[Stacomir-commits] r244 - in pkg/stacomir: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jan 24 12:31:16 CET 2017
Author: briand
Date: 2017-01-24 12:31:15 +0100 (Tue, 24 Jan 2017)
New Revision: 244
Added:
pkg/stacomir/man/BilanAgedemer-class.Rd
pkg/stacomir/man/calcule-BilanAgedemer-method.Rd
pkg/stacomir/man/charge-BilanAgedemer-method.Rd
pkg/stacomir/man/choice_c-BilanAgedemer-method.Rd
pkg/stacomir/man/choice_c-RefTextBox-method.Rd
pkg/stacomir/man/connect-BilanAgedemer-method.Rd
pkg/stacomir/man/funplotBilanAgedemer.Rd
pkg/stacomir/man/funtableBilanAgedemer.Rd
pkg/stacomir/man/interface_BilanAgedemer.Rd
pkg/stacomir/man/plot-BilanAgedemer-missing-method.Rd
pkg/stacomir/man/print-BilanAgedemer-method.Rd
pkg/stacomir/man/summary-BilanAgedemer-method.Rd
pkg/stacomir/man/write_database-BilanAgedemer-method.Rd
Removed:
pkg/stacomir/man/plot.Rd
Modified:
pkg/stacomir/DESCRIPTION
pkg/stacomir/NAMESPACE
pkg/stacomir/R/BilanAgedemer.r
pkg/stacomir/R/BilanArgentee.r
pkg/stacomir/R/Refpar.r
pkg/stacomir/man/BilanAnnuels-class.Rd
pkg/stacomir/man/BilanArgentee-class.Rd
pkg/stacomir/man/BilanEspeces-class.Rd
pkg/stacomir/man/BilanFonctionnementDC-class.Rd
pkg/stacomir/man/BilanFonctionnementDF-class.Rd
pkg/stacomir/man/BilanMigration-class.Rd
pkg/stacomir/man/BilanMigrationConditionEnv-class.Rd
pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
pkg/stacomir/man/BilanMigrationMult-class.Rd
pkg/stacomir/man/Bilan_carlot-class.Rd
pkg/stacomir/man/Bilan_poids_moyen-class.Rd
pkg/stacomir/man/Bilan_stades_pigm-class.Rd
pkg/stacomir/man/Bilan_taille-class.Rd
pkg/stacomir/man/RefTextBox-class.Rd
pkg/stacomir/man/calcule.Rd
pkg/stacomir/man/charge-RefTextBox-method.Rd
pkg/stacomir/man/charge.Rd
pkg/stacomir/man/charge_avec_filtre.Rd
pkg/stacomir/man/charge_complement.Rd
pkg/stacomir/man/choice-RefTextBox-method.Rd
pkg/stacomir/man/choice.Rd
pkg/stacomir/man/choice_c.Rd
pkg/stacomir/man/choicemult.Rd
pkg/stacomir/man/createmessage.Rd
pkg/stacomir/man/envir_stacomi.Rd
pkg/stacomir/man/f_stade_Durif.Rd
pkg/stacomir/man/getvalue.Rd
pkg/stacomir/man/model.Rd
pkg/stacomir/man/out.Rd
pkg/stacomir/man/supprime.Rd
pkg/stacomir/man/write_database.Rd
Log:
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/DESCRIPTION 2017-01-24 11:31:15 UTC (rev 244)
@@ -1,6 +1,6 @@
Package: stacomiR
Version: 0.5.0
-Date: 2016-12-18
+Date: 2017-01-24
Title: Fish Migration Monitoring (stacomiR)
Authors at R: c(person("Cedric", "Briand", role = c("aut", "cre"), email = "cedric.briand00 at gmail.com"),
person("Marion", "Legrand", role = "aut", email="tableau-salt-loire at logrami.fr"))
@@ -11,13 +11,15 @@
License: GPL (>= 2)
Collate:
'create_generic.r'
- 'RefAnnee.r'
+ 'Refpar.r'
+ 'RefHorodate.r'
'RefStades.r'
'RefTaxon.r'
'RefDC.r'
+ 'ReftextBox.r'
+ 'BilanAgedemer.r'
+ 'RefAnnee.r'
'BilanAnnuels.r'
- 'Refpar.r'
- 'RefHorodate.r'
'BilanArgentee.r'
'utilitaires.r'
'RefStationMesure.r'
@@ -41,7 +43,6 @@
'Bilan_carlot.r'
'RefCoe.r'
'Bilan_poids_moyen.r'
- 'ReftextBox.r'
'RefCheckBox.r'
'Bilan_stades_pigm.r'
'Bilan_taille.r'
@@ -58,6 +59,7 @@
'funstatJournalier.r'
'funtable.r'
'funtraitement_poids.r'
+ 'interface_BilanAgedemer.r'
'interface_BilanAnnuels.r'
'interface_BilanArgentee.r'
'interface_BilanConditionEnv.r'
@@ -101,7 +103,8 @@
RGtk2,
lubridate,
dplyr,
- xtable
+ xtable,
+ mgcv
Suggests:
testthat,
viridis
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/NAMESPACE 2017-01-24 11:31:15 UTC (rev 244)
@@ -10,9 +10,11 @@
export(fundat)
export(fundensityBilan_carlot)
export(funout)
+export(funplotBilanAgedemer)
export(funplotBilanArgentee)
export(funpointBilan_carlot)
export(funstat)
+export(funtableBilanAgedemer)
export(funtableBilanArgentee)
export(funtableBilan_carlot)
export(funtraitement_poids)
@@ -27,6 +29,7 @@
export(split_per_day)
export(stacomi)
export(vector_to_listsql)
+exportClasses(BilanAgedemer)
exportClasses(BilanAnnuels)
