R/CM.par.r
In AntoniusGolly/cmgo: Derive principle Channel metrics from bank points
Defines functions
CM.par
Documented in
CM.par
#' Get the parameter object
#'
#' Create a parameter list containing all model and plotting parameters. Depending on the arguments passed to
#' \code{CM.par()}, the parameter list is either created from the defaults or from a specified parameter file.
#'
#' \code{CM.par()} creates or renews a parameter list based on the arguments passed to it. The list contains all
#' model and plot parameters and is stored within the global data object, for example \code{cmgo.obj$par}
#' (see \link[=cmgo]{package documentation}). Thus, the returned parameter object must be assigned to the global data
#' object as in \code{cmgo.obj$par = CM.par()}.
#'
#' If you call \code{CM.par()} without arguments (example #1), the default parameter list
#' is returned (see section "All default parameters and their defaults"). For larger projects, it can be desired to easily switch between
#' parameter sets, for example to reproduce different plots. You can save these customized parameter sets in files
#' (see section "Make a custom parameter file"). These files are loaded with \code{CM.par("path_to_parameter_file")} (example #2). The file is
#' \strong{not required} to host \strong{all} parameters, since the list will be merged with the defaults on loading. That means, a parameter file
#' has to host only those parameters differing from the defaults. As a third option, you can pass directly a list to
#' \code{CM.par()} (example #3). The directly passed parameters will be merged with defaults, as well.
#'
#' @template section_all_default_parameters
#'
#' @section Make a custom parameter file:
#' Create an empty .r-file with the following code:\preformatted{
#' par = list(
#' plot.to.file = TRUE,
#' other_par = "value"
#' # other_par = "other value"
#' )
#' }
#' A full list of available parameters can be found in the paragraph "All parameters and their defaults" above. In a parameter file you
#' don't have to specify \strong{all} parameters. Just list parameters that you like to differ from the defaults. The parameter object that
#' will be created by CM.par() if you specify a file name will be merged with the defaults, where specified parameters overwrite the defaults.
#'
#' @param par.set either NULL (default parameters are returned), of type string to specify a filename or of type list to specify parameters
#' @return The resulting parameters list.
#' @author Antonius Golly
#' @examples
#' # instantiate your global data object first, for example with CM.ini()
#' cmgo.obj = list()
#'
#' # example #1: get the default parameters
#' cmgo.obj$par = CM.par()
#'
#' # example #2: get parameters from a configuration file (see also "Make a custom parameter file")
#' #cmgo.obj$par = CM.par("par/custom_parameters.r")#'
#'
#' # example 3: get modified default parameters
#' cmgo.obj$par = CM.par(list(
#' plot.to.file = TRUE,
#' plot.directory = "/my_figures"
#' ))
#'
#' @export CM.par
CM.par <- function(par.set=NULL){
notice = function(x,prim=FALSE){cat(paste((if(prim) "\n--> " else " "), x, sep=""), sep="\n")}
error = function(x){stop(x, call.=FALSE)}
par.default = list(
# name of the parameter set
name = "default",
version = "0.2.0",
# workspace
workspace.read = TRUE, # if [TRUE] it is tried to load the global data object from a workspace file in CM.ini()
workspace.write = FALSE, # if [TRUE] a workspace with the global data object will be written in CM.writeData()
workspace.replace = FALSE, # if [TRUE] a workspace will be replaced when existing in CM.writeData()
workspace.filename = "user_workspace.RData", # the filename used in CM.ini() and CM.writeData()
# input settings
input.dir = "input", # the directory from which all input files will be read in by CM.ini()
input.sep = "\t", # the column separator sign, e.g. ",", ";", "\t" (tab) passed to read.table (?read.table for more information)
input.col.easting = "POINT_X", # the column name for the x-value
input.col.northing = "POINT_Y", # s.a.
input.col.elevation = "POINT_Z", # s.a.
