Puerto Rico Github issues

Date	Number	Title
April 1, 2021, 4:03 PM PDT	1139	[PR] Patch 03/07/21 data
April 1, 2021, 4:03 PM PDT	1139	[PR] Patch 03/07/21 data
February 11, 2021, 8:02 AM PST	1096	[PR] Patch 10/01/20 - 02/10/21 Total PCR tests (specimens), Negative PCR tests (specimens), Positive PCR tests (specimens)
February 11, 2021, 8:02 AM PST	1096	[PR] Patch 10/01/20 - 02/10/21 Total PCR tests (specimens), Negative PCR tests (specimens), Positive PCR tests (specimens)
November 7, 2020, 4:51 PM PST	938	[PR] Probable cases totals for Nov. 5-6
November 7, 2020, 12:47 PM PST	937	[PR] Clear PR Probable Cases History
November 6, 2020, 4:53 PM PST	936	[PR] Puerto Rico to redefine "probable" cases to mean antigen testing
October 23, 2020, 10:19 AM PDT	910	[PR] Update 10/23/20
September 30, 2020, 11:32 AM PDT	878	[PR] Total Tests, Positive Tests, and Negative Tests(PCR) Backfill 8/28/20-9/30/20
September 14, 2020, 11:31 AM PDT	829	[PR] Backfill probable cases time-series starting on 4/24
July 30, 2020, 7:38 AM PDT	703	[PR] PCL Cases Historicals
July 24, 2020, 11:32 AM PDT	669	[PR] New Puerto Rico testing count report for July 24
July 19, 2020, 3:57 PM PDT	649	[PR] Confirmed + probable cases is a bad metric for Puerto Rico
July 17, 2020, 6:40 PM PDT	645	[PR] Puerto Rico Department of Health testing data API
July 11, 2020, 1:18 AM PDT	604	[PR] Historical Puerto Rico hospitalizations data
July 10, 2020, 2:24 PM PDT	603	[PR] New Puerto Rico testing data report (as of 2020-07-09)
July 2, 2020, 1:40 PM PDT	568	[PR] Official testing data for Puerto Rico
April 23, 2020, 3:17 PM PDT	276	[States Daily CSV] PR positiveIncrease is negative for 2020-04-22
April 21, 2020, 9:45 AM PDT	247	GA data discrepancy (~ APR 20)
April 17, 2020, 1:25 PM PDT	211	PR Test Data Note [Dept of Health has been double/triple counting]
March 27, 2020, 5:32 AM PDT	65	PR: Correct URL for Puerto Rico

#1139: [PR] Patch 03/07/21 data

Issue number 1139

hmhoffman opened this issue on April 1, 2021, 4:03 PM PDT

Open in Github

State: PR

Dates affected: 03/07/21

Describe the issue: On March 7, 2021, Puerto Rico relocated their data to another link. To allow our data quality team time to investigate this source, we did not update their data on March 7, 2021. We're backfilling their data for March 7, 2021, from screenshots of their new dashboard and their COVID-19 report from the day.

Screenshots: https://covid-tracking-project-data.s3.amazonaws.com/state_screenshots/PR/manual/PR-data-dashboard-20210307-171200.png https://covid-tracking-project-data.s3.amazonaws.com/state_screenshots/PR/manual/PR-data-dashboard-20210307-171201.png

Comments

hmhoffman commented on April 1, 2021, 4:11 PM PDT

Open in Github

Rows edited: 1 PR 2021-03-07 positive: 101632 (was 101327) hospitalizedCurrently: 134 (was 147) inIcuCurrently: 21 (was 24) onVentilatorCurrently: 19 (was 18) death: 2062 (was 2059) deathConfirmed: 1752 (was 1749) probableCases: 8012 (was 7991) positiveCasesViral: 93620 (was 93336) positiveTestsAntibody: 85241 (was 84115) lastUpdateTime: 2021-03-07 05:00:00+00:00 (was 2021-03-06 05:00:00+00:00)

#1139: [PR] Patch 03/07/21 data

Issue number 1139

hmhoffman opened this issue on April 1, 2021, 4:03 PM PDT

Open in Github

State: PR

Dates affected: 03/07/21

Comments

hmhoffman commented on April 1, 2021, 4:11 PM PDT

Open in Github

#1096: [PR] Patch 10/01/20 - 02/10/21 Total PCR tests (specimens), Negative PCR tests (specimens), Positive PCR tests (specimens)

Issue number 1096

hmhoffman opened this issue on February 11, 2021, 8:02 AM PST

Open in Github

State: PR

Dates affected: 10/01/20 - 02/10/21

Describe the issue: On October 1, 2020, we received a press release from Dept. de Salud with updated Total PCR tests (specimens), Negative PCR tests (specimens), and Positive PCR tests (specimens) for Puerto Rico dating back to August 28, 2020. We backfilled these values from August 28, 2020 through September 30, 2020, however due to an error in the backfill process, we did not begin capturing these new values on subsequent dates. On February 11, 2021, we corrected this error and backfilled our timeseries of Total PCR tests (specimens), Negative PCR tests (specimens), and Positive PCR tests (specimens) for October 1, 2020 through February 10, 2020 with the values from the August 28, 2020 press release. Our data quality team continues to search for updated data for these metrics.

