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Changelog

TOSTER v0.9.0

New Features

  • New trans_rank_prob() function for transforming probability-scale effect sizes between four scales: probability (concordance), difference (rank-biserial), log-odds, and odds. Supports bidirectional transformation via from and to arguments with delta-method standard errors and monotonic CI endpoint mapping.

  • brunner_munzel() gains a scale argument to report results on alternative scales (“probability”, “difference”, “logodds”, “odds”) without changing the underlying test. The default scale = "probability" preserves existing behavior.

  • ses_calc() estimate labels now use probability notation (e.g., P(X>Y) - P(X<Y) instead of Rank-Biserial Correlation). The $method string and data frame row names retain human-readable names. Code that parses names(result$estimate) may need updating.

  • ses_calc() paired sample labels use P(Z>0) notation (where Z = X - Y); one-sample labels use P(X>0).

  • Effect size calculators now support hypothesis testing and htest output:

    • ses_calc and boot_ses_calc updated with output, alternative, and null.value arguments
      • Default output is now "htest" class; use output = "data.frame" for legacy format
      • Supports "two.sided", "less", "greater", "equivalence", and "minimal.effect" alternatives
      • New Agresti/Lehmann placement-based SE method (se_method = "agresti") with log-odds scale hypothesis testing
      • Continuity correction for boundary cases (complete separation)
    • smd_calc and boot_smd_calc updated with output, alternative, null.value, and test_method arguments
      • Default output is now "htest" class; use output = "data.frame" for legacy format
      • Supports the same alternative hypothesis options as ses_calc
      • test_method argument ("z" or "t") controls the reference distribution for smd_calc
      • Degrees of freedom included in output when test_method = "t"
      • Bootstrap p-values for boot_smd_calc computed from empirical distribution
      • New denom argument for direct denominator selection ("z", "rm", "pooled", "avg", "glass1", "glass2"), overriding glass, rm_correction, and var.equal as needed; informative messages on conflicts

  • Added hodges_lehmann function for robust location testing

    • Implements Hodges-Lehmann estimators (HL1 for one-sample/paired, HL2 for two-sample)
    • Supports exact permutation, randomization, and asymptotic (KDE-based) inference
    • Full support for equivalence and minimal effect testing
    • Consistent sign convention with wilcox.test (x - y for two-sample tests)
    • Formula and default methods available

  • Added perm_t_test function to allow for permutation tests for equivalence using TOST

  • Added plot_htest_est() function to create simple estimate plots from any htest object

    • Displays point estimate with confidence interval
    • Handles null values (single or equivalence bounds) as reference lines
    • Automatically handles two-sample t-test estimates by computing mean difference

  • Added BCa (bias-corrected and accelerated) bootstrap confidence intervals as a new boot_ci = "bca" option for:

    • boot_t_test, boot_t_TOST, boot_log_TOST, boot_smd_calc, boot_ses_calc, and boot_cor_test
    • BCa intervals provide second-order accuracy by correcting for bias and skewness in the bootstrap distribution
    • Acceleration factor computed via leave-one-out jackknife (pooled jackknife for two-sample designs)
    • Informative errors for degenerate cases with suggestion to use boot_ci = "perc" as fallback

