---
title: "rangeModelMetadata Function Directory"
author: "Cory Merow, Brian S. Maitner, Hannah L. Owens, Jamie Kass, Brian Enquist, Rob Guralnick"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{rangeModelMetadata Function Directory}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---


The rangeModelMetadata package is designed to provide functionality for working with rangeModelMetadata (`rmm`) objects.  These `rmm` objects are nested lists that hierarchically store data associated with species range/niche/distribution models.  These objects are designed to be flexible to accommodate a wide variety of modeling frameworks while also making modeling decisions transparent. 

For full information on each function, see the associated help file.

### Primary functions

* `rmmTemplate` Creates an empty `rmm` object that can then be populated by the user.
<!-- * `rmmCheckFull` Prints only the rmm fields that have been populated. -->
* `rmmCheckEmpty` Checks for empty values in the rmm object.
* `rmmSuggest` Provides suggested values for rmm object fields.


### `rmm` Autofill functions

Functions to automatically populate the relevant fields in an `rmm` object.  

* `rmmAutofillPackageCitation` Takes in a vector of packages used by the user in a workflow and returns a vector of Bibtex citations that can be inserted into the rmm object.
* `rmmAutofillEnvironment` Takes in environmental rasters used in modeling and adds relevant information to the `rmm` object.
* `rmmAutofillENMeval` Populates `rmm` objects with data taken from an `ENMeval` object.
* `rmmAutofillBIEN` Populates occurrence field in an `rmm` object with output from a `BIEN_occurrence_...` query.
* `rmmAutofillspocc` Populates occurrence field in an `rmm` object with output from a spocc query.

### `rmm` Check functions

Functions to check for common errors in `rmm` objects.

* `rmmCheckName` Identifies non-standard name fields in an rmm object.
* `rmmCheckValue` Checks a subset of `rmm` values against commonly used values and returns information on possible errors.
* `rmmCheckMissingNames` Identify obligate fields that are missing.
* `rmmCheckEmpty` Identify empty fields in an `rmm` object and classify these into obligate and optional fields.
* `rmmCleanNULLs` Remove NULL entries in an `rmm` object.
* `rmmCheckFinalize` Run all checking functions (`rmmCheck...`) sequentially to detect non-standard and missing values and fields

### `rmm` Utilities

* `rmmFamilies` View entity family names.
* `rmmDataDictionary` View the data dictionary.
* `rmmToCSV` Converts the `rmm` object to a CSV file.
* `csvTormm` Create `rmm` object From .csv File