Rescale SDM predictions and (if applicable) associated uncertainties
Arguments
- x
object of class
sf
- x.idx
vector of column names or column indices; indicates columns in
x
with prediction values that will be rescaled- y
rescaling method; must be either "abundance" or "sumto1". See 'Details' section for descriptions of the rescaling methods
- y.abund
numeric value; ignored if
y
is not"abundance"
- x.var.idx
vector of column names or column indices; indicates columns in
x
with variance values that will be rescaled. Ifx.var.idx
is specified, it must be the same length asx.idx
. Usex.var.idx = NULL
(the default) if none of the predictions have associated uncertainty values; see the 'Details' section for more information
Value
The sf
object x
with the columns specified by x.idx
and x.var.idx
rescaled.
The agr
attributes of x
will be conserved
Details
ensemble_rescale
is intended to be used after overlaying predictions with
overlay_sdm
and before creating ensembles with ensemble_create
.
The provided rescaling methods are:
'abundance' - Rescale the density values so that the predicted abundance is
y.abund
'sumto1' - Rescale the density values so their sum is 1
SDM uncertainty values must be rescaled differently than the prediction values.
Columns specified in x.var.idx
must contain variance values.
These values will be rescaled using the formula var(c * x) = c^2 * var(x)
,
where c
is the rescaling factor for the associated predictions.
If x.var.idx
is not NULL
, then the function assumes
x.var.idx[1]
contains the variance values associated with the predictions in x.idx[1]
,
x.var.idx[2]
contains the variance values associated with the predictions in x.idx[2]
, etc.
Use NA
in x.var.idx
to indicate a set of predictions that does not have
associated uncertainty values (e.g., x.var.idx = c(4, NA, 5)
)
Examples
ensemble_rescale(preds.1, c("Density", "Density2"), "abundance", 50)
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> Simple feature collection with 325 features and 4 fields
#> Attribute-geometry relationships: constant (4)
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: -123 ymin: 32 xmax: -117 ymax: 35
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> Geodetic CRS: WGS 84
#> First 10 features:
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> Density Density2 Var1 Var2
#> 1 7.974472e-05 1.529132e-04 0.0006178977 6.782811e-03
#> 2 1.236210e-05 2.112553e-04 0.0041072496 7.100138e-03
#> 3 2.900737e-05 1.013395e-04 0.0060756461 2.152463e-03
#> 4 1.276122e-05 5.107520e-04 0.0030639979 7.415022e-03
#> 5 1.609208e-05 9.854752e-06 0.0009543514 2.318842e-03
#> 6 2.054191e-05 3.323853e-04 0.0081108828 1.309096e-05
#> 7 1.032142e-05 3.907932e-04 0.0068363941 2.566385e-04
#> 8 1.270168e-05 5.116246e-04 0.0047392882 7.242310e-03
#> 9 1.872979e-05 2.752257e-05 0.0038668358 5.157556e-03
#> 10 6.482159e-05 3.565201e-04 0.0071928494 7.077782e-03
#> geometry
#> 1 POLYGON ((-122.875 32.125, ...
#> 2 POLYGON ((-122.625 32.125, ...
#> 3 POLYGON ((-122.375 32.125, ...
#> 4 POLYGON ((-122.125 32.125, ...
#> 5 POLYGON ((-121.875 32.125, ...
#> 6 POLYGON ((-121.625 32.125, ...
#> 7 POLYGON ((-121.375 32.125, ...
#> 8 POLYGON ((-121.125 32.125, ...
#> 9 POLYGON ((-120.875 32.125, ...
#> 10 POLYGON ((-120.625 32.125, ...
ensemble_rescale(preds.1, c(1, 2), "sumto1")
#> Simple feature collection with 325 features and 4 fields
#> Attribute-geometry relationships: constant (4)
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: -123 ymin: 32 xmax: -117 ymax: 35
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> Geodetic CRS: WGS 84
#> First 10 features:
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> Density Density2 Var1 Var2
#> 1 0.0009493594 0.0017608119 0.0006178977 6.782811e-03
#> 2 0.0001471706 0.0024326274 0.0041072496 7.100138e-03
#> 3 0.0003453322 0.0011669347 0.0060756461 2.152463e-03
#> 4 0.0001519221 0.0058813643 0.0030639979 7.415022e-03
#> 5 0.0001915759 0.0001134785 0.0009543514 2.318842e-03
#> 6 0.0002445511 0.0038274525 0.0081108828 1.309096e-05
#> 7 0.0001228764 0.0045000253 0.0068363941 2.566385e-04
#> 8 0.0001512133 0.0058914121 0.0047392882 7.242310e-03
#> 9 0.0002229778 0.0003169253 0.0038668358 5.157556e-03
#> 10 0.0007716998 0.0041053668 0.0071928494 7.077782e-03
#> geometry
#> 1 POLYGON ((-122.875 32.125, ...
#> 2 POLYGON ((-122.625 32.125, ...
#> 3 POLYGON ((-122.375 32.125, ...
#> 4 POLYGON ((-122.125 32.125, ...
#> 5 POLYGON ((-121.875 32.125, ...
#> 6 POLYGON ((-121.625 32.125, ...
#> 7 POLYGON ((-121.375 32.125, ...
#> 8 POLYGON ((-121.125 32.125, ...
#> 9 POLYGON ((-120.875 32.125, ...
#> 10 POLYGON ((-120.625 32.125, ...
ensemble_rescale(
preds.1, c("Density", "Density2"), "abundance", 100, c(3,4)
)
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> Simple feature collection with 325 features and 4 fields
#> Attribute-geometry relationships: constant (4)
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: -123 ymin: 32 xmax: -117 ymax: 35
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> Geodetic CRS: WGS 84
#> First 10 features:
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> Density Density2 Var1 Var2
#> 1 1.594894e-04 3.058264e-04 4.771354e-10 8.081463e-09
#> 2 2.472421e-05 4.225106e-04 3.171583e-09 8.459546e-09
#> 3 5.801473e-05 2.026789e-04 4.691563e-09 2.564579e-09
#> 4 2.552245e-05 1.021504e-03 2.365993e-09 8.834719e-09
#> 5 3.218416e-05 1.970950e-05 7.369421e-10 2.762813e-09
#> 6 4.108382e-05 6.647706e-04 6.263155e-09 1.559739e-11
#> 7 2.064285e-05 7.815864e-04 5.279006e-09 3.057751e-10
#> 8 2.540336e-05 1.023249e-03 3.659638e-09 8.628939e-09
#> 9 3.745958e-05 5.504514e-05 2.985938e-09 6.145034e-09
#> 10 1.296432e-04 7.130402e-04 5.554258e-09 8.432909e-09
#> geometry
#> 1 POLYGON ((-122.875 32.125, ...
#> 2 POLYGON ((-122.625 32.125, ...
#> 3 POLYGON ((-122.375 32.125, ...
#> 4 POLYGON ((-122.125 32.125, ...
#> 5 POLYGON ((-121.875 32.125, ...
#> 6 POLYGON ((-121.625 32.125, ...
#> 7 POLYGON ((-121.375 32.125, ...
#> 8 POLYGON ((-121.125 32.125, ...
#> 9 POLYGON ((-120.875 32.125, ...
#> 10 POLYGON ((-120.625 32.125, ...