect_equal(pred1, pred2)
## subset
ran <- sample(1:150,100)
# formula, data
fit <- wqda(formula = Species ~ ., data = iris, subset = ran)
pred1 <- predict(fit)
pred2 <- predict(fit, newdata = iris[ran,])
expect_equal(pred1, pred2)
# y, x
fit <- wqda(x = iris[,-5], grouping = iris$Species, subset = ran)
pred1 <- predict(fit)
pred2 <- predict(fit, newdata = iris[ran,-5])
expect_equal(pred1, pred2)
})
test_that("predict.wqda works with one single predictor variable", {
data(iris)
ran <- sample(1:150,100)
fit <- wqda(Species ~ Petal.Width, data = iris, subset = ran)
expect_equal(ncol(fit$means), 1)
expect_equal(dim(fit$covs[[1]]), rep(1, 2))
predict(fit, newdata = iris[-ran,])
})
test_that("predict.wqda works with one single test observation", {
data(iris)
ran <- sample(1:150,100)
fit <- wqda(Species ~ Petal.Width, data = iris, subset = ran)
pred <- predict(fit, newdata = iris[5,])
expect_equal(length(pred$class), 1)
expect_equal(dim(pred$posterior), c(1, 3))
a <- factor("setosa", levels = c("setosa", "versicolor", "virginica"))
names(a) = "5"
expect_equal(pred$class, a)
pred <- predict(fit, newdata = iris[58,])
expect_equal(length(pred$class), 1)
expect_equal(dim(pred$posterior), c(1, 3))
a <- factor("versicolor", levels = c("setosa", "versicolor", "virginica"))
names(a) = "58"
expect_equal(pred$class, a)
})
test_that("predict.wqda works with one single predictor variable and one single test observation", {
data(iris)
ran <- sample(1:150,100)
fit <- wqda(Species ~ Petal.Width, data = iris, subset = ran)
expect_equal(ncol(fit$means), 1)
expect_equal(dim(fit$covs[[1]]), rep(1, 2))
pred <- predict(fit, newdata = iris[5,])
expect_equal(length(pred$class), 1)
expect_equal(dim(pred$posterior), c(1, 3))
})
test_that("predict.wqda: NA handling in newdata works", {
data(iris)
ran <- sample(1:150,100)
irisna <- iris
irisna[1:17,c(1,3)] <- NA
fit <- wqda(Species ~ ., data = iris, subset = ran)
expect_warning(pred <- predict(fit, newdata = irisna))
expect_equal(all(is.na(pred$class[1:17])), TRUE)
expect_equal(all(is.na(pred$posterior[1:17,])), TRUE)
})
test_that("predict.wqda: misspecified arguments", {
data(iris)
ran <- sample(1:150,100)
fit <- wqda(Species ~ Petal.Width, data = iris, subset = ran)
# errors in newdata
expect_error(predict(fit, newdata = TRUE))
expect_error(predict(fit, newdata = -50:50))
# errors in prior
expect_error(predict(fit, prior = rep(2,length(levels(iris$Species))), newdata = iris[-ran,]))
expect_error(predict(fit, prior = TRUE, newdata = iris[-ran,]))
expect_error(predict(fit, prior = 0.6, newdata = iris[-ran,]))
})
#=================================================================================================================
context("wqda: mlr interface code")
test_that("wqda: mlr interface works", {
library(mlr)
source("../../../../mlr/classif.wqda.R")
task <- makeClassifTask(data = iris, target = "Species")
# class prediction
lrn <- makeLearner("classif.wqda")
tr1 <- train(lrn, task)
pred1 <- predict(tr1, task = task)
tr2 <- wqda(Species ~ ., data = iris, method = "ML")
pred2 <- predict(tr2)
expect_equivalent(pred2$class, pred1@df$response)
# posterior prediction
lrn <- makeLearner("classif.wqda", par.vals = list(method = "ML"), predict.type = "prob")
tr1 <- train(lrn, task)
pred1 <- predict(tr1, task = task)
tr2 <- wqda(Species ~ ., data = iris, method = "ML")
pred2 <- predict(tr2)
expect_true(all(pred2$posterior == pred1@df[,3:5]))
expect_equivalent(pred2$class, pred1@df$response)
})
#=================================================================================================================
# test_that("wqda works", {
# data(iris)
# ## formula
# # wrong variable names
# expect_error(wqda(formula = Species ~ V1, data = iris))
# # numeric grouping variable
# expect_warning(wqda(formula = Petal.Width ~ ., data = iris))
# # wrong class
# expect_error(wqda(formula = iris, data = iris))
# ## data.frame/matrix
# # numeric grouping variable
# expect_warning(wqda(grouping = iris[,1], x = iris[,-1]))
# # target variable also in x
# #expect_error(wqda(grouping = iris$Species, x = iris)) ## funktioniert, sollte aber nicht
# # missing x
# expect_error(wqda(grouping = iris$Species))
# ## subset
# # wrong class
# expect_error(wqda(Species ~ ., data = iris, subset = iris[1:10,]))
# expect_error(wqda(Species ~ ., data = iris, subset = FALSE))
# expect_error(wqda(Species ~ ., data = iris, subset = 0))
# # nonsensical indices
# expect_error(wqda(Species ~ ., data = iris, subset = -10:50))
# ## na.action
# irisna <- iris
# irisna[1:10,c(1,3)] <- NA
# # default na.omit
# expect_warning(wqda(Species ~ ., data = irisna, subset = 6:60),"group virginica is empty or weights in this group are all zero")
