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Commit 23e613a3 authored by philippe.verley_ird.fr's avatar philippe.verley_ird.fr
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Incremented ADS version to 1.5-6. Fixed documentation according to CRAN notes.

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DESCRIPTION
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Package: ads
Type: Package
Title: Spatial Point Patterns Analysis
Version: 1.5-5
Date: 2021-03-15
Authors@R: c(person("Raphael", "Pelissier", role="aut", email="raphael.pelissier@ird.fr"),
person("Francois", "Goreau", role="aut"),
person("Philippe", "Verley", role=c("ctb", "cre"), email="philippe.verley@ird.fr"))
Version: 1.5-6
Date: 2022-05-11
Author: Raphael Pelissier [aut], Francois Goreau [aut], Philippe Verley [ctb, cre]
Maintainer: Raphael Pelissier <Raphael.Pelissier@ird.fr>
Maintainer: Raphael Pelissier <raphael.pelissier@ird.fr>
Imports: ade4, spatstat.geom
Description: Perform first- and second-order multi-scale analyses derived from Ripley K-function (Ripley B. D. (1977) <doi:10.1111/j.2517-6161.1977.tb01615.x>), for univariate,
multivariate and marked mapped data in rectangular, circular or irregular shaped sampling windows, with tests of
......@@ -16,5 +13,5 @@ Depends: R (>= 3.5.0)
License: GPL-2
NeedsCompilation: yes
Repository: CRAN
RoxygenNote: 7.1.1
RoxygenNote: 7.1.2
Language: en-GB
MD5
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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
d912451f743e11a9fbe50c8a6ef13b15 man/Couepia.Rd
d7b568c5332aad81bf4fb9f2bd4efed7 man/demopat.Rd
9b09cc667ab5d522e4a3a77c8b711159 man/dval.Rd
cd9ec1a82e0ee4e372e7ebd9c11233e4 man/inside.swin.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
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
301f8891de7b1d08e3acd6c76d550ffb R/fads.R
9f002a8b5ed00aaf26b4d7dc2f914f40 R/vads.R
b9f4aaeac158d6b0a7a231501e93baae R/zzz.R
7a71372e86fd8aadfc770b261cd953ca R/mimetic.R
7603ca1f27dbbaf85b7b2ec19e059d7d R/plot.fads.R
154b26509aa63d97c2e0cc646e6681a8 R/plot.vads.R
665a029a2927079c9d67198225bac08d R/swin.R
318472a4c160e2ac070b5fb390add04e R/triangulate.R
f3446ce87d2b9555674084cdc00495f7 R/fads.R
e3a02bd4932f3428d46df0d3aba92833 R/util.R
b85a2aa0125801e94f5b4ce8b0f22a12 R/print.fads.R
1a420e10243f4c0df000ac22e0bab60e R/print.vads.R
154b26509aa63d97c2e0cc646e6681a8 R/plot.vads.R
c4b216a6fb57acb020f5e21682f7ed13 R/spp.R
1a420e10243f4c0df000ac22e0bab60e R/print.vads.R
bbb6ddd2e55fabe14c9e9dfcdfc495e7 R/summary.vads.R
c5d76ac2aa5f6fa68c0cfd08f197989e R/swin.R
ba0e4bccaaaf969605faa35b7e01c578 R/triangulate.R
42d0d005b506098da453471b2f327362 R/util.R
9f002a8b5ed00aaf26b4d7dc2f914f40 R/vads.R
3d7a3f0a98ac75ad014cc91fbe2d0579 src/adssub.c
bd1503ee73c209191dc005b9be944175 src/adssub.h
1565adf6ba6c523f85ec70e89faca21c src/init.c
8a3dad68f1826270eef7ea08e098dfc5 src/spatstatsub.f
978998deca214a86ca6405d41a0d3b8f src/triangulate.c
0d9b249698185de8002c8aa767699d04 src/triangulate.h
