API Reference

Visualization

confints	Make a horizontal plot of centers/conf ints with error bars.
fill_between	Create a filled region between two curves.
qqplot	Generate a Q-Q plot.
contour	Make a contour plot, possibly overlaid on an image.
predictive_ecdf	Plot a predictive ECDF from samples.
predictive_regression	Plot a predictive regression plot from samples.
sbc_rank_ecdf	Make a rank ECDF plot from simulation-based calibration.
parcoord	Make a parallel coordinate plot of MCMC samples.
trace	Make a trace plot of MCMC samples.
corner	Make a corner plot of sampling results.
contour_lines_from_samples	Get lines for a contour plot from (x, y) samples.
cdf_to_staircase	Convert discrete values of CDF to staircase for plotting.
q_to_color	Convert a quantitative value to a color.
mpl_cmap_to_color_mapper	Convert a Matplotlib colormap to a bokeh.models.LinearColorMapper instance.
to_ColumnDataSource

Bootstrap methods

seed_rng	Seed random number generators for Numpy and Numba'd functions.
draw_bs_reps	Generate bootstrap replicates out of data using func.
draw_bs_reps_pairs	Perform pairs bootstrap for single statistic.
draw_bs_reps_mle	Draw bootstrap replicates of maximum likelihood estimator.
draw_perm_reps	Generate permutation replicates of func from data_1 and data_2
diff_of_means	Difference in means of two arrays.
studentized_diff_of_means	Studentized difference in means of two arrays.
pearson_r	Compute the Pearson correlation coefficient between two samples.

Hamiltonian Monte Carlo utilities

install_cmdstan_colab	Install CmdStan with Google Colab.
include_path	Return path to include files for Stan.
clean_cmdstan	Remove all .hpp, .o, .d, and executable files resulting from compilation of Stan models using CmdStanPy.
cmdstan_version	Determine CmdStan version
df_to_datadict_hier	Convert a tidy data frame to a data dictionary for a hierarchical Stan model.
convert_samples	Converts samples to a new format.
extract_variable	Extracts sample of a variable as a Numpy array.
check_hmc_diagnostics	Check to all HMC diagnostics that are included in Stan's output (divergences, EFMI, tree depth, acceptance rate).
check_expectand_diagnostics	Check all expectand-specific diagnostics for a collection of Markov chains (tail xi_hats, empirical variance, split Rhat, incremental integrated autocorrelation time, and effective sample size).
check_all_diagnostics	Check all MCMC diagnostics, both HMC and expectand diagnostics.
tau_hat	Compute the empirical integrated autocorrelation time for each expectand for each chain.
tail_xi_hat	Compute the empirical generalized Pareto shape (xi_hat) for the upper and lower tails of a sample of expectand values, ignoring any autocorrelation between the values.
ess_hat	Compute the empirical effective sample size for all expectand output ensembles across a collection of Markov chains.
split_rhat	Compute split Rhat for all expectand output ensembles across a collection of Markov chains.
check_variance	Compute the variance of each variable for each chain and report True if the variance if nonzero and False if the variance is zero.
decode_warning_code	Parse a binary diagnostic warning code from check_all_diagnostics() into individual failures and print the results.
inferential_calibration	Perform simulation-based calibration on a Stan Model.
disable_logging	Context manager for disabling logging when doing MCMC sampling.

Gaussian process utilities

append_sort_index	Add the entries of X to Xstar, sort the result, and find indices in the results where the entries in X appear.
linear_kernel	Linear kernel.
polynomial_kernel	Polynomial kernel: (sigma_0^2 + sigma_p^2 x1 .
se_kernel	Squared exponential kernel.
exp_quad_kernel	Exponentiated quadratic (a.k.a.
matern_kernel	Matern kernel.
periodic_kernel	Periodic kernel.
d1_se_kernel	Derivative of first variable of squared exponential kernel.
d1_exp_quad_kernel	Derivative of first variable of the exponentiated quadratic (a.k.a.
d2_se_kernel	Derivative of second variable of squared exponential kernel.
d2_exp_quad_kernel	Derivative of the exponentiated quadratic (a.k.a.
d1_d2_se_kernel	Mixed second derivative of squared exponential kernel.
d1_d2_exp_quad_kernel	Mixed second derivative of exponentiated quadratic (a.k.a.
d1_matern_kernel	Derivative of the Matern kernel with respect to the first variable.
d2_matern_kernel	Derivative of the Matern kernel with respect to the second parameter.
d1_d2_matern_kernel	Mixed second derivative of Matern kernel.
cov_exp_quad	Return covariance matrix for exponentiated quadratic (a.k.a.
cov_se	Return covariance matrix for squared exponential kernel.
cov_d1_exp_quad	Return covariance matrix for exponentiated quadratic (a.k.a.
cov_d1_se	Return covariance matrix for squared exponential kernel differentiated by the first variable.
cov_d1_d2_exp_quad	Return covariance matrix for exponentiated quadratic (a.k.a.
cov_d1_d2_se	Return covariance matrix for squared exponential kernel differentiated once by the first variable and once by the second.
cov_matern	Return covariance matrix for a Matérn kernel.
cov_d1_matern	Return covariance matrix for Matérn kernel differentiated by the first variable.
cov_d1_d2_matern	Return covariance matrix for Matérn kernel differentiated once by the first variable and once by the second.
cov_periodic	Return covariance matrix for a perdioic kernel.
cov_from_kernel	Return covariance matrix for specified kernel.
posterior_mean_cov	Compute the posterior mean vector and covariance matrix for a posterior Gaussian process derived from a Normal likelihood and Gaussian process prior.
posterior_mean_cov_deriv	Compute the posterior mean vector and covariance matrix for the derivative of a posterior Gaussian process derived from a Normal likelihood and Gaussian process prior.

HoloViews defaults

set_defaults	Set convenient HoloViews defaults.
no_xgrid_hook	Hook for disabling x-grid lines.
no_ygrid_hook	Hook for disabling x-grid lines.

Image processing utilities

imshow	Display an image in a Bokeh figure.
record_clicks	Display and record mouse clicks on a Bokeh plot of an image.
draw_rois	Draw and record polygonal regions of interest on a plot of a Bokeh image.
roicds_to_df	Convert a ColumnDataSource outputted by draw_rois() to a Pandas DataFrame.
im_merge	Merge channels to make RGB image.
rgb_to_rgba32	Convert an RGB image to a 32 bit-encoded RGBA image.
rgb_frac_to_hex	Convert fractional RGB values to hexidecimal color string.
simple_image_collection	Load a collection of images.
verts_to_roi	Converts list of vertices to an ROI and ROI bounding box
costes_coloc	Perform Costes colocalization analysis on a pair of images.

General utilities

unpivot_csv

Converts a CSV file in wide format, possibly with a hierarchical column, index to tall format via a unpivot operation.