ReadMe

README.md

@@ -0,0 +1,30 @@
+# Statsmed
+
+Statsmed is designed to perform statistical analysis of medical data, but may also be used for various datasets. It gives you an fast overview of your data and allows you to perform test and create figures. 
+There are examples for some functions.
+
+- [Example 1](https://github.com/segemart/statsmed/blob/main/examples/example1/Tests_normal_distribution.ipynb) - Test for normal distribution
+- [Example 2](https://github.com/segemart/statsmed/blob/main/examples/example2/DescriptiveStatistic.ipynb) - Descriptive Statistic - Mean; Confidence Interval - Median; Inter-quartile range
+- [Example 3](https://github.com/segemart/statsmed/blob/main/examples/example3/Correlations.ipynb) - Pearson's and Spearman's correlation with figures
+- [Example 4](https://github.com/segemart/statsmed/blob/main/examples/example4/Comparision_continuous.ipynb) - Comparison of two groups with continuous variables
+- [Example 5](https://github.com/segemart/statsmed/blob/main/examples/example5/Bland-Altman-Plots.ipynb) - Bland-Altman plots
+
+### Installation
+
+Statsmed works on Ubuntu, Mac, and Windows and on CPU and GPU.
+
+Please make sure you have a running version of Python (>= 3.8.8), pip and git.
+
+Install Statsmed
+```
+pip install git+https://github.com/segemart/statsmed.git
+```
+
+
+### Usage
+
+Statsmed also allows you to generate figures quickly. See for example [Example 3](https://github.com/segemart/statsmed/blob/main/examples/example3/Correlations.ipynb) or [Example 5](https://github.com/segemart/statsmed/blob/main/examples/example5/Bland-Altman-Plots.ipynb), where we generated plots to show some correlations and Bland-Altman plots.
+
+![Correlations](examples/example3/Corr_subplots.png)
+
+![Bland-Altman plots](examples/example3/Corr_subplots.png)

examples/example3/Correlations.ipynb

@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -96,7 +96,7 @@
        "       [ 0.   ,  0.12 ,  0.   ,  0.06 ,  0.17 ]])"
       ]
      },
-     "execution_count": 1,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -140,7 +140,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -169,7 +169,7 @@
        "       [0.  , 0.35, 0.  , 0.25, 0.44]])"
       ]
      },
-     "execution_count": 2,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -188,7 +188,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -218,7 +218,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -278,7 +278,7 @@
     "statsmed.corr_scatter_figure(data['age'][data['iliopsoas_left_volume'] >= 10],data['iliopsoas_left_volume'][data['iliopsoas_left_volume'] >= 10]/1000,x4,'Left Iliopsoas','Age in years','Volume of left Iliopsoas (ml)',color = 'blue')\n",
     "plt.gcf().subplots_adjust(bottom=0.15)\n",
     "plt.tight_layout()\n",
-    "plt.savefig('Corr_subplots.tiff',transparent=False) # saves the figure\n"
+    "plt.savefig('Corr_subplots.png',transparent=False) # saves the figure\n"
    ]
   },
   {

examples/example5/Bland-Altman-Plots.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Example 5 - Bland Altman plots"
+    "### Example 5 - Bland-Altman plots"
    ]
   },
   {
@@ -27,7 +27,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
@@ -67,7 +67,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -106,7 +106,7 @@
     "statsmed.bland_altman_plot(new_data_left_iliopsoas['iliopsoas_left_volume_R1'],new_data_left_iliopsoas['iliopsoas_left_volume_R2'],x4,'Left Iliopsoas','Mean of R1 and R2 (ml)','Volume difference (ml)')\n",
     "plt.gcf().subplots_adjust(bottom=0.15)\n",
     "plt.tight_layout()\n",
-    "plt.savefig('Bland_Altman_subplots.tiff',transparent=False) # saves the figure"
+    "plt.savefig('Bland_Altman_subplots.png',transparent=False) # saves the figure"
    ]
   },
   {

setup.py

@@ -2,7 +2,7 @@
 
 
 setup(name='statsmed',
-        version='0.0.5',
+        version='0.0.6',
         description='Statistics with Figures for medical data analysis',
         url='https://github.com/segemart/statsmed',
         author='Martin Segeroth',