[Stacomir-commits] r366 - in pkg/stacomir: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue May 16 16:51:04 CEST 2017
Author: briand
Date: 2017-05-16 16:51:03 +0200 (Tue, 16 May 2017)
New Revision: 366
Added:
pkg/stacomir/man/choice-PasDeTempsJournalier-method.Rd
pkg/stacomir/man/connect-BilanMigrationCar-method.Rd
Modified:
pkg/stacomir/DESCRIPTION
pkg/stacomir/R/BilanMigrationCar.r
pkg/stacomir/man/BilanArgentee-class.Rd
pkg/stacomir/man/BilanEspeces-class.Rd
pkg/stacomir/man/BilanMigrationCar-class.Rd
pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
pkg/stacomir/man/BilanMigrationMult-class.Rd
pkg/stacomir/man/BilanOperation-class.Rd
pkg/stacomir/man/bil_CE.Rd
pkg/stacomir/man/bmC.Rd
pkg/stacomir/man/bmi.Rd
pkg/stacomir/man/calcule-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/charge-BilanMigrationCar-method.Rd
pkg/stacomir/man/model-Bilan_poids_moyen-method.Rd
pkg/stacomir/man/plot-BilanMigrationCar-missing-method.Rd
Log:
Roxygen documentation
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/DESCRIPTION 2017-05-16 14:51:03 UTC (rev 366)
@@ -106,5 +106,5 @@
Marion Legrand [aut],
Timothee Besse [aut]
Maintainer: Cedric Briand <cedric.briand00 at gmail.com>
-RoxygenNote: 6.0.1
+RoxygenNote: 5.0.1
NeedsCompilation: no
Modified: pkg/stacomir/R/BilanMigrationCar.r
===================================================================
--- pkg/stacomir/R/BilanMigrationCar.r 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/R/BilanMigrationCar.r 2017-05-16 14:51:03 UTC (rev 366)
@@ -30,7 +30,7 @@
#' @slot time.sequence An object of class "POSIXct" inherited from \link{BilanMigration-class}
#' @family Bilan Objects
#' @aliases BilanMigrationMult bilanMigrationMult
-#' @note program : default two parameter choice, checking box "aucun" will allow the program to ignore the parameter
+#' @note program : default two parameter choice, checking box "none" will allow the program to ignore the parameter
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @concept Bilan Object
#' @keywords classes
Modified: pkg/stacomir/man/BilanArgentee-class.Rd
===================================================================
--- pkg/stacomir/man/BilanArgentee-class.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/BilanArgentee-class.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -72,7 +72,7 @@
# stages are in bilanArg at calcdata[["6"]][,"stage"]
#look at data structure using str(bilanArg at calcdata[["6"]])
-# standard plot as drawn by Laurent Beaulaton (Analyse des donnees d'argenture acquises en France)
+# 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(bilanArg, plot.type=1)
Modified: pkg/stacomir/man/BilanEspeces-class.Rd
===================================================================
--- pkg/stacomir/man/BilanEspeces-class.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/BilanEspeces-class.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -37,13 +37,14 @@
Other Bilan Classes
\code{\linkS4class{Bilan_carlot}},
\code{\linkS4class{Bilan_poids_moyen}},
+\code{\linkS4class{Bilan_stades_pigm}}, \code{\linkS4class{Bilan_taille}},
\code{\linkS4class{BilanConditionEnv}}, \code{\linkS4class{BilanEspeces}},
\code{\linkS4class{BilanFonctionnementDC}},
\code{\linkS4class{BilanFonctionnementDF}},
\code{\linkS4class{BilanMigration}},
-\code{\linkS4class{BilanMigrationMultConditionEnv}},
+\code{\linkS4class{BilanMigrationConditionEnv}},
\code{\linkS4class{BilanMigrationInterAnnuelle}},
-\code{\linkS4class{BilanMigrationCar}}
+\code{\linkS4class{BilanMigrationPar}}
Other Bilan.Objects: \code{\link{BilanAgedemer-class}},
\code{\link{BilanAnnuels-class}},
Modified: pkg/stacomir/man/BilanMigrationCar-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationCar-class.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/BilanMigrationCar-class.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -3,7 +3,7 @@
\docType{class}
\name{BilanMigrationCar-class}
\alias{BilanMigrationCar-class}
-%\alias{BilanMigrationMult}
+\alias{BilanMigrationMult}
\alias{bilanMigrationMult}
\title{Migration report along with quantitative and
qualitative characteristics}
@@ -18,6 +18,8 @@
\section{Slots}{
\describe{
+\item{\code{calcdata}}{A "list" of calculated data, filled in by the calcule method}
+
\item{\code{parquan}}{An object of class \link{Refparquan-class}, quantitative parameter}
\item{\code{parqual}}{An object of class \link{Refparqual-class}, quanlitative parameter}
@@ -42,7 +44,7 @@
The main difference between this class and \link{Bilan_carlot-class} is that this class allows to
select (or not) the samples, and that it handles quantitative and qualitative parameters separately.
