.Rhistory

covr()
code_coverage()
package_coverage()
devtools::load_all(".")
package_coverage()
devtools::load_all(".")
plot(hystar_fit(hystar_sim(z_sim())$data)
)
(1:10)[[c(4, 5)]]
(1:10)[[2]]
a <- c(b = 4, c = 5)
a[["b"]]
devtools::load_all(".")
plot(hystar_fit(hystar_sim(z_sim())$data))
devtools::load_all(".")
plot(hystar_fit(hystar_sim(z_sim())$data))
devtools::load_all(".")
plot(hystar_fit(hystar_sim(z_sim())$data), name_regime0 = "margo")
plot(hystar_fit(hystar_sim(z_sim())$data), name_regime0 = "margo", color_regime1 = "red")
?call
body(hystar_fit)
lm(x ~ y, data = matrix(rnorm(100), nrow = 50))
lm(x ~ y, data = data.frame(x = rnorm(100), y = rnorm(100)))
lm
?match.call
test <- function(a, b) {
return(match.call())
}
test(a = 4, b = 5)
a <- test(a = 4, b = 5)
class(a)
print(a)
test <- function(a, b = 4) {
return(match.call())
}
a <- test(a = 4)
a
lm
devtools::load_all(".")
hystar_fit(hystar_sim(z_sim())$data)
hystar_fit(hystar_sim(z_sim())$data)$call
devtools::load_all(".")
devtools::load_all(".")
hystar_fit(hystar_sim(z_sim())$data)$call
hystar_fit(hystar_sim(z_sim())$data)
devtools::load_all(".")
hystar_fit(hystar_sim(z_sim())$data)
?eval
?quote
a <- hystar_fit(hystar_sim(z_sim())$data)$call
a
cat(a)
print(a)
cat(as.character(a))
devtools::load_all(".")
a <- hystar_fit(hystar_sim(z_sim())$data)
a
a <- hystar_fit(hystar_sim(z_sim())$data)$call
a
quote(a)
cat(quote(a))
cat(enquote(a))
lm
print.lm
lm.print
cat(enquote(a))
enquote(a)
substitute(a)
?deparse
devtools::load_all(".")
a <- hystar_fit(hystar_sim(z_sim())$data)$call
a <- hystar_fit(hystar_sim(z_sim())$data)
a
a <- hystar_sim(z_sim())
a
devtools::load_all(".")
document()
?plot.hystar_fit
document()
?plot.hystar_fit
?plot
devtools::load_all(".")
plot(hystar_sim(z_sim()))
devtools::load_all(".")
test_that("plot function does not return", {
z <- z_sim(n_t = 50, n_switches = 3,
start_regime = 1, start_hyst = TRUE,
range = c(-1, 1))
sim <- hystar_sim(z = z, r = c(-.5, .5), d = 5,
phi_R0 = c(0, .6), phi_R1 = c(1. -.3),
resvar = c(1, .9),
start_regime = 1)
fit <- hystar_fit(sim$data)
expect_equal(plot(sim), NULL)
expect_equal(plot(fit), NULL)
})
sim <- hystar_sim(z_sim())
hystar_sim(sim$data$y)
hystar_fit(sim$data$y)
plot(sim)
fit <- hystar_fit(sim$data$y)
plot(fit)
check()
usethis::use_package_doc()
devtools::load_all(".")
document()
vignette()
library(devtools)
devtools::load_all(".")
?apply
?lapply
?replicate
vignette
clean_vignettes()
devtools::load_all(".")
check()
test_active_file()
hystar_info()
hystar_fit(hystar_sim(z_sim())$data)
control_variable <- z_sim(n_t = 100)
simulated_hystar_model <- hystar_sim(z = control_variable)
fitted_hystar_model <- hystar_fit(data = simulated_hystar_model$data)
summary(fitted_hystar_model)
?knitr
packageVersion("knitr")
install.packages("knitr")
install.packages("knitr")
install.packages("knitr")
install.packages("knitr")
library(knitr)
detach("package:knitr", unload = TRUE)
detach("package::knitr", unload = TRUE)
packageVersion("xfun")
search()
update.packages(ask = FALSE, checkBuilt = TRUE)
library(devtools)
devtools::load_all(".")
devtools::load_all(".")
check()
install()
test_that("users should provide data", {
expect_error(hystar_fit(),
"Argument `data` is missing, with no default.")
})
alphabet()
letters
test_that("data must be numeric", {
expect_error(hystar_fit(data.frame(letters, letters)),
"Argument `data` is missing, with no default.")
