Updated release date

Author: JAnns98

CHANGELOG.md

@@ -2,32 +2,30 @@
 
 <!-- do not remove -->
 
-## v2025.03.14
+## v2025.03.27
 
 ### New Features
 
-- **Horizontal Plots**: This new feature allows users to create horizontal plots instead of the regular vertical plots, providing a more compact visualization of data. This can be utilized by setting `horizontal=True` in the `plot()` method.
+- **Horizontal Plots**: Users can now create horizontal layout plots, providing compact data visualization. This can be achieved by setting `horizontal=True` in the `plot()` method.
 
-- **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.
+- **Forest Plots**: Forest plots provide a simple and intuitive way to visualize many delta-delta (or Deltas’ g), mini-meta, or regular delta effect sizes at once from multiple different dabest objects without presenting the raw data.
 
-- **Gridkey**: This new feature allows users to create a gridkey to represent the labels of the groups in the plot. This can be utilized with the `gridkey_rows` argument in the `plot()` method.
+- **Gridkey**: Users can now represent their experimental labels in a gridkey format. This can be accessed with the `gridkey` argument in the `plot()` method. 
 
 - **Aesthetic Updates**: We have made several aesthetic improvements to the plots, including:
-   - **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.
+   - **Raw, Contrast, and Summary bars**: We added bars highlighting the various groups' differences. These bars can be customized to suit the user’s needs. Raw and contrast bars are provided by default, summary bars can be added by the user.
 
-   - **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.
+   - **Delta-Delta and Mini-Meta Plots**: We have adjusted the spacing of delta-delta and mini-meta plots to reduce whitespace. The new format brings the added effect size closer to the regular effect sizes. In addition, delta-delta plots now have a gap in the zeroline to separate the delta-delta and regular effect sizes.
 
-   - **Delta-delta Effect Sizes for Proportion Plots**: Delta-delta effect sizes for proportion plots are now available.
-  
-   - **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.
+   - **Delta-delta Effect Sizes for Proportion Plots**: Delta-delta experimental plotting now supports binary data.
 
-   - **Proportion Plots Sample Sizes**: We have updated the proportion plots to show sample sizes for each group. These can be toggled on or off via the `prop_sample_counts` parameter.
+   - **Proportion Plots Sample Sizes**: The sample size of each binary option for each group can now be displayed. These can be toggled on or off via the `prop_sample_counts` parameter.
 
-   - **Effect Size Lines for Paired Plots**: Effect size lines for paired plots are now available. These can be toggled on or off via the `es_paired_lines` parameter.
+   - **Effect Size Lines for Paired Plots**: Paired plots now display lines linking the effect sizes within a group together in the contrast axes. These can be toggled on or off via the `contrast_paired_lines` parameter.
 
-   - **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).
+   - **Baseline Error Curves**: Baseline error dot and curve are now available to represent the baseline/control group in the contrast axes. The dot is shown by default, while the curve can be toggled on/off by the user (via the `show_baseline_ec` parameter).
 
-   - **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.
+   - **Delta Text**: Effect size deltas are now displayed as text next to their respective effect size. This can be toggled on or off via the `delta_text` parameter.
 
    - **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.
 
@@ -38,9 +36,10 @@
 - **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.
 
 - **Terminology Updates**: We have made several updates to the documentation and terminology to improve clarity and consistency. For example:
-    - 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).
+    - Plot arguments have been adjusted to bring more clarity and consistency in naming. Arguments relating to the rawdata plot axis will now be typically referred to with ‘raw’ while arguments relating to the contrast axis will be referred to with ‘contrast’. For example, ‘raw_label’ replaces ‘swarm_label’ and ‘bar_label’. The various kwargs relating to each different type of plot (e.g., swarmplot_kwargs) remain unchanged. 
+    - The method to utilise the Deltas’ g effect size is now via the .hedges_g.plot() method 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).
 
-- **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!.
+- **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!
 
 - **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.
 

