aohMixS: aohMixS: mapping the species' AOH by mixing data from EOO and...

In thaisdoria/habitaR: Tools for mapping the species’ area of habitat (AOH) from geospatial data

Description

Through a mix approach combining the species' spatial-informed distribution with modelling techniques, thresholds the distribution models (e.g. SDMs) based on EOO's geometry to generate models-derived EOOs. Here, EOOs might correspond to the alpha hulls (ahull) or Minimum Polygon Convex (MCP) and a geographical similarity approach is used to estimate the shape of the species' distribution based on models. It is develop by adapting the approach described in Syfert et al. (2014), so that the species' area of habitat (AOH) can be interpreted as the SDMs-derived EOOs.

Usage

aohMixS (eooSp = eooSp, modSp = modSp, thresInitial = NULL , thresIncrement = NULL,
continuous = TRUE, poly = NULL, cropToPoly = FALSE, progress = TRUE,
removeTempFile = TRUE, stack = TRUE )

Arguments

eooSp	Spatial distribution data of the species representing the original (i.e. not refined) extent of occurrence (EOO). It might correspond to: path for a folder with spatial distribution files (ESRI shapefile format). SpatialPolygonsDataFrame (see readShp to obtain such class of object). aHull object with elements of 'SpatialPolygons' class created from occurrences records (see aHull to obtain such class of object). a list of 'RasterLayer' objects created from occurrences records (see aHull to obtain such class of object). 'RasterLayer', 'RasterStack' or 'RasterBrick' objects. NOTE: Input data for EOOs might correspond to Alpha Hull or to Minimum Polygon Convex (MCP), which can be generated, for example, with the convaHull or mcp functions.
modSp	Species distribution derived from modelling techniques (eg. SDMs). It might correspond to: path for a folder with species distribution models files (.asc or .tif format). a list of 'RasterLayer' objects (see readRas to obtain such class of object). 'RasterLayer', 'RasterStack' or 'RasterBrick' objects.
thresInitial	The minimum value of threshold to indicate the presence of the species in the cell. NOTE: From this initial value all threshold spectrum will be considered up to maximum value of 1.0 based on the increment value defined by threIncrement.
thresIncrement	The amount to sequentially increase the initial threshold with each iteration until find the value that maximizes the geographical overlap (maxJSI) between EOO and distribution models. See details.
poly	Optional. A polygon (ESRI shapefile in a 'SpatialPolygonsDataFrame' class) of a given area to be used as a mask to crop and restrict the models-derived EOOs to the area corresponding to provided polygon.
cropToPoly	(logical) Whether the output should be cropped by the provided poly. Only used if 'poly' is provided. If TRUE, the resulting maps will be restricted to the area of the poly. Default is FALSE.
progress	(logical) A bar showing the progress of the function. Default is TRUE.
removeTempFile	(logical) Whether the temporary files generated in each iteration should be deleted. It is recommended if the user wants to analyse a high volume of data at the same time. Default is TRUE.
stack	(logical) Whether the output maps should be returned as a stack of 'RasterLayer' files. Default is TRUE.

Details

Models-derived EOOs are generated through an adapted approach presented by Syfert et al. (2014) to setting thresholds by maximizing (across all spectrum of probabilities) the geographical similarity between the EOO (i.e. a polygon drawn based on the presence records, such as alpha hull or minimum polygon convex) and the polygon derived from models (e.g. SDMs predicted presences). In each iteration, based on the increment value defined by threIncrement, is searched the threshold that return the most similar distribution between the provided model and the EOO through the Jaccard Similarity Index (JSI), calculated as:

• JSI = C / (A + B) - C

A: area of alpha hull / B: area of SDM / C: overlapped area between A and B.

Value

By default, aohMixS returns a list with two elements:

• A 'RasterStack' (if stack = TRUE) or list of 'RasterLayer' objects (if stack = FALSE) of maps representing SDMs-derived EOOs.

• A data.frame of species and measures relative to SDM-derived EOO's construction and evaluation, as follow:

  • Threshold - Threshold value maximizing the geographical similarity between distribution from EOO and from model.

  • MaxJSI - Value of Jaccard Similarity Index (JSI) measured from comparison between the EOO and the model returning the maximum geographical similarity.

  • DifSizes - Difference (in number of cells) between the EOO and the SDMs-derived EOOs. This measure can be used to evaluate the performance of this analysis (see Syfert et al. 2014 for more details).

  • Prop - Proportion of the EOO maintained in the resulting SDMs-derived EOOs. This measure can be used to evaluate the performance of this analysis (see Syfert et al. 2014 for more details).

Author(s)

Thaís Dória & Daniel Gonçalves-Souza

References

1. Syfert M.M., Joppa L.N., Smith M.J, Coomes D., Bachman S.P. & Brummitt N.A. (2014). Using species distribution models to inform IUCN Red List assessments. Biological Conservation. 177.

2. Sangermano F., Eastman J.R. (2012). A GIS framework for the refinement of species geographic ranges. International Journal of Geographical Information Science 26, 39-55.

Examples

### Path for folder as Input ###

## Not run: 

# Binary Output #
aohmix_bin <- aohMixS (eooSp = path_eoo, modSp = path_mod,
thresInitial = 0.05, thresIncrement = 0.25, continuous = FALSE, cropToPoly = TRUE,
poly = poly, progress = TRUE, stack = TRUE)

# Continuous Output #
aohmix_con <- aohMixS (eooSp = path_eoo, modSp = path_mod,
thresInitial = 0.05, thresIncrement = 0.25, continuous = TRUE, cropToPoly = TRUE,
poly = poly, progress = TRUE, stack = TRUE)


## End(Not run)


### Shapefile as Input ('aHull' or 'SpatialPolygonsDataFrame' class) ###

# Binary Output #

aohmixS_bin <- aohMixS (eooSp = aHull_plantShp, modSp = sdm_plantRas,
thresInitial = 0.05, thresIncrement = 0.25, continuous = FALSE, cropToPoly = TRUE,
poly = poly, progress = TRUE, stack = TRUE)

aohmixS_bin <- aohMixS (eooSp = spdf_plantShp, modSp = sdm_plantRas,
thresInitial = 0.05, thresIncrement = 0.25, continuous = FALSE, cropToPoly = TRUE,
poly = poly, progress = TRUE, stack = TRUE)

# Continuous Output #

aohmixS_con <- aohMixS (eooSp = aHull_plantShp, modSp = sdm_plantRas,
thresInitial = 0.05, thresIncrement = 0.25, continuous = TRUE, cropToPoly = TRUE,
poly = poly, progress = TRUE, stack = TRUE)

aohmixS_con <- aohMixS (eooSp = spdf_plantShp, modSp = sdm_plantRas,
thresInitial = 0.05, thresIncrement = 0.25, continuous = TRUE, cropToPoly = TRUE,
poly = poly, progress = TRUE, stack = TRUE)


### Raster as Input ###

# Binary Output #

aohmixR_bin <- aohMixS (eooSp = aHull_plantRas, modSp = sdm_plantRas,
thresInitial = 0.05, thresIncrement = 0.25, continuous = FALSE, cropToPoly = TRUE,
poly = poly, progress = TRUE, stack = TRUE)

# Continuous Output #

aohmixR_con <- aohMixS (eooSp = aHull_plantRas, modSp = sdm_plantRas,
thresInitial = 0.05, thresIncrement = 0.25, continuous = TRUE, cropToPoly = TRUE,
poly = poly, progress = TRUE, stack = TRUE)

thaisdoria/habitaR documentation built on Dec. 18, 2020, 8:09 p.m.