Skip to contents

Changelog

Source: NEWS.md

SimplyAgree 0.4.0

Results that change

Several fixes change results from earlier versions:

  • ICC intervals (reli_stats(), reli_aov()) are now two-sided; a “95%” interval was previously 90%. Old results at level c equal new results at 1 - 2 * (1 - c).
  • CCC for replicate and nested data (ccc_test(), agree_reps(), agree_nest()): new variance-components estimate for replicate data, and subject-level (jackknife) standard errors; the old intervals were too narrow.
  • Tolerance limits (tolerance_limit()) with variance functions, clustered data or the bootstrap; prediction limits are unchanged unless a variance function is used.
  • Deming joint tests (joint_test(), plot_joint(), and the joint power of deming_power_sim()/deming_sample_size()) now use Sadler’s sum-of-squares F test. Version 0.3.0 used a chi-squared Wald test from the jackknife variance-covariance matrix, which rejected a true identity line up to 14% of the time at n = 10 (nominal 5%); method = "wald", test_method = "asymptotic" reproduces it.
  • pb_reg(): error.ratio != 1 is now an error; bootstrap standard errors were 4-5 times too small before; tie-corrected slope intervals.
  • find_n() can return a sample size one larger; agreement_limit(data_type = "reps") and "nest" change with unbalanced or missing data.

Reliability

  • New icc_test() (one ICC as an htest, two-sided F intervals, REML for missing data, optional subject bootstrap), reli_err_test() (SEM, SEE, SEP and CVs), and mdc_test() (minimal detectable change).
  • New reli_facet_test() (experimental; its name may change) for subjects measured more than once by each rater or device: exchangeable repeats within subject-by-rater cells, or shared occasions (occasion, e.g. every rater on day 1 and day 2). Intra-rater, inter-rater and overall coefficients and SEMs from the generalizability-theory model, in consistency or agreement forms, with D-study projections, exact or MLS/Satterthwaite intervals, REML for unbalanced data, and the subject bootstrap. icc_test() and reli_err_test() point to it when the data have repeats, and mdc_test() accepts its SEMs.
  • New power_icc() and precision_icc() for ICC power and interval-width sample sizes, including missing data.
  • New summary(), plot() and check() methods for these results, with a new section in the power vignette.
  • reli_stats() and reli_aov() are superseded and now use the same engine. Beyond the two-sided intervals: observed-data degrees of freedom with missing data, subject bootstrap, delta-method intervals for SEE/SEP/CV, ANOVA variance components, and stricter data checks.
  • The jamovi reliability analysis uses the new functions.

Categorical ratings

  • New cac_test() (Gwet’s AC1/AC2, Fleiss’ kappa, Krippendorff’s alpha, percent agreement; matches irrCAC) and ord_kappa_test() (model-based kappa for ordinal ratings from many raters, with group comparisons; #63), with summary() and plot() methods.
  • New vignette, “Agreement for Categorical and Ordinal Ratings”.
  • agree_coef() is superseded by cac_test(); it gains categories and weights, and no longer fails or mislabels in edge cases.

Agreement

  • New ccc_test(): concordance correlation coefficient as an htest, with an opt-in studentized subject bootstrap for replicate data.
  • agreement_limit() gains bound_type ("iu" default, unchanged; "joint"), and prints within-subject SDs for replicate data.
  • tolerance_limit():
    • limits now use the residual SD for each row when there is a variance function (they were too narrow);
    • new bound_type, model = "lme" (including nested id), and conf_level;
    • corrected analytic limits for clustered data, and a fixed, faster bootstrap (tol_method = "boot_cal", formerly "perc");
    • its returned model now works with update() and emmeans().
  • loa_lme() is deprecated in favour of tolerance_limit(model = "lme").
  • Fixed plots failing after saving and reloading (e.g. in jamovi; #76), and plot()/print() failing when settings were expressions (#50).

