diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 0209418..75a1c08 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -3,8 +3,8 @@ on: branches: - main - master - schedule: - - cron: "0 0 * * *" + # schedule: + # - cron: "0 0 * * *" name: build @@ -16,41 +16,41 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v2 - with: - extra-repositories: 'https://tbep-tech.r-universe.dev' - - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-tinytex@v2 - - name: Setup Ubuntu dependencies - run: | - sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable - sudo apt-get update - sudo apt-get install libudunits2-dev libgdal-dev libgeos-dev libproj-dev libsqlite0-dev - - name: Setup R dependencies - uses: r-lib/actions/setup-r-dependencies@v2 - with: - packages: | - any::dplyr - any::knitr - any::rmarkdown - any::ggmap - any::ggrepel - any::here - any::tibble - any::ggplot2 - any::patchwork - any::Hmisc - any::tinytex - any::pdftools - url::https://cran.r-project.org/src/contrib/Archive/git2r/git2r_0.33.0.tar.gz - tbeptools - - - name: Build report card - run: Rscript -e 'source("build.R")' - - name: Commit results - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - git add -A - git commit -m 'Re-build data' || echo "No changes to commit" - git push origin || echo "No changes to commit" \ No newline at end of file + # - uses: r-lib/actions/setup-r@v2 + # with: + # extra-repositories: 'https://tbep-tech.r-universe.dev' + # - uses: r-lib/actions/setup-pandoc@v2 + # - uses: r-lib/actions/setup-tinytex@v2 + # - name: Setup Ubuntu dependencies + # run: | + # sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable + # sudo apt-get update + # sudo apt-get install libudunits2-dev libgdal-dev libgeos-dev libproj-dev libsqlite0-dev + # - name: Setup R dependencies + # uses: r-lib/actions/setup-r-dependencies@v2 + # with: + # packages: | + # any::dplyr + # any::knitr + # any::rmarkdown + # any::ggmap + # any::ggrepel + # any::here + # any::tibble + # any::ggplot2 + # any::patchwork + # any::Hmisc + # any::tinytex + # any::pdftools + # url::https://cran.r-project.org/src/contrib/Archive/git2r/git2r_0.33.0.tar.gz + # tbeptools + # + # - name: Build report card + # run: Rscript -e 'source("build.R")' + # - name: Commit results + # run: | + # git config --local user.email "actions@github.com" + # git config --local user.name "GitHub Actions" + # git add -A + # git commit -m 'Re-build data' || echo "No changes to commit" + # git push origin || echo "No changes to commit" \ No newline at end of file diff --git a/README.md b/README.md index 3f847d9..5902e34 100644 --- a/README.md +++ b/README.md @@ -12,8 +12,8 @@ For this repository: 1. Take downloaded data from wq-static CI build ('Results_Updated.xls') and copy in provisional data from EPC 1. Check if all data present, should be 10 samples in HB, 8 in LTB, 12 in MTB, 15 in OTB 1. Save new file, 'Results_Provisional.xlsx' (okay to save as new file format), in data-raw folder -1. In wq1.Rnw comment lines 64, 68, uncomment lines 63, 67, make sure line 70 is F -1. In wq2.Rnw comment lines 62, 66, uncomment lines 61, 65, make sure line 68 is F +1. In wq1.Rnw comment lines 63, 67, uncomment lines 62, 66, make sure line 69 is F +1. In wq2.Rnw comment lines 61, 65, uncomment lines 60, 64, make sure line 67 is F 1. Run build.R through line 27 1. Comment lines 6-7, 19-56 on .github/workflows/build.yaml to disable CI (w/o error) 1. Update text and any other static graphics diff --git a/data-raw/Results_Provisional.xlsx b/data-raw/Results_Provisional.xlsx index d18bb1a..efc35e3 100644 Binary files a/data-raw/Results_Provisional.xlsx and b/data-raw/Results_Provisional.xlsx differ diff --git a/data-raw/Results_Updated.xls b/data-raw/Results_Updated.xls index 2768be4..d1b6ecb 100644 Binary files a/data-raw/Results_Updated.xls and b/data-raw/Results_Updated.xls differ diff --git a/figure/attainmat.pdf b/figure/attainmat.pdf index 0ef28af..adc632c 100644 Binary files a/figure/attainmat.pdf and b/figure/attainmat.pdf differ diff --git a/figure/chlboxplot.pdf b/figure/chlboxplot.pdf index dbcb4f2..c0395f9 100644 Binary files a/figure/chlboxplot.pdf and b/figure/chlboxplot.pdf