cdpop: Internal CDPOP function
In nspope/radishDGS: Functions to conduct genetic simulations for DGS project

Function to run CDPOP from R

cdpop(
  CDPOP.py,
  sim_name = "output_",
  pts,
  sim_dir,
  resist_rast,
  resist_mat = NULL,
  agefilename = NULL,
  mcruns = 1,
  looptime = 400,
  output_years = 50,
  gridformat = "genepop",
  cdclimgentime = 0,
  matemoveno = 2,
  matemoveparA = 0,
  matemoveparB = 0,
  matemoveparC = 0,
  matemovethresh = "max",
  output_matedistance = "N",
  sexans = "Y",
  Freplace = "N",
  Mreplace = "N",
  philopatry = "N",
  multiple_paternity = "N",
  selfans = "N",
  Fdispmoveno = NULL,
  FdispmoveparA = 0,
  FdispmoveparB = 0,
  FdispmoveparC = 0,
  Fdispmovethresh = NULL,
  Mdispmoveno = NULL,
  MdispmoveparA = 0,
  MdispmoveparB = 0,
  MdispmoveparC = 0,
  Mdispmovethresh = NULL,
  offno = 2,
  MeanFecundity = 5,
  Femalepercent = 50,
  EqualsexratioBirth = "N",
  TwinningPercent = 0,
  popModel = "exp",
  r = 1,
  K_env = length(pts),
  subpopmortperc = 0,
  muterate = 5e-04,
  mutationtype = "random",
  loci = 1000,
  intgenesans = "random",
  allefreqfilename = "N",
  alleles = 2,
  mtdna = "N",
  startGenes = 0,
  cdevolveans = "N",
  startSelection = 0,
  betaFile_selection = "N",
  epistasis = "N",
  epigeneans = "N",
  startEpigene = 0,
  betaFile_epigene = "N",
  cdinfect = "N",
  transmissionprob = 0,
  deme_size = 1,
  n_demes = NULL,
  python = NULL
)

`CDPOP.py`	Full path to the CDPOP.py file
`sim_name`	Name for simulation results. Defaults to 'output'
`pts`	Spatial points object
`sim_dir`	Directory where simulation results will be written
`resist_rast`	Resistance surface
`agefilename`	Path to age file. Default will create and use a non-overlapping generations file.
`mcruns`	Default = 1
`looptime`	Default = 401; Number generations to conduct simulation
`output_years`	Default = 50; Interval to write out simulation results
`gridformat`	Default = 'genepop'; c('genepop', 'genalex', 'structure', 'cdpop')
`cdclimgentime`	Default = 0. To initiate the CDClimate module, this is the generation/year that the next effective distance matrix will be read in at. You can specify multiple generations by separating each generation to read in the next cost distance matrix by ‘\|’. Then in the following surface columns, a separate file can be given for each generation.
`matemoveno`	Default = 2; Uses Inverse Square (1 / (Cost Distance^2)). This function gets rescaled to min and threshold of the inverse square cost distance.
`matemoveparA`	Not used with inverse square movement
`matemoveparB`	Not used with inverse square movement
`matemoveparC`	Not used with inverse square movement
`matemovethresh`	Default = 'max'; The maximum movement is the maximum resistance distance
`output_matedistance`	Does mate movement distance differ (Default = 'N')
`sexans`	Default = 'N'; No selfing
`Freplace`	Default = 'N'; Females mate without replacement
`Mreplace`	Default = 'N'; Males mate without replacement
`philopatry`	Default = 'N';
`multiple_paternity`	Default = 'N'; No philopatry of Males or Females
`selfans`	Default = 'N'; No selfing
`Fdispmoveno`	Default = NULL. Will be set equal to matemoveno
`FdispmoveparA`	Not used with inverse square movement
`FdispmoveparB`	Not used with inverse square movement
`FdispmoveparC`	Not used with inverse square movement
`Fdispmovethresh`	Default = NULL. Will be set to matemovethresh
`Mdispmoveno`	Default = NULL. Will be set equal to matemoveno
`MdispmoveparA`	Not used with inverse square movement
`MdispmoveparB`	Not used with inverse square movement
`MdispmoveparC`	Not used with inverse square movement
`Mdispmovethresh`	Default = NULL. Will be set to matemovethresh
`offno`	Default = 2; Poisson draw around ‘mean fecundity’
`MeanFecundity`	Default = 5; Specifies mean fecundity in age variable file.
`Femalepercent`	Default = 50
`EqualsexratioBirth`	Default = 'N'
`TwinningPercent`	Default = 0
`popModel`	Default = 'exp'
`r`	Population growth rate. No applicable when using exponential growth rate
`K_env`	Equal to the number of individuals simulated
`subpopmortperc`	Default = 0\|0\|0\|0; Not using subpopulation features
`muterate`	Default = 0.0005
`mutationtype`	Default = 'forward'
`loci`	Default = 1000; For simulating SNP-like markers
`intgenesans`	Default = 'random'; Random initiation of alleles
`allefreqfilename`	Default = 'N'
`alleles`	Default = 2; For simulating SNP-like markers
`mtdna`	Default = 'N'
`startGenes`	Default = 0;
`cdevolveans`	Default = 'N'; No loci are under selection
`startSelection`	Default = 0; No selection
`betaFile_selection`	Default = 'N'; No selection
`epistasis`	Default = 'N'; No epigenetics
`epigeneans`	Default = 'N'; No epigenetics
`startEpigene`	Default = 0; No epigenetics
`betaFile_epigene`	Default = 'N'; No epigenetics
`cdinfect`	Default = 'N'; No epigenetics
`transmissionprob`	Default = 0; No epigenetics
`deme_size`	Number of individuals within each deme
`n_demes`	Number of demes on the landscape
`python`	Optional. Only needed if Python 2.7 is not in your system path. If needed, specify the full path to the Python 2.7x program file.