-program : default two parameter choice, checking box "aucun" will allow the program to ignore the parameter
+program : default two parameter choice, checking box "none" will allow the program to ignore the parameter
}
\section{Objects from the Class}{
Objects can be created by calls of the form
Modified: pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -26,6 +26,8 @@
\item{\code{anneeFin}}{Object of class \code{\link{RefAnnee-class}}
refAnnee allows to choose last year of the Bilan}
+
+\item{\code{calcdata}}{A "list" of calculated data, filled in by the calcule method}
}}
\examples{
require(stacomiR)
@@ -72,7 +74,7 @@
requireNamespace("viridis", quietly = TRUE)){
g<-get("g",envir=envir_stacomi)
g+ggplot2::scale_fill_manual(values=viridis::viridis(22))+
- ggplot2::ggtitle(iconv("Saisonnalite de la migration aux Enfrenaux","UTF8"))
+ ggplot2::ggtitle(iconv("Saisonalité de la migration aux Enfrenaux","UTF8"))
}
# the standard plot is showing daily values
plot(bmi,plot.type="standard",silent=TRUE)
@@ -120,10 +122,10 @@
plot(bmi,plot.type="pointrange",timesplit="mois",silent=TRUE)
plot(bmi,plot.type="step",silent=TRUE)
-if (requireNamespace("ggplot2", quietly = TRUE)&requireNamespace("viridis", quietly = TRUE)){
- g<-get("g",envir=envir_stacomi) + ggplot2::theme_minimal()
- g+viridis::scale_color_viridis(discrete=TRUE)+
- ggplot2::ggtitle("Cumulated migration step plot at les Enfrenaux eel trap")
+ if (requireNamespace("ggplot2", quietly = TRUE)&requireNamespace("viridis", quietly = TRUE)){
+ g<-get("g",envir=envir_stacomi) + ggplot2::theme_minimal()
+ g+viridis::scale_color_viridis(discrete=TRUE)+
+ ggplot2::ggtitle("Cumulated migration step plot at les Enfrenaux eel trap")
}
}
Modified: pkg/stacomir/man/BilanMigrationMult-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationMult-class.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/BilanMigrationMult-class.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -2,7 +2,7 @@
% Please edit documentation in R/BilanMigrationMult.r
\docType{class}
\name{BilanMigrationMult-class}
-%\alias{BilanMigrationMult}
+\alias{BilanMigrationMult}
\alias{BilanMigrationMult-class}
\alias{bilanMigrationMult}
\title{Migration reports for multiple DC / species / stages}
@@ -93,8 +93,7 @@
# for yellow eel and other taxa
# stopped, 1...5 types of operation, ponctuel, expert, calcule,mesure,working,
plot(bMM_Arzal,plot.type="standard",
- color=c("#DEF76B","#B950B5","#9ABDDA","#781A74","#BF9D6E","#FFC26E",
- "#A66F24","#012746","#6C3E00","#DC7ED8","#8AA123"),
+ color=c("#DEF76B","#B950B5","#9ABDDA","#781A74","#BF9D6E","#FFC26E","#A66F24","#012746","#6C3E00","#DC7ED8","#8AA123"),
color_ope=c("#5589B5","#FFDB6E","#FF996E","#1C4D76"),
silent=TRUE)
Modified: pkg/stacomir/man/BilanOperation-class.Rd
===================================================================
--- pkg/stacomir/man/BilanOperation-class.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/BilanOperation-class.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -21,14 +21,16 @@
\seealso{
Other Bilan Class \code{\linkS4class{Bilan_carlot}}
\code{\linkS4class{Bilan_poids_moyen}}
+\code{\linkS4class{Bilan_stades_pigm}}
+\code{\linkS4class{Bilan_taille}}
\code{\linkS4class{BilanConditionEnv}}
\code{\linkS4class{BilanEspeces}}
