[Stacomir-commits] r363 - in pkg/stacomir: . R inst/config man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue May 16 14:52:23 CEST 2017 

Author: legrand
Date: 2017-05-16 14:52:23 +0200 (Tue, 16 May 2017)
New Revision: 363

Added:
   pkg/stacomir/man/bil_CE.Rd
   pkg/stacomir/po/
Modified:
   pkg/stacomir/R/BilanMigrationCar.r
   pkg/stacomir/R/funSousListeBilanMigrationPar.r
   pkg/stacomir/R/stacomi.r
   pkg/stacomir/inst/config/stacomi_manual_launch.r
   pkg/stacomir/man/BilanEspeces-class.Rd
   pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
   pkg/stacomir/man/BilanMigrationMult-class.Rd
   pkg/stacomir/man/BilanOperation-class.Rd
   pkg/stacomir/man/calcule-BilanMigrationInterAnnuelle-method.Rd
   pkg/stacomir/man/model-Bilan_poids_moyen-method.Rd
Log:


Modified: pkg/stacomir/R/BilanMigrationCar.r
===================================================================
--- pkg/stacomir/R/BilanMigrationCar.r	2017-05-15 14:44:18 UTC (rev 362)
+++ pkg/stacomir/R/BilanMigrationCar.r	2017-05-16 12:52:23 UTC (rev 363)
@@ -391,8 +391,9 @@
 #' @param x An object of class BilanMigrationCar
 #' @param y not used there
 #' @param plot.type One of "qual", "quant" "crossed" default to qual
-#' @param color A named vector for the colors of either parameters (if plot.type=quant) or levels for
+#' @param color_parm A named vector for the colors of either parameters (if plot.type=quant) or levels for
 #' parameters (if plot.type=qual).
+#' @param silent Boolean default FALSE, if TRUE information messages not displayed
 #' @param ... Additional parameters
 #' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
 setMethod("plot",signature=signature(x="BilanMigrationCar",y="missing"),definition=function(x,color_parm=NULL,plot.type="qual",...){ 

Modified: pkg/stacomir/R/funSousListeBilanMigrationPar.r
===================================================================
--- pkg/stacomir/R/funSousListeBilanMigrationPar.r	2017-05-15 14:44:18 UTC (rev 362)
+++ pkg/stacomir/R/funSousListeBilanMigrationPar.r	2017-05-16 12:52:23 UTC (rev 363)
@@ -6,7 +6,7 @@
 #' 
 #' 
 #' @param bilanMigrationPar an object of class
-#' \code{\linkS4class{BilanMigrationPar}}
+#' \code{\linkS4class{BilanMigrationCar}}
 funSousListeBilanMigrationPar=function(bilanMigrationPar) {
 	
 	# *********************

Modified: pkg/stacomir/R/stacomi.r
===================================================================
--- pkg/stacomir/R/stacomi.r	2017-05-15 14:44:18 UTC (rev 362)
+++ pkg/stacomir/R/stacomi.r	2017-05-16 12:52:23 UTC (rev 363)
@@ -82,7 +82,7 @@
 #' @param ... additional parameters
 hTail=function(h,...){
 	funout(gettext("Lengths summary\n",domain="R-stacomiR"),wash=TRUE)
-	eval(interface_BilanTaille(),envir = .GlobalEnv)
+	#eval(interface_BilanTaille(),envir = .GlobalEnv)
 }
 #' handler function used by the main interface
 #' @param h handler

Modified: pkg/stacomir/inst/config/stacomi_manual_launch.r
===================================================================
--- pkg/stacomir/inst/config/stacomi_manual_launch.r	2017-05-15 14:44:18 UTC (rev 362)
+++ pkg/stacomir/inst/config/stacomi_manual_launch.r	2017-05-16 12:52:23 UTC (rev 363)
@@ -23,7 +23,12 @@
 # pour voir apparaitre toutes les requetes dans R
 # assign("showmerequest",1,envir=envir_stacomi)
 source ("F:/workspace/stacomir/pkg/stacomir/inst/config/libraries.r")
+<<<<<<< .mine
+
+source ("C:/Users/logrami/workspace/stacomir/pkg/stacomir/inst/config/libraries.r")
+=======
 #source ("C:/Users/logrami/workspace/stacomir/pkg/stacomir/inst/config/libraries.r")
+>>>>>>> .r359
 
 libraries()
 

