2023 provisional update all months

.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@v2
-      - 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::gridExtra
-            any::Hmisc
-            any::tinytex
-            any::pdftools
-            any::git2r
-            tbeptools
-
-      - name: Build report card
-        run: Rscript -e 'source("build.R")'
-      - name: Commit results
-        run: |
-          git config --local user.email "[email protected]"
-          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"
+      # - 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::gridExtra
+      #       any::Hmisc
+      #       any::tinytex
+      #       any::pdftools
+      #       any::git2r
+      #       tbeptools
+      # 
+      # - name: Build report card
+      #   run: Rscript -e 'source("build.R")'
+      # - name: Commit results
+      #   run: |
+      #     git config --local user.email "[email protected]"
+      #     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"

README.md

@@ -14,8 +14,8 @@ For this repository:
 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. Run build.R
-1. Comment lines 6-7, 19-48 on .github/workflows/build.yaml to disable CI (w/o error)
+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
 
 Updating the wq dashboard with provisional data (wq-dash repo):

wq1.Rnw

@@ -60,14 +60,14 @@ library(gridExtra)
 # 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 <- 2023
-partialyr <- T
+partialyr <- F
 
 # get legend from an existing ggplot object
 g_legend<-function(a.gplot){
@@ -152,7 +152,7 @@ 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 Hillsborough Bay (HB), Middle Tampa Bay (MTB), and Lower Tampa Bay (LTB)(Table \ref{tab:segtab}, Figure \ref{fig:thrplot}). Unlike the past seven years, 2022 water quality conditions in Old Tampa Bay (OTB) were also supportive of seagrass with annual averages of chlorophyll and light penetration remaining below management targets.  Chlorophyll and light penetration was supportive of seagrass in all other segments using existing targets (Table \ref{tab:segtab}). However, water quality conditions in OTB and HB remain under investigation based on recent seagrass coverage trends.
+Water quality remained supportive of seagrass in Hillsborough Bay (HB), Middle Tampa Bay (MTB), and Lower Tampa Bay (LTB)(Table \ref{tab:segtab}, Figure \ref{fig:thrplot}). 2023 water quality conditions in Old Tampa Bay (OTB) were also supportive of seagrass similar to 2022 with annual averages of chlorophyll and light penetration remaining below management targets.  Chlorophyll and light penetration was supportive of seagrass in all other segments using existing targets (Table \ref{tab:segtab}). However, water quality conditions in OTB and HB remain under investigation based on recent seagrass coverage trends.
 \end{minipage}
 \hspace{0.1in}
 \begin{minipage}{0.5\textwidth}

wq2.Rnw

@@ -58,14 +58,14 @@ 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 <- 2023
-partialyr <- T
+partialyr <- F
 
 # get legend from an existing ggplot object
 g_legend<-function(a.gplot){
@@ -116,12 +116,12 @@ 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 satisfied requirements for approval during the next five year period. During 2022, all bay segments met FDEP criteria for chlorophyll. Tampa Bay Nitrogen Management Consortium participants continue to pursue actions that ensure water quality criteria are met for the next RA period from 2022-2026. The first RA annual assessment report for the 2022-2026 period will be submitted in April 2023.
+\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 satisfied requirements for approval during the next five year period. During 2022, all bay segments met FDEP criteria for chlorophyll. Tampa Bay Nitrogen Management Consortium participants continue to pursue 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.
 \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 2022 compared to years prior, which allowed the chlorophyll criteria to be met for the first time in three years.  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 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 2022 compared to years prior, which allowed the chlorophyll criteria to be met again similar to 2022.  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.
 \end{block}
 
 <<chlboxplot, echo = F, fig = F, include = F, eval = T>>=
@@ -196,7 +196,7 @@ dev.off()
 
 \vspace{-0.1in}
 
-\tiny \textit{\textbf{Note}: 2022 nutrient management compliance assessment available from Beck, M.W., Burke, M., Sherwood, E. 2023. TBEP Technical Report \#05-23.  Please cite this document as Beck, M.W., Burke, M., Sherwood, E. 2023. 2022 Tampa Bay Water Quality Assessment. TBEP Technical Report \#03-23, St. Petersburg, FL.} \\
+\tiny \textit{\textbf{Note}: 2023 nutrient management compliance assessment available from Beck, M.W., Burke, M., Sherwood, E. 2024. TBEP Technical Report \#xx-24.  Please cite this document as Beck, M.W., Burke, M., Sherwood, E. 2024. 2023 Tampa Bay Water Quality Assessment. TBEP Technical Report \#xx-23, St. Petersburg, FL.} \\
 
 \end{column}