Calculate how well feature representation targets are met by a solution to
a conservation planning problem()
.
It is useful for understanding if features are adequately represented by
a solution.
Note that this function can only be used with problems that contain
targets.
eval_target_coverage_summary(x, solution, include_zone, include_sense)
# S3 method for default
eval_target_coverage_summary(x, solution, include_zone, include_sense)
# S3 method for ConservationProblem
eval_target_coverage_summary(
x,
solution,
include_zone = number_of_zones(x) > 1,
include_sense = number_of_zones(x) > 1
)
problem()
(i.e., ConservationProblem
) object.
numeric
, matrix
, data.frame
,
Raster
, Spatial
,
or sf::sf()
object.
The argument should be in the same format as the planning unit cost
data in the argument to x
.
See the Solution format section for more information.
logical
include the zone
column in the output?
Defaults to TRUE
for problems that contain multiple zones.
logical
include the sense
column in the output?
Defaults to TRUE
for problems that contain multiple zones.
tibble::tibble()
object.
Here, each row describes information for a different target.
It contains the following columns:
character
name of the feature associated with each
target.
list
of character
zone names associated with each target.
This column is in a list-column format because a single target can
correspond to multiple zones (see add_manual_targets()
for details
and examples).
For an example of converting the list-column format to a standard
character
column format, please see the Examples section.
This column is only included if the argument to include_zones
is TRUE
.
character
sense associated with each target.
Sense values specify the nature of the target.
Typically (e.g., when using the add_absolute_targets()
or
add_relative_targets()
functions), targets are specified using sense
values indicating that the total amount of a feature held within a
solution (ideally) be greater than or equal to a threshold amount
(i.e., a sense value of ">="
).
Additionally, targets (i.e., using the add_manual_targets()
function)
can also be specified using sense values indicating that the total
amount of a feature held within a solution must be equal to a
threshold amount (i.e., a sense value of "="
) or smaller than or equal
to a threshold amount (i.e., a sense value of "<="
).
This column is only included if the argument to include_sense
is
TRUE
.
numeric
total amount of the feature available across
the entire conservation planning problem for meeting each target
(not just planning units selected within the solution).
For problems involving a single zone, this column is calculated
as the sum of all of the values for a given feature
(similar to values in the total_amount
column produced by the
eval_feature_representation_summary()
function).
For problems involving multiple zones,
this column is calculated as the sum of the values for the
feature associated with target (per the "feature"
column),
across the zones associated with the target (per the "zone"
column).
numeric
total threshold amount associated with
each target.
numeric
total amount held within the solution for
the feature and (if relevant) zones associated with each target (per the
"feature"
and "zone"
columns, respectively).
This column is calculated as the sum of the feature data,
supplied when creating a problem()
object
(e.g., presence/absence values), weighted by the status of each
planning unit in the solution (e.g., selected or not for
prioritization).
numeric
total amount by which the solution
fails to meet each target.
This column is calculated as the difference between the total amount
held within the solution for the feature and (if relevant) zones
associated with the target (i.e., "absolute_held"
column) and the
target total threshold amount (i.e., "absolute_target"
column), with
values set to zero depending on the sense specified for the target
(e.g., if the target sense is >=
then the difference is
set to zero if the value in the "absolute_held"
is smaller than
that in the "absolute_target"
column).
numeric
proportion threshold amount associated
with each target.
This column is calculated by dividing the total threshold amount
associated with each target (i.e., "absolute_target"
column) by
the total amount associated with each target
(i.e., "total_amount"
column).
numeric
proportion held within the solution for the
feature and (if relevant) zones associated with each target (per the
"feature"
and "zone"
columns, respectively).
This column is calculated by dividing the total amount held
for each target (i.e., "absolute_held"
column) by the
total amount for with each target
(i.e., "total_amount"
column).
numeric
proportion by which the solution fails
to meet each target.
This column is calculated by dividing the total shortfall for
each target (i.e., "absolute_shortfall"
column) by the
total amount for each target (i.e., "total_amount"
column).
logical
indicating if each target is met by the solution. This
column is calculated by checking if the total shortfall associated
with each target (i.e., "absolute_shortfall
" column) is equal to
zero.
Broadly speaking, the argument to solution
must be in the same format as
the planning unit data in the argument to x
.
Further details on the correct format are listed separately
for each of the different planning unit data formats:
x
has numeric
planning unitsThe argument to solution
must be a
numeric
vector with each element corresponding to a different planning
unit. It should have the same number of planning units as those
in the argument to x
. Additionally, any planning units missing
cost (NA
) values should also have missing (NA
) values in the
argument to solution
.
x
has matrix
planning unitsThe argument to solution
must be a
matrix
vector with each row corresponding to a different planning
unit, and each column correspond to a different management zone.