Improvements

  • Correlation SE improvements for z_cor_test() and corsum_test():
    • Spearman’s rho now uses the Bonett-Wright ρ-dependent SE formula (sqrt((1 + r^2/2) / (n - 3))) instead of the fixed 1.06 constant, providing better calibration across the full range of rho.
    • z_cor_test() gains a se_method argument ("analytic" or "jackknife") for computing the standard error via leave-one-out resampling on the Fisher z scale. The jackknife SE is used consistently for both the test statistic and the confidence interval.
    • Both functions now return stderr as a named vector with z.se (Fisher z scale, used for inference) and cor.se (delta method SE on the correlation scale, for descriptive purposes).
    • The method string in the returned htest object now indicates the SE type used (e.g., "Pearson's product-moment correlation with approximate SE" or "Spearman's rank correlation rho with jackknifed SE").
  • simple_htest(), boot_t_test(), perm_t_test(), and hodges_lehmann() now produce more informative estimate labels that indicate the direction of calculation (e.g., "mean difference (treatment - control)" when using the formula interface).
  • For two-sample mean-based tests (simple_htest with t-test, boot_t_test, perm_t_test), the mean difference is now appended as a third element of $estimate, while preserving existing group means at positions 1-2 (backwards-compatible).
  • Paired test estimates are labeled to clarify the differencing operation, e.g., "mean of the differences (z = x - y)".
  • Wilcoxon/Mann-Whitney estimates in simple_htest() are labeled as "Hodges-Lehmann estimate" with direction indicated.
  • hodges_lehmann() estimate labels updated for clarity: "pseudomedian of x" for one-sample, "Hodges-Lehmann estimate (x - y)" for two-sample, and "Hodges-Lehmann estimate (z = x - y)" for paired tests.
  • Trimmed mean labels in boot_t_test() and perm_t_test() now include the trimming proportion, e.g., "trimmed mean difference (x - y, tr = 0.1)".
  • A $sample_size element (named numeric vector) is now included in the returned htest object for all four functions. For two-sample formula calls, names reflect the actual factor levels.
  • Permutation test terminology: Clarified distinction between “Exact Permutation” (all permutations enumerated) and “Randomization” (permutations sampled with replacement) tests across perm_t_test, hodges_lehmann, and brunner_munzel
  • p_method auto-selection: Added intelligent default for p_method argument in permutation-based functions:
    • NULL (default): Automatically selects “exact” for exact permutation tests and “plusone” for randomization tests
    • “exact”: Uses b/R, appropriate when all permutations are enumerated
    • “plusone”: Uses (b+1)/(R+1) following Phipson & Smyth (2010), provides exact Type I error control for randomization tests
  • Update brunner_munzel function to allow TOST directly
  • Update functions to disallow paired = TRUE when formula method utilized.
  • Improved plot.TOSTt for type = "simple":
    • Raw estimate plot now appears on top (was on bottom)
    • Decision text and equivalence bounds now displayed at top of plot
    • Added layout parameter: “stacked” (default) or “combined” for a single faceted plot
  • Improved plot.TOSTt for type = "tnull":
    • Now shows only one-sided rejection regions appropriate to the test type
    • Equivalence tests: lower bound shows right tail, upper bound shows left tail
    • Minimal effect tests: lower bound shows left tail, upper bound shows right tail

TOSTER v0.8.7

  • Update documentation to make it clear what the “eqb” argument does within the wilcox_TOST function.

TOSTER v0.8.6

CRAN release: 2025-08-22

  • Add warning message about error control with MET
  • Fix unit tests for boot_ses_calc to catch errors when estimates contain infinite values or when ses is not “rb”

TOSTER v0.8.5

  • Big update to package documentation to make things more detailed.
  • Added extra message when permutation tests are used for the Brunner-Munzel test.
  • Added more alternative hypotheses to boot_compare_smd.
  • Expanded functionality of power_eq_f function.

TOSTER v0.8.4

CRAN release: 2025-02-06

  • Added simple plot for TOSTt methods
  • Small fix to output for printed method for TOSTt
  • Added fix to power_z_cor to provide “zero” power for scenarios where the effect is undetectable

TOSTER v0.8.3

CRAN release: 2024-05-08

  • Change in the standard error formulation to Glass delta for independent samples
    • Hat tip to Paul Dudgeon for catching an error in the code that led to this development
    • Other small changes to standard error calcs (see vignettes for details)
  • Small modification to plot_smd to catch errors when attempting to plot
  • Brunner-Munzel updates
    • Added more warning messages
    • Changed default for simple_htest to 0.5 rather than 0

TOSTER v0.8.2

CRAN release: 2024-04-16

  • Fixed error with describe method for minimal effects test for TOSTt objects.

TOSTER v0.8.1

CRAN release: 2024-03-21

  • Small correction to the displayed equation for Cohen’s ds standard error. Thank you to Matthew B Jané for finding this error.
  • Added bootstrap options such as boot_smd_calc and boot_ses_calc.
    • Many functions also now allow for different CI methods for bootstrapped results.

TOSTER v0.8.0

CRAN release: 2023-09-14

  • Added Brunner-Munzel test
  • Updated documentation to include lifecycle labels
  • Created new function for two proportions tests (twoprop_test)
    • And power power_twoprop
  • Created new function for power for correlations (power_z_cor)
  • Deprecated old functions

TOSTER v0.7.1

CRAN release: 2023-04-05

  • Fixing the ggplot2 error related to after_stat update from that package.
  • Update documentation.

