[Mmsar-commits] r11 - pkg/man www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Feb 6 20:03:59 CET 2010
Author: fguilhaumon
Date: 2010-02-06 20:03:59 +0100 (Sat, 06 Feb 2010)
New Revision: 11
Modified:
pkg/man/asymp.Rd
pkg/man/expo.Rd
pkg/man/logist.Rd
pkg/man/lomolino.Rd
pkg/man/monod.Rd
pkg/man/negexpo.Rd
pkg/man/ratio.Rd
www/index.php
Log:
Fix manpages, the package should now compile for windows and Mac.
Modified: pkg/man/asymp.Rd
===================================================================
--- pkg/man/asymp.Rd 2009-12-22 11:03:58 UTC (rev 10)
+++ pkg/man/asymp.Rd 2010-02-06 19:03:59 UTC (rev 11)
@@ -2,40 +2,32 @@
\Rdversion{1.1}
\alias{asymp}
\docType{data}
-\title{
-%% ~~ data name/kind ... ~~
-}
-\description{
-%% ~~ A concise (1-5 lines) description of the dataset. ~~
-}
+\title{The asymptotic SAR regression model}
+\description{S == c - z * f^A}
\usage{data(asymp)}
\format{
The format is:
-List of 9
- $ name : chr "asymptotic regression"
- $ formula : expression(S == c - z * f^A)
- $ paramnumber: num 3
- $ paramnames : chr [1:3] "c" "z" "f"
- $ limits : num [1:2, 1:3] 0 Inf 0 Inf 0 ...
- $ parLim : chr [1:3] "Rplus" "Rplus" "unif"
- $ fun :function (par, data)
- ..- attr(*, "source")= chr "function(par,data){if(length(data)>1) d=data[[1]] else d=data; s = par[1] - par[2] * par[3]^data[[1]]; as.vector(s)}"
- $ rssfun :function (par, data, opt)
- ..- attr(*, "source")= chr "function(par,data,opt){if(opt)par=backLink(par,asymp$parLim) ; sum( ( data[[2]] - (par[1] - par[2] * par[3]^data[[1]]) )^2 ) }"| __truncated__
- $ init :function (data)
- ..- attr(*, "source")= chr [1:10] "function(data){#Ratkowsky 1983 p178" ...
+List of 8
+ $ name : "asymptotic regression"
+ $ formula : expression(S == c - z * f^A)
+ $ paramnumber: 3
+ $ paramnames : "c" "z" "f"
+ $ parLim : "Rplus" "Rplus" "unif"
+ $ fun : model function
+ $ rssfun : Residual Sum of Squares function
+ $ init : initial values calculation from Ratkowsky (1983) p178
}
-\details{
-%% ~~ If necessary, more details than the __description__ above ~~
+\details{This model is convex asymptotic. Parameter c is the upper asymptote.
}
-\source{
-%% ~~ reference to a publication or URL from which the data were obtained ~~
-}
+\source{Tjørve (2003).}
\references{
-%% ~~ possibly secondary sources and usages ~~
+Ratkowsky, D.A. (1983) Nonlinear regression modelling: a unified approach. Marcel Dekker, New York.
+
+Tjørve, E. (2003) Shapes and functions of species–area curves: a review of possible models. Journal of Biogeography, 30, 827–835.
+
}
\examples{
+#loading the asymp model object before using it
data(asymp)
-## maybe str(asymp) ; plot(asymp) ...
}
-\keyword{datasets}
+\keyword{mmSAR model object, non linear regression}
Modified: pkg/man/expo.Rd
===================================================================
--- pkg/man/expo.Rd 2009-12-22 11:03:58 UTC (rev 10)
+++ pkg/man/expo.Rd 2010-02-06 19:03:59 UTC (rev 11)
@@ -2,40 +2,36 @@
\Rdversion{1.1}
\alias{expo}
\docType{data}
-\title{
-%% ~~ data name/kind ... ~~
-}
-\description{
-%% ~~ A concise (1-5 lines) description of the dataset. ~~
-}
+\title{The exponetial SAR regression model}
+\description{s == z * log(a) + c}
\usage{data(expo)}
\format{
The format is:
-List of 9
- $ name : chr "Exponential"
- $ formula : expression(s == z * log(a) + c)
- $ paramnumber: num 2
- $ paramnames : chr [1:2] "c" "z"
- $ limits : num [1:2, 1:2] 0 Inf 0 Inf
- $ parLim : chr [1:2] "R" "Rplus"
- $ fun :function (par, data)
- ..- attr(*, "source")= chr "function(par,data){if(length(data)>1) d=data[[1]] else d=data; s = par[2] * log(d) + par[1]; names(s)=c(\"s.expo\"); as.vector("| __truncated__
- $ rssfun :function (par, data, opt)
- ..- attr(*, "source")= chr "function(par,data,opt){if(opt)par=backLink(par,expo$parLim) ; sum( (data[[2]] - (par[2] * log(data[[1]]) + par[1]) ) ^2 )"| __truncated__
- $ init :function (data)
- ..- attr(*, "source")= chr [1:7] "function(data){" ...
