NEWS.md

In extras: Helper Functions for Bayesian Analyses

extras 0.8.0

• Added a scalar case to log_lik_beta_binom() to improve speed for scalar inputs.
• Add memoization (if memoize package is installed) and data has > 800 rows to gain speed from repeated function calls.
• Use a vectorized optimization to improve speed of optimization required for deviance calculation.

extras 0.7.3.9002

• Remove dependency on MASS package so minimum R version can be brought down to 4.0.0 from 4.3.0.

extras 0.7.3.9001

• Register poissontemplate usage.
• Fix actions.
• Perform upkeep on package.

extras 0.7.3

• Ensure all tests, examples, and vignettes run conditionally for packages listed in suggests.

extras 0.7.2

• Fix behaviour of dev_beta_binom() when size \< x.

extras 0.7.1

• Refactored log_lik_beta_binom() to speed up optimization required in dev_beta_binom().
• Styled all code in package.

extras 0.7.0

• Added sensitivity functions to produce list of new parameters that vary standard deviations (sens_xxx()).
• Added Skew Normal family of functions (ran_skewnorm(), log_lik_skewnorm(), res_skewnorm(), dev_skewnorm()).
• Added Skew Normal distribution functions (rskewnorm(), dskewnorm(), pskewnorm(), qskewnorm()).
• Added log2()<-, log10()<-, ilog2(), and ilog10() functions.
• Added exp2() and exp10() functions.

extras 0.6.1

• Fixed M1mac test

extras 0.6.0

New Features

• Added family of functions for the following distributions

• xx_gamma()

• xx_student()

• xx_beta_binomial()

• Added standardized residuals to residual functions for all distributions

Bug Fixes

• Exported pbern(), qbern() and rbern().

Internal

• Fix for dev testthat
• Fix tests for dev waldo

extras 0.5.0

• Added following zero-inflated gamma Poisson functions
• log_lik_gamma_pois_zi()
• ran_gamma_pois_zi()
• dev_gamma_pois_zi()
• res_gamma_pois_zi() Fixed bugs in
• dev_binom()
• dev_pois_zi()
• Set R >= 3.5

extras 0.4.0

• Added log_odds() and log_odds()<-.
• Added dbern(), pbern(), qbern(), rbern().

extras 0.3.0

Added

• Added the following functions
• step() R version of JAGS function.
• ilog().
• inv_logit().
• inv_odds() and odds()<-.
• odds_ratio2() and log_odds_ratio2().
• proportional_change(), proportional_difference().
• ran_pois_zi(), log_lik_pois_zi(), res_pois_zi() and dev_pois_zi().
• pzeros() to calculate proportion of zeros in a numeric object.

Modifications

• res_xx() functions now return data (actual or simulated) if type = 'data'.

Bug Fixes

• Fixed normal and log-normal deviances which were out by a factor of 2 and 1.41 respectively.

extras 0.2.0

Added

Functions

• Added the following function families
• ran_xx() (random samples)
• log_lik_xx() (log-likelihood)
• dev_xx() (deviances)
• res_xx() (residuals)

for the following distributions - _bern, (Bernoulli), - _binom (binomial) - _pois (Poisson) - _norm (normal) - _lnorm (log-normal) - _gamma (gamma) - _gamma_pois (gamma-Poisson)

• Added odds(), odd_ratio() and log_odds_ratio() to calculate odds, odds ratio and log odds ratio.
• Added moments functions xtr_mean(), xtr_sd(), variance(), skewness() and kurtosis().
• Added xtr_median() to calculate the median.
• Added invlogit() to calculate the inverse logistic transform.
• Added fabs() to calculate the absolute value of x. Used in TMB as replacement for abs().
• Added zeros() function to sum number of 0 values in a numeric (or MCMC object).

Arguments

• Added threshold = 0 argument to pvalue() and svalue().
• Added na_rm = FALSE argument to lower(), upper(), pvalue(), svalue() and zscore().

Deprecated

• Soft-deprecated as_list_unnamed() for as_list().
• Soft-deprecated pextreme() and sextreme().

extras 0.1.0

• Added chk_indices() and vld_indices() to check (validate) if an object is a list of indices ie a vector of one or more positive integer values.
• Added par_pattern() to provide string of regular expression for a parameter name.
• Added as_list_unnamed() generic which by default strips all attributes except names.
• Modified chk_pars() and vld_pars() to permit missing values and duplicates.

extras 0.0.1

• Initial submission to CRAN.

extras documentation built on April 4, 2025, 2:40 a.m.