input.units = "m", # units of input coordinates (will be used for axis labels in plotting functions)
input.col.bank = "Name", # the column name of the side (left/right bank)
bank.code.left = "left", # the string code used for the left bank
bank.code.right = "right", # the string code used for the right bank
bank.reverse.left = FALSE, # reverse bank points of left bank from input data
bank.reverse.right = FALSE, # reverse bank points of right bank from input data
# output settings
output.replace = FALSE, # if [TRUE] the output files are replaced when existing in CM.writeFiles()
output.write.centerline = FALSE, # if [TRUE] the geometry of the centerline will be written in CM.writeFiles()
output.write.metrics = TRUE, # if [TRUE] the calculated channel metrics will be written in CM.writeFiles()
output.write.metrics.d = TRUE, # switch on/off the variable d.r and d.l (distances from centerline to banks)
output.write.metrics.w = TRUE, # switch on/off the variable w (channel width)
output.write.metrics.r = TRUE, # switch on/off the variable r.r and r.l (direction factor of d.r and d.l)
output.write.metrics.diff = TRUE, # switch on/off the variable diff.r and diff.l (distances between two banks)
output.write.steps = FALSE, #
output.dir = "output",
output.sep = "\t",
# enable/disable plots and configure them
plot.polygoncheck = TRUE, # if [TRUE], a three-column plot is generated showing the entire river and both ends to rouhgly check the polygon consitency (see also CM.generatePolygon())
plot.polygoncheck.colors = FALSE, # if [TRUE], a polygoncheck will be colored
plot.planview = TRUE, # create a plan view overview plot
plot.planview.secondary = TRUE, # in the plan view plot, add a secodary data set for comparison (will be displayed in dashed lines)
plot.planview.bankpoints = FALSE, # in the plan view plot, add the bank points of a data set
plot.planview.bankpoints.col= FALSE, # if [TRUE] bank points will be colored by side (left/right)
plot.planview.bankpoints.interpolated = FALSE, # in the plan view plot, add the interpolated bank points of a data set
plot.planview.polygon = TRUE, # in the plan view plot, add the channel borders
plot.planview.voronoi = FALSE, # in the plan view plot, add voronoi polygons in plan view plot
plot.planview.cl.original = FALSE, # in the plan view plot, add the rough centerline (before smoothing)
plot.planview.cl.smoothed = TRUE, # in the plan view plot, add the smoothed centerline
plot.planview.cl.points = FALSE, # when a centerline is plotted should the points representing the line be emphasized
plot.planview.cl.tx = FALSE, # in the plan view plot, add a label with the number next to the centerline points
plot.planview.cl.selection = TRUE, # if [TRUE] and plot window is determined by cl points (see docu) the cl points are highlighted
plot.planview.cl.binned = FALSE, # if [TRUE] plot the re-binned centerline produced by CM.resampleCenterline()
plot.planview.transects = FALSE, # in the plan view plot, add transects (perpendiculars to centerline)
plot.planview.transects.len = 20, # give the length of transects in the unit of the input coordinates
plot.planview.dist2banks = TRUE, # in the plan view plot, add transect segments from centerline to the banks (left and right)
plot.planview.grid = TRUE, # in the plan view plot, add a grid in the background
plot.planview.grid.dist = NULL, # the distance of the grid lines in the unit of the input coordinates, if NULL it will be calculated automatically
plot.planview.legend = TRUE, # in the plan view plot, add a legend
plot.planview.legend.pos = "topleft", # keyword to position legend (see ?legend)
plot.planview.scalebar = TRUE, # in the plan view plot, add a scalebar (width of one plot.planview.grid.dist)
plot.planview.use.names = TRUE, # if [TRUE] set names will be used for display, otherwise "set1", "set2", etc.
plot.metrics.use.names = TRUE, # if [TRUE] set names will be used for display, otherwise "set1", "set2", etc.