README.md

@@ -14,7 +14,7 @@ citation](https://zenodo.org/badge/DOI/10.1038/s41592-019-0470-3.svg)](https://r
 
 ## Recent Version Update
 
-We are proud to announce **DABEST Version Dadar (v2025.03.14)** This new
+We are proud to announce **DABEST Version Dadar (v2025.03.27)** This new
 version of the DABEST Python library includes several new features and
 performance improvements. It’s a big one!
 

dabest/__init__.py

@@ -12,4 +12,4 @@
     if not _NUMBA_COMPILED:
         precompile_all()
 
-__version__ = "2025.03.14"
+__version__ = "2025.03.27"

nbs/02-about.ipynb

@@ -17,7 +17,7 @@
     "\n",
     "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",
     "\n",
-    "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",
+    "Features in v2025.03.27 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",
     "\n",
     "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",
     "\n",

nbs/read_me.ipynb

@@ -29,7 +29,7 @@
    "source": [
     "## Recent Version Update\n",
     "\n",
-    "We are proud to announce **DABEST Version Dadar (v2025.03.14)** This new version of the DABEST Python library includes several new features and performance improvements. It's a big one!\n",
+    "We are proud to announce **DABEST Version Dadar (v2025.03.27)** This new version of the DABEST Python library includes several new features and performance improvements. It's a big one!\n",
     "\n",
     "1. **Python 3.13 Support**: DABEST now supports Python 3.10-3.13.\n",
     "\n",

nbs/tutorials/01-basics.ipynb

@@ -34,15 +34,15 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Compiling numba functions: 100%|██████████| 11/11 [00:00<00:00, 42.13it/s]"
+      "Compiling numba functions: 100%|██████████| 11/11 [00:00<00:00, 68.51it/s]"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "Numba compilation complete!\n",
-      "We're using DABEST v2025.03.14\n"
+      "We're using DABEST v2025.03.27\n"
      ]
     },
     {
@@ -318,11 +318,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:21:31 2025.\n",
+       "The current time is Fri Mar 14 15:56:31 2025.\n",
        "\n",
        "Effect size(s) with 95% confidence intervals will be computed for:\n",
        "1. Test 1 minus Control 1\n",
@@ -361,11 +361,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:21:31 2025.\n",
+       "The current time is Fri Mar 14 15:56:31 2025.\n",
        "\n",
        "Effect size(s) with 90% confidence intervals will be computed for:\n",
        "1. Test 1 minus Control 1\n",
@@ -416,11 +416,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:21:33 2025.\n",
+       "The current time is Fri Mar 14 15:56:33 2025.\n",
        "\n",
        "The unpaired mean difference between Control 1 and Test 1 is 0.48 [95%CI 0.205, 0.774].\n",
        "The p-value of the two-sided permutation t-test is 0.001, calculated for legacy purposes only. \n",
@@ -709,7 +709,7 @@
     "**Note:**\n",
     "A research paper [Phipson & Smyth (2010)](https://doi.org/10.2202/1544-6115.1585) suggested that permutation p-values should never be zero, and provided a slightly adjusted formula to compute permutation p-values. \n",
     "\n",
-    "Since **v2025.03.14**, DABEST provides a `ps_adjust` parameter in the `.load()` function. This parameter allows you to adjust the permutation p-values using the formula suggested by Phipson & Smyth (2010). By default, DABEST uses the unadjusted p-values."
+    "Since **v2025.03.27**, DABEST provides a `ps_adjust` parameter in the `.load()` function. This parameter allows you to adjust the permutation p-values using the formula suggested by Phipson & Smyth (2010). By default, DABEST uses the unadjusted p-values."
    ]
   },
   {
@@ -821,11 +821,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:21:34 2025.\n",
+       "The current time is Fri Mar 14 15:56:34 2025.\n",
        "\n",
        "The unpaired Hedges' g between Control 1 and Test 1 is 1.03 [95%CI 0.317, 1.62].\n",
        "The p-value of the two-sided permutation t-test is 0.001, calculated for legacy purposes only. \n",
@@ -1247,11 +1247,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:21:35 2025.\n",
+       "The current time is Fri Mar 14 15:56:34 2025.\n",
        "\n",
        "Effect size(s) with 95% confidence intervals will be computed for:\n",
        "1. Test 1 minus Control 1\n",
@@ -1297,7 +1297,7 @@
     "   \n",
     "6.  [Forest Plot](07-forest_plot.html)\n",
     "   \n",
-    "In addition, as of Dabest **v2025.03.14**, we introduce a new plotting orientation: **[horizontal plots](08-horizontal_plot.html)**. \n",
+    "In addition, as of Dabest **v2025.03.27**, we introduce a new plotting orientation: **[horizontal plots](08-horizontal_plot.html)**. \n",
     "\n",
     "Lastly, we have a whole tutorial page for making [aesthetic changes to dabest plots](09-plot_aesthetics.html).\n"
    ]

