NEWS.md

In rstatix: Pipe-Friendly Framework for Basic Statistical Tests

rstatix 0.7.2

Minor changes

• Required tidyselect versions is >= 1.2.0

Bug fixes

• emmeans_test(): restoring grouping variable class (factor) in the final results emmeans_test() (#169)
• Fix warning in emmeans_test(): "Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0."

rstatix 0.7.1

Minor changes

• cor_plot() now accepts additional arguments to pass to corrplot() (#66)
• suppressMessages() used to suppress this message ("Coefficient covariances computed by hccm()") generated by car::Anova().
• get_comparisons() now drops unused levels before creating possible comparisons (#67)
• Now, the function get_summary_stats() keeps the order of columns specified by the user (#46).
• internal two_sample_test() now counts group sizes (n1 and n2) by the number of non-NA values #104

Bug fixes

• Name collisions bug fixes in the shapiro_test() function. Shapiro_test() throws an error if the input data contains column names "value" or "variable". This is fixed now (#52).
• Bug fixed in the cor_test() function, where there was a tidy evaluation conflict when the input data contains "x" and "y" as column names (#68).
• The dunn_test() documentation is updated to describe the discrepancy between the default behavior of the rstatix::dunn_test() compared to other packages (dunn.test and jamovi). The default of the rstatix::dunn_test() function is to perform a two-sided Dunn test like the well known commercial softwares, such as SPSS and GraphPad. This is not the case for some other R packages (dunn.test and jamovi), where the default is to perform one-sided test (#50).
• Now, the function get_summary_stats() handles the user defined probabilities for grouped data (#78)

rstatix 0.7.0

New features

• New function to extract information from rstatix statistical tests:
  • get_n() to extract sample count (n) from statistical test results.
  • get_description to extract stat test description or name
  • remove_ns() to remove non-significant rows.

Major changes

• Rewriting add_x_position() to better support different situations (#73).
• Now, the output of the function dunn_test() include estimate1 and estimate2 when the argument detailed = TRUE is specified. The estimate1 and estimate2 values represent the mean rank values of the two groups being compared, respectively (#59).

Minor changes

• cor_spread() doc updated, error is explicitly shown if the input data doesn't contain the columns "var1", "var2" and "cor" (#95)
• Maintenance updates of the functions emmeans_test() and levene_test() to adapt to broom release 0.7.4 (#89)
• The documentation of the function anova_test() is updated to explain the internal contrast setting (#74).
• Now, p_mark_significance() works when all p-values are NA. Empty character ("") is returned for NA (#64).
• Classes (rstatix and grouped_anova_test) added to grouped ANOVA test (#61)
• New argument scales added in the function get_y_position(). If the specified value is "free" or "free_y", then the step increase of y positions will be calculated by plot panels. Note that, using "free" or "free_y" gives the same result. A global step increase is computed when scales = "fixed" (#56).

Bug fixes

• The function anova_test() computes now repeated measures ANOVA without error when unused columns are present in the input data frame (#55)

rstatix 0.6.0

Minor changes

• Adapted to upcoming broom v0.7.0 release (#49)
• New argument stack added in get_y_position() to compute p-values y position for stacked bar plots (#48).
• wilcox_test(): Now, if detailed = TRUE, an estimate of the location parameter (Only present if argument detailed = TRUE). This corresponds to the pseudomedian (for one-sample case) or to the difference of the location parameter (for two-samples case) (#45).

Bug fixes

• anova_test() function: Changing R default contrast setting (contr.treatment) into orthogonal contrasts (contr.sum) to have comparable results to SPSS when users define the model using formula (@benediktclaus, #40).
• Now, the option type = "quantile" of get_summary_stats() works properly (@Boyoron, #39).

rstatix 0.5.0

New features

• New functions added for easy data frame manipulation. These functions are internally used in the rstatix and the ggpubr package and makes it easy to program with tidyverse packages using non standard evaluation.
  • df_select
  • df_arrange
  • df_group_by
  • df_nest_by
  • df_split_by
  • df_unite
  • df_get_var_names
  • df_label_both
  • df_label_value

Minor changes

• Now, in freq_table() the option na.rm removes only missing values in the variables used to create the frequency table (@JuhlinF, #25).
• Missing values are now correctly handled in anova_test() (@benediktclaus, #31)
• Maintenance for adapting to the future dplyr 1.0.0 version #32

Bug fixes

• An informative message is now displayed when users try to apply Hedge's correction when computing the Cohen's D for one sample test (@GegznaV, #36).
• Bug fixes in the games_howell_test() function : the t-statistic is now calculated using the absolute mean difference between groups (@GegznaV, #37).
• x position is now correctly computed when when making custom comparisons (@barrel0luck, #28).

rstatix 0.4.0

New features

• The cohens_d() function now supports Hedge's correction. New argument hedge.correction added . logical indicating whether apply the Hedges correction by multiplying the usual value of Cohen's d by (N-3)/(N-2.25) (for unpaired t-test) and by (n1-2)/(n1-1.25) for paired t-test; where N is the total size of the two groups being compared (N = n1 + n2) (@IndrajeetPatil, #9).

Minor changes

• Now, the function cohens_d() outputs values with directionality. The absolute value is no longer returned. It can now be positive or negative depending on the data (@narunpat, #9).

