Deletes on request all files produced by the PSPManalysis package.
Description
PSPMclean deletes all PSPManalysis result files (default) and/or
all executables (hit 'F') in the current directory.
Usage
PSPMclean(str = NULL)
Arguments
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.
Value
None.
Examples
## Not run:
PSPMclean()
PSPMclean("F")
## End(Not run)
Demographic analysis of a structured population model
Description
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
Usage
PSPMdemo(
modelname = NULL,
curvepars = NULL,
parameters = NULL,
options = NULL,
clean = FALSE,
force = FALSE,
debug = FALSE,
silent = FALSE
)
Arguments
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:
curvepars[1]: the index of the parameter to vary
(in case the model is specified in R, this can be
a string with the name of the parameter as specified
in the variable 'DefaultParameters')
curvepars[2]: the initial value of the parameter
curvepars[3]: the step size in the parameter value
curvepars[4]: lower threshold, below which value of the
parameter the computation stops
curvepars[5]: upper threshold, above which value of the
parameter the computation stops
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:
"isort", "<index>": Index of i-state variable to use as
ruling variable for sorting the
structured populations
"report", "<value>": Interval between consecutive output of
computed points to the console ( >= 1). Minimum value of 1
implies output of every point
"test": Perform only a single integration over
the life history, reporting dynamics
of survival, R0, i-state and
interaction variables
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
Details
output <- PSPMdemo(modelname = NULL, curvepars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE)
Value
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).
Examples
## Not run:
PSPMdemo("Medfly", c(2, 11, 0.1, 11, 16))
## End(Not run)
Ecological dynamics of a structured population model computed using the Escalator Boxcar Train
Description
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 .
Usage
PSPMecodyn(
modelname = NULL,
startstate = NULL,
timepars = NULL,
bifpars = NULL,
parameters = NULL,
options = NULL,
clean = FALSE,
force = FALSE,
debug = FALSE,
silent = FALSE
)
Arguments
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:
timepars[1]: Cohort cycle time, i.e. time interval between starts of new
boundary cohorts
timepars[2]: Output time interval, i.e. time interval between data output
to .out file
timepars[3]: State output interval, i.e. time interval between complete
state output to .csb file
timepars[4]: Maximum integration time, i.e. maximum time value until which
to continue the 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.
bifpars[1]: Index of the bifurcation parameter
bifpars[2]: Starting value of the bifurcation parameter
bifpars[3]: Step size in the bifurcation parameter
bifpars[4]: Final value of the bifurcation parameter
bifpars[5]: Period of producing data output during each bifurcation interval
bifpars[6]: Period of producing state output during each bifurcation interval
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:
"info", "<index>": Level of performance information on the DOPRI5
integrator written to .err file (1, 2, 3 or 4)
"report", "<index>": Interval between reporting of data output to
console ( > 0)
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
Details
output <- PSPMecodyn(modelname = NULL, startstate = NULL, timepars = NULL, bifpars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE)
Value
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)
Examples
## 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)
Bifurcation analysis of a structured population model
Description
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.
Usage
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
)
Arguments
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:
parbnds[1]: the index of the first bifurcation parameter
(in case the model is specified in R, this can be
a string with the name of the parameter as specified
in the variable 'DefaultParameters')
parbnds[2]: lower threshold, below which value of the
first bifurcation parameter the computation stops
parbnds[3]: upper threshold, above which value of the
first bifurcation parameter the computation stops
In case of two-parameter bifurcations, the second triplet specifies:
parbnds[4]: the index of the second bifurcation parameter
(in case the model is specified in R, this can be
a string with the name of the parameter as specified
in the variable 'DefaultParameters')
parbnds[5]: lower threshold, below which value of the
second bifurcation parameter the computation stops
parbnds[6]: upper threshold, above which value of the
second bifurcation parameter the computation stops
In case of ESS continuation, consecutive sets of 4 values specify:
parbnds[4*n]: the index of population that is impacted by the
parameter at its ESS value
(in case the model is specified in R, this can be
a string with the name of the parameter as specified
in the variable 'DefaultParameters')
parbnds[4*n+1]: the index of the parameter at its ESS value
parbnds[4*n+2]: lower threshold, below which value of this ESS
parameter the computation stops
parbnds[4*n+3]: upper threshold, above which value of this ESS
parameter the computation stops
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:
"envBP", "<index>": Index of environment variable, of which
to continue the transcritical bifurcation
"popBP", "<index>": Index of structured population, of which
to continue the transcritical bifurcation
"popEVO", "<index>": Index of structured population, for
which to compute the selection gradient or
perform PIP continuation
"parEVO", "<index>": Index of parameter, for which to
compute the selection gradient
"envZE", "<index>": Index of environment variable in
trivial equilibrium (can be used
multiple times)
"popZE", "<index>": Index of structured population in
trivial equilibrium (can be used
multiple times)
"isort", "<index>": Index of i-state variable to use as
ruling variable for sorting the
structured populations
"report", "<value>": Interval between consecutive output of
computed points to the console ( >= 1).
