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*Python* and *R*. They are two of the most popular programming languages

for science. They are both free, both of them have a strong user

community and both of them work pretty well.

Personally, I find *Python* way more intuitive than *R* (at least for

people who, like me, have a classical mathematics background). Thinking

in terms of data frames is great when you work with statistical data,

but it gets a bit annoying when you are more interested in analysis. To

uneven the score even more, *Python’s* libraries like *NumPy*, *SciPy*,

*SimPy* and *Matplotlib* are the perfect toolbox for anyone doing

mathematical research of any kind.

But… I chose *R*. Why?

There is only one reason for doing so: *knitr*[1]. *knitr* is a package

that turns a combination of text **and code** (the *RMarkdown* file)

into almost any format of human readable text, including a *pdf* report,

slides, or a blog page like the one you are reading now. The interesting

point is the integration of the code with the text. This means that an

*RMarkdown* document is not passive. This allows one to write papers

that, quite literally, recalculate themselves any time needed. *knitr*,

combined with research code structured as an *R* package, is clearly my

favourite way of writing research. The package structure keeps my code

tidy and tested, and *knitr* allows me to do all and the figures the

writing in a single file. The result is a rock-solid, reproducible

output. Let me put it like this: *knitr* is like *LaTeX* on steroids![2]

But… I keep finding *R* annoying. A few days ago, after looking for

hours for a nice way of ploting phase planes, I gave up. All the

possibilities I found were terribly ugly. I had to go back to *Python’s*

*Matplotlib* and its function *streamplot*. See for yourself:

With *R*:

With *Python*:

After a bit of googling, I found an *R* library called *reticulate* that

allows to run *Python* code from inside *R*. If this works (I thought) I

can keep the best of both approaches! And, so far, it works flawlessly!

## How to do it

First of all, *R* and *Python* are obviously reequired. *reticulate* can

be installed and loaded as usual in *R*:

```
install.packages("reticulate")
library(reticulate)
```

For some

reason

I still don’t fully understand, I had to add these two lines to make

*Matplotlib* work properly.

```
matplotlib <- import("matplotlib", convert = TRUE)
matplotlib$use("Agg")
```

Now, we can insert python chunks in *Rmarkdown*:

```
```{python, eval=TRUE}
import numpy as np
x = np.pi
y = np.sin(x/4)
print(y)
```
## 0.707106781187
```

## Interaction

*reticulate* works creating two different sessions, one of *R* and

another of *Python*. In order to unleash all the power of this

combination, we need a way of passing variables between both sessions.

This is done via the dataframe `py`

. See examples below:

### From *R* to *Python*

Create a variable and store it as a field of `py`

:

```
```{r}
py$foo <- "Hi!"
```
```

The variable will be available in the *Python* session:

```
```{python}
print(foo)
```
## Hi!
```

### From *Python* to *R*

Create a variable inside the *Python* session:

```
```{python}
bar = "How are you?"
```
```

The variable will be available as a field of the dataframe `py`

in the

*R* session:

```
```{r}
py$bar
```
## [1] "How are you?"
```

This entry appears in R-bloggers.com

[1] Actually, there is a second (and less important) reason: *Shiny*.

[2] It is true that *Python* also has *Jupyter* for reproducible

research, but the results are just not as neat as with *R*.

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**PabRod - R**.

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