+List of 8
+ $ name : "Exponential"
+ $ formula : expression(s == z * log(a) + c)
+ $ paramnumber: 2
+ $ paramnames : "c" "z"
+ $ parLim : "R" "Rplus"
+ $ fun : model function
+ $ rssfun : Residual Sum of Squares function
+ $ init : initial values calculation
}
-\details{
-%% ~~ If necessary, more details than the __description__ above ~~
+\details{This model is convex non asymptotic.
}
-\source{
-%% ~~ reference to a publication or URL from which the data were obtained ~~
+\source{Gleason (1922, 1925), Fisher et al. (1943), Tjørve (2003).
}
\references{
-%% ~~ possibly secondary sources and usages ~~
+Fisher, R.A., Corbet, A.S. & Williams, C.B. (1943) The relation between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology, 12, 42–58.
+
+Gleason, H.A. (1922) On the relation between species and area. Ecology, 3, 158–162.
+
+Gleason, H.A. (1925) Species and area. Ecology, 6, 66–74.
+
+Tjørve, E. (2003) Shapes and functions of species–area curves: a review of possible models. Journal of Biogeography, 30, 827–835.
}
\examples{
+#loading the expo model object before using it
data(expo)
-## maybe str(expo) ; plot(expo) ...
}
-\keyword{datasets}
+\keyword{mmSAR model object, non linear regression}
Modified: pkg/man/logist.Rd
===================================================================
--- pkg/man/logist.Rd 2009-12-22 11:03:58 UTC (rev 10)
+++ pkg/man/logist.Rd 2010-02-06 19:03:59 UTC (rev 11)
@@ -2,42 +2,33 @@
\Rdversion{1.1}
\alias{logist}
\docType{data}
-\title{
-%% ~~ data name/kind ... ~~
-}
-\description{
-%% ~~ A concise (1-5 lines) description of the dataset. ~~
-}
+\title{The logistic SAR regression model}
+\description{S == over(c, (1 + exp(-z * A + f)))}
\usage{data(logist)}
\format{
The format is:
-List of 10
- $ name : chr "Logistic function"
- $ formula : expression(S == over(c, (1 + exp(-z * A + f))))
- $ Formula :Class 'formula' length 3 s ~ over(par1, (1 + exp(-par2 * a + par3)))
- .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
- $ paramnumber: num 3
- $ paramnames : chr [1:3] "c" "z" "f"
- $ limits : num [1:2, 1:3] 0 Inf 0 Inf -Inf ...
- $ parLim : chr [1:3] "Rplus" "Rplus" "R"
- $ fun :function (par, data)
- ..- attr(*, "source")= chr "function(par,data){if(length(data)>1) d=data[[1]] else d=data; s = par[1] / (1 + exp(-par[2]*d+par[3])) ; as.vector(s)}"
- $ rssfun :function (par, data, opt)
- ..- attr(*, "source")= chr "function(par,data,opt){if(opt)par=backLink(par,logist$parLim) ; sum( ( data[[2]] - (par[1] / (1 + exp(-par[2]*data[[1]]+par[3])"| __truncated__
- $ init :function (data)
- ..- attr(*, "source")= chr [1:14] "function(data){" ...
+List of 8
+ $ name : "Logistic function"
+ $ formula : expression(S == over(c, (1 + exp(-z * A + f))))
+ $ paramnumber: 3
+ $ paramnames : "c" "z" "f"
+ $ parLim : "Rplus" "Rplus" "R"
+ $ fun : model function
+ $ rssfun : Residual Sum of Squares function
+ $ init : initial values calculation
}
-\details{
-%% ~~ If necessary, more details than the __description__ above ~~
+\details{This model is sigmoid asymptotic. Parameter c is the upper asymptote. The function is symmetrical about the inflection point. The curve has a lower asymptote of zero, and the intersection with the y-axis depends on all three parameters. Thus it never goes through the origin.
}
-\source{
-%% ~~ reference to a publication or URL from which the data were obtained ~~
+\source{Ratkowsky (1990), Tjørve (2003).
