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library(recipes)
library(caret)
library(testthat)
# ------------------------------------------------------------------------------
context('updating objects')
diff_coef <- function(x, y) {
x_nm <- names(x$fit$finalModel$coefficients)
y_nm <- names(y$fit$finalModel$coefficients)
delta <- c(setdiff(x_nm, y_nm), setdiff(y_nm, x_nm))
length(delta) > 0
}
# ------------------------------------------------------------------------------
set.seed(3545)
dat <- SLC14_1(100)
y_ind <- which(names(dat) == "y")
# ------------------------------------------------------------------------------
test_that("train updating", {
ctrl <- trainControl(method = "cv")
lm_obj_form <- train(y ~ Var01 + Var02, data = dat, method = "lm", trControl = ctrl)
lm_obj_form_2 <- update(lm_obj_form, list(intercept = FALSE))
expect_equal(length(lm_obj_form_2$finalModel$coefficients), 2)
rec <- recipe(y ~ Var01 + Var02, data = dat) %>%
step_mutate(Var01 = Var01/2)
lm_obj_rec <- train(rec, data = dat, method = "lm", trControl = ctrl)
lm_obj_rec_2 <- update(lm_obj_rec, list(intercept = FALSE))
expect_equal(length(lm_obj_rec_2$finalModel$coefficients), 2)
})
# ------------------------------------------------------------------------------
test_that("safs updating", {
ctrl <- safsControl(functions = caretSA, method = "cv", number = 3)
set.seed(3997)
sa_xy <-
safs(x = dat[, -y_ind],
y = dat$y,
safsControl = ctrl,
iters = 2,
differences = FALSE,
method = "lm",
trControl = trainControl(method = "cv")
)
new_iter <- ifelse(sa_xy$optIter == 1, 2, 1)
sa_xy_2 <- update(sa_xy, iter = new_iter, x = dat[, -y_ind], y = dat$y)
expect_true(diff_coef(sa_xy, sa_xy_2))
expect_error(update(sa_xy, iter = new_iter))
rec <- recipe(y ~ ., data = dat) %>%
step_mutate(Var01 = Var01/2)
set.seed(3997)
sa_rec <-
safs(rec,
data = dat,
safsControl = ctrl,
iters = 2,
differences = FALSE,
method = "lm",
trControl = trainControl(method = "cv")
)
new_iter <- ifelse(sa_rec$optIter == 1, 2, 1)
sa_rec_2 <- update(sa_rec, iter = new_iter)
expect_true(diff_coef(sa_rec, sa_rec_2))
sa_rec$recipe$template <- NULL
expect_error(update(sa_rec, iter = new_iter))
})
# ------------------------------------------------------------------------------
test_that("gafs updating", {
ctrl <- gafsControl(functions = caretGA, method = "cv", number = 3)
set.seed(3997)
ga_xy <-
gafs(x = dat[, -y_ind],
y = dat$y,
gafsControl = ctrl,
popSize = 4,
iters = 2,
differences = FALSE,
method = "lm",
trControl = trainControl(method = "cv")
)
new_iter <- ifelse(ga_xy$optIter == 1, 2, 1)
ga_xy_2 <- update(ga_xy, iter = new_iter, x = dat[, -y_ind], y = dat$y)
expect_true(diff_coef(ga_xy, ga_xy_2))
expect_error(update(ga_xy, iter = new_iter))
rec <- recipe(y ~ ., data = dat) %>%
step_mutate(Var01 = Var01/2)
set.seed(3997)
ga_rec <-
gafs(rec,
data = dat,
gafsControl = ctrl,
popSize = 4,
iters = 2,
differences = FALSE,
method = "lm",
trControl = trainControl(method = "cv")
)
new_iter <- ifelse(ga_rec$optIter == 1, 2, 1)
ga_rec_2 <- update(ga_rec, iter = new_iter)
expect_true(diff_coef(ga_rec, ga_rec_2))
ga_rec$recipe$template <- NULL
expect_error(update(ga_rec, iter = new_iter))
})
# ------------------------------------------------------------------------------
test_that("rfe updating", {
ctrl <- rfeControl(functions = caretFuncs, method = "cv", number = 3)
set.seed(3997)
rfe_xy <-
rfe(x = dat[, -y_ind],
y = dat$y,
rfeControl = ctrl,
sizes = 1:5,
method = "lm",
trControl = trainControl(method = "none")
)
rfe_xy_2 <- expect_warning(update(rfe_xy, size = 5, x = dat[, -y_ind], y = dat$y))
expect_equal(length(rfe_xy_2$fit$finalModel$coefficients), 6)
expect_error(update(rfe_xy, size = 5))
rec <- recipe(y ~ ., data = dat) %>%
step_mutate(Var01 = Var01/2)
set.seed(3997)
rfe_rec <-
rfe(rec,
data = dat,
rfeControl = ctrl,
sizes = 1:5,
method = "lm",
trControl = trainControl(method = "none")
)
expect_warning(rfe_rec_2 <- update(rfe_rec, size = 5))
expect_equal(length(rfe_rec_2$fit$finalModel$coefficients), 6)
rfe_rec$recipe$template <- NULL
expect_error(update(rfe_rec, size = 5))
})
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