NEWS.md
N.B. All statistical analysis in ggstatsplot
is carried out in statsExpressions
. Thus, to see changes related to statistical expressions, read the NEWS
for that package: https://indrajeetpatil.github.io/statsExpressions/news/index.html
MAJOR CHANGES
ggscatterstats
, ggstatsplot
now relies on ggside
package instead of ggExtra
. This was done to remove a glaring inconsistency in the API. All functions in ggstatsplot
produced ggplot
objects and could be further modified with ggplot2
functions, except ggscatterstats
, which led to a lot of confusion among users (e.g. #28). This change gets rid of this inconsistency. But it comes at a cost: there is no more marginal.type
argument that lets you change the type of marginal distribution graphic and the densigram (density plus histogram,i.e.) is the only possible option. Note that this is not a breaking change. Your past code will continue to work but it will now always produce a densigram instead of other marginal graphic you might have chosen. Additionally, the densigrams will look slightly different due to differences in how these packages compute density plots for marginal distributions (for more, see: https://github.com/jtlandis/ggside/issues/18).
MINOR CHANGES
Online vignette about combine_plots
has been removed. In case you want to create a grid of plots, it is highly recommended that you use patchwork
package directly and not this wrapper around it which is mostly useful with ggstatsplot
plots.
ggscatterstats
labeling arguments accept only unquoted inputs now, and not quoted or string inputs. Allowing this was a bad design choice in the past since most functions in ggstatsplot
, inspired by tidyverse
, expect unquoted (x
) - and not quoted ("x"
) - arguments. So this function was the odd one out.
Gets rid of ipmisc
dependency.
Removes movies_wide
dataset, which was virtually identical to movies_long
dataset and was not used anywhere in the package.
NEW FUNCTIONS
extract_stats
function to extract dataframes containing statistical details.MAJOR CHANGES
There is finally a publication for ggstatsplot
package! https://joss.theoj.org/papers/10.21105/joss.03167
The ggcoefstats
function defaults to NULL
for xlab
and ylab
arguments, which lets users change these labels if they wish to do so. Additionally, the x-axis label, if not specified, now defaults to "estimate"
. Whether this estimate corresponds to regression coefficient or effect size like partial eta-squared should be clear from the label itself.
To reduce the dependency load, ggcorrplot
moves from Imports
to Suggests
.
The bar.fill
argument in gghistostats
is retired in favor of the new bin.args
argument that can be used to pass aesthetic arguments to ggplot2::stat_bin
.
ggstatsplot.layer
argument has been retired. If the user chooses a certain ggplot2
theme, it means they want that theme, and not ggstatsplot
’s varnish on it. So the previous behavior was undesirable. This is a backward compatible change, so the plots should not look different.
MINOR CHANGES
The pch
size for ggcorrmat
has been increased to 14 (#579) to increase its visibility compared to the correlation value text.
ggwithinstats
gains point.args
to change geom_point
.
Minor change to ggcorrmat
legend title - content in parentheses is now shown outside of it.
BUG FIXES
ggcoefstats
didn’t work when statistic for the given model was chi-squared. This has been fixed.MAJOR CHANGES
To reduce the dependency load, ggExtra
moves from Imports
to Suggests
.
All functions are more robust in the sense that when statistical analysis fails, they will return only the plots with no subtitles/captions. This helps avoid difficult-to-diagnose edge case failures when the primary functions are used in grouped_
functions (e.g., #559). The ggpiestats
and ggbarstats
functions always behaved this way, but the rest of the functions now also mimic this behavior.
MINOR CHANGES
ggcoefstats
labels do not contain degrees of freedom when they are not available instead of displaying Inf
.MAJOR CHANGES
title.prefix
is now removed. It led to redundant title prefixes across different facets of the plot. Given that grouped_
functions require users to set grouping.var
, it is fair to assume what variable the levels in the title correspond to.MINOR CHANGES
Adapts to changes made in statsExpressions 1.0.0
.
sample.size.label
argument is retired for ggbetweenstats
, ggwithinstats
, and ggbarstats
. I do not think it is ever a good idea to not do this. If the users wish to not display sample sizes, they can easily do this using scale_*
functions from ggplot2
.
In ggpiestats
and ggbarstats
, parametric proportion tests are now turned off when type = "bayes"
.
BREAKING CHANGES
combine_plots
has been completely revised to rely not on patchwork
, but on patchwork
, to combine a list of ggplot
together. This was done to have a leaner syntax. With this revision, its vestigial twin combine_plots
is no longer needed and has been removed. This should not break any of the existing instances of grouped_
functions, although it will lead to changed graphical layouts. The only instance in which this change will lead to a breakage is when you specified labels
argument. So, if you used plotgrid.args = list(labels = "auto")
, you will now have to replace it with plotgrid.args = list(tag_level = "keep")
. You can also use annotation.args
(e.g., annotation.args = list(tag_levels = "a")
to customize labels (this will create labels with pattern a
, b
, c
, etc.). Another instance of breakage is if you had used combine_plots
function and provided individual plots to ...
instead as a list
.
To avoid confusion among users, the default trimming level for all functions is now changed from tr = 0.1
to tr = 0.2
(which is what WRS2
defaults to).
MAJOR CHANGES
All robust tests in this package were based on trimmed means, except for correlation test. This has been changed: the robust correlation measure is now Winsorized correlation, which is based on trimming. Therefore, the beta
argument has been replaced by tr
argument. This should result only in minor changes in correlation coefficient estimates.
Using annotate
instead of geom_label
had significantly slowed down gghistostats
and ggdotplotstats
functions. This has been fixed.
Removes the vestigial notch
and notchwidth
arguments for ggbetweenstats
and ggwithinstats
.
All Bayesian expression templates are now explicit about the type of estimate being displayed.
For gghistostats
and ggdotplotstats
, the centrality measure labels used to be attached to the vertical line, but this occluded the underlying data. Now this label is instead shown on the top x
-axis. Note that this means that if you make any further changes to the resulting plot using the ggplot2::scale_x_continuous
function, this label will likely disappear. The centrality.k
argument is retired in favor of k
.
