Piney Point Data and Analysis

# Piney Point Data and Analysis
### <a href="mailto:mbeck@tbep.org">Dr. Marcus Beck</a> <span class="math inline">•</span> <a href="https://twitter.com/fawda123">@fawda123</a> <span class="math inline">•</span> <a href="https://twitter.com/hashtag/TampaBayOpenSci?src=hashtag_click">#TampaBayOpensci</a>
### Tampa Bay Estuary Program
### 6/15/2021

---

* Understand the available data
* Understand how to access the available data
* Analyses to date
* Develop analysis goals and plan of attack
* Meeting notes [here](https://docs.google.com/document/d/1gWFnNe5kPj5rLmgmrLbVlt2UsxfE4pX1v6Gfdh8HbZc/edit)

---

* All raw data from partners are here (spreadsheet, GoogleDrive): https://bit.ly/3wtC5gz
* All compiled/formatted data are here (.RData, GitHub): https://github.com/tbep-tech/piney-point/tree/main/data)

---

* __Water quality__: 17 parameters
* __Phytoplankton__: qualitative, quantitative
* __Seagrass, macroalgae__: Freq. occurrence by species, groups
* __Contaminants__: mostly metals
* __Baseline__: water quality and seagrass
* __Spatial__: monitoring stations by type

---

* All data pulled from GoogleDrive and synthesized using [this](https://github.com/tbep-tech/piney-point/blob/main/R/dat_proc.R) R script 
     * Compile by source (e.g., DEP, Manatee Co., etc.)
     * Standardize names, units, etc.
     * Organize in tidy format for ease of analysis
* Each time data are updated, several automated [tests](https://github.com/tbep-tech/piney-point/tree/main/tests/testthat) are run to check accuracy, e.g., 
     * Are the units, names correct?
     * Are the station names matching between files?
     * Are their duplicates, missing values?

---

* All files are in .RData binary formats, access in R (I can make csv if needed)
* Files follow a loose naming convention, e.g.,
   * `rswqdat`: response water quality data
   * `bswqdat`: baseline water quality data
   * `rstrndat`: response SAV, macroalgae transect data
   * `rsphydat`: response phytoplankton data
   * `rstrnpts`: response transect spatial data (points)
   
---

* All files are "tidy" and able to join by station, source and/or date

```r
load(url('https://tbep-tech.github.io/piney-point/data/rswqdat.RData'))
rswqdat
```

```
## # A tibble: 7,065 x 12
##    station date       source var   uni     val qual  bswqstation lbs     nrmrng 
##    <chr>   <date>     <chr>  <chr> <chr> <dbl> <chr> <chr>       <chr>   <chr>  
##  1 16      2021-03-23 epchc  do    mgl    6.62 <NA>  16          DO (mg~ 6.07-6~
##  2 19      2021-03-23 epchc  do    mgl    6.56 <NA>  19          DO (mg~ 6.08-6~
##  3 21      2021-03-23 epchc  do    mgl    6.56 <NA>  202         DO (mg~ 6.29-7~
##  4 22      2021-03-23 epchc  do    mgl    7.7  <NA>  362         DO (mg~ 6.92-7~
##  5 23      2021-03-23 epchc  do    mgl    6.5  <NA>  23          DO (mg~ 6.01-6~
##  6 24      2021-03-23 epchc  do    mgl    6.82 <NA>  24          DO (mg~ 5.87-6~
##  7 25      2021-03-23 epchc  do    mgl    7.32 <NA>  25          DO (mg~ 6.34-8~
##  8 28      2021-03-23 epchc  do    mgl    6.66 <NA>  28          DO (mg~ 6.03-7~
##  9 82      2021-03-23 epchc  do    mgl    6.92 <NA>  82          DO (mg~ 6.17-7~
## 10 84      2021-03-23 epchc  do    mgl    6.64 <NA>  84          DO (mg~ 5.83-6~
## # ... with 7,055 more rows, and 2 more variables: lbunis <chr>, inrng <chr>
```

---

* Some preliminary stuff: [https://github.com/tbep-tech/piney-point-analysis](https://github.com/tbep-tech/piney-point-analysis)
     * [Interpolation example](https://tbep-tech.github.io/piney-point-analysis/chlinterp): chlorophyll response
     * [Trends synthesis](https://tbep-tech.github.io/piney-point-analysis/trends): poor attempt at broad analysis
     * [Seasonal analysis](https://tbep-tech.github.io/piney-point-analysis/seasonal): deviation from baseline
* The data folder in this repo is synced daily with the source data on the Piney Point dashboard repo
* Open for GitHub Pull Requests

---

* We know there was an initial water column algal response
* We need to show other responses, the nutrients did not go away: 
     * Nutrient recycling between parts of the bay
     * Broad vs local changes
     * Deviation from baseline
     * Link to modelling data
* Immediate concern is documenting impacts, but long-term plan is publication