spGetStrata: Spatial wrapper - Extracts point attribute values and pixel...

In FIESTA: Forest Inventory Estimation and Analysis

Spatial wrapper - Extracts point attribute values and pixel counts for strata and estimation unit spatial layers.

Description

Wrapper to extract attribute and area from a polygon or raster estimation unit layer and a polygon or raster layer with strata pixel categories.

Usage

spGetStrata(
  xyplt,
  xyplt_dsn = NULL,
  unit_layer,
  unit_dsn = NULL,
  uniqueid = "PLT_CN",
  unitvar = NULL,
  unit.filter = NULL,
  strattype = "RASTER",
  strat_layer = NULL,
  strat_dsn = NULL,
  strvar = NULL,
  strat_lut = NULL,
  areaunits = "acres",
  rast.NODATA = NULL,
  keepNA = FALSE,
  showext = FALSE,
  returnxy = FALSE,
  savedata = FALSE,
  exportsp = FALSE,
  exportNA = FALSE,
  spMakeSpatial_opts = NULL,
  savedata_opts = NULL,
  vars2keep = NULL,
  gui = FALSE
)

Arguments

xyplt	Data frame, sf object, full pathname to *.csv or *shp, or layer name in a geodatabase. Includes XY coordinates and unique identifier. If non-spatial, include options in spMakeSpatial_opts parameter.
xyplt_dsn	String. Name of database where xyplt is. The dsn varies by driver. See gdal OGR vector formats (https://www.gdal.org/ogr_formats.html).
unit_layer	sf R object or String. Name of estimation unit spatial layer. Can be a spatial polygon object, full pathname to a shapefile, name of a polygon layer within a database, or a full pathname to raster file.
unit_dsn	String. Data source name (dsn; e.g., sqlite or shapefile pathname) of unit_layer. The dsn varies by driver. See gdal OGR vector formats (https://www.gdal.org/ogr_formats.html). Optional if unit_layer is sf object.
uniqueid	String.* Unique identifier of xyplt records. Note: raster unit layers are converted to polygon.
unitvar	String. If unittype="POLY", name of attribute in unit_layer defining estimation units. If NULL, the unit_layer represents one estimation unit.
unit.filter	String. Filter to subset unit_layer spatial layer.
strattype	String. Spatial layer type of strat_layer ("POLY", "RASTER"). Note: polygon strata layers are converted to raster.
strat_layer	sf R object or full pathname of spatial stratification layer. Can be a spatial polygon object, full pathname to a shapefile, name of a polygon layer within a database, or a full pathname to raster file.
strat_dsn	String. Data source name (dsn; e.g., sqlite or shapefile pathname) of strat_layer. The dsn varies by driver. See gdal OGR vector formats (https://www.gdal.org/ogr_formats.html). Optional if unit_layer is sf object.
strvar	String. If strattype="POLY", name of strata attribute in strat_layer.
strat_lut	Data frame. A look-up table of codes to aggregate. The format of table includes 2 columns, one column same name as strvar. If strattype="RASTER", strvar="value".
areaunits	String. Output area units ("acres", "hectares", "sqmeters").
rast.NODATA	Numeric. NODATA value if stratlayer is raster (See notes). This values will be converted to NA and removed from output. if keepNA=TRUE, NA values will not be in included in stratalut but will remain in pltassgn table.
keepNA	Logical. If TRUE, returns data frame of NA values.
showext	Logical. If TRUE, layer extents are displayed in plot window.
returnxy	Logical. If TRUE, returns xy data as sf object (spxyplt).
savedata	Logical. If TRUE, the input data with extracted values are saved to outfolder.
exportsp	Logical. If savedata=TRUE and returnxy=TRUE, If TRUE, the extracted strata point data are exported to outfolder.
exportNA	Logical. If TRUE and keepNA=TRUE, NA values are exported to outfolder as a point shapefile.
spMakeSpatial_opts	List. See help(spMakeSpatial_options()) for a list of options. Use to convert X/Y values to simple feature (sf) coordinates.
savedata_opts	List. See help(savedata_options()) for a list of options. Only used when savedata = TRUE.
vars2keep	String vector. Attributes in SAdoms, other than domvar to include in dunitlut output and extract to pltassgn points.
gui	Logical. If gui, user is prompted for parameters.