Previous GH issues: https://github.com/COVID19Tracking/issues/issues/878

Comments

hmhoffman commented on February 11, 2021, 8:05 AM PST

Open in Github

Rows edited: 133 PR 2021-02-10 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-02-09 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-02-08 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-02-07 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-02-06 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-02-05 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-02-04 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-02-03 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-02-02 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-02-01 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-31 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-30 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-29 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-28 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-27 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-26 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-25 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-24 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-23 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-22 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-21 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-20 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-19 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-18 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-17 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-16 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-15 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-14 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-13 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-12 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-11 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-10 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-09 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-08 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-07 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-06 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-05 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-04 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-03 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-02 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2021-01-01 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-31 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-30 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-29 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-28 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-27 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-26 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-25 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-24 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-23 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-22 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-21 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-20 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-19 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-18 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-17 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-16 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-15 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-14 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-13 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-12 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-11 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-10 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-09 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-08 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-07 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-06 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-05 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-04 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-03 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-02 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-12-01 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-30 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-29 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-28 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-27 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-26 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-25 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-24 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-23 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-22 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-21 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-20 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-19 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-18 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-17 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-16 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-15 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-14 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-13 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-12 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-11 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-10 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-09 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-08 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-07 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-06 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-05 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-04 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-03 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-02 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-11-01 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-31 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-30 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-29 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-28 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-27 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-26 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-25 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-24 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-23 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-22 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-21 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-20 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-19 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-18 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-17 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-16 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-15 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-14 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-13 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-12 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-11 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-10 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-09 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-08 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-07 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-06 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-05 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-04 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-03 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-02 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412) PR 2020-10-01 totalTestsViral: 415664 (was 310546) positiveTestsViral: 20103 (was 7002) negativeTestsViral: 395291 (was 303412)

#1096: [PR] Patch 10/01/20 - 02/10/21 Total PCR tests (specimens), Negative PCR tests (specimens), Positive PCR tests (specimens)

Issue number 1096

hmhoffman opened this issue on February 11, 2021, 8:02 AM PST

Open in Github

State: PR

Dates affected: 10/01/20 - 02/10/21

Previous GH issues: https://github.com/COVID19Tracking/issues/issues/878

Comments

hmhoffman commented on February 11, 2021, 8:05 AM PST

Open in Github

#938: [PR] Probable cases totals for Nov. 5-6

Issue number 938

sacundim opened this issue on November 7, 2020, 4:51 PM PST

Labels Data quality

Open in Github

State or US: Puerto Rico

As reported in https://github.com/COVID19Tracking/issues/issues/936, Puerto Rico on Nov. 7, 2020 changed its case classification to reclassify cases supported by only an antibody test as "suspect," and use the "probable" label for cases arising from antigen testing. As a response to this, https://github.com/COVID19Tracking/issues/issues/937 cleared the probable case history, and the Nov. 7 daily update picked up the 77 probable cases total for that day.

But the Puerto Rico Department of Health's daily report (released Nov. 7 data up to Nov. 6 inside) actually has a footnote documenting the probable cases total for a couple of earlier dates:

fn4

...which reads at the beginning: "The total of probable cases from October 10, 2020 to November 4, 2020 was seventy two (72): [detail list of the dates and counts by sample date]." From this we can backfill the count of probable cases on Nov. 5 and 6 as 72. (Yes, Nov. 5 and 6. See below.)

NOTE ON OFF-BY-ONE DATES: The way the Puerto Rico Department of Health daily reports are dated is that the front page has a "data update date" field ("fecha de actualización de los datos"), and then they are published on the next date, which makes the dates inside the official report systematically one date earlier than the COVID Tracking Project's scraper-based capture. So while the Project's data currently says 37,490 confirmed cases in Puerto Rico on Nov. 7, the Department of Health gives that as its Nov. 6 total. Therefore, the Nov. 4 date on the footnote above should be read as Nov. 5 using the Project's dating convention. And that implies:

72 cases as of Nov. 4 (PRDoH) ⟹ 72 cases on Nov. 5 (COVID Tracking)
5 new, 77 total on Nov. 6 (PRDoH) ⟹ 72 on Nov. 6 and 77 on Nov. 7 (COVID Tracking)

Sources:

Puerto Rico Department of Health daily report released Nov. 7, 2020 (data up to Nov. 6)

Screenshot of front page of this report. Note that it reads November 6, 2020, but the filename says Nov. 7 and the totals it reports are what the Project tracks as Nov. 7.

2020-11-06_announcement

Comments

MattHilliard commented on November 10, 2020, 4:20 PM PST

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Thank you as always @sacundim for helping us have the best data possible for PR!

Before:

After:

#937: [PR] Clear PR Probable Cases History

Issue number 937

karaschechtman opened this issue on November 7, 2020, 12:47 PM PST

Labels Data quality

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State or US: PR

Describe the problem As reported in #936, PR is changing probable case reporting to reflect antigen instead of antibody reporting, moving to report antibody in a suspected category. Probable cases have dropped to 77. To avoid the appearance of a ~33,000 case drop today nationally and to reflect most up to date CSTE August definition, we are clearing PR's probable case history.

Link to data source PR dash Screen Shot 2020-11-07 at 3 37 39 PM

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karaschechtman commented on November 7, 2020, 12:50 PM PST

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karaschechtman commented on November 7, 2020, 1:01 PM PST

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I am also duplicating confirmed into confirmed+probable to reflect that antigen cases were 0 during this period. This only applies to April 24 onward, when we have a breakdown. Screen Shot 2020-11-07 at 4 00 57 PM

#936: [PR] Puerto Rico to redefine "probable" cases to mean antigen testing

Issue number 936

sacundim opened this issue on November 6, 2020, 4:53 PM PST

Labels Data quality stale

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State or US: Puerto Rico

Puerto Rico's Department of Health announced today that it's going to revise its COVID-19 dashboard to adopt the case classification in the Council of State and Territorial Epidemiologists' Coronavirus Disease 2019 (COVID-19) 2020 Interim Case Definition, Approved August 5, 2020, so that:

Confirmed case: Positive PCR test
Probable case: Positive antigen test
Suspect case: Positive antibody test

Previous to this, the "probable case" category was (mis)used to cover cases that generally all they had was a positive antibody test. These cases will now be reclassified as "suspect," which means that the number of cases labeled as "probable" will soon drop from the current 33,615 to something in the neighborhood of 160 (my estimate using PRDoH testing API data).

