Package index • stom

Stan

Working with cmdstanr.

stan(): Compile and sample with cmdstanr

save_model(): Save CmdStanFit object as RDS with a cross-platform consistent name

precis() extract() erect(): Posterior summary and extraction from CmdStanFit objects

extract2(): R6 representation of posterior samples

get_pars(): Select/Filter parameters from precis/extract data frames

as_posterior_array(): Convert posterior data frame to a list of array

get_sim_param_info(): Get parameter information of a simulation

get_stan_param_info(): Infer parameter data structure from Stan's parameter names

test_cmdstanr(): Test cmdstanr compilation

prepare_drive_model(): Gather Stan models for Google Drive upload

Stats

Utilities for stats.

rbern(): Bernoulli Random Number Generator

rordlogit(): Random Number Generator from Ordered Logit Distribution

rtnorm(): Random Number Generator for Truncated Normal Distribution

rgampois2(): Random Number Generator from Gamma-Poisson Distribution

rlkjcorr(): Random Number Generator for Cholesky LKJ Correlation Distribution

logit() inv_logit() logistic(): Links and Inverse Links for Logistic Regression

erf() inv_erf() inv_tanh(): Links for mapping reals to values between -1 and 1.

softmax(): Numerically stable softmax function

standardize(): Standardize a vector to fixed mean and std

simplex() min_max(): Commonly used statistical transformation

log_mix(): log_mix from stan

Linguisitics

Utilities for linguistics.

TTR() MATTR() MSTTR() HDD() ATTR() MTLD() YuleK(): Lexical diversity measures

VOCD(): Implementation of CLAN's VOCD command

Evaluation

Utilities for evaluating models.

prob_input() confusion_input(): Sensitivity and Specificity calculation

Wrangling

Utilities for data wrangling.

as_vec(): Handy vector construction from string

year() month() day(): Extract Year/Month/Day from date string

fstem(): R equivalent of Python pathlib's Path.stem

Plotting

Utilities for plotting.

plot_forest(): Forest plot for multiple densities

col.alpha() shade(): Functions stolen from the rethinking package

curve_mvnorm(): Add multivariate normal contour to plot

par2(): Get graphical parameters

vals2cols(): Convert numerical values to divergent colors

Image conversion

Conversion between various image formats

pdf2png() pdf2svg() svg2pdf() svg2png(): Vector graphics conversion

mutool_convert(): Convert PDF to images by mutool

Data I/O

Reading and writing data.

write_tcsv() read_tcsv(): I/O for data frames and typed CSVs

Documentation

Helpers for documenting scripts in Markdown.

image_combine(): Joining multiple images into a single one

as_vec(): Handy vector construction from string

inline() inline_zh(): Format vectors as inline text

as_c_num() as_c_chr(): Vector object as R input string

xclip() fclip(): Copy to and from clipboard

export_docs() export_docs_pdf() export_docs_html(): Extract docstring from R script to various output formats

inkscape_pdf_pager(): Construct output file paths based on input PDF page numbers

pandoc_pdf() pandoc_html(): Pandoc wrappers for converting markdown to pre-styled documents

pdf2png() pdf2svg() svg2pdf() svg2png(): Vector graphics conversion

Command Line Builder

Helpers for command line programs.

get_cli_programs(): Get stom cmd programs

to_unix_path() to_gitbash_path() print_paths(): Normalize to Unix paths

cmd_get_value() cmd_has() cmd_parse_date(): Primitive parsing of command line arguments

cmd_parse_args() cmd_parse_key_val(): (Deprecated) Full parsing of command line arguments

Index

All functions.

array_type(): Simplified array data type of R to match Stan's parameter dimensions Vector: 1D; matrix: 2D; array: 3D or above

as_c_num() as_c_chr(): Vector object as R input string

as_posterior_array(): Convert posterior data frame to a list of array

as_vec(): Handy vector construction from string

bin_ext(): Returns binary extension depending on OS

cmd_get_value() cmd_has() cmd_parse_date(): Primitive parsing of command line arguments

cmd_parse_args() cmd_parse_key_val(): (Deprecated) Full parsing of command line arguments

col.alpha() shade(): Functions stolen from the rethinking package

curve_mvnorm(): Add multivariate normal contour to plot

erf() inv_erf() inv_tanh(): Links for mapping reals to values between -1 and 1.

export_docs() export_docs_pdf() export_docs_html(): Extract docstring from R script to various output formats

extract2(): R6 representation of posterior samples

fstem(): R equivalent of Python pathlib's Path.stem

get_cli_programs(): Get stom cmd programs

get_pars(): Select/Filter parameters from precis/extract data frames

get_sim_param_info(): Get parameter information of a simulation

get_stan_param_info(): Infer parameter data structure from Stan's parameter names

ignore_dollars_with_begin_equation(): Spcial function to deal with conflicts between $$ and equation env in latex

image_combine(): Joining multiple images into a single one

inkscape_pdf_pager(): Construct output file paths based on input PDF page numbers

inkscape_run_through_pages(): Run Inkscape through pages of PDF input, where page info is given by the out_info arg obtained through inkscape_pdf_pager()

inline() inline_zh(): Format vectors as inline text

logit() inv_logit() logistic(): Links and Inverse Links for Logistic Regression

log_mix(): log_mix from stan

lst2message(): Print named lists as formatted messages

mutool_convert(): Convert PDF to images by mutool

n_samples(): Get number of samples (chains combined) from CmdStanFit

pandoc_pdf() pandoc_html(): Pandoc wrappers for converting markdown to pre-styled documents

par2(): Get graphical parameters

pat_depth(): Stan parameter regex pattern

pdf2png() pdf2svg() svg2pdf() svg2png(): Vector graphics conversion

plot_forest(): Forest plot for multiple densities

precis() extract() erect(): Posterior summary and extraction from CmdStanFit objects

prepare_drive_model(): Gather Stan models for Google Drive upload

prob_input() confusion_input(): Sensitivity and Specificity calculation

rbern(): Bernoulli Random Number Generator

replace_file_ext(): Replace file extension

rgampois2(): Random Number Generator from Gamma-Poisson Distribution

rlkjcorr(): Random Number Generator for Cholesky LKJ Correlation Distribution

rordlogit(): Random Number Generator from Ordered Logit Distribution

rtnorm(): Random Number Generator for Truncated Normal Distribution

save_model(): Save CmdStanFit object as RDS with a cross-platform consistent name

simplex() min_max(): Commonly used statistical transformation

softmax(): Numerically stable softmax function

stan(): Compile and sample with cmdstanr

stan2bin(): Convert stan file path to stan binary file path

standardize(): Standardize a vector to fixed mean and std

test_cmdstanr(): Test cmdstanr compilation

to_unix_path() to_gitbash_path() print_paths(): Normalize to Unix paths

TTR() MATTR() MSTTR() HDD() ATTR() MTLD() YuleK(): Lexical diversity measures

vals2cols(): Convert numerical values to divergent colors

VOCD(): Implementation of CLAN's VOCD command

write_tcsv() read_tcsv(): I/O for data frames and typed CSVs

xclip() fclip(): Copy to and from clipboard

year() month() day(): Extract Year/Month/Day from date string