NEW FEATURES
More models supported in ggcoefstats
: crr
, eglm
, elm
, varest
.
ggbetweenstats
, ggwithinstats
, gghistostats
, ggdotplotstats
gain argument centrality.type
that can be used to specify which centrality parameter is to be displayed. So one can have type = "robust"
and still show median as centrality parameter by choosing centrality.type = "nonparametric"
.
MAJOR CHANGES
gghistostats
removes bar.measure
argument. The function now defaults to showing the count
information on the x
-axis and the proportion
information on the duplicated x
-axis.
ggscatterstats
removes method
and method.args
arguments. It will no longer be possible to use this function to visualize data for when the model is not linear. It also retires margins
argument.
For ggbetweenstats
and ggwithinstats
functions, the arguments of type mean.*
have all been replaced by centrality.*
. This is because now these functions decide which central tendency measure to show depending on the type
argument (mean for parametric, median for non-parametric, trimmed mean for robust, and MAP estimator for Bayes).
Similarly, gghistostats
and ggdotplotstats
functions also decide which central tendency measure to show depending on the type
argument (mean for parametric, median for non-parametric, trimmed mean for robust, and MAP estimator for Bayes). Therefore, centrality.parameter
argument has been removed. If you want to turn off displaying centrality measure, set centrality.plotting = FALSE
.
gghistostats
and ggdotplotstats
functions remove the functionality to display a vertical line corresponding to test.value
. This feature was turned off by default in prior releases. Accordingly, all related arguments from these two functions have been removed.
ggscatterstats
defaults to densigram
as the marginal distribution visualization.
ggbetweenstats
and ggwithinstats
now display the centrality tendency measure in such a way that the label doesn’t occlude any of the raw data points (#429).
mean.ci
argument is retired for ggbetweenstats
and ggwithinstats
. Future ggstatsplot
releases will be providing different centrality measures depending on the type
argument and it is not guaranteed that all of them will have CIs available. So, for the sake of consistency, this argument is just going to be retired.
MINOR CHANGES
ggcorrmat
uses pretty formatting to display sample size information.
ggcoefstats
now also displays degrees of freedom for chi-squared tests.
Expects minor changes in some of the effect sizes and their confidence intervals due to changes in statsExpressions
.
NEW FEATURES
More models supported in ggcoefstats
: fixest
, ivFixed
, ivprobit
, riskRegression
.
ggcorrmat
supports partial correlations.
BREAKING CHANGES
ggcoefstats
no longer supports exponentiate
argument. If it is specified, the user will have to themselves adjust the scales appropriately.
ggcorrmat
defaults have changed significantly:
As a matter of good practice, the p-values are adjusted by default for multiple comparisons.
The default matrix is upper type, and not the full matrix, which features many redundant comparisons and self-correlations diagonally.
Default text size for legend has been increased to 15 and background grid has been removed.
BUG FIXES
In the prior release, when the GitHub version of BayesFactor
wasn’t present, ggwithinstats
just outright failed to run for ANOVA designs. This has been fixed.
Setting mean.path = FALSE
in ggwithinstats
produced incorrect colors for points (#470). This bug was introduced in 0.6.5
and is now fixed.
If user had set options(scipen = 999)
in their session, the p-value formatting for ggpiestats
and ggcoefstats
looked super-ugly (#478). This has been fixed.
MAJOR CHANGES
Drops broomExtra
from dependencies. All regression modeling-related analysis now relies on easystats
ecosystem.
ggpiestats
and ggbarstats
don’t support returning dataframes. See FAQ vignette on how to get these dataframes: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/faq.html#faq-1
ggpiestats
and ggbarstats
were not supposed to support returning Bayes Factor for paired contingency table analysis, which is not supported in BayesFactor
itself.
ggcoefstats
defaults to displaying the intercept term. Also, when the degrees of freedom are not available for t
-statistic, they are displayed to be Inf
, in keeping with easystats
conventions.
Instead of showing significance of p-values with APA’s asterisks conventions, ggbarstats
now instead shows the actual p-values from one-sample proportion tests.
NEW FEATURES
ggcoefstats
: Glm
.BREAKING CHANGES
ggpiestats
and ggbarstats
no longer have the vestigial arguments main
and condition
, which are superseded by x
and y
, respectively.MAJOR CHANGES
For consistency and to reduce confusion, all Bayes Factor (irrespective of whether in the subtitle or caption) are always in favor of null over alternative (BF01
).
Retires centrality parameter tagging functionality of ggscatterstats
. Although it was not the default, when turned on, it definitely created a cluttered plot.
MAJOR CHANGES
ggbetweenstats
and ggwithinstats
functions now default to pairwise.comparisons = TRUE
.MINOR CHANGES
Plot borders are now removed from the default theme.
Small p-values (< 0.001) are now displayed in scientific notation.
BREAKING CHANGES
pairwiseComparisons
re-exports are deprecated.NEW FEATURES
More models supported in ggcoefstats
: BFBayesFactor
, betamfx
, crq
, coxph.penal
, geeglm
, glht
, glmm
, lm_robust
, lqm
, lqmm
, manova
, maov
, margins
, negbinmfx
, logitmfx
, logitsf
, margins
, poissonmfx
, betaor
, negbinirr
, logitor
, metafor
, metaplus
, orm
, poissonirr
, semLm
, semLme
, vgam
.
ggpiestats
gains label.repel
argument to cover contexts in which the labels might overlap. Setting it to TRUE
will minimize such an overlap.
ggbetweenstats
and ggwithinstats
gain ggsignif.args
argument to make it easy to change aesthetics of the pairwise comparison geom.
The subtitle and caption for Bayes Factor tests now also provide information about posterior estimates, when relevant.
MAJOR CHANGES
Removed unused intent_morality
dataset.
ggcoefstats
retires caption.summary
argument. So, by default, the caption is going to contain as much information as it can and the users can then choose to modify the default caption using ggplot2
functions.
MINOR CHANGES
The argument method
for ggcorrmat
has been renamed to matrix.method
, since it was confusing whether this method referred to correlation method.
For both ggpiestats
and ggbarstats
, the count labels no longer include n =
in them as this was confusing since all labels had n =
in them with no further explanation about how this n
differed from n
in the proportion test.
