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Commit 9e3b1b5d authored by philippe.verley_ird.fr's avatar philippe.verley_ird.fr
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Deleted transpose function in utils.R since the C function is absent from... 

Deleted transpose function in utils.R since the C function is absent from utils.c. Deleted it as well from internal.Rd
Deleted utils.c and moved function triangulate to triangulate.c
Renamed C function triangulate into c_triangulate and updated triangulate.R
Added new file init.c to declare C and Fortran functions as recommanded by outputs of tools::package_native_routine_registration_skeleton(".")
Updated NAMESPACE "useDynLib(ads, .registration=TRUE)" as recommanded for R >= 3.4
Updated MD5
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DESCRIPTION
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− 2
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......@@ -13,8 +13,6 @@ Description: Perform first- and second-order multi-scale analyses derived from R
multivariate and marked mapped data in rectangular, circular or irregular shaped sampling windows, with tests of
statistical significance based on Monte Carlo simulations.
License: GPL-2
Packaged: 2015-01-13 12:09:18 UTC; root
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-01-13 14:49:23
RoxygenNote: 6.0.1
INDEX
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− 23
View file @ 9e3b1b5d
Allogny Spatial pattern of oaks suffering from frost shake in Allogny, France.
BPoirier Tree spatial pattern in Beau Poirier plot, Haye forest, France.
Couepia Spatial pattern of Couepia caryophylloides in Paracou, a canopy tree
species of French Guiana.
demopat Artificial data point pattern from \code{spatstat} package.
Paracou15 Spatial pattern of trees in plot 15 of Paracou experimental station,
French Guiana.
Couepia Spatial pattern of Couepia caryophylloides in Paracou, a canopy tree species of French Guiana.
demopat Artificial data point pattern from \code{spatstat} package.
Paracou15 Spatial pattern of trees in plot 15 of Paracou experimental station, French Guiana.
area.swin Area of a sampling window.
dval Multiscale local density of a spatial point pattern.
inside.swin Test wether points are inside a sampling window.
k12fun Multiscale second-order neigbourhood analysis of a bivariate spatial
point pattern.
k12val Multiscale local second-order neighbour density of a bivariate spatial
point pattern.
kdfun Multiscale second-order neigbourhood analysis of phylogentic/functional
spatial structure of a multivariate spatial point pattern.
kfun Multiscale second-order neigbourhood analysis of an univariate spatial
point pattern.
kmfun Multiscale second-order neigbourhood analysis of a marked spatial point
pattern.
kp.fun (Formerly ki.fun) Multiscale second-order neigbourhood analysis of a
multivariate spatial point pattern.
kpqfun (Formerly kijfun) Multiscale second-order neigbourhood analysis of a
multivariate spatial point pattern.
krfun Multiscale second-order neigbourhood analysis of a multivariate spatial
point pattern using Rao quadratic entropy.
ksfun Multiscale second-order neigbourhood analysis of a multivariate spatial
point pattern using Simpson diversity.
k12fun Multiscale second-order neigbourhood analysis of a bivariate spatial point pattern.
k12val Multiscale local second-order neighbour density of a bivariate spatial point pattern.
kdfun Multiscale second-order neigbourhood analysis of phylogentic/functional spatial structure of a multivariate spatial point pattern.
kfun Multiscale second-order neigbourhood analysis of an univariate spatial point pattern.
kmfun Multiscale second-order neigbourhood analysis of a marked spatial point pattern.
kp.fun (Formerly ki.fun) Multiscale second-order neigbourhood analysis of a multivariate spatial point pattern.
kpqfun (Formerly kijfun) Multiscale second-order neigbourhood analysis of a multivariate spatial point pattern.
krfun Multiscale second-order neigbourhood analysis of a multivariate spatial point pattern using Rao quadratic entropy.
ksfun Multiscale second-order neigbourhood analysis of a multivariate spatial point pattern using Simpson diversity.
kval Multiscale local second-order neighbour density of a spatial point pattern.
mimetic Univariate point pattern replication by mimetic point process.
plot.fads Plot second-order neigbourhood functions.
......