nbs/tutorials/02-two_group.ipynb

@@ -34,15 +34,15 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Compiling numba functions: 100%|██████████| 11/11 [00:00<00:00, 71.84it/s]"
+      "Compiling numba functions: 100%|██████████| 11/11 [00:00<00:00, 44.00it/s]"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "Numba compilation complete!\n",
-      "We're using DABEST v2025.03.14\n"
+      "We're using DABEST v2025.03.27\n"
      ]
     },
     {
@@ -334,11 +334,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:21:55 2025.\n",
+       "The current time is Fri Mar 14 15:57:59 2025.\n",
        "\n",
        "The unpaired mean difference between Control 1 and Test 1 is 0.48 [95%CI 0.205, 0.774].\n",
        "The p-value of the two-sided permutation t-test is 0.001, calculated for legacy purposes only. \n",
@@ -543,7 +543,7 @@
     "plot](https://en.wikipedia.org/wiki/Forest_plot), commonly used in\n",
     "meta-analyses to aggregate and to compare data from different experiments.\n",
     "\n",
-    "**Note: If you're interested in just plotting the contrast ax (the violin plots), you may be interested in the new [forest plot](07-forest_plot.html) feature added in v2025.03.14!**"
+    "**Note: If you're interested in just plotting the contrast ax (the violin plots), you may be interested in the new [forest plot](07-forest_plot.html) feature added in v2025.03.27!**"
    ]
   },
   {

nbs/tutorials/03-shared_control_and_repeated_measures.ipynb

@@ -47,15 +47,15 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Compiling numba functions: 100%|██████████| 11/11 [00:00<00:00, 35.80it/s]"
+      "Compiling numba functions: 100%|██████████| 11/11 [00:00<00:00, 39.60it/s]"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "Numba compilation complete!\n",
-      "We're using DABEST v2025.03.14\n"
+      "We're using DABEST v2025.03.27\n"
      ]
     },
     {
@@ -148,11 +148,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:24:49 2025.\n",
+       "The current time is Fri Mar 14 15:58:46 2025.\n",
        "\n",
        "Effect size(s) with 95% confidence intervals will be computed for:\n",
        "1. Test 1 minus Control 1\n",
@@ -186,11 +186,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:24:50 2025.\n",
+       "The current time is Fri Mar 14 15:58:47 2025.\n",
        "\n",
        "The unpaired mean difference between Control 1 and Test 1 is 0.48 [95%CI 0.205, 0.774].\n",
        "The p-value of the two-sided permutation t-test is 0.001, calculated for legacy purposes only. \n",
@@ -262,11 +262,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:24:51 2025.\n",
+       "The current time is Fri Mar 14 15:58:47 2025.\n",
        "\n",
        "Effect size(s) with 95% confidence intervals will be computed for:\n",
        "1. Test 1 minus Control 1\n",
@@ -300,11 +300,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:24:52 2025.\n",
+       "The current time is Fri Mar 14 15:58:48 2025.\n",
        "\n",
        "The unpaired mean difference between Control 1 and Test 1 is 0.48 [95%CI 0.205, 0.774].\n",
        "The p-value of the two-sided permutation t-test is 0.001, calculated for legacy purposes only. \n",
@@ -396,11 +396,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:24:52 2025.\n",
+       "The current time is Fri Mar 14 15:58:49 2025.\n",
        "\n",
        "Paired effect size(s) for repeated measures against baseline \n",
        "with 95% confidence intervals will be computed for:\n",
@@ -430,11 +430,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:24:53 2025.\n",
+       "The current time is Fri Mar 14 15:58:49 2025.\n",
        "\n",
        "The paired mean difference for repeated measures against baseline \n",
        "between Control 1 and Test 1 is 0.48 [95%CI 0.241, 0.749].\n",
@@ -493,11 +493,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:24:53 2025.\n",
+       "The current time is Fri Mar 14 15:58:49 2025.\n",
        "\n",
        "Paired effect size(s) for the sequential design of repeated-measures experiment \n",
        "with 95% confidence intervals will be computed for:\n",
@@ -527,11 +527,11 @@
     {
      "data": {
       "text/plain": [
-       "DABEST v2025.03.14\n",
+       "DABEST v2025.03.27\n",
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Wed Mar 12 17:24:54 2025.\n",
+       "The current time is Fri Mar 14 15:58:50 2025.\n",
        "\n",
        "The paired mean difference for the sequential design of repeated-measures experiment \n",
        "between Control 1 and Test 1 is 0.48 [95%CI 0.241, 0.749].\n",