\code{\linkS4class{BilanFonctionnementDC}}
\code{\linkS4class{BilanFonctionnementDF}}
\code{\linkS4class{BilanMigration}}
-\code{\linkS4class{BilanMigrationMultConditionEnv}}
+\code{\linkS4class{BilanMigrationConditionEnv}}
\code{\linkS4class{BilanMigrationInterAnnuelle}}
-\code{\linkS4class{BilanMigrationCar}}
+\code{\linkS4class{BilanMigrationPar}}
}
\concept{
Bilan Object
Modified: pkg/stacomir/man/bil_CE.Rd
===================================================================
--- pkg/stacomir/man/bil_CE.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/bil_CE.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -3,8 +3,23 @@
\docType{data}
\name{bil_CE}
\alias{bil_CE}
-\title{Dayly temperature at Gabion station during the year 2008}
-\format{An object of class \link{BilanConditionEnv-class} with data slot loaded.}
+\title{An object of class BilanConditionEnv with data loaded}
+\format{An object of class \link{BilanConditionEnv-class} with data slot loaded:
+\describe{
+ \item{stationMesure}{the \code{RefStationMesure} object with 5 slots filled with data corresponding to the iav postgres schema}
+ \item{horodatedebut}{object of class \code{RefHorodate-class} : the start date selected}
+ \item{horodatefin}{object of class \code{RefHorodate-class} : the end date selected}
+ \item{data}{ A dataframe with 723 rows and 6 variables
+ \describe{
+ \item{env_date_debut}{start date}
+ \item{env_date_fin}{end date}
+ \item{env_methode_obtention}{method of data collection, measured, calculated...}
+ \item{env_val_identifiant}{the value of the parameter if qualitative}
+ \item{env_valeur_quantitatif}{the value of the parameter if quantitative}
+ \item{env_stm_identifiant}{station id}
+ }
+ }
+}}
\usage{
bil_CE
}
Modified: pkg/stacomir/man/bmC.Rd
===================================================================
--- pkg/stacomir/man/bmC.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/bmC.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -3,13 +3,33 @@
\docType{data}
\name{bmC}
\alias{bmC}
-\title{BLABLABLABLA}
-\format{An object of class \code{BilanMigrationCar} of length 0.}
+\title{An object of class BilanMigrationCar with data loaded}
+\format{An object of class \link{BilanConditionEnv-class} with data slot loaded:
+\describe{
+ \item{calcdata}{slot to be filled with the calcule method}
+ \item{data}{ A list of 2 elements
+ \describe{
+ \item{parqual}{values of all the qualitative parameters}
+ \item{parquan}{values of all the quantitative parameters}
+ }
+ }
+ \item{dc}{the \code{RefDC} : the control devices selected}
+ \item{taxons}{the \code{RefTaxon} : Salmo salar selected}
+ \item{stades}{the \code{RefStades} : the stages selected}
+ \item{par}{Object of class \link{Refpar-class}: the parameters used}
+ \item{horodatedebut}{object of class \code{RefHorodate-class} : the start date selected}
+ \item{horodatefin}{object of class \code{RefHorodate-class} : the end date selected}
+}}
\usage{
bmC
}
\description{
-BLABLABLABLA
+The dataset corresponds to the caracteristics (qualitative and quantitative) of salmo salar migrating
+at Decize (Loire river) and Vichy (Allier river) counting device in 2012.
}
+\details{
+the dataset has been loaded as an example for the BilanMigrationCar-class. It has been
+kindly given by Loire Grands Migrateurs.