f44e3b71761cdf40a551c450517d20cd src/Zlibs.c
91f57a5dcc09e9babc1b761e95b8e446 src/Zlibs.h
705c1b8142d8d69a8b6df81b00d34739 DESCRIPTION
68a58538a504c7cfa73472d87053be45 INDEX
639184324c5b727794789ee4c72accb1 NAMESPACE
0cda74fcbb52beb428a91e4fb270a921 src/util.o
84e6de2d2fae1da249c5f98b4b4773f9 src/Zlibs.o
2a2482c6213d4b438ecf4d56c22cd347 src/init.o
1c1b148fdc049d409209e4af81f1b171 src/Zlibs.h
c3c9323f8a885d4393bd7d9dbebbaa20 src/adssub.c
12a29495568f318dc34a5ca932801771 src/init.c
64a89b3fe173b3bb94d59d39703c81b8 src/Zlibs.c
e482b9d18794f53adaed3f2c98edd19a src/triangulate.h
6b36548eb7273a4fa62cf299292f2690 src/triangulate.o
fb07aec2cf6396cab654966e2757ab5c src/util.c
5aa9f5862ef5b0e8bbcc327021e1489a src/triangulate.c
da81d39dc9915bc8bb0fcfd460a4cda0 src/adssub.o
d58a1f617f64e4c7d04360cca89ef75b src/ads.so
07d89d5db81d8de60ffa2807da747e6f src/adssub.h
fa794261fe3c8f96f8701947b1a58b23 NAMESPACE
941c40c291485c31ca187da74d692ac1 INDEX
4f0da7352d2317c6750447a088ec70bb data/Paracou15.rda
674867657e9a3df07b6eced02aa022a1 data/demopat.rda
31fa89b542936dac1031133b12ef530c data/Allogny.rda
24fea786746fc897f8918300f2f2c544 data/Couepia.rda
5450b84c345240671b3410af7c70bc44 data/BPoirier.rda
ae90188ce7c0a45afbaa041a725a434b inst/CITATION
ba137a8fe81d56c2436eee072ea5195a DESCRIPTION
a93ef3f8bfc9909d60ba25bbe511facc man/Couepia.Rd
9f351cb219c8c7aa8c70bc20507da3be man/internal.Rd
34bcb89b0e7144697d21f288d8b469c8 man/Paracou15.Rd
1c25c8c336747bbd2d185704a5b67652 man/plot.vads.Rd
0b30c3a2b2b7509c153c4a7614ef8bdc man/kfun.Rd
84a056aa039ef0001d0a85781d4ee62e man/area.swin.Rd
d2d6f00f6a5fa5e516ec2c2bcac7d869 man/krfun.Rd
48f981054c040eeaf06c64f39eef39d9 man/spp.Rd
759b9259c437125168eb9a766a57df4f man/mimetic.Rd
8a6700ec288bb0b867fce8b00ab518a9 man/demopat.Rd
7aecbe0cb1088e36c41cc7c2e4aae910 man/kdfun.Rd
1b8dcd354991b592cb4ffec83eb96404 man/inside.swin.Rd
7b39f7b6aa823df824b8713c9b88d2d0 man/kpqfun.Rd
fd18b66179f59eefe782c07467c73309 man/k12fun.Rd
0b3c74dfa223d983966a99a2cb556194 man/BPoirier.Rd
b55f1fe8cf3e1cda2c5ff86183838c57 man/k12val.Rd
4e242b5a91fbe5cc4c7b39fc4db9e9f4 man/swin.Rd
2cb7ce4baa084527191f98fde748556a man/kmfun.Rd
fe27b8d65a850f4ff019c832d16485cd man/Allogny.Rd
09a262d26506576ce4f6e998e5efea21 man/kval.Rd
b1f043130dd56c50ec79a5a2a1539ab3 man/triangulate.Rd
dbcfcb0f39464bd739c18d8423facc63 man/ksfun.Rd
ea1d40c0dc836014b34a13cac934daba man/plot.spp.Rd
6cda3b09fdc5e9e4b47e6a0d1aecb0f8 man/plot.fads.Rd
6da15dc4d56b3349a577a69644f1d41c man/kp.fun.Rd
b7757ca3c5f8a40ccfb65ed3dfe5de11 man/dval.Rd
R/util.R
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......@@ -278,7 +278,7 @@ overlap.trapez <- function(xa, ya, xb, yb, verb=FALSE) {
}
#Points on boundary are considered outside. No alternative option implemented yet.
in.poly<-function(x,y,poly,bdry=TRUE) {
in.poly<-function(x,y,poly,bdry=FALSE) {
if(bdry) {
bdry<-FALSE
warning("argument 'bdry' automatically set to FALSE. No alternative implemented yet")
......
