Title: | Analysis of Physiologically Structured Population Models |
---|---|
Description: | Performs demographic, bifurcation and evolutionary analysis of physiologically structured population models, which is a class of models that consistently translates continuous-time models of individual life history to the population level. A model of individual life history has to be implemented specifying the individual-level functions that determine the life history, such as development and mortality rates and fecundity. M.A. Kirkilionis, O. Diekmann, B. Lisser, M. Nool, B. Sommeijer & A.M. de Roos (2001) <doi:10.1142/S0218202501001264>. O.Diekmann, M.Gyllenberg & J.A.J.Metz (2003) <doi:10.1016/S0040-5809(02)00058-8>. A.M. de Roos (2008) <doi:10.1111/j.1461-0248.2007.01121.x>. |
Authors: | Andre M. de Roos [aut, cre], Ernst Hairer [ctb], Gerhard Wanner [ctb] |
Maintainer: | Andre M. de Roos <A.M.deRoos@uva.nl> |
License: | GPL-3 |
Version: | 0.3.9 |
Built: | 2025-03-07 04:19:01 UTC |
Source: | https://github.com/cran/PSPManalysis |
csbread
reads a CSB file, which is generated by PSPMdemo
,
PSPMequi
, PSPMecodyn
and PSPMevodyn
to save the entire state of the environmental variables and physiologically
structured populations during computations.
csbread(csbfile = NULL, state = -1)
csbread(csbfile = NULL, state = -1)
csbfile |
(string, required) Name of the CSB file to be read with or without '.csb' extension. |
state |
(integer, optional) If not specified |
output <- csbread(csbfile = NULL, state = -1)
If a specific state is specified and found in the file, the state is returned as a list.
## Not run: PSPMdemo("Medfly", c(2, 11, 0.1, 11, 15), clean = TRUE) csbread("Medfly-PGR-0000") csbread("Medfly-PGR-0000", 1) ## End(Not run)
## Not run: PSPMdemo("Medfly", c(2, 11, 0.1, 11, 15), clean = TRUE) csbread("Medfly-PGR-0000") csbread("Medfly-PGR-0000", 1) ## End(Not run)
PSPMclean
deletes all PSPManalysis result files (default) and/or
all executables (hit 'F') in the current directory.
PSPMclean(str = NULL)
PSPMclean(str = NULL)
str |
Character (optional). Only valid argument is 'F'. If not or wrongly specified the user will be asked whether to do a full clean up or whether to quit the clean up. |
None.
## Not run: PSPMclean() PSPMclean("F") ## End(Not run)
## Not run: PSPMclean() PSPMclean("F") ## End(Not run)
PSPMdemo
computes the population growth rate of a physiologically structured
population model and its sensitivities with respect to all model parameters.
PSPMdemo
either carries out these computation for a single parameter set or
varies one of the parameters over a range of values specified by the user
PSPMdemo( modelname = NULL, curvepars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE )
PSPMdemo( modelname = NULL, curvepars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE )
modelname |
(string, required) Basename of the file with model specification. The file should have extension ".h". For example, the model "Medfly" is specified in the file "Medfly.h". If the model is specified in R include the .R extension explicitly, i.e. specify the model name as "Medfly.R" |
curvepars |
(row vector, optional, can be left equal to its default NULL) Vector of length 5, specifying:
|
parameters |
(row vector, optional, can be left equal to its default NULL) Vector of length PARAMETER_NR (set in the model program file; This is the length of the variable 'DefaultParameters' if the model is specified in R), specifying the values for the model parameters to use in the computation. Vectors of other lengths, including an empty vector will be ignored. |
options |
(row vector of strings, optional, can be left equal to its default NULL) Vector with pairs of strings, consisting of an option name and a value (for example c("isort", "1")) or single options (i.e. c("test")). Possible option names and their values are:
|
clean |
(Boolean, optional argument) Specify clean = TRUE as argument to remove all the result files of the model before the computation |
force |
(Boolean, optional argument) Specify force = TRUE as argument to force a rebuilding of the model before the computation |
debug |
(Boolean, optional argument) Specify debug = TRUE as argument to compile the model in verbose mode and with debugging flag set |
silent |
(Boolean, optional argument) Specify silent = TRUE as argument to suppress reporting of compilation commands and results on the console |
output <- PSPMdemo(modelname = NULL, curvepars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE)
The output is a list containing the following elements:
curvepoints
: Matrix with output for all computed points along the curve
curvedesc
: Column vector with strings, summarizing the numerical details
of the computed curve (i.e., initial point, parameter values,
numerical settings used).
