evolution_reporting.Rmd

---
title: "Evolution of the water quality reporting tool"
author: "[Dr. Marcus Beck](mailto:marcusb@sccwrp.org) $\\bullet$ [\\@fawda123](https://twitter.com/fawda123)	$\\bullet$ [#TampaBayOpensci](https://twitter.com/hashtag/TampaBayOpenSci?src=hashtag_click)"
institute: "Southern California Coastal Water Research Project"
date: "9/5/2019"
output:
  xaringan::moon_reader:
    lib_dir: libs
    nature:
      highlightStyle: github
      highlightLines: true
      countIncrementalSlides: false
---

```{r, message = F, echo = F, warning = F}
library(knitr)
library(icon)

# global knitr options
opts_chunk$set(message = FALSE, dev.args = list(family = 'serif'), echo = F, warning = F)

# chunk hook for par
knit_hooks$set(par = function(before, options, envir){
  if (before && options$fig.show!='none') par(mar=c(4,4,.1,.1))
})
```

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# How did we apply open science principles to the water quality reporting tool?

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# Chapter 1: A history lesson

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```{r, out.width = '70%'}
knitr::include_graphics('figure/tbepreport.png')
```

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# Buried deep in the appendix... some clues!

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## Defining magnitude and duration of water quality exceedances

```{r, out.width = '90%'}
knitr::include_graphics('figure/outints.png')
```

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## Combining different water quality indicators

```{r, out.width = '90%'}
knitr::include_graphics('figure/outmats.PNG')
```

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## Developing a management narrative

```{r, out.width = '90%'}
knitr::include_graphics('figure/cats.PNG')
```

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# Chapter 2: Entering the modern age 

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```{r, out.width = '90%'}
knitr::include_graphics('figure/epchcftp.PNG')
```

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```{r, out.width = '100%'}
knitr::include_graphics('figure/reportall.png')
```

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### A primitive langauge...

```{r, out.width = '70%'}
knitr::include_graphics('figure/sascode.PNG')
```

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# Chapter 3: Ed goes to California

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```{r, out.width = '100%'}
knitr::include_graphics('figure/nceasoss.PNG')
```

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#### Dabbling in reproducibility

```{r, out.width = '80%'}
knitr::include_graphics('figure/initialrmd.PNG')
```

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# Chapter 4: Let's try open science

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# The first three chapters gave us the raw materials, now we can try better science in less time!

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## Build an R package!

```{r, out.width = '70%'}
knitr::include_graphics('figure/packagestructure.png')
```

###### http://r-pkgs.had.co.nz/package.html

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## The tbeptools package

```{r, out.width = '100%'}
knitr::include_graphics('figure/tbeptoolshome.PNG')
```

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## Full documentation

```{r, out.width = '90%'}
knitr::include_graphics('figure/examplehelp.PNG')
```

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## Vignettes (how to in plain language)

```{r, out.width = '80%'}
knitr::include_graphics('figure/vignetteexample.PNG')
```

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## Interactive dashboards

```{r, out.width = '100%'}
knitr::include_graphics('figure/dashboard.PNG')
```

##### https://shiny.tbeptech.org/tbeptools/inst/wq-dash/wq-dash.Rmd

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# These are prototypes, this is what we can do for all CCMP indicators!