MD5
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− 24
View file @ 9e3b1b5d
f6aac0fb4ef187df6521cbb2d9ffc9cf R/fads.R
7a71372e86fd8aadfc770b261cd953ca R/mimetic.R
7603ca1f27dbbaf85b7b2ec19e059d7d R/plot.fads.R
154b26509aa63d97c2e0cc646e6681a8 R/plot.vads.R
b85a2aa0125801e94f5b4ce8b0f22a12 R/print.fads.R
1a420e10243f4c0df000ac22e0bab60e R/print.vads.R
c4b216a6fb57acb020f5e21682f7ed13 R/spp.R
bbb6ddd2e55fabe14c9e9dfcdfc495e7 R/summary.vads.R
c5d76ac2aa5f6fa68c0cfd08f197989e R/swin.R
318472a4c160e2ac070b5fb390add04e R/triangulate.R
a322bba8d53aff07f9a8ce9a69c89aef R/util.R
9f002a8b5ed00aaf26b4d7dc2f914f40 R/vads.R
31fa89b542936dac1031133b12ef530c data/Allogny.rda
5450b84c345240671b3410af7c70bc44 data/BPoirier.rda
24fea786746fc897f8918300f2f2c544 data/Couepia.rda
674867657e9a3df07b6eced02aa022a1 data/demopat.rda
a014cac4bc9abd4f40123a762939c8ca data/Paracou15.rda
c7cd00087730e79e06e8c0d937d0b1f7 inst/CITATION
94a8b147b3d2730b0c3869a7e1a2592f man/Allogny.Rd
b3c89a3bcb5db0d5fc9e93d8305df8c8 man/area.swin.Rd
1755cf31329228337e0b8039af2b6daf man/BPoirier.Rd
......@@ -22,14 +11,13 @@ d912451f743e11a9fbe50c8a6ef13b15 man/Couepia.Rd
d7b568c5332aad81bf4fb9f2bd4efed7 man/demopat.Rd
9b09cc667ab5d522e4a3a77c8b711159 man/dval.Rd
cd9ec1a82e0ee4e372e7ebd9c11233e4 man/inside.swin.Rd
e85df8cba02e1d7ae44b447ef05f0e3f man/internal.Rd
0656e69ec81de59af7b29e52639eee85 man/internal.Rd
18f7794bc004e9b9599486a725f7da5b man/k12fun.Rd
26a82fbf3be668f7c74dd4f1b9fd93e4 man/k12val.Rd
f4c594ec01933acd9d9cae7e797685fe man/kdfun.Rd
aa725a3e6b7183290f7dd758d594810c man/kfun.Rd
ea3edb1e20ecd5aa794f48c9fa5ee0e5 man/kmfun.Rd
0e606a71b6ec6f730bdd0d1498834dbc man/kp.fun.Rd
b45ac5f58b213884c5b1d9c79d5d1599 man/kpfun.Rd
500b63ba993de0b1f8a7d7f92765403b man/kpqfun.Rd
d388b950333aad22313c76d82f51c749 man/krfun.Rd
9970f6e4573f2e241de12d62ab201e23 man/ksfun.Rd
......@@ -42,7 +30,7 @@ c30babaf1b550ec45fa0f1bd89f967e5 man/plot.vads.Rd
2c61afcc548ad6440240664252a645a5 man/spp.Rd
cfe40689a11ec983e9b9bb4b759aaa26 man/swin.Rd
c04839dd6cd8eb396d512260a23dc7fd man/triangulate.Rd
f6aac0fb4ef187df6521cbb2d9ffc9cf R/fads.R
301f8891de7b1d08e3acd6c76d550ffb R/fads.R
7a71372e86fd8aadfc770b261cd953ca R/mimetic.R
7603ca1f27dbbaf85b7b2ec19e059d7d R/plot.fads.R
154b26509aa63d97c2e0cc646e6681a8 R/plot.vads.R
......@@ -51,17 +39,17 @@ b85a2aa0125801e94f5b4ce8b0f22a12 R/print.fads.R
c4b216a6fb57acb020f5e21682f7ed13 R/spp.R
bbb6ddd2e55fabe14c9e9dfcdfc495e7 R/summary.vads.R
c5d76ac2aa5f6fa68c0cfd08f197989e R/swin.R
318472a4c160e2ac070b5fb390add04e R/triangulate.R
a322bba8d53aff07f9a8ce9a69c89aef R/util.R
ba0e4bccaaaf969605faa35b7e01c578 R/triangulate.R