+}
\keyword{data}
Modified: pkg/stacomir/man/bmi.Rd
===================================================================
--- pkg/stacomir/man/bmi.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/bmi.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -1,11 +1,12 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.r
+\docType{data}
\name{bmi}
\alias{bmi}
\title{Daily glass eel and elver migration from 1984 to 2016 in the Sevre Niortaise}
\format{An object of class \link{BilanMigrationInterAnnuelle-class} with data loaded.}
\usage{
-bmi(wt, ht)
+bmi
}
\description{
The first eel trapping ladder in France was built by Antoine Legault and the team from Rennes
Modified: pkg/stacomir/man/calcule-BilanMigrationInterAnnuelle-method.Rd
===================================================================
--- pkg/stacomir/man/calcule-BilanMigrationInterAnnuelle-method.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/calcule-BilanMigrationInterAnnuelle-method.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -9,7 +9,7 @@
timesplit = "mois")
}
\arguments{
-\item{object}{An object of class \code{\link{BilanMigrationInterAnnuelle-class}}}
+\item{object}{An object of class \code{\link{BilanMigrationInterannuelle-class}}}
\item{silent}{Boolean, if TRUE, information messages are not displayed, only warnings and errors}
Modified: pkg/stacomir/man/charge-BilanMigrationCar-method.Rd
===================================================================
--- pkg/stacomir/man/charge-BilanMigrationCar-method.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/charge-BilanMigrationCar-method.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -8,7 +8,7 @@
\S4method{charge}{BilanMigrationCar}(object, silent = FALSE)
}
\arguments{
-\item{object}{An object of class \link{BilanMigrationMult-class}}
+\item{object}{An object of class \link{BilanMigrationCar-class}}
\item{silent}{Default FALSE, if TRUE the program should not display messages}
}
Added: pkg/stacomir/man/choice-PasDeTempsJournalier-method.Rd
===================================================================
--- pkg/stacomir/man/choice-PasDeTempsJournalier-method.Rd (rev 0)
+++ pkg/stacomir/man/choice-PasDeTempsJournalier-method.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PasDeTempsJournalier.r
+\docType{methods}
+\name{choice,PasDeTempsJournalier-method}
+\alias{choice,PasDeTempsJournalier-method}
+\title{Method to select timesteps from the graphical interface}
+\usage{
+\S4method{choice}{PasDeTempsJournalier}(object)
+}
+\arguments{
+\item{object}{An object of class \link{PasDeTempsJournalier-class}}
+}
+\description{
+Method to select timesteps from the graphical interface
+}
+
Added: pkg/stacomir/man/connect-BilanMigrationCar-method.Rd
===================================================================
--- pkg/stacomir/man/connect-BilanMigrationCar-method.Rd (rev 0)
+++ pkg/stacomir/man/connect-BilanMigrationCar-method.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/BilanMigrationCar.r
+\docType{methods}
+\name{connect,BilanMigrationCar-method}
+\alias{connect,BilanMigrationCar-method}
+\title{connect method for BilanMigrationCar}
+\usage{
+\S4method{connect}{BilanMigrationCar}(object, silent = FALSE)
+}
+\arguments{
+\item{object}{An object of class \link{BilanMigrationCar-class}}
+
+\item{silent}{Boolean default FALSE, if TRUE information messages not displayed}
+}
+\value{
+BilanMigrationCar with slot @data filled from the database
+}
+\description{
+uses the BilanMigrationMult method
+}
+
Modified: pkg/stacomir/man/model-Bilan_poids_moyen-method.Rd
===================================================================
--- pkg/stacomir/man/model-Bilan_poids_moyen-method.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/model-Bilan_poids_moyen-method.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -12,9 +12,11 @@
model(object,model.type=c("seasonal","seasonal1","seasonal2","manual"),silent=FALSE)
}
\arguments{
-\item{object}{An object of class \link{Bilan_poids_moyen-class}}
+\item{object}{An object of class \link{Bilan_pois_moyen-class}}
\item{model.type}{default "seasonal", "seasonal1","seasonal2","manual".}
+
+\item{silent}{Default FALSE, if TRUE the program should no display messages}
}
\description{
model method for Bilan_poids_moyen'
Modified: pkg/stacomir/man/plot-BilanMigrationCar-missing-method.Rd
===================================================================
--- pkg/stacomir/man/plot-BilanMigrationCar-missing-method.Rd 2017-05-16 14:46:31 UTC (rev 365)
+++ pkg/stacomir/man/plot-BilanMigrationCar-missing-method.Rd 2017-05-16 14:51:03 UTC (rev 366)
@@ -6,13 +6,15 @@
\title{plot method for BilanMigrationCar}
\usage{
\S4method{plot}{BilanMigrationCar,missing}(x, color_parm = NULL,
- plot.type = "qual", ...)
+ plot.type = "qual", silent = FALSE, ...)
}
\arguments{
\item{x}{An object of class BilanMigrationCar}
\item{plot.type}{One of "qual", "quant" "crossed" default to qual}
+\item{silent}{Boolean default FALSE, if TRUE information messages not displayed}
+
\item{...}{Additional parameters}
\item{y}{not used there}
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