diff --git a/docs/api/afhsb.md b/docs/api/afhsb.md index fccdcee78..f0e29ca32 100644 --- a/docs/api/afhsb.md +++ b/docs/api/afhsb.md @@ -31,7 +31,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | --- | --- | --- | | `auth` | password | string | | `epiweeks` | epiweeks | `list` of epiweeks | -| `locations` | locations | `list` of [region](../../labels/regions.txt), [state](../../labels/states.txt), or 3-letter country code labels | +| `locations` | locations | `list` of [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt), [state](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/states.txt), or 3-letter country code labels | | `flu_types` | flu types | `list` of disjoint (`flu1`, `flu2-flu1`, `flu3-flu2`, `ili-flu3`) or subset (`flu2`, `flu3`, `ili`) flu type labels | ## Response diff --git a/docs/api/cdc.md b/docs/api/cdc.md index b79e8927b..97a6fc478 100644 --- a/docs/api/cdc.md +++ b/docs/api/cdc.md @@ -31,7 +31,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | --- | --- | --- | | `auth` | password | string | | `epiweeks` | epiweeks | `list` of epiweeks | -| `locations` | locations | `list` of [region](../../labels/regions.txt)/[state](../../labels/states.txt) labels | +| `locations` | locations | `list` of [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt)/[state](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/states.txt) labels | ## Response diff --git a/docs/api/covid_hosp.md b/docs/api/covid_hosp.md index ca312e3ed..863d7c48a 100644 --- a/docs/api/covid_hosp.md +++ b/docs/api/covid_hosp.md @@ -143,7 +143,7 @@ https://delphi.cmu.edu/epidata/covid_hosp_state_timeseries/?states=MA&dates=2020 # Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following sample shows how to import the library and fetch MA on 2020-05-10 (per most recent issue). diff --git a/docs/api/covid_hosp_facility.md b/docs/api/covid_hosp_facility.md index 82508d5b1..f85f324d0 100644 --- a/docs/api/covid_hosp_facility.md +++ b/docs/api/covid_hosp_facility.md @@ -190,7 +190,7 @@ https://delphi.cmu.edu/epidata/covid_hosp_facility/?hospital_pks=390119&collecti # Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following sample shows how to import the library and fetch Moses Taylor Hospital (Scranton, PA) on the first collection week of December 2020 (per most recent issue). diff --git a/docs/api/covid_hosp_facility_lookup.md b/docs/api/covid_hosp_facility_lookup.md index bd98c4788..1fea970fe 100644 --- a/docs/api/covid_hosp_facility_lookup.md +++ b/docs/api/covid_hosp_facility_lookup.md @@ -99,7 +99,7 @@ https://delphi.cmu.edu/epidata/covid_hosp_facility_lookup/?city=southlake # Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following sample shows how to import the library and fetch facilities in the city of Southlake (TX). diff --git a/docs/api/covidcast_meta.md b/docs/api/covidcast_meta.md index 67f8b5867..82c4579e2 100644 --- a/docs/api/covidcast_meta.md +++ b/docs/api/covidcast_meta.md @@ -73,7 +73,7 @@ https://api.covidcast.cmu.edu/epidata/covidcast_meta/ ## Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following samples show how to import the library and fetch Delphi's COVID-19 Surveillance Streams metadata. ### JavaScript (in a web browser) diff --git a/docs/api/flusurv.md b/docs/api/flusurv.md index c04923750..fb990220a 100644 --- a/docs/api/flusurv.md +++ b/docs/api/flusurv.md @@ -37,7 +37,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | Parameter | Description | Type | | --- | --- | --- | | `epiweeks` | epiweeks | `list` of epiweeks | -| `locations` | locations | `list` of [location](../../labels/flusurv_locations.txt) labels | +| `locations` | locations | `list` of [location](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/flusurv_locations.txt) labels | ### Optional @@ -105,7 +105,7 @@ https://delphi.cmu.edu/epidata/flusurv/?locations=ca&epiweeks=202001 # Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following samples show how to import the library and fetch CA FluView Clinical data for epiweeks `201940` and `202001-202010` (11 weeks total). ### JavaScript (in a web browser) diff --git a/docs/api/fluview.md b/docs/api/fluview.md index ad37c32c0..688089d25 100644 --- a/docs/api/fluview.md +++ b/docs/api/fluview.md @@ -18,7 +18,7 @@ General topics not specific to any particular endpoint are discussed in the Influenza-like illness (ILI) from U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet). - Data source: [United States Centers for Disease Control and Prevention](http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html) (CDC) - Temporal Resolution: Weekly* from 1997w40 - - Spatial Resolution: National, [HHS regions](http://www.hhs.gov/iea/regional/), [Census divisions](http://www.census.gov/econ/census/help/geography/regions_and_divisions.html), most States and Territories, and some Cities (full list [here](../../src/acquisition/fluview/fluview_locations.py)) + - Spatial Resolution: National, [HHS regions](http://www.hhs.gov/iea/regional/), [Census divisions](http://www.census.gov/econ/census/help/geography/regions_and_divisions.html), most States and Territories, and some Cities (full list [here](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/acquisition/fluview/fluview_locations.py)) - Open access \* Data is usually released on Friday @@ -36,7 +36,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | Parameter | Description | Type | | --- | --- | --- | | `epiweeks` | epiweeks | `list` of epiweeks | -| `regions` | regions | `list` of [region](../../labels/regions.txt) labels | +| `regions` | regions | `list` of [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt) labels | ### Optional @@ -120,7 +120,7 @@ https://delphi.cmu.edu/epidata/fluview/?regions=nat&epiweeks=201453&issues=20150 # Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following samples show how to import the library and fetch national FluView data for epiweeks `201440` and `201501-201510` (11 weeks total). diff --git a/docs/api/fluview_clinical.md b/docs/api/fluview_clinical.md index 11906bde7..5583abcc4 100644 --- a/docs/api/fluview_clinical.md +++ b/docs/api/fluview_clinical.md @@ -31,7 +31,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | Parameter | Description | Type | | --- | --- | --- | | `epiweeks` | epiweeks | `list` of epiweeks | -| `regions` | regions | `list` of [region](../../labels/regions.txt) labels | +| `regions` | regions | `list` of [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt) labels | ### Optional @@ -94,7 +94,7 @@ https://delphi.cmu.edu/epidata/fluview_clinical/?regions=nat&epiweeks=202001 # Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following samples show how to import the library and fetch national FluView Clinical data for epiweeks `201940` and `202001-202010` (11 weeks total). ### JavaScript (in a web browser) diff --git a/docs/api/gft.md b/docs/api/gft.md index b373b517b..21d9676fb 100644 --- a/docs/api/gft.md +++ b/docs/api/gft.md @@ -18,7 +18,7 @@ General topics not specific to any particular endpoint are discussed in the Estimate of influenza activity based on volume of certain search queries. Google has discontinued Flu Trends, and this is now a static endpoint. - Source: [Google](https://www.google.org/flutrends/) - Temporal Resolution: Weekly from 2003w40 until 2015w32 - - Spatial Resolution: National, [HHS regions](http://www.hhs.gov/iea/regional/) ([1+10](../../labels/regions.txt)); by state/territory ([50+1](../../labels/states.txt)); and by city ([97](../../labels/cities.txt)) + - Spatial Resolution: National, [HHS regions](http://www.hhs.gov/iea/regional/) ([1+10](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt)); by state/territory ([50+1](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/states.txt)); and by city ([97](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/cities.txt)) - Open access # The API @@ -34,7 +34,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | Parameter | Description | Type | | --- | --- | --- | | `epiweeks` | epiweeks | `list` of epiweeks | -| `locations` | locations | `list` of [region](../../labels/regions.txt)/[state](../../labels/states.txt)/[city](../../labels/cities.txt) labels | +| `locations` | locations | `list` of [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt)/[state](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/states.txt)/[city](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/cities.txt) labels | ## Response @@ -69,7 +69,7 @@ https://delphi.cmu.edu/epidata/gft/?locations=nat&epiweeks=201501 # Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following samples show how to import the library and fetch Google Flu Trends data for epiweeks `201440` and `201501-201510` (11 weeks total). ### JavaScript (in a web browser) diff --git a/docs/api/ght.md b/docs/api/ght.md index 2bc6f935a..db333ef6c 100644 --- a/docs/api/ght.md +++ b/docs/api/ght.md @@ -31,7 +31,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | --- | --- | --- | | `auth` | password | string | | `epiweeks` | epiweeks | `list` of epiweeks | -| `locations` | locations | `list` of [state](../../labels/states.txt) and/or `US` labels | +| `locations` | locations | `list` of [state](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/states.txt) and/or `US` labels | | `query` | search query or topic ID (see https://www.freebase.com/) | string | ## Response diff --git a/docs/api/nidss_dengue.md b/docs/api/nidss_dengue.md index eec6cb737..330963ad6 100644 --- a/docs/api/nidss_dengue.md +++ b/docs/api/nidss_dengue.md @@ -18,7 +18,7 @@ General topics not specific to any particular endpoint are discussed in the Counts of confirmed dengue cases from Taiwan's NIDSS. - Data source: [Taiwan CDC](http://nidss.cdc.gov.tw/en/SingleDisease.aspx?dc=1&dt=4&disease=061&position=1) - Temporal Resolution: Weekly from 2003w01 - - Spatial Resolution: By [hexchotomy region](https://en.wikipedia.org/wiki/Regions_of_Taiwan#Hexchotomy) ([6+1](../../labels/nidss_regions.txt)) and by [city/county](https://en.wikipedia.org/wiki/List_of_administrative_divisions_of_Taiwan) ([22](../../labels/nidss_locations.txt)) + - Spatial Resolution: By [hexchotomy region](https://en.wikipedia.org/wiki/Regions_of_Taiwan#Hexchotomy) ([6+1](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/nidss_regions.txt)) and by [city/county](https://en.wikipedia.org/wiki/List_of_administrative_divisions_of_Taiwan) ([22](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/nidss_locations.txt)) - Open access # The API @@ -34,7 +34,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | Parameter | Description | Type | | --- | --- | --- | | `epiweeks` | epiweeks | `list` of epiweeks | -| `locations` | locations | `list` of [region](../../labels/nidss_regions.txt) and/or [location](../../labels/nidss_locations.txt) labels | +| `locations` | locations | `list` of [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/nidss_regions.txt) and/or [location](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/nidss_locations.txt) labels | ## Response @@ -69,7 +69,7 @@ https://delphi.cmu.edu/epidata/nidss_dengue/?locations=nationwide&epiweeks=20150 # Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following samples show how to import the library and fetch national NIDSS Dengue data for epiweeks `201440` and `201501-201510` (11 weeks total). ### JavaScript (in a web browser) diff --git a/docs/api/nidss_flu.md b/docs/api/nidss_flu.md index 591493531..8231aa0d7 100644 --- a/docs/api/nidss_flu.md +++ b/docs/api/nidss_flu.md @@ -18,7 +18,7 @@ General topics not specific to any particular endpoint are discussed in the Outpatient ILI from Taiwan's National Infectious Disease Statistics System (NIDSS). - Source: [Taiwan CDC](http://nidss.cdc.gov.tw/en/CDCWNH01.aspx?dc=wnh) - Temporal Resolution: Weekly* from 2008w14 - - Spatial Resolution: By [hexchotomy region](https://en.wikipedia.org/wiki/Regions_of_Taiwan#Hexchotomy) ([6+1](../../labels/nidss_regions.txt)) + - Spatial Resolution: By [hexchotomy region](https://en.wikipedia.org/wiki/Regions_of_Taiwan#Hexchotomy) ([6+1](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/nidss_regions.txt)) - Open access \* Data is usually released on Tuesday @@ -36,7 +36,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | Parameter | Description | Type | | --- | --- | --- | | `epiweeks` | epiweeks | `list` of epiweeks | -| `regions` | regions | `list` of [region](../../labels/nidss_regions.txt) labels | +| `regions` | regions | `list` of [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/nidss_regions.txt) labels | ### Optional @@ -90,7 +90,7 @@ https://delphi.cmu.edu/epidata/nidss_flu/?regions=nationwide&epiweeks=201501 # Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following samples show how to import the library and fetch national NIDSS Flu data for epiweeks `201440` and `201501-201510` (11 weeks total). ### JavaScript (in a web browser) diff --git a/docs/api/nowcast.md b/docs/api/nowcast.md index eb295659e..51f33835c 100644 --- a/docs/api/nowcast.md +++ b/docs/api/nowcast.md @@ -18,7 +18,7 @@ General topics not specific to any particular endpoint are discussed in the A nowcast of U.S. national, regional, and state-level (weighted) %ILI, available seven days (regionally) or five days (state-level) before the first ILINet report for the corresponding week. - Source: [Delphi's ILI Nearby system](https://delphi.cmu.edu/nowcast/) - Temporal Resolution: Weekly, from 2010w30* - - Spatial Resolution: National, [HHS regions](http://www.hhs.gov/iea/regional/), [Census divisions](http://www.census.gov/econ/census/help/geography/regions_and_divisions.html) ([1+10+9](../../labels/regions.txt)), and by state/territory ([51](../../labels/states.txt)) + - Spatial Resolution: National, [HHS regions](http://www.hhs.gov/iea/regional/), [Census divisions](http://www.census.gov/econ/census/help/geography/regions_and_divisions.html) ([1+10+9](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt)), and by state/territory ([51](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/states.txt)) - Open access \* Data is usually released on Friday and updated on Sunday and Monday @@ -36,7 +36,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | Parameter | Description | Type | | --- | --- | --- | | `epiweeks` | epiweeks | `list` of epiweeks | -| `locations` | locations | `list` of [region](../../labels/regions.txt)/[state](../../labels/states.txt) labels | +| `locations` | locations | `list` of [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt)/[state](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/states.txt) labels | ## Response @@ -73,7 +73,7 @@ https://delphi.cmu.edu/epidata/nowcast/?locations=nat&epiweeks=202001 # Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following samples show how to import the library and fetch national ILI Nearby data for epiweeks `201940` and `202001-202010` (11 weeks total). ### JavaScript (in a web browser) diff --git a/docs/api/quidel.md b/docs/api/quidel.md index 2e269810f..3f5c39115 100644 --- a/docs/api/quidel.md +++ b/docs/api/quidel.md @@ -33,7 +33,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | --- | --- | --- | | `auth` | password | string | | `epiweeks` | epiweeks | `list` of epiweeks | -| `locations` | locations | `list` of `hhs<#>` [region](../../labels/regions.txt) labels | +| `locations` | locations | `list` of `hhs<#>` [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt) labels | ## Response diff --git a/docs/api/sensors.md b/docs/api/sensors.md index e4dc93e02..a00669d13 100644 --- a/docs/api/sensors.md +++ b/docs/api/sensors.md @@ -40,7 +40,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | Parameter | Description | Type | | --- | --- | --- | | `epiweeks` | epiweeks | `list` of epiweeks | -| `locations` | locations | `list` of [region](../../labels/regions.txt)/[state](../../labels/states.txt) labels | +| `locations` | locations | `list` of [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt)/[state](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/states.txt) labels | | `names` | sensor names | `list` of string | Notes: @@ -90,7 +90,7 @@ https://delphi.cmu.edu/epidata/sensors/?names=sar3&locations=nat&epiweeks=202001 # Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following samples show how to import the library and fetch national Delphi's Digital Surveillance SAR3 Sensor data for epiweeks `201940` and `202001-202010` (11 weeks total). ### JavaScript (in a web browser) diff --git a/docs/api/twitter.md b/docs/api/twitter.md index 2bdb415a8..10564dcf9 100644 --- a/docs/api/twitter.md +++ b/docs/api/twitter.md @@ -18,7 +18,7 @@ General topics not specific to any particular endpoint are discussed in the