differ diff --git a/figure/chlmat.pdf b/figure/chlmat.pdf index 59a137e..eebcecb 100644 Binary files a/figure/chlmat.pdf and b/figure/chlmat.pdf differ diff --git a/figure/sitemap-1.pdf b/figure/sitemap-1.pdf index 7cfc47d..4246122 100644 Binary files a/figure/sitemap-1.pdf and b/figure/sitemap-1.pdf differ diff --git a/figure/sitemap.pdf b/figure/sitemap.pdf index 1c0efa7..f62bd6c 100644 Binary files a/figure/sitemap.pdf and b/figure/sitemap.pdf differ diff --git a/figure/thrplot.pdf b/figure/thrplot.pdf index 13f9349..74d2f99 100644 Binary files a/figure/thrplot.pdf and b/figure/thrplot.pdf differ diff --git a/wq.pdf b/wq.pdf index 5f9184b..a697f6d 100644 Binary files a/wq.pdf and b/wq.pdf differ diff --git a/wq1.Rnw b/wq1.Rnw index 24c8b1e..582bf04 100644 --- a/wq1.Rnw +++ b/wq1.Rnw @@ -59,14 +59,14 @@ library(patchwork) # devtools::load_all('../tbeptools/.') # local file path -# xlsx <- here('data-raw', 'Results_Provisional.xlsx') -xlsx <- here('data-raw', 'Results_Updated.xls') +xlsx <- here('data-raw', 'Results_Provisional.xlsx') +# xlsx <- here('data-raw', 'Results_Updated.xls') # import and download if new -# epcdata <- read_importwq(xlsx, download_latest = F) -epcdata <- read_importwq(xlsx, download_latest = T) +epcdata <- read_importwq(xlsx, download_latest = F) +# epcdata <- read_importwq(xlsx, download_latest = T) maxyr <- 2024 -partialyr <- T +partialyr <- F @ \title{\Large \Sexpr{maxyr} Tampa Bay Water Quality Assessments} @@ -144,7 +144,7 @@ Year to year algae abundance (measured as chlorophyll-a concentrations) and visi \vspace{-0.1in} \begin{minipage}{0.45\textwidth} \footnotesize -Water quality remained supportive of seagrass in all bay segments and continued to improve in comparison to prior years. Annual averages of chlorophyll-a and light penetration remained below management targets in Old Tampa Bay (OTB), Hillsborough Bay (HB), Middle Tampa Bay (MTB), and Lower Tampa Bay (LTB)(Table \ref{tab:segtab}, Figure \ref{fig:thrplot}). Despite these improvements, water quality conditions in OTB and HB remain under investigation based on observations of significant decreases in seagrass coverage between 2016 and 2022. +Water quality remained supportive of seagrass in most bay segments in comparison to prior years (Table \ref{tab:segtab}, Figure \ref{fig:thrplot}). One tropical storm and two hurricanes affected the region in the fall. As a result, management targets for chlorophyll-a were exceeded in Old Tampa Bay (OTB) and Middle Tampa Bay (MTB). Light attenuation targets were exceeded in Lower Tampa Bay (LTB), causing the bay segment to receive a "Caution" outcome. Water quality conditions in OTB remain under investigation based on observations of significant decreases in seagrass coverage between 2016 and 2022. \end{minipage} \hspace{0.1in} \begin{minipage}{0.5\textwidth} diff --git a/wq2.Rnw b/wq2.Rnw index a62764c..f01289a 100644 --- a/wq2.Rnw +++ b/wq2.Rnw @@ -57,14 +57,14 @@ library(ggplot2) # devtools::load_all('../tbeptools/.') # local file path -# xlsx <- here('data-raw', 'Results_Provisional.xlsx') -xlsx <- here('data-raw', 'Results_Updated.xls') +xlsx <- here('data-raw', 'Results_Provisional.xlsx') +# xlsx <- here('data-raw', 'Results_Updated.xls') # import and download if new -# epcdata <- read_importwq(xlsx, download_latest = F) -epcdata <- read_importwq(xlsx, download_latest = T) +epcdata <- read_importwq(xlsx, download_latest = F) +# epcdata <- read_importwq(xlsx, download_latest = T) maxyr <- 2024 -partialyr <- T +partialyr <- F @ \begin{document} @@ -108,12 +108,12 @@ dev.off() \begin{column}{.79\linewidth} \begin{block}{Maintaining Reasonable Assurance \& TMDL Compliance} -\footnotesize On behalf of the Tampa Bay Nitrogen Management Consortium, TBEP submitted the 2022 Reasonable Assurance (RA) Update for the 2017-2021 period to FDEP in December 2022. FDEP concluded that the RA Update satisifies efforts to maintain water quality during the next five year period. During 2023, all bay segments met FDEP numeric nutrient criteria. Tampa Bay Nitrogen Management Consortium participants continue to implement actions that ensure water quality criteria are met