Uganda Ebola SitReps and Line List

IMPORTANT - As of Dec. 13th, SitRep 73 the data are no longer being updated.

We are digitizing the daily SitReps from the Ebola outbreak in Uganda that are being posted online here. The most current line list from the processed SitReps is location in Data/Line List. However, we're storing all the generated line lists, so choose the one with the most recent date.

It's critical to point out that we haven't yet performed proper validation on these data and would very much welcome contributors who are either interested in suggesting code changes, validating data, and/or contributing new data sets. In addition, please see the specific license, warranty, and copyright information for our code and each individual data set.

Known issues with the list list

IMPORTANT - As of Dec. 13th, SitRep 73 the data are no longer being updated.

1. As of Dec. 13th, SitRep 73, the Uganda MoH reports 141 confirmed cases. The line list currently has 212.
2. Beginning with SitRep 50, a new set of sub-county information started being reported, which does not align with previous SitReps. This includes two major changes. First, Butoloogo had previously only had a single case reported, beginning with SitRep 50 and proceeding through current SitReps (68 as of this commit) Butoloogo was reported to have 10 cases. Second, Kassanda had 2 or 5 (depending on the SitRep), but again, as of SitRep 50 (and onwards) reports 9. There were a few other smaller changes, which were probably due to prior SitReps where sub-county was not reported and could not be determined conclusively.
3. Prior to Oct 31st, the line lists contained date errors. These were not back corrected, so line lists prior to 10-31-2022 have some incorrect dates. These errors will cause inflated growth rate estimates.
4. The Kikandwa sub-county is listed as MITYANA (District) MITYANA (County) KIKANDWA (Sub-county) in the government shapefile. However, all SitReps report Kikandwa as being in the Kassanda district. There is no other Kikandwa sub-county listed in the shapefile. For now, we map to the shapefile and place Kikandwa in Mityana district.
5. Gomba and Busiro are listed as sub-counties, but do not appear as sub-counties in the government shapefile and are not listed as sub-counties online.
6. Kiruuma and Kirwanyi are not listed a sub-counties in the government shapefile, but are listed as sub-counties in Mubende on the Mubende gov. website. For these two we do not have a county identified, but list them as Mubende district.
7. There are multiple sub-counties for Kasambya, and the Eastern, Western, and Southern Districts. Currently, these are all mapped to Mubende.
8. The SitReps report a sub-county called Butologo, which does not appear in the government shapefile. However, a Butoloogo sub-county does appear and is in the same district, so we map to that.
9. Prior to SitRep 25, Bageza sub-county in Mubende was listed at Bayeza. We have mapped everything to Bageza. As best as we can tell, there does not appear to be a Bayeza in Uganda.
10. The gov. shapefile lists a Bagezza, Mubende, but not a Bageza. The Mubende website spells the sub-county Bageza, which is the spelling listed in the SitRep. We map to Bagezza to match the shapefile.
11. In SitRep 33, a Nanssana, Wakiso appears, but that sub-county isn't present in the shapefile. In SitRep 35, that changes to Nansana, Wakiso, which is in the shapefile. We map to Nansana.
12. SitRep 39 does not contain information on sub-county. There was one case in Kassanda in SitRep 39 and another in SitRep 40. Based on SitRep 40, which does contain sub-county information, the case reported in SitRep 39 was either in Kalwana or Kikandwa. We put the case in SitRep 39 in Kalwana.
13. In SitRep 40, there is a sub-county spelled BUTOLOGOA. This is almost certainly a misspelling of BUTOLOGO, as this sub-county does not appear in SitRep 40. We correct BUTOLOGOA -> BUTOLOGO and map to BUTOLOOGO.
14. In SitRep 45, 3 confirmed cases are reported in the header. However, in the district table (there is no subcounty table) they report 4 new cases, 2 in KAS, 1 in WAK, and 1 in KLA. However, the cases in WAK and KLA do not appear in future sitreps. In addition, in SitRep 46, which does contain subcounty, they report 1 new case in KLA. Putting this all together, we record only 3 new cases in the CSV and all in KAS -> Kalwana.
15. In SitRep 47, a new case is reported in Kyegegwa. Subcounties are not reported in SitRep 47. However, while subcounties are reported in SitRep 48, no additional cases appear in Kyegegwa relative to past sitreps. We record a case in SitRep 47 in KYE - > Kasule. However, this case does not appear in the CSV for SitRep 48.
16. In SitRep 48, there is a Buelnga TC, which does not appear in the shapefile. Googling suggests this should be Buwenge TC. We map Buelnga to Buwenge.
17. In SitRep 48, there is a Kimanya-Kyabakuza, which does not appear in the shapefile. However there is a Kimaanya-Kyabakuza (note the extra "a"). We map to this location.
18. SitRep 48 is missing a row for Kirwanyi, Mubende. This is almost certainly an error in the SitRep. However, this deletion is recorded in the CSV.
19. SitRep 48 reports only 1 new confirmed case, but according to the subcounty table there are 10 previously unreported cases. Given the number of errors in SitRep 48, this is likely a mistake.