42d0d005b506098da453471b2f327362 R/util.R
9f002a8b5ed00aaf26b4d7dc2f914f40 R/vads.R
3d7a3f0a98ac75ad014cc91fbe2d0579 src/adssub.c
bd642dbad07c62b2f39fae4c5640f93a src/adssub.h
bd1503ee73c209191dc005b9be944175 src/adssub.h
1565adf6ba6c523f85ec70e89faca21c src/init.c
8a3dad68f1826270eef7ea08e098dfc5 src/spatstatsub.f
5aa9f5862ef5b0e8bbcc327021e1489a src/triangulate.c
e482b9d18794f53adaed3f2c98edd19a src/triangulate.h
fb07aec2cf6396cab654966e2757ab5c src/util.c
978998deca214a86ca6405d41a0d3b8f src/triangulate.c
0d9b249698185de8002c8aa767699d04 src/triangulate.h
f44e3b71761cdf40a551c450517d20cd src/Zlibs.c
109615f7005a5a6e02b98bcf1a904551 src/Zlibs.h
d9ae8cc82c07551b180991f6d508aedf NAMESPACE
a32d955da46938603fc72e218ce86101 DESCRIPTION
91f57a5dcc09e9babc1b761e95b8e446 src/Zlibs.h
705c1b8142d8d69a8b6df81b00d34739 DESCRIPTION
68a58538a504c7cfa73472d87053be45 INDEX
639184324c5b727794789ee4c72accb1 NAMESPACE
NAMESPACE
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......@@ -80,4 +80,4 @@ S3method(summary, k12val, summary.vads.k12val)
S3method(summary, kval, summary.vads.kval)
# load DLL
useDynLib(ads)
useDynLib(ads, .registration=TRUE)
R/triangulate.R
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......@@ -44,7 +44,7 @@ triangulate<-function(outer.poly,holes) {
vertY<-outer.poly$y
nbtri<-(nbpts-2)
}
tri<-.C("triangulate",
tri<-.C("c_triangulate",
as.integer(nbpoly),as.integer(nbpts),as.integer(nbptot),as.double(vertX),as.double(vertY),as.integer(nbtri),
X1=double(nbtri),Y1=double(nbtri),X2=double(nbtri),Y2=double(nbtri),X3=double(nbtri),Y3=double(nbtri),
PACKAGE="ads")
......
R/util.R
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− 10
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......@@ -307,16 +307,6 @@ read.tri<-function(X) {
return(res)
}
transpose<-function(x,y) {
nbTri<-length(x)/3
res<-.C("transpose",x=as.double(x),y=as.double(y),nbTri=as.integer(nbTri),
x1=double(nbTri),y1=double(nbTri),x2=double(nbTri),y2=double(nbTri),
x3=double(nbTri),y3=double(nbTri),PACKAGE="ads")
list(x1=res$x1,y1=res$y1,x2=res$x2,y2=res$y2,x3=res$x3,y3=res$y3)
}
##############
#subsetting dist objects
#sub is a logical vector of True/False
......
man/internal.Rd
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......@@ -32,7 +32,6 @@
\alias{summary.vads.kval}
\alias{testIC}
\alias{testInteger}
\alias{transpose}
\alias{subsetdist}
\title{Internal ads functions}
\description{
......@@ -59,7 +58,6 @@ sortmat(dis,ind)
subsetdist(dis,sub)
testIC(nbSimu, lev)
testInteger(i)
transpose(x, y)
}
\details{
These are usually not to be called by the user.