## Not run: PSPMdemo("Medfly", c(2, 11, 0.1, 11, 16)) ## End(Not run)
## Not run: PSPMdemo("Medfly", c(2, 11, 0.1, 11, 16)) ## End(Not run)
PSPMecodyn
computes the dynamics of a physiologically structured population model
starting from an environmental and population state that is computed with PSPMequi
.
If starting from an arbitrary state is required, the list specifying the initial state should
have the same layout as produced by PSPMequi
.
PSPMecodyn( modelname = NULL, startstate = NULL, timepars = NULL, bifpars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE )
PSPMecodyn( modelname = NULL, startstate = NULL, timepars = NULL, bifpars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE )
modelname |
(string, required) Basename of the file with the model specification. The file should have an extension ".h". For example, the model "PNAS2002" is specified in the file "PNAS2002.h". If the model is specified in R include the .R extension explicitly, i.e. specify the model name as "PNAS2002.R" |
startstate |
(list, required) The initial environmental and population state from which to start the simulation of the dynamics. This list should have the identical layout as a list returned by the function csbread(). As a minimum, the list should contain a vector 'Environment' specifying the initial values of the environmental variables, and a matrix 'Pop00' (assuming there is only a single population in the model), which specifies on each row the number and individual state variables of a cohort of while the different rows specify all the cohorts in the population. |
timepars |
(row vector of length 4, required) Vector of length 4 specifying the settings for the time integration:
|
bifpars |
(row vector of length 6, optional) Vector of length 6 specifying the settings for the bifurcation settings. If not specified a normal time integration is carried out.
|
parameters |
(row vector, optional, can be left equal to its default NULL) Vector of length PARAMETER_NR (set in the model program file; This is the length of the variable 'DefaultParameters' if the model is specified in R), specifying the values for the model parameters to use in the computation. Vectors of other lengths, including an empty vector will be ignored. |
options |
(row vector of strings, optional, can be left equal to its default NULL) Vector with pairs of strings, consisting of an option name and a value (for example c("info", "1")). Possible option names and their values are:
|
clean |
(Boolean, optional argument) Specify clean = TRUE as argument to remove all the result files of the model before the computation |
force |
(Boolean, optional argument) Specify force = TRUE as argument to force a rebuilding of the model before the computation |
debug |
(Boolean, optional argument) Specify debug = TRUE as argument to compile the model in verbose mode and with debugging flag set |
silent |
(Boolean, optional argument) Specify silent = TRUE as argument to suppress reporting of compilation commands and results on the console |
output <- PSPMecodyn(modelname = NULL, startstate = NULL, timepars = NULL, bifpars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE)
The output is a list containing the following elements:
curvepoints
: Matrix with output for all computed points along the curve
curvedesc
: Column vector with strings, summarizing the numerical details
of the computed curve (i.e., initial point, parameter values,
numerical settings used)
## Not run: initstate <- list(Environment = c(1.561e-04, 1.270e-04, 4.008e-06), Pop00 = matrix(c(0.001, 0, 7.0, 1.0E-5, 300, 111), ncol = 3, byrow = TRUE)) PSPMecodyn("PNAS2002", initstate, c(1, 1, 10, 100)) ## End(Not run)
## Not run: initstate <- list(Environment = c(1.561e-04, 1.270e-04, 4.008e-06), Pop00 = matrix(c(0.001, 0, 7.0, 1.0E-5, 300, 111), ncol = 3, byrow = TRUE)) PSPMecodyn("PNAS2002", initstate, c(1, 1, 10, 100)) ## End(Not run)
PSPMequi
computes bifurcation curves for a physiologically structured
population model as a function of one or two parameters and detects bifurcation
points along these curves.
When computing equilibrium curves of a physiologically structured population model
as a function of one parameter, PSPMequi
can detect transcritical
bifurcation points (branching points, BP) of both the structured populations as
well as environment variables (BPE), limit points (LP) in the equilibrium curve
and evolutionary stationary points (ESS). The location of these bifurcation points
can subsequently be computed as a function of second parameter.
In addition PSPMequi
can compute the pairwise invasion plot (PIP) as a
function of the resident and a mutant value for one evolving parameter.