No longer relies on groupedstats
package.
BREAKING CHANGES
The pairwise.annotation
argument for ggbetweenstats
and ggwithinstats
is deprecated. This was done because-
Different fields have different schema for what significance levels asterisks represent.
The p-value labels also contain information about whether they are adjusted for multiple comparisons.
The normality_message
and bartlett_message
helper functions have been removed. This is because model assumption checks don’t really fall under the purview of this package. There are excellent visualization tools out there for model assumption checks (ggResidpanel
, performance
, DHARMa
, olsrr
, etc.), which should be preferred over unhelpful messages with only p-values that these functions were printing. For what it’s worth, the functions where these messages were displayed (ggbetweenstats
or ggwithinstats
) feature visualizations rich enough and defaults sensible enough that most of the time one can either assess these assumptions from the plots or need not worry about them.
MAJOR CHANGES
ggcoefstats
has been refactored to reflect that broomExtra::tidy_parameters
now defaults to parameters
package instead of broom
. It also loses the following vestigial arguments: p.adjust.method
and coefficient.type
.
Reverts aligning title and subtitle with the plot and not the axes, since it looked pretty ugly (esp., ggcoefstats
) and was causing problems for labels.
factor.levels
(for ggpiestats
) and labels.legend
(for ggbarstats
) are deprecated. If users would like to changes the names for factor levels, this should be done outside of ggstatsplot
.
The non-parametric post hoc test for between-subjects design has been changed from Dwass-Steel-Crichtlow-Fligner test to Dunn test.
NEW FEATURES
ggcoefstats
: bayesGARCH
, clm2
, clmm2
, mcmc.list
, robmixglm
.BREAKING CHANGES
ggcorrmat
no longer returns matrices of correlation coefficients or other details. It now returns either a plot or a dataframe and this can dataframe can then be used to create matrices.
ggbarstats
loses x.axis.orientation
argument. This argument was supposed to help avoid overlapping x-axis label, but now ggplot2 3.3.0
has a better way to handle this: https://www.tidyverse.org/blog/2020/03/ggplot2-3-3-0/#rewrite-of-axis-code
NEW FEATURES
More models supported in ggcoefstats
: bayesx
, BBmm
, brmultinom
, lmerModLmerTest
, lrm
.
Specifying output = "proptest"
for ggpiestats
and ggbarstats
functions will now return a dataframe containing results from proportion test.
ggbetweenstats
and ggwithinstats
will display pairwise comparisons even if results.subtitle
is set to FALSE
.
ggcorrmat
supports computing Bayes Factors for Pearson’s r correlation.
ggbetweenstats
and ggwithinstats
now support pairwise comparisons for Bayes Factor test.
MAJOR CHANGES
For changes related to subtitle details, see changes made in new version of statsExpressions 4.0.0
: https://CRAN.R-project.org/package=statsExpressions/news/news.html
ggbetweenstats
and ggwithinstats
no longer print dataframes containing results from pairwise comparisons tests because this is too cluttering for the user’s console. The users are now instead advised to either extract this dataframe using ggplot2::ggplot_build()
function or use the pairwiseComparisons::pairwise_comparisons()
function used in the background by ggstatsplot
to carry out this analysis.
Due to changes in one of the downstream dependencies, ggstatsplot
now expects the minimum R version to be 3.6.0
.
MINOR CHANGES
ggcorrmat
now internally relies on correlation
for correlation analyses.
ggbarstats
no longer displays "percent"
for Y-axis label as this was redundant information.
Continuing the argument cleanup that began in 0.3.0
, ggcoefstats
gains point.args
argument instead of individuals point.*
arguments.
The subtitles are more explicit about the details of the test. For the same reason stat.title
argument from all relevant functions is retired since this argument was supposed to be for entering some additional details about the test. Additionally, the plot titles and subtitles for some of the plots are aligned with the plot.
ggcorrmat
legend, in case of missing values, shows mode - instead of median - for the distribution of sample pairs.
The following vestigial arguments are retired:
caption.default
in ggcorrmat
k.caption.summary
in ggcoefstats
This is a hotfix release to correct some of the failing tests and other minor breakages resulting from the new release of ggplot2 3.3.0
.
MAJOR CHANGES
ggpiestats
loses sample.size.label
argument since this information is included in the goodness of fit test results itself. So setting proportion.test
to FALSE
will suppress this information.BREAKING CHANGES
To give users more flexibility in terms of modifying the aesthetic defaults for all geoms
included in the ggstatsplot
plots (each plot typically has multiple geoms), the package now uses a new form of syntax. Previously, each geom
had a separate argument to specify each aesthetic (e.g., geom_point
would get arguments like point.size
, point.color
, etc.), which resulted in functions with a massive number of arguments and was unsustainable in the long run. Instead, ggstatsplot
functions now expect a list of such arguments for the respective geom (e.g., geom_point
will have point.args
argument where a list of arguments list(size = 5, color = "darkgreen", alpha = 0.8)
can be supplied).
All grouped_
functions have been refactored to reduce the number of arguments. These functions now internally use the new combine_plots
instead of combine_plots
. The additional arguments to primary functions can be provided through ...
. These changes will not necessarily break the existing code but will lead to some minor graphical changes (e.g., if you were providing labels
argument explicitly, it will be ignored).
All functions lose the return
argument, which was supposed to be alternative to enter output
. But this was just leading to more confusion on the user’s part. The biggest user-visible impact this is going to have is that ggcorrmat
will no longer be backward-compatible. The older scripts will still work but if the return
argument was anything except "plot"
, it will just be ignored.
ggcorrmat
no longer has corr.method
argument. To be consistent with rest of the functions in this package, the type of statistics should be specified using type
argument. Additional, it gains a new argument ggcorrplot.args
, which can be used to pass additional arguments to the underlying plotting function (ggcorrplot::ggcorrplot
).
Both gghistostats
and ggdotplotstats
now use the following arguments to modify geom
s corresponding to the lines and labels: test.value.line.args
, test.value.label.args
, centrality.line.args
, centrality.label.args
. This helps avoid specifying millions of arguments.
