NEWS (original) (raw)

• 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.
• Remove dependency on MASS package so minimum R version can be brought down to 4.0.0 from 4.3.0.
• Register poissontemplate usage.
• Fix actions.
• Perform upkeep on package.
• Ensure all tests, examples, and vignettes run conditionally for packages listed in suggests.
• Fix behaviour of dev_beta_binom() when size < x.
• Refactored log_lik_beta_binom() to speed up optimization required in dev_beta_binom().
• Styled all code in package.
• 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.
• Fixed M1mac test

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() andrbern().

Internal

• Fix for dev testthat
• Fix tests for dev waldo
• 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
• Added log_odds() and log_odds()<-.
• Added dbern(), pbern(),qbern(), rbern().

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.

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() andlog_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() andzscore().

Deprecated

• Soft-deprecated as_list_unnamed() foras_list().
• Soft-deprecated pextreme() andsextreme().
• 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.
• Initial submission to CRAN.