califlopp: Calculation of the Integrated Flow of Particles between...
In RCALI: Calculation of the Integrated Flow of Particles Between Polygons
califlopp R Documentation
Calculation of the Integrated Flow of Particles
between Polygons
Description
Calculation of the flow of particles between polygons by two integration methods: integration by a cubature method and
integration on a grid of points.
Usage
califlopp(file, dispf=c(1,2), param=NULL, resfile = NULL)
Arguments
file
Pathname of the polygons-file. See details.
dispf
The required dispersion functions. Vector of integers or vector of R functions. The maximum length of this vector is 5.
If vector of integers, the dispersion functions are
then compiled. Five are provided. To modify them, see
Details.
By default,
1 is for dispersal of oilseed rape pollen, 2 for dispersal
of oilseed rape seed (dispersals of oilseed rape are the ones
defined in GeneSys - see References),
3 for the constant function, 4 for an
anisotropic version of the dispersal of yellow rust of wheat defined
in Soubeyrand and all, 5 for a discontinuous function.
These functions are viewable in the C file src/functions.cc.
To modify them, see Details.
If vector of functions, the dispersion functions are coded in R
(more time consuming than compiled version). Two R dispersal functions are provided, fpollen and
fseed, the functions used in Genesys.
To specify your own function, see details.
param
Optional list of parameters. Valid components are
input, output,
verbose, warn.poly, warn.conv,delim,
poly, send.and.receive, method, dz, dp.
In addition, when method is “cub”: maxpts,
reler, abser, tz.
When method is “grid”: seed,
step, nr.
See details.
resfile
Optional pathname of a result-file. When set,
the results are written on it. This file can be read
by using function
getRes or read.table. See details, as to the content of the file.
Details
The polygons-file
The coordinates of the polygons should be provided in an ASCII file,
denoted here "polygons-file". The unit is the meter. The vertices should
be ordered clockwise. The polygons can be closed
or not, but without holes. The first line contains the number of polygons.
The following lines depend of the input
parameter:
input=1 Two lines per polygon: on the first one,
an identifier (a positive
integer), followed by the x-coordinates,
on the second one, the same identifier
followed by the y-coordinates. The function
export.listpoly generates such a file from R structures
input=2 Three lines per polygon: on the first one,
an identifier (a positive
integer), followed by a name for the polygon and
by the number of its vertices, on the second one, the x-coordinates,
and on the third one, the y-coordinates.
The individual dispersion functions
The individual dispersion functions can either be compiled
or R functions.
-
Compiled function: Five compiled dispersal functions are
provided (see argument dispf). To replace them by yours,
you have to download the source of RCALI,
modify and compile it.
Suppose that you have download the tar-archive
in the directory MyDir.
The steps to customize the dispersion functions are:
1/ Replace one or several functions in
MyDir/RCALI/src/functions.cc by yours:
The dispersion function has one argument,
the current point, p, of class Point.
You can use p.getX()
and p.getY() to get the coordinates of the current point
(in meters*SCALE, where SCALE is the rescaling
parameter defined in the file src/calicinfig.h),
p.dist0(), the distance of p
from the origin (in meters*SCALE)
and p.angle0(), the angle (in degrees, in [-PI, +PI]) between the line (0,p)
and the horizontal line.
2/ Create a directory MyDir/RCALI/libs,
place you in MyDir/RCALI/src and type in:
R CMD SHLIB -o ../libs/RCALI.so *.cc
to create the compiled shared library.
3/ To use in a R-session:
source("MyDir/RCALI/R/sourceDir.R")
sourceDir("MyDir/RCALI/R")
dyn.load("MyDir/RCALI/libs/RCALI.so")
The help-files are viewable by opening in a browser
MyDir/RCALI/inst/doc/html/00Index.html
You can also build the tar.gz file again, after modifications,
and install it as a library
by using the standard R commands R CMD build and
R CMD INSTALL --html.
R function: Two R dispersal functions are provided, fpollen and
fseed, the functions used in Genesys.
You can define your own R dispersal function:
it should have one vector
argument, the localization of the current point, p.
The first element of this vector is the distance of p from the origin
(in meters) and the second one is the angle (in degrees, in [-PI, +PI]) between the line (0,p)
and the horizontal line (i.e, stating x and y are the coordinates
of p, the angle is
atan2(y,x)*180/PI)
The parameters
The argument param is a list which valid components are:
input format of the polygons-file. 1 or 2 (see above).