})
data.frame(letters, letters)
test_that("data must be numeric", {
expect_error(hystar_fit(data.frame(letters, letters)),
"numeric")
})
test_that("data must be a vector, matrix or df", {
expect_error(hystar_fit(mean),
"vector, matrix or data.frame")
})
test_that("data cannot have missings", {
expect_error(hystar_fit(data.frame(1:20, c(1:19, NA))),
"not have missing values")
})
library(covr)
codecov()
test_that("data cannot have missings", {
expect_error(hystar_fit(c(1:20, NA)),
"not have missing values")
})
test_that("r must be numeric", {
expect_error(check_r_fit(letters), "numeric")
})
devtools::load_all(".")
test_that("r must be numeric", {
expect_error(check_r_fit(letters), "numeric")
})
test_that("r must be a proper interval", {
expect_error(check_r_fit(c(3, 2)), "interval")
})
test_that("a matrix for r must have correct thresholds if TAR is specified", {
r <- matrix(c(1, 2,
3, 3),
nrow = 2, byrow = TRUE)
expect_error(check_r_fit(r), "TAR")
})
test_that("a matrix for r must have correct thresholds", {
r <- matrix(c(1, 2,
2, 1),
nrow = 2, byrow = TRUE)
expect_error(check_r_fit(r), "The second threshold value should")
})
test_that("a matrix for r must have correct thresholds if TAR is specified", {
r <- matrix(c(1, 2,
3, 3),
nrow = 2, byrow = TRUE)
expect_error(check_r_fit(r, tar = TRUE), "TAR")
})
test_that("user is notified that they are fitting a TAR model", {
r <- matrix(c(2, 2,
3, 3),
nrow = 2, byrow = TRUE)
expect_error(check_r_fit(r, tar = FALSE), "TAR")
})
test_that("user is notified that they are fitting a TAR model", {
r <- matrix(c(2, 2,
3, 3),
nrow = 2, byrow = TRUE)
expect_warning(check_r_fit(r, tar = FALSE), "TAR")
})
test_that("`r` must be in the range of `z`", {
expect_error(check_rz(r = matrix(c(2, 20), nrow = 1),
z = 1:10), "range")
})
test_that("z should be present", {
expect_error(hystar_sim(),
"`z` is missing")
})
?hystar_sim
test_that("r must be numeric", {
expect_error(hystar_sim(1:10, r = c("a", "b")),
"numeric")
})
test_that("r must be length 2", {
expect_error(hystar_sim(1:10, r = 1:3),
"two threshold values")
})
test_that("r must be a proper interval", {
expect_error(hystar_sim(1:10, r = c(4, 2)),
"second threshold should be larger")
})
test_that("p cannot exceed d + 10", {
expect_error(hystar_sim(1:10, p0 = 15, d = 4),
"maximum order can not be")
})
test_that("p cannot exceed d + 10", {
expect_error(hystar_sim(1:10, phi_R0 = rep(.01, times = 15), d = 4),
"maximum order can not be")
})
test_that("p cannot exceed d + 10", {
expect_error(hystar_sim(1:100, phi_R0 = rep(.01, times = 15), d = 4),
"maximum order can not be")
})
test_that("p cannot exceed d + 10", {
expect_error(hystar_sim(1:100, r = c(5, 6), phi_R0 = rep(.01, times = 15), d = 4),
"maximum order can not be")
})
test_that("p cannot exceed d + 10", {
expect_error(hystar_sim(1:100, r = c(5, 6), phi_R0 = rep(.01, times = 15), d = 3),
"maximum order can not be")
})
test_that("residual variances must be numeric", {
expect_error(hystar_sim(-5:100, resvar = c(TRUE, TRUE)))
})
test_that("phi must be numeric", {
expect_error(hystar_sim(-5:10, phi_R0 = c(), "at least 1 value"))
})
test_that("there must be more than 1 switch", {
expect_error(z_sim(n_switches = 1), "must be at least 2"))
test_that("there must be more than 1 switch", {
expect_error(z_sim(n_switches = 1), "must be at least 2")
})
test_that("start regime in hystar_sim matches that in z_sim", {
expect_error(hystar_sim(z_sim(start_regime = 0), start_regime = 1), "does not match")
})
test_that("start regime in hystar_sim matches that in z_sim", {
expect_warning(hystar_sim(z_sim(start_regime = 0), start_regime = 1), "does not match")
})
?z-sim
?z_sim
z_sim(start_regime = NULL)
typeof(NULL)
?hystar_sim
devtools::load_all(".")
