test_sim <- function() {
mySim <- load_safe("sim.RDS")
no_error_in_expr({ extract_ysim(mySim) })
no_error_in_expr({ extract_zsim(mySim) })
invisible()
}
test_stanfit <- function() {
myFit <- load_safe("draw_samples.RDS")
no_error_in_expr({ print(myFit) })
no_error_in_expr({ show(myFit) })
no_error_in_expr({ extract_alpha(myFit) })
no_error_in_expr({ extract_data(myFit) })
no_error_in_expr({ extract_diagnostics(myFit) })
no_error_in_expr({ extract_filename(myFit) })
no_error_in_expr({ extract_gamma(myFit) })
no_error_in_expr({ extract_K(myFit) })
no_error_in_expr({ extract_n_chains(myFit) })
no_error_in_expr({ extract_model(myFit) })
no_error_in_expr({ extract_obs_parameters(myFit) })
no_error_in_expr({ extract_parameter_names(myFit) })
no_error_in_expr({ extract_parameters(myFit) })
no_error_in_expr({ extract_quantity(myFit, par = "A") })
no_error_in_expr({ extract_R(myFit) })
no_error_in_expr({ extract_seed(myFit) })
no_error_in_expr({ extract_spec(myFit) })
no_error_in_expr({ extract_T(myFit) })
no_error_in_expr({ extract_time(myFit) })
no_error_in_expr({ extract_y(myFit) })
no_error_in_expr({ extract_ypred(myFit) })
no_error_in_expr({ extract_ysim(myFit) })
no_error_in_expr({ extract_zpred(myFit) })
no_error_in_expr({ extract_zsim(myFit) })
no_error_in_expr({ extract_zstar(myFit) })
invisible()
}
test_plots <- function() {
myFit <- load_safe("draw_samples.RDS")
no_error_in_expr({ plot_series(myFit) })
no_error_in_expr({ plot_state_probability(myFit) })
no_error_in_expr({
plot_ppredictive(
myFit,
type = c("density", "cumulative", "boxplot",
"histogram", "scatterplot", "ks"),
fun = mean, fun1 = mean, fun2 = mean
)
})
invisible()
}
test_optimizing <- function() {
myOpt <- load_safe("optimizing_all.RDS")
no_error_in_expr({ extract_grid(myOpt, pars = "mu") })
no_error_in_expr({ extract_best(myOpt) })
myOpt <- extract_best(myOpt)
no_error_in_expr({ extract_data(myOpt) })
no_error_in_expr({ extract_filename(myOpt) })
no_error_in_expr({ extract_gamma(myOpt) })
no_error_in_expr({ extract_K(myOpt) })
no_error_in_expr({ extract_model(myOpt) })
no_error_in_expr({ extract_obs_parameters(myOpt) })
no_error_in_expr({ extract_parameter_names(myOpt) })
no_error_in_expr({ extract_parameters(myOpt) })
no_error_in_expr({ extract_quantity(myOpt, par = "A") })
no_error_in_expr({ extract_R(myOpt) })
no_error_in_expr({ extract_seed(myOpt) })
no_error_in_expr({ extract_spec(myOpt) })
no_error_in_expr({ extract_T(myOpt) })
no_error_in_expr({ extract_time(myOpt) })
no_error_in_expr({ extract_y(myOpt) })
no_error_in_expr({ extract_ypred(myOpt) })
no_error_in_expr({ extract_ysim(myOpt) })
no_error_in_expr({ extract_zpred(myOpt) })
no_error_in_expr({ extract_zsim(myOpt) })
no_error_in_expr({ extract_zstar(myOpt) })
invisible()
}
testExtractors <- function() {
myFit <- load_safe("draw_samples.RDS")
no_error_in_expr({ extract_alpha(myFit, reduce = NULL, combine = NULL, chain = "all") })
no_error_in_expr({ extract_alpha(myFit, reduce = NULL, combine = NULL, chain = 3) })
no_error_in_expr({ extract_alpha(myFit, reduce = mean, combine = NULL, chain = 1) })
no_error_in_expr({ extract_alpha(myFit, reduce = mean, combine = NULL, chain = "all") })
no_error_in_expr({ extract_alpha(myFit, reduce = mean, combine = c, chain = 1) })
no_error_in_expr({ extract_alpha(myFit, chain = "all") })
no_error_in_expr({ extract_alpha(myFit) })
no_error_in_expr({ classify_alpha(myFit, reduce = NULL, chain = "all") })
no_error_in_expr({ classify_alpha(myFit, reduce = median, chain = "all") })
no_error_in_expr({ classify_alpha(myFit, reduce = median, chain = 1) })
no_error_in_expr({ classify_alpha(myFit, reduce = mean, chain = 1) })
no_error_in_expr({ classify_alpha(myFit, chain = 1) })
no_error_in_expr({ classify_alpha(myFit) })
no_error_in_expr({ extract_gamma(myFit, reduce = NULL, combine = NULL, chain = "all") })
