EcotonerSettings-class: An S4-class to represent the settings of an 'ecotoner'...
In dschlaep/ecotoner: ecotoner - ecotones / ecological boundaries across environmental gradients
Description
An S4-class to represent the settings of an 'ecotoner' project
Slots
transect_typeAn integer. This flag selects the method to locate a transect, i.e., index to get("transect_types", envir = etr_vars). See package?ecotoner. Default is 4 corresponding to the method by 'sufficient area of homogeneous aspect'.
transect_type_descA character string. A string describing the method selected by transect_type. One of get("transect_types", envir = etr_vars).
candidate_THAs_NAn integer. The number of candidate transects that should be created if transect_type == 4. Default is 20.
transect_azimuthA numeric. The orientation of the environmental gradient within a transect. Defaults to 3 / 2 * pi, i.e., "left is low & right is high".
cores_NAn integer. This project is attempted to be run on the local machine in parallel with cores_N cores, but not with more than the actual number of cores of this machine.
rng_seedAn integer. This is the seed to set the (global) random number generator if used.
reproducibleA logical. If TRUE then this flag sets the transect number as the seed of the random number generator for each transect function call.
searchpoints_NAn integer. The target number of search points to randomly sample.
inhibit_searchpointsA logical. If TRUE then search points to initiate a transect search are sampled by a random simple sequential inhibition process; if FALSE, then a random (stratified) process is used to sample search points.
transect_NAn integer. The number of search points generated to initiate a transect search in the neighborhood of size(s) neighborhoods.
neighborhoodsAn integer vector. The number(s) of cells per side of a square representing local grid window(s) around a search point within which the transect methods searches for a suitable transect. Neighborhood(s) must be odd. Note: Below a neighborhood of 333 cells, the density function may become unreliable.
neighbors_NAn integer. The number of neighborhoods.
stepsHullEdgeAn integer vector. The step length(s), in grid cells, of the hull edge method by Gastner et al.
clumpAreaClasses_m2A numeric vector of length 2. The first number is the limit between small and medium patches, and the second number is the limit between medium and large patches.
res_rotate_gridAn integer. This number is used in the call to extract_tband_grids(); it represents variable 'fact' in raster::disaggregate(). The rotation of the grid from geographical to transect orientation requires a high resolution in cells because not all resulting cells would otherwise be represented well after the rotation. Instead, they would need to be interpolated which is tricky with categorical data such as vegetation cover. Hence, the results, e.g., patches, flowpaths, are relatively sensitive to this factor. 2 produced only a coarse representation of the rotated grids; 4 improved the resolution after rotation; 6 and 8 produced mostly similar results, but only 8 was satisfactorily. Default is thus 8.
Aspect_SDof201Mean_MaximumA numeric. If transect_type == 4, then this option limits the search area for line-starting points to areas of low standard variation of the mean aspect; default is 75 * pi / 180 = 1.31
Aspect_DeviationAlongCandidateLines_MaximumA numeric. If transect_type == 4, then this option sets the limit by which the mean aspect along candidate lines may differ from the mean aspect at the starting point differs; default is 30 * pi / 180 = 0.52
vegDefiningDensityTransect_lowA numeric. Determines the start of an ecotone transect by setting a critical vegetation density which should not be reached during the first run of sufficiently low values; default is 0.05
vegDefiningDensityTransect_highA numeric. Determines the start of an ecotone transect by setting a critical vegetation density which should be reached during the first run of sufficiently high values; default is 0.75
vegDefiningDensityTransectExtended_minA numeric. Determines the location of an ecotone transect by setting a critical vegetation density which should be maintained; default is 0.5
bandTransect_width_cellNAn integer. The width, in grid cell numbers, of the extracted band transect, half of which is on either side of the line transect. If transect_type == 4, then this number must match the smoothing window width of EcotonerGrids@grid_aspect_mean and EcotonerGrids@grid_aspect_sd.
min_slope_with_aspectA numeric. The minimum gradient, above which an aspect can be meaningfully measured/calculated. If transect_type == 4, then this number must match the used during production of EcotonerGrids@grid_aspect_mean and EcotonerGrids@grid_aspect_sd. Default is 2 * pi / 180 = 0.035 based for elevational slopes.
type_exclA TypeInfo object. This 'type' is to be excluded from 'grid_veg'.
type_veg1A TypeInfo object. This 'type' is one of the two vegetation (types) from 'grid_veg'.
type_veg2A TypeInfo object. This 'type' is one of the two vegetation (types) from 'grid_veg'.
dir_prjAn 'EcotonerPath' object, i.e., a character string representing a path. The path to the project directory.
dir_bigAn 'EcotonerPath' object or NA. If not NA, then the path where the transect data will be stored.
