mp.results: Calculates various endpoints using results from RAMAS MP...

In mlammens/demgsa: Global Sensitivity Analyses Of Demographic Matrix Projection Models

Description

mp.results Calculates various endpoints from the results of an MP simulation as carried out in RAMAS. Use for Metapop version 5 and 5.1 file formats. Based on ResOut.exe program written by R. Akcakaya

Usage

mp.results(
  mpFile,
  spatial = FALSE,
  ptc = FALSE,
  ptcFiles = "no file",
  ptcFileIter = "",
  habdyn = FALSE,
  hdhFile = "no file",
  verbose = FALSE
)

Arguments

spatial	TRUE/FALSE - should spatial parameters be extracted from the *.mp file, including factors such as dispersal, correlation, and factors included in *.ptc files, if included
ptc	TRUE/FALSE - Is a *.ptc file included? If yes, some spatial information can be extracted from this file
ptcFiles	A single path to a ptc file or a vector of ptc files with which to extract data from.
ptcFileIter	For each ptcFile, the corresponding iteration as noted in the HabDyn history file. If no history file is used, iter values can be some user defined values, however an error will be generated if the length of ptcfiles and ptcFileIter do not match.
habdyn	TRUE/FALSE - Was HabDyn module used? Is there a corresponding HabDyn history file?
hdhFile	The full path name to the HabDyn history (.txt) file
verbose	Print function progress and checkpoints.
mpList	The full list object of an MP file that has been run (i.e., has results)

Details

The resulting data.frame includes several parameters and endpoints. Each is discribed below.

• mpFile Name of the MP file the data for a particular row are associated with

• metapop.initab Initial population abundance for metapopulation

• EigenVal Growth rate based on Stage (Age) Matrix (i.e., Eigen value of this matrix)

• GenTime Generation time, as calculated using generation.time from the popbio package

• dd.type Density dependence type

• Rmax Population level maximum growth rate, use if density dependence is contest or scramble type.

• GrowthRt The effective growth rate - either the EigenVal or Rmax, depending on density dependence model

• fec.stdev.avg Average standard deviation of fecundity

• surv.stdev.avg Average standard deviation of survival

• stdev.avg Average standard deviation of fecundity and survival

• fec.cv.avg Average coefficient of variation for fecundity

• surv.cv.avg Average coefficient of variation for survival

• cv.avg Average coefficient of variation for fecundity and survival

• N.maxVmin.10 Ratio of maximum versus minum population size at time step 10

• N.plusVmin.SD N(+1S.D.)/N(-1S.D.) for average abundance for time step 10

• N.CV.10 CV of N (calculated as (N(+1S.D) - N(-1S.D.)/(2*Navg), from Average Abundance for time step 10)

• St.First.Rep Stage level of first reproduction

• St.First.Rep.Name Name of stage level of first reproduction

• ext.risk Exinction risk = (# reps resulting in extinction) / (total # of reps)

• threshold The quasi-extinction threshold. Value set in Stochasticity section of MP Module.

• prob.thresh.maxt Risk of falling below the Threshold at least once by the final time step. Calculated using information regarding the time of first crossing of the extinction

• med.time.cross Median time to fall below the quasi-extinction threshold

• prob.50 Prob(50): Risk of falling below a population size of 50 individuals at least once by the final

• prob.250 Prob(250): Risk of falling below a population size of 250 individuals at least once by the final

• prob.1000 Prob(1000): Risk of falling below a population size of 1000 individuals at least once by the final

• prob.Thr.50 Prob(50 the intial metapop size at least once

• exp.min.n ExpMinN: Expected minimum total abundance (also known as EMA)

• sderr.ema SdErr.ExpMinN: Standard error of EMA

• n.mean N(maxt): Mean metapopulation abundance at the final time step maxt

• n.stdev SD of N: Standard deviation of metapopulation occupancy at the final time step maxt

• metapop.chng Percent change in total metapopulation size compared to initial metapopulation size

• occ.maxt Mean metapopulation occupance at the final time step maxt

• occ.stdev.maxt Standard deviation of metapopulation occupancy at the final time step maxt

• quant.* Quantiles of Terminal Population Trajectory. 5

• harv.* Harvest Results: Average total harvest, St.Dev. of total harvest, Minimum of total harvest

• use.disp.dist.func Was dispersal distance function used?

• disp.dist.func.* Values for disperal distance function parameters a, b, c, and Dmax

• mean.t0.disp.rate Mean dispersal rate at time 0

• loquart.t0.disp.rate Lower quartile dispersal rate at time 0

• hiquart.t0.disp.rate Upper quartile dispersal rate at time 0

• *.t0.Ngt0.disp.rate Mean, lower, and upper quartile dispersal rates at time 0, considering only populations with non-zero population size

• *.t0.nearest.disp.rate Mean, lower, and upper quartile dispersal rates to nearest neighboring population

• *.t0.Ngt0.nearest.disp.rate Mean, lower, and upper quartile dispersal rates to nearest neighboring population, considering only populations with non-zero population size

• use.corr.dist.func Use the correlation distance function?

• avg.corr.dist.b Average correlation distance, based on b value of the correlation distance function

Value

res.summ.df A data frame of the endpoints calculated.

mlammens/demgsa documentation built on Aug. 4, 2020, 1:16 a.m.