index.qmd

---
title: "Introduction to MassWateR"
author: 
   - name: Dr. Marcus Beck, <mbeck@tbep.org>
institute: "Tampa Bay Estuary Program"
date: "09/16/2022"
format:
  revealjs:
    logo: figure/logo.png
    transition: slide
    footer: "<https://massbays-tech.github.io/MassWateR>"
    theme: styles.scss
    link-external-icon: true
    linkcolor: "#64C147"
    link-external-newwindow: true
execute: 
  echo: true
---

```{r}
#| echo: false
#| include: false
library(knitr)
library(MassWateR)

# results data
respth <- system.file('extdata/ExampleResults.xlsx', package = 'MassWateR')
resdat <- readMWRresults(respth, warn = F, runchk = F)

# dqo accuracy data
accpth <- system.file('extdata/ExampleDQOAccuracy.xlsx', package = 'MassWateR')
accdat <- readMWRacc(accpth, runchk = F)

# dqo completeness data
frecompth <- system.file('extdata/ExampleDQOFrequencyCompleteness.xlsx', package = 'MassWateR')
frecomdat <- readMWRfrecom(frecompth, runchk = F)

# site metadata
sitpth <- system.file('extdata/ExampleSites.xlsx', package = 'MassWateR')
sitdat <- readMWRsites(sitpth, runchk = F)

# wqx metadata
wqxpth <- system.file('extdata/ExampleWQX.xlsx', package = 'MassWateR')
wqxdat <- readMWRwqx(wqxpth)
```

------------------------------------------------------------------------

## WHAT IS MASSWATER?

::: columns
::: {.column width="60%"}
An R package for working with Massachusetts surface water quality data

-   Summarize quality control checks and create reports
-   Evaluate outliers
-   Plot trends by site, date
-   Create maps
-   Format results for upload to WQX
:::

::: {.column width="40%"}
![](figure/logo.png){fig-align="center" width="250px"}
:::
:::

------------------------------------------------------------------------

## WHAT IS MASSWATER?

A workflow to solve your data woes!

![](figure/workflow.PNG){fig-align="center"}

------------------------------------------------------------------------

## WEBSITE

Installation instructions, function help files, vignettes!

![](figure/website.png){fig-align="center"}

------------------------------------------------------------------------

## REQUIRED DATA

-   [Water quality data results file](https://massbays-tech.github.io/MassWateR/MassWateR_Results_Template.xlsx){style="color: #64C147"}
-   Data quality objective files ([accuracy](https://massbays-tech.github.io/MassWateR/MassWateR_DQOAccuracy_Template.xlsx){style="color: #64C147"}, [frequency, completeness](https://massbays-tech.github.io/MassWateR/MassWateR_DQOFreqComp_Template.xlsx){style="color: #64C147"})
-   [Site metadata](https://massbays-tech.github.io/MassWateR/MassWateR_Sites_Template.xlsx){style="color: #64C147"} (location, site groups, etc.)
-   [WQX metadata](https://massbays-tech.github.io/MassWateR/MassWateR_WQXMeta_Template.xlsx){style="color: #64C147"}

::: callout-note
## Templates

All data must be formatted using available templates, which you are already have! The package includes automated data checks to verify the correct format.
:::

------------------------------------------------------------------------

## QC REVIEW

```{r}
#| eval: false
qcMWRreview(res = resdat, acc = accdat, frecom = frecomdat, output_dir = getwd())
```

![](figure/qcreport.png){fig-align="center" fig-height="80%" width="579"}

[view report](supp/qcreview.pdf){style="color: #64C147"}

------------------------------------------------------------------------

## OUTLIER REVIEW

```{r}
anlzMWRoutlier(res = resdat, param = "DO", acc = accdat, group = "month")
```

------------------------------------------------------------------------

## SEASONAL ANALYSIS

```{r}
anlzMWRseason(res = resdat, param = "DO", acc = accdat, thresh = "fresh", group = "month", type = "jitterbar")
```

------------------------------------------------------------------------

## TIME-SERIES ANALYSIS

```{r}
anlzMWRdate(res = resdat, param = "DO", acc = accdat, thresh = "fresh", group = "site", site = c("ABT-026", "ABT-077"))
```

------------------------------------------------------------------------

## SITE ANALYSIS

```{r}
anlzMWRsite(res = resdat, param = "DO", acc = accdat, thresh = "fresh", type = "bar", confint = T)
```

------------------------------------------------------------------------

## MAP ANALYSIS

```{r}
anlzMWRmap(res = resdat, param = "DO", acc = accdat, sit = sitdat, addwater = "medium", warn = F)
```

------------------------------------------------------------------------

## WQX FORMATTING

```{r}
#| eval: false
tabMWRwqx(res = resdat, acc = accdat, sit = sitdat, wqx = wqxdat, output_dir = getwd())
```

![](figure/wqxtab.PNG){fig-align="center" fig-height="80%"}

[view output](supp/wqxtab.xlsx){style="color: #64C147"}