Default 2
output output required on the screen:
0 nothing, 1: all results, 2: progression numbers,
3: the integrated flows and their means per squared meter.
Default 1
verbose TRUE, if output is required about polygons convexity
and landscape translation. Default FALSE
warn.poly TRUE, if output is required about polygons simplification. Default FALSE
warn.conv TRUE, if output is required when
cubature convergence is not reached. Default TRUE
delim separator character between values in the polygons-file. Default: tabulate
send.and.receive TRUE, if results are required from
sending polygons to target polygons and from target polygons to
sending polygons (case of anisotropic functions). Default FALSE
poly required pairs of polygons.
List of vectors of length 2, or two-columns matrix.
If only one pair is required, it may be a vector of length 2.
Default: all pairs of polygons.
method string equal to cub for cubature method, grid for the grid
method. Default: cub
dz integer vector, whose length is greater or equal to the number of
required dispersion functions. dz[i] is the distance in meters
beyond which the ist dispersion function is considered as
nul. Default in a standard configuration: 0,21,0,1000,0
for functions number 1 to 5, respectively.
dp integer vector, whose length is greater or equal
to the number of
required dispersion functions. dp[i] is the distance in meters
beyond which the ist dispersion function is calculated between
centroids only. Default in a standard configuration: 100, 0, 0,
500, 0
for functions number 1 to 5, respectively.
In addition, when method is cub:
maxpts maximal
number of evaluation points required for each function.
Vector of length equal to the number of required functions.
Default in a standard configuration: 100000
reler relative error required for each function.
Vector of length equal to the number of required functions.
Should be positive when method is cubature.
Default in a standard configuration: 1.0e-3
abser absolute error required for each function.
Vector of length equal to the number of required functions.
Should be positive when method is cubature.
Default in a standard configuration: 1.0e-3
tz integer vector, whose length is greater
or equal to the number of
required dispersion functions. Mode of triangulation for the
cubature method.
tz[i] should be 1, if, for the ist dispersion
function,
triangulation from (0,0) has to be done
when (0,0) is included in the integration area and, 0 if not.
1 is recommended when the dispersion function is very "sharp"
at the origin. Default in a standard configuration: 0,1,0,0,0
for functions number 1 to 5, respectively.
When method is grid:
seed seed of the random generator.
step step of the grid on the x-axis and on the y-axis
in meter. Vector of length 2.
nr maximal number of replications or grids.
The result-file
When the argument resfile is set, a file is created.
On this file, the values are separated by tabulates.
Its contains, when the method is cub,
on the first line: "npoly:", "input-file:",
"nfunc:", "method:", each of these identifiers
followed by the actual values.
on each of the following lines, the results for a couple of
polygons: the identifiers of both polygons;
the integrated flow divided by the area of the second
polygon, for
each dispersal function;
the areas of both polygons; then, for
each dispersal function,
the integrated flow, the lower and upper bounds
of the confidence interval, the absolute error, and the
number of evaluations.
Its contains, when the method is grid,
on the first line: "npoly:", "input-file:",
"nfunc:", "method:", "stepx:", "stepy:", each of these identifiers
followed by the actual values.
on each of the following lines, the results for a couple of
polygons: the identifiers of both polygons;
the integrated flow divided by the area of the second
polygon, for
each dispersal function;
the areas of both polygons; then, for
each dispersal function,
the integrated flow, and the standard deviation.
This file can be read in a R-session by using the function
getRes or read.table, with option
skip=1.
Value
Nothing. To store the results, set the argument resfile,
then use the function
getRes or read.table, with option
skip=1
Side effect
This function creates a temporary file to store the
parameters, usually in the directory tmp of the user. This file
is destroyed at the end of execution.
Author(s)
A. Bouvier
References
- The CaliFloPP software: http://genome.jouy.inra.fr/logiciels/califlopp/
- Main reference paper: A. Bouvier, K. Kieu, K. Adamczyk, and H. Monod. Computation of
integrated flow of particles between polygons. Environmental Modelling
& Software, 24:843–849, 2009.