Sources:

Journalist's Twitter thread with press release
Puerto Rico Department of Health press release (attached below)

2020-11-06_reclassification

Comments

muamichali commented on November 6, 2020, 7:10 PM PST

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Thank you so much @sacundim for letting us know!

stale[bot] commented on November 21, 2020, 9:26 PM PST

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This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions!

stale[bot] commented on December 1, 2020, 9:32 PM PST

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This issue has been closed because it was stale for 15 days, and there was no further activity on it for 10 days. You can feel free to re-open it if the issue is important, and label it as "not stale."

#910: [PR] Update 10/23/20

Issue number 910

esquared opened this issue on October 23, 2020, 10:19 AM PDT

Labels Data quality

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Target Date: 10/23/20 Overview: Update via press release from PR Dept. of Salud PR 231020 Update1 PR 231020 Update2 PR 231020 Update3 PR 231020 Update4

. Contribution to milestone: Explain how the issue contributes to the overall milestone. Other benefits: Explain any side benefits we could get from completing this issue. Potential challenges: Explain any potential blockers. Editorial: The specific editorial content we expect to come out of this issue.

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esquared commented on October 27, 2020, 6:16 AM PDT

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Translation: The report from the Dept of Health reported 8 deaths by COVID-19; meanwhile, 1114 confirmed cases and 878 additional probable cases were registered.[breakdown of 8 deaths, 2 of which are probable]With these additional deaths, confirmed deaths rose to 682 and probable deaths to 189 so that the total deceased are 791. It’s important to remember that any deaths registered after this report will be reflected in later reports.The change in the number of deaths should not be interpreted as those which might have occurred in the last 24 hours. IN the same manner, it’s important to note that the death reports can vary, owed to the registration process and coding of the cause of death, which can take various days.From another part, the total results of confirmed COVID-19 cases is 30,956, of which 16,665 are women and 14,291 are men. The total of the confirmed cases was adjusted after adding 43 cases with test-taking dates from July 25- October 9; additionally, 5 duplicate cases were subtracted. The reported cases are those which have a positive PCR test, with a test-taking date from Oct. 10- Oct. 20.As part of the report, 878 additional probable cases were registered, with the understood test-taking date between Oct. 10- Oct. 20. In this row, the total is 30,028 after being adjusted, when subtracting 105 cases which later had a positive molecular test and which are added to the registered cases as part of this report; additionally, 28 cases were added with the test-taking date of April 22 - Oct 9, and 6 duplicate cases were subtracted. The probable cases divide into 16,742 women and 13,286 men.The private clinical labs and the Dept. of Health continue working to optimize the reporting of the COVID-19 tests to the BioPortal in an electronic manner. In the past days, work is being done to electronically connect one of the systems which manages the information used by the clinical labs with the BioPortal. This new connection will permit the reporting of results of COVID-19 tests in a more efficient, complete, and rapid manner. During this period, various records of COVID-19 test results have accumulated, which were entered late, simultaneously. This explains the high number of cases reported in today’s report; however, this does not represent a significant change in the epidemiological curve. En the graph of confirmed cases, the distribution of cases according to the test-taking date can be observed.Additional Confirmed Cases = 1114 Additional Confirmed Cases Adjusted = 43Title of graph: Confirmed Cases(molecular test) not duplicated, not previously reported, with test-taking date from Oct. 10 - 20, 2020Title of 2nd graph: Confirmed cases(molecular test) not duplicated, not previously reported, with test-taking date from July 25 - Oct. 9, 2020The adjustments of totals are done as part of an effort by the Dept. of Health, entities, and clinical labs to ensure that all COVID-19 tests performed are registered in the BioPortal, independently of the date it was taken.Summary of Dept of Health Report: Additional confirmed cases: 1114 Total confirmed cases: 30,956Additional probable cases: 878 Total probable cases: 30,028Additional confirmed deaths: 6 Total confirmed deaths: 602Additional probable deaths: 2 Total probable deaths: 189Total reported deaths: 791

esquared commented on October 27, 2020, 9:08 AM PDT

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Data already captured. Patch note filed.

#878: [PR] Total Tests, Positive Tests, and Negative Tests(PCR) Backfill 8/28/20-9/30/20

Issue number 878

esquared opened this issue on September 30, 2020, 11:32 AM PDT

Labels Data quality

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State or US: [Puerto Rico]

Describe the problem Received press release from Dept. de Salud with values updated to 8/28/20.

Action Plan Backfill from 8/28/20-9/30/20 for Total Tests(PCR), Positive Tests(PCR), and Negative Tests(PCR).

Link to data source Actualización de los resultados de las pruebas moleculares y serológicas para Covid-19 registradas en Bioportal del Depto. de Salud..pdf

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esquared commented on October 1, 2020, 9:41 AM PDT

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Before and after values PR Backfill Github Issue #878.xlsx

#829: [PR] Backfill probable cases time-series starting on 4/24

Issue number 829

muamichali opened this issue on September 14, 2020, 11:31 AM PDT

Labels Data quality

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State or US: Puerto Rico

Describe the problem CTP did not separately capture what they report as probable cases, though we do lump that number with the confirmed to make the Positive Cases (People, confirmed + probable) number.

Action Plan

[x] Backfill Probable Cases from 4/29-now from Positive Antibody Tests
[x] Update Positive Cases (PCR) on 5/18 to 1195 from 2710
[x] Backfill Probable Cases & Positive Antibody Tests from 4/24-4/28 from total-confirmed

Link to data source https://covidtracking.com/screenshots/PR/PR-secondary-20200424-181629.png https://covidtracking.com/screenshots/PR/PR-secondary-20200518-184759.png

Previous Issue https://github.com/COVID19Tracking/issues/issues/703

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muamichali commented on September 14, 2020, 11:39 AM PDT

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Before and After values in the attached sheet Probable Timeseries Backfill - PR.xlsx

#703: [PR] PCL Cases Historicals

Issue number 703

qpmnguyen opened this issue on July 30, 2020, 7:38 AM PDT

Labels Backfill Data quality PCL/SVP Historicals not stale

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State or US: PR

Describe the problem There exists data for probable confirmed breakdown for PR prior to the implementation of the new case breakdown columns on 4/29. The dates affected extend from 4/24 to 4/28. PR also updated in the morning at 6:00 AM, so using the 6:00 pm screenshots of the date of interest can accurately capture the data.