Removes the vestigial ggplot_converter
function.
ggpiestats
and ggbarstats
remove the following vestigial arguments: facet.wrap.name
, bias.correct
, bar.outline.color
. The bar.proptest
and facet.proptest
arguments were difficult to remember and confusing and are replaced by a common proportion.test
argument. Additionally, the following arguments have all been removed and replaced by label
argument: slice.label
, bar.label
, data.label
. These plethora of options was a headache to remember.
gghistostats
loses the following arguments: fill.gradient
, low.color
, high.color
. It made no sense to add a color gradient to this plot when the Y-axis already displayed the information about what the bar represented.
ggscatterstats
loses the following arguments: palette
and package
. Since this function requires only two colors, it didn’t make much sense to use color palettes to specify this. They can be instead specified using xfill
and yfill
. You can always use paletteer::paletteer_d
to get a vector of color values and then provide values of your choosing to xfill
and yfill
.
Removes sorting options in ggbetweenstats
and ggwithinstats
functions. This is something the users can easily do before entering the data in these functions.
MAJOR CHANGES
ggcorrmat
was never supposed to work with Kendall’s correlation coefficient but it accidentally did. This is no longer the case.
ggstatsplot
now has a logo, thanks to Sarah! :)
The default theme_ggstatsplot
changes slightly. The biggest change is that the title and the subtitle for plots are now aligned to the left of the plot. This change also forced the legend for ggpiestats
to be displayed on the right side of the plot rather than at the bottom.
MINOR CHANGES
More models supported in ggcoefstats
: BBreg
, bcplm
, bife
, cglm
, crch
, DirichReg
, LORgee
, zcpglm
, zeroinfl
.
Following functions are now re-exported from ipmisc
: bartlett_message
, normality_message
. A few other internal data wrangling functions now reside in ipmisc
.
BREAKING CHANGES
To have a more manageable length of function arguments, additional aesthetic specifications for any given geom can be provided via a dedicated *.args
argument. For example, all aesthetic arguments for geom_vline
can be provided via vline.args
, for geom_errorbarh
via errorbar.args
, etc.
ggstatsplot
continues with its conscious uncoupling that started in 0.1.0
release: The following functions have now been moved to statsExpressions
package: subtitle_meta_parametric
and bf_meta_message
and follow a more logical nomenclature. For the same reason, lm_effsize_ci
function is also no longer exported and lives in the groupedstats
package.
MAJOR CHANGES
The summary caption no longer displays log-likelihood value because it tends to be not available for a number of regression model objects and so the caption was unnecessarily being skipped.
Supports robust and Bayes Factors for random-effects meta-analysis.
MINOR CHANGES
New dataset included: bugs_wide
More models supported in ggcoefstats
: cgam
, cgamm
, coxme
, cpglm
, cpglmm
, complmrob
, feis
, flexsurvreg
, glmx
, hurdle
, iv_robust
, mixor
, rqss
, truncreg
, vgam
.
Removed vestigial arguments from ggcorrmat
(e.g., exact
, continuity
, etc.) and ggpiestats
(bf.prior
, simulate.p.value
, B
, etc.).
BUG FIXES
ggbetweenstats
and ggwithinstats
no longer produce error with variables with pattern mean
(#336).MAJOR CHANGES
pairwise_p
has been reintroduced as a number of users found it useful to call the function from ggstatsplot
itself rather than using pairwiseComparisons
package.MINOR CHANGES
ggbetweenstats
and ggwithinstats
use [
instead of (
to display confidence intervals. Additionally, μ denoted sample mean, but was confused with population mean by some users. So these functions instead display μ̂.
More models supported in ggcoefstats
: bmlm
, coeftest
Adapts to the new syntax provided in paletteer
package.
MAJOR CHANGES
ggrepel
in ggcoefstats
function have been removed. The users can instead provide all such arguments in a list to stats.labels.args
argument.BUG FIXES
ggbetweenstats
and ggwithinstats
no longer produce incorrect label if the dataframe already contains a variable named n
(#317) or variables with pattern mean
(#322).
ggbetweenstats
and ggwithinstats
mean labels respect k
argument (#331).
MINOR
ggcoefstats
now uses parameters::p_value
instead of sjstats::p_value
, as requested by the maintainer of that package. This might lead to differences in p-values for lmer
models.
More models supported in ggcoefstats
: blavaan
, bracl
, brglm2
, glmc
, lavaan
, nlreg
, slm
, wbgee
.
ggcoefstats
gains only.significant
argument to only display display stats labels for significant effects. This can be helpful when a large number of regression coefficients are to be displayed in a single plot.
MINOR
magrittr
, ellipsis
, purrrlyr
.MAJOR
ggbetweenstats
and ggwithinstats
pairwise comparisons were adjusted or not for multiple comparisons.ANNOUNCEMENTS
ggstatsplot
is undergoing conscious uncoupling whereby all the statistical processing functions that make stats subtitles are being moved to a new package called statsExpressions
. This new package will act as a backend that handles all things statistical processing. This will not affect the end users of ggstatsplot
unless you have been using the helper functions.
Additionally, multiple pairwise comparison tests are being moved to an independent package called pairwiseComparisons
.
This uncoupling is designed to achieve two things:
Make the code base of more manageable size in ggstatsplot
, which will make package development a bit easier.
Make the workflow more customizable since now you can prepare your own plots and then use statsExpressions
to display results in the plot rather than relying on ggstatsplot
default plots which are heavily opinionated and not appealing to everyone.
BREAKING CHANGES
All helper functions subtitle_*
and bf_*
have been moved to the new statsExpressions
package.
To be consistent with all the other subtitle_
and bf_
functions, subtitle_contingency_tab
and bf_contingency_tab
now use the arguments x
and y
instead of main
and condition
.
MAJOR CHANGES
Major refactoring to reduce the codesize and to rely fully on rlang
.
There was confusion about what did the red point in ggbetweenstats
and ggbetweenstats
plots represents. Now the label also contains μ to highlight that what is being displayed is a mean value.
To be consistent with the rest of the functions, ggpiestats
and ggbarstats
now uses the following aliases for arguments: x
for main
and y
for condition
. This change is backward-compatible and should not pose any problems for scripts that used main
and condition
arguments in these functions.
