m_whole_climate_analysis: Whole climate analysis

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

Description

All-encompassing function to run all different scenarios at once (present & futures), given the input.

Usage

m_whole_climate_analysis(
  times = c("present"),
  rcps = c("none"),
  data_dir = getwd(),
  liz_file = "Darkness_Morpho_Data_Adjusted.csv",
  species,
  loc_file = "Coordinates_Clean_notransect_MOK.csv",
  loc_mean = TRUE,
  morpho_mean = FALSE,
  physio_file = "Physio_info.csv",
  nyears = 1,
  ndays = 12,
  burrow = TRUE,
  burrowtype = "sunshade",
  burrowdepth = 9,
  DEB = FALSE,
  shade = c(0, 50),
  plot = FALSE,
  save_plot = FALSE,
  monthly = FALSE
)

Arguments

times	Vector of strings listing the different time periods to run the model on. Be aware that you need to have downloaded the according climate data and saved it in the appropriate folders. Default is the time period of 1961 to 1990 ("present") used in New et al. (2002), the standard climate dataset used in NicheMapR (Kearney & Porter, 2017). Options: "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.
rcps	Vector of strings listing the Representative Concentration Pathway (RCP) scenarios of greenhouse gas concentrations. "45" and "85" stand for RCP4.5 and RCP8.5, respectively.
data_dir	The path containing the data files. Will be set as working directory.
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).
loc_mean	Boolean whether the microclimate model should be run with location means to decrease computational demand (loc_mean = TRUE) or if it should be run per individual (FALSE). ONLY works when individual location an terrain data is supplied in loc_file!!
morpho_mean	Boolean whether the biophysical model should be run on the populations mean morphology (TRUE) rather than individual data (FALSE) to save time.
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. !!!NOT FULLY IMPLEMENTED AND TESTED YET!!!
shade	Vector of 2 numerics defining minimum and maximum shade. Default is 0 % minimum shade, 50 % maximum shade.
plot	Boolean whether to produce plots of activity pattern of individual lizards or not.
save_plot	Boolean whether plots shall be saved or not.
monthly	Boolean whether the final dataframe should be organised per individual or per month at each location.

Value

Dataframe with the collective physiological and activity data of all individuals or populations and their respective climatic environments.

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