exportClasses(BilanArgentee)
exportClasses(BilanConditionEnv)
Modified: pkg/stacomir/R/BilanAgedemer.r
===================================================================
--- pkg/stacomir/R/BilanAgedemer.r 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/R/BilanAgedemer.r 2017-01-24 11:31:15 UTC (rev 244)
@@ -1,21 +1,21 @@
#' Class "BilanAgedemer"
#'
-#' the BilanAgedemer class is used to calculate various statistics about the silver eel run
+#' the BilanAgedemer class is used to dispatch adult salmons to age class according
+#' their size and to basin dependent limits set by the user. Once checked with graphs and summary
+#' statistics, the results are to be written to the database.
+#' @include create_generic.r
+#' @include ReftextBox.r
#' @include RefDC.r
#' @include RefTaxon.r
#' @include RefStades.r
#' @include RefHorodate.r
#' @include Refpar.r
-#' @note This class is displayed by interface_bilan_admentee
+#' @note This class is displayed by interface_bilan_agedemer
#' @slot data A data frame with data generated from the database
-#' @slot calcdata A list of dc with processed data. Each dc contains a data frame with
+#' @slot calcdata A list of dc with processed data. This lists consists of two elements
#' \itemize{
-#' \item (1) qualitative data on body contrast (CONT), presence of punctuation on the lateral line (LINP)
-#' \item (2) quantitative data "BL" Body length,"W" weight,"Dv" vertical eye diameter,"Dh" horizontal eye diameter,"FL" pectoral fin length
-#' \item (3) calculated durif stages, Pankhurst's index, Fulton's body weight coefficient K_ful
-#' \item (4) other columns containing data pertaining to the sample and the control operation: lot_identifiant,ope_identifiant,
-#' ope_dic_identifiant,ope_date_debut,ope_date_fin,dev_code (destination code of fish),
-#' dev_libelle (text for destination of fish)
+#' \item (1) data A dataset with age set to be used by the plot and summary methods
+#' \item (2) tj_caracteristitiquelot_car A dataset to import into the database
#' }
#' @slot dc Object of class \link{RefDC-class}: the control devices
#' @slot taxons Object of class \link{RefTaxon-class}: the speciess
@@ -23,12 +23,14 @@
#' @slot par Object of class \link{Refpar-class}: the parameters used
#' @slot horodatedebut An object of class \code{RefHorodate-class}
#' @slot horodatefin An object of class \code{RefHorodate-class}
+#' @slot limit1hm The size limit, in mm between 1 sea winter fishes and 2 sea winter fishes
+#' @slot limit2hm The size limit, in mm between 3 sea winter fishes and 3 sea winter fishes
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("BilanAgedemer", ...)}
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @family Bilan Objects
#' @keywords classes
-#' @example inst/examples/bilan_admentee_example.R
+#' @example inst/examples/bilanAgedemer_example.R
#' @export
setClass(Class="BilanAgedemer",
representation= representation(
@@ -274,14 +276,13 @@
ylab("Effectif")
print(p)
assign("p",p,envir=envir_stacomi)
- funout("L'objet graphique est écrit dans l'environnement stacomi, tappez p<-get('p',envir=envir_stacomi))")
+ funout("The graphical object is written is env_stacomi, type p<-get('p',envir=envir_stacomi))")
}
######################################
# Migration according to stage, month and year
######################################
- if (plot.type=="2"){
-
+ if (plot.type=="2"){
p<-ggplot(dat)+geom_histogram(aes(x=car_valeur_quantitatif,fill=factor(age)),alpha=0.8)+
geom_vline(xintercept=les_coupes,lty=2,lwd=1)+
theme_minimal()+
@@ -292,186 +293,8 @@
print(p)
assign("p",p,envir=envir_stacomi)
funout("L'objet graphique est écrit dans l'environnement stacomi, tappez p<-get('p',envir=envir_stacomi))")
-
-
}
- ######################################
- # Series of graphs showing proportion of stage, mean Fulton's coefficient, Pankhurst eye index,
- # body weight, body size, sex ratio.