Bug fixes

• The value of mu is now considered when calculating cohens_d() for one sample t-test (@mllewis, #22).
• The function tukey_hsd() now handles situation where minus - symbols are present in factor levels (@IndrajeetPatil, #19).

rstatix 0.3.1

Minor changes

• tidyr > 1.0.0 now required
• know, identify_outliers returns a basic data frame instead of tibble when nrow = 0 (for nice printing)
• new argument detailed added in dunn_test(). If TRUE, then estimate and method columns are shown in the results.

rstatix 0.3.0

New features

• prop_test(), pairwise_prop_test() and row_wise_prop_test(). Performs one-sample and two-samples z-test of proportions. Wrappers around the R base function prop.test() but have the advantage of performing pairwise and row-wise z-test of two proportions, the post-hoc tests following a significant chi-square test of homogeneity for 2xc and rx2 contingency tables.
• fisher_test(), pairwise_fisher_test() and row_wise_fisher_test(): Fisher's exact test for count data. Wrappers around the R base function fisher.test() but have the advantage of performing pairwise and row-wise fisher tests, the post-hoc tests following a significant chi-square test of homogeneity for 2xc and rx2 contingency tables.
• chisq_test(), pairwise_chisq_gof_test(), pairwise_chisq_test_against_p() : Chi-square test for count data.
• binom_test(), pairwise_binom_test(), pairwise_binom_test_against_p() and multinom_test(): performs exact binomial and multinomial tests. Alternative to the chi-square test of goodness-of-fit-test when the sample.
• counts_to_cases(): converts a contingency table or a data frame of counts into a data frame of individual observations.
• New functions mcnemar_test() and cochran_qtest() for comparing two ore more related proportions.
• prop_trend_test(): Performs chi-squared test for trend in proportion. This test is also known as Cochran-Armitage trend test.

Minor changes

• Now get_test_label() and get_pwc_label() return expression by default
• Unit testing and spelling check added
• Code rewritten to adapt tidyr 1.0.0

rstatix 0.2.0

Minor changes

• get_anova_table() supports now an object of class grouped_anova_test
• ANOVA table is now correctly returned when correction = "none" for repeated measures ANOVA
• NAs are now automatically removed before quantile computation for identifying outliers (@IndrajeetPatil, #10).
• Unquoted factor variable name is now supported in factor manipulation functions: set_ref_level(), reorder_levels() and make_valid_levels()
• New argument model added in the function emmeans_test()
• Adapting to tidyr v1.0.0 (@jennybc, #6)

New features

• New function welch_anova_test(): Welch one-Way ANOVA test. A wrapper around the base function stats::oneway.test(). This is is an alternative to the standard one-way ANOVA in the situation where the homogeneity of variance assumption is violated.
• New function friedman_effsize(), computes the effect size of Friedman test using the Kendall's W value.
• New function friedman_test(), provides a pipe-friendly framework to perform a Friedman rank sum test, which is the non-parametric alternative to the one-way repeated measures ANOVA test.
• New function games_howell_test(): Performs Games-Howell test, which is used to compare all possible combinations of group differences when the assumption of homogeneity of variances is violated.
• New function kruskal_effsize() for computing effect size for Kruskal-Wallis test.
• New functions added to round and format p-values: p_round(), p_format(), p_mark_significant().
• New function wilcox_effsize() added for computing effect size (r) for wilcoxon test.
• New function get_anova_table() added to extract ANOVA table from anova_test() results. Can apply sphericity correction automatically in the case of within-subject (repeated measures) designs.
• New functions added to extract information from statistical tests: get_anova_label()
• New function emmeans_test() added for pairwise comparisons of estimated marginal means.

Minor changes

• the unnecessary column comparison removed from tukey_hsd() results (breaking change).
• New column n (sample count) added to statistical tests results: t_test(), wilcox_test(), sign_test(), dunn_test() and kruskal_test() (@ShixiangWang, #4).
• rstatix_test class added to anova_test() results
• the results of kruskal_test() is now an object of class rstatix_test that has an attribute named args for holding the test arguments.
• In get_y_position(), y positions and test data are merged now for grouped plots.
• New argument y.trans added in get_y_position() for y scale transformation.
• significance column added in tukey_hsd() results.
• adjust_pvalue() now supports grouped data

Bug fixes

• detailed arguments correctly propagated when grouped stats are performed

rstatix 0.1.1

New features

• New function get_pvalue_position added to autocompute p-value positions for plotting significance using ggplot2.
• New function get_comparisons() added to create a list of possible pairwise comparisons between groups.
• New function dunn_test() added for multiple pairwise comparisons following Kruskal-Wallis test.
• New function sign_test() added.

Minor changes

• get_summary_stats() now supports type = "min", "max", "mean" or "median"
• the results of t_test(), wilcox_test(), dunn_test() and sign_test() are now an object of class rstatix_test that has an attribute named args for holding the test arguments.
• The results of cohens_d() is now a data frame containing the Cohen's d and the magnitude.

Bug fixes

• the argument detatiled is now passed to compare_pairs().

rstatix 0.1.0

First release

rstatix documentation built on Feb. 16, 2023, 6:10 p.m.