}
\references{
-%% ~~ possibly secondary sources and usages ~~
+
+Ratkowsky, D.A. (1990) Handbook of nonlinear regression models. Marcel Dekker, New York.
+
+Tjørve, E. (2003) Shapes and functions of species–area curves: a review of possible models. Journal of Biogeography, 30, 827–835.
}
\examples{
+#loading the logist model object before using it
data(logist)
-## maybe str(logist) ; plot(logist) ...
}
-\keyword{datasets}
+\keyword{mmSAR model object, non linear regression}
Modified: pkg/man/lomolino.Rd
===================================================================
--- pkg/man/lomolino.Rd 2009-12-22 11:03:58 UTC (rev 10)
+++ pkg/man/lomolino.Rd 2010-02-06 19:03:59 UTC (rev 11)
@@ -2,40 +2,32 @@
\Rdversion{1.1}
\alias{lomolino}
\docType{data}
-\title{
-%% ~~ data name/kind ... ~~
-}
-\description{
-%% ~~ A concise (1-5 lines) description of the dataset. ~~
-}
+\title{The lomolino SAR regression model}
+\description{S == c / 1 + z^log(f/A)}
\usage{data(lomolino)}
\format{
The format is:
-List of 9
- $ name : chr "Lomolino model"
- $ formula : expression(S == over(c, 1 + z^log(over(f, A))))
- $ paramnumber: num 3
- $ paramnames : chr [1:3] "c" "z" "f"
- $ limits : num [1:2, 1:3] 0 Inf 0 Inf 0 ...
- $ parLim : chr [1:3] "Rplus" "Rplus" "Rplus"
- $ fun :function (par, data)
- ..- attr(*, "source")= chr "function(par,data){if(length(data)>1) d=data[[1]] else d=data; s = par[1] / (1 + par[2]^log(par[3]/d)) ; as.vector(s)}"
- $ rssfun :function (par, data, opt)
- ..- attr(*, "source")= chr "function(par,data,opt){if(opt)par=backLink(par,lomolino$parLim) ; sum( ( data[[2]] - par[1] / (1 + par[2]^log(par[3]/data[[1]]"| __truncated__
- $ init :function (data)
- ..- attr(*, "source")= chr [1:11] "function(data){" ...
+List of 8
+ $ name : "Lomolino"
+ $ formula : expression(S == over(c, 1 + z^log(over(f, A))))
+ $ paramnumber: 3
+ $ paramnames : "c" "z" "f"
+ $ parLim : "Rplus" "Rplus" "Rplus"
+ $ fun : model function
+ $ rssfun : Residual Sum of Squares function
+ $ init : initial values calculation
}
-\details{
-%% ~~ If necessary, more details than the __description__ above ~~
+\details{The lomolino model is sigmoid asymptotic. Parameter c is the upper asymptote.
}
-\source{
-%% ~~ reference to a publication or URL from which the data were obtained ~~
+\source{Lomolino, M.V. (2000), Tjørve (2003).
}
\references{
-%% ~~ possibly secondary sources and usages ~~
+Lomolino, M.V. (2000) Ecology’s most general, yet protean pattern: the species–area relationship. Journal of Biogeography, 27, 17–26.
+
+Tjørve, E. (2003) Shapes and functions of species–area curves: a review of possible models. Journal of Biogeography, 30, 827–835.
}
\examples{
+#loading the lomolino model object before using it
data(lomolino)
-## maybe str(lomolino) ; plot(lomolino) ...
}
-\keyword{datasets}
+\keyword{mmSAR model object, non linear regression}
Modified: pkg/man/monod.Rd
===================================================================
--- pkg/man/monod.Rd 2009-12-22 11:03:58 UTC (rev 10)
+++ pkg/man/monod.Rd 2010-02-06 19:03:59 UTC (rev 11)
@@ -2,40 +2,32 @@
\Rdversion{1.1}
\alias{monod}
\docType{data}
-\title{
-%% ~~ data name/kind ... ~~
-}
-\description{
-%% ~~ A concise (1-5 lines) description of the dataset. ~~
-}
+\title{The Monod function SAR regression model}
+\description{s == c * a /z + a}
\usage{data(monod)}
\format{
The format is:
-List of 9
- $ name : chr "Monod"
- $ formula : expression(s == over(c * a, z + a))
- $ paramnumber: num 2
- $ paramnames : chr [1:2] "c" "z"
- $ limits : num [1:2, 1:2] 0 Inf 0 Inf
- $ parLim : chr [1:2] "Rplus" "Rplus"
- $ fun :function (par, data)
- ..- attr(*, "source")= chr "function(par,data){if(length(data)>1) d=data[[1]] else d=data; s = (par[1]*d) / (par[2]+d) ; names(s)=c(\"s.monod\"); as.vector"| __truncated__
- $ rssfun :function (par, data, opt)
- ..- attr(*, "source")= chr "function(par,data,opt){if(opt)par=backLink(par,monod$parLim) ; sum( ( data[\"s\"] - (par[1]*data[\"a\"]) / (par[2]+data[\"a\"]"| __truncated__
- $ init :function (data)
- ..- attr(*, "source")= chr [1:12] "function(data){" ...