It should have the same number of planning units and zones
as those in the argument to x
. Additionally, any planning units
missing cost (NA
) values for a particular zone should also have a
missing (NA
) values in the argument to solution
.
x
has Raster
planning unitsThe argument to solution
be a Raster
object where different grid cells (pixels) correspond
to different planning units and layers correspond to
a different management zones. It should have the same dimensionality
(rows, columns, layers), resolution, extent, and coordinate reference
system as the planning units in the argument to x
. Additionally,
any planning units missing cost (NA
) values for a particular zone
should also have missing (NA
) values in the argument to solution
.
x
has data.frame
planning unitsThe argument to solution
must
be a data.frame
with each column corresponding to a different zone,
each row corresponding to a different planning unit, and cell values
corresponding to the solution value. This means that if a data.frame
object containing the solution also contains additional columns, then
these columns will need to be subsetted prior to using this function
(see below for example with sf::sf()
data).
Additionally, any planning units missing cost
(NA
) values for a particular zone should also have missing (NA
)
values in the argument to solution
.
x
has Spatial
planning unitsThe argument to solution
must be a Spatial
object with each column corresponding to a
different zone, each row corresponding to a different planning unit, and
cell values corresponding to the solution value. This means that if the
Spatial
object containing the solution also contains additional
columns, then these columns will need to be subsetted prior to using this
function (see below for example with sf::sf()
data).
Additionally, the argument to solution
must also have the same
coordinate reference system as the planning unit data.
Furthermore, any planning units missing cost
(NA
) values for a particular zone should also have missing (NA
)
values in the argument to solution
.
x
has sf::sf()
planning unitsThe argument to solution
must be
a sf::sf()
object with each column corresponding to a different
zone, each row corresponding to a different planning unit, and cell values
corresponding to the solution value. This means that if the
sf::sf()
object containing the solution also contains additional
columns, then these columns will need to be subsetted prior to using this
function (see below for example).
Additionally, the argument to solution
must also have the same
coordinate reference system as the planning unit data.
Furthermore, any planning units missing cost
(NA
) values for a particular zone should also have missing (NA
)
values in the argument to solution
.
See summaries for an overview of all functions for summarizing solutions.
Other summaries:
eval_asym_connectivity_summary()
,
eval_boundary_summary()
,
eval_connectivity_summary()
,
eval_cost_summary()
,
eval_feature_representation_summary()
,
eval_n_summary()
# \dontrun{
# set seed for reproducibility
set.seed(500)
# load data
data(sim_pu_raster, sim_pu_sf, sim_features,
sim_pu_zones_sf, sim_features_zones)
# build minimal conservation problem with raster data
p1 <- problem(sim_pu_raster, sim_features) %>%
add_min_set_objective() %>%
add_relative_targets(0.1) %>%
add_binary_decisions() %>%
add_default_solver(verbose = FALSE)
# solve the problem
s1 <- solve(p1)
# print solution
print(s1)
#> class : RasterLayer
#> dimensions : 10, 10, 100 (nrow, ncol, ncell)
#> resolution : 0.1, 0.1 (x, y)
#> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax)
#> crs : NA
#> source : memory
#> names : layer
#> values : 0, 1 (min, max)
#>
# plot solution
plot(s1, main = "solution", axes = FALSE, box = FALSE)
# calculate target coverage by the solution
r1 <- eval_target_coverage_summary(p1, s1)
print(r1, width = Inf) # note: `width = Inf` tells R to print all columns
#> # A tibble: 5 × 9
#> feature met total_amount absolute_target absolute_held absolute_shortfall
#> <chr> <lgl> <dbl> <dbl> <dbl> <dbl>
#> 1 layer.1 TRUE 83.3 8.33 8.91 0
#> 2 layer.2 TRUE 31.2 3.12 3.13 0
#> 3 layer.3 TRUE 72.0 7.20 7.34 0
#> 4 layer.4 TRUE 42.7 4.27 4.35 0
#> 5 layer.5 TRUE 56.7 5.67 6.01 0
#> relative_target relative_held relative_shortfall
#> <dbl> <dbl> <dbl>
#> 1 0.1 0.107 0
#> 2 0.1 0.100 0
#> 3 0.1 0.102 0
#> 4 0.1 0.102 0
#> 5 0.1 0.106 0
# build minimal conservation problem with polygon (sf) data
p2 <- problem(sim_pu_sf, sim_features, cost_column = "cost") %>%
add_min_set_objective() %>%
add_relative_targets(0.1) %>%
add_binary_decisions() %>%
add_default_solver(verbose = FALSE)
# solve the problem
s2 <- solve(p2)
# print first six rows of the attribute table
print(head(s2))
#> Simple feature collection with 6 features and 4 fields
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: 0 ymin: 0.9 xmax: 0.6 ymax: 1
#> CRS: NA
#> cost locked_in locked_out solution_1 geometry
#> 1 215.8638 FALSE FALSE 0 POLYGON ((0 1, 0.1 1, 0.1 0...
