[Stacomir-commits] r365 - in pkg/stacomir: . R inst/config man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue May 16 16:46:31 CEST 2017
Author: legrand
Date: 2017-05-16 16:46:31 +0200 (Tue, 16 May 2017)
New Revision: 365
Modified:
pkg/stacomir/DESCRIPTION
pkg/stacomir/R/BilanMigrationCar.r
pkg/stacomir/R/BilanMigrationInterAnnuelle.r
pkg/stacomir/R/Bilan_poids_moyen.r
pkg/stacomir/R/PasDeTempsJournalier.r
pkg/stacomir/R/data.r
pkg/stacomir/R/fungraph.r
pkg/stacomir/R/stacomi.r
pkg/stacomir/inst/config/generate_Roxygen2.R
pkg/stacomir/man/BilanArgentee-class.Rd
pkg/stacomir/man/BilanMigrationCar-class.Rd
pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
pkg/stacomir/man/BilanMigrationMult-class.Rd
pkg/stacomir/man/funSousListeBilanMigrationPar.Rd
Log:
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/DESCRIPTION 2017-05-16 14:46:31 UTC (rev 365)
@@ -106,5 +106,5 @@
Marion Legrand [aut],
Timothee Besse [aut]
Maintainer: Cedric Briand <cedric.briand00 at gmail.com>
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1
NeedsCompilation: no
Modified: pkg/stacomir/R/BilanMigrationCar.r
===================================================================
--- pkg/stacomir/R/BilanMigrationCar.r 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/R/BilanMigrationCar.r 2017-05-16 14:46:31 UTC (rev 365)
@@ -12,11 +12,12 @@
#' @include Refparqual.r
#' @include RefChoix.r
#' @include Bilan_carlot.r
-#' @note The main difference between this class and \link{Bilan_carlot} is that this class allows to
+#' @note 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.
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("BilanMigrationCar", ...)}. they are loaded by the interface
#' using interface_BilanMigrationCar function.
+#' @slot calcdata A "list" of calculated data, filled in by the calcule method
#' @slot parquan An object of class \link{Refparquan-class}, quantitative parameter
#' @slot parqual An object of class \link{Refparqual-class}, quanlitative parameter
#' @slot echantillon An object of class \link{RefChoix-class}, vector of choice
@@ -185,7 +186,14 @@
return(bmC)
})
-
+#' connect method for BilanMigrationCar
+#'
+#'
+#' uses the BilanMigrationMult method
+#' @param object An object of class \link{BilanMigrationCar-class}
+#' @param silent Boolean default FALSE, if TRUE information messages not displayed
+#' @return BilanMigrationCar with slot @data filled from the database
+#' @export
setMethod("connect",signature=signature("BilanMigrationCar"),definition=function(object,silent=FALSE){
bmC<-object
if (!bmC at echantillon@selectedvalue) {
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-05-16 14:46:31 UTC (rev 365)
@@ -14,6 +14,7 @@
#' @slot anneeDebut Object of class \code{\link{RefAnnee-class}}. refAnnee allows to choose year of beginning
#' @slot anneeFin Object of class \code{\link{RefAnnee-class}}
#' refAnnee allows to choose last year of the Bilan
+#' @slot calcdata A "list" of calculated data, filled in by the calcule method
#'
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @family Bilan Objects
Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/R/Bilan_poids_moyen.r 2017-05-16 14:46:31 UTC (rev 365)
@@ -287,6 +287,7 @@
#' glass eel or yellow eels.
#' @param object An object of class \link{Bilan_pois_moyen-class}
#' @param model.type default "seasonal", "seasonal1","seasonal2","manual".
+#' @param silent Default FALSE, if TRUE the program should no display messages
#' @usage model(object,model.type=c("seasonal","seasonal1","seasonal2","manual"),silent=FALSE)
#' @details
#' Depending on model.type several models are produced
Modified: pkg/stacomir/R/PasDeTempsJournalier.r
===================================================================
--- pkg/stacomir/R/PasDeTempsJournalier.r 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/R/PasDeTempsJournalier.r 2017-05-16 14:46:31 UTC (rev 365)
@@ -55,6 +55,9 @@
return(ifelse( rep1 & rep2 & rep3 ,TRUE,retValue) )
})
# pour test #object=new("PasDeTempsJournalier")
+
+#' Method to select timesteps from the graphical interface
+#' @param object An object of class \link{PasDeTempsJournalier-class}
setMethod("choice",signature=signature("PasDeTempsJournalier"),definition=function(object) {
if (length(LesPasDeTemps$LabelPasDeTemps) > 0){
hwinpa=function(h,...){
Modified: pkg/stacomir/R/data.r
===================================================================
--- pkg/stacomir/R/data.r 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/R/data.r 2017-05-16 14:46:31 UTC (rev 365)
@@ -337,6 +337,53 @@
"bilan_adm"
-#' BLABLABLABLA
+#' An object of class BilanConditionEnv with data loaded
+#'
+#' The dataset corresponds to the dayly temperature at Gabion station during the year 2008. This environmental station is used to
+#' analyse conditions in which fish migrated at Arzal dam
+#'
+#' @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}
+#' }
+#' }
+#' }
#' @keywords data
+"bil_CE"
+
+
+#' An object of class BilanMigrationCar with data loaded
+#'
+#' 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.
+#'
+#' the dataset has been loaded as an example for the BilanMigrationCar-class. It has been
+#' kindly given by Loire Grands Migrateurs.
