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Updated readme and about page
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‎README.md‎

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@@ -14,37 +14,95 @@ citation](https://zenodo.org/badge/DOI/10.1038/s41592-019-0470-3.svg)](https://r
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## Recent Version Update
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We are proud to announce **DABEST Version Ondeh (v2024.03.29)**. This
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new version of the DABEST Python library provides several new features
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and includes performance improvements.
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1. **New Paired Proportion Plot**: This feature builds upon the
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existing proportional analysis capabilities by introducing advanced
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aesthetics and clearer visualization of changes in proportions
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between different groups, inspired by the informative nature of
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Sankey Diagrams. It’s particularly useful for studies that require
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detailed examination of how proportions shift in paired
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observations.
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2. **Customizable Swarm Plot**: Enhancements allow for tailored swarm
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plot aesthetics, notably the adjustment of swarm sides to produce
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asymmetric swarm plots. This customization enhances data
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representation, making visual distinctions more pronounced and
33-
interpretations clearer.
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3. **Standardized Delta-delta Effect Size**: We added a new metric akin
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to a Hedges’ g for delta-delta effect size, which allows comparisons
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between delta-delta effects generated from metrics with different
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units.
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4. **Miscellaneous Improvements**: This version also encompasses a
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broad range of miscellaneous enhancements, including bug fixes,
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Bootstrapping speed improvements, new templates for raising issues,
43-
and updated unit tests. These improvements are designed to
44-
streamline the user experience, increase the software’s stability,
45-
and expand its versatility. By addressing user feedback and
46-
identified issues, DABEST continues to refine its functionality and
47-
reliability.
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We are proud to announce **DABEST Version TBC (v2025.03.14)** This new
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version of the DABEST Python library provides several new features and
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includes performance improvements. It’s a big one!
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1. **Python 3.13 Support**: DABEST now supports Python 3.10-3.13.
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2. **Horizontal Plots**: This new feature allows users to create
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horizontal plots instead of the regular vertical plots, providing a
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more compact visualization of data.
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3. **Forest Plots**: This new feature allows users to create forest
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plots! Forest plots provide a simple and intuitive way to visualize
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many delta-delta (or Deltas’ g) or mini-meta effect sizes at once
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from multiple different dabest objects without presenting the raw
31+
data.
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4. **Aesthetic Updates**: We have made several aesthetic improvements
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to the plots, including:
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36+
- **Swarm, Contrast, and Summary bars**: We have added bars to
37+
better highlight the various groups and their differences. These
38+
bars can be customized to suit the user’s needs. The swarm and
39+
contrast bars are provided by default, while the summary bars can
40+
be added by the user.
41+
42+
- **Delta-Delta Plots**: We have modified the delta-delta plot
43+
format to be more compact and easier to read. The new format
44+
brings the delta-delta (or Deltas’ g) effect size closer to the
45+
regular effect sizes. In addition, a gap has been added to the
46+
zeroline to separate the delta-delta and regular effect sizes.
47+
48+
- **Delta-delta Effect Sizes for Proportion Plots**: Delta-delta
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effect sizes for proportion plots are now available.
50+
51+
- **Mini-Meta Plots**: We have modified the mini-meta plot format to
52+
be more compact and easier to read. The new format brings the
53+
mini-meta effect size closer to the regular effect sizes
54+
55+
- **Proportion Plots Sample Sizes**: We have updated the proportion
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plots to show sample sizes for each group.
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- **Effect Size Lines for Paired Plots**: Effect size lines for
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paired plots are now available.
60+
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- **Baseline Error Curves**: Plots now include a baseline error dot
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and curve to show the error of the baseline/control group. By
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default, the dot is shown, while the curve can be added by the
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user (via the `show_baseline_ec` parameter).
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- **Delta Text**: There is now an option to display delta text on
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the contrast axes. It displays the effect size of the contrast
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group relative to the reference group. This can be toggled on or
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off via the `delta_text` parameter. It is on by default.
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- **Empty Circle Color Palette**: A new swarmplot color palette
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modification is available for unpaired plots via the
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`empty_circle` parameter in the `plot()` method. This option
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modifies the two-group swarmplots to have empty circles for the
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control group and filled circles for the experimental group.
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5. **Miscellaneous Improvements & Adjustments**
78+
79+
- **Numba for Speed Improvements**: We have included Numba to speed
80+
up the various calculations in DABEST. This should make the
81+
calculations faster and more efficient. Importing DABEST may take
82+
a little longer than before, and a progress bar will appear during
83+
the import process to show the calculations being performed. Once
84+
imported, loading and plotting data should now be faster.
85+
86+
- **Terminology Updates**: We have made several updates to the
87+
documentation and terminology to improve clarity and consistency.
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For example:
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- The method to utilise the Deltas’ g effect size is now via the
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`.hedges_g.plot()` method now rather than creating a whole new
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`Delta_g` object as before. The functionality remains the same,
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it plots hedges_g effect sizes and then the Deltas’ g effect
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size alongside these (if a delta-delta experiment was loaded
95+
correctly).
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- **Updated Tutorial Pages**: We have updated the tutorial pages to
98+
reflect the new features and changes. The tutorial pages are now
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more comprehensive and hopefully more intuitive!.
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- **Results Dataframe for Delta-delta and Mini-meta Plots**: A
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results dataframe can now be extracted for both the delta-delta
103+
and mini-meta effect size data (similar to the results dataframe
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for the regular effect sizes). These can be found via the
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`.results` attribute of the `.delta_delta` or `.mini_meta` object.
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## Contents
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‎nbs/02-about.ipynb‎