- N. Colbach, and all.Genesys: a model of the influence of cropping
system on gene escape from herbicide tolerant rapeseed crops to rape
volunteers. Agriculture, Ecosystems and Environnement, 83:235–270, 2001.
See Also
getRes
Examples
# Grid method with compiled constant and seed dispersion functions:
param <- list(method="grid", grid=list(step=c(50,50)))
## Not run: califlopp("MyPolygonsFile",dispf=c(3,1), param=param)
# Cubature method with a R dispersion function:
param <- list( output=1, input=2, dz=0, dp=100, tz=0)
## Not run: califlopp("MyPolygonsFile", dispf=fpollen, param=param)
RCALI documentation built on Jan. 13, 2023, 5:12 p.m.
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| califlopp | R Documentation |
Calculation of the Integrated Flow of Particles between Polygons
Description
Calculation of the flow of particles between polygons by two integration methods: integration by a cubature method and integration on a grid of points.
Usage
califlopp(file, dispf=c(1,2), param=NULL, resfile = NULL)
Arguments
file |
Pathname of the polygons-file. See details. |
dispf |
The required dispersion functions. Vector of integers or vector of R functions. The maximum length of this vector is 5.
|
param |
Optional list of parameters. Valid components are
|
resfile |
Optional pathname of a result-file. When set,
the results are written on it. This file can be read
by using function
|
Details
The polygons-file
The coordinates of the polygons should be provided in an ASCII file,
denoted here "polygons-file". The unit is the meter. The vertices should
be ordered clockwise. The polygons can be closed
or not, but without holes. The first line contains the number of polygons.
The following lines depend of the input
parameter:
input=1Two lines per polygon: on the first one, an identifier (a positive integer), followed by the x-coordinates, on the second one, the same identifier followed by the y-coordinates. The function export.listpoly generates such a file from R structuresinput=2Three lines per polygon: on the first one, an identifier (a positive integer), followed by a name for the polygon and by the number of its vertices, on the second one, the x-coordinates, and on the third one, the y-coordinates.
The individual dispersion functions
The individual dispersion functions can either be compiled or R functions.
-
Compiled function: Five compiled dispersal functions are provided (see argument
dispf). To replace them by yours, you have to download the source ofRCALI, modify and compile it.
Suppose that you have download the tar-archive in the directory
MyDir. The steps to customize the dispersion functions are:1/ Replace one or several functions in
MyDir/RCALI/src/functions.ccby yours: The dispersion function has one argument, the current point,p, of classPoint. You can usep.getX()andp.getY()to get the coordinates of the current point (in meters*SCALE, whereSCALEis the rescaling parameter defined in the filesrc/calicinfig.h),p.dist0(), the distance ofpfrom the origin (in meters*SCALE) andp.angle0(), the angle (in degrees, in [-PI, +PI]) between the line (0,p) and the horizontal line.2/ Create a directory
MyDir/RCALI/libs, place you inMyDir/RCALI/srcand type in:R CMD SHLIB -o ../libs/RCALI.so *.cc
to create the compiled shared library.
3/ To use in a R-session:
source("MyDir/RCALI/R/sourceDir.R") sourceDir("MyDir/RCALI/R") dyn.load("MyDir/RCALI/libs/RCALI.so")The help-files are viewable by opening in a browser
MyDir/RCALI/inst/doc/html/00Index.htmlYou can also build the tar.gz file again, after modifications, and install it as a library by using the standard R commandsR CMD buildandR CMD INSTALL --html. R function: Two R dispersal functions are provided,
fpollenandfseed, the functions used in Genesys.