PSPMequi( modelname = NULL, biftype = NULL, startpoint = NULL, stepsize = NULL, parbnds = NULL, parameters = NULL, minvals = NULL, maxvals = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE )
PSPMequi( modelname = NULL, biftype = NULL, startpoint = NULL, stepsize = NULL, parbnds = NULL, parameters = NULL, minvals = NULL, maxvals = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE )
modelname |
(string, required) Basename of the file with the model specification. The file should have an extension ".h". For example, the model "PNAS2002" is specified in the file "PNAS2002.h". If the model is specified in R include the .R extension explicitly, i.e. specify the model name as "PNAS2002.R" |
biftype |
(string, required) Type of bifurcation to compute: "BP", "BPE", "EQ", "LP", "ESS" or "PIP" |
startpoint |
(row vector, required) The initial point from which to start the continuation of the curve |
stepsize |
(double value, required) Value of the step size in the first bifurcation parameter |
parbnds |
(row vector, required) Vector of length 3 for EQ continuation, length 6 for BP, BPE, LP and PIP continuation and 3+4*N for ESS continuation. The first triplet specifies: Each triples specifies:
In case of two-parameter bifurcations, the second triplet specifies:
In case of ESS continuation, consecutive sets of 4 values specify:
|
parameters |
(row vector, optional, can be left equal to its default NULL) Vector of length PARAMETER_NR (set in the model program file; This is the length of the variable 'DefaultParameters' if the model is specified in R), specifying the values for the model parameters to use in the computation. Vectors of other lengths, including an empty vector will be ignored. |
minvals |
(row vector, optional, can be left equal to its default NULL) Vector of length (ENVIRON_DIM + POPULATION_NR), specifying minimum values for the environmental variables and the population birth rates, at which computations will stop. Vectors of other lengths, including an empty vector will be ignored. |
maxvals |
(row vector, optional, can be left equal to its default NULL) Vector of length (ENVIRON_DIM + POPULATION_NR), specifying maximum values for the environmental variables and the population birth rates, at which computations will stop. Vectors of other lengths, including an empty vector will be ignored. |
options |
(row vector of strings, optional, can be left equal to its default NULL) Vector with pairs of strings, consisting of an option name and a value (for example c("popBP", "1")) or single options (i.e. c("test")). Possible option names and their values are:
|
clean |
(Boolean, optional argument) Specify clean = TRUE as argument to remove all the result files of the model before the computation |
force |
(Boolean, optional argument) Specify force = TRUE as argument to force a rebuilding of the model before the computation |
debug |
(Boolean, optional argument) Specify debug = TRUE as argument to compile the model in verbose mode and with debugging flag set |
silent |
(Boolean, optional argument) Specify silent = TRUE as argument to suppress reporting of compilation commands and results on the console |
output <- PSPMequi(modelname = NULL, biftype = NULL, startpoint = NULL, stepsize = NULL, parbnds = NULL, parameters = NULL, minvals = NULL, maxvals = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE)
The output is a list containing the following elements:
curvepoints
: Matrix with output for all computed points along the curve
curvedesc
: Column vector with strings, summarizing the numerical details
of the computed curve (i.e., initial point, parameter values,
numerical settings used)
bifpoints
: Matrix with the located bifurcation points along the curve
biftypes
: Column vector of strings, containing a description of the
type of bifurcation for each of the located bifurcation points
## Not run: PSPMequi("Indet_growth", "EQ", c(1, 0.22, 0), -0.1, c(6, 0.8, 1.0), options = c("popEVO", "0"), silent = TRUE) ## End(Not run)
## Not run: PSPMequi("Indet_growth", "EQ", c(1, 0.22, 0), -0.1, c(6, 0.8, 1.0), options = c("popEVO", "0"), silent = TRUE) ## End(Not run)
PSPMevodyn
computes the dynamics of a physiologically structured population model
over evolutionary time for an arbitrary number of evolving parameters. The
evolutionary trajectory of these evolving parameters is determined by the
canonical equation of Adaptive Dynamics, which is solved using a simple
Euler integration scheme.
PSPMevodyn( modelname = NULL, startpoint = NULL, curvepars = NULL, evopars = NULL, covars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE )
PSPMevodyn( modelname = NULL, startpoint = NULL, curvepars = NULL, evopars = NULL, covars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE )
modelname |
(string, required) Basename of the file with the model specification. The file should have an extension ".h". For example, the model "PNAS2002" is specified in the file "PNAS2002.h". If the model is specified in R include the .R extension explicitly, i.e. specify the model name as "PNAS2002.R" |
startpoint |
(row vector, required) The initial point from which to start the simulation of the dynamics over evolutionary time, including the initial values of the evolving parameters |
curvepars |
(row vector of length 2, required) Vector of length 2 specifying:
|
evopars |
(row vector of length n*4, required) Vector of length n*4 specifying:
......