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"\n",
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"DABEST is written in Python by [Joses W. Ho](https://twitter.com/jacuzzijo), with design and input from [Adam Claridge-Chang](https://twitter.com/adamcchang) and other [lab members](https://www.claridgechang.net/people.html).\n",
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"\n",
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"Features in v2025.03.14 were added by [Jonathan Anns](https://github.com/JAnns98), [Zinan Lu](https://github.com/Jacobluke-), [Kah Seng Lian](https://github.com/sunroofgod), and [Lucas Wang Zhuoyu](https://github.com/Lucas1213WZY).\n",
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"\n",
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"Features in v2024.03.29 were added by [Zinan Lu](https://github.com/Jacobluke-), [Kah Seng Lian](https://github.com/sunroofgod), [Ana Rosa Castillo](https://github.com/cyberosa).\n",
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"\n",
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"Features in v2023.02.14 were added by [Yixuan Li](https://github.com/LI-Yixuan), [Zinan Lu](https://github.com/Jacobluke-) and [Rou Zhang](https://github.com/ZHANGROU-99).\n",
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"POSSIBILITY OF SUCH DAMAGE.\n",
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"</div>\n"
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]
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},
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{
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"cell_type": "markdown",
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"id": "e1dcfc63",
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"metadata": {},
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"source": []
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}
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],
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"metadata": {

