.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "_examples/pandas/plot_format04_therapy_all.py"
.. LINE NUMBERS ARE GIVEN BELOW.
.. only:: html
.. note::
:class: sphx-glr-download-link-note
Click :ref:`here <sphx_glr_download__examples_pandas_plot_format04_therapy_all.py>`
to download the full example code
.. rst-class:: sphx-glr-example-title
.. _sphx_glr__examples_pandas_plot_format04_therapy_all.py:
04. Format MIMIC therapy (all)
===============================
Description...
.. GENERATED FROM PYTHON SOURCE LINES 7-13
.. code-block:: default
:lineno-start: 7
# Generic libraries
import pandas as pd
# Show in terminal
TERMINAL = False
.. GENERATED FROM PYTHON SOURCE LINES 14-15
First, lets load and do some basic formatting on the data.
.. GENERATED FROM PYTHON SOURCE LINES 15-54
.. code-block:: default
:lineno-start: 16
# -----------------------------
# Constants
# -----------------------------
# Path
path = './data/mimic-therapy/ICU_diagnoses_antibiotics.csv'
# -----------------------------
# Load data
# -----------------------------
# Read data
data = pd.read_csv(path,
dayfirst=True,
parse_dates=['starttime',
'stoptime'])
# Keep only useful columns
data = data[['subject_id',
'hadm_id',
'stay_id',
'icd_code',
'antibiotic',
'route',
'starttime',
'stoptime']]
# Reformat (time info and str)
data.starttime = data.starttime.dt.date
data.stoptime = data.stoptime.dt.date
data.antibiotic = data.antibiotic \
.str.lower() \
.str.strip()
# Show
if TERMINAL:
print("\nData:")
print(data)
data
.. raw:: html
<div class="output_subarea output_html rendered_html output_result">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
vertical-align: top;
}
.dataframe thead th {
text-align: right;
}
</style>
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>subject_id</th>
<th>hadm_id</th>
<th>stay_id</th>
<th>icd_code</th>
<th>antibiotic</th>
<th>route</th>
<th>starttime</th>
<th>stoptime</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>10656173</td>
<td>25778760</td>
<td>30001555</td>
<td>J95851</td>
<td>ceftriaxone</td>
<td>IV</td>
<td>2177-09-27</td>
<td>2177-10-02</td>
</tr>
<tr>
<th>1</th>
<td>10656173</td>
<td>25778760</td>
<td>37985659</td>
<td>J95851</td>
<td>cefepime</td>
<td>IV</td>
<td>2177-09-19</td>
<td>2177-09-23</td>
</tr>
<tr>
<th>2</th>
<td>10656173</td>
<td>25778760</td>
<td>37985659</td>
<td>J95851</td>
<td>cefepime</td>
<td>IV</td>
<td>2177-09-11</td>
<td>2177-09-12</td>
</tr>
<tr>
<th>3</th>
<td>10656173</td>
<td>25778760</td>
<td>37985659</td>
<td>J95851</td>
<td>cefepime</td>
<td>IV</td>
<td>2177-09-10</td>
<td>2177-09-11</td>
</tr>
<tr>
<th>4</th>
<td>10656173</td>
<td>25778760</td>
<td>37985659</td>
<td>J95851</td>
<td>cefepime</td>
<td>IV</td>
<td>2177-09-12</td>
<td>2177-09-12</td>
</tr>
<tr>
<th>...</th>
<td>...</td>
<td>...</td>
<td>...</td>
<td>...</td>
<td>...</td>
<td>...</td>
<td>...</td>
<td>...</td>
</tr>
<tr>
<th>21541</th>
<td>15689523</td>
<td>23914765</td>
<td>39918058</td>
<td>99731</td>
<td>metronidazole (flagyl)</td>
<td>IV</td>
<td>2159-07-13</td>
<td>2159-07-25</td>
</tr>
<tr>
<th>21542</th>
<td>15689523</td>
<td>23914765</td>
<td>39918058</td>
<td>99731</td>
<td>metronidazole (flagyl)</td>
<td>IV</td>
<td>2159-06-27</td>
<td>2159-06-27</td>
</tr>
<tr>
<th>21543</th>
<td>15689523</td>
<td>23914765</td>
<td>39918058</td>
<td>99731</td>
<td>sulfamethoxazole-trimethoprim</td>
<td>IV</td>
<td>2159-06-25</td>
<td>2159-06-26</td>
</tr>
<tr>
<th>21544</th>
<td>15689523</td>
<td>23914765</td>
<td>39918058</td>
<td>99731</td>
<td>sulfamethoxazole-trimethoprim</td>
<td>IV</td>
<td>2159-06-26</td>
<td>2159-07-02</td>
</tr>
<tr>
<th>21545</th>
<td>15689523</td>
<td>23914765</td>
<td>39918058</td>
<td>99731</td>
<td>sulfamethoxazole-trimethoprim</td>
<td>IV</td>
<td>2159-06-29</td>
<td>2159-06-29</td>
</tr>
</tbody>
</table>
<p>21546 rows × 8 columns</p>
</div>
</div>
<br />
<br />
.. GENERATED FROM PYTHON SOURCE LINES 55-63
Lets transform the data
.. note:: You might need to add ``NaNs`` for missing days per patient.