......
src/init.c 0 → 100644
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#include <R_ext/RS.h>
#include <stdlib.h> // for NULL
#include <R_ext/Rdynload.h>
#include "Zlibs.h"
#include "triangulate.h"
/* .Fortran calls */
extern void F77_NAME(inpoly)(void *, void *, void *, void *, void *, void *, void *, void *);
static const R_CMethodDef CEntries[] = {
{"corr_disq", (DL_FUNC) &corr_disq, 11},
{"corr_disq_ic", (DL_FUNC) &corr_disq_ic, 19},
{"corr_rect", (DL_FUNC) &corr_rect, 12},
{"corr_rect_ic", (DL_FUNC) &corr_rect_ic, 20},
{"corr_tr_disq", (DL_FUNC) &corr_tr_disq, 18},
{"corr_tr_disq_ic", (DL_FUNC) &corr_tr_disq_ic, 26},
{"corr_tr_rect", (DL_FUNC) &corr_tr_rect, 19},
{"corr_tr_rect_ic", (DL_FUNC) &corr_tr_rect_ic, 27},
{"density_disq", (DL_FUNC) &density_disq, 12},
{"density_rect", (DL_FUNC) &density_rect, 13},
{"density_tr_disq", (DL_FUNC) &density_tr_disq, 19},
{"density_tr_rect", (DL_FUNC) &density_tr_rect, 20},
{"intertype_disq", (DL_FUNC) &intertype_disq, 13},
{"intertype_disq_ic", (DL_FUNC) &intertype_disq_ic, 29},
{"intertype_rect", (DL_FUNC) &intertype_rect, 14},
{"intertype_rect_ic", (DL_FUNC) &intertype_rect_ic, 30},
{"intertype_tr_disq", (DL_FUNC) &intertype_tr_disq, 20},
{"intertype_tr_disq_ic", (DL_FUNC) &intertype_tr_disq_ic, 36},
{"intertype_tr_rect", (DL_FUNC) &intertype_tr_rect, 21},
{"intertype_tr_rect_ic", (DL_FUNC) &intertype_tr_rect_ic, 37},
{"intertypelocal_disq", (DL_FUNC) &intertypelocal_disq, 13},
{"intertypelocal_rect", (DL_FUNC) &intertypelocal_rect, 14},
{"intertypelocal_tr_disq", (DL_FUNC) &intertypelocal_tr_disq, 20},
{"intertypelocal_tr_rect", (DL_FUNC) &intertypelocal_tr_rect, 21},
{"mimetic_disq", (DL_FUNC) &mimetic_disq, 19},
{"mimetic_rect", (DL_FUNC) &mimetic_rect, 20},
{"mimetic_tr_disq", (DL_FUNC) &mimetic_tr_disq, 26},
{"mimetic_tr_rect", (DL_FUNC) &mimetic_tr_rect, 27},
{"rao_disq", (DL_FUNC) &rao_disq, 19},
{"rao_disq_ic", (DL_FUNC) &rao_disq_ic, 27},
{"rao_rect", (DL_FUNC) &rao_rect, 20},
{"rao_rect_ic", (DL_FUNC) &rao_rect_ic, 28},
{"rao_tr_disq", (DL_FUNC) &rao_tr_disq, 26},
{"rao_tr_disq_ic", (DL_FUNC) &rao_tr_disq_ic, 34},
{"rao_tr_rect", (DL_FUNC) &rao_tr_rect, 27},
{"rao_tr_rect_ic", (DL_FUNC) &rao_tr_rect_ic, 35},
{"ripley_disq", (DL_FUNC) &ripley_disq, 10},
{"ripley_disq_ic", (DL_FUNC) &ripley_disq_ic, 22},
{"ripley_rect", (DL_FUNC) &ripley_rect, 11},
{"ripley_rect_ic", (DL_FUNC) &ripley_rect_ic, 23},
{"ripley_tr_disq", (DL_FUNC) &ripley_tr_disq, 17},
{"ripley_tr_disq_ic", (DL_FUNC) &ripley_tr_disq_ic, 29},
{"ripley_tr_rect", (DL_FUNC) &ripley_tr_rect, 18},
{"ripley_tr_rect_ic", (DL_FUNC) &ripley_tr_rect_ic, 30},
{"ripleylocal_disq", (DL_FUNC) &ripleylocal_disq, 10},
{"ripleylocal_rect", (DL_FUNC) &ripleylocal_rect, 11},
{"ripleylocal_tr_disq", (DL_FUNC) &ripleylocal_tr_disq, 17},
{"ripleylocal_tr_rect", (DL_FUNC) &ripleylocal_tr_rect, 18},