|
covars |
(row vector or matrix, optional, can be left equal to its default NULL) Vector of length N*N or NxN matrix, where N is the number of evolving parameters. The vector or matrix elements specify the values of the covariance matrix in the selection gradients. Vectors of other lengths, including an empty vector will be ignored. |
parameters |
(row vector, optional, can be left equal to its default NULL) Vector of length PARAMETER_NR (set in the model program file), specifying the values for the model parameters to use in the computation. Vectors of other lengths, including an empty vector will be ignored. |
options |
(row vector of strings, optional, can be left equal to its default NULL) Vector with pairs of strings, consisting of an option name and a value (for example c("popZE", "1")) or single options (i.e. c("test")). Possible option names and their values are:
|
clean |
(Boolean, optional argument) Specify clean = TRUE as argument to remove all the result files of the model before the computation |
force |
(Boolean, optional argument) Specify force = TRUE as argument to force a rebuilding of the model before the computation |
debug |
(Boolean, optional argument) Specify debug = TRUE as argument to compile the model in verbose mode and with debugging flag set |
silent |
(Boolean, optional argument) Specify silent = TRUE as argument to suppress reporting of compilation commands and results on the console |
output <- PSPMevodyn(modelname = NULL, startpoint = NULL, curvepars = NULL, evopars = NULL, covars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE)
The output is a list containing the following elements:
curvepoints
: Matrix with output for all computed points along the curve
curvedesc
: Column vector with strings, summarizing the numerical details
of the computed curve (i.e., initial point, parameter values,
numerical settings used)
## Not run: PSPMevodyn("Indet_growth", c(0.22, 0.03554, 1.0), c(0.05, 1), c(0, 6, 0.5, 1.5)) ## End(Not run)
## Not run: PSPMevodyn("Indet_growth", c(0.22, 0.03554, 1.0), c(0.05, 1), c(0, 6, 0.5, 1.5)) ## End(Not run)
PSPMhelp
opens the manual of the the PSPManalysis package in html format.
PSPMhelp()
PSPMhelp()
The manual is created in bookdown format. A PDF version can be downloaded via the PDF icon in the menu bar.
None.
## Not run: PSPMhelp() ## End(Not run)
## Not run: PSPMhelp() ## End(Not run)
PSPMind
is a utility function to compute the individual life history as
defined by a physiologically structured population model, given a specific
set of values for the environmental variables
PSPMind( modelname = NULL, environment = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE )
PSPMind( modelname = NULL, environment = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE )
modelname |
(string, required) Basename of the file with the model specification. The file should have an extension ".h". For example, the model "PNAS2002" is specified in the file "PNAS2002.h". If the model is specified in R include the .R extension explicitly, i.e. specify the model name as "PNAS2002.R" |
environment |
(row vector, required) Vector of length ENVIRON_DIM (set in the model program file; This is the length of the variable 'EnvironmentState' if the model is specified in R), specifying the value of the environmental variables at which to calculate the individual life history. This vector can also be extended with values of the birth rates for all structured populations in the model, which would scale the output of the model with these birth rates. |
parameters |
(row vector, optional, can be left equal to its default NULL) Vector of length PARAMETER_NR (set in the model program file; This is the length of the variable 'DefaultParameters' if the model is specified in R), specifying the values for the model parameters to use in the computation. Vectors of other lengths, including an empty vector will be ignored. |
options |
(row vector of strings, optional, can be left equal to its default NULL) Vector with a pair of strings, consisting of an option name and a value (for example c("isort", "1")). The only possible option name and its values is:
|
clean |
(Boolean, optional argument) Specify clean = TRUE as argument to remove all the result files of the model before the computation |
force |
(Boolean, optional argument) Specify force = TRUE as argument to force a rebuilding of the model before the computation |
debug |
(Boolean, optional argument) Specify debug = TRUE as argument to compile the model in verbose mode and with debugging flag set |
silent |
(Boolean, optional argument) Specify silent = TRUE as argument to suppress reporting of compilation commands and results on the console |
output <- PSPMind(modelname = NULL, environment = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE)
The output is a structure with the population state as normally stored in the
.csb output file of PSPMdemo
, PSPMequi
, PSPMecodyn
and
PSPMevodyn
.
## Not run: PSPMind("PNAS2002_5bs", c(1.30341E-05, 3.84655E-05, 4.00802E-06), options = c("isort", "1"), clean=TRUE, force=TRUE) ## End(Not run)
## Not run: PSPMind("PNAS2002_5bs", c(1.30341E-05, 3.84655E-05, 4.00802E-06), options = c("isort", "1"), clean=TRUE, force=TRUE) ## End(Not run)
showpspm
displays the file contents of one of the physiologically structured
population models that is provided as an example.
showpspm(modelname = NULL)
showpspm(modelname = NULL)
modelname |
(string) Name of the example model to be displayed. |
showpspm(modelname = NULL)
## Not run: showpspm("Medfly.R") ## End(Not run)
## Not run: showpspm("Medfly.R") ## End(Not run)