for the next RA period from 2022-2026. The second RA annual assessment report for the 2022-2026 period will be submitted in April 2024. +\footnotesize On behalf of the Tampa Bay Nitrogen Management Consortium, TBEP submitted the 2022 Reasonable Assurance (RA) Update for the 2017-2021 period to FDEP in December 2022. FDEP concluded that the RA Update satisifies efforts to maintain water quality during the next five year period. During 2023, all bay segments met FDEP numeric nutrient criteria. Tampa Bay Nitrogen Management Consortium participants continue to implement actions that ensure water quality criteria are met for the current RA period from 2022-2026. The second RA annual assessment report for the 2022-2026 period will be submitted in April 2025. \end{block} \begin{block}{\Sexpr{maxyr} Chl-a Monthly Variation Compared to 1974-\Sexpr{maxyr - 1}} \footnotesize -Chlorophyll-a concentrations were evaluated within the bay on a monthly basis during \Sexpr{maxyr} and compared to prior years' levels (Figure \ref{fig:chlboxplot}). Summer concentrations in Old Tampa Bay were lower in 2023 compared to prior years, which allowed the chlorophyll criteria to again be met over the 2022-2023 period. Understanding and mitigating summer blooms of \textit{Pyrodinium bahamense} in OTB continue to be the focus of research and management efforts for improving water quality in OTB. +Chlorophyll-a concentrations were elevated within the bay during late summer/fall months in \Sexpr{maxyr} due to tropical storm activity in the region (Figure \ref{fig:chlboxplot}). Summer concentrations in Old Tampa Bay were slightly elevated but on average were lower compared to prior years, which allowed the chlorophyll criteria to again be met over the 2022-2024 period. Understanding and mitigating summer blooms of \textit{Pyrodinium bahamense} in OTB continue to be the focus of research and management efforts. \end{block} <>= @@ -155,7 +155,7 @@ dev.off() \vspace{0in} \begin{minipage}{0.6\textwidth} \footnotesize -Tampa Bay's total seagrass coverage remains below the 40,000 acre recovery goal defined in the \href{https://tbep.org/habitat-master-plan-update/}{Habitat Master Plan Update}. The 2022 baywide estimate was 30,137 acres, representing a decrease of 11,518 acres since peak conditions in 2016 (Figure \ref{fig:sgtrnd}). The next SWFWMD seagrass coverage estimates will be developed from aerial photographs acquired during the 2023-2024 winter period. The largest coverage decreases were observed in Old Tampa Bay and Hillsborough Bay where increases in the attached algae \textit{Caulerpa prolifera} were also observed. However, 2023 seagrass transect data indicate this attached algae species is now in decline. More information on the bay's seagrass trends using transect monitoring data can be found at \href{https://shiny.tbep.org/seagrasstransect-dash/}{https://shiny.tbep.org/seagrasstransect-dash/} and using the coverage estimates can be found at \href{https://shiny.tbep.org/seagrass-analysis/}{https://shiny.tbep.org/seagrass-analysis/}. +Tampa Bay's total seagrass coverage remains below the 40,000 acre recovery goal defined in the \href{https://tbep.org/habitat-master-plan-update/}{Habitat Master Plan Update}. The 2022 baywide estimate was 30,137 acres, representing a decrease of 11,518 acres since peak conditions in 2016 (Figure \ref{fig:sgtrnd}). The next SWFWMD seagrass coverage estimates will be developed from aerial photographs acquired during the 2023-2024 winter period. The largest coverage decreases were observed in Old Tampa Bay and Hillsborough Bay where increases in the attached algae \textit{Caulerpa prolifera} were also observed. However, 2024 seagrass transect data indicate this attached algae species is now in decline. More information on the bay's seagrass trends using transect monitoring data can be found at \href{https://shiny.tbep.org/seagrasstransect-dash/}{https://shiny.tbep.org/seagrasstransect-dash/} and using the coverage estimates can be found at \href{https://shiny.tbep.org/seagrass-analysis/}{https://shiny.tbep.org/seagrass-analysis/}. \end{minipage} \hspace{0.2in} \begin{minipage}{0.32\textwidth}