{"shen", (DL_FUNC) &shen, 13},
{"shen_ic", (DL_FUNC) &shen_ic, 21},
{"shimatani_disq", (DL_FUNC) &shimatani_disq, 14},
{"shimatani_disq_ic", (DL_FUNC) &shimatani_disq_ic, 23},
{"shimatani_rect", (DL_FUNC) &shimatani_rect, 15},
{"shimatani_rect_ic", (DL_FUNC) &shimatani_rect_ic, 24},
{"shimatani_tr_disq", (DL_FUNC) &shimatani_tr_disq, 21},
{"shimatani_tr_disq_ic", (DL_FUNC) &shimatani_tr_disq_ic, 30},
{"shimatani_tr_rect", (DL_FUNC) &shimatani_tr_rect, 22},
{"shimatani_tr_rect_ic", (DL_FUNC) &shimatani_tr_rect_ic, 31},
{"c_triangulate", (DL_FUNC) &c_triangulate, 12},
{NULL, NULL, 0}
};
static const R_FortranMethodDef FortranEntries[] = {
{"inpoly", (DL_FUNC) &F77_NAME(inpoly), 8},
{NULL, NULL, 0}
};
void R_init_ads(DllInfo *dll)
{
R_registerRoutines(dll, CEntries, NULL, FortranEntries, NULL);
R_useDynamicSymbols(dll, FALSE);
}
\ No newline at end of file
src/triangulate.c
+ 78
− 0
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......@@ -2126,3 +2126,81 @@ int is_point_inside_polygon(vertex)
return _greater_than_equal_to(&seg[rseg].v1, &seg[rseg].v0);
}
int c_triangulate(int *npoly, int *tabpt, int *nptTot,double *vertX, double *vertY, int *ntri, double *X1, double *Y1,double *X2, double *Y2,double *X3, double *Y3) {
int i,j,k,l;
int **triangles;
double **vertices;
double *x,*y;
tabintalloc(&triangles,*ntri,3);
taballoc(&vertices,*nptTot+1,2);
l=0;
for(i=0;i<*npoly;i++) {
int npt=tabpt[i];
vecalloc(&x,npt+1);
vecalloc(&y,npt+1);
for(j=1;j<=npt;j++) {
k=j+l-1;
x[j]=vertX[k];
y[j]=vertY[k];
}
if(i==0) {
if(testclock(x,y,npt)) { /*clockwise order*/
k=npt;
for(j=1;j<=npt;j++) {
vertices[j+l][0]=x[k];
vertices[j+l][1]=y[k];
k--;
}
}
else { /*anti-clockwise order*/
for(j=1;j<=npt;j++) {
vertices[j+l][0]=x[j];
vertices[j+l][1]=y[j];
}
}
}
else {
if(!testclock(x,y,npt)) { /*anti-clockwise order*/
k=npt;
for(j=1;j<=npt;j++) {
vertices[j+l][0]=x[k];
vertices[j+l][1]=y[k];
k--;
}
}
else { /*clockwise order*/
for(j=1;j<=npt;j++) {
vertices[j+l][0]=x[j];
vertices[j+l][1]=y[j];
}
}
}
l+=npt;
freevec(x);
freevec(y);
}
/*Test de l'unicite des points*/
for(i=2;i<=*nptTot;i++) {
for(j=1;j<i;j++) {
if((vertices[i][0]==vertices[j][0])&&(vertices[i][1]==vertices[j][1])) {
Rprintf("Error : Duplicate input vertices\n");
return -1;
}
}
}
triangulate_polygon(*npoly,tabpt,vertices,triangles);
for(i=0;i<*ntri;i++) {
X1[i]=vertices[triangles[i][2]][0];
Y1[i]=vertices[triangles[i][2]][1];
X2[i]=vertices[triangles[i][1]][0];
Y2[i]=vertices[triangles[i][1]][1];
X3[i]=vertices[triangles[i][0]][0];
Y3[i]=vertices[triangles[i][0]][1];
}
freeinttab(triangles);
freetab(vertices);
return 0;
}
src/triangulate.h
+ 2
− 8
View file @ 9e3b1b5d
......@@ -88,7 +88,7 @@ typedef struct {
#define LASTPT 2
#define INFINITY 1<<30
#define INFINITY 1<<30
#define C_EPS 1.0e-7 /* tolerance value: Used for making */