plot.metrics.width = TRUE, # if [TRUE] plot width
# plot options
plot.zoom = TRUE, # if [TRUE] the plan view plot is zoomed in (see also CM.plotPlanView())
plot.zoom.extent.length = NULL, # zoom window extent for the plan view plot in the unit of the input coordinates
plot.zoom.extent = "e1", # applied zoom window name (see also CM.plotPlanView())
plot.zoom.extents = list( # presets (customizable list) of zoom windows
e1 = c(400480, 3103130),
e2 = c(399445, 3096220),
e3 = c(401623, 3105925)
),
plot.cl.range = "cl1", # applied zoom cl range (see also CM.plotPlanView)
plot.cl.ranges = list( # presets (customizable list) of cl ranges
cl1 = c(1235, 1260)
),
plot.cl.range.use.reference = TRUE, # determines whether to look for reference centerline [TRUE] or current centerline when centering around cl.range
plot.to.file = FALSE, # if [TRUE] all plots will be copied to file devices
plot.to.pdf = TRUE, # if [TRUE] the plot will be saved as pdf
plot.to.png = TRUE, # if [TRUE] the plot will be saved as png
plot.index = 0, # numbering for filenames (see also CM.plotPlanView())
plot.directory = "plots/", # directory for saving plots if plot.to.file = TRUE
plot.filename = "documentation", # plot file name
# model parameters
force.calc.voronoi = FALSE, # if [TRUE] the voronoi polygons are always re-calculated and never taken from cache
force.calc.cl = FALSE, # if [TRUE] the centerline is always re-calculated and never taken from cache
bank.interpolate = TRUE, # if [TRUE] the provided bank points are linearly interpolated to generate a denser polygon (see CM.generatePolygon())
bank.interpolate.max.dist = 6, # if bank.interpolate is [TRUE] this is the maximum distance all bank points will have
bank.reduce = FALSE, # if [TRUE] the provided bank points are reduced by points that are closer to each other than bank.reduce.min.dist
bank.reduce.min.dist = 0.5, # if bank.reduce is [TRUE] this is the minimum distance all bank point will have
bank.filter2.max.it = 20, # number of the maximum iterations for filter 2 to prevent the program to run infinitely
centerline.smoothing.width = 7, # smoothing window width of mean filter in number of observations (see CM.calculateCenterline())
centerline.local.slope.range= 15,
transects.span = 3, # span of centerline points used for calculating the transects (see CM.processCenterline())
centerline.bin.length = 5, # for simplifying the centerline give the spacing in the unit of the input coordinates (see CM.reduceCenterline())
centerline.use.reference = FALSE, # sets method for calculating distance centerline to banks, if [FALSE] (default) each river profile will be compared to its own centerline, if [TRUE] the centerline of centerline.reference will be taken (see CM.processCenterline())
centerline.reference = "set1", # sets the reference data set if centerline.use.reference is [TRUE]
force.calc.metrics = FALSE, # if [TRUE] the metrics are always re-calculated and never taken from cache
calculate.metrics = TRUE, # if [TRUE] all centerline metrics are calculated (see CM.processCenterline())
calculate.metrics.dw = FALSE, # defines whether or not the change of the width shall be calculated
metrics.local.change.range = 5, # the upstream range over which metric changes are derived (e.g. width change)
# step identification after Zimmermann et. al 2008 [Zimmermann, A.E., Church, M., and Hassan, M. a., 2008, Identification of steps and pools from stream longitudinal profile data: Geomorphology, v. 102, no. 3–4, p. 395–406, doi: 10.1016/j.geomorph.2008.04.009.)]
steps.identify = FALSE,
steps.verbose = FALSE, # should there be information printed to the screen during step identification
steps.thalweg.dist = "3d", # chose method of distance calculation "3d" or "2d"
steps.minimum.step.length = 2.25, # as percentage of Wb [%]
steps.maximum.step.length = 200, # as percentage of Wb [%]
steps.minimum.pool.length = 10, # as percentage of Wb [%]
steps.minimum.residual.depth= 0.23, # as percentage of Wb [%]
steps.minimum.drop.height = 3.3, # as percentage of Wb [%]
steps.bank.full.width.fix = TRUE, # TRUE: use a fix bank full width for the whole stream, FALSE: calculate from banks
steps.bank.full.width = 3.7, # [m]
steps.average.slope.fix = FALSE,
steps.average.slope = 12.5, # 8.34, #12.5, # [deg]
# ignore
dummy = TRUE
)
notice("load parameters", TRUE)
# par.set is not specified: return default or existing parameter set
if(is.null(par.set)){
# set to default
par = par.default
tx = "default parameters"
}
# par.set is a filename: open file and merge with defaults
if(typeof(par.set) == "character"){
# check if parameter file exists
if(!file.exists(par.set)) error(paste("parameter file ", par.set, " does not exist!", sep=""))
# source parameter file
source(par.set, local=TRUE)
# check for a valid par list
if(!exists("par")) error(paste("parameter file", par.set, "does not contain a parameter list!"))
if(typeof(par) != "list") error(paste("parameter file", par.set, "does not contain a parameter list!"))
# merge with defaults (specified parameters have higher priorities
par = modifyList(par.default, par)
tx = paste("parameters from file '", par.set, "' merged with defaults", sep="")
}
if(typeof(par.set) == "list"){
par = modifyList(par.default, par.set)
tx = "passed parameters merged with defaults"
}
# manipulate defaults
if(is.null(par$centerline.smoothing.width)) par$centerline.smoothing.width = ceiling(par$bank.interpolate.max.dist)
notice(paste("parameter set:", tx))
return(par)
}
AntoniusGolly/cmgo documentation built on Sept. 24, 2021, 1:33 a.m.
