R/eval_feature_representation_summary.R
eval_feature_representation_summary.Rd
Calculate how well features are represented by a solution
to a conservation planning problem()
.
These summary statistics are reported for each and every feature,
and each and every zone, within a conservation planning problem.
eval_feature_representation_summary(x, solution)
# S4 method for ConservationProblem,numeric
eval_feature_representation_summary(x, solution)
# S4 method for ConservationProblem,matrix
eval_feature_representation_summary(x, solution)
# S4 method for ConservationProblem,data.frame
eval_feature_representation_summary(x, solution)
# S4 method for ConservationProblem,Spatial
eval_feature_representation_summary(x, solution)
# S4 method for ConservationProblem,sf
eval_feature_representation_summary(x, solution)
# S4 method for ConservationProblem,Raster
eval_feature_representation_summary(x, solution)
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.
tibble::tibble()
object describing feature representation.
Here, each row describes a specific summary statistic
(e.g., different management zone) for a specific feature.
It contains the following columns:
character
description of the summary statistic.
The statistic associated with the "overall"
value
in this column is calculated using the entire solution
(including all management zones if there are multiple zones).
If multiple management zones are present, then summary statistics
are also provided for each zone separately
(indicated using zone names).
character
name of the feature.
numeric
total amount of each feature available
in the entire conservation planning problem
(not just planning units selected within the solution).
It is calculated as the sum of the feature data,
supplied when creating a problem()
object
(e.g., presence/absence values).
numeric
total amount of each feature secured within
the solution. It 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
proportion of
each feature secured within the solution. It is calculated
by dividing values in the "absolute_held"
column by those in the
"total_amount"
column.
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_n_summary()
,
eval_target_coverage_summary()
# \dontrun{
# set seed for reproducibility
set.seed(500)
# load data
data(sim_pu_raster, sim_pu_polygons, sim_pu_zones_sf, sim_features,
sim_pu_zones_stack, sim_features_zones)
# create a simple conservation planning dataset so we can see exactly
# how feature representation is calculated
pu <- data.frame(id = seq_len(10), cost = c(0.2, NA, runif(8)),
spp1 = runif(10), spp2 = c(rpois(9, 4), NA))
# create problem
p1 <- problem(pu, c("spp1", "spp2"), cost_column = "cost") %>%
add_min_set_objective() %>%
add_relative_targets(0.1) %>%
add_binary_decisions() %>%
add_default_solver(verbose = FALSE)
# create a solution
# specifically, a data.frame with a single column that contains
# binary values indicating if each planning units was selected or not
s1 <- data.frame(s = c(1, NA, rep(c(1, 0), 4)))
print(s1)
#> s
#> 1 1
#> 2 NA
#> 3 1
#> 4 0
#> 5 1
#> 6 0
#> 7 1
#> 8 0
#> 9 1
#> 10 0
# calculate feature representation
r1 <- eval_feature_representation_summary(p1, s1)
print(r1)
#> # A tibble: 2 × 5
#> summary feature total_amount absolute_held relative_held
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 overall spp1 5.76 3.12 0.541
