05-Background.Rmd

# Create Backgound Data
This chapter will describe the process used to calculate background data for input to the Maxent model. Background point data are used to define the habitat available to mussels within the study area.  

```{r echo=FALSE, fig.cap="HREP Mussel Modeling Workflow, Calculate Background Step."}
include_graphics("docs/images/workflow_calculate_background.png")
```

## Create Background Data
Create a background to constrain points to aquatic areas (more data resolution) and reduce Maxent run times.

* Use the Create Random Points (Data Management) tool to create a background restricted to aquatic areas:

    * Output location: `\\mvrdfs\EGIS\Work\EMP\HREP_Projects\SteamboatSlough\Mussels\SteamboatMusselModel\Data\SB_Mussels.gdb\`
    * Output feature class: `background`
    * Constraining feature class:`aquatic_areas_20m`
    * Number of points: 10000
    * Minimum allowed distance: 25m
    * Leave all others as defaults
    * Click OK to run the tool

* In the `background` feature class, add 3 fields, one named `species`, Type = Text and Length=20; one named `longitude`, Type = Double; and one named `latitude`, Type = Double. 
* For the `species` field use the Field Calculator tool to set the value of the field to `species` = "background". 
* Use the Calculate Geometry tool to populate the `longitude` and `latitude` fields, ensuring that the coordinate system is set to `NAD 1983 2011 US Feet` and `StatePlane Illinois West FIPS 1202` and the units are set to `US feet`. 


## Export to Maxent "SWD" Format
The purpose of this step is to assign the environmental predictor values (AdH hydraulic variables and optionally the wind/wave variables) to each of the background points. The Maxent documentation refers to this format as the "Samples With Data" (SWD) format because it contains the samples (i.e., sample identifier, latitude, longitude) with the environmental predictor variables (e.g., q5_velocity, q5_depth, q5_slope, etc.). 

* Ensure all environmental predictor layers have the same spatial reference as the `background` feature class. 
* Use the Extract Multi Values to Points (spatial analyst) tool to write new values (velocity, depth, slope, and ss) onto the `background` feature class.

     * Input point features: `\\mvrdfs\EGIS\Work\EMP\HREP_Projects\SteamboatSlough\Mussels\SteamboatMusselModel\Data\SB_Mussels.gdb\background`
     * Input rasters: `q5_velocity`, `q5_depth`, `q5_ss`, `q5_froude`, `q5_reynolds`, `q5_slope`, `q95_velocity`, `q95_depth`, `q95_ss`, `q95_froude`, `q95_reynolds`, `q95_slope`. 
     
* Export the `background` feature class attribute table as a `.csv` file. Ensure the `ObjectID` field is deleted using Excel prior to use in Maxent.