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Defines functions CM.par
Documented in CM.par
#' Get the parameter object
#'
#' Create a parameter list containing all model and plotting parameters. Depending on the arguments passed to
#' \code{CM.par()}, the parameter list is either created from the defaults or from a specified parameter file.
#'
#' \code{CM.par()} creates or renews a parameter list based on the arguments passed to it. The list contains all
#' model and plot parameters and is stored within the global data object, for example \code{cmgo.obj$par}
#' (see \link[=cmgo]{package documentation}). Thus, the returned parameter object must be assigned to the global data
#' object as in \code{cmgo.obj$par = CM.par()}.
#'
#' If you call \code{CM.par()} without arguments (example #1), the default parameter list
#' is returned (see section "All default parameters and their defaults"). For larger projects, it can be desired to easily switch between
#' parameter sets, for example to reproduce different plots. You can save these customized parameter sets in files
#' (see section "Make a custom parameter file"). These files are loaded with \code{CM.par("path_to_parameter_file")} (example #2). The file is
#' \strong{not required} to host \strong{all} parameters, since the list will be merged with the defaults on loading. That means, a parameter file
#' has to host only those parameters differing from the defaults. As a third option, you can pass directly a list to
#' \code{CM.par()} (example #3). The directly passed parameters will be merged with defaults, as well.
#'
#' @template section_all_default_parameters
#'
#' @section Make a custom parameter file:
#' Create an empty .r-file with the following code:\preformatted{
#' par = list(
#' plot.to.file = TRUE,
#' other_par = "value"
#' # other_par = "other value"
#' )
#' }
#' A full list of available parameters can be found in the paragraph "All parameters and their defaults" above. In a parameter file you
#' don't have to specify \strong{all} parameters. Just list parameters that you like to differ from the defaults. The parameter object that
#' will be created by CM.par() if you specify a file name will be merged with the defaults, where specified parameters overwrite the defaults.
#'
#' @param par.set either NULL (default parameters are returned), of type string to specify a filename or of type list to specify parameters
#' @return The resulting parameters list.
#' @author Antonius Golly
#' @examples
#' # instantiate your global data object first, for example with CM.ini()
#' cmgo.obj = list()
#'
#' # example #1: get the default parameters
#' cmgo.obj$par = CM.par()
#'
#' # example #2: get parameters from a configuration file (see also "Make a custom parameter file")
#' #cmgo.obj$par = CM.par("par/custom_parameters.r")#'
#'
#' # example 3: get modified default parameters
#' cmgo.obj$par = CM.par(list(
#' plot.to.file = TRUE,
#' plot.directory = "/my_figures"
#' ))
#'
#' @export CM.par
CM.par <- function(par.set=NULL){
notice = function(x,prim=FALSE){cat(paste((if(prim) "\n--> " else " "), x, sep=""), sep="\n")}
error = function(x){stop(x, call.=FALSE)}
par.default = list(
# name of the parameter set
name = "default",
version = "0.2.0",
# workspace
workspace.read = TRUE, # if [TRUE] it is tried to load the global data object from a workspace file in CM.ini()
workspace.write = FALSE, # if [TRUE] a workspace with the global data object will be written in CM.writeData()
workspace.replace = FALSE, # if [TRUE] a workspace will be replaced when existing in CM.writeData()
workspace.filename = "user_workspace.RData", # the filename used in CM.ini() and CM.writeData()
# input settings
input.dir = "input", # the directory from which all input files will be read in by CM.ini()
input.sep = "\t", # the column separator sign, e.g. ",", ";", "\t" (tab) passed to read.table (?read.table for more information)
input.col.easting = "POINT_X", # the column name for the x-value
input.col.northing = "POINT_Y", # s.a.
input.col.elevation = "POINT_Z", # s.a.
