results: Extract simulation results from RAMAS Metapop .mp files

In johnbaums/mptools: RAMAS Metapop Tools

Description

Extract population size simulation results (mean, sd, min and max), including expected minimum abundance (EMA) and its standard deviation, from a RAMAS Metapop .mp file.

Usage

results(mp)

Arguments

mp	A character string containing the path to a RAMAS Metapop .mp file containing simulation results. Metapop .mp files are plain text files that store settings describing RAMAS metapopulation models, and the results of simulating population dynamics according to those models.

Value

A list containing:

version	The version of RAMAS Metapop from which the file indicated by mp originated (if identifiable).
results	An array containing simulation results extracted from file. The number of rows is equal to the number of time steps in the simulation. The array has four columns, containing mean, sd, min and max of population size across iterations at each time step (i.e. each row), and the number of array slices is equal to the number of populations. The third dimension is named according to population names (numeric component only).
iter_min	A sorted vector of minimum abundance, across time steps, for each iteration.
iter_max	A sorted vector of maximum abundance, across time steps, for each iteration.
iter_terminal	A sorted vector of terminal abundance for each iteration.
qe_thr	The quasi-extinction threshold. When the total abundance is beneath qe_thr, the metapopulation is considered to be quasi-extinct.
qe_prob	The probability and cumulative probability of exceeding the quasi-extinction threshold (qe_thr) at each time step.
EMA	The mean minimum abundance (i.e. the mean, across iterations, of the minimum abundance for each simulation trajectory).
SDMA	The standard deviation of minimum abundance (i.e. the sd, across iterations, of the minimum abundance for each simulation trajectory).
timestamp	A POSIXlt object representing the date and time at which the simulation was completed.
n_pops	The number of populations in the simulation.
duration	The number of time steps in the simulation
n_iters	The number of iterations performed.

Note

mptools has been tested with outputs generated by RAMAS Metapop version 5, and may produce unexpected results for other versions. A warning is issued if the user attempts to access files originating from other versions of RAMAS Metapop.

References

• Akcakaya, H. R., Burgman, M. A., Kindvall, O., Wood, C. C., Sjogren-Gulve, P., Hatfield, J. S., & McCarthy, M. A. (2004). Species Conservation and Management: Case Studies. New York: Oxford University Press.

• RAMAS Software

• RAMAS GIS and RAMAS Metapop Frequently Asked Questions

See Also

meta

Examples

mp <- system.file('example.mp', package='mptools')
res <- results(mp)
str(res)

# look at the simulation results for the first array slice (NB: this slice is
# all pops combined):
res$results[,, 1]
# equivalently, subset by name:
res$results[,, 'ALL']
res$results[,, 'Pop 190']
res$results[,, '240A24']
dimnames(res$results)[[3]] # population names

# return a matrix of mean population sizes, where columns represent
# populations and rows are time steps:
res$results[, 1, ] # or res$results[, 'mean', ]

# sd across iterations:
res$results[, 2, ] # or res$results[, 'sd', ]

# min pop sizes across iterations:
res$results[, 3, ] # or res$results[, 'min', ]

# max pop sizes across iterations:
res$results[, 4, ] # or res$results[, 'max', ] 

johnbaums/mptools documentation built on May 19, 2019, 3:03 p.m.