#> 2 overall spp2 33 14 0.424
# let's verify that feature representation calculations are correct
# by manually performing the calculations and compare the results with r1
## calculate total amount for each feature
print(setNames(
c(sum(pu$spp1, na.rm = TRUE),
sum(pu$spp2, na.rm = TRUE)),
c("spp1", "spp2")))
#> spp1 spp2
#> 5.755739 33.000000
## calculate absolute amount held for each feature
print(setNames(
c(sum(pu$spp1 * s1$s, na.rm = TRUE),
sum(pu$spp2 * s1$s, na.rm = TRUE)),
c("spp1", "spp2")))
#> spp1 spp2
#> 3.116052 14.000000
## calculate relative amount held for each feature
print(setNames(
c(sum(pu$spp1 * s1$s, na.rm = TRUE) / sum(pu$spp1, na.rm = TRUE),
sum(pu$spp2 * s1$s, na.rm = TRUE) / sum(pu$spp2, na.rm = TRUE)),
c("spp1", "spp2")))
#> spp1 spp2
#> 0.5413818 0.4242424
# solve the problem using an exact algorithm solver
s1_2 <- solve(p1)
print(s1_2)
#> id cost spp1 spp2 solution_1
#> 1 1 0.2000000 0.8288314 4 1
#> 2 2 NA 0.7115770 3 NA
#> 3 3 0.8336000 0.2820609 1 0
#> 4 4 0.7250118 0.8928427 6 0
#> 5 5 0.9753142 0.7647062 1 0
#> 6 6 0.4676038 0.1643470 4 0
#> 7 7 0.8122781 0.7320744 3 0
#> 8 8 0.2056958 0.2531062 6 0
#> 9 9 0.5121819 0.5083795 5 0
#> 10 10 0.9254660 0.6178138 NA 0
# calculate feature representation in this solution
r1_2 <- eval_feature_representation_summary(
p1, s1_2[, "solution_1", drop = FALSE])
print(r1_2)
#> # A tibble: 2 × 5
#> summary feature total_amount absolute_held relative_held
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 overall spp1 5.76 0.829 0.144
#> 2 overall spp2 33 4 0.121
# build minimal conservation problem with raster data
p2 <- 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
s2 <- solve(p2)
# print solution
print(s2)
#> 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)
#>
# calculate feature representation in the solution
r2 <- eval_feature_representation_summary(p2, s2)
print(r2)
#> # A tibble: 5 × 5
#> summary feature total_amount absolute_held relative_held
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 overall layer.1 83.3 8.91 0.107
#> 2 overall layer.2 31.2 3.13 0.100
#> 3 overall layer.3 72.0 7.34 0.102
#> 4 overall layer.4 42.7 4.35 0.102
#> 5 overall layer.5 56.7 6.01 0.106
# plot solution
plot(s2, main = "solution", axes = FALSE, box = FALSE)
# build minimal conservation problem with polygon (Spatial) data
p3 <- problem(sim_pu_polygons, 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
s3 <- solve(p3)
# print first six rows of the attribute table
print(head(s3))
#> cost locked_in locked_out solution_1
#> 1 215.8638 FALSE FALSE 0
#> 2 212.7823 FALSE FALSE 0
#> 3 207.4962 FALSE FALSE 0
#> 4 208.9322 FALSE TRUE 0
#> 5 214.0419 FALSE FALSE 0
#> 6 213.7636 FALSE FALSE 0
# calculate feature representation in the solution
r3 <- eval_feature_representation_summary(p3, s3[, "solution_1"])
print(r3)
#> # A tibble: 5 × 5
#> summary feature total_amount absolute_held relative_held
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 overall layer.1 74.5 8.05 0.108
#> 2 overall layer.2 28.1 2.83 0.101
#> 3 overall layer.3 64.9 6.65 0.103
#> 4 overall layer.4 38.2 3.87 0.101
#> 5 overall layer.5 50.7 5.41 0.107
# plot solution
spplot(s3, zcol = "solution_1", main = "solution", axes = FALSE, box = FALSE)
# build multi-zone conservation problem with raster data
p4 <- problem(sim_pu_zones_stack, sim_features_zones) %>%
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
s4 <- solve(p4)
# print solution
print(s4)
#> class : RasterStack
#> dimensions : 10, 10, 100, 3 (nrow, ncol, ncell, nlayers)
#> resolution : 0.1, 0.1 (x, y)
#> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax)
#> crs : NA
#> names : zone_1, zone_2, zone_3
#> min values : 0, 0, 0
#> max values : 1, 1, 1
#>
# calculate feature representation in the solution
r4 <- eval_feature_representation_summary(p4, s4)
print(r4)
#> # A tibble: 20 × 5
#> summary feature total_amount absolute_held relative_held
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 overall feature_1 250. 45.8 0.183
#> 2 overall feature_2 93.6 17.7 0.189
#> 3 overall feature_3 216. 40.2 0.186
#> 4 overall feature_4 128. 23.7 0.186
#> 5 overall feature_5 170. 31.2 0.183
#> 6 zone_1 feature_1 83.3 16.0 0.192
#> 7 zone_1 feature_2 31.2 5.07 0.162
#> 8 zone_1 feature_3 72.0 13.2 0.183
#> 9 zone_1 feature_4 42.7 7.04 0.165
#> 10 zone_1 feature_5 56.7 11.2 0.197
#> 11 zone_2 feature_1 83.3 16.0 0.192
#> 12 zone_2 feature_2 31.2 6.45 0.207
#> 13 zone_2 feature_3 72.0 15.1 0.210
#> 14 zone_2 feature_4 42.7 8.22 0.193
#> 15 zone_2 feature_5 56.7 10.4 0.184
#> 16 zone_3 feature_1 83.3 13.8 0.166
#> 17 zone_3 feature_2 31.2 6.16 0.197
#> 18 zone_3 feature_3 72.0 11.9 0.165
#> 19 zone_3 feature_4 42.7 8.49 0.199
#> 20 zone_3 feature_5 56.7 9.58 0.169
# plot solution
plot(category_layer(s4), main = "solution", axes = FALSE, box = FALSE)
# build multi-zone conservation problem with polygon (sf) data
p5 <- 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
s5 <- solve(p5)
# print first six rows of the attribute table
print(head(s5))
#> 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 1 0 POLYGON ((0 1, 0.1 1, 0.1 0...
#> 2 0 0 POLYGON ((0.1 1, 0.2 1, 0.2...
#> 3 0 0 POLYGON ((0.2 1, 0.3 1, 0.3...
#> 4 0 0 POLYGON ((0.3 1, 0.4 1, 0.4...
#> 5 0 0 POLYGON ((0.4 1, 0.5 1, 0.5...
#> 6 0 0 POLYGON ((0.5 1, 0.6 1, 0.6...
# calculate feature representation in the solution
r5 <- eval_feature_representation_summary(
p5, s5[, c("solution_1_zone_1", "solution_1_zone_2", "solution_1_zone_3")])
print(r5)
#> # A tibble: 20 × 5
#> summary feature total_amount absolute_held relative_held
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 overall feature_1 225. 40.9 0.182
#> 2 overall feature_2 83.9 13.8 0.164
#> 3 overall feature_3 195. 34.3 0.176
#> 4 overall feature_4 114. 18.7 0.164
#> 5 overall feature_5 154. 28.3 0.184
#> 6 zone_1 feature_1 75.1 14.9 0.198
#> 7 zone_1 feature_2 28.0 4.77 0.170
#> 8 zone_1 feature_3 65.0 12.7 0.195
#> 9 zone_1 feature_4 38.0 6.39 0.168
#> 10 zone_1 feature_5 51.2 10.2 0.200
#> 11 zone_2 feature_1 75.1 15.0 0.199
#> 12 zone_2 feature_2 28.0 5.02 0.179
#> 13 zone_2 feature_3 65.0 12.9 0.199
#> 14 zone_2 feature_4 38.0 6.03 0.158
#> 15 zone_2 feature_5 51.2 10.2 0.199
#> 16 zone_3 feature_1 75.1 11.1 0.148
#> 17 zone_3 feature_2 28.0 3.98 0.142
#> 18 zone_3 feature_3 65.0 8.71 0.134
#> 19 zone_3 feature_4 38.0 6.33 0.166
#> 20 zone_3 feature_5 51.2 7.84 0.153
# create new column representing the zone id that each planning unit
# was allocated to in the solution
s5$solution <- category_vector(
s5[, c("solution_1_zone_1", "solution_1_zone_2", "solution_1_zone_3")])
s5$solution <- factor(s5$solution)
# plot solution
plot(s5[, "solution"])
# }