mp.read: Read RAMAS (c) *.MP file

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

Description

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.

Usage

mp.read(mpFile, verbose = FALSE, results = FALSE)

Arguments

mpFile	The name of the *.MP file to be read.
verbose	Print function progress and checkpoints.
results	Read results saved in the *.MP file.

Details

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.

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

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

3. Demog_Stoch: Use demographic stochasticity? (boolean)

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

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

6. 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

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

8. DDActing: Information regarding density dependence

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

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

11. dispCV: Coefficient of variation for dispersal

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

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

14. DispersalDependsOnTargetPopK: Just like the variable name implie; boolean

15. DDBasis: Density basis type (char)

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

17. DDforAllPop: Density dependence type for all populations (char)

18. UserDllFileName: Filename for user-defined density dependence function

19. TimeStepSize: Time step size

20. TimeStepUnits: Time step units

21. SexStructure: Description of Sex Structure (char)

22. FemaleStages: Number of female stages

23. MatingSystem: Description of Mating system selected (char)

24. FemalesPerMale: Number of females per male as given by user

25. MalesPerFemale: Number of males per female as given by user

26. CVerror: sampling error for N

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

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

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

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

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

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

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

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

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

36. 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

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

38. 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

39. ConstraintsMatr: Constraints Matrix

40. StMig: Stage Relative Migration (Dispersal) Rates

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

42. Cat1EffNst: Catastrophe 1 effects on abundances

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

44. Cat2EffNst: Catastrophe 2 effects on abundances

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

46. 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

47. NPopManage: Number of population managment actions

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

49. ExtinctThr: Extinction threshold

50. ExplodeThr: Explosion threshold

51. stepsize: step size

52. PopData_df: Population level information in data.frame format

Value

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.

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