import os
from typing import Union
import pandas as pd
[docs]
def busan_beach(
inputs: list = None,
target: Union[list, str] = 'tetx_coppml'
) -> pd.DataFrame:
"""
Loads the Antibiotic resitance genes (ARG) data from a recreational beach
in Busan, South Korea along with environment variables.
The data is in the form of
mutlivariate time series and was collected over the period of 2 years during
several precipitation events. The frequency of environmental data is 30 mins
while that of ARG is discontinuous. The data and its pre-processing is described
in detail in `Jang et al., 2021 <https://doi.org/10.1016/j.watres.2021.117001>`_
Arguments
---------
inputs :
features to use as input. By default all environmental data
is used which consists of following parameters
- tide_cm
- wat_temp_c
- sal_psu
- air_temp_c
- pcp_mm
- pcp3_mm
- pcp6_mm
- pcp12_mm
- wind_dir_deg
- wind_speed_mps
- air_p_hpa
- mslp_hpa
- rel_hum
target :
feature/features to use as target/output. By default
`tetx_coppml` is used as target.
Logically one or more from following can be considered as target
- ecoli
- 16s
- inti1
- Total_args
- tetx_coppml
- sul1_coppml
- blaTEM_coppml
- aac_coppml
- Total_otus
- otu_5575
- otu_273
- otu_94
Returns
-------
pd.DataFrame
a pandas dataframe with inputs and target and indexed
with pandas.DateTimeIndex
Examples
--------
>>> from water_quality import busan_beach
>>> dataframe = busan_beach()
>>> dataframe.shape
(1446, 14)
>>> dataframe = busan_beach(target=['tetx_coppml', 'sul1_coppml'])
>>> dataframe.shape
(1446, 15)
See usage `here <https://tabulight.readthedocs.io/en/latest/auto_examples/busan_beach.html>`_ for more details.
"""
path = os.path.join(os.path.dirname(os.path.dirname(__file__)), "data")
if not os.path.exists(path):
os.makedirs(path)
fpath = os.path.join(path, "arg_busan.csv")
if os.path.exists(fpath):
df = pd.read_csv(fpath, index_col="index")
else:
df = pd.read_csv(
"https://raw.githubusercontent.com/AtrCheema/AI4Water/ec2a4a426673b11e3589b64cef9d7160b1de28d4/ai4water/datasets/arg_busan.csv",
index_col="index")
df.to_csv(fpath, index=True, index_label="index")
df.index = pd.to_datetime(df.index)
default_inputs = ['tide_cm', 'wat_temp_c', 'sal_psu', 'air_temp_c', 'pcp_mm', 'pcp3_mm', 'pcp6_mm',
'pcp12_mm', 'wind_dir_deg', 'wind_speed_mps', 'air_p_hpa', 'mslp_hpa', 'rel_hum'
]
default_targets = [col for col in df.columns if col not in default_inputs]
if inputs is None:
inputs = default_inputs
if not isinstance(target, list):
if isinstance(target, str):
target = [target]
elif isinstance(target, list):
pass
else:
target = default_targets
assert isinstance(target, list)
df = df[inputs + target]
return df