tbep-tech / wq-static

water quality reporting static documents

README

Repository for building static water quality reporting tool documents.

Updating report card with provisional Nov/Dec data in January

For this repository:

1. First week of jan, request Nov/Dec provisional water quality data for HB, OTB, LTB, MTB from EPC (SM)
2. Take downloaded data from wq-static CI build ('Results_Updated.xls') and copy in provisional data from EPC
3. Check if all data present, should be 10 samples in HB, 8 in LTB, 12 in MTB, 15 in OTB
4. Save new file, 'Results_Provisional.xlsx' (okay to save as new file format), in data-raw folder
5. In wq1.Rnw comment lines 64, 68, uncomment lines 63, 67, make sure line 70 is F
6. In wq2.Rnw comment lines 62, 66, uncomment lines 61, 65, make sure line 68 is F
7. Run build.R through line 27
8. Comment lines 6-7, 19-56 on .github/workflows/build.yaml to disable CI (w/o error)
9. Update text and any other static graphics

Updating the wq dashboard with provisional data (wq-dash repo):

1. After the data are updated on the wq-static repo, save the epcdata RData object created on line 67 of wq1.Rnw to the wq-dash repo data folder
2. Convert the sq_q column in epcdata to logical, as in line 12 in R/dat_build.R, save epcdata again to data folder
3. In wq-dash.Rmd, comment line 42, uncomment line 41, change line 49 to current year
4. In R/dat_proc.R, comment line 14, uncomment line 13, change line 20 to current year, run R/dat_proc.R
5. In R/dat_build.R, comment lines 6 - 20 so CI actions don't overwrite epcdata

Updating state of the bay (state of the bay repo):

1. Copy 'Results_Provisional.xlsx' to state of the bay repo data-raw folder
2. In docs/water-quality-decision-matrix.Rmd, comment lines 13, 17, uncomment lines 14, 18, change line 10 to current year
3. Knit docs/water-quality-decision-matrix.Rmd and verify changes

Note that once the Nov/Dec data are no longer provisional (on EPC FTP), undo the above, set maxyr as next year. For next year's provisional report card, this can only be done once January data are available. Also make sure line 70 in wq1.Rnw and line 68 in wq2.Rnw is T for partialyr.

wq-static's Issues

Fix Travis builds for Rnw files

Use tinytex https://yihui.org/tinytex/

Graph background

Looking good! I think the graphs need a different background (maybe white-ish), colors are fading into the green for me

piney point reference

consider moving the piney point and red tide sentences to the chlorophyll section, provide a little separation from the regulatory compliance?

Remove Janicki Logo

We need to remove the Janicki logo from the header since they are no longer on contract for NMC tech support

gh actions build not pulling recent data from EPC

It works running the build file locally, but it's not pulling it on build.yaml

Page 2 Subheadings

Capitalize "Initiative"
Capitalize TMDL "Compliance"

Review text for 2023 update

Draft 2023 report card with provisional Nov/Dec EPC data is available: https://tbep-tech.github.io/wq-static/wq.pdf

Please review the text and make the appropriate edits to wq1.Rnw (first page) and wq2.Rnw (second page).

Compliance report link

Link/biblio for the 2nd report:

https://www.tbeptech.org/TBEP_TECH_PUBS/2019/TBEP_11-19_TBNMC_2018_RA_Annual_Assessment.pdf

2018 Tampa Bay Estuary Nutrient Management Compliance Assessment. 2019. Technical Report #11-19 of the Tampa Bay Estuary Program (E.T. Sherwood and M. Burke). 15 pp.

text edit p.2

fig. 7 seagrass acreage source change SWFMD to "SWFWMD"

Create build file for two-pager

Scrape content from Google Docs, manual year entry, combine separate pdfs into one

Decision Matrix Results

Verify results for OTB. Management result shouldn't be yellow if regulatory threshold is not met/result red.

Add interim results

See issue here tbep-tech/tbeptools#19

2020 text edits

Figures 1 & 5 add note about missing data

2020 Decision Matrix Results
The nuisance alga, Pyrodinium bahamense, was again reported in Old Tampa Bay (OTB) during June - September 2020, contributing to a large magnitude chlorophyll-a exceedance that has persisted for a long duration (6 yrs).

Page 1 Note: Add hyphen to "#4-00"

Maintaining Reasonable Assurance & TMDL Compliance
During 2020, the COVID-19 pandemic precluded water quality data collection in April and May. As a result, compliance determinations have not been made for any bay segments. Results shown in Figure 5 depict chlorophyll-a concentrations in relation to regulatory criteria, as calculated without observations from the months noted above. The fourth RA annual assessment report for the 2017-2021 period will be submitted in April 2021.

2020 Chl-a Monthly Variation
summer months. and DELETE "Lower Tampa Bay also showed elevated concentrations in August 2019, potentially due to non-harmful algae blooms."

Tampa Bay Seagrass Recovery
SWFWMD coverage estimates from the winter 2019-20 period will be available in spring 2021. More information on assessments of the bay’s seagrass recovery using transect monitoring data can be found at https://shiny.tbep.org/seagrasstransect-dash/.

Progress Towards Meeting Regulatory Goals
Update note at bottom--
Note: : 2020 Tampa Bay Reasonable Assurance Assessment available from Sherwood, E., Burke, M. 2021. TBEP Technical Report #XX-21. Please cite this document as Beck, M.W., Burke, M., Raulerson, G. 2020. 2020 Tampa Bay Water Quality Assessment. Tampa Bay Estuary Program Technical Report #XX-21, St. Petersburg, FL.

Language into doc about compliance assessment

Paragraph 2.1, last sentence:

"...report for the 2017-2021 period was submitted in March 2019."

(Changing from future to past tense)

Links to blue font?

Suggest making links (I found HMPU & 2 shiny apps in seagrass section) a different color, maybe standard blue?

Seagrass target change

Bottom of page 2, the seagrass target, per the 2020 HMPU, is now 40,000 acres (not 38k). Per Maya change the text now and we'll wait for the 2020 seagrass numbers to update the graph?

And I was poking a few things, couldn't figure out where to try and make the change myself. I think I looked at all of the text-ish files but no joy.