tutorial and various notebook updates

Author: JAnns98

nbs/01-getting_started.ipynb

@@ -46,7 +46,7 @@
    "id": "e4c2e459",
    "metadata": {},
    "source": [
-    "DABEST powers [estimationstats.com](estimationstats.com), allowing everyone access to high-quality estimation plots."
+    "DABEST powers [estimationstats.com](https://www.estimationstats.com/#/), allowing everyone access to high-quality estimation plots."
    ]
   },
   {

nbs/tutorials/01-basics.ipynb

@@ -34,7 +34,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Compiling numba functions: 100%|██████████| 11/11 [00:00<00:00, 60.60it/s]"
+      "Compiling numba functions: 100%|██████████| 11/11 [00:00<00:00, 42.13it/s]"
      ]
     },
     {
@@ -322,7 +322,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:54:36 2025.\n",
+       "The current time is Wed Mar 12 17:21:31 2025.\n",
        "\n",
        "Effect size(s) with 95% confidence intervals will be computed for:\n",
        "1. Test 1 minus Control 1\n",
@@ -365,7 +365,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:54:36 2025.\n",
+       "The current time is Wed Mar 12 17:21:31 2025.\n",
        "\n",
        "Effect size(s) with 90% confidence intervals will be computed for:\n",
        "1. Test 1 minus Control 1\n",
@@ -420,7 +420,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:54:36 2025.\n",
+       "The current time is Wed Mar 12 17:21:33 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",
@@ -454,7 +454,7 @@
     "\n",
     "Since v0.3.0, DABEST will report the p-value of the [non-parametric two-sided approximate permutation t-test](https://en.wikipedia.org/wiki/Resampling_(statistics)#Permutation_tests). This is also known as *the Monte Carlo permutation test*.\n",
     "\n",
-    "For unpaired comparisons, the p-values and test statistics of [Welch's t test](https://en.wikipedia.org/wiki/Welch%27s_t-test>), \n",
+    "For unpaired comparisons, the p-values and test statistics of [Welch's t test](https://en.wikipedia.org/wiki/Welch%27s_t-test), \n",
     "[Student's t test](https://en.wikipedia.org/wiki/Student%27s_t-test), \n",
     "and [Mann-Whitney U test](https://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U_test) can be found. For paired comparisons, the p-values and test statistics of the \n",
     "[paired Student's t](https://en.wikipedia.org/wiki/Student%27s_t-test#Paired_samples)\n",
@@ -547,7 +547,7 @@
        "      <td>[-0.17259843762502491, 0.03802293852634886, -0...</td>\n",
        "      <td>0.001</td>\n",
        "      <td>5000</td>\n",
-       "      <td>[0.026356588154404337, 0.027102495439046997, 0...</td>\n",
+       "      <td>[0.26356588154404337, 0.2710249543904699, 0.26...</td>\n",
        "      <td>0.002094</td>\n",
        "      <td>-3.308806</td>\n",
        "      <td>0.002057</td>\n",
@@ -584,7 +584,7 @@
        "0               0.001               5000   \n",
        "\n",
        "                                    permutations_var  pvalue_welch  \\\n",
-       "0  [0.026356588154404337, 0.027102495439046997, 0...      0.002094   \n",
+       "0  [0.26356588154404337, 0.2710249543904699, 0.26...      0.002094   \n",
        "\n",
        "   statistic_welch  pvalue_students_t  statistic_students_t  \\\n",
        "0        -3.308806           0.002057             -3.308806   \n",
@@ -825,7 +825,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:54:37 2025.\n",
+       "The current time is Wed Mar 12 17:21:34 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",
@@ -933,7 +933,7 @@
        "      <td>[-0.329508986559053, 0.07158401210924781, -0.2...</td>\n",
        "      <td>0.001</td>\n",
        "      <td>5000</td>\n",
-       "      <td>[0.026356588154404337, 0.027102495439046997, 0...</td>\n",
+       "      <td>[0.26356588154404337, 0.2710249543904699, 0.26...</td>\n",
        "      <td>0.002094</td>\n",
        "      <td>-3.308806</td>\n",
        "      <td>0.002057</td>\n",
@@ -967,7 +967,7 @@
        "0  [-0.329508986559053, 0.07158401210924781, -0.2...               0.001   \n",
        "\n",
        "   permutation_count                                   permutations_var  \\\n",
-       "0               5000  [0.026356588154404337, 0.027102495439046997, 0...   \n",
+       "0               5000  [0.26356588154404337, 0.2710249543904699, 0.26...   \n",
        "\n",
        "   pvalue_welch  statistic_welch  pvalue_students_t  statistic_students_t  \\\n",
        "0      0.002094        -3.308806           0.002057             -3.308806   \n",
@@ -1126,7 +1126,7 @@
     "\n",
     "For more details on wide vs long or 'melted' data, refer to this\n",
     "[Wikipedia article](https://en.wikipedia.org/wiki/Wide_and_narrow_data). The\n",
-    "[pandas documentation](https://pandas.pydata.org/pandas-docs/stable/generated/pandas.melt.html)\n",
+    "[pandas documentation](https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.melt.html)\n",
     "provides recipes for melting dataframes.\n"
    ]
   },
@@ -1251,7 +1251,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:54:38 2025.\n",
+       "The current time is Wed Mar 12 17:21:35 2025.\n",
        "\n",
        "Effect size(s) with 95% confidence intervals will be computed for:\n",
        "1. Test 1 minus Control 1\n",
@@ -1284,24 +1284,23 @@
    "source": [
     "The ``dabest`` package implements a range of estimation plot\n",
     "designs aimed at depicting common experimental designs:\n",
-    "1. Two-Group\n",
-    "2. Multi Two-Group\n",
-    "3. Shared Control (Unpaired) and Repeated Measures (Paired)\n",
-    "4. Multi-Groups\n",
-    "5. Proportion plots\n",
-    "6. Mini-Meta\n",
-    "7. Delta-Delta\n",
-    "8. Forest Plot\n",
+    "\n",
+    "1. [Two-Group](02-two_group.html)\n",
+    "   \n",
+    "2. [Shared Control (Unpaired) and Repeated Measures (Paired)](03-shared_control_and_repeated_measures.html)\n",
+    "   \n",
+    "3. [Proportion plots](04-proportion_plot.html)\n",
+    "   \n",
+    "4. [Mini-Meta](05-mini_meta.html)\n",
+    "   \n",
+    "5. [Delta-Delta](06-delta_delta.html)\n",
     "   \n",
-    "In addition, as of Dabest **v2025.03.14**, we introduce a new plotting orientation: **horizontal plots**. \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",
     "\n",
-    "Lastly, we have a whole tutorial page for making aesthetic changes to dabest plots.\n"
+    "Lastly, we have a whole tutorial page for making [aesthetic changes to dabest plots](09-plot_aesthetics.html).\n"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
   }
  ],
  "metadata": {

