def test_save_tree_plot():
fit = get_fit()
fit2 = get_fit_larger_uncertainties()
fits = [fit, fit2]
values_no_error_bars = [{
"mu": 1.1,
"tau": 3.1,
}]
tree_params = TreePlotParams()
tree_params.labels = [
"Normal",
"Larger uncertainties",
"Exact",
]
outdir = "tarpan/cmdstanpy/model_info/tree_plot_test"
if os.path.isdir(outdir):
shutil.rmtree(outdir)
save_tree_plot(fits,
extra_values=values_no_error_bars,
param_names=["mu", "tau"],
tree_params=tree_params)
assert os.path.isfile(os.path.join(outdir, "summary.pdf"))
def test_save_compare_parameters__extra_values():
fit = get_fit()
fit2 = get_fit_larger_uncertainties()
fits = [fit, fit2]
outdir = "tarpan/cmdstanpy/model_info/compare_parameters_test"
if os.path.isdir(outdir):
shutil.rmtree(outdir)
extra_values = [{
"mu": 1.1,
"tau": 2.1,
"eta.1": 3.1,
"eta.2": 5.2
}, {
"mu": 10.1,
"tau": 20.1,
"eta.1": 30.1,
"eta.2": 35.3
}]
save_compare_parameters(fits,
labels=['One', 'Two', 'Extra 1', 'Extra 2'],
extra_values=extra_values,
param_names=["mu", "tau", "eta.1"])
assert os.path.isfile(os.path.join(outdir, "parameters_compared.txt"))
with open(os.path.join(outdir, "parameters_compared.txt"), 'r') as file:
data = file.read()
assert "2.36 (+5.41, -2.35)" in data
assert "Extra 1" in data
assert "Extra 2" in data
assert "30.1" in data
def test_save_pair_plot():
fit = get_fit()
outdir = "tarpan/cmdstanpy/model_info/pair_plot_test"
if os.path.isdir(outdir):
shutil.rmtree(outdir)
save_pair_plot(fit, param_names=["mu", "tau", 'eta.1'])
assert os.path.isfile(os.path.join(outdir, "pair_plot.pdf"))
def test_save_traceplot():
fit = get_fit()
outdir = "tarpan/cmdstanpy/model_info/histogram_test"
if os.path.isdir(outdir):
shutil.rmtree(outdir)
save_histogram(fit)
assert os.path.isfile(os.path.join(outdir, "histogram_01.pdf"))
assert os.path.isfile(os.path.join(outdir, "histogram_01.pdf"))
assert os.path.isfile(os.path.join(outdir, "histogram_01.pdf"))
def test_save_summary():
fit = get_fit()
outdir = "tarpan/cmdstanpy/model_info/summary_test"
if os.path.isdir(outdir):
shutil.rmtree(outdir)
save_summary(fit, param_names=["mu", "tau", 'eta.1'])
assert os.path.isfile(os.path.join(outdir, "summary.txt"))
assert os.path.isfile(os.path.join(outdir, "summary.csv"))
def test_print_summary(capsys):
fit = get_fit()
result = print_summary(fit,
param_names=["mu", "tau", 'eta.1'],
summary_params=SummaryParams(hpdis=[0.05, 0.99]))
assert "8.05" in capsys.readouterr().out
assert result["df"].shape == (3, 11)
assert "8.05" in result["table"]
assert result["samples"].shape == (4000, 3)
def test_save_summary_specify_hpdi():
fit = get_fit()
outdir = "tarpan/cmdstanpy/model_info/summary_test"
if os.path.isdir(outdir):
shutil.rmtree(outdir)
save_summary(fit,
param_names=["mu", "tau", 'eta.1'],
summary_params=SummaryParams(hpdis=[0.05, 0.99]))
assert os.path.isfile(os.path.join(outdir, "summary.txt"))
assert os.path.isfile(os.path.join(outdir, "summary.csv"))
def test_save_compare_parameters():
fit = get_fit()
fit2 = get_fit_larger_uncertainties()
fits = [fit, fit2]
outdir = "tarpan/cmdstanpy/model_info/compare_parameters_test"
if os.path.isdir(outdir):
shutil.rmtree(outdir)
save_compare_parameters(fits,
labels=['One', 'Two'],
param_names=["mu", "tau", "eta.1"])
assert os.path.isfile(os.path.join(outdir, "parameters_compared.txt"))
with open(os.path.join(outdir, "parameters_compared.txt"), 'r') as file:
data = file.read()
assert "2.36 (+5.41, -2.35)" in data
def test_save_analysis():
fit = get_fit()
outdir = "tarpan/cmdstanpy/model_info/analyse_test"
if os.path.isdir(outdir):
shutil.rmtree(outdir)
save_analysis(fit)
# Diagnostic
assert os.path.isfile(os.path.join(outdir, "diagnostic.txt"))
# Check summary files
# ---------------
assert os.path.isfile(os.path.join(outdir, "summary.txt"))
assert os.path.isfile(os.path.join(outdir, "summary.csv"))
# Tree plot
assert os.path.isfile(os.path.join(outdir, "summary.pdf"))
# Trace plots
# ----------
assert os.path.isfile(os.path.join(outdir, "traceplot_01.pdf"))
assert os.path.isfile(os.path.join(outdir, "traceplot_02.pdf"))
assert os.path.isfile(os.path.join(outdir, "traceplot_03.pdf"))
# Histograms of posterior distributions
# ----------
assert os.path.isfile(os.path.join(outdir, "histogram_01.pdf"))
assert os.path.isfile(os.path.join(outdir, "histogram_02.pdf"))
assert os.path.isfile(os.path.join(outdir, "histogram_03.pdf"))
# Pair plot
assert os.path.isfile(os.path.join(outdir, "pair_plot.pdf"))