| spGetStrata {FIESTA} | R Documentation |
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,
unitvar2 = NULL,
unit.filter = NULL,
strattype = "RASTER",
strat_layer = NULL,
strat_dsn = NULL,
strvar = NULL,
strat_lut = NULL,
areaunits = "acres",
rast.NODATA = NULL,
keepNA = FALSE,
ncores = 1,
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. |
unitvar2 |
String. If unittype="POLY", name of attribute in unit_layer defining a second, hierarchical larger, estimation unit (e.g., Statecd). |
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. |
ncores |
Integer. Number of cores to use for extracting 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)