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extras 0.10.0.9003

  • Rename skewnorm and skewlnorm parameters and fix definitions (#164).

  • Treat near-zero negative deviances as 0 in dev_res() (#167).

extras 0.10.0.9002

  • Fix raw and standardized residuals in res_skewnorm() (#152, #153) (#161) (#152).

  • Document shape as unbounded for sens_skewnorm() and sens_skewlnorm() (#158) (#162) (#158).

extras 0.10.0.9001

  • Move the fledge preamble back to the first line of NEWS.md (#150).

  • Fix dev_skewnorm() residual sign to use the mode, not the mean (#144).

extras 0.10.0

  • Add probability_direction() and directional_information() (#106).
  • Add functions to calculate s-values and information from vectors of probabilities: p2svalue() and p2info() (#122).
  • Add functions to calculate the Region of Practical Equivalence (ROPE) and credible intervals: xtr_ci(), xtr_ci_eti(), xtr_ci_hdi(), xtr_rope() (#110).
  • Add skew-lognormal distribution family (dskewlnorm(), pskewlnorm(), qskewlnorm(), rskewlnorm(), ran_skewlnorm(), sens_skewlnorm(), quant_skewlnorm(), dev_skewlnorm(), res_skewlnorm(), log_lik_skewlnorm(), prob_skewlnorm()) (#127).
  • Add skeptical argument to pvalue(), svalue(), and directional_information(), defaulting to TRUE (#133).
  • Advance deprecation of as_list_unnamed(), pextreme(), and sextreme() from soft-deprecated to warnings (#140).

extras 0.9.0

  • Add log_lik_exp(), log_lik_beta(), and log_lik_unif() (#93, #94, #95).
  • Allow one-sided p-values and s-values via the side argument of pvalue() and svalue(); tighten pvalue()'s sample-size correction to only apply when it would otherwise return exactly 0 (#100, #105).
  • Add truncation arguments (tlower, tupper) to log_lik_*() functions; add prob_*() and quant_*() function families (#119).

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.
  • 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

  • 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.