Running the code

1. You need to create a directory in Data called "tmp" in order to run the script build_csv.R

Information on data files

1. As of Oct 27th, SitReps 1 - 9 are missing, so data start on Sept 29th, 2022, and SitRep 11 is missing.
2. SitReps 10 - 18 only contain country-wide data.
3. Regional information on cases begins for SitRep 19, which means that SitRep 20 is the first where line list cases can be disaggregated by region. That is Oct 9th, 2022.
4. Data were hand curated prior to SitRep 20.
5. Ebola_SitReps_Uganda_2022/Data/Ebola SitReps Uganda Baseline.csv contains the hand-curated line-list through SitRep 20.
6. Automated linelist curation begins with cases reported in SitReps 21 (Oct 10th, 2022)
7. SitReps 22, 28, 31, 32, and 34 were hand curated. This is noted in the CSVs.
8. SitRep 22 couldn't be digitized.
9. SitRep 28 has a different format than all other SitReps. In addition, you can tell the death reported in SitRep 28 occurred in Kiganda, Kassanda District despite the SitRep only listing Kassanda district because the following SitRep (29) reports no new deaths, but includes a death in Kiganda, Kassanda District not reported in the SitRep prior to 28 (i.e., 27).
10. SitRep 31 had a bespoke format. Unfortunately, the three cases reported in Mubende cannot be place in sub-county, because SitRep 32 also did not contain sub-country information, but reported new cases in Mubende as well.
11. SitRep 32 also had a bespoke format and had cases in Mubende that could not be place in sub-counties.
12. SitRep 32 reports a death in Entebbe and a case in Wakiso. These were treated as separate even though Entebbe is in Wakiso. The death was not previously reported as a case, so we marked both a case and a death so that the case would appear in the line list.
13. SitRep 34 is missing a PDF, but does report cases on the html page for the WHO. However, cases were only reported at the District level.
14. Beginning with SitRep 37, Oct. 27th, we updated the geo-coding. As a result, we have two line lists for Oct 27th, one with the old geo-coding and one with the new. Going forward, we will only report the new geo-coding.
15. SitRep 41 had to be manually entered and did not report sub-counties. However, SitRep 42 reported no new confirmed cases, so it's possible to determine the sub-county for the reported case in SitRep 41.
16. SitRep 44 had to be manually entered, but did not report any new cases (confirmed or probable).
17. SitReps 45, 47, and 48 had to be manually entered.
18. SitRep 48 contains subcounty information, but the table is broken across a page. If this persists, the code should be updated to accommodate.
19. SitRep 49 had to be manually entered, but did contain subcounty information.
20. SitRep 50 had to be manually entered, but the sub-county information on the case was listed in the text.
21. SitReps 51 - 73 had to be manually entered.

Additional license, warranty, and copyright information

We provide a license for our code (see LICENSE) and do not claim ownership, nor the right to license, the data we have obtained. Please cite the appropriate agency, paper, and/or individual in publications and/or derivatives using these data, contact them regarding the legal use of these data, and remember to pass-forward any existing license/warranty/copyright information. THE DATA AND SOFTWARE ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE DATA AND/OR SOFTWARE OR THE USE OR OTHER DEALINGS IN THE DATA AND/OR SOFTWARE.