- ######################################
- if (plot.type=="3"){
- layout(matrix(c(1,2,3,4,4,5,6,6,7), 3, 3, byrow = TRUE),
- widths=c(3,3,1), heights=c(3,1,3))
- # width 331 sets the last column relative width
- # same for rows
- par(mar=c(3,4.1,4.1,2.1))# ressetting to default
- datdc<-chnames(datdc,"ope_dic_identifiant","dc")
- lesdc<-unique(datdc$dc)
- datdc$sex<-"F"
- datdc$sex[datdc$BL<450]<-"M"
-
- #############
- # Fulton
- #############
- moy<-tapply(datdc$K_ful,list(datdc$dc,datdc$sex),mean,na.rm=TRUE)
- sd<- tapply(datdc$K_ful,list(datdc$dc,datdc$sex),sd,na.rm=TRUE) # sample standard deviation
- n<-tapply(datdc$K_ful,list(datdc$dc,datdc$sex),length)
- SE = sd/sqrt(n)
- plotTop=max(moy+3*SE,na.rm=TRUE)
-
-
- bp<-barplot(moy,
- beside = TRUE, las = 1,
- ylim = c(0, plotTop),
- cex.names = 0.75,
- main = "Fulton coefficient (+-2SE)",
- ylab = "Fulton K",
- xlab = "",
- border = "black", axes = TRUE,
- #legend.text = TRUE,
- #adms.legend = list(title = "DC",
- # x = "topright",
- # cex = .7)
- )
- graphics::segments(bp, moy - SE * 2, bp,
- moy + SE * 2, lwd = 2)
-
- graphics::arrows(bp, moy - SE * 2, bp,
- moy + SE * 2, lwd = 2, angle = 90,
- code = 3, length = 0.05)
-
-
- #############
- # Pankhurst
- #############
- moy<-tapply(datdc$Pankhurst,list(datdc$dc,datdc$sex),mean,na.rm=TRUE)
- sd<- tapply(datdc$Pankhurst,list(datdc$dc,datdc$sex),sd,na.rm=TRUE) # sample standard deviation
- n<-tapply(datdc$Pankhurst,list(datdc$dc,datdc$sex),length)
- SE = sd/sqrt(n)
- plotTop=max(moy+3*SE,na.rm=TRUE)
-
-
- bp<-barplot(moy,
- beside = TRUE, las = 1,
- ylim = c(0, plotTop),
- cex.names = 0.75,
- main = "Pankhurst (+-2SE)",
- ylab = "Pankhurst eye index",
- xlab = "",
- border = "black", axes = TRUE,
- #legend.text = TRUE,
- #adms.legend = list(title = "DC",
- # x = "topright",
- # cex = .7)
- )
- segments(bp, moy - SE * 2, bp,
- moy + SE * 2, lwd = 2)
-
- arrows(bp, moy - SE * 2, bp,
- moy + SE * 2, lwd = 2, angle = 90,
- code = 3, length = 0.05)
-
- #############
- # empty plot
- #############
- op<-par(mar=c(1,1,1,1))
- plot(1, type="n", axes=F, xlab="", ylab="")
- legend("center",fill =grDevices::grey.colors(nrow(moy)),legend=unique(datdc$dc))
- # grey.colors is the default color generation for barplot
- #############
- # size hist
- #############
- par(mar=c(1,4.1,1,1))
- for (i in 1:length(lesdc)){
- indexdc<-datdc$dc==lesdc[i]
- histxn<-graphics::hist(datdc$BL[indexdc],breaks=seq(250,1000,by=50),plot=FALSE)$density
- if (i==1) histx<-histxn else histx<-cbind(histx,histxn)
- }
- if (length(lesdc)>1) colnames(histx)<-lesdc
- barplot(height=t(histx),space=0,beside=FALSE, las = 1,horiz=FALSE,legend.text = FALSE,axes=FALSE)
- #############
- # empty plot
- #############
- op<-par(mar=c(1,1,1,1))
- plot(1, type="n", axes=F, xlab="", ylab="")
-
- #############
- # size -weight
- #############
- par(mar=c(5.1,4.1,1,1)) # blur bottom left up right
- plot(datdc$BL,datdc$W,type="n",
- xlab=get("msg",envir=envir_stacomi)$BilanAgedemer.9,
- ylab=get("msg",envir=envir_stacomi)$BilanAgedemer.10,
- xlim=c(250,1000),ylim=c(0,2000))
- abline(v=seq(250,1000,by=50), col = "lightgray",lty=2)
- abline(h=seq(0,2000,by=100),col="lightgray",lty=2)
- # some alpha blending to better see the points :
- lescol<-ggplot2::alpha(grDevices::grey.colors(nrow(moy)),0.8)
- for (i in 1:length(lesdc)){
- indexdc<-datdc$dc==lesdc[i]
- points(datdc$BL[indexdc],datdc$W[indexdc],pch=16,col=lescol[i],cex=0.8)
-
- }
- ######################"
- # Size - weight model using robust regression
- ######################
- subdatdc<-datdc[,c("BL","W")]
- subdatdc$BL3<-(subdatdc$BL/1000)^3
- # plot(subdatdc$W~subdatdc$BL3)
-
- rlmmodb<-MASS::rlm(W~0+BL3,data=subdatdc)
- #summary(rlmmodb)
- newdata<-data.frame("BL"=seq(250,1000,by=50),"BL3"=(seq(250,1000,by=50)/1000)^3)
- pred<-predict(rlmmodb,newdata=newdata,se.fit=TRUE,type="response",interval="prediction")
- newdata$predlm<-pred$fit[,1]
- newdata$predlowIC<-pred$fit[,2]
- newdata$predhighIC<-pred$fit[,3]
-
- points(newdata$BL,newdata$predlm,type="l")
- points(newdata$BL,newdata$predlowIC,type="l",lty=2,col="grey50")
- points(newdata$BL,newdata$predhighIC,type="l",lty=2,col="grey50")
-
- text(400,1500,stringr::str_c("W=",round(coefficients(rlmmodb),1)," BL^3"))
-
- #############
- # weight hist rotate
- #############
- par(mar=c(5.1,1,1,1))
- for (i in 1:length(lesdc)){
- indexdc<-datdc$dc==lesdc[i]
- histyn<-hist(datdc$W[indexdc],plot=FALSE,breaks=seq(0,2000,by=100))$density
- if (i==1) histy<-histyn else histy<-cbind(histy,histyn)
-
- }
- if (length(lesdc)>1) colnames(histy)<-lesdc
- barplot(height=t(histy),space=0,beside=FALSE, las = 1,horiz=TRUE,legend.text = FALSE,axes=FALSE)
-
-
- }
- if (plot.type=="4"){
- #creating a shingle with some overlaps
- my.settings <- list(
- superpose.polygon=list(
- col=c("Lime green","#420A68E6","#932667E6","#DD513AE6","#FCA50AE6",blue_for_males),
- alpha=c(0.9,0.9,0.9,0.9,0.9,0.9)
- ),
- superpose.line=list(
- col=c("#FBA338","#420A68E6","#932667E6","#DD513AE6","#FCA50AE6",blue_for_males)
- ),
- #colfn<-colorRampPalette(c("#1C4587", "#BBC7DB"),space = "Lab")
- #colfn(7)
- strip.background=list(col=c("#1B4586","#3E5894","#596DA2","#7282B0","#8A98BE","#A2AFCC","#BAC6DA")),
- strip.border=list(col="black")
- )
- lattice::trellis.par.set(my.settings)
-
- ccc<-lattice::cloud(Pankhurst ~ W * BL|ouv, data = datdc,group=stage,
- screen = list(x = -90, y = 70), distance = .4, zoom = .6,strip = lattice::strip.custom(par.strip.text=list(col="white")))
- return(ccc)
- }
-
-
})
#' summary for BilanAgedemer
Modified: pkg/stacomir/R/BilanArgentee.r
===================================================================
--- pkg/stacomir/R/BilanArgentee.r 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/R/BilanArgentee.r 2017-01-24 11:31:15 UTC (rev 244)
@@ -1,6 +1,7 @@
#' Class "BilanArgentee"
#'
#' the BilanArgentee class is used to calculate various statistics about the silver eel run
+#' @include create_generic.r
#' @include RefDC.r
#' @include RefTaxon.r
#' @include RefStades.r
Modified: pkg/stacomir/R/Refpar.r
===================================================================
--- pkg/stacomir/R/Refpar.r 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/R/Refpar.r 2017-01-24 11:31:15 UTC (rev 244)
@@ -6,7 +6,7 @@
#' Class "Refpar"
#'
#' Class enabling to load the list of parameters and select one of them
-#'
+#' @include create_generic.r
#' @slot data A data.frame
#' @slot par_selectionne A character vector corresponding to par_code
#' @section Objects from the Class: Objects can be created by calls of the form
Added: pkg/stacomir/man/BilanAgedemer-class.Rd
===================================================================
--- pkg/stacomir/man/BilanAgedemer-class.Rd (rev 0)
+++ pkg/stacomir/man/BilanAgedemer-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -0,0 +1,107 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/BilanAgedemer.r
+\docType{class}
+\name{BilanAgedemer-class}
+\alias{BilanAgedemer-class}
+\title{Class "BilanAgedemer"}
+\description{
+the BilanAgedemer class is used to dispatch adult salmons to age class according
+their size and to basin dependent limits set by the user. Once checked with graphs and summary
+statistics, the results are to be written to the database.
+}
+\section{Slots}{
+
+\describe{
+\item{\code{data}}{A data frame with data generated from the database}
+
+\item{\code{calcdata}}{A list of dc with processed data. This lists consists of two elements
+\itemize{
+\item (1) data A dataset with age set to be used by the plot and summary methods
+\item (2) tj_caracteristitiquelot_car A dataset to import into the database
+}}
+
+\item{\code{dc}}{Object of class \link{RefDC-class}: the control devices}
+
+\item{\code{taxons}}{Object of class \link{RefTaxon-class}: the speciess}
+
+\item{\code{stades}}{Object of class \link{RefStades-class} : the stages of the fish}
+
+\item{\code{par}}{Object of class \link{Refpar-class}: the parameters used}
+
+\item{\code{horodatedebut}}{An object of class \code{RefHorodate-class}}
+
+\item{\code{horodatefin}}{An object of class \code{RefHorodate-class}}
+
+\item{\code{limit1hm}}{The size limit, in mm between 1 sea winter fishes and 2 sea winter fishes}
+
+\item{\code{limit2hm}}{The size limit, in mm between 3 sea winter fishes and 3 sea winter fishes}
+}}
+\note{
+This class is displayed by interface_bilan_agedemer
+}
+\section{Objects from the Class}{
+ Objects can be created by calls of the form
+\code{new("BilanAgedemer", ...)}
+}
+\examples{
+require(stacomiR)
+# launching stacomi without selecting the scheme or interface
+stacomi(gr_interface=FALSE,
+ login_window=FALSE,
+ database_expected=TRUE)
+# the following script will load data from the two Anguillere monitored in the Somme
+
+\dontrun{
+ #create an instance of the class
+ bilan_adm<-new("BilanAgedemer")
+ baseODBC<-get("baseODBC",envir=envir_stacomi)
+ baseODBC[c(2,3)]<-rep("logrami",2)
+ assign("baseODBC",baseODBC,envir_stacomi)
+ sch<-get("sch",envir=envir_stacomi)
+ assign("sch","logrami.",envir_stacomi)
+ bilan_adm<-choice_c(bilan_adm,
+ dc=c(107,108,101),
+ horodatedebut="2012-01-01",
+ horodatefin="2012-12-31",
+ limit1hm=675,
+ limit2hm=875,
+ silent=FALSE
+ )
+ bilan_adm<-connect(bilan_adm)
+
+}
+# load the dataset generated by previous lines
+data("bilan_adm")
+# the calculation will fill the slot calcdata
+bilan_adm<-calcule(bilan_adm)
+# stages are in bilan_adm at calcdata[["6"]][,"stage"]
+#look at data structure using str(bilan_adm at calcdata[["6"]])
+
+# standard plot as drawn by Laurent Beaulaton (Analyse des données d'argenture acquises en France)
+# showing Durif's stage according to size and eye diameter
+plot(bilan_adm, plot.type=1)
+
+
+# print a summary statistic, and save the output in a list for later use
+stats<-summary(bilan_adm)
+}
+\author{
+Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+}
+\seealso{
+Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+ \code{\link{BilanArgentee-class}},
+ \code{\link{BilanEspeces-class}},
+ \code{\link{BilanFonctionnementDC-class}},
+ \code{\link{BilanFonctionnementDF-class}},
+ \code{\link{BilanMigration-class}},
+ \code{\link{BilanMigrationConditionEnv-class}},
+ \code{\link{BilanMigrationInterAnnuelle-class}},
+ \code{\link{BilanMigrationMult-class}},
+ \code{\link{Bilan_carlot-class}},
+ \code{\link{Bilan_poids_moyen-class}},
+ \code{\link{Bilan_stades_pigm-class}},
+ \code{\link{Bilan_taille-class}}
+}
+\keyword{classes}
+
Modified: pkg/stacomir/man/BilanAnnuels-class.Rd
===================================================================
--- pkg/stacomir/man/BilanAnnuels-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/BilanAnnuels-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -95,7 +95,8 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other Bilan Objects: \code{\link{BilanArgentee-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanArgentee-class}},
\code{\link{BilanEspeces-class}},
\code{\link{BilanFonctionnementDC-class}},
\code{\link{BilanFonctionnementDF-class}},
Modified: pkg/stacomir/man/BilanArgentee-class.Rd
===================================================================
--- pkg/stacomir/man/BilanArgentee-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/BilanArgentee-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -95,7 +95,8 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanAnnuels-class}},
\code{\link{BilanEspeces-class}},
\code{\link{BilanFonctionnementDC-class}},
\code{\link{BilanFonctionnementDF-class}},
Modified: pkg/stacomir/man/BilanEspeces-class.Rd
===================================================================
--- pkg/stacomir/man/BilanEspeces-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/BilanEspeces-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -46,7 +46,8 @@
\code{\linkS4class{BilanMigrationInterAnnuelle}},
\code{\linkS4class{BilanMigrationPar}}
-Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanAnnuels-class}},
\code{\link{BilanArgentee-class}},
\code{\link{BilanFonctionnementDC-class}},
\code{\link{BilanFonctionnementDF-class}},
Modified: pkg/stacomir/man/BilanFonctionnementDC-class.Rd
===================================================================
--- pkg/stacomir/man/BilanFonctionnementDC-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/BilanFonctionnementDC-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -65,7 +65,8 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanAnnuels-class}},
\code{\link{BilanArgentee-class}},
\code{\link{BilanEspeces-class}},
\code{\link{BilanFonctionnementDF-class}},
Modified: pkg/stacomir/man/BilanFonctionnementDF-class.Rd
===================================================================
--- pkg/stacomir/man/BilanFonctionnementDF-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/BilanFonctionnementDF-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -67,7 +67,8 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanAnnuels-class}},
\code{\link{BilanArgentee-class}},
\code{\link{BilanEspeces-class}},
\code{\link{BilanFonctionnementDC-class}},
Modified: pkg/stacomir/man/BilanMigration-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigration-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/BilanMigration-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -77,7 +77,6 @@
#Individual plot for all DC (standard), taxon and stage where data present
#silent argument to stop all messages
plot(bM_Arzal,plot.type="standard",silent=TRUE)
-
#cumulated migration at the station (all stages and DC grouped)
plot(bM_Arzal,plot.type="step")
@@ -96,7 +95,8 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanAnnuels-class}},
\code{\link{BilanArgentee-class}},
\code{\link{BilanEspeces-class}},
\code{\link{BilanFonctionnementDC-class}},
Modified: pkg/stacomir/man/BilanMigrationConditionEnv-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationConditionEnv-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/BilanMigrationConditionEnv-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -23,7 +23,8 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanAnnuels-class}},
\code{\link{BilanArgentee-class}},
\code{\link{BilanEspeces-class}},
\code{\link{BilanFonctionnementDC-class}},
Modified: pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -131,7 +131,8 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanAnnuels-class}},
\code{\link{BilanArgentee-class}},
\code{\link{BilanEspeces-class}},
\code{\link{BilanFonctionnementDC-class}},
Modified: pkg/stacomir/man/BilanMigrationMult-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationMult-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/BilanMigrationMult-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -106,7 +106,8 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanAnnuels-class}},
\code{\link{BilanArgentee-class}},
\code{\link{BilanEspeces-class}},
\code{\link{BilanFonctionnementDC-class}},
Modified: pkg/stacomir/man/Bilan_carlot-class.Rd
===================================================================
--- pkg/stacomir/man/Bilan_carlot-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/Bilan_carlot-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -111,7 +111,8 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanAnnuels-class}},
\code{\link{BilanArgentee-class}},
\code{\link{BilanEspeces-class}},
\code{\link{BilanFonctionnementDC-class}},
Modified: pkg/stacomir/man/Bilan_poids_moyen-class.Rd
===================================================================
--- pkg/stacomir/man/Bilan_poids_moyen-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/Bilan_poids_moyen-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -46,7 +46,8 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanAnnuels-class}},
\code{\link{BilanArgentee-class}},
\code{\link{BilanEspeces-class}},
\code{\link{BilanFonctionnementDC-class}},
Modified: pkg/stacomir/man/Bilan_stades_pigm-class.Rd
===================================================================
--- pkg/stacomir/man/Bilan_stades_pigm-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/Bilan_stades_pigm-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -77,7 +77,8 @@
\url{http://www.eptb-vilaine.fr/site/index.php/les-migrateurs/documents/publications-scientifiques/46-publications-migrateurs/60-dynamique-de-population-et-de-migration-des-civelles-en-estuaire-de-vilaine}
}
\seealso{
-Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanAnnuels-class}},
\code{\link{BilanArgentee-class}},
\code{\link{BilanEspeces-class}},
\code{\link{BilanFonctionnementDC-class}},
Modified: pkg/stacomir/man/Bilan_taille-class.Rd
===================================================================
--- pkg/stacomir/man/Bilan_taille-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/Bilan_taille-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -53,7 +53,8 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other Bilan Objects: \code{\link{BilanAnnuels-class}},
+Other Bilan Objects: \code{\link{BilanAgedemer-class}},
+ \code{\link{BilanAnnuels-class}},
\code{\link{BilanArgentee-class}},
\code{\link{BilanEspeces-class}},
\code{\link{BilanFonctionnementDC-class}},
Modified: pkg/stacomir/man/RefTextBox-class.Rd
===================================================================
--- pkg/stacomir/man/RefTextBox-class.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/RefTextBox-class.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -1,11 +1,13 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ReftextBox.r
+% Please edit documentation in R/reftextBox.r, R/ReftextBox.r
\docType{class}
\name{RefTextBox-class}
\alias{RefTextBox-class}
\title{RefTextBox referencial class}
\description{
allows to a put a value within a glabel
+
+allows to a put a value within a glabel
}
\section{Slots}{
@@ -15,8 +17,16 @@
\item{\code{labels}}{the logical parameters choice}
\item{\code{checked}}{a vector}
+
+\item{\code{title="character"}}{the title of the box giving the possible choices}
+
+\item{\code{labels}}{the logical parameters choice}
+
+\item{\code{checked}}{a vector}
}}
\author{
cedric.briand"at"eptb-vilaine.fr
+
+cedric.briand"at"eptb-vilaine.fr
}
Added: pkg/stacomir/man/calcule-BilanAgedemer-method.Rd
===================================================================
--- pkg/stacomir/man/calcule-BilanAgedemer-method.Rd (rev 0)
+++ pkg/stacomir/man/calcule-BilanAgedemer-method.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/BilanAgedemer.r
+\docType{methods}
+\name{calcule,BilanAgedemer-method}
+\alias{calcule,BilanAgedemer-method}
+\title{Calcule method for BilanAgedemer, this method will pass the data from long to wide format
+( one line per individual) and calculate Durif silvering index and Pankhurst and Fulton's K.}
+\usage{
+\S4method{calcule}{BilanAgedemer}(object, silent)
+}
+\arguments{
+\item{object}{An object of class \code{\link{BilanAgedemer-class}}}
+
+\item{silent}{Boolean, if TRUE, information messages are not displayed, only warnings and errors}
+}
+\description{
+Calcule method for BilanAgedemer, this method will pass the data from long to wide format
+( one line per individual) and calculate Durif silvering index and Pankhurst and Fulton's K.
+}
+\author{
+Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+}
+
Modified: pkg/stacomir/man/calcule.Rd
===================================================================
--- pkg/stacomir/man/calcule.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/calcule.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -5,16 +5,26 @@
\title{Generic method for calculations}
\usage{
calcule(object, ...)
+
+calcule(object, ...)
}
\arguments{
\item{object}{Object}
\item{...}{Additional parms}
+
+\item{object}{Object}
+
+\item{...}{Additional parms}
}
\description{
Generic method for calculations
+
+Generic method for calculations
}
\author{
cedric.briand
+
+cedric.briand
}
Added: pkg/stacomir/man/charge-BilanAgedemer-method.Rd
===================================================================
--- pkg/stacomir/man/charge-BilanAgedemer-method.Rd (rev 0)
+++ pkg/stacomir/man/charge-BilanAgedemer-method.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/BilanAgedemer.r
+\docType{methods}
+\name{charge,BilanAgedemer-method}
+\alias{charge,BilanAgedemer-method}
+\title{charge method for BilanAgedemer class}
+\usage{
+\S4method{charge}{BilanAgedemer}(object, h)
+}
+\arguments{
+\item{object}{An object of class \link{BilanAgedemer-class}}
+
+\item{h}{a handler}
+}
+\value{
+An object of class \link{BilanAgedemer-class} with slots filled with user choice
+
+An object of the class
+}
+\description{
+this method verifies that boxes have been clicked in the user interface and gets the objects pasted in
+envir_stacomi
+}
+\author{
+Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+}
+
Modified: pkg/stacomir/man/charge-RefTextBox-method.Rd
===================================================================
--- pkg/stacomir/man/charge-RefTextBox-method.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/charge-RefTextBox-method.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -1,11 +1,13 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ReftextBox.r
+% Please edit documentation in R/reftextBox.r, R/ReftextBox.r
\docType{methods}
\name{charge,RefTextBox-method}
\alias{charge,RefTextBox-method}
\title{Loading method for ReTextBox referential objects}
\usage{
\S4method{charge}{RefTextBox}(object, title, label)
+
+\S4method{charge}{RefTextBox}(object, title, label)
}
\arguments{
\item{object}{An object of class \link{RefTextBox-class}}
@@ -13,20 +15,36 @@
\item{title}{A title for the frame}
\item{label}{A label for the TextBox}
+
+\item{object}{An object of class \link{RefTextBox-class}}
+
+\item{title}{A title for the frame}
+
+\item{label}{A label for the TextBox}
}
\value{
An S4 object of class RefTextBox
+
+An S4 object of class RefTextBox
}
\description{
Loading method for ReTextBox referential objects
+
+Loading method for ReTextBox referential objects
}
\examples{
\dontrun{
object=new("RefTextBox")
charge(object,title="un titre",label="20")
}
+\dontrun{
+ object=new("RefTextBox")
+charge(object,title="un titre",label="20")
}
+}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+
+Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
Modified: pkg/stacomir/man/charge.Rd
===================================================================
--- pkg/stacomir/man/charge.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/charge.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -5,16 +5,26 @@
\title{Generic method to load referentials}
\usage{
charge(object, ...)
+
+charge(object, ...)
}
\arguments{
\item{object}{Object}
\item{...}{Additional parms}
+
+\item{object}{Object}
+
+\item{...}{Additional parms}
}
\description{
Generic method to load referentials
+
+Generic method to load referentials
}
\author{
cedric.briand
+
+cedric.briand
}
Modified: pkg/stacomir/man/charge_avec_filtre.Rd
===================================================================
--- pkg/stacomir/man/charge_avec_filtre.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/charge_avec_filtre.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -5,16 +5,26 @@
\title{Generic method to load referentials, with filters from the parent object in the database}
\usage{
charge_avec_filtre(object, ...)
+
+charge_avec_filtre(object, ...)
}
\arguments{
\item{object}{Object}
\item{...}{Additional parms}
+
+\item{object}{Object}
+
+\item{...}{Additional parms}
}
\description{
Generic method to load referentials, with filters from the parent object in the database
+
+Generic method to load referentials, with filters from the parent object in the database
}
\author{
cedric.briand
+
+cedric.briand
}
Modified: pkg/stacomir/man/charge_complement.Rd
===================================================================
--- pkg/stacomir/man/charge_complement.Rd 2017-01-23 16:49:42 UTC (rev 243)
+++ pkg/stacomir/man/charge_complement.Rd 2017-01-24 11:31:15 UTC (rev 244)
@@ -5,16 +5,26 @@
\title{Generic method to load additional data}
\usage{
charge_complement(object, ...)
+
+charge_complement(object, ...)
}
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 244
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