Example usage

To use covid_tracker in a project:

import covid_tracker
from covid_tracker.get_covid_data import get_covid_data
from covid_tracker.plot_geographical import plot_geographical
from covid_tracker.plot_time_series import plot_ts
from covid_tracker.calculate_stat_summary import calculate_stat_summary

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Input In [1], in <module>
      1 import covid_tracker
----> 2 from covid_tracker.get_covid_data import get_covid_data
      3 from covid_tracker.plot_geographical import plot_geographical
      4 from covid_tracker.plot_time_series import plot_ts

ModuleNotFoundError: No module named 'covid_tracker.get_covid_data'

Retrieve the Data

We first retrieve the data using the get_covid_data function, and in this case we are using data_type = ‘active’ and all locations and dates by default.

covid_df = get_covid_data('active')
covid_df

	active_cases	active_cases_change	cumulative_cases	cumulative_deaths	cumulative_recovered	date_active	province
0	0	0	0	0	0	25-01-2020	Alberta
1	0	0	0	0	0	26-01-2020	Alberta
2	0	0	0	0	0	27-01-2020	Alberta
3	0	0	0	0	0	28-01-2020	Alberta
4	0	0	0	0	0	29-01-2020	Alberta
...	...	...	...	...	...	...	...
10229	213	-16	2820	15	2592	20-01-2022	Yukon
10230	196	-17	2849	16	2637	21-01-2022	Yukon
10231	196	0	2849	16	2637	22-01-2022	Yukon
10232	196	0	2849	16	2637	23-01-2022	Yukon
10233	194	-2	2959	16	2749	24-01-2022	Yukon

10234 rows × 7 columns

Plot Map

We can then plot a chloropleth map showing the cumulative number of deaths in each province across Canada.

plot_geographical(covid_df,'cumulative_deaths')

<Figure size 432x288 with 0 Axes>

Plot Time Series

We can also plot a time series graph showing the number of active cases over time.

plot_ts(covid_df, "active_cases")

---------------------------------------------------------------------------
MaxRowsError                              Traceback (most recent call last)
File ~\miniconda3\envs\covtrack\lib\site-packages\altair\vegalite\v4\api.py:2020, in Chart.to_dict(self, *args, **kwargs)
   2018     copy.data = core.InlineData(values=[{}])
   2019     return super(Chart, copy).to_dict(*args, **kwargs)
-> 2020 return super().to_dict(*args, **kwargs)

File ~\miniconda3\envs\covtrack\lib\site-packages\altair\vegalite\v4\api.py:374, in TopLevelMixin.to_dict(self, *args, **kwargs)
    372 copy = self.copy(deep=False)
    373 original_data = getattr(copy, "data", Undefined)
--> 374 copy.data = _prepare_data(original_data, context)
    376 if original_data is not Undefined:
    377     context["data"] = original_data

File ~\miniconda3\envs\covtrack\lib\site-packages\altair\vegalite\v4\api.py:89, in _prepare_data(data, context)
     87 # convert dataframes  or objects with __geo_interface__ to dict
     88 if isinstance(data, pd.DataFrame) or hasattr(data, "__geo_interface__"):
---> 89     data = _pipe(data, data_transformers.get())
     91 # convert string input to a URLData
     92 if isinstance(data, str):

File ~\miniconda3\envs\covtrack\lib\site-packages\toolz\functoolz.py:630, in pipe(data, *funcs)
    610 """ Pipe a value through a sequence of functions
    611 
    612 I.e. ``pipe(data, f, g, h)`` is equivalent to ``h(g(f(data)))``
   (...)
    627     thread_last
    628 """
    629 for func in funcs:
--> 630     data = func(data)
    631 return data

File ~\miniconda3\envs\covtrack\lib\site-packages\toolz\functoolz.py:306, in curry.__call__(self, *args, **kwargs)
    304 def __call__(self, *args, **kwargs):
    305     try:
--> 306         return self._partial(*args, **kwargs)
    307     except TypeError as exc:
    308         if self._should_curry(args, kwargs, exc):

File ~\miniconda3\envs\covtrack\lib\site-packages\altair\vegalite\data.py:19, in default_data_transformer(data, max_rows)
     17 @curried.curry
     18 def default_data_transformer(data, max_rows=5000):
---> 19     return curried.pipe(data, limit_rows(max_rows=max_rows), to_values)

File ~\miniconda3\envs\covtrack\lib\site-packages\toolz\functoolz.py:630, in pipe(data, *funcs)
    610 """ Pipe a value through a sequence of functions
    611 
    612 I.e. ``pipe(data, f, g, h)`` is equivalent to ``h(g(f(data)))``
   (...)
    627     thread_last
    628 """
    629 for func in funcs:
--> 630     data = func(data)
    631 return data

File ~\miniconda3\envs\covtrack\lib\site-packages\toolz\functoolz.py:306, in curry.__call__(self, *args, **kwargs)
    304 def __call__(self, *args, **kwargs):
    305     try:
--> 306         return self._partial(*args, **kwargs)
    307     except TypeError as exc:
    308         if self._should_curry(args, kwargs, exc):

File ~\miniconda3\envs\covtrack\lib\site-packages\altair\utils\data.py:80, in limit_rows(data, max_rows)
     78         return data
     79 if max_rows is not None and len(values) > max_rows:
---> 80     raise MaxRowsError(
     81         "The number of rows in your dataset is greater "
     82         "than the maximum allowed ({}). "
     83         "For information on how to plot larger datasets "
     84         "in Altair, see the documentation".format(max_rows)
     85     )
     86 return data

MaxRowsError: The number of rows in your dataset is greater than the maximum allowed (5000). For information on how to plot larger datasets in Altair, see the documentation

alt.Chart(...)

Calculate Summary

Lastly, we can create a summary of our covid tracking information.

calculate_stat_summary(covid_df, 'active')

	date_active	province	active_cases	active_cases_change	cumulative_cases	cumulative_deaths	cumulative_recovered	active_cases_max	active_cases_mean
718	2022-12-01	Alberta	61229	2616	424322	3367	359726	72368	8045
1449	2022-12-01	BC	39544	464	288692	2455	246693	40269	4622
2180	2022-12-01	Manitoba	35048	1431	105406	1429	68929	41708	2535
3642	2022-12-01	NL	6346	213	10827	23	4458	6346	178
5835	2022-12-01	NWT	1145	120	3467	12	2310	1306	58
2911	2022-12-01	New Brunswick	7060	-289	21249	174	14015	7935	367
4373	2022-12-01	Nova Scotia	6867	-545	28194	117	21210	8597	418
5104	2022-12-01	Nunavut	186	-8	1036	4	846	285	15
6566	2022-12-01	Ontario	116623	-3454	921332	10406	794303	126695	15272
7297	2022-12-01	PEI	1922	228	3427	0	1505	2514	71
8028	2022-12-01	Quebec	100448	-5802	758576	12028	646100	123058	12467
8759	2022-12-01	Repatriated	0	0	13	0	13	13	0
9490	2022-12-01	Saskatchewan	8707	477	95174	960	85507	13291	1551
10221	2022-12-01	Yukon	429	138	2515	15	2071	429	28