Minimum value of 1 implies output of every
point
"noBP": Do not check for branching points while
computing equilibrium curves
"noLP": Do not check for limit points while
computing equilibrium curves
"single": Only compute the first point of the
solution curve, do not continue the curve
"test": Perform only a single integration over
the life history, reporting dynamics
of survival, R0, i-state and
interaction variables
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
Details
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)
Value
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
Examples
## 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)
Evolutionary dynamics for a structured population model computed following the canonical equation
Description
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.
Usage
PSPMevodyn(
modelname = NULL,
startpoint = NULL,
curvepars = NULL,
evopars = NULL,
covars = NULL,
parameters = NULL,
options = NULL,
clean = FALSE,
force = FALSE,
debug = FALSE,
silent = FALSE
)
Arguments
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:
curvepars[1]: the maximum step size in evolutionary time during
the integration of the canonical equation
curvepars[2]: the maximum evolutionary time at which to stop
the integration of the canonical equation
evopars
(row vector of length n*4, required)
Vector of length n*4 specifying:
evopars[1]: the index of the structured population whose
life history is influenced by the first evolving
parameter
evopars[2]: the index of the first evolution parameter
(in case the model is specified in R, this can be
a string with the name of the parameter as specified
in the variable 'DefaultParameters')
evopars[3]: lower threshold, below which value of the
first evolution parameter the computation stops
evopars[4]: upper threshold, above which value of the
first evolution parameter the computation stops
......
evopars[n*4-3]: the index of the structured population whose
life history is influenced by the last evolving
parameter
evopars[n*4-2]: the index of the last evolution parameter
(in case the model is specified in R, this can be
a string with the name of the parameter as specified
in the variable 'DefaultParameters')
evopars[n*4-1]: lower threshold, below which value of the
last evolution parameter the computation stops
evopars[n*4]: upper threshold, above which value of the
last evolution parameter the computation stops
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:
"envZE", "<index>": Index of environment variable in
trivial equilibrium (can be used
multiple times)
"popZE", "<index>": Index of structured population in
trivial equilibrium (can be used
multiple times)
"isort", "<index>": Index of i-state variable to use as
ruling variable for sorting the
structured populations
"report", "<value>": Interval between consecutive output of
computed points to the console ( >= 1).
Minimum value of 1 implies output of every
point
"test": Perform only a single integration over
the life history, reporting dynamics
of survival, R0, i-state and
interaction variables
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
Details
output <- PSPMevodyn(modelname = NULL, startpoint = NULL, curvepars = NULL, evopars = NULL, covars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE)
Value
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)
Examples
## 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)
Opens the PSPManalysis manual
Description
PSPMhelp opens the manual of the the PSPManalysis package in html format.
Usage
PSPMhelp()
Details
The manual is created in bookdown format. A PDF version can be downloaded via the PDF icon in the menu bar.
Value
None.
Examples
## Not run:
PSPMhelp()
## End(Not run)
Computes the individual life history of a physiologically structured population model in a given environment
Description
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
Usage
PSPMind(
modelname = NULL,
environment = NULL,
parameters = NULL,
options = NULL,
clean = FALSE,
force = FALSE,
debug = FALSE,
silent = FALSE
)
Arguments
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:
"isort", "<index>": Index of i-state variable to use as
ruling variable for sorting the
structured populations
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
Details
output <- PSPMind(modelname = NULL, environment = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE)
Value
The output is a structure with the population state as normally stored in the
.csb output file of PSPMdemo , PSPMequi , PSPMecodyn and
PSPMevodyn .
Examples
## 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)
Reads the state of a structured population model from a CSB file
Description
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.
Usage
csbread(csbfile = NULL, state = -1)
Arguments
csbfile
(string, required)
Name of the CSB file to be read with or without '.csb' extension.
state
(integer, optional)
If not specified csbread will list the states that are
stored in the CSB file. If specified, it should be the name or index
of one of the states in the CSB file.
Details
output <- csbread(csbfile = NULL, state = -1)
Value
If a specific state is specified and found in the file, the state is returned as a list.
Examples
## 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)
Shows the model definition file of one of the example models provided with PSPManalysis
Description
showpspm displays the file contents of one of the physiologically structured
population models that is provided as an example.
Usage
showpspm(modelname = NULL)
Arguments
modelname
(string)
Name of the example model to be displayed.
Details
showpspm(modelname = NULL)
Examples
## Not run:
showpspm("Medfly.R")
## End(Not run)