# # na.fail
# expect_error(wqda(Species ~ ., data = irisna, subset = 6:60, na.action = na.fail))
# # check if na.omit works correctly
# fit1 <- wqda(Species ~ ., data = irisna, subset = 6:60, na.action = na.omit)
# fit2 <- wqda(Species ~ ., data = irisna, subset = 11:60)
# expect_equal(fit1[-c(8, 11)], fit2[-8])
# #fit1 <- wqda(Species ~ ., data = irisna, weights = 1:150, subset = 6:60, na.action = na.omit)
# # one predictor variable
# wqda(Species ~ Petal.Width, data = iris, subset = 6:60)
# # one training observation
# #expect_error(wqda(Species ~ ., data = iris, subset = 1)) ## funktioniert???
# # one training observation in one predictor variable
# #expect_error(wqda(Species ~ Petal.Width, data = iris, subset = 1)) ## funktioniert
# # check if weighted solution with weights = 1 equals weighted batch solution
# l2 <- wqda(Species ~ ., data = iris, weights = rep(1,150))
# l1 <- wqda(Species ~ ., data = iris)
# expect_equal(l1[c(1:3,5:7)],l2[c(1:3,5:7)])
# expect_equal(length(l1$weights), 150)
# # check if updated solution with lambda = 0.8 equals weighted batch solution
# # l <- onlda(Species ~ ., data = iris, subset = 1:110)
# # l2 <- onlda(Species ~ ., data = iris, object = l, subset = 111:150, lambda = 0.8)
# # l1 <- wqda(Species ~ ., data = iris, weights = c(rep(0.8,110), rep(1,40)))
# # checkEquals(l1[c(1,3,5)],l2[c(1,3,5)]) ### ???
# ## updates in conjunction with missing classes
# # check if updated solution with lambda = 0.8 equals weighted batch solution
# # l <- onlda(Species ~ ., data = iris, subset = 1:60)
# # l2 <- onlda(Species ~ ., data = iris, object = l, subset = 61:110, lambda = 0.8)
# # l1 <- wqda(Species ~ ., data = iris[-(111:150),], weights = c(rep(0.8,60), rep(1,50)))
# # checkEquals(l1[c(1,3,5)],l2[c(1,3,5)]) ### ???
# ## wrong weights
# # weights in a matrix
# weight <- matrix(seq(1:150),nrow=50)
# expect_error(wqda(Species ~ ., data = iris, weights = weight))
# # weights < 0
# expect_error(wqda(Species ~ ., data = iris, weights = rep(-5, 150)))
# # weights true/false
# expect_error(wqda(Species ~ ., data = iris, weights = TRUE))
# ## wrong method argument
# # missing quotes
# expect_error(wqda(Species ~ ., data = iris, method = ML))
# # method as vector
# expect_error(wqda(Species ~ ., data = iris, method = c("ML","unbiased")))
# })
# test_that("predict.wqda works", {
# data(iris)
# ran <- sample(1:150,100)
# # missing classes
# expect_warning(fit <- wqda(Species ~ ., data = iris, subset = 1:100))
# p <- predict(fit, newdata = iris[-ran,])
# expect_equal(nlevels(p$class), 3)
# expect_equal(ncol(p$posterior), 2)
# # one predictor variable
# fit <- wqda(Species ~ Petal.Width, data = iris, subset = ran)
# expect_equal(ncol(fit$means), 1)
# expect_equal(dim(fit$cov[[1]]), rep(1, 2))
# predict(fit, newdata = iris[-ran,])
# # one predictor variable and one test observation
# fit <- wqda(Species ~ Petal.Width, data = iris, subset = ran)
# expect_equal(ncol(fit$means), 1)
# expect_equal(dim(fit$cov[[1]]), rep(1, 2))
# pred <- predict(fit, newdata = iris[5,])
# expect_equal(length(pred$class), 1)
# expect_equal(dim(pred$posterior), c(1, 3))
# #
# fit <- wqda(formula = Species ~ ., data = iris, subset = ran)
# predict(fit, newdata = iris[-ran,])
# # one test observation
# pred <- predict(fit, newdata = iris[5,])
# expect_equal(length(pred$class), 1)
# expect_equal(dim(pred$posterior), c(1, 3))
# a <- factor("setosa", levels = c("setosa", "versicolor", "virginica"))
# names(a) = "5"
# expect_equal(pred$class, a)
# pred <- predict(fit, newdata = iris[58,])
# expect_equal(length(pred$class), 1)
# expect_equal(dim(pred$posterior), c(1, 3))
# a <- factor("versicolor", levels = c("setosa", "versicolor", "virginica"))
# names(a) = "58"
# expect_equal(pred$class, a)
# # errors in newdata
# expect_error(predict(fit, newdata = TRUE))
# expect_error(predict(fit, newdata = -50:50))
# # errors in prior
# expect_error(predict(fit, prior = rep(2,length(levels(iris$Species))), newdata = iris[-ran,]))
# expect_error(predict(fit, prior = TRUE, newdata = iris[-ran,]))
# expect_error(predict(fit, prior = 0.6, newdata = iris[-ran,]))
# irisna <- iris
# irisna[1:17,c(1,3)] <- NA
# # NA in newdata
# fit <- wqda(Species ~ ., data = iris, subset = ran)
# expect_warning(pred <- predict(fit, newdata = irisna))
# expect_equal(all(is.na(pred$class[1:17])), TRUE)
# expect_equal(all(is.na(pred$posterior[1:17,])), TRUE)
# })
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