test_that("start regime must be 0 or 1", {
expect_error(z_sim(start_regime = 2), "must be 0 or 1")
})
test_that("start regime can be NULL for hystar_sim", {
expect_no_error(hystar_sim(z_sim()))
})
test_that("range must be numeric", {
expect_error(z_sim(range = letters), "numeric")
})
test_that("range must contain exactly two values", {
expect_error(z_sim(range = 1:3), "of length 2")
})
test_that("range must be an interval", {
expect_error(z_sim(range = c(1, 1)), "a proper interval")
})
test()
devtools::load_all(".")
test()
devtools::load_all(".")
hystar_sim(start_regime = "a")
hystar_sim(1:10, start_regime = "a")
hystar_sim(-1:10, start_regime = "a")
hystar_sim(z_sim(), r = c(-2, -.5), start_regime = "a")
hystar_sim(z_sim(start_hyst = TRUE), start_regime = "a")
hystar_sim(c(4:10, 10:1), r = c(3, 5), start_regime = "a")
hystar_sim(c(4:10, 10:1), r = c(3, 5))
devtools::load_all(".")
test()
r_search <- hystar_fit(hystar_sim(z_sim)$data, tar = TRUE)
r_search <- hystar_fit(hystar_sim(z_sim())$data, tar = TRUE)
r_search
r_search <- hystar_fit(hystar_sim(z_sim())$data, tar = TRUE)$r_search
r_search
test_that("tar = TRUE makes sure that r_search is a TAR search", {
grid <- create_grid_r(1:10, r = c(3, 6), thin = FALSE, tar = TRUE)
expect_true(all(grid[, 1] == grid[, 2]))
})
test_that("tar = TRUE makes sure that r_search is a TAR search", {
grid <- create_grid_r(1:10, r = c(.1, .4), thin = FALSE, tar = TRUE)
expect_true(all(grid[, 1] == grid[, 2]))
})
length(from = .1, to = .2, by = .01)
length(seq(from = .1, to = .2, by = .01))
test_that("thin works", {
grid <- create_grid_r(1:10, r = c(.1, .2), thin = TRUE, tar = TRUE)
expect_equal(nrow(grid), 11)
})
create_grid_r(1:10, r = c(.1, .2), thin = TRUE, tar = TRUE)
test_that("thin works", {
grid <- create_grid_r(1:10, r = c(.1, .2), thin = TRUE, tar = TRUE)
expect_equal(nrow(grid), 10)
})
test_that("p_select must be a valid choice", {
expect_error(hystar_fit(1:100, p_select = 1),
"character")
expect_error(hystar_fit(data.frame(y = 1:10, z = 1:10), p_select = "bla"),
"aic")
p_select <- check_hystar_fit_input(
z = 1:4, d = 1, p0 = 1, p1 = 1,
p_select = "aic", r = c(.8, .9), thin = TRUE, tar = FALSE
)
expect_equal(p_select, "aic")
})
class(NA)
devtools::load_all(".")
test()
devtools::load_all(".")
test()
devtools::load_all(".")
test()
devtools::load_all(".")
test()
devtools::load_all(".")
test_that("`r` must be numeric", {
expect_error(hystar_fit(hystar_sim(z_sim()$data, r = c("a", "b"))))
})
test_that("r must be numeric", {
expect_error(hystar_sim(1:10, r = c("a", "b")),
"numeric")
})
test_that("delay must be numeric", {
expect_error(hystar_sim(1:10, d = "1"),
"numeric")
})
test_that("things run normally with certain arguments off-default", {
expect_no_error({
hystar_fit(hystar_sim(z_sim())$data, show_progress = TRUE)
})
})
test_that("phi must be numeric", {
expect_error(hystar_sim(-5:10, phi_R0 = c(), "at least 1 value"))
})
test_that("phi contain values", {
expect_error(hystar_sim(-5:10, phi_R0 = c())), "at least 1 value")
test_that("phi contain values", {
expect_error(hystar_sim(-5:10, phi_R0 = c()), "at least 1 value")
})
c()
test_that("phi contain values", {
expect_error(hystar_sim(-5:10, phi_R0 = numeric(0)), "at least 1 value")
})
check_resvar(c(0, 2))
test_that("zero or negative residual variances are not allowed", {
expect_error(check_resvar(c(0, 2)), "positive")
})
devtools::load_all(".")