#> 2 212.7823 FALSE FALSE 0 POLYGON ((0.1 1, 0.2 1, 0.2...
#> 3 207.4962 FALSE FALSE 0 POLYGON ((0.2 1, 0.3 1, 0.3...
#> 4 208.9322 FALSE TRUE 0 POLYGON ((0.3 1, 0.4 1, 0.4...
#> 5 214.0419 FALSE FALSE 0 POLYGON ((0.4 1, 0.5 1, 0.5...
#> 6 213.7636 FALSE FALSE 0 POLYGON ((0.5 1, 0.6 1, 0.6...
# plot solution
plot(s2[, "solution_1"])
# calculate target coverage by the solution
r2 <- eval_target_coverage_summary(p2, s2[, "solution_1"])
print(r2, width = Inf)
#> # A tibble: 5 × 9
#> feature met total_amount absolute_target absolute_held absolute_shortfall
#> <chr> <lgl> <dbl> <dbl> <dbl> <dbl>
#> 1 layer.1 TRUE 74.5 7.45 8.05 0
#> 2 layer.2 TRUE 28.1 2.81 2.83 0
#> 3 layer.3 TRUE 64.9 6.49 6.65 0
#> 4 layer.4 TRUE 38.2 3.82 3.87 0
#> 5 layer.5 TRUE 50.7 5.07 5.41 0
#> relative_target relative_held relative_shortfall
#> <dbl> <dbl> <dbl>
#> 1 0.1 0.108 0
#> 2 0.1 0.101 0
#> 3 0.1 0.103 0
#> 4 0.1 0.101 0
#> 5 0.1 0.107 0
# build multi-zone conservation problem with polygon (sf) data
p3 <- problem(sim_pu_zones_sf, sim_features_zones,
cost_column = c("cost_1", "cost_2", "cost_3")) %>%
add_min_set_objective() %>%
add_relative_targets(matrix(runif(15, 0.1, 0.2), nrow = 5,
ncol = 3)) %>%
add_binary_decisions() %>%
add_default_solver(verbose = FALSE)
# solve the problem
s3 <- solve(p3)
# print first six rows of the attribute table
print(head(s3))
#> Simple feature collection with 6 features and 9 fields
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: 0 ymin: 0.9 xmax: 0.6 ymax: 1
#> CRS: NA
#> cost_1 cost_2 cost_3 locked_1 locked_2 locked_3 solution_1_zone_1
#> 1 215.8638 183.3344 205.4113 FALSE FALSE FALSE 0
#> 2 212.7823 189.4978 209.6404 FALSE FALSE FALSE 0
#> 3 207.4962 193.6007 215.4212 TRUE FALSE FALSE 0
#> 4 208.9322 197.5897 218.5241 FALSE FALSE FALSE 0
#> 5 214.0419 199.8033 220.7100 FALSE FALSE FALSE 0
#> 6 213.7636 203.1867 224.6809 FALSE FALSE FALSE 0
#> solution_1_zone_2 solution_1_zone_3 geometry
#> 1 0 0 POLYGON ((0 1, 0.1 1, 0.1 0...
#> 2 0 1 POLYGON ((0.1 1, 0.2 1, 0.2...
#> 3 0 0 POLYGON ((0.2 1, 0.3 1, 0.3...
#> 4 0 1 POLYGON ((0.3 1, 0.4 1, 0.4...
#> 5 0 1 POLYGON ((0.4 1, 0.5 1, 0.5...
#> 6 0 0 POLYGON ((0.5 1, 0.6 1, 0.6...