Link to data source http://covid-tracking-project-data.s3-website.us-east-1.amazonaws.com/state_screenshots/PR/

Comments

qpmnguyen commented on July 30, 2020, 7:46 AM PDT

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Fixing now... BEFORE: AFTER:

qpmnguyen commented on July 30, 2020, 7:48 AM PDT

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@MattHilliard @muamichali said there might be a better source for PR than screenshots -- assigning this to you for now.

#669: [PR] New Puerto Rico testing count report for July 24

Issue number 669

sacundim opened this issue on July 24, 2020, 11:32 AM PDT

Labels Data quality

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State or US: Puerto Rico

The Puerto Rico Department of Health shared a new Bioportal report with its testing counts as of July 23. As usual, it just shares them with some journalists who share it on Twitter:

https://twitter.com/angelicaserran0/status/1286690476968599555
https://twitter.com/RobbyCortes/status/1286697081705566208

As usual as well, I have a CSV with all the data of all these irregular reports:

https://github.com/sacundim/covid-19-puerto-rico/blob/master/assets/data/cases/PuertoRico-bioportal.csv

Images of the report (2 pages):

2020-07-23_bioportal

2020-07-23_bioportal_p2

Comments

muamichali commented on July 24, 2020, 3:39 PM PDT

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Thank you @sacundim and @MattHilliard so much!

MattHilliard commented on July 24, 2020, 4:25 PM PDT

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OK, so there was a miscommunication after the last update I made and the daily data entry team continued carrying over the previous (6/29) numbers on 7/12 and after. So I not only put in @sacundim's new numbers for 7/23 and 7/24, I also fixed the data for previous two weeks. This time I will make sure we handle this correctly in tomorrow's data entry shift.

I did this right after today's publication, so these numbers aren't factored into the test numbers in today's tweets. The website however should pick them up in an hour or so.

PCR columns before:

PCR columns after:

Negative column before:

Negative column after:

One anomaly here is that on 7/15 the data entry team reported a new number for Positive Cases (PCR) that is lower than the data point we had for 7/9. I'm not sure what happened there yet but wanted to get the data fixed first.

As always, thanks so much @sacundim for keeping us informed of these data releases!

MattHilliard commented on July 24, 2020, 4:28 PM PDT

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Quick update: I don't see anything in the data entry conversations to indicate where the Positive Cases (PCR) data point on 7/15 came from. Since this data source contradicts it, I'm not too worried about losing it.

#649: [PR] Confirmed + probable cases is a bad metric for Puerto Rico

Issue number 649

sacundim opened this issue on July 19, 2020, 3:57 PM PDT

Labels Data quality stale

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State or US: Puerto Rico

I figure this isn't an easy issue to tackle, but I'm growing more and more concerned that the Project's choice to foreground the confirmed + probable cases figures for Puerto Rico, it's not giving the best quality of information available. Perhaps this can be summed up with this chart that I make with my Puerto Rico COVID-19 data collection and visualization project:

This shows, by date sample taken (which I'm aware is different from reported date as the Project uses):

Blue: New confirmed cases
Orange: New probable cases

Lines are 7-day averages, dots are the raw values straight from charts in Puerto Rico's Department of Health's official daily PDF reports, samples of which I attach at the bottom of this issue.

The very striking pattern I wish to highlight in my chart is the following:

New probable cases (orange line) have been found at a more or less flat rate (70-100) since early May.
New confirmed cases, on the other hand, fell from 51.4/day on April 1st to 4.9/day on May 27, and have been on an exponential rise since then (162.1/day on July 13).

And the key observation I'd like to make is that if one tracks of Puerto Rico's epidemic by the sum of confirmed and probable cases, one doesn't spot the exponential climb until very recently, because the probable cases figures—which have in many ways behaved as background noise—mask it out.

Some additional facts that are worth remarking:

Puerto Rico's Department of Health, in its daily case count bulletins (here's the most recent), defines a "confirmed case" as one that has a positive RT-PCR test (footnote 1) and a "probable case" as one that has a positive serological test (footnote 3).
There were numerous news reports during May from officials in Puerto Rico that large volumes of persons being indiscriminately given serological tests was producing a large number of "false positives" that were later testing negative on PCR. (I put "false positives" in scare quotes because the people making the complaints didn't seem to clearly distinguish between people with antibodies who no longer had the virus and false positive proper.) See for example this May 24 news story: "52 school cafeteria employees who were positive to COVID-19 in serological tests give negative to molecular tests", and note that these 52 were all of the positive cases—not a single one from this incident tested positive on molecular!

Data sources

Puerto Rico Department of Health daily COVID-19 reports, which have daily charts of COVID-19 cases by test sample date, with separate charts for probable and for confirmed cases.
My Puerto Rico COVID-19 tracking project, which has data files where I've transcribed all of the PRDoH cases charts I've seen since April 22nd

2020-07-18_confirmed_part1

2020-07-18_confirmed

2020-07-18_probable

Comments

muamichali commented on July 19, 2020, 6:30 PM PDT

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Hi @sacundim

I haven't looked at your post in detail yet, but this is something we are working towards, not just with PR but in general. https://github.com/COVID19Tracking/issues/issues/578

sacundim commented on July 19, 2020, 9:10 PM PDT

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Ah, @muamichali,

Didn't see that, good to hear.

muamichali commented on July 26, 2020, 1:02 PM PDT

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@sacundim Would you mind sending me your email to michal.mart@covidtracking.com or post it here? I would like to have another way to communicate outside github as well. Thanks again for everything you do to help us!