dir_initAn 'EcotonerPath' object. The path to the folder where the search points and other data are stored before transects can be searched for and extracted. This path is automatically generated.
dir_outAn 'EcotonerPath' object. The path that contains the outputs. This path is automatically generated from dir_prj or from dir_big if not NA.
dir_out_figAn 'EcotonerPath' object. The path that contains the folders where the transect figures are stored. This path is automatically generated.
dir_out_datAn 'EcotonerPath' object. The path that contains the folders where the transect data are stored. This path is automatically generated.
dir_envAn 'EcotonerPath' object. The path to where the raster grid representing the environmental gradient 'grid_env' is stored.
dir_vegAn 'EcotonerPath' object. The path to where the raster grid representing the vegetation 'grid_veg' is stored.
dir_veg1An 'EcotonerPath' object. The path to where the raster grid representing the vegetation 'grid_veg1' is stored.
dir_veg2An 'EcotonerPath' object. The path to where the raster grid representing the vegetation 'grid_veg2' is stored.
dir_flowAn 'EcotonerPath' object. The path to where the raster grid representing the flow paths 'grid_flow' is stored (required with transect_type == 3).
dir_abutAn 'EcotonerPath' object. The path to where the raster grid representing the abutting cells of vegetation types 1 and 2 'grid_abut' is stored (required with transect_type == 4).
dir_aspect_meanAn 'EcotonerPath' object. The path to where the raster grid representing the mean smoothed aspect 'grid_aspect_mean' is stored (required with transect_type == 4).
dir_aspect_sdAn 'EcotonerPath' object. The path to where the raster grid representing the standard deviation of the smoothed aspect 'grid_aspect_sd' is stored (required with transect_type == 4).
file_searchpointsAn 'EcotonerFile' object. The entire file path to where the search points are/will be stored.
file_initwindowAn 'EcotonerFile' object. The entire file path to where the owin object for the search point generation with inihibition is/will be stored.
file_timing_locateAn 'EcotonerFile' object. The entire file path to the timing of each transect location call will be stored, e.g., used by the call that removes unused temporary raster files.
file_etsummaryAn 'EcotonerFile' object. The entire file path to where the table of the transect summary are stored.
file_etsummary_tempAn 'EcotonerFile' object. The entire file path to where temporary table of the transect summary are stored.
file_etmeasure_baseAn 'EcotonerFile' object. The entire file path (minus a flag indicating which measure type) to where temporary tables of the transect measures are stored.
dschlaep/ecotoner documentation built on May 15, 2019, 2:57 p.m.
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Description
An S4-class to represent the settings of an 'ecotoner' project
Slots
transect_typeAn integer. This flag selects the method to locate a transect, i.e., index to
get("transect_types", envir = etr_vars). Seepackage?ecotoner. Default is4corresponding to the method by 'sufficient area of homogeneous aspect'.transect_type_descA character string. A string describing the method selected by
transect_type. One ofget("transect_types", envir = etr_vars).candidate_THAs_NAn integer. The number of candidate transects that should be created if
transect_type == 4. Default is20.transect_azimuthA numeric. The orientation of the environmental gradient within a transect. Defaults to
3 / 2 * pi, i.e., "left is low & right is high".cores_NAn integer. This project is attempted to be run on the local machine in parallel with
cores_Ncores, but not with more than the actual number of cores of this machine.rng_seedAn integer. This is the seed to set the (global) random number generator if used.
reproducibleA logical. If
TRUEthen this flag sets the transect number as the seed of the random number generator for each transect function call.searchpoints_NAn integer. The target number of search points to randomly sample.
inhibit_searchpointsA logical. If
TRUEthen search points to initiate a transect search are sampled by a random simple sequential inhibition process; ifFALSE, then a random (stratified) process is used to sample search points.transect_NAn integer. The number of search points generated to initiate a transect search in the neighborhood of size(s)
neighborhoods.neighborhoodsAn integer vector. The number(s) of cells per side of a square representing local grid window(s) around a search point within which the transect methods searches for a suitable transect. Neighborhood(s) must be odd. Note: Below a neighborhood of 333 cells, the density function may become unreliable.
neighbors_NAn integer. The number of
neighborhoods.stepsHullEdgeAn integer vector. The step length(s), in grid cells, of the hull edge method by Gastner et al.
clumpAreaClasses_m2A numeric vector of length
2. The first number is the limit between small and medium patches, and the second number is the limit between medium and large patches.res_rotate_gridAn integer. This number is used in the call to extract_tband_grids(); it represents variable 'fact' in raster::disaggregate(). The rotation of the grid from geographical to transect orientation requires a high resolution in cells because not all resulting cells would otherwise be represented well after the rotation. Instead, they would need to be interpolated which is tricky with categorical data such as vegetation cover. Hence, the results, e.g., patches, flowpaths, are relatively sensitive to this factor.
