Description Usage Arguments Details Value

`mp.read`

reads in the *.MP file used in the RAMAS Metapop software.
The *.MP file is a simple text file containing all of the values necessary
to configure a metapopulation simulation.

1 |

`mpFile` |
The name of the *.MP file to be read. |

`verbose` |
Print function progress and checkpoints. |

`results` |
Read results saved in the *.MP file. |

mp.file 'list' structure elements. Most element names from RAMAS Metapop source code The assignment of each element of the mp.file list is based on the Metapopulation input file type for version 5.0.

MaxRep: maximum number of replications (integer; 1-10000)

MaxDur: Duration of simulation (integer; 1-500)

Demog_Stoch: Use demographic stochasticity? (boolean)

Stages: Number of stages (integer; 1-50)

Stages.IgnoreConstraints: Ingore constraints? (boolean - TRUE/FALSE)

Cat1: Information associated with catastrophe 1 This information is subdivided in RAMAS Input, but will not be subdivided in the first version of the sensitivity analysis package

Cat2: Information associated with catastrophe 2 See note associated with Cat1

DDActing: Information regarding density dependence

Distrib: Distribution (Normal or Lognormal) to use for Environmental Stochasticity.

AdvancedStochSetting: Advanced Environmental Stoch. Settings: (0 or PoolVar or NegSurvCorr)

dispCV: Coefficient of variation for dispersal

WhenBelow: When below local threshold (count in total or don't count or assume dead)

corrwith: Within population correlation - 1 - (F, S, K Correlated) 2 - (F and S correlated, K independent) 3 - (F, S, K independent

DispersalDependsOnTargetPopK: Just like the variable name implie; boolean

DDBasis: Density basis type (char)

PopSpecificDD: Density dependence type is population specific (boolean - Yes/No)

DDforAllPop: Density dependence type for all populations (char)

UserDllFileName: Filename for user-defined density dependence function

TimeStepSize: Time step size

TimeStepUnits: Time step units

SexStructure: Description of Sex Structure (char)

FemaleStages: Number of female stages

MatingSystem: Description of Mating system selected (char)

FemalesPerMale: Number of females per male as given by user

MalesPerFemale: Number of males per female as given by user

CVerror: sampling error for N

FirstTforRisk: Initial number of time steps to exclude from risk calculations Population Parameters

PopList: Individual population data - saved as a 'nested list' structure, one 'list' for each population. Dispersal (Migration) Parameters

UseDispDistFunc: True if dispersal rates are based on dispersal distance function; false if they are specified in the dispersal matrix

DispDistFunc: Dispersal-distance function parameters - a, b, c, Dmax - Mij = a exp(-Dij^c/b)

DispMatr: Dispersal matrix, as defined or calculated in 'fill.matrix.df.r' Correlation Parameters

UseCorrDistFunc: True if correlations between populations is based on correlation distance function; False if they are specified in the correlation matrix

CorrDistFunc: Correlation-distance function parameters - a, b, c - Cij = a exp(-Dij^c/b)

CorrMatr: User specified correlation matrix, as defined or calculated in 'fill.matrix.df.r' Stage Matrices Information

StMatrNumber: number of stage matrices defined by user in *.mp file

StMatr: a 'list' object containing information about each stage matrix. For each stage matrix the following information is stored: StMatrName: Name of the stage matrix StMatrSurvMult: Survival multiplier for stage matrix (for generating new matrices; not used in simulation) StMatrFecMult: Fecundity multiplier for stage matrix (for generating new matrices; not used in simulation) Matr: a matrix object with numeric values Standard Deviation Matrices Information

SDMatrNumber: number of st. dev. matrices defined by user in *.mp file

SDMatr: a 'list' object containing information for each st.dev. matrix. For each st.dev. matrix the following information is stored: SDMatrName: Name of the st.dev. matrix Matr: a matrix object of numeric values

ConstraintsMatr: Constraints Matrix

StMig: Stage Relative Migration (Dispersal) Rates

Cat1EffMat: Catastrophe 1 effects on vital rates; one row per stage, seperated by spaces

Cat1EffNst: Catastrophe 1 effects on abundances

Cat2EffMat: Catastrophe 2 effects on vital rates; one row per stage, seperated by spaces

Cat2EffNst: Catastrophe 2 effects on abundances

StInit: Initial Abundance for each stage for each population Stage Properties

StProp: a 'list' object containing the following information for each stage StName: Name of stage StWeight: Relative weight of stage StExclude: Exclude from total (boolean: TRUE or FALSE) StBasisForDD: Basis for density-dependence (boolean: TRUE or FALSE) StBreeding: Proportion of stage physically capable of breeding Population Management Actions

NPopManage: Number of population managment actions

PopManageProp: All of the lines associated with population management, unpartitioned

ExtinctThr: Extinction threshold

ExplodeThr: Explosion threshold

stepsize: step size

PopData_df: Population level information in data.frame format

`mp.read`

returns a nested list object. The first level includes
two elements, the version of the *.MP file and list names "mp.file". The
"mp.file" list is composed of 52 elements that provide all of the information
found in the *.MP file.

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