Calculation of the Integrated Flow of Particles Between Polygons

Description

Calculate the flow of particles between polygons by two integration methods: integration by a cubature method and integration on a grid of points.

Details

Author(s)

Annie Bouvier <annie.bouvier@inra.fr>

Create an object of class 'poly'

Description

Create an object of class "poly" from two vectors or from a matrix.

Usage

as.poly(x, y=NULL)

Arguments

Value

An object of class "poly", i.e a two-columns matrix labelled "xcoord", "ycoord".

See Also

crpoly

Examples

# A triangle
a <- as.poly(matrix(c(2,2,2,3,3,3), ncol=2, byrow=TRUE))

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

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)*\frac{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)

Create an object of class 'listpoly' from objects of class 'poly'

Description

Create an object of class "listpoly" from objects of class "poly"

Usage

crlistpoly(...)

Arguments

Value

An object of class "listpoly" : a list where each component is a 'poly' object (see poly-class).

See Also

poly-class

Examples

# A triangle:
a <- as.poly(matrix(c(2,2,2,3,3,3), ncol=2, byrow=TRUE))
# A square:
b <- as.poly(matrix(c(2.5,2,2.5,2.5,3,2.5,3,2), ncol=2, byrow=TRUE))
# The both:
 z <- crlistpoly(a,b)

Create un object of class 'poly' by clicking on points

Description

Create un object of class "poly" by clicking on a graphic: the locations of the clicks will be the vertices of the polygon.

Usage

crpoly()

Details

The system prompts the user to enter points on the current graphic using the mouse or other pointing device. The points are joined on the screen with the current line symbol. A polygon of the points entered is drawn on the current graphics device and returned as a 'poly' object.

Value

An object of class "poly" i.e a two-columns matrix with the coordinates.

Warning

A plot should be drawn on the current graphics device before.

See Also

as.poly, getpoly of the package splancs

Examples

## Not run: plot(x=c(1,10), y=c(1,10), type='n')
## Not run: a<-crpoly()
#    Enter points with button 1
#    Finish with button 2

Generic for 'export'

Description

Generic function for 'export'

Usage

export(x, filename)

Arguments

Value

None.

See Also

export.listpoly

export.default method

Description

Default method export

Usage

  ## Default S3 method:
export(x, filename)

Arguments

Value

None.

See Also

export.listpoly

Create a polygons file in format 1.

Description

From an object of class "listpoly", create a polygons file for input to the software CaliFloPP or to the function califlopp. The format of this file corresponds to the format 1 of them, i.e you should set the param input to 1 when used as input to califlopp.

Usage

  ## S3 method for class 'listpoly'
export(x, filename)

Arguments

Value

None.

Individual pollen dispersion function

Description

From a vector of distances, calculate the individual pollen dispersion function used in Genesys

Usage

fpollen(point)

Arguments

Value

The calculated dispersions.

References

Colbach, N. and Clermont-Dauphin, C. and Meynard, J.M. Genesys: a model of the influence of cropping system on gene escape from herbicide tolerant rapeseed crops to rape volunteers. i. temporal evolution of a population of rapeseed volunteers in a field. Agriculture, Ecosystems and Environnement, 83:235-253, 2001.

See Also

fseed

Examples

distance = seq(1,1.5, by=0.05)
a=matrix(distance, ncol=1)
b= apply(a,1,fpollen)
par(pty="s")
plot(x=distance, y =b)
lines(x=distance, y = apply(a,1,fseed))

Individual seed dispersion function

Description

From a vector of distances, calculate the individual seed dispersion function used in Genesys

Usage

fseed(point)

Arguments

Value

The calculated dispersions.

References

Colbach, N. and Clermont-Dauphin, C. and Meynard, J.M. Genesys: a model of the influence of cropping system on gene escape from herbicide tolerant rapeseed crops to rape volunteers. i. temporal evolution of a population of rapeseed volunteers in a field. Agriculture, Ecosystems and Environnement, 83:235-253, 2001.

See Also

fpollen

Examples

distance = seq(1,1.5, by=0.05)
a=matrix(distance, ncol=1)
b= apply(a,1,fseed)
par(pty="s")
plot(x=distance, y =b)

Generate a regular grid of polygons

Description

Generate a regular grid of polygons and optionally write them on a file for input to califlopp

Usage

generPoly(step = 5, np = 10, file = "data", plot = TRUE)

Arguments

Details

When file is not NULL, a polygons file is created. It is in the format 2 of califlopp and the values separator is tabulate.

Value

An object of class "listpoly"

Note

The polygons are numbered from 1, from the left to the right, then from bottom to top.

See Also

"listpoly-class", plot.listpoly

Examples

a <- generPoly(np=3, file=NULL)

Generate the neighbors of each polygon of a regular grid

Description

For each polygon of a regular grid, generate the indexes of its neighbour polygons

Usage

generVois(np = 10, nvois = 1)

Arguments

Details

For each polygon P of a regular grid made of np polygons along each axis, the indexes of its neighbours are generated: the neighbours are the polygons included in the square made of nvois polygons below, above, at the right and left sides of P, in the limit of the grid bounds.

Value

A two-columns matrix, of all pairs of neighbourgs.

See Also

generPoly, califlopp

Examples

generVois(np=3)

Read a result-file of 'califlopp'

Description

Return the results stored on a file created by califlopp.

Usage

getRes(ficres)

Arguments

Value

A data.frame with as many rows as pairs of polygons on the file. The columns are:

Note

This function works when RCALI has been configured with OUTPUT_FILE_FORMAT = LIGHT only (this is the default; see the file src/caliconfig.h to be sure your configuration is compatible).

Details about the returned values can be found in the Reference Manual.

See Also

califlopp

Class 'listpoly'

Description

A class to store a suite of polygons and its methods.

Objects from the Class

Objects can be created by calls of the function crlistpoly and generPoly

Slots

list

List where each component is an object of poly-class

Methods

plot.listpoly, range.listpoly, export.listpoly

See Also

poly-class

Plot of an object of class 'listpoly'

Description

Plot all the polygons of an object of class "listpoly", optionnaly with colors.

Usage

## S3 method for class 'listpoly'
plot(x, add = F, color = T, ...)

Arguments

Value

None.

Note

To make a zoom, type in: zoom() (see 'splancs') then use this function with argument “add=TRUE”.

Plot of an object of class 'poly'

Description

Plot an object of class "poly" via the function polymap of the library splancs.

Usage

## S3 method for class 'poly'
plot(x, ...)

Arguments

Value

None.

Class 'poly'

Description

A class to store the coordinates of a polygons and its methods.

Objects from the Class

Objects can be created by calls of the functions as.poly and crpoly

Slots

m

Matrix with two columns xcoord and ycoord

Methods

plot.poly

See Also

listpoly-class

Range of the coordinates of an object of class 'listpoly'

Description

Return the minimum and maximum coordinates over all the polygones of an object of class "listpoly".

Usage

## S3 method for class 'listpoly'
range(x, ...)

Arguments

Value

Matrix ; its two columns are “xrange” and “yrange” and its two lines are “lower” and “upper”.

Read a polygons file in format 1

Description

Create an object of class "listpoly" from the values read on a polygons file in format 1.

Usage

readpoly1(filename, delim=" ")

Arguments

Value

An object of class "listpoly", i.e a list, each component of which is an object of class "poly"

See Also

readpoly2

Read a polygons file in format 2

Description

Create an object of class "listpoly" from the values read on a polygons file in format 2.

Usage

readpoly2(filename, delim="\t")

Arguments

Value

An object of class "listpoly", i.e a list, each component of which is an object of class "poly"

See Also

readpoly1