1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
|
"""
Loading a RDS file from a URL
=============================
A simple example showing how to read a dataset in the RDS format from a URL.
"""
# sphinx_gallery_thumbnail_path = '_static/download.png'
# %%
# If the data to read is accesible at a particular URL, we can open it as a
# file using the function :external+python:func:`urllib.request.urlopen`.
# Thus, we need to import that function as well as the rdata package.
from urllib.request import urlopen
import rdata
# %%
# For this example we will use a dataset hosted at
# `Zenodo <https://zenodo.org/records/7425539>`_.
# This is a small dataset containing information about some fungal pathogens.
#
dataset_url = (
"https://zenodo.org/records/7425539/files/core_fungal_pathogens.rds"
)
# %%
# The object resulting from calling
# :external+python:func:`~urllib.request.urlopen` can be then
# passed to :func:`~rdata.parser.parse_file` as if it were a normal file.
with urlopen(dataset_url) as dataset:
parsed = rdata.parser.parse_file(dataset)
# %%
# RDS files do not have a special magic number that identifies them.
# Thus, when reading a RDS file, rdata has to suppose that the file is a valid
# RDS file, and warns about that.
# We can omit this warning by passing manually the extension of the file
# instead.
with urlopen(dataset_url) as dataset:
parsed = rdata.parser.parse_file(dataset, extension=".rds")
# %%
# This parsed object contains a lossless representation of the internal data
# contained in the file.
# This data mimics the internal format used in R, and is thus not directly
# usable.
# However, we can retrieve some information about the file that will be lost
# after the conversion to a Python object, such as the version of the format
# employed or the encoding used for the strings.
print(parsed.versions.format)
print(parsed.extra.encoding)
# %%
# In order to convert it to Python objects we need to use the function
# :func:`rdata.conversion.convert`.
converted = rdata.conversion.convert(parsed)
# %%
# RDS files contain just one R object.
# In this particular case, it is a R dataframe object, that will be converted
# to a Pandas dataframe by default.
converted
# %%
# As usually we just want to parse and convert a given dataset, the convenience
# functions :func:`rdata.read_rds` and :func:`rdata.read_rda` can be used with
# that purpose.
with urlopen(dataset_url) as dataset:
data = rdata.read_rds(dataset)
data
|