stale[bot] commented on August 10, 2020, 1:14 PM PDT

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This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions!

stale[bot] commented on August 21, 2020, 11:21 AM PDT

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#645: [PR] Puerto Rico Department of Health testing data API

Issue number 645

sacundim opened this issue on July 17, 2020, 6:40 PM PDT

Labels Data quality not stale

Open in Github

State or US: Puerto Rico

Just saw an informal announcement from a biostatistician collaborating with Puerto Rico's Department of Health that they now have an API for downloading test data:

Tweet with the info: https://twitter.com/rafalab/status/1284292056697929730
API: https://bioportal.salud.gov.pr/api/administration/reports/minimal-info-unique-tests

Note that when I hit the latter URL with a regular browser I get an authorization failure message, but when I wget from it I get a 48.78M JSON data file:

$ wget https://bioportal.salud.gov.pr/api/administration/reports/minimal-info-unique-tests
--2020-07-17 18:20:34--  https://bioportal.salud.gov.pr/api/administration/reports/minimal-info-unique-tests
Resolving bioportal.salud.gov.pr (bioportal.salud.gov.pr)... 54.210.0.6
Connecting to bioportal.salud.gov.pr (bioportal.salud.gov.pr)|54.210.0.6|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/json]
Saving to: ‘minimal-info-unique-tests’

minimal-info-unique-t     [                    <=> ]  48.78M  4.06MB/s    in 13s     

2020-07-17 18:21:46 (3.79 MB/s) - ‘minimal-info-unique-tests’ saved [51154578]

$ cat minimal-info-unique-tests |jq |head -n 30
[
  {
    "collectedDate": "7/2/2020",
    "reportedDate": "7/3/2020",
    "ageRange": "60 to 69",
    "testType": "Molecular",
    "result": "Negative",
    "patientCity": "Ceiba",
    "createdAt": "07/07/2020 13:34"
  },
  {
    "collectedDate": "6/24/2020",
    "reportedDate": "6/25/2020",
    "ageRange": "60 to 69",
    "testType": "Molecular",
    "result": "Negative",
    "patientCity": "Bayamón",
    "createdAt": "06/26/2020 11:26"
  },
  {
    "collectedDate": "6/10/2020",
    "reportedDate": "6/16/2020",
    "ageRange": "50 to 59",
    "testType": "Molecular",
    "result": "Negative",
    "patientCity": "San Sebastián",
    "createdAt": "06/16/2020 17:07"
  },
  {
    "collectedDate": "5/26/2020",

The file is a single big JSON list with individual records for each test. I saw an earlier version of this data the other day (it was shared as an Excel file) and there's some data quality issues. Summary of the ones I'm aware of:

result field not normalized. I just treat the ones that match Positive anywhere inside as positive, rest as negative.
A couple thousand records (out of 275K+) don't have some of the date fields.
Some records have individually nonsensical date values, like from 1937
A couple thousand records have collectedDate > reportedDate

Here are the cleanups I ended up doing on it if it's of any help:

https://github.com/sacundim/covid-19-puerto-rico/blob/master/postgres/020-load-data.sql#L34

Comments

muamichali commented on July 17, 2020, 6:46 PM PDT

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Wow, @sacundim! Thank you so much for this and all the helpful info you provide us about PR. We are going to follow this closely.

Nosferican commented on July 17, 2020, 7:41 PM PDT

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Agreed. I watched the governor's press conference yesterday which included some of the work by @rafalab et at. Thanks for sharing the API announcement @sacundim!

Nosferican commented on July 17, 2020, 8:08 PM PDT

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I seems the license of the data falls under the EULA

No se pueden descargar, republicar, revender, duplicar o hacer "web scraping", en su totalidad o en parte, de los datos de propiedad de los sitios web y / o servicios del DSPR para ningún fin que no sea el uso personal permitido en estos Términos de Uso.

Which basically says it can only be used for personal use. Hopefully we can get the all clear from the copyright holders to incorporate the API in the project (ref: https://twitter.com/Nosferican/status/1284323770694619136).

space-buzzer commented on July 17, 2020, 8:31 PM PDT

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All the tests are tagged as Molecular, so I can't understand the result field:

Negative
Positive 2019-nCoV
COVID-19 Negative
COVID-19 Positive
Positive
Inconclusive
Invalid
Other
Not Valid
Not Tested
Presumptive Positive : Does it mean that the test is inconclusive? "presumptive positive" by CDC's definition?
Positive IgM Only
Positive IgM and IgG

So "Molecular* test type does not mean PCR?

sacundim commented on July 17, 2020, 8:44 PM PDT

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I'm afraid I haven't seen any real documentation, @space-buzzer. The number of records in the spreadsheet I saw earlier this week was about 275K, which is consistent with all tests being PCR based on other information.

The approach I took, personally, is that the strange values like "Positive IgM Only" and "Positive IgM and IgG" are very infrequent so they don't make a big dent on the counts, which are only going to be an approximation anyway due to issues with date data. I personally assumed that they're positive PCR results.

Some context (that I don't fully understand): the data are extracted a the PRDoH's website ("Bio Portal") that has a web form for labs to report test results. So I think these are probably a mix of data entry errors by users and bugs in that web UI that allowed weird values to be entered.

sacundim commented on July 17, 2020, 8:45 PM PDT

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Oops, I hit "Close issue" by accident.

sacundim commented on July 17, 2020, 8:46 PM PDT

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@Nosferican Do you have a link to that EULA?

Nosferican commented on July 17, 2020, 8:49 PM PDT

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@Nosferican Do you have a link to that EULA?

It's under the terms and services agreement when signing up for an account at the bioportal.

sacundim commented on July 17, 2020, 9:22 PM PDT

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I am not a lawyer nor a professional translator, but I'll take a stab at this specific section:

Intellectual property

Most of the content of our web sites is public domain and doesn't include copyright or other intellectual property statements.

