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Commit 2f2ebbb7 authored by philippe.verley_ird.fr's avatar philippe.verley_ird.fr
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In src/*.h cosmetic changes to declare the same way all functions. In fads.R... 

In src/*.h cosmetic changes to declare the same way all functions. In fads.R there was a wrong call to ripley_tr_disq_ic instead of coor_tr_disq_ic. Deleted comments en plot.vads.R that were problematic according to devtools:check() function. Updated DESCRIPTION, NAMESPACE and MD5 files
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DESCRIPTION
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View file @ 2f2ebbb7
......@@ -2,10 +2,11 @@ Package: ads
Type: Package
Title: Spatial point patterns analysis
Version: 1.5-3
Date: 2018-03-28
Authors@R: c(person("Raphael", "Pelissier", role=c("aut", "cre"), email="raphael.pelissier@ird.fr"),
Date: 2018-03-29
Authors@R: c(person("Raphael", "Pelissier", role=c("aut"), email="raphael.pelissier@ird.fr"),
person("Francois", "Goreau", role="aut"),
person("Philippe", "Verley", role="ctb"))
person("Philippe", "Verley", role=c("ctb", "cre"), email="philippe.verley@ird.fr"))
Author: Raphael Pelissier [aut], Francois Goreau [aut], Philippe Verley [ctb, cre]
Maintainer: Raphael Pelissier <raphael.pelissier@ird.fr>
Imports: ade4, spatstat
Description: Perform first- and second-order multi-scale analyses derived from Ripley K-function, for univariate,
......@@ -16,3 +17,4 @@ 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
MD5
+ 67
− 55
View file @ 2f2ebbb7
2755553481e78a8f5b6ef00d43e983a5 *DESCRIPTION
68a58538a504c7cfa73472d87053be45 *INDEX
7478c6d745db573c9d03ebc59bdc969c *NAMESPACE
f6aac0fb4ef187df6521cbb2d9ffc9cf *R/fads.R
7a71372e86fd8aadfc770b261cd953ca *R/mimetic.R
e87bd01e08a83a7b1c52b2a4a7e5df35 *R/plot.fads.R
95d2bc01bd2779736c826a21c83b62f3 *R/plot.vads.R
6317d29d7e9045d55b1a41906e867462 *R/print.fads.R
d0f79442970e383cf8c3bd1677320b53 *R/print.vads.R
c4b216a6fb57acb020f5e21682f7ed13 *R/spp.R
96dada922fee237e190207f544de8ed3 *R/summary.vads.R
c5d76ac2aa5f6fa68c0cfd08f197989e *R/swin.R
34b15c6ed440f88d868d3ab3b93db3b8 *R/triangulate.R
a322bba8d53aff07f9a8ce9a69c89aef *R/util.R
f2c452832a53eb1ed6d168b59918d52a *R/vads.R
31fa89b542936dac1031133b12ef530c *data/Allogny.rda
5450b84c345240671b3410af7c70bc44 *data/BPoirier.rda
24fea786746fc897f8918300f2f2c544 *data/Couepia.rda
a014cac4bc9abd4f40123a762939c8ca *data/Paracou15.rda
674867657e9a3df07b6eced02aa022a1 *data/demopat.rda
c7cd00087730e79e06e8c0d937d0b1f7 *inst/CITATION
94a8b147b3d2730b0c3869a7e1a2592f *man/Allogny.Rd
1755cf31329228337e0b8039af2b6daf *man/BPoirier.Rd
d912451f743e11a9fbe50c8a6ef13b15 *man/Couepia.Rd
4f272a7a2e7528da43c0d2ef8685921b *man/Paracou15.Rd
b3c89a3bcb5db0d5fc9e93d8305df8c8 *man/area.swin.Rd
d7b568c5332aad81bf4fb9f2bd4efed7 *man/demopat.Rd
9b09cc667ab5d522e4a3a77c8b711159 *man/dval.Rd
cd9ec1a82e0ee4e372e7ebd9c11233e4 *man/inside.swin.Rd
e85df8cba02e1d7ae44b447ef05f0e3f *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