no_error_in_expr({ extract_gamma(myFit, reduce = NULL, combine = NULL, chain = 3) })
no_error_in_expr({ extract_gamma(myFit, reduce = mean, combine = NULL, chain = 1) })
no_error_in_expr({ extract_gamma(myFit, reduce = mean, combine = NULL, chain = "all") })
no_error_in_expr({ extract_gamma(myFit, reduce = mean, combine = c, chain = 1) })
no_error_in_expr({ extract_gamma(myFit, chain = "all") })
no_error_in_expr({ extract_gamma(myFit) })
no_error_in_expr({ classify_gamma(myFit, reduce = NULL, chain = "all") })
no_error_in_expr({ classify_gamma(myFit, reduce = median, chain = "all") })
no_error_in_expr({ classify_gamma(myFit, reduce = median, chain = 1) })
no_error_in_expr({ classify_gamma(myFit, reduce = mean, chain = 1) })
no_error_in_expr({ classify_gamma(myFit, chain = 1) })
no_error_in_expr({ classify_gamma(myFit) })
no_error_in_expr({ extract_zstar(myFit, reduce = NULL, combine = NULL, chain = "all") })
no_error_in_expr({ extract_zstar(myFit, reduce = NULL, combine = NULL, chain = 3) })
no_error_in_expr({ extract_zstar(myFit, reduce = mean, combine = NULL, chain = 1) })
no_error_in_expr({ extract_zstar(myFit, reduce = mean, combine = NULL, chain = "all") })
no_error_in_expr({ extract_zstar(myFit, reduce = mean, combine = c, chain = 1) })
no_error_in_expr({ extract_zstar(myFit, chain = "all") })
no_error_in_expr({ extract_zstar(myFit) })
no_error_in_expr({ classify_zstar(myFit, reduce = NULL, chain = "all") })
no_error_in_expr({ classify_zstar(myFit, reduce = median, chain = "all") })
no_error_in_expr({ classify_zstar(myFit, reduce = median, chain = 1) })
no_error_in_expr({ classify_zstar(myFit, reduce = mean, chain = 1) })
no_error_in_expr({ classify_zstar(myFit, chain = 1) })
no_error_in_expr({ classify_zstar(myFit) })
no_error_in_expr({ extract_ypred(myFit, reduce = NULL, combine = NULL, chain = "all") })
no_error_in_expr({ extract_ypred(myFit, reduce = NULL, combine = NULL, chain = 3) })
no_error_in_expr({ extract_ypred(myFit, reduce = mean, combine = NULL, chain = 1) })
no_error_in_expr({ extract_ypred(myFit, reduce = mean, combine = NULL, chain = "all") })
no_error_in_expr({ extract_ypred(myFit, reduce = mean, combine = c, chain = 1) })
no_error_in_expr({ extract_ypred(myFit, chain = "all") })
no_error_in_expr({ extract_ypred(myFit) })
no_error_in_expr({ extract_zpred(myFit, reduce = NULL, combine = NULL, chain = "all") })
no_error_in_expr({ extract_zpred(myFit, reduce = NULL, combine = NULL, chain = 3) })
no_error_in_expr({ extract_zpred(myFit, reduce = mean, combine = NULL, chain = 1) })
no_error_in_expr({ extract_zpred(myFit, reduce = mean, combine = NULL, chain = "all") })
no_error_in_expr({ extract_zpred(myFit, reduce = mean, combine = c, chain = 1) })
no_error_in_expr({ extract_zpred(myFit, chain = "all") })
no_error_in_expr({ extract_zpred(myFit) })
no_error_in_expr({ extract_quantity(myFit, par = "mu*", reduce = median, combine = cbind, chain = "all") })
no_error_in_expr({ extract_quantity(myFit, par = "mu*", reduce = mean, combine = c, chain = 1) })
invisible()
}
testPlots <- function() {
myFit <- load_safe("draw_samples.RDS")
no_error_in_expr({
for (s in c("filtered", "smoothed", "viterbi")) {
plot_series(
myFit, r = 1,
features = c(
"stateShade", "yColoredLine", "yColoredDots",
"bottomColoredMarks", "topColoredMarks"
),
stateProbability = s
)
}
for (s in c("filtered", "smoothed")) {
plot_state_probability(
myFit, r = 1,
features = c(
"stateShade", "probabilityColoredLine", "probabilityColoredDots",
"probabilityFan", "bottomColoredMarks", "topColoredMarks"
),
stateProbability = s
)
}
plot_ppredictive(
myFit,
type = c(
"density", "cumulative", "boxplot", "histogram", "scatterplot",
"ks", "kl"
),
fun = mean, fun1 = mean, fun2 = sd,
klControl = list(yNBins = 20, yPredNBins = 20)
)
})
}
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