Details

*If variable = NULL, then it will prompt user for input.

If spatial layers have different projections, the polygon spatial layer is transformed to the projection of raster (See note about on-the-fly projection conversion). If both layers are long/lat coordinate system, they are transformed to default coordinate system (Conus Albers, NAD83).

Value

pltassgn	Data frame. Input xyplt data with extracted estimation unit and strata values appended.
unitarea	Data frame. Area by estimation unit.
unitvar	Data frame. Variable name for estimation unit in unitarea.
acrevar	Data frame. Variable name for area in unitarea.
stratalut	Data frame. Strata proportions (weights) by estimation unit and strata.
strvar	Data frame. Variable name for strata values in stratalut.
NAlst	sf List. If keepNA=TRUE, and NA values exist after data extraction, the spatial NA points are returned.
pltassgnid	String. Unique identifier of plot.
spxy	Simple feature. If returnxy=TRUE, Spatial coordinates.
xy.uniqueid	String. If returnxy=TRUE, unique identifier of spxy.

If savedata=TRUE, pltassgn and unitarea are saved to outfolder.
If exportsp=TRUE, the spatial sf points object is exported to outfolder.
. If exportNA=TRUE and NA values exist after data extraction, the spatial NA points are exported to outfolder.

Note

rast.NODATA
NODATA values are raster pixel values that have no data of interest, including pixels within the extent of the layer, but outside the area of interest. Sometimes these pixels have been defined previously. The defined NODATA pixels are imported to R as NULL values. When not previously defined, the pixels outside the area of interest will be the minimum or maximum value depending on the data type (e.g., 16-bit signed: min=-32,768; max=32,768) or byte size (1 byte: min=0; max=255). These NODATA values will be added to the zonal statistic calculations if not specified in rast.NODATA.

If exportsp=TRUE:
If out_fmt="shp", the st_write (sf) function is called. The ArcGIS driver truncates variable names to 10 characters or less. Variable names are changed before export using an internal function (trunc10shp). If Spatial object has more than 1 record, it will be returned but not exported.

On-the-fly projection conversion
The spTransform (sf) method is used for on-the-fly map projection conversion and datum transformation using PROJ.4 arguments. Datum transformation only occurs if the +datum tag is present in the both the from and to PROJ.4 strings. The +towgs84 tag is used when no datum transformation is needed. PROJ.4 transformations assume NAD83 and WGS84 are identical unless other transformation parameters are specified. Be aware, providing inaccurate or incomplete CRS information may lead to erroneous data shifts when reprojecting. See spTransform help documentation for more details.

unitarea
Area by estimation unit is calculated and returned as object named unitarea. Area is based on the projection of unit_layer. If no unit_layer input, than area is calculated from pixel counts.

polygon to raster
If strattype="POLY", a raster template is created based on the masked extent of strat_layer, with strat_layer projected coordinate system and 30 meter pixel size.

Author(s)

Tracey S. Frescino

Examples

# Create a `SpatialPoints` object from `WYplt`
WYspplt <- spMakeSpatialPoints(xyplt = WYplt, 
                               xy.uniqueid = "CN", 
                               xvar = "LON_PUBLIC", 
                               yvar = "LAT_PUBLIC", 
                               xy.crs = 4269)
                               
# Set up stratification from object in `FIESTA`
fornffn <- system.file("extdata",
                       "sp_data/WYbighorn_forest_nonforest_250m.tif",
                       package = "FIESTA")
                       
# Set up data from FIESTA
WYbhfn <- system.file("extdata",
                      "sp_data/WYbighorn_adminbnd.shp",
                      package = "FIESTA")
                               
# Run `spGetStrata`
spGetStrata(WYspplt, 
            uniqueid = "CN", 
            unit_layer = WYbhfn, 
            strattype = "RASTER", 
            strat_layer = fornffn) 

FIESTA documentation built on Nov. 22, 2023, 1:07 a.m.