search_for_approximating_lognormal: Search for approximating lognormal

In langfob/bdpg: Package For Building and Testing Biodiversity Problem Generators

Search for approximating lognormal

Description

Function to search for a lognormal that comes close to meeting the constraints specified in the argument list, i.e.,

1. to generate roughly the given number of species but never more than the given number (tot_num_spp_after_wrapping)

2. to come close to the given number of species that occur on exactly 2 PUs without ever falling below that minimum value (min_num_spp_on_2_PUs)

3. to have the most abundant generated species have roughly the target value (target_max_abundance_ct), but never exceed the given max value (max_max_abundance).

Usage

search_for_approximating_lognormal(
  seed_value,
  tot_num_spp_after_wrapping,
  min_num_spp_on_2_PUs,
  max_max_abundance,
  target_max_abundance_ct,
  initial_meanlog,
  initial_sdlog,
  max_iterations,
  add_one_to_abundances,
  outfile
)

Arguments

seed_value	random seed to pass to optim function
tot_num_spp_after_wrapping	number of species to generate in distribution
min_num_spp_on_2_PUs	minimum number of species that occur on exactly 2 patches in distribution
max_max_abundance	largest maximum abundance allowed in distribution
target_max_abundance_ct	desired maximum abundance in distribution
initial_meanlog	initial value of lognormal's meanlog in search for distribution
initial_sdlog	initial value of lognormal's sdlog in search for distribution
max_iterations	maximum number of iterations allowed for search
add_one_to_abundances	boolean flag to indicate whether to add 1 to all abundances
outfile	output file

Value

Returns the best lognormal found in the given maximum number of search iterations (max_iterations). The value returned is a structure containing the following information about the best lognormal curve found: $meanlog - the meanlog used in specifying the curve, e.g., 1.035326 $sdlog - the sdlog used in specifying the curve, e.g., 0.9283901 $score - the EF score for the curve, i.e., how well does it fit the given constraints (where smaller is better), e.g., 0.1 $abundance_data - a structure containing specifics of the curve, e.g., $abundance_data$rounded_abundances - a vector of the number of PUs each species occurs on, e.g., [1] 2 4 3 2 7 3 8 15 5 5 9 6 10 4 13 4 7 4 6 6 6 2 2 14 3 9 4 5 5 [30] 2 2 2 2 1 2 3 2 2 4 3 5 3 3 10 17 4 15 3 6 2 5 28 6 4 2 10 2 3 [59] 8 23 4 2 5 2 4 4 3 8 8 3 6 2 2 1 4 3 1 5 3 16 2 6 9 3 2 5 7 [88] 4 3 4 6 2 4 3 3 6 2 3 5 3 $abundance_data$num_spp_on_exactly_2_patches - number of species that occur on exactly 2 PUs, e.g., 22 $abundance_data$max_abundance_ct - number of PUs that the most abundant species occurs on, e.g., 28

langfob/bdpg documentation built on Dec. 8, 2022, 5:33 a.m.