Agreement power and sample size

Method comparison regression

  • joint_test() and plot_joint() gain method. For Deming fits the default is Sadler’s (2010) sum-of-squares F test and its exact region. The jackknife Wald ellipse (method = "wald") rejected a true identity line about 8.5% of the time at n = 10 and 7.4% at n = 20 with the F reference (test_method = "F", its default), and 14% and 10% with the chi-squared reference that 0.3.0 used (nominal 5%); Sadler’s test held 4.3-5.9% (references/general/eiv_sims). Passing-Bablok fits use the Wald test; Dufey (2020) fits are refused (8-11%).
  • deming_power_sim() now uses joint_test() (new joint_method), so its power matches the test users run; it previously overstated joint power. deming_sample_size(use_joint = ) now takes effect.
  • pb_reg():
    • pairs bootstrap replaces a wild bootstrap that gave standard errors 4-5 times too small;
    • new se_method ("bootstrap", "jackknife", "dufey");
    • error.ratio != 1 is now an error (it biased the slope in simulations; use dem_reg());
    • id averages replicates and now works with missing values;
    • fixed tie-corrected slope intervals and reject_h0 on tied data.
  • plot_joint() takes ideal_intercept before ideal_slope, like joint_test(), and both default to the model’s confidence level.
  • The documentation of dem_reg(error.ratio) now correctly states var(x)/var(y), as computed (thanks to Hugo Lachuer).

SimplyAgree 0.3.0

CRAN release: 2026-01-21

  • Add enhanced support for Deming regression.
    • Updated dem_reg function to include options for confidence intervals and plotting.
  • Added more power and sample size determination functions for limits of agreement.
  • Added Passing-Bablok regression function (pb_reg) for method comparison studies.
  • Updated methods for simple_eiv objects to be more extensive and act like other statistical models

SimplyAgree 0.2.2

  • Small fixes to errors related to plotting and df for lmer based results.

SimplyAgree 0.2.1

CRAN release: 2025-02-24

  • Add sympercent options for log transformed results in tolerance_limit and agreement_limit
  • Add argument to agreement_limit to allow of asymptotic confidence intervals to avoid errors related emmeans calculations
    • Only a problem for “big” data with > 1000 observations
  • Small edit to reli_stats documentation to remove references to BCa confidence intervals

SimplyAgree 0.2.0

CRAN release: 2024-03-21

  • Add universal tolerance limits function: tolerance_limit
  • Add universal agreement limits function: agreement_limit

SimplyAgree 0.1.5

  • Add option to drop “CCC” calculation from agree_reps and agree_nest functions.

SimplyAgree 0.1.4

SimplyAgree 0.1.3

  • Added chisq type of confidence intervals for “Other” CIs for reli_stats and reli_aov

SimplyAgree 0.1.2

CRAN release: 2022-12-14

  • Fix to agree_np plot. (colors now align with order of LoA elements).
  • Added reli_aov function for sums of squares approach.

SimplyAgree 0.1.1

  • Minor cosmetic updates for jamovi submission.
  • Minor cosmetic changes to plots (transparent backgrounds)

SimplyAgree 0.1.0

CRAN release: 2022-08-24

  • Updated CV calculations for reli_stats with the cv_calc argument.
    • Options now included CV for the model residuals, mean-squared error (MSE), or for the standard error of measurement (SEM).
    • Parametric bootstrap CI for all “other” statistics (CV, SEM, SEE, and SEP)
  • Updated plots to include the delta argument on plot if specified, and estimate of LoA.
  • Line-of-identity plot now includes trend line from Deming regression rather than OLS.
  • Deming regression function (dem_reg) has been added to the package.
  • Agreement coefficients (agree_coef), otherwise known as
  • Added agreement coefficient function (agree_coef).
  • Added loa_lme function
    • loa_mixed now deprecated
    • loa_lme allows for heterogenous variance by condition
    • New function is faster and relies on parametric bootstrap
  • Assumptions checks are added for all “simple-agree” class results
    • Checks include: normality, heteroscedasticity, and proportional bias
  • Assumptions checks are added for all “simple-reli” class results
    • Checks include: normality and heteroscedasticity
  • All jamovi functions updated with new UI layout
  • Big thanks go to Greg Atkinson and Ivan Jukic for the many suggestions leading to this update.

SimplyAgree 0.0.3

CRAN release: 2022-03-14

  • Fixed error in agree_nest and agree_reps; now properly handles missing values
  • Remove dependencies on sjstats and cccrm packages

SimplyAgree 0.0.2

CRAN release: 2021-05-18

  • Fixes typos in jamovi/jmv functions
  • Adds more descriptive errors to jamovi output
  • Remove dontrun from examples in documentation
  • Add more details and references to the package’s functions