example_python_in_rstudio.Rmd

---
title: "Example: python in RStudio"
date: "Last knitted `r format(Sys.Date(), '%d %b %Y')`"
output:
  html_document: 
    df_print: paged
    number_sections: yes
    toc: yes
    toc_float: true
    toc_depth: 3
    code_folding: show
editor_options:
  chunk_output_type: inline
---

> Click into a code cell (the gray blocks below) to select or edit it. To run a selected code cell, hit `Ctrl`+`Shift`+`Enter` (Windows & Linux) / `Command`+`Shift`+`Enter` (MacOS). Make sure that each code cell runs successfully before you move on to the next one.

```{r, include = FALSE, message = FALSE}
# required behind the scenes to find the correct python installation
library(reticulate)

# include the following command to activate a specific conda environment:
#use_condaenv(condaenv = "my_env", required = TRUE)

# note that this may get stuck knitting automatically in RStudio but will work 
# if you knit manually using the following command from the console:
#rmarkdown::render("example_python_in_rstudio.Rmd")
```

# $\LaTeX$ Math

This is just markdown that can include latex math.

$$
\begin{align}
\dot{x} & = \sigma(y-x) \\
\dot{y} & = \rho x - y - xz \\
\dot{z} & = -\beta z + xy
\end{align}
$$

# System Info

```{python}
# load IPython library for comprehensive system info
import IPython
print(IPython.sys_info())
```


# Custom Function

```{python}
# custom function from scripts/functions.py
from scripts.functions import test_add
test_add(2,5)
```

# Data

```{python}
# create dataset using pandas and numpy
import pandas as pd
import numpy as np
curve = pd.DataFrame(np.arange(0.0, 2.0, 0.01), columns = list('t'))
curve['y'] = 1 + np.sin(2 * np.pi * curve['t'])
curve[1:10] # first 10 rows
```

```{r}
# sidenote: you can access all python variables in R
py$curve
```

# Plot

```{r, include = FALSE}
# make sure the correct display is used for matplotlib
matplotlib <- import("matplotlib", convert = TRUE)
matplotlib$use("Agg")
```


```{python}
# plot using pyplot
import matplotlib.pyplot as plt
plt.rcParams['figure.figsize'] = [8, 6]
plt.plot(curve['t'], curve['y'])
plt.show()
```