500b63ba993de0b1f8a7d7f92765403b *man/kpqfun.Rd
d388b950333aad22313c76d82f51c749 *man/krfun.Rd
9970f6e4573f2e241de12d62ab201e23 *man/ksfun.Rd
d5d294338860db9a406208f219f05f5e *man/kval.Rd
1037e7421f3a50f15fcb07e88dcc260c *man/mimetic.Rd
5bff5bb53402d742900fe12ed542877b *man/plot.fads.Rd
7e88d95ac70e452257a939a70f9a1a76 *man/plot.spp.Rd
c30babaf1b550ec45fa0f1bd89f967e5 *man/plot.vads.Rd
2c61afcc548ad6440240664252a645a5 *man/spp.Rd
cfe40689a11ec983e9b9bb4b759aaa26 *man/swin.Rd
c04839dd6cd8eb396d512260a23dc7fd *man/triangulate.Rd
22fae7567dd07dddf2ea00cb023c2be5 *src/Zlibs.c
109615f7005a5a6e02b98bcf1a904551 *src/Zlibs.h
3d7a3f0a98ac75ad014cc91fbe2d0579 *src/adssub.c
bd642dbad07c62b2f39fae4c5640f93a *src/adssub.h
8a3dad68f1826270eef7ea08e098dfc5 *src/spatstatsub.f
5aa9f5862ef5b0e8bbcc327021e1489a *src/triangulate.c
e482b9d18794f53adaed3f2c98edd19a *src/triangulate.h
fb07aec2cf6396cab654966e2757ab5c *src/util.c
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
94a8b147b3d2730b0c3869a7e1a2592f man/Allogny.Rd
b3c89a3bcb5db0d5fc9e93d8305df8c8 man/area.swin.Rd
1755cf31329228337e0b8039af2b6daf man/BPoirier.Rd
d912451f743e11a9fbe50c8a6ef13b15 man/Couepia.Rd
d7b568c5332aad81bf4fb9f2bd4efed7 man/demopat.Rd
9b09cc667ab5d522e4a3a77c8b711159 man/dval.Rd
cd9ec1a82e0ee4e372e7ebd9c11233e4 man/inside.swin.Rd
e85df8cba02e1d7ae44b447ef05f0e3f 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
d5d294338860db9a406208f219f05f5e man/kval.Rd
1037e7421f3a50f15fcb07e88dcc260c man/mimetic.Rd
4f272a7a2e7528da43c0d2ef8685921b man/Paracou15.Rd
5bff5bb53402d742900fe12ed542877b man/plot.fads.Rd
7e88d95ac70e452257a939a70f9a1a76 man/plot.spp.Rd
c30babaf1b550ec45fa0f1bd89f967e5 man/plot.vads.Rd
2c61afcc548ad6440240664252a645a5 man/spp.Rd
cfe40689a11ec983e9b9bb4b759aaa26 man/swin.Rd
c04839dd6cd8eb396d512260a23dc7fd man/triangulate.Rd
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
3d7a3f0a98ac75ad014cc91fbe2d0579 src/adssub.c
bd642dbad07c62b2f39fae4c5640f93a src/adssub.h
8a3dad68f1826270eef7ea08e098dfc5 src/spatstatsub.f
5aa9f5862ef5b0e8bbcc327021e1489a src/triangulate.c
e482b9d18794f53adaed3f2c98edd19a src/triangulate.h
fb07aec2cf6396cab654966e2757ab5c src/util.c
f44e3b71761cdf40a551c450517d20cd src/Zlibs.c
109615f7005a5a6e02b98bcf1a904551 src/Zlibs.h
d9ae8cc82c07551b180991f6d508aedf NAMESPACE
a32d955da46938603fc72e218ce86101 DESCRIPTION
68a58538a504c7cfa73472d87053be45 INDEX
NAMESPACE
+ 2
− 2
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......@@ -4,8 +4,8 @@ importFrom(spatstat,"border","bounding.box.xy","area.owin")
importFrom("graphics", "abline", "barplot", "layout", "lines", "par",
"plot", "plot.default", "points", "polygon", "symbols",
"text")
importFrom("stats", "as.dist", "var")
importFrom("utils", "read.table", "str")
importFrom("stats", "as.dist", "var")
importFrom("utils", "read.table", "str")
# Export all names (should be improved in the future)
export(
......
R/fads.R
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This diff is collapsed.