# create new column representing the zone id that each planning unit
# was allocated to in the solution
s3$solution <- category_vector(
s3[, c("solution_1_zone_1", "solution_1_zone_2", "solution_1_zone_3")])
s3$solution <- factor(s3$solution)
# plot solution
plot(s3[, "solution"])
# calculate target coverage by the solution
r3 <- eval_target_coverage_summary(
p3, s3[, c("solution_1_zone_1", "solution_1_zone_2", "solution_1_zone_3")])
print(r3, width = Inf)
#> # A tibble: 15 × 11
#> feature zone sense met total_amount absolute_target absolute_held
#> <chr> <list> <chr> <lgl> <dbl> <dbl> <dbl>
#> 1 feature_1 <chr [1]> >= TRUE 75.1 13.8 14.9
#> 2 feature_2 <chr [1]> >= TRUE 28.0 4.82 5.14
#> 3 feature_3 <chr [1]> >= TRUE 65.0 12.8 12.8
#> 4 feature_4 <chr [1]> >= TRUE 38.0 5.58 6.64
#> 5 feature_5 <chr [1]> >= TRUE 51.2 9.27 9.96
#> 6 feature_1 <chr [1]> >= TRUE 75.1 9.06 15.0
#> 7 feature_2 <chr [1]> >= TRUE 28.0 4.23 5.58
#> 8 feature_3 <chr [1]> >= TRUE 65.0 12.5 13.6
#> 9 feature_4 <chr [1]> >= TRUE 38.0 6.96 7.14
#> 10 feature_5 <chr [1]> >= TRUE 51.2 8.76 9.96
#> 11 feature_1 <chr [1]> >= TRUE 75.1 9.63 13.3
#> 12 feature_2 <chr [1]> >= TRUE 28.0 5.29 5.65
#> 13 feature_3 <chr [1]> >= TRUE 65.0 11.5 11.8
#> 14 feature_4 <chr [1]> >= TRUE 38.0 4.43 7.71
#> 15 feature_5 <chr [1]> >= TRUE 51.2 8.86 9.04
#> absolute_shortfall relative_target relative_held relative_shortfall
#> <dbl> <dbl> <dbl> <dbl>
#> 1 0 0.183 0.198 0
#> 2 0 0.173 0.184 0
#> 3 0 0.198 0.198 0
#> 4 0 0.147 0.175 0
#> 5 0 0.181 0.195 0
#> 6 0 0.121 0.200 0
#> 7 0 0.151 0.200 0
#> 8 0 0.193 0.210 0
#> 9 0 0.183 0.188 0
#> 10 0 0.171 0.195 0
#> 11 0 0.128 0.177 0
#> 12 0 0.189 0.202 0
#> 13 0 0.176 0.181 0
#> 14 0 0.116 0.203 0
#> 15 0 0.173 0.177 0
# create a new column with character values containing the zone names,
# by extracting these data out of the zone column
# (which is in list-column format)
r3$zone2 <- vapply(r3$zone, FUN.VALUE = character(1), paste, sep = " & ")
# print r3 again to show the new column
print(r3, width = Inf)
#> # A tibble: 15 × 12
#> feature zone sense met total_amount absolute_target absolute_held
#> <chr> <list> <chr> <lgl> <dbl> <dbl> <dbl>
#> 1 feature_1 <chr [1]> >= TRUE 75.1 13.8 14.9
#> 2 feature_2 <chr [1]> >= TRUE 28.0 4.82 5.14
#> 3 feature_3 <chr [1]> >= TRUE 65.0 12.8 12.8
#> 4 feature_4 <chr [1]> >= TRUE 38.0 5.58 6.64
#> 5 feature_5 <chr [1]> >= TRUE 51.2 9.27 9.96
#> 6 feature_1 <chr [1]> >= TRUE 75.1 9.06 15.0
#> 7 feature_2 <chr [1]> >= TRUE 28.0 4.23 5.58
#> 8 feature_3 <chr [1]> >= TRUE 65.0 12.5 13.6
#> 9 feature_4 <chr [1]> >= TRUE 38.0 6.96 7.14
#> 10 feature_5 <chr [1]> >= TRUE 51.2 8.76 9.96
#> 11 feature_1 <chr [1]> >= TRUE 75.1 9.63 13.3
#> 12 feature_2 <chr [1]> >= TRUE 28.0 5.29 5.65
#> 13 feature_3 <chr [1]> >= TRUE 65.0 11.5 11.8
#> 14 feature_4 <chr [1]> >= TRUE 38.0 4.43 7.71
#> 15 feature_5 <chr [1]> >= TRUE 51.2 8.86 9.04
#> absolute_shortfall relative_target relative_held relative_shortfall zone2
#> <dbl> <dbl> <dbl> <dbl> <chr>
#> 1 0 0.183 0.198 0 zone_1
#> 2 0 0.173 0.184 0 zone_1
#> 3 0 0.198 0.198 0 zone_1
#> 4 0 0.147 0.175 0 zone_1
#> 5 0 0.181 0.195 0 zone_1
#> 6 0 0.121 0.200 0 zone_2
#> 7 0 0.151 0.200 0 zone_2
#> 8 0 0.193 0.210 0 zone_2
#> 9 0 0.183 0.188 0 zone_2
#> 10 0 0.171 0.195 0 zone_2
#> 11 0 0.128 0.177 0 zone_3
#> 12 0 0.189 0.202 0 zone_3
#> 13 0 0.176 0.181 0 zone_3
#> 14 0 0.116 0.203 0 zone_3
#> 15 0 0.173 0.177 0 zone_3
# }