nbs/tutorials/02-two_group.ipynb

@@ -34,7 +34,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Compiling numba functions: 100%|██████████| 11/11 [00:03<00:00,  2.82it/s]"
+      "Compiling numba functions: 100%|██████████| 11/11 [00:00<00:00, 71.84it/s]"
      ]
     },
     {
@@ -275,7 +275,9 @@
     "We can achieve this by supplying the dataframe to `dabest.load()`. Additionally, we must provide the groups to be compared in the `idx` argument as a tuple or list.\n",
     "\n",
     "For this tutorial, we will create two separate analyses: \n",
-    "- A singular two-group comparison between Control 1 and Test 1\n",
+    "\n",
+    "- A singular two-group comparison between Control 1 and Test 1.\n",
+    "  \n",
     "- A multi two-group comparison between Control 1 and Test 1, and between Control 2 and Test 2. \n",
     "  \n",
     "The **multi two-group estimation plot** tiles two or more Cumming plots\n",
@@ -299,9 +301,9 @@
    "source": [
     "In addition, we can specify the `paired` argument to indicate paired data.\n",
     "\n",
-    " `paired` can be set as 'baseline' or 'sequential' or left as None (unpaired). \n",
+    " `paired` can be set as `'baseline'` or `'sequential'` or left as `None` (unpaired). \n",
     " \n",
-    " **Note: For two-group, both 'baseline' and 'sequential' are equivalent.**"
+    " **Note: For two-group, both `'baseline'` and `'sequential'` are equivalent.**"
    ]
   },
   {
@@ -336,7 +338,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:54:22 2025.\n",
+       "The current time is Wed Mar 12 17:21:55 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",
@@ -539,7 +541,9 @@
     "\n",
     "The lower axes in the Cumming plot is effectively a [forest\n",
     "plot](https://en.wikipedia.org/wiki/Forest_plot), commonly used in\n",
-    "meta-analyses to aggregate and to compare data from different experiments."
+    "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!**"
    ]
   },
   {

nbs/tutorials/03-shared_control_and_repeated_measures.ipynb

@@ -47,7 +47,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Compiling numba functions: 100%|██████████| 11/11 [00:00<00:00, 77.31it/s]"
+      "Compiling numba functions: 100%|██████████| 11/11 [00:00<00:00, 35.80it/s]"
      ]
     },
     {
@@ -152,7 +152,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:55:53 2025.\n",
+       "The current time is Wed Mar 12 17:24:49 2025.\n",
        "\n",
        "Effect size(s) with 95% confidence intervals will be computed for:\n",
        "1. Test 1 minus Control 1\n",
@@ -190,7 +190,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:55:54 2025.\n",
+       "The current time is Wed Mar 12 17:24:50 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",
@@ -266,7 +266,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:55:54 2025.\n",
+       "The current time is Wed Mar 12 17:24:51 2025.\n",
        "\n",
        "Effect size(s) with 95% confidence intervals will be computed for:\n",
        "1. Test 1 minus Control 1\n",
@@ -304,7 +304,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:55:55 2025.\n",
+       "The current time is Wed Mar 12 17:24:52 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",
@@ -372,7 +372,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "DABEST version 2023.02.14 expands the repertoire of plots for experiments with repeated-measures designs. DABEST now allows the visualization of paired experiments with one control and multiple test \n",
+    "DABEST **v2023.02.14** expands the repertoire of plots for experiments with repeated-measures designs. DABEST now allows the visualization of paired experiments with one control and multiple test \n",
     "groups, as well as repeated measurements of the same group. This is an improved version of paired data plotting in previous versions, which only supported computations involving one test group and one control group.\n",
     "\n",
     "The repeated-measures function supports the calculation of effect sizes for\n",
@@ -400,7 +400,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:55:55 2025.\n",
+       "The current time is Wed Mar 12 17:24:52 2025.\n",
        "\n",
        "Paired effect size(s) for repeated measures against baseline \n",
        "with 95% confidence intervals will be computed for:\n",
@@ -434,7 +434,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:55:56 2025.\n",
+       "The current time is Wed Mar 12 17:24:53 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",
@@ -497,7 +497,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:55:56 2025.\n",
+       "The current time is Wed Mar 12 17:24:53 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",
@@ -531,7 +531,7 @@
        "==================\n",
        "                  \n",
        "Good afternoon!\n",
-       "The current time is Fri Mar  7 13:55:57 2025.\n",
+       "The current time is Wed Mar 12 17:24:54 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",