The government's information is normally public domain. Public domain information can be used and copied freely. However, you're authorized to use our contractor's computer software and the related database only for informational ends and not for direct or indirect commercial purposes. Also, other materials in the web sites and/or services that is not government material cannot [sic] be copyright protected and cannot be used for any direct or indirect commercial purpose. Any use not authorized in this document is forbidden. Any copy made of materials must conserve all copyrights and other warnings. Except as explicitly provided in these Terms of Use, you may not reproduce, modify, publish, transmit, show, produce, distribute, disseminate, disseminate [sic] or disseminate any materials to third parties, nor participate in the transfer or sale, create derived works or in any manner exploit the contents of the web sites and/or services of the PRDoH or in any part of these without prior written consent by PRDoH.

I've put "[sic]" on some bits that rendered literally but understand are flat out wrong. In particular, the part that says that "other materials in the web sites and/or services that is not government material cannot [sic] be copyright protected and cannot be used for any direct or indirect commercial purpose" is just contradictory and I think it is intended to read "may."

I think one important piece of context is that this Bioportal web site is normally used as a web UI for:

Doctors to order tests from the PRDoH labs and view their results.
Private labs to submit their test results to PRDoH.

And they've apparently added a public API endpoint to publish the testing data that the system contains.

Original Spanish:

Propiedad intelectual

La mayor parte del contenido de nuestros sitios web es de dominio público y no incluye avisos de derechos de autor u otros avisos de propiedad intelectual.

La información del gobierno normalmente es de dominio público. La información de dominio público se puede distribuir y copiar libremente. Sin embargo, está autorizado a utilizar el software de la computadora de nuestro contratista y la base de datos relacionada solo con fines informativos y no con fines comerciales directos o indirectos. Además, otro material en los sitios web y / o servicios que no sea material del gobierno no puede estar protegido por derechos de autor por entidades privadas y no puede usarse para ningún propósito comercial directo o indirecto. Cualquier uso no autorizado en este documento está prohibido. Cualquier copia que haga de los materiales debe conservar todos los derechos de autor y otros avisos. Salvo lo dispuesto expresamente en estos Términos de Uso, no puede reproducir, modificar, publicar, transmitir, mostrar, realizar, distribuir, difundir, difundir o transmitir ningún material a terceros, ni participar en la transferencia o venta de, crear trabajos derivados o de cualquier manera explotar el contenido de los sitios web y / o servicios del DSPR o cualquier parte de estos sin el previo consentimiento por escrito del DSPR.

Nosferican commented on July 17, 2020, 9:36 PM PDT

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In this case, a simple written notice from the copyright holder / publisher saying the generic catch-all EULA doesn't apply to the dataset and that it can be used freely should suffice.

The generic boilerplate seems to suggest the API may not be that well maintained. However, if we can get a contact person / data steward for basic questions such as the ones @space-buzzer mentioned, that would be great. The data curation can occur upstream but that still requires some basic data lineage / governance information. @rafalab might be able to help with making that initial contact with the dept.

sacundim commented on July 18, 2020, 2:31 AM PDT

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Observations from playing a little bit with the API:

The createdAt field might be more reliable than reportedDate. With two downloads that I've done about 8 hours apart on 2020-07-17 and 2020-07-18, I'm noting some differences in aggregates for createdDate and reportedDate between 2020-07-09 to 2020-07-16 (inclusive). Looks like there is some lag such that data with reportedDate in this range was still being added to the data set on the night of the 17th to 18th.
The timezone of the createdAt field seems to be UTC.

edusoccer1121 commented on July 18, 2020, 10:13 AM PDT

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Hi @Nosferican,

@gabynevada can help clarifying some of the provided data he is the lead maintainer of the public API.

Good day.

space-buzzer commented on July 19, 2020, 2:29 PM PDT

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I set a cron job to download it daily, but noting will happen until we figure out:

Licensing issues
What kind of tests are we talking about?
Consistent data sanitizing strategies we can take

gabynevada commented on July 20, 2020, 1:30 AM PDT

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Hey all, I'm the project manager for the BioPortal system.

I'll start inquiring on what we need on the legal side for this to proceed.

On the data side, we're on the process of cleaning it up as much as possible.

The data is directly reported from the island's testing facilities.
If it comes via interface it comes in mostly as is, later we run missing or incorrect value identification and send notifications to the testing facilities to fix their reported data.
We have teams cleaning up the data, but are focusing on the tests for the positive Covid-19 cases as those are of the most importance to us.
Data may change as it's cleaned/verified by our personnel or the testing facilities.

Some answers to the questions here:

Molecular in this case are PCR tests.
The test results vary depending on the kit being used.
Presumptive Positive in most cases means that it requires additional confirmation, it depends on the kit that was used
The createdAt field is just a timestamp of when it was reported or uploaded into the system, it has no other correlation to the data.
The missing collectedDate and reportedDate fields are caused by testing facilities not reporting all required data. The system was implemented after the pandemic had begun and the prior process was mostly manual. We're still on the process of improving the data collection methods for the tests.

I'm available for any questions and i'll see what I can do to help in this process.

Regards

muamichali commented on July 21, 2020, 7:28 PM PDT

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Hey @gabynevada! Thank you so much for interacting with us here. I will send you an email so we can have a better way to find out what is the status on the legal side.

stale[bot] commented on August 5, 2020, 8:10 PM PDT

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This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions!

Nosferican commented on August 9, 2020, 8:49 PM PDT

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Any updates on this? @gabynevada, any updates on the data quality issues?

gabynevada commented on August 15, 2020, 9:03 AM PDT

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@Nosferican The test results that did not matched with the test types were verified and cleaned. We're still working on additional interfaces with Laboratory Information Systems to get as much electronic information as possible.

We're working with the legal side on the Terms and Conditions on the API. It's taking longer than expected.

stale[bot] commented on August 30, 2020, 9:42 AM PDT

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This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions!