/* all decisions about collinearity or */
/* left/right of segment. Decrease */
......@@ -140,26 +140,20 @@ extern node_t qs[QSIZE]; /* Query structure */
extern trap_t tr[TRSIZE]; /* Trapezoid structure */
extern segment_t seg[SEGSIZE]; /* Segment table */
/* Functions */
extern int c_triangulate(int*, int *, int *,double *, double *, int *, double *, double *,double *, double *,double *, double *);
extern int triangulate_polygon(int, int *, double**,int**);
extern int is_point_inside_polygon(double *);
int triangulate_polygon(int, int [], double**, int**);
int testclock(double *,double *,int);
extern int monotonate_trapezoids(int);
extern int triangulate_monotone_polygons(int, int, int**);
extern int _greater_than(point_t *, point_t *);
extern int _equal_to(point_t *, point_t *);
extern int _greater_than_equal_to(point_t *, point_t *);
extern int _less_than(point_t *, point_t *);
extern int locate_endpoint(point_t *, point_t *, int);
extern int construct_trapezoids(int);
extern int generate_random_ordering(int);
extern int choose_segment(void);
extern int read_segments(char *, int *);
......
src/util.c deleted 100755 → 0
+ 0
− 80
View file @ 2f2ebbb7
#include "adssub.h"
#include "triangulate.h"
int triangulate(int *npoly, int *tabpt, int *nptTot,double *vertX, double *vertY, int *ntri,
double *X1, double *Y1,double *X2, double *Y2,double *X3, double *Y3) {
int i,j,k,l;
int **triangles;
double **vertices;
double *x,*y;
tabintalloc(&triangles,*ntri,3);
taballoc(&vertices,*nptTot+1,2);
l=0;
for(i=0;i<*npoly;i++) {
int npt=tabpt[i];
vecalloc(&x,npt+1);
vecalloc(&y,npt+1);
for(j=1;j<=npt;j++) {
k=j+l-1;
x[j]=vertX[k];
y[j]=vertY[k];
}
if(i==0) {
if(testclock(x,y,npt)) { /*clockwise order*/
k=npt;
for(j=1;j<=npt;j++) {
vertices[j+l][0]=x[k];
vertices[j+l][1]=y[k];
k--;
}
}
else { /*anti-clockwise order*/
for(j=1;j<=npt;j++) {
vertices[j+l][0]=x[j];
vertices[j+l][1]=y[j];
}
}
}
else {
if(!testclock(x,y,npt)) { /*anti-clockwise order*/
k=npt;
for(j=1;j<=npt;j++) {
vertices[j+l][0]=x[k];
vertices[j+l][1]=y[k];
k--;
}
}
else { /*clockwise order*/
for(j=1;j<=npt;j++) {
vertices[j+l][0]=x[j];
vertices[j+l][1]=y[j];
}
}
}
l+=npt;
freevec(x);
freevec(y);
}
/*Test de l'unicite des points*/
for(i=2;i<=*nptTot;i++) {
for(j=1;j<i;j++) {
if((vertices[i][0]==vertices[j][0])&&(vertices[i][1]==vertices[j][1])) {
Rprintf("Error : Duplicate input vertices\n");
return -1;
}
}
}
triangulate_polygon(*npoly,tabpt,vertices,triangles);
for(i=0;i<*ntri;i++) {
X1[i]=vertices[triangles[i][2]][0];
Y1[i]=vertices[triangles[i][2]][1];
X2[i]=vertices[triangles[i][1]][0];
Y2[i]=vertices[triangles[i][1]][1];
X3[i]=vertices[triangles[i][0]][0];
Y3[i]=vertices[triangles[i][0]][1];
}
freeinttab(triangles);
freetab(vertices);
return 0;
}
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