---
title: "Getting Started"
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  %\VignetteIndexEntry{Getting Started With StreamCatTools StreamCatTools}
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---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>", 
  warning = FALSE, 
  message = FALSE
)
```

## Installing and loading StreamCatTools
To install, currently you need to install from GitHub using devtools
```{r, message=FALSE, eval=FALSE}
library(devtools)
install_github('USEPA/StreamCatTools')
```

After installing load the library
```{r, message=FALSE}
library(StreamCatTools)
```

## Background
The `StreamCatTools` package was designed to simplify the use of [StreamCat](https://www.epa.gov/national-aquatic-resource-surveys/streamcat-dataset) data in R, leveraging the new [API for StreamCat](https://api.epa.gov/StreamCat/streams/metrics). 

## StreamCat API
We can  pull data into R from the [StreamCat API](https://usepa.github.io/StreamCatWebServices_Public/#/) by simply passing a URL to extract from json.  We have to hard-wire parameters though and are limited in the number of records returned through a `GET` request.
```{r API}
res <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/streams/metrics?name=fert&areaOfInterest=cat&comid=179")
res$items
```

## List API parameters
List StreamCat parameters: Get a list of available StreamCat values for certain parameters using the `sc_get_params` function via the API
```{r params}
region_params <- sc_get_params(param='areaOfInterest')

name_params <- sc_get_params(param='metric_names')

print(paste0('region parameters are: ', paste(region_params,collapse = ', ')))
print(paste0('A selection of available StreamCat metrics include: ',paste(name_params[1:10],collapse = ', ')))
```
We can also see what metrics are available for what areas of interest and what years using the `sc_get_params` function (which returns a tibble of information about StreamCat metrics):
```{r params2}
var_info <- sc_get_params(param='variable_info')
head(var_info)
```

We can look up the display name or names for a metric using the `sc_fullname` function via the API
```{r fullnames}
metric='pcthbwet2011'
fullname <- sc_fullname(metric)
fullname
```

```{r fullnames2}
metric='pctdecid2019,fert'
fullname <- sc_fullname(metric)
fullname
```
We can additionally get a data frame of state FIPS codes, abbreviations and names, and the same information for counties as well using `sc_get_params`:
```{r states}
states <- sc_get_params(param='state')
head(states)
```

```{r counties}
counties <- sc_get_params(param='county')
head(counties)
```

## Get data for COMIDs
In this example we access several variables, for several areas of interest, and for several COMIDs using the `sc_get_data` function.  Loads data into a tibble we can view.
```{r get_data}
df <- sc_get_data(metric='pcturbmd2006,damdens,tridens', aoi='rp100cat,cat,ws', comid='179,1337,1337420')
knitr::kable(df)
```

## Get data for county
In this example we access a couple variables at the watershed scale for the area of interest of a county (Benton County in this case) using the `sc_get_data` function. 
```{r countydata}
df <- sc_get_data(metric='pctwdwet2006', aoi='ws', county='41003')
knitr::kable(head(df))
```

## Get all metrics for COMIDs or an Area of Interest
We can also get all StreamCat metrics for a set of COMIDs or an area of interest.  **Please do not request metric='all' and aoi='conus' in order not to overload requests to the server.  Requesting metric='all' for a state or multiple states or hydroregions will also take a long time to process**.
```{r all}
df <- sc_get_data(comid='179', aoi='cat', metric='all')
knitr::kable(head(df))
```

## Get NLCD data
In this example we access National Land Cover Dataset (NLCD) data for 2001, just at the catchment level for several COMIDs using the `sc_nlcd` function.  Loads data into a tibble we can view.
```{r get_nlcd}
df <- sc_nlcd(year='2001', aoi='cat',
              comid='179,1337,1337420')
knitr::kable(df)
```

We can also pass a couple years for a different area of interest for another region like a county.
```{r get_nlcd2}
df <- sc_nlcd(year='2006, 2019', aoi='ws',
              county='41003')
knitr::kable(head(df))
```

## Get COMIDs
In this example we use the `sc_get_comid` function to find COMIDs for USGS stream gages we load into R. We use a .csv file with coordinate columns and a known coordinate reference system.
```{r comids, eval=FALSE}
gages = readr::read_csv(system.file("extdata","Gages_flowdata.csv", package = "StreamCatTools"),show_col_types = FALSE)
# we'll just grab a few variables to keep things simple
gages <- gages[,c('SOURCE_FEA','STATION_NM','LON_SITE','LAT_SITE')]
gages_coms <- sc_get_comid(gages, xcoord='LON_SITE',                   ycoord='LAT_SITE', crsys=4269)

# Add the COMID we found back to gages data frame
gages$COMID <- strsplit(gages_coms, ",")[[1]]
df <- sc_get_data(metric='huden2010', aoi='ws', comid=gages_coms)
df$COMID <- as.character(df$comid)
gages <- dplyr::left_join(gages, df, by='COMID')
knitr::kable(head(gages))
```

## Get data for a hydroregion
In this example we access a couple watershed-only metrics for a particular NHDPlus hydroregion using the `sc_get_data` function.
```{r hydroregion}
df <- sc_get_data(metric='pctwdwet2006', aoi='ws', region='Region17')
knitr::kable(head(df))
```

## Get data for CONUS
In this example we access a metric for conus using the `sc_get_data` function - this is shown for demonstration but not run as it takes a bit of time
```{r conus, eval=FALSE}
# df <- sc_get_data(metric='om', aoi='ws', conus='true')
# knitr::kable(head(df))
```