#604: [PR] Historical Puerto Rico hospitalizations data

Issue number 604

sacundim opened this issue on July 11, 2020, 1:18 AM PDT

Labels Data quality

Open in Github

State or US: Puerto Rico

Describe the problem

So, on Thursday (July 9) the number of COVID-19 hospitalizations in Puerto Rico climbed to 147, prompting a leading local paper to publish a story pointing out that, according to the data they had, this was a record high:

"Record patients: hospitalizations for COIVD-19 increase to 147" El Nuevo Día, July 9, 2020.

This seemingly didn't sit well with the Secretary of Health, who responded by saying that his department's records refute this and that there were 201 hospitalizations on April 30:

https://twitter.com/DeptSaludPR/status/1281261229403713537

And as part of this, he also shared a table of historical hospitalization data with some journalists. It goes from April 18 to July 9, and also breaks the totals down by region:

https://twitter.com/angelicaserran0/status/1281256666881802241
https://twitter.com/RobbyCortes/status/1281536898230558720

I have dutifully transcribed this data into a CSV, and used a spreadsheet to check that the regional totals add up to the listed totals:

https://github.com/sacundim/covid-19-puerto-rico/blob/master/assets/data/PuertoRico-hospitalizations.csv

Comments

MattHilliard commented on July 11, 2020, 4:46 PM PDT

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Thank you yet again @sacundim! Your CSV made this really easy for me to check against our numbers. All our recent data matched, just a discrepancy or two around the edges of our gaps. And of course this fills in a vastly better picture of the "first wave" than we had before.

Our existing current hospitalization data:

Fixed data:

Details, including before/after of States Daily

#603: [PR] New Puerto Rico testing data report (as of 2020-07-09)

Issue number 603

sacundim opened this issue on July 10, 2020, 2:24 PM PDT

Labels Data quality

Open in Github

State or US: Puerto Rico

This is a continuation of https://github.com/COVID19Tracking/issues/issues/568

As infuriatingly usual, the only way to get official data on the number of tests in Puerto Rico is to follow certain journalists on Twitter who pester the Department of Health periodically for the numbers. We just got a new set today:

https://twitter.com/angelicaserran0/status/1281694446233497602
https://twitter.com/RobbyCortes/status/1281697289279545344

I've got the images and copied the data into a CSV file with all of the previous ones here:

https://github.com/sacundim/covid-19-puerto-rico/blob/master/assets/data/PuertoRico-bioportal.csv
https://github.com/sacundim/covid-19-puerto-rico/blob/master/assets/source_material/2020-07-09/2020-07-09_bioportal.jpg
https://github.com/sacundim/covid-19-puerto-rico/blob/master/assets/source_material/2020-07-09/2020-07-09_bioportal_p2.jpg

Comments

MattHilliard commented on July 10, 2020, 6:50 PM PDT

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PCR Columns Before:

PCR Columns After:

Negative column before:

Negative column after (using Total Tests PCR - Positive Cases PCR from first day (258001 - 2235 = 255766) per extensive discussion with @muamichali last time:

MattHilliard commented on July 10, 2020, 6:51 PM PDT

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Oh and thank you so much @sacundim for passing along this data! Your help is very much appreciated!

#568: [PR] Official testing data for Puerto Rico

Issue number 568

sacundim opened this issue on July 2, 2020, 1:40 PM PDT

Labels Data quality

Open in Github

State or US: Puerto Rico

Describe the problem

Since Puerto Rico's Department of Health doesn't publish tests data regularly, and when it does it doesn't do so in any manner or medium that's amenable to automatic capture, the testing data in the Project for Puerto Rico is very sorely out of date, leading to reports that show, for example, Puerto Rico's COVID-19 positive test rate at 100% which then get picked up by the press.

I have been manually compiling a set of the official data that has been available. The official reports linked below are shared with some journalists by the Department of Health, with no appreciable schedule. These journalists tweet images of these reports out, which I have collected and copied their data into a CSV (also linked) over at my repo for my Puerto Rico data project:

https://github.com/sacundim/covid-19-puerto-rico

Insomuch as it is required I grant permission for you to use my CSVs (which I understand are facts and therefore not copyrightable anyway).

While there is no evident path to automating the capture of this data, even a small one-time manual update to your numbers would likely avoid some modest amount of public misinformation.

Comments

MattHilliard commented on July 7, 2020, 9:49 AM PDT

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@sacundim, thank you for bringing this to our attention! I've updated our historical data based on these five data points. It should be visible on the web site within an hour. Hopefully we can get a more reliable official source at some point, but in the meantime if you catch more things like this, please don't hesitate to open more Github issues!

muamichali commented on July 7, 2020, 4:35 PM PDT

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@sacundim would you kindly share with us the twitter handles of the journalists that post this info so we can follow them as well?

sacundim commented on July 8, 2020, 2:51 AM PDT

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@muamichali The two journalists I follow who post these on Twitter are @angelicaserran0 and @RobbyCortes.