test_that("zero or negative residual variances are not allowed", {
expect_error(check_resvar(c(0, 2)), "positive")
})
test_that("zero or negative residual variances are not allowed", {
expect_error(check_resvar(c(0, 2)), "nonnegative")
})
test_that("whole error has correct variable name", {
hey <- 4.4
expect_error(error_whole(hey), "`hey` must be a whole number")
joe <- "a"
expect_error(error_whole(hey), "`joe` must benumeric")
})
hey <- 4.4
expect_error(error_whole(hey), "`hey` must be a whole number")
joe <- "a"
expect_error(error_whole(joe), "`joe` must benumeric")
test_that("whole error has correct variable name", {
hey <- 4.4
expect_error(error_whole(hey), "`hey` must be a whole number")
joe <- "a"
expect_error(error_whole(joe), "`joe` must benumeric")
})
test_that("whole error has correct variable name", {
hey <- 4.4
expect_error(check_whole_nn(hey), "`hey` must be a whole number")
joe <- "a"
expect_error(check_whole_nn(joe), "`joe` must benumeric")
})
hystar_sim(z_sim(), d = .2)
hystar_sim(z_sim(), d = "a")
devtools::load_all(".")
joe <- "a"
check_whole_nn(joe)
substitute(joe)
z_sim(n_t = 2.5)
devtools::load_all(".")
z_sim(n_t = 2.5)
?substitute
test_that("custom errors have correct variable name", {
expect_error(error_numeric(hey = TRUE), "`hey` must be numeric")
expect_error(error_nonnegative(hey = -9), "`hey` must be nonnegative")
expect_error(error_nonnegative(hey = 0.6), "`hey` must be a whole")
})
error_numeric()
test_that("custom errors have correct variable name", {
all <- TRUE
expect_error(error_numeric(all), "`all` must be numeric")
night <-  -9
expect_error(error_nonnegative(night), "`night` must be nonnegative")
long <-  0.6
expect_error(error_nonnegative(long), "`long` must be a whole")
})
test_that("custom errors have correct variable name", {
all <- TRUE
expect_error(error_numeric(all), "`all` must be numeric")
night <-  -9
expect_error(error_nonnegative(night), "`night` must be nonnegative")
long <-  0.6
expect_error(error_whole(long), "`long` must be a whole")
})
test_that("whole numbers are correctly checked", {
expect_true(is_whole(5))
expect_false(is_whole(pi))
})
test_that("custom errors have correct variable name", {
hey <- TRUE
expect_error(error_numeric(hey), "`hey` must be numeric")
mister <-  -9
expect_error(error_nonnegative(mister), "`mister` must be nonnegative")
blue <-  0.6
expect_error(error_whole(long), "`blue` must be a whole")
skye <-  7
expect_error(error_logical(skye), "`skye` must be logical")
})
test_that("custom errors have correct variable name", {
hey <- TRUE
expect_error(error_numeric(hey), "`hey` must be numeric")
mister <-  -9
expect_error(error_nonnegative(mister), "`mister` must be nonnegative")
blue <-  0.6
expect_error(error_whole(long), "`blue` must be a whole")
skye <-  7
expect_error(error_logical(skye), "`skye` must be TRUE or FALSE")
})
test_that("custom errors have correct variable name", {
hey <- TRUE
expect_error(error_numeric(hey), "`hey` must be numeric")
mister <-  -9
expect_error(error_nonnegative(mister), "`mister` must be nonnegative")
blue <-  0.6
expect_error(error_whole(blue), "`blue` must be a whole")
skye <-  7
expect_error(error_logical(skye), "`skye` must be TRUE or FALSE")
})
test()
test_active_file()
use_test()
test_that("hystar info does not throw error", {
expect_no_error(hystar_info())
expect_invisible(hystar_info())
})
hystar_info()
test_that("fit throws no errors with certain off-default settings", {
expect_no_error({
hystar_fit(1:100, show_progress = TRUE)
})
})
check()
document()
check()
?hystar
test_that("n_t and n_switches must be correct", {
expect_error(check_n_t_switches("a", 100), "numeric")
expect_error(check_n_t_switches(.3, 100), "whole")
expect_error(check_n_t_switches(-1, 100), "nonnegative")
expect_error(check_n_t_switches(5, "100"), "numeric")
expect_error(check_n_t_switches(5, .5), "whole")
expect_error(check_n_t_switches(5, -5), "nonnegative")
})
test_that("delay must be numeric, whole and nonnegative", {
expect_error(check_d("1"), "numeric")
expect_error(check_d(.6), "whole")
expect_error(check_d(-10), "nonnegative")
})
test_that("orders are checked correctly", {
expect_error(check_p0("a"), "numeric")
expect_error(check_p0(.4), "whole")
expect_error(check_p0(-1), "nonnegative")
expect_error(check_p1("a"), "numeric")
expect_error(check_p1(.4), "whole")
expect_error(check_p1(-1), "nonnegative")
})
devtools::load_all(".")