First changes on documentation

Author: cyberosa

nbs/01-getting_started.ipynb

@@ -70,7 +70,7 @@
    "source": [
     "2. Using Github\n",
     "\n",
-    "Clone the [DABEST-python repo](https://github.com/ACCLAB/DABEST-python) locally (see instructions [here] (https://help.github.com/articles/cloning-a-repository/).\n",
+    "Clone the [DABEST-python repo](https://github.com/ACCLAB/DABEST-python) locally (see instructions [here](https://help.github.com/articles/cloning-a-repository/)).\n",
     "\n",
     "Then, navigate to the cloned repo in the command line and run\n",
     "\n",

nbs/02-about.ipynb

@@ -66,6 +66,7 @@
     "\n",
     "     * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.\n",
     "\n",
+    "<div style=\"padding: 15px; border: 1px solid transparent; border-color: transparent; margin-bottom: 20px; border-radius: 4px; color: #8a6d3b;; background-color: #fcf8e3; border-color: #faebcc;\">\n",
     "NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY\n",
     "THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND\n",
     "CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT\n",
@@ -77,7 +78,8 @@
     "BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER\n",
     "IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)\n",
     "ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE\n",
-    "POSSIBILITY OF SUCH DAMAGE.\n"
+    "POSSIBILITY OF SUCH DAMAGE.\n",
+    "</div>\n"
    ]
   },
   {

nbs/read_me.ipynb

@@ -62,13 +62,13 @@
     "\n",
     "DABEST is a package for **D**ata **A**nalysis using **B**ootstrap-Coupled **EST**imation.\n",
     "\n",
-    "[Estimation statistics](https://en.wikipedia.org/wiki/Estimation_statistics) is a [simple framework](https://thenewstatistics.com/itns/) that avoids the [pitfalls](https://www.nature.com/articles/nmeth.3288) of significance testing. It uses familiar statistical concepts: means, mean differences, and error bars. More importantly, it focuses on the effect size of one's experiment/intervention, as opposed to a false dichotomy engendered by *P* values.\n",
+    "[Estimation statistics](https://en.wikipedia.org/wiki/Estimation_statistics) are a [simple framework](https://thenewstatistics.com/itns/) that avoids the [pitfalls](https://www.nature.com/articles/nmeth.3288) of significance testing. It employs familiar statistical concepts such as means, mean differences, and error bars. More importantly, it focuses on the effect size of one's experiment or intervention, rather than succumbing to a false dichotomy engendered by *P* values.\n",
     "\n",
-    "An estimation plot has two key features.\n",
+    "An estimation plot comprises two key features.\n",
     "\n",
-    "1. It presents all datapoints as a swarmplot, which orders each point to display the underlying distribution.\n",
+    "1. It presents all data points as a swarm plot, ordering each point to display the underlying distribution.\n",
     "\n",
-    "2. It presents the effect size as a **bootstrap 95% confidence interval** on a **separate but aligned axes**.\n",
+    "2. It illustrates the effect size as a **bootstrap 95% confidence interval** on a **separate but aligned axis**.\n",
     "\n",
     "![The five kinds of estimation plots](showpiece.png \"The five kinds of estimation plots.\")\n",
     "\n",
@@ -116,7 +116,7 @@
     "import pandas as pd\n",
     "import dabest\n",
     "\n",
-    "# Load the iris dataset. Requires internet access.\n",
+    "# Load the iris dataset. This step requires internet access.\n",
     "iris = pd.read_csv(\"https://github.com/mwaskom/seaborn-data/raw/master/iris.csv\")\n",
     "\n",
     "# Load the above data into `dabest`.\n",
@@ -172,13 +172,13 @@
    "metadata": {},
    "source": [
     "### A wish list for new features\n",
-    "Currently, DABEST offers functions to handle data traditionally analyzed with Student's paired and unpaired t-tests. It also offers plots for multiplexed versions of these, and the estimation counterpart to a 1-way analysis of variance (ANOVA), the shared-control design. While these five functions execute a large fraction of common biomedical data analyses, there remain three others: 2-way data, time-series group data, and proportional data. We aim to add these new functions to both the R and Python libraries.\n",
+    "Currently, DABEST offers functions to handle data traditionally analyzed with Student's paired and unpaired t-tests. It also provides plots for multiplexed versions of these, and the estimation counterpart to a 1-way analysis of variance (ANOVA), known as the shared-control design. While these five functions cover a large fraction of common biomedical data analyses, three others are yet to be implemented: 2-way data, time-series group data, and proportional data. We aim to add these new functions to both the R and Python libraries.\n",
     "\n",
-    "- In many experiments, four groups are investigate to isolate an interaction, for example: a genotype × drug effect. Here, wild-type and mutant animals are each subjected to drug or sham treatments; the data are traditionally analysed with a 2×2 ANOVA. We have received requests by email, Twitter, and GitHub to implement an estimation counterpart to the 2-way ANOVA. To do this, we will implement $\\Delta\\Delta$ plots, in which the difference of means ($\\Delta$) of two groups is subtracted from a second two-group $\\Delta$. **Implemented in v2023.02.14.**\n",
+    "- In many experiments, four groups are investigated to isolate an interaction, for example: a genotype × drug effect. Here, wild-type and mutant animals are each subjected to drug or sham treatments; the data are traditionally analysed with a 2×2 ANOVA. We have received requests via email, Twitter, and GitHub to implement an estimation counterpart to the 2-way ANOVA. To address this, we will implement $\\Delta\\Delta$ plots, in which the difference of means ($\\Delta$) of two groups is subtracted from a second two-group $\\Delta$. **Implemented in v2023.02.14.**\n",
     "\n",
     "- Currently, DABEST can analyse multiple paired data in a single plot, and multiple groups with a common, shared control. However, a common design in biomedical science is to follow the same group of subjects over multiple, successive time points. An estimation plot for this would combine elements of the two other designs, and could be used in place of a repeated-measures ANOVA. **Implemented in v2023.02.14**\n",
     "\n",
-    "- We have observed that proportional data are often analyzed in neuroscience and other areas of biomedical research. However, compared to other data types, the charts are frequently impoverished: often, they omit error bars, sample sizes, and even P values—let alone effect sizes. We would like DABEST to feature proportion charts, with error bars and a curve for the distribution of the proportional differences. **Implemented in v2023.02.14**\n",
+    "- We have observed that proportional data are often analyzed in neuroscience and other areas of biomedical research. However, compared to other data types, the charts are frequently impoverished: often omitting error bars, sample sizes, and even P values—let alone effect sizes. We would like DABEST to feature proportion charts, with error bars and a curve for the distribution of the proportional differences. **Implemented in v2023.02.14**\n",
     "\n",
     "We encourage contributions for the above features. "
    ]
@@ -195,9 +195,9 @@
     "\n",
     "## Testing\n",
     "\n",
-    "To test DABEST, you will need to install [pytest](https://docs.pytest.org/en/latest).\n",
+    "To test DABEST, you need to install [pytest](https://docs.pytest.org/en/latest).\n",
     "\n",
-    "Run `pytest` in the root directory of the source distribution. This runs the test suite in the folder `dabest/tests`. The test suite will ensure that the bootstrapping functions and the plotting functions perform as expected.\n",
+    "Run `pytest` in the root directory of the source distribution. This runs the test suite in the folder `dabest/tests`. The test suite ensures that the bootstrapping functions and the plotting functions perform as expected.\n",
     "\n",
     "\n",
     "## DABEST in other languages\n",