Most subtitle expressions now report details about the design. In case of between-subjects design, this will be n_obs, while in case of repeated measures design, this will be n_pairs.
pairwise.annotation
now defaults to "p.value"
rather than "asterisk"
for ggbetweenstats
and ggwithinstats
(and their grouped_
variants) functions. This was done because the asterisk conventions are not consistent across various scientific disciplines.
MINOR CHANGES
New dataset included: bugs_long
, for repeated measures designs with NA
s present in the data.
ggstatsplot
now uses rcompanion
to compute Spearman’s rho and Kendall’s W. Therefore, DescTools
is removed from dependencies.
ggcoefstats
supports following objects: bglmerMod
, blmerMod
, lme
, mclogit
, mmclogit
, tobit
, wblm
.
ggcoefstats
now respects conf.int
. It internally always defaulted to conf.int = TRUE
in broom::tidy
irrespective of what was specified by the user.
It was painfully confusing for a lot of users what exactly the asterisks in each facet of ggpiestats
signified. So instead now ggpiestats
displays more detailed results from a goodness of fit (gof) test. No such change is made for ggbarstats
because there is no space to include more details above the bar.
Removed conf.method
and conf.type
arguments for ggcoefstats
. Also, p.kr
argument removed because ggcoefstats
will begin to rely on parameters
instead of sjstats
package to compute p-values for some regression models.
BUG FIXES
ggwithinstats
caption, displayed by default, was incorrect. This has been fixed. This stemmed from a line of code which should have been paired = TRUE
, but was instead paired = FALSE
.MAJOR CHANGES
MINOR CHANGES
ggcoefstats
defaults to bf.message = TRUE
to be consistent with the rest of the functions in the package.
ggcoefstats
supports the following class of objects: epi.2by2
, negbin
, emmGrid
, lmrob
, glmrob
, glmmPQL
, data.table
.
bf_ttest
is introduced as a general function. The previously exported bf_one_sample_ttest
and bf_two_sample_ttest
become its aliases.
bf_meta_message
syntax changes to adapt to updates made to metaBMA
package (thanks to #259).
BREAKING CHANGES
The vestigial arguments axis.text.x.margin.t
, axis.text.x.margin.r
, axis.text.x.margin.b
, axis.text.x.margin.l
for ggcorrmat
have been removed. The margins can be adjusted using ggplot2::margin()
.
gghistostats
no longer allows data
argument to be NULL
. This is to make this function’s syntax consistent with rest of the functions in this package (none of which allow data
to be NULL
). This also removes confusion that arose for some users when data
couldn’t be NULL
for its grouped_
cousin (grouped_gghistostats
).
outlier_df
function is no longer exported since it was always meant to be an internal function and was accidently exported during initial release and was retained for a while for backward compatibility.
BREAKING CHANGES
Instead of having two separate functions that dealt with repeated measures (subtitle_friedman_nonparametric
) and between-subjects (subtitle_kw_nonparametric
), a single function subtitle_anova_nonparametric
handles both of these designs with the paired
argument determining which test is run.
All functions that supported Bayes Factor analysis (type = "bf"
) will only return BF value and the scale used. Previously, this was a mix of parametric statistics and BF, which was confusing and often times misleading since these two types of analyses relied on different tests.
The default for bf.message
has been changed from FALSE
to TRUE
. This is to make the Bayes Factor analysis more visible to the user.
MAJOR CHANGES
ggscatterstats
returns only plot (without any statistical details) when the specified model is not linear (i.e., either when method
argument is not "lm"
or when formula
is not y ~ x
).NEW FEATURES
New functions ggwithinstats
(and its grouped_
variant) are introduced as a counterpart to ggbetweenstats
to handle repeated measures designs.
For repeated measures ANOVA, subtitle_anova_nonparametric
now returns confidence intervals for Kendall’s W.
All functions get return
argument that can be used to return either "plot"
, "subtitle"
, or "caption"
. This makes it unnecessary to remember which subtitle function is to be used where. As a result, in the next release, all subtitle making functions will not be exported and are encouraged not be used either by other developers or by users.
Both subtitle_anova_robust
and subtitle_anova_parametric
gain a new argument paired
to support repeated measures designs.
ggcoefstats
can support following new model objects: drc
, mlm
.
ggcoefstats
gains bf.message
argument to display a caption containing results from Bayesian random-effects meta-analysis. It therefore gains a new dependency: metaBMA
.
ggpiestats
and ggcatstats
will now display Cramer’s V as effect size for one-sample proportion tests.
All functions gain stat.title
argument (NULL
by default) that can be used to prefix the subtitle with a string of interest. This is possibly useful for specifying the details of the statistical test.
MINOR CHANGES
pairwise_p()
function no longer outputs conf.low
and conf.high
columns when parametric post hoc tests are run. This is because these values were accurate only when no p-value adjustment was carried out.
Instead of using the internal function cor_test_ci
, ggscatterstats
instead used SpearmanRho
function from DescTools
package. This was done to reduce number of custom internal functions used to compute CIs for various effect sizes. ggstatsplot
therefore gains DescTools
as a dependency.
The sampling.plan
argument default for ggbarstats
function has been changed from "indepMulti"
to "jointMulti"
to be consistent with its sister function ggpiestats
.
NEW FEATURES
ggcoefstats
can support following new model objects: rjags
.
New VR_dilemma
dataset for toying around with within-subjects design.
subtitle_t_onesample
supports both Cohen’s d and Hedge’s g as effect sizes and also produces their confidence intervals. Additionally, non-central variants of these effect sizes are also supported. Thus, gghistostats
and its grouped_
variant gets two new arguments: effsize.type
, effsize.noncentral
.
ggpiestats
used to display odds ratio as effect size for paired designs (McNemar test). But this was only working when the analysis was a 2 x 2 contingency table. It now instead displays Cohen’s G as effect size, which generalizes to any kind of design.