input.units = "m", # units of input coordinates (will be used for axis labels in plotting functions)
input.col.bank = "Name", # the column name of the side (left/right bank)
bank.code.left = "left", # the string code used for the left bank
bank.code.right = "right", # the string code used for the right bank
bank.reverse.left = FALSE, # reverse bank points of left bank from input data
bank.reverse.right = FALSE, # reverse bank points of right bank from input data
# output settings
output.replace = FALSE, # if [TRUE] the output files are replaced when existing in CM.writeFiles()
output.write.centerline = FALSE, # if [TRUE] the geometry of the centerline will be written in CM.writeFiles()
output.write.metrics = TRUE, # if [TRUE] the calculated channel metrics will be written in CM.writeFiles()
output.write.metrics.d = TRUE, # switch on/off the variable d.r and d.l (distances from centerline to banks)
output.write.metrics.w = TRUE, # switch on/off the variable w (channel width)
output.write.metrics.r = TRUE, # switch on/off the variable r.r and r.l (direction factor of d.r and d.l)
output.write.metrics.diff = TRUE, # switch on/off the variable diff.r and diff.l (distances between two banks)
output.write.steps = FALSE, #
output.dir = "output",
output.sep = "\t",
# enable/disable plots and configure them
plot.polygoncheck = TRUE, # if [TRUE], a three-column plot is generated showing the entire river and both ends to rouhgly check the polygon consitency (see also CM.generatePolygon())
plot.polygoncheck.colors = FALSE, # if [TRUE], a polygoncheck will be colored
plot.planview = TRUE, # create a plan view overview plot
plot.planview.secondary = TRUE, # in the plan view plot, add a secodary data set for comparison (will be displayed in dashed lines)
plot.planview.bankpoints = FALSE, # in the plan view plot, add the bank points of a data set
plot.planview.bankpoints.col= FALSE, # if [TRUE] bank points will be colored by side (left/right)
plot.planview.bankpoints.interpolated = FALSE, # in the plan view plot, add the interpolated bank points of a data set
plot.planview.polygon = TRUE, # in the plan view plot, add the channel borders
plot.planview.voronoi = FALSE, # in the plan view plot, add voronoi polygons in plan view plot
plot.planview.cl.original = FALSE, # in the plan view plot, add the rough centerline (before smoothing)
plot.planview.cl.smoothed = TRUE, # in the plan view plot, add the smoothed centerline
plot.planview.cl.points = FALSE, # when a centerline is plotted should the points representing the line be emphasized
plot.planview.cl.tx = FALSE, # in the plan view plot, add a label with the number next to the centerline points
plot.planview.cl.selection = TRUE, # if [TRUE] and plot window is determined by cl points (see docu) the cl points are highlighted
plot.planview.cl.binned = FALSE, # if [TRUE] plot the re-binned centerline produced by CM.resampleCenterline()
plot.planview.transects = FALSE, # in the plan view plot, add transects (perpendiculars to centerline)
plot.planview.transects.len = 20, # give the length of transects in the unit of the input coordinates
plot.planview.dist2banks = TRUE, # in the plan view plot, add transect segments from centerline to the banks (left and right)
plot.planview.grid = TRUE, # in the plan view plot, add a grid in the background
plot.planview.grid.dist = NULL, # the distance of the grid lines in the unit of the input coordinates, if NULL it will be calculated automatically
plot.planview.legend = TRUE, # in the plan view plot, add a legend
plot.planview.legend.pos = "topleft", # keyword to position legend (see ?legend)
plot.planview.scalebar = TRUE, # in the plan view plot, add a scalebar (width of one plot.planview.grid.dist)
plot.planview.use.names = TRUE, # if [TRUE] set names will be used for display, otherwise "set1", "set2", etc.
plot.metrics.use.names = TRUE, # if [TRUE] set names will be used for display, otherwise "set1", "set2", etc.