+List of 8
+ $ name : "Monod"
+ $ formula : expression(s == over(c * a, z + a))
+ $ paramnumber: 2
+ $ paramnames : "c" "z"
+ $ parLim : "Rplus" "Rplus"
+ $ fun : model function
+ $ rssfun : Residual Sum of Squares function
+ $ init : initial values calculation
}
-\details{
-%% ~~ If necessary, more details than the __description__ above ~~
+\details{The Monod function SAR model is convex asymptotic.
}
-\source{
-%% ~~ reference to a publication or URL from which the data were obtained ~~
+\source{Monod (1950), Tjørve (2003).
}
\references{
-%% ~~ possibly secondary sources and usages ~~
+Monod, J. (1950) La technique de culture continue, the´orie et applications. Annales de l’Institut Pasteur, 79, 390–410.
+
+Tjørve, E. (2003) Shapes and functions of species–area curves: a review of possible models. Journal of Biogeography, 30, 827–835.
}
\examples{
+#loading the monod model object before using it
data(monod)
-## maybe str(monod) ; plot(monod) ...
}
-\keyword{datasets}
+\keyword{mmSAR model object, non linear regression}
Modified: pkg/man/negexpo.Rd
===================================================================
--- pkg/man/negexpo.Rd 2009-12-22 11:03:58 UTC (rev 10)
+++ pkg/man/negexpo.Rd 2010-02-06 19:03:59 UTC (rev 11)
@@ -2,40 +2,36 @@
\Rdversion{1.1}
\alias{negexpo}
\docType{data}
-\title{
-%% ~~ data name/kind ... ~~
-}
-\description{
-%% ~~ A concise (1-5 lines) description of the dataset. ~~
-}
+\title{The negative exponential SAR regression model}
+\description{s == c * (1 - exp(-z * a))}
\usage{data(negexpo)}
\format{
The format is:
-List of 9
- $ name : chr "Negative exponential"
- $ formula : expression(s == c * (1 - exp(-z * a)))
- $ paramnumber: num 2
- $ paramnames : chr [1:2] "c" "z"
- $ limits : num [1:2, 1:2] 0 Inf 0 1
- $ parLim : chr [1:2] "Rplus" "unif"
- $ fun :function (par, data)
- ..- attr(*, "source")= chr "function(par,data){if(length(data)>1) d=data[[1]] else d=data; s = par[1]*(1 - exp(-par[2]*d)) ; names(s)=c(\"s.negexpo\"); as."| __truncated__
- $ rssfun :function (par, data, opt)
- ..- attr(*, "source")= chr "function(par,data,opt){if(opt)par=backLink(par,negexpo$parLim) ; sum( ( data[[2]] - par[1] * (1 - exp(-par[2] * data[[1]]) ) )"| __truncated__
- $ init :function (data)
- ..- attr(*, "source")= chr "function(data){c=max(data[[2]]); Z=( -log( (-data[[2]]/(max(data[[2]])+1))+1))/data[[1]]; z = mean(Z); c(c,z)}"
+List of 8
+ $ name : "Negative exponential"
+ $ formula : expression(s == c * (1 - exp(-z * a)))
+ $ paramnumber: 8
+ $ paramnames : "c" "z"
+ $ parLim : "Rplus" "unif"
+ $ fun : model function
+ $ rssfun : Residual Sum of Squares function
+ $ init : initial values calculation
}
-\details{
-%% ~~ If necessary, more details than the __description__ above ~~
+\details{The negative exponential model is convex asymptotic.
}
-\source{
-%% ~~ reference to a publication or URL from which the data were obtained ~~
+\source{Holdridge et al. (1971), Miller & Wiegert (1989), Ratkowsky (1990), Tjørve (2003).
}
\references{
-%% ~~ possibly secondary sources and usages ~~
+Holdridge, L.R., Grenke, W.C., Hatheway, W.H., Liang, T. & Tosi, J.A. (1971) Forest environments in tropical life zones. Pergamon Press, Oxford.
+
+Miller, R.I. & Wiegert, R.G. (1989) Documenting completeness, species–area relations, and the species abundance distribution of a regional flora. Ecology, 70, 16–22.
+
+Ratkowsky, D.A. (1990) Handbook of nonlinear regression models. Marcel Dekker, New York.
+
+Tjørve, E. (2003) Shapes and functions of species–area curves: a review of possible models. Journal of Biogeography, 30, 827–835.
}
\examples{
+#loading the negexpo model object before using it
data(negexpo)
-## maybe str(negexpo) ; plot(negexpo) ...
}
-\keyword{datasets}
+\keyword{mmSAR model object, non linear regression}
Modified: pkg/man/ratio.Rd
===================================================================
--- pkg/man/ratio.Rd 2009-12-22 11:03:58 UTC (rev 10)
+++ pkg/man/ratio.Rd 2010-02-06 19:03:59 UTC (rev 11)
@@ -2,40 +2,32 @@
\Rdversion{1.1}
\alias{ratio}
\docType{data}
-\title{
-%% ~~ data name/kind ... ~~
-}
-\description{
-%% ~~ A concise (1-5 lines) description of the dataset. ~~
-}
+\title{The rational function SAR regression model}
+\description{S == (c + z * A) / (1 + f * A)}
\usage{data(ratio)}
\format{
The format is:
-List of 9
- $ name : chr "Rational function"
- $ formula : expression(S == over((c + z * A), (1 + f * A)))
- $ paramnumber: num 3
- $ paramnames : chr [1:3] "c" "z" "f"
- $ limits : num [1:2, 1:3] -Inf Inf -Inf Inf -Inf ...
- $ parLim : chr [1:3] "R" "R" "R"
- $ fun :function (par, data)
- ..- attr(*, "source")= chr "function(par,data){if(length(data)>1) d=data[[1]] else d=data; s = (par[1] + par[2] * d) / (1 + par [3]*d) ; as.vector(s)}"
- $ rssfun :function (par, data, opt)
- ..- attr(*, "source")= chr "function(par,data,opt){if(opt)par=backLink(par,ratio$parLim) ; sum( ( data[[2]] - ((par[1] + par[2] * data[[1]]) / (1 + par [3]"| __truncated__
- $ init :function (data)
- ..- attr(*, "source")= chr "function(data){c(0,0,0)}"
+List of 8
+ $ name : "Rational function"
+ $ formula : expression(S == over((c + z * A), (1 + f * A)))
+ $ paramnumber: 3
+ $ paramnames : "c" "z" "f"
+ $ parLim : "R" "R" "R"
+ $ fun : model function
+ $ rssfun : Residual Sum of Squares function
+ $ init : initial values calculation
}
-\details{
-%% ~~ If necessary, more details than the __description__ above ~~
+\details{The rational function model (Ratkowsky, 1990) is convex asymptotic. Each parameter in the model affects several curve aspects (shape, upper asymptote and y-axis intersection).
}
-\source{
-%% ~~ reference to a publication or URL from which the data were obtained ~~
+\source{Ratkowsky (1990), Tjørve (2003).
}
\references{
-%% ~~ possibly secondary sources and usages ~~
+Ratkowsky, D.A. (1990) Handbook of nonlinear regression models. Marcel Dekker, New York.
+
+Tjørve, E. (2003) Shapes and functions of species–area curves: a review of possible models. Journal of Biogeography, 30, 827–835.
}
\examples{
+#loading the ratio model object before using it
data(ratio)
-## maybe str(ratio) ; plot(ratio) ...
}
-\keyword{datasets}
+\keyword{mmSAR model object, non linear regression}
Modified: www/index.php
===================================================================
--- www/index.php 2009-12-22 11:03:58 UTC (rev 10)
+++ www/index.php 2010-02-06 19:03:59 UTC (rev 11)
@@ -43,7 +43,7 @@
<!-- end of project description -->
-
+<p> The <strong>project summary page</strong> you can find <a href="http://<?php echo $domain; ?>/projects/<?php echo $group_name; ?>/"><strong>here</strong></a>. </p>
<br/>
<strong>Installing and loading mmSAR</strong>
<br/>
@@ -246,14 +246,7 @@
return the following :
<br/>
<code>expression(s == c * a^z)</code>
-
-
-
-
-
-
-
-<p> The <strong>project summary page</strong> you can find <a href="http://<?php echo $domain; ?>/projects/<?php echo $group_name; ?>/"><strong>here</strong></a>. </p>
-
+<br/>
+<br/><br/><br/>
</body>
</html>
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