‎nbs/read_me.ipynb‎

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"source": [
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"## Recent Version Update\n",
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"\n",
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"We are proud to announce **DABEST Version Ondeh (v2024.03.29)**. This new version of the DABEST Python library provides several new features and includes performance improvements.\n",
32+
"We are proud to announce **DABEST Version TBC (v2025.03.14)** This new version of the DABEST Python library provides several new features and includes performance improvements. It's a big one!\n",
3333
"\n",
34-
"1. **New Paired Proportion Plot**: This feature builds upon the existing proportional analysis capabilities by introducing advanced aesthetics and clearer visualization of changes in proportions between different groups, inspired by the informative nature of Sankey Diagrams. It's particularly useful for studies that require detailed examination of how proportions shift in paired observations.\n",
34+
"1. **Python 3.13 Support**: DABEST now supports Python 3.10-3.13.\n",
3535
"\n",
36-
"2. **Customizable Swarm Plot**: Enhancements allow for tailored swarm plot aesthetics, notably the adjustment of swarm sides to produce asymmetric swarm plots. This customization enhances data representation, making visual distinctions more pronounced and interpretations clearer.\n",
36+
"1. **Horizontal Plots**: This new feature allows users to create horizontal plots instead of the regular vertical plots, providing a more compact visualization of data.\n",
3737
"\n",
38-
"3. **Standardized Delta-delta Effect Size**: We added a new metric akin to a Hedges’ g for delta-delta effect size, which allows comparisons between delta-delta effects generated from metrics with different units. \n",
38+
"2. **Forest Plots**: This new feature allows users to create forest plots! Forest plots provide a simple and intuitive way to visualize many delta-delta (or Deltas' g) or mini-meta effect sizes at once from multiple different dabest objects without presenting the raw data.\n",
3939
"\n",
40-
"4. **Miscellaneous Improvements**: This version also encompasses a broad range of miscellaneous enhancements, including bug fixes, Bootstrapping speed improvements, new templates for raising issues, and updated unit tests. These improvements are designed to streamline the user experience, increase the software's stability, and expand its versatility. By addressing user feedback and identified issues, DABEST continues to refine its functionality and reliability.\n"
40+
"3. **Aesthetic Updates**: We have made several aesthetic improvements to the plots, including:\n",
41+
" - **Swarm, Contrast, and Summary bars**: We have added bars to better highlight the various groups and their differences. These bars can be customized to suit the user's needs. The swarm and contrast bars are provided by default, while the summary bars can be added by the user.\n",
42+
" \n",
43+
" - **Delta-Delta Plots**: We have modified the delta-delta plot format to be more compact and easier to read. The new format brings the delta-delta (or Deltas' g) effect size closer to the regular effect sizes. In addition, a gap has been added to the zeroline to separate the delta-delta and regular effect sizes.\n",
44+
"\n",
45+
" - **Delta-delta Effect Sizes for Proportion Plots**: Delta-delta effect sizes for proportion plots are now available.\n",
46+
" \n",
47+
" - **Mini-Meta Plots**: We have modified the mini-meta plot format to be more compact and easier to read. The new format brings the mini-meta effect size closer to the regular effect sizes\n",
48+
"\n",
49+
" - **Proportion Plots Sample Sizes**: We have updated the proportion plots to show sample sizes for each group.\n",
50+
"\n",
51+
" - **Effect Size Lines for Paired Plots**: Effect size lines for paired plots are now available.\n",
52+
"\n",
53+
" - **Baseline Error Curves**: Plots now include a baseline error dot and curve to show the error of the baseline/control group. By default, the dot is shown, while the curve can be added by the user (via the `show_baseline_ec` parameter).\n",
54+
"\n",
55+
" - **Delta Text**: There is now an option to display delta text on the contrast axes. It displays the effect size of the contrast group relative to the reference group. This can be toggled on or off via the `delta_text` parameter. It is on by default.\n",
56+
"\n",
57+
" - **Empty Circle Color Palette**: A new swarmplot color palette modification is available for unpaired plots via the `empty_circle` parameter in the `plot()` method. This option modifies the two-group swarmplots to have empty circles for the control group and filled circles for the experimental group.\n",
58+
"\n",
59+
"\n",
60+
"\n",
61+
"4. **Miscellaneous Improvements & Adjustments**\n",
62+
" - **Numba for Speed Improvements**: We have included Numba to speed up the various calculations in DABEST. This should make the calculations faster and more efficient. Importing DABEST may take a little longer than before, and a progress bar will appear during the import process to show the calculations being performed. Once imported, loading and plotting data should now be faster.\n",
63+
" \n",
64+
" - **Terminology Updates**: We have made several updates to the documentation and terminology to improve clarity and consistency. For example:\n",
65+
" \n",
66+
" - The method to utilise the Deltas' g effect size is now via the `.hedges_g.plot()` method now rather than creating a whole new `Delta_g` object as before. The functionality remains the same, it plots hedges_g effect sizes and then the Deltas' g effect size alongside these (if a delta-delta experiment was loaded correctly).\n",
67+
"\n",
68+
" - **Updated Tutorial Pages**: We have updated the tutorial pages to reflect the new features and changes. The tutorial pages are now more comprehensive and hopefully more intuitive!.\n",
69+
"\n",
70+
" - **Results Dataframe for Delta-delta and Mini-meta Plots**: A results dataframe can now be extracted for both the delta-delta and mini-meta effect size data (similar to the results dataframe for the regular effect sizes). These can be found via the `.results` attribute of the `.delta_delta` or `.mini_meta` object.\n",
71+
"\n"
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]
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},
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{

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