plot.metrics.width = TRUE, # if [TRUE] plot width
# plot options
plot.zoom = TRUE, # if [TRUE] the plan view plot is zoomed in (see also CM.plotPlanView())
plot.zoom.extent.length = NULL, # zoom window extent for the plan view plot in the unit of the input coordinates
plot.zoom.extent = "e1", # applied zoom window name (see also CM.plotPlanView())
plot.zoom.extents = list( # presets (customizable list) of zoom windows
e1 = c(400480, 3103130),
e2 = c(399445, 3096220),
e3 = c(401623, 3105925)
),
plot.cl.range = "cl1", # applied zoom cl range (see also CM.plotPlanView)
plot.cl.ranges = list( # presets (customizable list) of cl ranges
cl1 = c(1235, 1260)
),
plot.cl.range.use.reference = TRUE, # determines whether to look for reference centerline [TRUE] or current centerline when centering around cl.range
plot.to.file = FALSE, # if [TRUE] all plots will be copied to file devices
plot.to.pdf = TRUE, # if [TRUE] the plot will be saved as pdf
plot.to.png = TRUE, # if [TRUE] the plot will be saved as png
plot.index = 0, # numbering for filenames (see also CM.plotPlanView())
plot.directory = "plots/", # directory for saving plots if plot.to.file = TRUE
plot.filename = "documentation", # plot file name
# model parameters
force.calc.voronoi = FALSE, # if [TRUE] the voronoi polygons are always re-calculated and never taken from cache
force.calc.cl = FALSE, # if [TRUE] the centerline is always re-calculated and never taken from cache
bank.interpolate = TRUE, # if [TRUE] the provided bank points are linearly interpolated to generate a denser polygon (see CM.generatePolygon())
bank.interpolate.max.dist = 6, # if bank.interpolate is [TRUE] this is the maximum distance all bank points will have
bank.reduce = FALSE, # if [TRUE] the provided bank points are reduced by points that are closer to each other than bank.reduce.min.dist
bank.reduce.min.dist = 0.5, # if bank.reduce is [TRUE] this is the minimum distance all bank point will have
bank.filter2.max.it = 20, # number of the maximum iterations for filter 2 to prevent the program to run infinitely
centerline.smoothing.width = 7, # smoothing window width of mean filter in number of observations (see CM.calculateCenterline())
centerline.local.slope.range= 15,
transects.span = 3, # span of centerline points used for calculating the transects (see CM.processCenterline())
centerline.bin.length = 5, # for simplifying the centerline give the spacing in the unit of the input coordinates (see CM.reduceCenterline())
centerline.use.reference = FALSE, # sets method for calculating distance centerline to banks, if [FALSE] (default) each river profile will be compared to its own centerline, if [TRUE] the centerline of centerline.reference will be taken (see CM.processCenterline())
centerline.reference = "set1", # sets the reference data set if centerline.use.reference is [TRUE]
force.calc.metrics = FALSE, # if [TRUE] the metrics are always re-calculated and never taken from cache
calculate.metrics = TRUE, # if [TRUE] all centerline metrics are calculated (see CM.processCenterline())
calculate.metrics.dw = FALSE, # defines whether or not the change of the width shall be calculated
metrics.local.change.range = 5, # the upstream range over which metric changes are derived (e.g. width change)
# step identification after Zimmermann et. al 2008 [Zimmermann, A.E., Church, M., and Hassan, M. a., 2008, Identification of steps and pools from stream longitudinal profile data: Geomorphology, v. 102, no. 3–4, p. 395–406, doi: 10.1016/j.geomorph.2008.04.009.)]
steps.identify = FALSE,
steps.verbose = FALSE, # should there be information printed to the screen during step identification
steps.thalweg.dist = "3d", # chose method of distance calculation "3d" or "2d"
steps.minimum.step.length = 2.25, # as percentage of Wb [%]
steps.maximum.step.length = 200, # as percentage of Wb [%]
steps.minimum.pool.length = 10, # as percentage of Wb [%]
steps.minimum.residual.depth= 0.23, # as percentage of Wb [%]
steps.minimum.drop.height = 3.3, # as percentage of Wb [%]
steps.bank.full.width.fix = TRUE, # TRUE: use a fix bank full width for the whole stream, FALSE: calculate from banks
steps.bank.full.width = 3.7, # [m]
steps.average.slope.fix = FALSE,
steps.average.slope = 12.5, # 8.34, #12.5, # [deg]
# ignore
dummy = TRUE
)
notice("load parameters", TRUE)
# par.set is not specified: return default or existing parameter set
if(is.null(par.set)){
# set to default
par = par.default
tx = "default parameters"
}
# par.set is a filename: open file and merge with defaults
if(typeof(par.set) == "character"){
# check if parameter file exists
if(!file.exists(par.set)) error(paste("parameter file ", par.set, " does not exist!", sep=""))
# source parameter file
source(par.set, local=TRUE)
# check for a valid par list
if(!exists("par")) error(paste("parameter file", par.set, "does not contain a parameter list!"))
if(typeof(par) != "list") error(paste("parameter file", par.set, "does not contain a parameter list!"))
# merge with defaults (specified parameters have higher priorities
par = modifyList(par.default, par)
tx = paste("parameters from file '", par.set, "' merged with defaults", sep="")
}
if(typeof(par.set) == "list"){
par = modifyList(par.default, par.set)
tx = "passed parameters merged with defaults"
}
# manipulate defaults
if(is.null(par$centerline.smoothing.width)) par$centerline.smoothing.width = ceiling(par$bank.interpolate.max.dist)
notice(paste("parameter set:", tx))
return(par)
}
R Package Documentation
Browse R Packages
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