Estimate of influenza activity based on analysis of language used in tweets. - Source: [HealthTweets](http://www.healthtweets.org/) - Temporal Resolution: Daily and weekly from 2011-12-01 (2011w48) - - Spatial Resolution: National, [HHS regions](http://www.hhs.gov/iea/regional/), and [Census divisions](http://www.census.gov/econ/census/help/geography/regions_and_divisions.html) ([1+10+9](../../labels/regions.txt)); and by state/territory ([51](../../labels/states.txt)) + - Spatial Resolution: National, [HHS regions](http://www.hhs.gov/iea/regional/), and [Census divisions](http://www.census.gov/econ/census/help/geography/regions_and_divisions.html) ([1+10+9](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt)); and by state/territory ([51](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/states.txt)) - Restricted access: Delphi doesn't have permission to share this dataset # The API @@ -34,7 +34,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | Parameter | Description | Type | | --- | --- | --- | | `auth` | password | string | -| `locations` | locations | `list` of [region](../../labels/regions.txt)/[state](../../labels/states.txt) labels | +| `locations` | locations | `list` of [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt)/[state](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/states.txt) labels | | `dates` | dates | `list` of dates | | `epiweeks` | epiweeks | `list` of epiweeks | diff --git a/docs/api/wiki.md b/docs/api/wiki.md index 58249b394..81bc105e2 100644 --- a/docs/api/wiki.md +++ b/docs/api/wiki.md @@ -19,7 +19,7 @@ Number of page visits for selected English, Influenza-related wikipedia articles - Source: [Wikimedia](https://dumps.wikimedia.org/other/pagecounts-raw/) - Temporal Resolution: Hourly, daily, and weekly from 2007-12-09 (2007w50) - Spatial Resolution: N/A - - Other resolution: By article ([54](../../labels/articles.txt)) + - Other resolution: By article ([54](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/articles.txt)) - Open access # The API @@ -34,7 +34,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | Parameter | Description | Type | | --- | --- | --- | -| `articles` | articles | list of [articles](../../labels/articles.md) | +| `articles` | articles | list of [articles](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/articles.md) | | `language` | language (currently `en`, `es`, and `pt` supported) | string | | `dates` | dates | `list` of dates | | `epiweeks` | epiweeks | `list` of epiweeks | @@ -107,7 +107,7 @@ https://delphi.cmu.edu/epidata/wiki/?language=en&articles=influenza&dates=202001 # Code Samples -Libraries are available for [JavaScript](../../src/client/delphi_epidata.js), [Python](../../src/client/delphi_epidata.py), and [R](../../src/client/delphi_epidata.R). +Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R). The following samples show how to import the library and fetch national Wikipedia Access data for article "influenza" on epiweeks `201940` and `202001-202010` (11 weeks total) for hours 0 and 12 in English. diff --git a/docs/epidata_development.md b/docs/epidata_development.md index 87602f8f0..5264d0b7b 100644 --- a/docs/epidata_development.md +++ b/docs/epidata_development.md @@ -69,10 +69,10 @@ These are both based on core Delphi images as defined in the above. The base images are built first, followed by the derived `epidata`-specific images. -- The [`delphi_web_epidata` image](../dev/docker/web/epidata/README.md) adds +- The [`delphi_web_epidata` image](https://github.com/cmu-delphi/delphi-epidata/blob/main/dev/docker/web/epidata/README.md) adds the Epidata API to the `delphi_web` image. - The - [`delphi_database_epidata` image](../dev/docker/database/epidata/README.md) + [`delphi_database_epidata` image](https://github.com/cmu-delphi/delphi-epidata/blob/main/dev/docker/database/epidata/README.md) adds the `epi` user account, `epidata` database, and relevant tables (initially empty) to the `delphi_database` image. @@ -246,8 +246,8 @@ Here's a full example based on the `fluview` endpoint: Writing an integration test is outside of the scope of this document. However, a number of existing integration tests