MINOR CHANGES
The internal function outlier_df
to add a column specifying outlier status of any given data point is now exported.
ggstatsplot
previously relied on an internal function chisq_v_ci
to compute confidence intervals for Cramer’s V using bootstrapping but it was pretty slow. It now instead relies on rcompanion
package to compute confidence intervals for V. ggstatsplot
, therefore, gains a new dependency.
subtitle_mann_nonparametric
and subtitle_t_onesample
now computes effect size r and its confidence intervals as $$Z/\sqrt{N}$$ (with the help of rcompanion
package), instead of using Spearman correlation.
BREAKING CHANGES
subtitle_t_onesample
no longer has data
as the optional argument. This was done to be consistent with other subtitle helper functions.NEW FEATURES
New function ggbarstats
(and its grouped_
variant) introduced for making bar charts (thanks to #78).
ggcoefstats
also displays a caption with model summary when meta-analysis is required.
gghistostats
and its grouped_
variant has a new argument normal.curve
to superpose a normal distribution curve on top of the histogram (#138).
ggcoefstats
can support following new regression model objects: brmsfit
, gam
, Gam
, gamlss
, mcmc
, mjoint
, stanreg
.
New function to convert plots which are not of gg
/ggplot
class to ggplot
class objects.
Instead of using effsize
to compute Cohen’s d and Hedge’s g, ggstatsplot
now relies on a new (#159) internal function effect_t_parametric
to compute them. This removes effsize
from dependencies.
To be consistent with other functions in this package, both ggbarstats
and ggpiestats
gain results.subtitle
which can be set to FALSE
if statistical analysis is not required, in which case subtitle
argument can be used to provide alternative subtitle.
MAJOR CHANGES
ggbetweenstats
now defaults to using noncentral-t distribution for computing Cohen’s d and Hedge’s g. To get variants with central-t distribution, use effsize.noncentral = FALSE
.MINOR CHANGES
All grouped_
functions had argument title.prefix
that defaulted to "Group"
. It now instead defaults to NULL
, in which case the prefix will variable name for grouping.var
argument.
To accommodate non-parametric tests, subtitle_template
function can now work with parameter = NULL
.
For ggbetweenstats
, details contained in the subtitle for non-parametric test are modified. It now uses Spearman’s rho-based effect size estimates. This removes coin
from dependencies.
ggbetweenstats
and its grouped_
variant gain a new argument axes.range.restrict
(which defaults to FALSE
). This restricts y
-axes limits to minimum and maximum of y
variable. This is what these functions were doing by default in the past versions, which created issues for additional ggplot components using the ggplot.component
argument.
All bayes factor related subtitle and captions replace prior.width
with r_{Cauchy}
.
ggcoefstats
passes dots (...
) to augment
method from broom
.
BUG FIXES
The helper function bf_extractor
no longer provides option to extract information about posterior distribution because these details were incorrect. The posterior = TRUE
details were not used anywhere in the package so nothing about the results changes.
ggcorrmat
didn’t output pair names when output == "ci"
was used. This is fixed.
NEW FEATURES
ggcoefstats
gains meta.analytic.effect
that can be used to carry out meta-analysis on regression estimates. This especially useful when a dataframe with regression estimates and standard error is available from prior analyses. The subtitle
is prepared with the new function subtitle_meta_ggcoefstats
which is also exported.
ggbetweenstats
, ggscatterstats
, gghistostats
, and ggdotplotstats
(and their grouped_
variants) all gain a new ggplot.component
argument. This argument will primarily be helpful to change the individual plots in a grouped_
plot.
ggcoefstats
can support following new regression model objects: polr
, survreg
, cch
, Arima
, biglm
, glmmTMB
, coxph
, ridgelm
, aareg
, plm
, nlrq
, ivreg
, ergm
, btergm
, garch
, gmm
, lmodel2
, svyolr
, confusionMatrix
, multinom
, nlmerMod
, svyglm
, MCMCglmm
, lm.beta
, speedlm
, fitdistr
, mle2
, orcutt
, glmmadmb
.
BUG FIXES
ggcoefstats
didn’t work when statistic
argument was set to NULL
. This was not expected behavior. This has been fixed. Now, if statistic
is not specified, only the dot-and-whiskers will be shown without any labels.
subtitle_t_parametric
was producing incorrect sample size information when paired = TRUE
and the data contained NA
s. This has been fixed.
MAJOR CHANGES
ggscatterstats
and its grouped_
variant accept both character and bare exressions as input to arguments label.var
and labe.expression
(#110).
To be consistent with rest of the functions in the package, both Pearson’s r, Spearman’s rho, and robust percentage bend correlations also display information about statistic associated with these tests.
ggscatterstats
, by default, showed jittered data points (because it relied on position_jitter
defaults). This could be visually inaccurate and, therefore, ggscatterstats
now displays points without any jitter. The user can introduce jitter if they wish to using point.width.jitter
and point.height.jitter
arguments. For similar reasons, for ggbetweenstats
and its grouped_
variant, point.jitter.height
default has been changed from 0.1
to 0
(no vertical jitter, i.e.).
MINOR CHANGES
Confidence interval for Kendall’s W is now computed using stats::kruskal.test
. As a result, PMCMRplus
removed from dependencies.
ggcoefstats
gains a caption
argument. If caption.summary
is set to TRUE
, the specified caption will be added on top of the caption.summary
.
BUG FIXES
ggcoefstats
was showing wrong confidence intervals for merMod
class objects due to a bug in the broom.mixed
package (https://github.com/bbolker/broom.mixed/issues/30#issuecomment-428385005). This was fixed in broom.mixed
and so ggcoefstats
should no longer have any issues.
specify_decimal_p
has been modified because it produced incorrect results when k < 3
and p.value = TRUE
(e.g., 0.002
was printed as < 0.001
).
ggpiestats
produced incorrect results if some levels of the factor had been filtered out prior to using this function. It now drops unused levels and produces correct results.
gghistostats
wasn’t filtering out NA
s properly. This has been fixed.
MAJOR CHANGES
New function ggdotplotstats
for creating a dot plot/chart for labelled numeric data.
All primary functions gain conf.level
argument to control confidence level for effect size measures.
As per APA guidelines, all results show results with two decimal places. That is, the default value for k
argument for all functions has been changed from 3
to 2
.