man/k12fun.Rd
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......@@ -62,8 +62,8 @@ k12fun(p, upto, by, nsim=0, H0=c("pitor","pimim","rl"), prec=0.01, nsimax=3000,
\item{g12 }{a data frame containing values of the bivariate pair density function \eqn{g12(r)}.}
\item{n12 }{a data frame containing values of the bivariate local neighbour density function \eqn{n12(r)}.}
\item{k12 }{a data frame containing values of the intertype function \eqn{K12(r)}.}
\item{l12 }{a data frame containing values of the modified intertype function \eqn{L12(r)}.\cr\cr}
\item{ }{Each component except \code{r} is a data frame with the following variables:\cr\cr}
\item{l12 }{a data frame containing values of the modified intertype function \eqn{L12(r)}.\cr}
Each component except \code{r} is a data frame with the following variables:\cr
\item{obs }{a vector of estimated values for the observed point pattern.}
\item{theo }{a vector of theoretical values expected under the selected null hypothesis.}
\item{sup }{(optional) if \code{nsim>0} a vector of the upper local confidence limits of the selected null hypothesis at a significant level \eqn{\alpha}.}
......
man/kdfun.Rd
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......@@ -39,8 +39,8 @@ kdfun(p, upto, by, dis, nsim=0, alpha = 0.01)
A list of class \code{"fads"} with essentially the following components:
\item{r }{a vector of regularly spaced out distances (\code{seq(by,upto,by)}).}
\item{gd }{a data frame containing values of the function \eqn{gd(r)}.}
\item{kd }{a data frame containing values of the function \eqn{Kd(r)}.\cr\cr}
\item{}{Each component except \code{r} is a data frame with the following variables:\cr\cr}
\item{kd }{a data frame containing values of the function \eqn{Kd(r)}.\cr}
Each component except \code{r} is a data frame with the following variables:\cr
\item{obs }{a vector of estimated values for the observed point pattern.}
\item{theo }{a vector of theoretical values expected under the null hypothesis of species equivalence.}
\item{sup }{(optional) if \code{nsim>0} a vector of the upper local confidence limits of a random distribution of the null hypothesis at a significant level \eqn{\alpha}.}
......
man/kfun.Rd
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......@@ -44,8 +44,8 @@ kfun(p, upto, by, nsim=0, prec=0.01, alpha=0.01)
\item{g }{a data frame containing values of the pair density function \eqn{g(r)}.}
\item{n }{a data frame containing values of the local neighbour density function \eqn{n(r)}.}
\item{k }{a data frame containing values of Ripley's function \eqn{K(r)}.}
\item{l }{a data frame containing values of the modified Ripley's function \eqn{L(r)}.\cr\cr}
\item{}{Each component except \code{r} is a data frame with the following variables:\cr\cr}
\item{l }{a data frame containing values of the modified Ripley's function \eqn{L(r)}.\cr}
Each component except \code{r} is a data frame with the following variables:\cr
\item{obs }{a vector of estimated values for the observed point pattern.}
\item{theo }{a vector of theoretical values expected for a Poisson pattern.}
\item{sup }{(optional) if \code{nsim>0} a vector of the upper local confidence limits of a Poisson pattern at a significant level \eqn{\alpha}.}
......
man/kmfun.Rd
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......@@ -38,8 +38,8 @@ kmfun(p, upto, by, nsim=0, alpha=0.01)
A list of class \code{"fads"} with essentially the following components:
\item{r }{a vector of regularly spaced out distances (\code{seq(by,upto,by)}).}
\item{gm }{a data frame containing values of the pair mark correlation function \eqn{gm(r)}.}
\item{km }{a data frame containing values of the mark correlation function \eqn{Km(r)}.\cr\cr}
\item{ }{Each component except \code{r} is a data frame with the following variables:\cr\cr}
\item{km }{a data frame containing values of the mark correlation function \eqn{Km(r)}.\cr}
Each component except \code{r} is a data frame with the following variables:\cr
\item{obs }{a vector of estimated values for the observed point pattern.}
\item{theo }{a vector of theoretical values expected for the null hypothesis of no correlation between marks.}
\item{sup }{(optional) if \code{nsim>0} a vector of the upper local confidence limits of the null hypothesis at a significant level \eqn{\alpha}.}
......