TOSTER v0.7.0

  • Add correlation functions z_cor_test, boot_cor_test, corsum_test, boot_compare_cor, and simple_htest
  • Add describe method to provide verbose output for analyses
    • Alternative describe_htest function for htest objects

TOSTER v0.6.0

CRAN release: 2022-12-13

  • Changed Glass’s delta SE for paired samples (minor).
  • Added smd_calc and ses_calc for just calculating the standardized effect sizes (no tests).
  • Default CIs for for SMDs are now NCT rather than the Goulet method.
  • compare_smd can be supplied with user provided standard errors.
  • Add log_TOST and boot_log_TOST function for comparing ratios of means.
  • Reduce the amount of text in the print methods

TOSTER v0.5.1

  • Formatting requirements for jamovi (all superficial changes)

TOSTER v0.5.0

  • Added “compare” functions.
    • compare_smd: Compare 2 SMDs from summary statistics
    • boot_compare_smd: Compare 2 SMDs from raw data
    • compare_cor: Compare 2 independent correlations
  • Added additional SMD options
    • Confidence intervals can now be estimated using other methods
    • smd_ci can be used to set the confidence interval method
    • Glass’s delta can now be calculated using the glass argument
  • Added additional standardized effect sizes for wilcox_TOST
    • ses argument can be set to “r”, “odds”, or “cstat”
    • Respectively, these will provide the rank-biserial correlation, odds, or concordance probability

TOSTER v0.4.2

CRAN release: 2022-09-20

  • Fix to Cohen’s drm calculation

TOSTER v0.4.1

CRAN release: 2022-03-23

  • jmv removed as dependency

TOSTER v0.4.0

CRAN release: 2022-02-04

“Avocado TOST” (Release date: 2022-02-05)

Changes:

  • New t_TOST function
    • Generalized function for TOST for any type of t-test
    • S3 generic methods to print and plot results
  • New power_t_TOST function
    • Generalized function for t_TOST power analysis
    • Outputs the an object of power.htest class
  • Updated all jamovi functions to allow minimal effect tests
    • Direction of one-sided tests now allows
  • Added equ_anova and equ_ftest
    • Now allows equivalence (also called non-inferiority)
  • jamovi functions using t-test have more plotting options
  • Error in powerTOSTtwo fixed when determining N
  • All old t-test based TOST functions now have message telling users they are defunct
  • All TOST procedures have text results changed to provide more appropriate feedback.

TOSTER v0.3.4

CRAN release: 2018-08-03

(Release date: 2018-08-05)

Changes:

  • Added a verbose = FALSE option to all functions.
  • Added Fisher’s z transformed CI to output of TOSTr.
  • Cleaned up the text and numeric output of the functions.
  • Renamed some variable names in the TOSTtwo.prop function for similarity with TOSTmeta.
  • Added warnings and error messages for possible incorrect input when using the functions.

TOSTER v0.3.3

CRAN release: 2018-05-08

(Release date: 2018-05-08)

Changes:

  • Error in order in which p-value 1 and p-value 2 were reported for TOSTr due to incorrect use of abs(r) in function. (thanks to Nils Kroemer and Dan Quintana)
  • Fixed error in powerTOSTr function - instead of based on conversion to d, new function calculates directly from r and is more accurate.
  • Added testthat folder and initial unit tests.

TOSTER v0.3.2

CRAN release: 2018-04-14

(Release date: 2018-04-14)

Changes:

  • Error in sensitivity analyses of powerTOSTpaired.raw, powerTOSTone.raw, powerTOSTtwo.raw where output was in Cohen’s d - now changed to output in raw scores, added sd to examples. (thanks to Lisa DeBruine)
  • Raw power functions still output ceiling N in message, but exact N in output value

TOSTER v0.3.1

CRAN release: 2018-04-06

(Release date: 2018-04-06)

Changes:

  • Error in TOSTpaired.raw where t-test for TOST multiplied by sdiff (copied from TOSTpaired function) removed. CI were correct, but p-values did not match. Now tests are correct. (thanks to ontogenerator)
  • Changed text in TOSTr function (text copied from t-test script now changed to correlation)