All helper functions for the ggbetweenstats
subtitles have been renamed to remove _ggbetween_
from their names as this was becoming confusing for the user. Some of these functions work both with the between- and within-subjects designs, so having _ggbetween_
in their names made users suspect if they could use these functions for within-subjects designs.
ggstatsplot
now depends on R 3.5.0
. This is because some of its dependencies require 3.5.0 to work (e.g., broom.mixed
).
All theme_
functions are now exported (theme_pie()
, theme_corrmat()
).
ggbetweenstats
now supports multiple pairwise comparison tests (parametric, nonparametric, and robust variants). It gains a new dependency ggsignif
.
ggbetweenstats
now supports eta-squared and omega-squared effect sizes for anova models. This function gains a new argument partial
.
Following functions are now reexported from the groupedstats
package to avoid repeating the same code in two packages: specify_decimal_p
, signif_column
, lm_effsize_ci
, and set_cwd
. Therefore, groupedstats
is now added as a dependency.
gghistostats
can now show both counts and proportions information on the same plot when bar.measure
argument is set to "mix"
.
ggcoefstats
works with tidy dataframes.
The helper function untable
has been deprecated in light of tidyr::uncount
, which does exactly what untable
was doing. The author wasn’t aware of this function when untable
was written.
All vignettes have been removed from CRAN
to reduce the size of the package. They are now available on the package website: https://indrajeetpatil.github.io/ggstatsplot/articles/.
subtitle_t_robust
function can now handle dependent samples and gains paired
argument.
A number of tidyverse operators are now reexported by ggstatsplot
: %>%
, %<>%
, %$%
.
MINOR CHANGES
ggscatterstats
, ggpiestats
, and their grouped_
variant support bayes factor tests and gain new arguments relevant to this test.
Effect size and their confidence intervals now available for Kruskal-Wallis test.
Minor stylistic changes to how symbols for partial-eta-/omega-squared were being displayed in subtitles.
ggbetweenstats
supports bayes factor tests for anova designs.
ggpiestats
(and its grouped_
version) gain slice.label
argument that decides what information needs to be displayed as a label on the slices of the pie chart: "percentage"
(which has been the default thus far), "counts"
, or "both"
.
ggcorrmat
can work with cor.vars = NULL
. In such case, all numeric variables from the provided dataframe will be used for computing the correlation matrix.
Given the constant changes to the default behavior of functions, the lifecycle badge has been changed from stable
to maturing
.
When the number of colors needed by a function exceeds the number of colors contained in a given palette, informative message is displayed to the user (with the new internal function palette_message()
).
Several users had requested an easier way to turn off subtitles with results from tests (which was already implemented in ggscatterstats
and gghistostats
with the argument results.subtitle
), so ggbetweenstats
also gains two new arguments to do this: results.subtitle
and subtitle
.
New dataset added: iris_long
.
More tests added and the code coverage has now jumped to over 75%.
To avoid code repetition, there is a now a function that produces a generic message any time confidence intervals for effect size estimate are computed using bootstrapping.
MAJOR CHANGES
The package now exports all functions used to create text expressions with results. This makes it easy for people to use these results in their own plots at any location they want (and not just in subtitle
, the current default for ggstatsplot
).
ggcorrmat
gains p.adjust.method
argument which allows p-values for correlations to be corrected for multiple comparisons.
ggscatterstats
gains label.var
and label.expression
arguments to attach labels to points.
gghistostats
now defaults to not showing (redundant) color gradient (fill.gradient = FALSE
) and shows both "count"
and "proportion"
data. It also gains a new argument bar.fill
that can be used to fill bars with a uniform color.
ggbetweenstats
, ggcoefstats
, ggcorrmat
, ggscatterstats
, and ggpiestats
now support all palettes contained in the paletteer
package. This helps avoid situations where people had large number of groups (> 12) and there were not enough colors in any of the RColorBrewer
palettes.
ggbetweenstats
gains bf.message
argument to display bayes factors in favor of the null (currently works only for parametric t-test).
gghistostats
function no longer has line.labeller.y
argument; this position is automatically determined now.
BREAKING CHANGES
legend.title.margin
function has been deprecated since ggplot2 3.0.0
has improved on the margin issues from previous versions. All functions that wrapped around this function now lose the relevant arguments (legend.title.margin
, t.margin
, b.margin
).
The argument ggstatsplot.theme
has been changed to ggstatsplot.layer
for ggcorrmat
function to be consistent across functions.
For consistency, conf.level
and conf.type
arguments for ggbetweenstats
have been deprecated. No other function in the package allowed changing confidence interval or their type for effect size estimation. These arguments were relevant only for robust
tests anyway.
ggocorrmat
argument type
has been changed to matrix.type
because for all other functions type
argument specifies the type of the test, while for this function it specified the display of the visualization matrix. This will make the syntax more consistent across functions.
ggscatterstats
gains new arguments to specify aesthetics for geom point (point.color
, point.size
, point.alpha
). To be consistent with this naming schema, the width.jitter
and height.jitter
arguments have been renamed to point.width.jitter
and point.height.jitter
, resp.
MINOR CHANGES
gghistostats
: To be compatible with JASP
, natural logarithm of Bayes Factors is displayed, and not base 10 logarithm.
ggscatterstats
gains method
and formula
arguments to modify smoothing functions.
ggcorrmat
can now show robust
correlation coefficients in the matrix plot.
For gghistostats
, binwidth
value, if not specified, is computed with (max-min)/sqrt(n)
. This is basically to get rid of the warnings ggplot2 produces. Thanks to Chuck Powell’s PR (#43).
ggcoefstats
gains a new argument partial
and can display eta-squared and omega-squared effect sizes for anovas, in addition to the prior partial variants of these effect sizes.
ggpiestats
gains perc.k
argument to show desired number of decimal places in percentage labels.
BUG FIXES
grouped_ggpiestats
wasn’t working when only main
variable was provided with counts
data. Fixed that.MAJOR CHANGES
For the sake of consistency, theme_mprl
is now called theme_ggstatsplot
. The theme_mprl
function will still be around and will not be deprecated, so feel free to use either or both of them since they are identical.
ggcoefstats
no longer has arguments effects
and ran_params
because only fixed effects are shown for mixed-effects models.
ggpiestats
can now handle within-subjects designs (McNemar test results will be displayed).