Modified: pkg/stacomir/man/BilanEspeces-class.Rd
===================================================================
--- pkg/stacomir/man/BilanEspeces-class.Rd	2017-05-15 14:44:18 UTC (rev 362)
+++ pkg/stacomir/man/BilanEspeces-class.Rd	2017-05-16 12:52:23 UTC (rev 363)
@@ -37,14 +37,13 @@
 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{BilanMigrationConditionEnv}},
+\code{\linkS4class{BilanMigrationMultConditionEnv}},
 \code{\linkS4class{BilanMigrationInterAnnuelle}},
-\code{\linkS4class{BilanMigrationPar}}
+\code{\linkS4class{BilanMigrationCar}}
 
 Other Bilan.Objects: \code{\link{BilanAgedemer-class}},
   \code{\link{BilanAnnuels-class}},

Modified: pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd	2017-05-15 14:44:18 UTC (rev 362)
+++ pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd	2017-05-16 12:52:23 UTC (rev 363)
@@ -120,10 +120,10 @@
 	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	2017-05-15 14:44:18 UTC (rev 362)
+++ pkg/stacomir/man/BilanMigrationMult-class.Rd	2017-05-16 12:52:23 UTC (rev 363)
@@ -93,7 +93,8 @@
 # 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	2017-05-15 14:44:18 UTC (rev 362)
+++ pkg/stacomir/man/BilanOperation-class.Rd	2017-05-16 12:52:23 UTC (rev 363)
@@ -21,16 +21,14 @@
 \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{BilanMigrationConditionEnv}}
+\code{\linkS4class{BilanMigrationMultConditionEnv}}
 \code{\linkS4class{BilanMigrationInterAnnuelle}}
-\code{\linkS4class{BilanMigrationPar}}
+\code{\linkS4class{BilanMigrationCar}}
 }
 \concept{
 Bilan Object

Added: pkg/stacomir/man/bil_CE.Rd
===================================================================
--- pkg/stacomir/man/bil_CE.Rd	                        (rev 0)
+++ pkg/stacomir/man/bil_CE.Rd	2017-05-16 12:52:23 UTC (rev 363)
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.r
+\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.}
+\usage{
+bil_CE
+}
+\description{
+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
+}
+\keyword{data}
+

Modified: pkg/stacomir/man/calcule-BilanMigrationInterAnnuelle-method.Rd
===================================================================
--- pkg/stacomir/man/calcule-BilanMigrationInterAnnuelle-method.Rd	2017-05-15 14:44:18 UTC (rev 362)
+++ pkg/stacomir/man/calcule-BilanMigrationInterAnnuelle-method.Rd	2017-05-16 12:52:23 UTC (rev 363)
@@ -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/model-Bilan_poids_moyen-method.Rd
===================================================================
--- pkg/stacomir/man/model-Bilan_poids_moyen-method.Rd	2017-05-15 14:44:18 UTC (rev 362)
+++ pkg/stacomir/man/model-Bilan_poids_moyen-method.Rd	2017-05-16 12:52:23 UTC (rev 363)
@@ -12,7 +12,7 @@
 model(object,model.type=c("seasonal","seasonal1","seasonal2","manual"),silent=FALSE)
 }
 \arguments{
-\item{object}{An object of class \link{Bilan_pois_moyen-class}}
+\item{object}{An object of class \link{Bilan_poids_moyen-class}}
 
 \item{model.type}{default "seasonal", "seasonal1","seasonal2","manual".}
 }

More information about the Stacomir-commits mailing list