m_run_biophysical: m_run_biophysical

In sebmader/LizardsAndNiches: Handleing specific data frames of lizard morphology and reflectance data

Description

This function runs a full analysis of the climate niche starting with importing our standard dataframe, running microclimate model and ectotherm function subsequently.

Usage

m_run_biophysical(
  liz_file,
  species,
  loc_file,
  morpho_mean = FALSE,
  physio_file,
  nyears = 1,
  ndays = 12,
  burrow = FALSE,
  burrowtype = "sunshade",
  burrowdepth = 9,
  DEB = FALSE,
  timeper = "present",
  rcp = "none",
  shade = c(0, 90),
  save_plot = FALSE
)

Arguments

liz_file	A file with lizard data (see example_lizard_data.csv) containing at least one individual with location, morphology and reflectance data.
species	The species to be looked at, which will be selected from the data frame and split into sub groups of morphs if present.
loc_file	File with information on locations (see example_coordinates.csv).
morpho_mean	Boolean whether the biophysical model should be run with location means to decrease computational demand (morpho_mean = TRUE) or if it should be run per individual (FALSE).
physio_file	File path with physiological data of the lizards per location (see 'example_lizard_data.csv' for structure of dataframe).
nyears	Number of years the model is run.
ndays	Number of days modeled per year.
burrow	Boolean whether lizard is allowed to seek shelter in burrow.
burrowtype	Character string defining the burrow type: "sun" (always in the sun), "shade" (always in the shade), "sunshade" (organism decides if burrow is in the sun or in the shade).
burrowdepth	The burrows depth in "soil nodes", a numeric ranging from 2 to 10. 2 equals to 2.5 cm, 3 to 5 cm, 4 to 10 cm, 5 to 15 cm, 6 to 20 cm, 7 to 30 cm, 8 to 50 cm, 9 to 100 cm and 10 to 200 cm. These are also the steps the lizard takes while burrowing.
DEB	Boolean stating wheather the ectotherm should be run with or without the Dynamic Energy Budget model.
timeper	Character string of the time period for the climate data / predictions ("present", "2040_2059", "2080_2099", "presentCCKP" to compare the 1961-1990 of CCKP with the one from NicheMapR, and "presentNASA" to use more recent (1983-2017) climate data).
rcp	Character string to specify the emission scenario in case of climate predictions ("none", "45", "85").
shade	Vector of 2 numerics defining minimum and maximum shade.
save_plot	Boolean whether plots shall be saved or not.

Value

List of lists with output of ectotherm function for each species/population/entity

sebmader/LizardsAndNiches documentation built on March 11, 2021, 6:08 p.m.