BUG FIXES
ggbetweenstats
was producing wrong axes labels when sample.size.label
was set to TRUE
and user had reordered factor levels before using this function. The new version fixes this.
ggcoefstats
wasn’t producing partial omega-squared for aovlist
objects. Fixed that with new version of sjstats
.
MINOR CHANGES
Removed the trailing comma from the robust correlation analyses.
gghistostats
has a new argument to remove color fill gradient.
ggbetweenstats
takes new argument mean.ci
to show confidence intervals for the mean values.
For lmer
models, p-values are now computed using sjstats::p_value
. This removes lmerTest
package from dependencies.
sjstats
no longer suggests apaTables
package to compute confidence intervals for partial eta- and omega-squared. Therefore, apaTables
and MBESS
are removed from dependencies.
ggscatterstats
supports densigram
with the development version of ggExtra
. It additionally gains few extra arguments to change aesthetics of marginals (alpha, size, etc.).
MAJOR CHANGES
New function: ggcoefstats
for displaying model coefficients.
All functions now have ggtheme
argument that can be used to change the default theme, which has now been changed from theme_grey()
to theme_bw()
.
The robust correlation is no longer MASS::rlm
, but percentage bend correlation, as implemented in WRS2::pbcor
. This was done to be consistent across different functions. ggcorrmat
also uses percentage bend correlation as the robust correlation measure. This also means that ggstatsplot
no longer imports MASS
and sfsmisc
.
The data
argument is no longer NULL
for all functions, except gghistostats
. In other words, the user must provide a dataframe from which variables or formulas should be selected.
All subtitles containing results now also show sample size information (n). To adjust for the inflated length of the subtitle, the default subtitle text size has been changed from 12
to 11
.
MINOR CHANGES
Switched back to Shapiro-Wilk test of normality to remove nortest
from imports.
ggbetweenstats
and ggpiestats
now display sample sizes for each level of the groping factor by default. This behavior can be turned off by setting sample.size.label
to FALSE
.
Three new datasets added: Titanic_full
, movies_wide
, movies_long
.
Added confidence interval for effect size for robust ANOVA.
The 95% CI for Cramer’V computed using boot::boot
. Therefore, the package no longer imports DescTools
.
To be consistent across correlations covered, all correlations now show estimates for correlation coefficients, confidence intervals for the estimate, and p-values. Therefore, t-values and regression coefficients are no longer displayed for Pearson’s r.
The legend.title.margin
arguments for gghistostats
and ggcorrmat
now default to FALSE
, since ggplot2 3.0.0
has better legend title margins.
ggpiestats
now sorts the summary dataframes not by percentages but by the levels of main
variable. This was done to have the same legends across different levels of a grouping variable in grouped_ggpiestats
.
To remove cluttered display of results in the subtitle, ggpiestats
no longer shows titles for the tests run (these were “Proportion test” and “Chi-Square test”). From the pie charts, it should be obvious to the user or reader what test was run.
gghistostats
also allows running robust version of one-sample test now (One-sample percentile bootstrap).
NEW FEATURES
The ggbetweenstats
function can now show notched box plots. Two new arguments notch
and notchwidth
control its behavior. The defaults are still standard box plots.
Removed warnings that were appearing when outlier.label
argument was of character
type.
The default color palette used for all plots is colorblind friendly.
gghistostats
supports proportion
and density
as a value measure for bar heights to show proportions and density. New argument bar.measure
controls this behavior.
grouped_
variants of functions ggcorrmat
, ggscatterstats
, ggbetweenstats
, and ggpiestats
introduced to create multiple plots for different levels of a grouping variable.
MAJOR CHANGES
To be internally consistent, all functions in ggstatsplot
use the spelling color
, rather than colour
in some functions, while color
in others.
Removed the redundant argument binwidth.adjust
from gghistostats
function. This argument was relevant for the first avatar of this function, but is no longer playing any role.
To be internally consistent, the argument lab_col
and lab_size
in ggcorrmat
have been changed to lab.col
and lab.size
, respectively.
MINOR CHANGES
Added a new argument to ggstatsplot.theme
function to control if ggstatsplot::theme_mprl
is to be overlaid on top of the selected ggtheme
(ggplot2 theme, i.e.).
Two new arguments added to gghistostats
to allow user to change colorbar gradient. Defaults are colorblind friendly.
Both gghistostats
and ggcorrmat
have a new argument legend.title.margin
to control margin adjustment between the title and the colorbar.
The vertical lines denoting test values and centrality parameters can be tagged with text labels with a new argument line.labeller
in gghistostats
function.
BUG FIXES
centrality.para
argument for ggscatterstats
was not working properly. Choosing "median"
didn’t show median, but the mean. This is fixed now.NEW FEATURES
Bayesian test added to gghistostats
and two new arguments to also display a vertical line for test.value
argument.
Vignette added for gghistostats
.
Added new function grouped_gghistostats
to facilitate applying gghistostats
for multiple levels of a grouping factor.
ggbetweenstats
has a new argument outlier.coef
to adjust threshold used to detect outliers. Removed bug from the same function when outlier.label
argument is of factor/character type.
MAJOR CHANGES
Functions signif_column
and grouped_proptest
are now deprecated. They were exported in the first release by mistake.
Function gghistostats
no longer displays both density and count since the density information was redundant. The density.plot
argument has also been deprecated.
ggscatterstats
argument intercept
has now been changed to centrality.para
. This was due to possible confusion about interpretation of these lines; they show central tendency measures and not intercept for the linear model. Thus the change.
The default for effsize.type = "biased"
effect size for ggbetweenstats
in case of ANOVA is partial omega-squared, and not omega-squared. Additionally, both partial eta- and omega-squared are not computed using bootstrapping with (default) 100 bootstrap samples.
MINOR CHANGES
More examples added to the README
document.
95% confidence intervals for Spearman’s rho are now computed using broom
package. RVAideMemoire
package is thus removed from dependencies.
95% confidence intervals for partial eta- and omega-squared for ggbetweenstats
function are now computed using sjstats
package, which allows bootstrapping. apaTables
and userfriendlyscience
packages are thus removed from dependencies.