+#' @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}
+#' }
+#' @keywords data
"bmC"
\ No newline at end of file
Modified: pkg/stacomir/R/fungraph.r
===================================================================
--- pkg/stacomir/R/fungraph.r 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/R/fungraph.r 2017-05-16 14:46:31 UTC (rev 365)
@@ -13,10 +13,10 @@
#' @param taxon The species
#' @param stade The stage
#' @param dc The DC
+#' @param silent Message displayed or not
#' @param color Default NULL, a vector of color in the following order, working, stopped, 1...5 types of operation
#' for the fishway or DC, measured, calculated, expert, direct observation. If null will be set to brewer.pal(12,"Paired")[c(8,10,4,6,1,2,3,5,7)]
#' @param color_ope Default NULL, a vector of color for the operations. Default to brewer.pal(4,"Paired")
-#' @param silent Message displayed or not
#' @param ... additional parameters passed to matplot, main, ylab, ylim, lty, pch, bty, cex.main,
#' it is currenly not a good idea to change xlim (numbers are wrong, the month plot covers all month, and legend placement is wrong
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
Modified: pkg/stacomir/R/stacomi.r
===================================================================
--- pkg/stacomir/R/stacomi.r 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/R/stacomi.r 2017-05-16 14:46:31 UTC (rev 365)
@@ -483,7 +483,8 @@
"taxon_stades","time.sequence","sum","variable","duree","Hdeb","Hfin","per_tar_code",
"per_etat_fonctionnement","std_libelle","sumduree","dc","stade","taxon","stage","ouv",
"Q0","Q100","Q5","Q50","Q95","age","bjo_annee","bjo_labelquantite","bjo_valeur","doy",
- "pred_weight","pred_weight_lwr","pred_weight_upr","total","w","year"))
+ "pred_weight","pred_weight_lwr","pred_weight_upr","total","w","year","sta","tableauCEst","stm_libelle",
+ "env_valeur_quantitatif","env_val_identifiant","DC"))
# variable used by dplyr
utils::globalVariables(c("n0","newid","xmin","xmax"))
Modified: pkg/stacomir/inst/config/generate_Roxygen2.R
===================================================================
--- pkg/stacomir/inst/config/generate_Roxygen2.R 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/inst/config/generate_Roxygen2.R 2017-05-16 14:46:31 UTC (rev 365)
@@ -35,6 +35,10 @@
require(stacomiR)
stacomi(FALSE,FALSE,FALSE)
require(roxygen2)
-roxygen2::roxygenise("F:/workspace/stacomir/pkg/stacomir");warnings()[1:10]
+#Pour Cédric
+#roxygen2::roxygenise("F:/workspace/stacomir/pkg/stacomir");warnings()[1:10]
+#Pour Marion
+roxygen2::roxygenise("C:/Users/logrami/workspace/stacomir/pkg/stacomir");warnings()[1:10]
+
Modified: pkg/stacomir/man/BilanArgentee-class.Rd
===================================================================
--- pkg/stacomir/man/BilanArgentee-class.Rd 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/man/BilanArgentee-class.Rd 2017-05-16 14:46:31 UTC (rev 365)
@@ -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 données d'argenture acquises en France)
+# standard plot as drawn by Laurent Beaulaton (Analyse des donnees d'argenture acquises en France)
# showing Durif's stage according to size and eye diameter
plot(bilanArg, plot.type=1)
Modified: pkg/stacomir/man/BilanMigrationCar-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationCar-class.Rd 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/man/BilanMigrationCar-class.Rd 2017-05-16 14:46:31 UTC (rev 365)
@@ -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}
@@ -39,7 +39,7 @@
\item{\code{time.sequence}}{An object of class "POSIXct" inherited from \link{BilanMigration-class}}
}}
\note{
-The main difference between this class and \link{Bilan_carlot} is that this class allows to
+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
Modified: pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd 2017-05-16 14:46:31 UTC (rev 365)
@@ -72,7 +72,7 @@
requireNamespace("viridis", quietly = TRUE)){
g<-get("g",envir=envir_stacomi)
g+ggplot2::scale_fill_manual(values=viridis::viridis(22))+
- ggplot2::ggtitle(iconv("Saisonalité de la migration aux Enfrenaux","UTF8"))
+ ggplot2::ggtitle(iconv("Saisonnalite de la migration aux Enfrenaux","UTF8"))
}
# the standard plot is showing daily values
plot(bmi,plot.type="standard",silent=TRUE)
Modified: pkg/stacomir/man/BilanMigrationMult-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationMult-class.Rd 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/man/BilanMigrationMult-class.Rd 2017-05-16 14:46:31 UTC (rev 365)
@@ -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}
Modified: pkg/stacomir/man/funSousListeBilanMigrationPar.Rd
===================================================================
--- pkg/stacomir/man/funSousListeBilanMigrationPar.Rd 2017-05-16 12:56:24 UTC (rev 364)
+++ pkg/stacomir/man/funSousListeBilanMigrationPar.Rd 2017-05-16 14:46:31 UTC (rev 365)
@@ -8,7 +8,7 @@
}
\arguments{
\item{bilanMigrationPar}{an object of class
-\code{\linkS4class{BilanMigrationPar}}}
+\code{\linkS4class{BilanMigrationCar}}}
}
\description{
see \code{funSousListeBilanMigration} This function is similar to
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