The other sample included in this repository for a single patient
:ref:`sphx_glr__examples_pandas_plot_format04_therapy_one.py`
achieves this by using the following code: ``aux = aux.asfreq('1D')``
Note it needs to be applied per patient!
.. GENERATED FROM PYTHON SOURCE LINES 63-92
.. code-block:: default
:lineno-start: 64
# -----------------------------
# Transform data
# -----------------------------
# .. note: The closed parameter indicates whether to include
# the first and/or last samples. None will keep both,
# left will keep only start date and right will keep
# also the right date.
# Create column with date range
data['startdate'] = data.apply(lambda x:
pd.date_range(start=x['starttime'],
end=x['stoptime'],
closed='left', # ignoring right
freq='D') ,axis=1)
# Explode such column
data = data.explode('startdate')
# Groupby
groupby = ['subject_id',
'hadm_id',
'stay_id',
'startdate']
# Create daily therapies
aux = data.groupby(groupby) \
.apply(lambda x: sorted(x.antibiotic \
.unique().tolist()))
.. GENERATED FROM PYTHON SOURCE LINES 93-94
Lets see the formatted data
.. GENERATED FROM PYTHON SOURCE LINES 94-102
.. code-block:: default
:lineno-start: 95
# Show
if TERMINAL:
print("\nFormatted:")
print(aux)
aux
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
subject_id hadm_id stay_id startdate
10004733 27411876 39635619 2174-12-04 [piperacillin-tazobactam, vancomycin]
2174-12-05 [piperacillin-tazobactam, vancomycin]
2174-12-06 [piperacillin-tazobactam, vancomycin]
2174-12-07 [piperacillin-tazobactam]
2174-12-08 [piperacillin-tazobactam, vancomycin]
...
19997367 20617667 35616526 2126-05-06 [ceftriaxone]
2126-05-07 [ceftriaxone]
2126-05-08 [ceftriaxone]
2126-05-09 [ceftriaxone]
2126-05-10 [ceftriaxone]
Length: 22936, dtype: object
.. GENERATED FROM PYTHON SOURCE LINES 103-104
Lets count the number of days
.. GENERATED FROM PYTHON SOURCE LINES 104-112
.. code-block:: default
:lineno-start: 105
# Show
if TERMINAL:
print("\nTherapies (number of days)")
print(aux.value_counts())
aux.value_counts()
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
[cefepime, vancomycin] 2630
[cefepime] 1802
[vancomycin] 1732
[piperacillin-tazobactam, vancomycin] 1490
[meropenem] 1378
...
[cefepime, gentamicin, gentamicin sulfate, vancomycin] 1
[ciprofloxacin, ciprofloxacin iv, vancomycin] 1
[doxycycline hyclate, metronidazole (flagyl)] 1
[cefepime, ciprofloxacin iv, metronidazole (flagyl), sulfamethoxazole-trimethoprim, vancomycin] 1
[ceftolozane-tazobactam, ceftolozane-tazobactam *nf*] 1
Length: 707, dtype: int64
.. rst-class:: sphx-glr-timing
**Total running time of the script:** ( 0 minutes 5.921 seconds)
.. _sphx_glr_download__examples_pandas_plot_format04_therapy_all.py:
.. only :: html
.. container:: sphx-glr-footer
:class: sphx-glr-footer-example
.. container:: sphx-glr-download sphx-glr-download-python
:download:`Download Python source code: plot_format04_therapy_all.py <plot_format04_therapy_all.py>`
.. container:: sphx-glr-download sphx-glr-download-jupyter
:download:`Download Jupyter notebook: plot_format04_therapy_all.ipynb <plot_format04_therapy_all.ipynb>`
.. only:: html
.. rst-class:: sphx-glr-signature
`Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_