R/plot.vads.R
+ 6
− 34
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......@@ -28,8 +28,7 @@ plot.vads.dval<-function (x,main,opt=c("dval","cval"),select,chars=c("circles","
val<-data.frame(adjust.marks.size(val,x$window,if(!missing(maxsize)) maxsize))
def.par <- par(no.readonly = TRUE)
on.exit(par(def.par))
#if(options()$device=="windows")
# csize<-0.75*csize
if (missing(main))
main <- deparse(substitute(x))
mylayout<-layout(matrix(c(rep(1,nf),seq(2,((nf*nf)+1),1)),(nf+1),nf,byrow=TRUE))
......@@ -54,14 +53,7 @@ plot.vads.dval<-function (x,main,opt=c("dval","cval"),select,chars=c("circles","
text(c(xl[1]+lms[1],xl[2]+lms[2],xl[3]+lms[3]),yl,labels=signif(lm,2),pos=4,cex=1.5)
}
}
#if(!is.null(main)) {
# mylayout<-layout(matrix(c(rep(1,nf),seq(2,((nf*nf)+1),1)),(nf+1),nf,byrow=TRUE))
# plot.default(x$xy$x,x$xy$y,type="n",axes=FALSE)
# text(mean(range(x$xy$x)),mean(range(x$xy$y)),pos=3,cex=2,labels=main)
#ajouter une lgende ???
#}
#else
# mylayout<-layout(matrix(seq(1,(nf*nf),1),nf,nf,byrow=TRUE))
ifelse(missing(cols),cols<-1,cols<-cols[1])
if(!missing(char0)||!missing(col0)) {
ifelse(missing(col0),col0<-cols,col0<-col0[1])
......@@ -82,7 +74,6 @@ plot.vads.dval<-function (x,main,opt=c("dval","cval"),select,chars=c("circles","
fg=cols,bg=cols,inches=FALSE,add=TRUE,...)
}
}
## mthode en courbes de niveaux ?
}
plot.vads.kval<-function (x,main,opt=c("lval","kval","nval","gval"),select,chars=c("circles","squares"),cols,maxsize,char0,col0,legend=TRUE,csize=1,...) {
......@@ -117,14 +108,12 @@ plot.vads.kval<-function (x,main,opt=c("lval","kval","nval","gval"),select,chars
else
stopifnot(opt%in%c("lval","kval","nval","gval"))
v<-val
#val<-data.frame(adjust.marks.size(val,x$window,if(!missing(maxsize)) maxsize))
val<-data.frame(adjust.marks.size(val,x$window))
if(!missing(maxsize))
val<-val*maxsize
def.par <- par(no.readonly = TRUE)
on.exit(par(def.par))
#if(options()$device=="windows")
# csize<-0.75*csize
if (missing(main))
main <- deparse(substitute(x))
mylayout<-layout(matrix(c(rep(1,nf),seq(2,((nf*nf)+1),1)),(nf+1),nf,byrow=TRUE))
......@@ -155,14 +144,7 @@ plot.vads.kval<-function (x,main,opt=c("lval","kval","nval","gval"),select,chars
}
}
#if(!is.null(main)) {
# mylayout<-layout(matrix(c(rep(1,nf),seq(2,((nf*nf)+1),1)),(nf+1),nf,byrow=TRUE))
# plot.default(x$xy$x,x$xy$y,type="n",axes=FALSE)
# text(mean(range(x$xy$x)),mean(range(x$xy$y)),pos=3,cex=2,labels=main)
#ajouter une lgende ???
#}
#else
# mylayout<-layout(matrix(seq(1,(nf*nf),1),nf,nf,byrow=TRUE))
ifelse(missing(cols),cols<-1,cols<-cols[1])
if(!missing(char0)||!missing(col0)) {
ifelse(missing(col0),col0<-cols,col0<-col0[1])
......@@ -194,7 +176,6 @@ plot.vads.kval<-function (x,main,opt=c("lval","kval","nval","gval"),select,chars