exist and can be used as a good starting point for additional tests. For example, see the tests for the -[`fluview` API endpoint](../integrations/server/test_fluview.py) and the -[`covidcast` ingestion pipeline](../integrations/acquisition/covidcast). +[`fluview` API endpoint](https://github.com/cmu-delphi/delphi-epidata/blob/main/integrations/server/test_fluview.py) and the +[`covidcast` ingestion pipeline](https://github.com/cmu-delphi/delphi-epidata/blob/main/integrations/acquisition/covidcast). To run the existing tests and any new tests that you write, you must follow the @@ -365,15 +365,15 @@ The command above mounts two specific files into the image. It may be tempting to bind mount the `src/server` directory rather than specific files, however that is currently problematic for a couple of reasons: -1. `server/.htaccess` [from the local repository](../src/server/.htaccess) uses +1. `server/.htaccess` [from the local repository](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/server/.htaccess) uses the `Header` directive. However, the webserver in the container doesn't have the corresponding module enabled. This causes the server to deny access to the API. 2. `server/database_config.php` - [in the image](../dev/docker/web/epidata/assets/database_config.php) contains + [in the image](https://github.com/cmu-delphi/delphi-epidata/blob/main/dev/docker/web/epidata/assets/database_config.php) contains database credentials for use in conjunction with the `delphi_database_epidata` container during development. However, the same - file from [the local repository](../src/server/database_config.php) only + file from [the local repository](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/server/database_config.php) only contains placeholder values. This prevents communication with the database. There is currently no benefit to bind-mounting sources into the database diff --git a/docs/new_endpoint_tutorial.md b/docs/new_endpoint_tutorial.md index c5739768c..87a1a3b11 100644 --- a/docs/new_endpoint_tutorial.md +++ b/docs/new_endpoint_tutorial.md @@ -55,7 +55,7 @@ is to extract the subset of metadata pertaining to `fluview` and return just tha data through a new endpoint. Each row in the `fluview` table contains -[a lot of data](../src/ddl/fluview.sql), but we're particularly interested in +[a lot of data](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/ddl/fluview.sql), but we're particularly interested in the following: - latest publication date @@ -83,7 +83,7 @@ what this looks like. Here's what we add to each client: -- [`delphi_epidata.js`](../src/client/delphi_epidata.js) +- [`delphi_epidata.js`](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js) ```javascript // within createEpidataAsync return { @@ -98,7 +98,7 @@ Here's what we add to each client: }; ``` -- [`delphi_epidata.d.ts`](../src/client/delphi_epidata.d.ts) +- [`delphi_epidata.d.ts`](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.d.ts) ```typescript export interface EpidataFunctions { // ... @@ -110,7 +110,7 @@ Here's what we add to each client: } ``` -- [`delphi_epidata.py`](../src/client/delphi_epidata.py) +- [`delphi_epidata.py`](https://pypi.org/project/delphi-epidata/) Note that this file, unlike the others, is released as a public package, available to install easily through Python's `pip` tool. That package should @@ -130,7 +130,7 @@ Here's what we add to each client: return Epidata._request(params) ``` -- [`delphi_epidata.R`](../src/client/delphi_epidata.R) +- [`delphi_epidata.R`](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R) ```R # Fetch FluView metadata @@ -164,7 +164,7 @@ needs to be an integration test. See more about integration testing in Delphi's Create an integration test for the new endpoint by creating a new file, `integrations/server/test_fluview_meta.py`. There's a good amount of boilerplate, but fortunately, this can be copied _almost_ verbatim from the -[`fluview` endpoint integration test](../integrations/server/test_fluview.py). +[`fluview` endpoint integration test](https://github.com/cmu-delphi/delphi-epidata/blob/main/integrations/server/test_fluview.py). Include the following pieces: