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Simulate multiple scenarios with animal surveys randomly excluded

Source: R/exclude_simulator.R
exclude_simulator.Rd

Randomly exclude either animal surveys or sampling points (and all their associated surveys) from a species community matrix. Each column of the community matrix should represent a unique species, while each row represents a single unique survey.

Usage

exclude_simulator(
  community_matrix,
  survey_ref,
  exclude_level = "survey",
  exclude_num,
  specify_areas = NULL,
  specify_points = NULL,
  specify_periods = NULL,
  specify_cycles = NULL,
  area_ignore = NULL,
  period_ignore = NULL,
  cycle_ignore = NULL,
  survey_id = "survey_id",
  point_id = "point_id",
  area = "area",
  period = "period",
  cycle = "cycle",
  rep = 100
)

Arguments

community_matrix

Dataframe of the species community matrix (one survey per row). It should a column containing the unique IDs for the animal surveys conducted (e.g. survey_id).

survey_ref

Dataframe containing information of the surveys conducted (e.g. survey_id, point_id, period, area, cycle). Values in the column survey_id should correspond to those in community_matrix.

exclude_level

Whether to exclude based on "survey" or "point". Defaults to "survey".

exclude_num

Number of surveys/points to exclude (remove) from the full dataset community_matrix. Value should be a single integer.

specify_areas

Specify the area(s) to randomly exclude surveys from (character string or vector). Defaults to NULL, which excludes surveys randomly across all areas.

specify_points

Specify the point_id(s) of sampling points to randomly exclude surveys from (character string or vector). Defaults to NULL, which excludes surveys randomly across all points.

specify_periods

Specify the survey period(s) to exclude surveys from (character string or vector). Defaults to NULL, which excludes surveys randomly across all periods.

specify_cycles

Specify the survey cycle(s) to exclude surveys from (character string or vector). Defaults to NULL, which excludes surveys randomly across all cycles.

area_ignore

Ignore specified area(s) from the simulation and output (character string or vector). Defaults to NULL, which includes all areas in the simulation.

period_ignore

Ignore specified period from the simulation and output (character string or vector). Defaults to NULL, which includes all periods in the simulation.

cycle_ignore

Ignore specified cycles(s) from the simulation and output (character string or vector). Defaults to NULL, which includes all cycles in the simulation.

survey_id

Column name of the unique identifier for each survey in community_matrix and survey_ref. Defaults to survey_id.

point_id

Column name of the unique identifier for each sampling point in survey_ref. Defaults to survey_id.

area

Column name of the area specified in survey_ref. Defaults to area.

period

Column name of the survey period specified in survey_ref. Defaults to period.

cycle

Column name of the survey cycle specified in survey_ref. Defaults to cycle.

rep

Specify number of repetitions (scenarios) to simulate. Defaults to 100.

Value

A dataframe containing the results of each iteration (column). The count of sampling points with each species (row) is shown. The column fullshows the breakdown of counts within the original dataset.

Examples

data(animal_observations)
data(animal_surveys)

# filter animal observations to taxon of interest
birds <- filter_observations(observations = animal_observations,
                            survey_ref = animal_surveys,
                            specify_taxon = "Aves")

# convert animal observations to community matrix
birds <- as.data.frame.matrix(xtabs(abundance ~ survey_id + species, data = birds))
birds <- cbind(survey_id = rownames(birds), birds) # convert rownames to col

# run function
set.seed(123)
exclude_simulator(birds, animal_surveys,
                 exclude_num = 15, exclude_level = "survey", # exclude 15 surveys
                 specify_cycles = 5, # exclude those in cycle 5 only
                 period_ignore = "2", # remove all data from period 2
                 rep = 10) # 10 scenarios only
#> # A tibble: 138 × 12
#>    species     full iter1 iter2 iter3 iter4 iter5 iter6 iter7 iter8 iter9 iter10
#>    <chr>      <int> <int> <int> <int> <int> <int> <int> <int> <int> <int>  <int>
#>  1 Accipiter…     1     1     1     1     1     1     1     1     1     1      1
#>  2 Accipitri…     1     1     1     1     1     1     1     1     1     1      1
#>  3 Acridothe…   157   157   157   157   157   157   157   157   157   157    157
#>  4 Acridothe…    52    51    51    52    52    52    52    52    52    52     51
#>  5 Acrocepha…     1     1     1     1     1     1     1     1     1     1      1
#>  6 Acrocepha…     1     1     1     1     1     1     1     1     1     1      1
#>  7 Actitis h…     4     4     4     4     4     4     4     4     4     4      4
#>  8 Aegithina…    68    67    67    68    68    67    67    66    67    67     67
#>  9 Aerodramu…     1     1     1     1     1     1     1     1     1     1      1
#> 10 Aerodramu…     1     1     1     1     1     1     1     1     1     1      1
#> # … with 128 more rows