You can define your own R dispersal function: it should have one vector argument, the localization of the current point,p. The first element of this vector is the distance ofpfrom the origin (in meters) and the second one is the angle (in degrees, in [-PI, +PI]) between the line (0,p) and the horizontal line (i.e, statingxandyare the coordinates ofp, the angle is atan2(y,x)*180/PI)
The parameters
The argument param is a list which valid components are:
inputformat of the polygons-file. 1 or 2 (see above). Default 2outputoutput required on the screen: 0 nothing, 1: all results, 2: progression numbers, 3: the integrated flows and their means per squared meter. Default 1verboseTRUE, if output is required about polygons convexity and landscape translation. Default FALSEwarn.polyTRUE, if output is required about polygons simplification. Default FALSEwarn.convTRUE, if output is required when cubature convergence is not reached. Default TRUEdelimseparator character between values in the polygons-file. Default: tabulatesend.and.receiveTRUE, if results are required from sending polygons to target polygons and from target polygons to sending polygons (case of anisotropic functions). Default FALSEpolyrequired pairs of polygons. List of vectors of length 2, or two-columns matrix. If only one pair is required, it may be a vector of length 2. Default: all pairs of polygons.methodstring equal tocubfor cubature method,gridfor the grid method. Default:cubdzinteger vector, whose length is greater or equal to the number of required dispersion functions.dz[i]is the distance in meters beyond which theist dispersion function is considered as nul. Default in a standard configuration: 0,21,0,1000,0 for functions number 1 to 5, respectively.dpinteger vector, whose length is greater or equal to the number of required dispersion functions.dp[i]is the distance in meters beyond which theist dispersion function is calculated between centroids only. Default in a standard configuration: 100, 0, 0, 500, 0 for functions number 1 to 5, respectively.
In addition, when method is cub:
maxptsmaximal number of evaluation points required for each function. Vector of length equal to the number of required functions. Default in a standard configuration: 100000relerrelative error required for each function. Vector of length equal to the number of required functions. Should be positive when method is cubature. Default in a standard configuration: 1.0e-3abserabsolute error required for each function. Vector of length equal to the number of required functions. Should be positive when method is cubature. Default in a standard configuration: 1.0e-3tzinteger vector, whose length is greater or equal to the number of required dispersion functions. Mode of triangulation for the cubature method.tz[i]should be 1, if, for theist dispersion function, triangulation from (0,0) has to be done when (0,0) is included in the integration area and, 0 if not. 1 is recommended when the dispersion function is very "sharp" at the origin. Default in a standard configuration: 0,1,0,0,0 for functions number 1 to 5, respectively.
When method is grid:
seedseed of the random generator.stepstep of the grid on the x-axis and on the y-axis in meter. Vector of length 2.nrmaximal number of replications or grids.
The result-file
When the argument resfile is set, a file is created.
On this file, the values are separated by tabulates.
Its contains, when the method is cub,
on the first line: "npoly:", "input-file:", "nfunc:", "method:", each of these identifiers followed by the actual values.
on each of the following lines, the results for a couple of polygons: the identifiers of both polygons; the integrated flow divided by the area of the second polygon, for each dispersal function; the areas of both polygons; then, for each dispersal function, the integrated flow, the lower and upper bounds of the confidence interval, the absolute error, and the number of evaluations.
Its contains, when the method is grid,
on the first line: "npoly:", "input-file:", "nfunc:", "method:", "stepx:", "stepy:", each of these identifiers followed by the actual values.
on each of the following lines, the results for a couple of polygons: the identifiers of both polygons; the integrated flow divided by the area of the second polygon, for each dispersal function; the areas of both polygons; then, for each dispersal function, the integrated flow, and the standard deviation.
This file can be read in a R-session by using the function
getRes or read.table, with option
skip=1.
Value
Nothing. To store the results, set the argument resfile,
then use the function
getRes or read.table, with option
skip=1
Side effect
This function creates a temporary file to store the
parameters, usually in the directory tmp of the user. This file
is destroyed at the end of execution.
Author(s)
A. Bouvier
References
- The CaliFloPP software: http://genome.jouy.inra.fr/logiciels/califlopp/
- Main reference paper: A. Bouvier, K. Kieu, K. Adamczyk, and H. Monod. Computation of
integrated flow of particles between polygons. Environmental Modelling
& Software, 24:843–849, 2009.
- N. Colbach, and all.Genesys: a model of the influence of cropping
system on gene escape from herbicide tolerant rapeseed crops to rape
volunteers. Agriculture, Ecosystems and Environnement, 83:235–270, 2001.
See Also
getRes
Examples
# Grid method with compiled constant and seed dispersion functions:
param <- list(method="grid", grid=list(step=c(50,50)))
## Not run: califlopp("MyPolygonsFile",dispf=c(3,1), param=param)
# Cubature method with a R dispersion function:
param <- list( output=1, input=2, dz=0, dp=100, tz=0)
## Not run: califlopp("MyPolygonsFile", dispf=fpollen, param=param)
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