I am using R on a MacBook. I have an Rmarkdown document and I’m trying to use reticulate in order to use python within R.
First I download the libraries:
```{r libraries, warning = FALSE, message = FALSE}
library(dplyr)
library(reticulate)
```
Next I look at an R chunk and figure out my working directory. Then I write mtcars to my desktop.
```{r chunk, warning = FALSE, message = FALSE}
getwd()
write.csv(mtcars, '/Users/name/Desktop/mtcars.csv', row.names = TRUE)
```
Then I try to use python instead to read in that csv that I just wrote to my desktop.
```{python}
import pandas as pd
mtcars = pd.read_csv('/Users/name/Desktop/mtcars.csv')
```
But I get this error:
ModuleNotFoundError: No module named 'pandas' NameError: name 'pd' is not defined
So I went to this R documentation website and discovered that with python you have to import packages differently. So I went to terminal and then I typed in
python -m pip install pandas
It seemed to download OK? But when I return to my Rmarkdown document I can’t seem to get the python code to run and read in the csv. I still get the same error message.
I also saw a similar question on this SO post but I’m certain that my RStudio version is newer than the version in this question, so I don’t the answer hits on the same error exactly.
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Answer
An option is to create a virtualenv, install the package and then specify the virtual env to be used
virtualenv_create("py-proj")
py_install("pandas", envname = "py-proj")
In the rmarkdown, we can use
---
title: "Testing"
output:
pdf_document: default
html_document: default
---
```{r libraries, warning = FALSE, message = FALSE}
library(reticulate)
use_virtualenv("py-proj")
```
```{r chunk, warning = FALSE, message = FALSE}
write.csv(mtcars, "/Users/name/Desktop/mtcars.csv", row.names = TRUE)
```
```{python}
import pandas as pd
mtcars = pd.read_csv("/Users/name/Desktop/mtcars.csv")
mtcars.head(5)
```
-output