2produced only a coarse representation of the rotated grids;4improved the resolution after rotation;6and8produced mostly similar results, but only8was satisfactorily. Default is thus8.Aspect_SDof201Mean_MaximumA numeric. If
transect_type == 4, then this option limits the search area for line-starting points to areas of low standard variation of the mean aspect; default is75 * pi / 180 = 1.31Aspect_DeviationAlongCandidateLines_MaximumA numeric. If
transect_type == 4, then this option sets the limit by which the mean aspect along candidate lines may differ from the mean aspect at the starting point differs; default is30 * pi / 180 = 0.52vegDefiningDensityTransect_lowA numeric. Determines the start of an ecotone transect by setting a critical vegetation density which should not be reached during the first run of sufficiently low values; default is
0.05vegDefiningDensityTransect_highA numeric. Determines the start of an ecotone transect by setting a critical vegetation density which should be reached during the first run of sufficiently high values; default is
0.75vegDefiningDensityTransectExtended_minA numeric. Determines the location of an ecotone transect by setting a critical vegetation density which should be maintained; default is
0.5bandTransect_width_cellNAn integer. The width, in grid cell numbers, of the extracted band transect, half of which is on either side of the line transect. If
transect_type == 4, then this number must match the smoothing window width ofEcotonerGrids@grid_aspect_meanandEcotonerGrids@grid_aspect_sd.min_slope_with_aspectA numeric. The minimum gradient, above which an aspect can be meaningfully measured/calculated. If
transect_type == 4, then this number must match the used during production ofEcotonerGrids@grid_aspect_meanandEcotonerGrids@grid_aspect_sd. Default is2 * pi / 180 = 0.035based for elevational slopes.type_exclA
TypeInfoobject. This 'type' is to be excluded from 'grid_veg'.type_veg1A
TypeInfoobject. This 'type' is one of the two vegetation (types) from 'grid_veg'.type_veg2A
TypeInfoobject. This 'type' is one of the two vegetation (types) from 'grid_veg'.dir_prjAn 'EcotonerPath' object, i.e., a character string representing a path. The path to the project directory.
dir_bigAn 'EcotonerPath' object or
NA. If notNA, then the path where the transect data will be stored.dir_initAn 'EcotonerPath' object. The path to the folder where the search points and other data are stored before transects can be searched for and extracted. This path is automatically generated.
dir_outAn 'EcotonerPath' object. The path that contains the outputs. This path is automatically generated from dir_prj or from dir_big if not NA.
dir_out_figAn 'EcotonerPath' object. The path that contains the folders where the transect figures are stored. This path is automatically generated.
dir_out_datAn 'EcotonerPath' object. The path that contains the folders where the transect data are stored. This path is automatically generated.
dir_envAn 'EcotonerPath' object. The path to where the raster grid representing the environmental gradient 'grid_env' is stored.
dir_vegAn 'EcotonerPath' object. The path to where the raster grid representing the vegetation 'grid_veg' is stored.
dir_veg1An 'EcotonerPath' object. The path to where the raster grid representing the vegetation 'grid_veg1' is stored.
dir_veg2An 'EcotonerPath' object. The path to where the raster grid representing the vegetation 'grid_veg2' is stored.
dir_flowAn 'EcotonerPath' object. The path to where the raster grid representing the flow paths 'grid_flow' is stored (required with transect_type == 3).
dir_abutAn 'EcotonerPath' object. The path to where the raster grid representing the abutting cells of vegetation types 1 and 2 'grid_abut' is stored (required with transect_type == 4).
dir_aspect_meanAn 'EcotonerPath' object. The path to where the raster grid representing the mean smoothed aspect 'grid_aspect_mean' is stored (required with transect_type == 4).
dir_aspect_sdAn 'EcotonerPath' object. The path to where the raster grid representing the standard deviation of the smoothed aspect 'grid_aspect_sd' is stored (required with transect_type == 4).
file_searchpointsAn 'EcotonerFile' object. The entire file path to where the search points are/will be stored.
file_initwindowAn 'EcotonerFile' object. The entire file path to where the owin object for the search point generation with inihibition is/will be stored.
file_timing_locateAn 'EcotonerFile' object. The entire file path to the timing of each transect location call will be stored, e.g., used by the call that removes unused temporary raster files.
file_etsummaryAn 'EcotonerFile' object. The entire file path to where the table of the transect summary are stored.
file_etsummary_tempAn 'EcotonerFile' object. The entire file path to where temporary table of the transect summary are stored.
file_etmeasure_baseAn 'EcotonerFile' object. The entire file path (minus a flag indicating which measure type) to where temporary tables of the transect measures are stored.
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