Final touches

Author: rzats

Makefile

@@ -25,6 +25,7 @@ test:
 	env/bin/pytest .
 
 doc:
+	env/bin/python docs/preprocess.py
 	env/bin/sphinx-build -b html docs docs/_build
 	env/bin/python -m webbrowser -t "docs/_build/index.html"
 

docs/data/endpoints.csv

@@ -0,0 +1,29 @@
+Endpoint,Description
+pub_covid_hosp_facility,Fetch COVID hospitalization data for specific facilities.
+pub_covid_hosp_facility_lookup,Lookup COVID hospitalization facility identifiers.
+pub_covid_hosp_state_timeseries,Fetch COVID hospitalization data.
+pub_covidcast,Fetch Delphi's COVID-19 Surveillance Streams
+pub_covidcast_meta,Fetch COVIDcast surveillance stream metadata.
+pub_delphi,Fetch Delphi's forecast.
+pub_dengue_nowcast,Fetch Delphi's dengue nowcast.
+pub_ecdc_ili,Fetch ECDC ILI data.
+pub_flusurv,Fetch FluSurv data.
+pub_fluview,
+pub_fluview_clinical,Fetch FluView clinical data.
+pub_fluview_meta,
+pub_gft,Fetch Google Flu Trends data.
+pub_kcdc_ili,Fetch KCDC ILI data.
+pub_meta,Fetch API metadata.
+pub_nidss_dengue,Fetch NIDSS dengue data.
+pub_nidss_flu,Fetch NIDSS flu data.
+pub_nowcast,Fetch Delphi's wILI nowcast.
+pub_paho_dengue,Fetch PAHO Dengue data.
+pub_wiki,Fetch Wikipedia access data.
+pvt_cdc,Fetch CDC page hits.
+pvt_dengue_sensors,Fetch Delphi's digital surveillance sensors.
+pvt_ght,Fetch Google Health Trends data.
+pvt_meta_norostat,Fetch NoroSTAT metadata.
+pvt_norostat,"Fetch NoroSTAT data (point data, no min/max)."
+pvt_quidel,Fetch Quidel data.
+pvt_sensors,Fetch Delphi's digital surveillance sensors.
+pvt_twitter,Fetch HealthTweets data.

docs/getting_started.rst

@@ -112,7 +112,9 @@ it supports ``*``.)
    print(apicall)
    print(apicall.df().head())
 
-We can fetch a subset of states by listing out the desired locations:
+Alternatively, we can fetch the full time series for a subset of states by 
+listing out the desired locations in the ``geo_value`` argument and using
+``*`` in the ``time_values`` argument:
 
 .. exec::
    :context: true
@@ -128,22 +130,6 @@ We can fetch a subset of states by listing out the desired locations:
    print(apicall)
    print(apicall.df().head())
 
-We can also request data for a single location at a time, via the ``geo_values`` argument.
-
-.. exec::
-   :context: true
-
-   apicall = epidata.pub_covidcast(
-      data_source = "fb-survey",
-      signals = "smoothed_cli",
-      geo_type = "state",
-      time_type = "day",
-      geo_values = "pa",
-      time_values = EpiRange(20210405, 20210410))
-
-   print(apicall)
-   print(apicall.df().head())
-
 Getting versioned data
 ----------------------
 
@@ -234,3 +220,21 @@ the data stream that you are most interested in.
 The Epidata documentation lists all the data sources and signals available
 through the API for `COVID-19 <https://cmu-delphi.github.io/delphi-epidata/api/covidcast_signals.html>`_
 and for `other diseases <https://cmu-delphi.github.io/delphi-epidata/api/README.html#source-specific-parameters>`_.
+
+Epiweeks and Dates
+------------------
+Epiweeks use the U.S. definition. That is, the first epiweek each year is the
+week, starting on a Sunday, containing January 4. See `this page
+<https://www.cmmcp.org/mosquito-surveillance-data/pages/epi-week-calendars-2008-2021>`_
+for more information.
+
+Formatting for epiweeks is YYYYWW and for dates is YYYYMMDD.
+
+Use individual values, comma-separated lists or, a hyphenated range of values to specify single or several dates.
+An ``EpiRange`` object can be also used to construct a range of epiweeks or dates. Examples include:
+
+- ``param = 201530`` (A single epiweek)
+- ``param = '201401,201501,201601'`` (Several epiweeks)
+- ``param = '200501-200552'`` (A range of epiweeks)
+- ``param = '201440,201501-201510'`` (Several epiweeks, including a range)
+- ``param = EpiRange(20070101, 20071231)`` (A range of dates)

docs/getting_started_with_epidatpy.rst

@@ -66,12 +66,10 @@ Contents
 .. toctree::
    :maxdepth: 2
 
-   getting_started
-
    getting_started_with_epidatpy
 
-   epidatpy
-
    signal_discovery
 
    versioned_data
+
+   epidatpy