man/kp.fun.Rd
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......@@ -27,8 +27,8 @@ kp.fun(p, upto, by)
\item{gp. }{a data frame containing values of the pair density function \eqn{g12(r)}.}
\item{np. }{a data frame containing values of the local neighbour density function \eqn{n12(r)}.}
\item{kp. }{a data frame containing values of the \eqn{K12(r)} function.}
\item{lp. }{a data frame containing values of the modified \eqn{L12(r)} function.\cr\cr}
\item{ }{Each component except \code{r} is a data frame with the following variables:\cr\cr}
\item{lp. }{a data frame containing values of the modified \eqn{L12(r)} function.\cr}
Each component except \code{r} is a data frame with the following variables:\cr
\item{obs }{a vector of estimated values for the observed point pattern.}
\item{theo }{a vector of theoretical values expected under the null hypothesis of population independence (see \code{\link{k12fun}}).}
}
......
man/kpqfun.Rd
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......@@ -27,8 +27,8 @@ A list of class \code{"fads"} with essentially the following components:
\item{gpq }{a data frame containing values of the pair density functions \eqn{g(r)} and \eqn{g12(r)}.}
\item{npq }{a data frame containing values of the local neighbour density functions \eqn{n(r)} and \eqn{n12(r)}.}
\item{kpq }{a data frame containing values of the \eqn{K(r)} and \eqn{K12(r)} functions.}
\item{lpq }{a data frame containing values of the modified \eqn{L(r)} and \eqn{L12(r)} functions.\cr\cr}
\item{ }{Each component except \code{r} is a data frame with the following variables:\cr}
\item{lpq }{a data frame containing values of the modified \eqn{L(r)} and \eqn{L12(r)} functions.\cr}
Each component except \code{r} is a data frame with the following variables:\cr
\item{obs }{a vector of estimated values for the observed point pattern.}
\item{theo }{a vector of theoretical values expected under the null hypotheses of spatial randomness (see \code{\link{kfun}}) and
population independence (see \code{\link{k12fun}}).}
......
man/krfun.Rd
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......@@ -43,8 +43,8 @@ The species equivalence hypothesis (H0 = "se") is tested by randomizing the betw
A list of class \code{"fads"} with essentially the following components:
\item{r }{a vector of regularly spaced out distances (\code{seq(by,upto,by)}).}
\item{gr }{a data frame containing values of the function \eqn{gr(r)}.}
\item{kr }{a data frame containing values of the function \eqn{Kr(r)}.\cr\cr}
\item{}{Each component except \code{r} is a data frame with the following variables:\cr\cr}
\item{kr }{a data frame containing values of the function \eqn{Kr(r)}.\cr}
Each component except \code{r} is a data frame with the following variables:\cr
\item{obs }{a vector of estimated values for the observed point pattern.}
\item{theo }{a vector of theoretical values expected under the selected null hypothesis.}
\item{sup }{(optional) if \code{nsim>0} a vector of the upper local confidence limits of a random distribution of the selected null hypothesis at a significant level \eqn{\alpha}.}
......
man/ksfun.Rd
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......@@ -41,8 +41,8 @@ ksfun(p, upto, by, nsim=0, alpha=0.01)
A list of class \code{"fads"} with essentially the following components:
\item{r }{a vector of regularly spaced out distances (\code{seq(by,upto,by)}).}
\item{gs }{a data frame containing values of the function \eqn{gs(r)}.}
\item{ks }{a data frame containing values of the function \eqn{Ks(r)}.\cr\cr}
\item{}{Each component except \code{r} is a data frame with the following variables:\cr\cr}
\item{ks }{a data frame containing values of the function \eqn{Ks(r)}.\cr}
Each component except \code{r} is a data frame with the following variables:\cr
\item{obs }{a vector of estimated values for the observed point pattern.}
\item{theo }{a vector of theoretical values expected under the null hypothesis of random labelling, i.e. 1 for all \eqn{r}.}
\item{sup }{(optional) if \code{nsim>0} a vector of the upper local confidence limits of a random distribution of species labels at a significant level \eqn{\alpha}.}
......
src/triangulate.h
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......@@ -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 */
......
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