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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

Bug Fixes

  • Consistent handling of mu in t_TOST(), tsum_TOST(), and boot_t_TOST():
    • The raw estimate, its confidence interval, and the raw equivalence bounds are now all reported on the original scale. Previously the raw estimate was estimate - mu while the confidence interval and bounds were not shifted. TOST p-values from t_TOST() and tsum_TOST() are unchanged.
    • The SMD and its bounds are now consistently relative to mu (e.g., (x - y - mu) / SD). Previously the two-sample SMD added mu, the paired SMD ignored mu, and tsum_TOST() ignored mu for all designs. Bounds given with eqbound_type = "SMD" are standardized distances from mu.
    • mu is now stored in the returned TOSTt object. print() reports the equivalence bounds and notes the scale of each row when mu is not zero, and describe() uses the stored mu (previously always 0 for tsum_TOST()).
    • The “Equivalence interval does not include zero” message now checks whether the bounds contain mu.
  • boot_t_TOST(): the studentized bootstrap p-values used a bootstrap t-statistic whose variance was centered incorrectly, which under-dispersed the reference distribution whenever the (difference in) means was far from zero. The p-values now use the same pivot as the studentized confidence interval, so they agree with the interval and with boot_t_test().
    • Paired resamples are now drawn in the same order as boot_t_test(), so both functions give identical p-values and confidence intervals for the same seed (results for a given seed differ from earlier versions).
    • The Welch two-sample bootstrap replicates now use the normal-approximation SMD standard error, as the other designs already did.
  • boot_t_test() with var.equal = TRUE: the studentized confidence interval used Welch standard errors for the bootstrap replicates while the observed standard error and p-value used the pooled standard error. The replicates now use the pooled standard error, so the interval and p-value agree.
  • smd_calc() and boot_smd_calc(): the one-sample SMD now uses mean(x) - mu correctly
  • jamovi one-sample TOST now passes the mu option to the analysis.
  • plot.TOSTt(type = "tnull"): fixed swapped internal labels for the CI limits.

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)