}
}
}
## mthode en courbes de niveaux ?
}
plot.vads.k12val<-function (x,main,opt=c("lval","kval","nval","gval"),select,chars=c("circles","squares"),cols,maxsize,char0,col0,legend=TRUE,csize=1,...) {
......@@ -235,8 +216,7 @@ plot.vads.k12val<-function (x,main,opt=c("lval","kval","nval","gval"),select,cha
val<-val*maxsize
def.par <- par(no.readonly = TRUE)
on.exit(par(def.par))
#if(options()$device=="windows")
# csize<-0.75*csize
if (missing(main))
main <- deparse(substitute(x))
mylayout<-layout(matrix(c(rep(1,nf),seq(2,((nf*nf)+1),1)),(nf+1),nf,byrow=TRUE))
......@@ -265,14 +245,7 @@ plot.vads.k12val<-function (x,main,opt=c("lval","kval","nval","gval"),select,cha
text(c(xl[1]+lms[1],xl[2]+lms[2],xl[3]+lms[3]),yl*0.5,labels=signif(-lm,2),pos=4,cex=1)
}
}
#if(!is.null(main)) {
# mylayout<-layout(matrix(c(rep(1,nf),seq(2,((nf*nf)+1),1)),(nf+1),nf,byrow=TRUE))
# plot.default(x$xy$x,x$xy$y,type="n",axes=FALSE)
# text(mean(range(x$xy$x)),mean(range(x$xy$y)),pos=3,cex=2,labels=main)
#ajouter une lgende ???
#}
#else
# mylayout<-layout(matrix(seq(1,(nf*nf),1),nf,nf,byrow=TRUE))
ifelse(missing(cols),cols<-1,cols<-cols[1])
if(!missing(char0)||!missing(col0)) {
ifelse(missing(col0),col0<-cols,col0<-col0[1])
......@@ -304,5 +277,4 @@ plot.vads.k12val<-function (x,main,opt=c("lval","kval","nval","gval"),select,cha
}
}
}
## mthode en courbes de niveaux ?
}
R/vads.R
+ 296
− 305
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src/Zlibs.h
+ 80
− 168
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This diff is collapsed.
src/adssub.h
+ 23
− 28
View file @ 2f2ebbb7
......@@ -3,31 +3,26 @@
#include <limits.h>
#include <R_ext/PrtUtil.h>
double Pi();
void progress(int,int*, int);
/*double alea ();*/
void freeintvec (int *);
void freetab (double **);
void freevec (double *);
void taballoc (double ***,int,int);
void tabintalloc (int ***,int,int);
void freeinttab (int **);
void vecalloc (double **vec, int n);
void vecintalloc (int **vec, int n);
double bacos(double a);
void decalVal(double *,int,double);
void decalRect(int,double *,double *,double *,double *,double *,double *);
void decalCirc(int,double *,double *,double *,double *,double);
void decalRectTri(int,double *,double *,double *,double *,double *,double *,
int,double *,double *,double *,double *,double *,double *);
void decalCircTri(int,double *,double *,double *,double *,double,
int,double *,double *,double *,double *,double *,double *);
void decalRect2(int,double *,double *,int,double *,double *,double *,double *,double *,double *);
void decalCirc2(int,double *,double *,int,double *,double *,double *,double *,double);
void decalRectTri2(int,double *,double *,int,double *,double *,double *,double *,double *,double *,
int,double *,double *,double *,double *,double *,double *);
void decalCircTri2(int,double *,double *,int,double *,double *,double *,double *,double,int,
double *,double *,double *,double *,double *,double *);
void decalSample(int,double *,double *,double,double);
double** taballoca(int,int *);
void complete_tab(int,double **,double **,int *,int *,int *,double *,double *);
double bacos(double);
void complete_tab(int,double**,double**,int*,int*,int*,double*,double*);
void decalCirc(int,double*,double*,double*,double*,double);
void decalCirc2(int,double*,double*,int,double*,double*,double*,double*,double);
void decalCircTri(int,double*,double*,double*,double*,double, int,double*,double*,double*,double*,double*,double*);
void decalCircTri2(int,double*,double*,int,double*,double*,double*,double*,double,int,double*,double*,double*,double*,double*,double*);
void decalRect(int,double*,double*,double*,double*,double*,double*);
void decalRect2(int,double*,double*,int,double*,double*,double*,double*,double*,double*);
void decalRectTri(int,double*,double*,double*,double*,double*,double*, int,double*,double*,double*,double*,double*,double*);
void decalRectTri2(int,double*,double*,int,double*,double*,double*,double*,double*,double*, int,double*,double*,double*,double*,double*,double*);
void decalSample(int,double*,double*,double,double);
void decalVal(double*,int,double);
void freeinttab(int**);
void freeintvec(int*);
void freetab(double**);
void freevec(double*);
double Pi();
void progress(int,int*,int);
void taballoc(double***,int,int);
double** taballoca(int,int*);
void tabintalloc(int***,int,int);
void vecalloc(double**,int);
void vecintalloc(int**,int);
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