#276: [States Daily CSV] PR positiveIncrease is negative for 2020-04-22

Issue number 276

hrushka opened this issue on April 23, 2020, 3:17 PM PDT

Open in Github

Source: https://covidtracking.com/api/v1/states/daily.csv

Reference: https://c19.dev/d/4S5AN4CZz/covid-19-us-state-data?panelId=5&fullscreen&orgId=1&from=now-45d&to=now&var-state=PR&var-population=3193694&var-density=0&var-total_cases=915&var-total_deaths=46

Comments

Nosferican commented on April 29, 2020, 1:56 PM PDT

Open in Github

See #211 for the explanation.

stale[bot] commented on May 14, 2020, 2:15 PM PDT

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This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions!

karaschechtman commented on May 20, 2020, 6:51 AM PDT

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Hi @hrushka, Thank you for pointing this out. As @Nosferican says, see issue 211 for an explanation. We will add a note about this to the PR data.

muamichali commented on May 27, 2020, 11:13 AM PDT

Open in Github

Hi @Nosferican Wanted to give you a heads up on this from our web team

We are now building the entire API to a repository. All the JSON/CSV files are built every 15 minutes and put into this repo. https://github.com/COVID19Tracking/covid-public-api

We have a test version of the website available that exposes that repo at the same exact endpoints we have now. https://5ece700c83e8e9b0cd122372--upbeat-lovelace-3e9fff.netlify.app/api

There is a new status endpoint that gives info on when the data was last updated. There's also a run number that we can use to go back and download a snapshot of the API at that moment. https://5ece700c83e8e9b0cd122372--upbeat-lovelace-3e9fff.netlify.app/api/v1/status.json https://github.com/COVID19Tracking/covid-public-api-build/actions/runs/116895561

I have reproduced the exact same file structure and format across the different endpoints. The only changes are some additional fields that were in current endpoints are now in every entry for US or states' daily data - for example, dataQualityGrade, There were also some odd time offsets in the old API for fields like dateModified that were presented as UTC, but were in fact not. So they are now UTC. Please take some time to test out the new API files and endpoint and give feedback. I hope to have this replace our production API build tool by the

end of this week. Any feedback filed as an issue in this repo https://github.com/COVID19Tracking/covid-public-api-build would be helpful!

#247: GA data discrepancy (~ APR 20)

Issue number 247

dcorbin opened this issue on April 21, 2020, 9:45 AM PDT

Labels Data source

Open in Github

On Apr 20, in Georgia, you're data table shows about ~ 700 new cases. I looked at the source page for that data (also visible in the screen shots). The only place on that page that I can find to extract a "new cases" is from a chart (hover), and it is showing 36 new cases. I strongly suspect there is a data inconsistency on the source page, but I need more information on how the GA data is extracted from that page.

Comments

muamichali commented on April 21, 2020, 9:58 AM PDT

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Hi @dcorbin

Thanks for writing The Georgia source page shows a total of 18,301 cases on 4/19 https://covidtracking.com/screenshots/GA/GA-20200419-180551.png

and a total of 18,947 cases on 4/20 https://covidtracking.com/screenshots/GA/GA-20200420-180537.png

18,947-18301 = 646 https://covidtracking.com/data/state/georgia#historical

#211: PR Test Data Note [Dept of Health has been double/triple counting]

Issue number 211

Nosferican opened this issue on April 17, 2020, 1:25 PM PDT

Open in Github

The Department of Health has been counting the RAPID and Molecular tests as a different subjects. The end result is that they might have two positive and one negative test results and they are all for the same subject. They had previously stated it was a per subject count. They are working on fixing the numbers by looking at the patient information.

Source: http://periodismoinvestigativo.com/2020/04/las-matematicas-de-salud-estan-mal/

Comments

goldfarb commented on April 20, 2020, 5:06 PM PDT

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Thank you so much for pointing that out, @Nosferican

We will keep an eye out for an update from the Department of Health, when they update the numbers.

sacundim commented on April 21, 2020, 4:39 PM PDT

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This revision just happened today. The # of positive cases has been revised down from 1,298 to 915:

https://www.theweeklyjournal.com/business/puerto-rico-businesses-expected-to-reopen-gradually/article_9e73d46c-840f-11ea-b9f1-7bca7219abcf.html

Fewer Cases Than Previously Informed

As the government continues to debate how to reinstate the economy, the Health Department acknowledged that it repeat-counted multiple confirmed cases of infection, meaning that the actual number of positives is lower than previously informed.

While the agency had stated that there were 1,298 confirmed cases, the real number is 915. Of these, 736 are molecular tests and 189 are serological tests.

I've seen no indication whether they plan to issue revised numbers for earlier dates. It's going to be rather infuriating if they don't.

PS the article that @Nosferican posted above is now available in English translation:

http://periodismoinvestigativo.com/2020/04/puerto-rico-health-departments-covid-19-math-is-wrong/

muamichali commented on April 22, 2020, 4:20 PM PDT

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Thank you @sacundim and @Nosferican

We revised today's number based on the new information and we will update the historical numbers if those are published.

gah-bo commented on April 30, 2020, 8:54 AM PDT

Open in Github

Dept. Health must have published the fixed data because two of the independent dashboards I use for research now have the accurate numbers

https://datastudio.google.com/u/0/reporting/1j-ZxP9IvddFJT-V0GQUJQQIV-G0YVVw4/page/ctiNB

https://app.powerbi.com/view?r=eyJrIjoiMzgzNjhiOTItNjM2Mi00OWRlLWE2ZTgtNDVhNzliYjUyMmQzIiwidCI6IjIxY2ZmMGY5LWQ1ZGQtNGEzOS04N2NlLTVmNjg4MzFmMjNjZCIsImMiOjF9

Unfortunately, they only name their source as the Dept. of Health and Dept. of Statistics, without providing links or anything of that sort. I will edit this comment if I manage to find an official source for developers to add. Else, I just wanted to leave these two links for other people to access in the meantime. The first of them allows for extracting data in .csv or Excel format.

Edit: Use this dashboard in the meantime https://www.covid19prdata.org/dashboard its made by the Code4PR team and is on gitbub. It contains all accurate info and is easily downloadable.

#65: PR: Correct URL for Puerto Rico

Issue number 65

amandafrench opened this issue on March 27, 2020, 5:32 AM PDT

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I think urlwatch might still be tracking an old Puerto Rico public health coronavirus page, since the Status column in the stats sheet says "URL Not Found Anymore" but the most trusted data source is now https://estadisticas.pr/en/covid-19. That URL is correct as of now on http://covidtracking.com and in the States column in the sheet.

Comments

schwartzadev commented on March 31, 2020, 8:59 PM PDT

Open in Github

This looks updated in the latest screenshots :+1: