Merge pull request #10 from lee14257/lee14257/package-eval

Initial documentation and data fetching guide (with examples)

Author: krivard

docs/covidcast_examples.rst

@@ -0,0 +1,62 @@
+Basic examples
+--------------
+
+To obtain all available sources of epidemiological data, we can use the following command:
+
+>>> from delphi_epidata.request import CovidcastEpidata, EpiRange
+>>> epidata = CovidcastEpidata()
+>>> print(list(epidata.source_names))
+['chng-cli', 'chng-covid', 'covid-act-now', 'doctor-visits', 'fb-survey', 'google-symptoms', 'hhs', 'hospital-admissions', 'indicator-combination-cases-deaths', 'jhu-csse', 'quidel-covid-ag', 'safegraph-weekly', 'usa-facts', 'ght', 'google-survey', 'indicator-combination-nmf', 'quidel-flu', 'safegraph-daily', 'nchs-mortality']
+
+
+To obtain smoothed estimates of COVID-like illness from our symptom survey,
+distributed through Facebook (`fb-survey`), for every county in the United States between
+2020-05-01 and 2020-05-07:
+
+>>> from delphi_epidata.request import EpiRange
+>>> apicall = epidata[("fb-survey", "smoothed_cli")].call(    
+...     'county', "*", EpiRange(20200501, 20200507),
+... )
+EpiDataCall(endpoint=covidcast, params={'data_source': 'fb-survey', 'signals': 'smoothed_cli', 'time_type': 'day', 'time_values': '20200501-20200507', 'geo_type': 'county', 'geo_values': '*'})
+>>> data = apicall.df()
+>>> data.head()
+      source        signal geo_type geo_value time_type time_value      issue  lag     value    stderr  sample_size  direction  missing_value   missing_stderr  missing_sample_size
+0  fb-survey  smoothed_cli   county     01000       day 2020-05-01 2020-09-03  125  0.825410  0.136003         1722        NaN              0                0                    0
+1  fb-survey  smoothed_cli   county     01001       day 2020-05-01 2020-09-03  125  1.299425  0.967136          115        NaN              0                0                    0   
+2  fb-survey  smoothed_cli   county     01003       day 2020-05-01 2020-09-03  125  0.696597  0.324753          584        NaN              0                0                    0   
+3  fb-survey  smoothed_cli   county     01015       day 2020-05-01 2020-09-03  125  0.428271  0.548566          122        NaN              0                0                    0   
+4  fb-survey  smoothed_cli   county     01031       day 2020-05-01 2020-09-03  125  0.025579  0.360827          114        NaN              0                0                    0   
+
+
+Each row represents one observation in one county on one day. The county FIPS
+code is given in the ``geo_value`` column, the date in the ``time_value``
+column. Here ``value`` is the requested signal---in this case, the smoothed
+estimate of the percentage of people with COVID-like illness, based on the
+symptom surveys. ``stderr`` is its standard error. The ``issue`` column
+indicates when this data was reported; in this case, the survey estimates for
+May 1st were updated on September 3rd based on new data, giving a ``lag`` of 125 days.
+See the `Delphi Epidata API <https://cmu-delphi.github.io/delphi-epidata/api/README.html#epidata-api-other-diseases>`_ documentation for details on all fields of the returned data frame.
+
+The API documentation lists each available signal and provides technical details
+on how it is estimated and how its standard error is calculated. In this case,
+for example, the `symptom surveys documentation page
+<https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/fb-survey.html>`_
+explains the definition of "COVID-like illness", links to the exact survey text,
+and describes the mathematical derivation of the estimates.
+
+Using the ``geo_values`` argument, we can request data for a specific geography,
+such as the state of Pennsylvania for the month of September 2021:
+
+>>> pa_data = epidata[("fb-survey", "smoothed_cli")].call(    
+...         'state', "pa", EpiRange(20210901, 20210930)
+...     ).df()
+>>> pa_data.head()
+      source        signal geo_type geo_value time_type time_value      issue  lag     value    stderr  sample_size  direction  missing_value  missing_stderr  missing_sample_size
+0  fb-survey  smoothed_cli    state        pa       day 2021-09-01 2021-09-06    5  0.928210  0.088187         9390        NaN              0               0                    0
+1  fb-survey  smoothed_cli    state        pa       day 2021-09-02 2021-09-07    5  0.894603  0.087308         9275        NaN              0               0                    0
+2  fb-survey  smoothed_cli    state        pa       day 2021-09-03 2021-09-08    5  0.922847  0.088324         9179        NaN              0               0                    0
+3  fb-survey  smoothed_cli    state        pa       day 2021-09-04 2021-09-09    5  0.984799  0.092566         9069        NaN              0               0                    0
+4  fb-survey  smoothed_cli    state        pa       day 2021-09-05 2021-09-10    5  1.010306  0.093357         9016        NaN              0               0                    0
+
+We can request multiple states by providing a list, such as ``["pa", "ny",
+"mo"]``.