[Stacomir-commits] r425 - pkg/stacomir pkg/stacomir/inst/examples www

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun Jun 25 22:14:07 CEST 2017 

Author: timothee_besse
Date: 2017-06-25 22:14:07 +0200 (Sun, 25 Jun 2017)
New Revision: 425

Added:
   pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
   pkg/stacomir/po/
Removed:
   pkg/stacomir/po/
Modified:
   www/index.php
Log:
correction chemin images

Copied: pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R (from rev 389, pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R)
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R	                        (rev 0)
+++ pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R	2017-06-25 20:14:07 UTC (rev 425)
@@ -0,0 +1,144 @@
+require(stacomiR)
+# launching stacomi without selecting the scheme or interface
+stacomi(gr_interface=FALSE,
+		login_window=FALSE,
+		database_expected=FALSE)
+# the following script will load the Arzal dataset if connected to iav schema
+\dontrun{
+	# overriding user schema to point to Parc Marais Poitevin 
+	# (longest historical dataset available
+	# in France for eel ...) this suppose you have access to the pmp schema...
+	# a glimpse of the dataset is still available in the bmi dataset 
+	# loaded in the package...
+	baseODBC<-get("baseODBC",envir=envir_stacomi)
+	baseODBC[c(2,3)]<-rep("pmp",2)
+	assign("baseODBC",baseODBC,envir_stacomi)
+	sch<-get("sch",envir=envir_stacomi)
+	assign("sch","pmp.",envir_stacomi)
+	bmi<-new("BilanMigrationInterAnnuelle")
+	bmi<-choice_c(bmi,
+			dc=c(16),
+			taxons=c("Anguilla anguilla"),
+			stades=c("AGJ"),
+			anneedebut="2007",
+			anneefin="2012",
+			silent=TRUE)
+	bmi<-connect(bmi)	
+}	
+# load the dataset generated by previous lines
+data("bmi")
+# the first plot is of little interest, it allows to see what data 
+# are available... simple lines
+# For irregular operations like those reported at the enfrenaux eel ladder....
+plot(bmi,plot.type="line",silent=TRUE)
+
+# a plot to show the seasonality, Here it has also to do with the monitoring period
+# the y unit has little sense in this graph
+plot(bmi,plot.type="density",silent=TRUE)
+
+bmi<-calcule(bmi,timesplit="semaine")
+
+#install.packages("viridis")
+\dontrun{
+	if (requireNamespace("ggplot2", quietly = TRUE)&
+		requireNamespace("viridis", quietly = TRUE)){
+	g<-get("g",envir=envir_stacomi)	
+	g+
+			ggplot2::scale_fill_manual(values=viridis::viridis(22))+
+			ggplot2::ggtitle("Saisonnalite de la migration aux Enfrenaux")
+}
+# the standard plot is showing daily values
+plot(bmi,plot.type="standard",silent=TRUE)
+# Manual edition of the graph produced
+if (requireNamespace("ggplot2", quietly = TRUE)){
+g1<-get("g1",envir=envir_stacomi)
+g1<-g1+ggplot2::ggtitle("Les Enfrenaux")+
+		ggplot2::scale_fill_manual(name="Source", 
+				values=c("purple","#0A0C01"),
+				labels = c("historical set","2015 values"))+
+		ggplot2::scale_colour_manual(name="Source", values="#B8EA00",
+				labels = c("historical mean"))	+
+		ggplot2::ylab("Nombre d'anguilles")
+print(g1)
+}
+
+# Another graph from scratch
+if (requireNamespace("ggplot2", quietly = TRUE)&
+	requireNamespace("viridis", quietly = TRUE)){
+dat<-funtraitementdate(bmi at data, # tableau de donnees a importer
+		"bjo_jour", # nom de la colonne
+		annee=FALSE,
+		mois=TRUE,
+		semaine =TRUE,
+		jour_mois=FALSE)
+# sum per month
+res<-dplyr::select(dat,bjo_valeur,bjo_annee,semaine)
+res<-dplyr::group_by(res,bjo_annee,semaine)
+res<-dplyr::summarize(res,effectif=sum(bjo_valeur))
+ggplot2::ggplot(res, ggplot2::aes(x = semaine, y = bjo_annee,fill=effectif)) +
+	ggplot2::geom_tile(colour="black") + ggplot2::coord_fixed() +
+	viridis::scale_fill_viridis(begin=0,option="D") + ggplot2::theme_bw()+
+	ggplot2::theme(panel.background= ggplot2::element_rect(fill = "#9360A9"),
+			panel.grid.major=ggplot2::element_line(colour="#C1DB39"),
+			panel.grid.minor=ggplot2::element_line(colour="#7DD632"))+
+	ggplot2::ylab("year")+ggplot2::xlab("week")+
+	ggplot2::ggtitle("Historical trend at Les Enfrenaux Eel trap")
+	
+}
+# available arguments for timesplit are "quinzaine" and "mois" and "semaine"
+# with the silent=TRUE argument, it's always the latest year that is selected
+plot(bmi,plot.type="barchart",timesplit="quinzaine",silent=TRUE)
+# Comparison with historical values. Each year and 2 weeks values 
+# is a point on the graph...
+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")
+	
+}
+
+data("bmi_vichy")
+bmi_vichy<-calcule(bmi_vichy,timesplit="jour",silent=TRUE)
+#bmi_vichy at calcdata
+
+bmi_vichy<-calcule(bmi_vichy,timesplit="semaine",silent=TRUE)
+#bmi_vichy at calcdata
+
+bmi_vichy<-calcule(bmi_vichy,timesplit="jour_365")
+#bmi_vichy at calcdata
+
+plot(bmi_vichy,plot.type="seasonal",timesplit="semaine",silent=TRUE)
+plot(bmi_vichy,plot.type="seasonal",timesplit="mois",silent=TRUE)
+plot(bmi_vichy,plot.type="seasonal",timesplit="jour",silent=TRUE)
+
+
+
+# A test with lampreys in the Descarte DF (Vienne)
+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)
+bmi_des<-new("BilanMigrationInterAnnuelle") #descartes
+bmi_des<-choice_c(bmi_des,
+		dc=c(23),
+		taxons=c("Petromyzon marinus"),
+		stades=c("5"),
+		anneedebut="2007",
+		anneefin="2014",
+		silent=TRUE)
+bmi_des<-charge(bmi_des)
+bmi_des<-connect(bmi_des)	
+bmi_des<-calcule(bmi_des,timesplit="semaine")
+plot(bmi_des,plot.type="seasonal",timesplit="semaine")
+plot(bmi_des,plot.type="seasonal",timesplit="jour")
+plot(bmi_des,plot.type="seasonal",timesplit="mois")
+}	
+
+
+

Modified: www/index.php
===================================================================
--- www/index.php	2017-06-25 20:11:07 UTC (rev 424)
+++ www/index.php	2017-06-25 20:14:07 UTC (rev 425)
@@ -75,7 +75,7 @@
 Timothée Besse LOGRAMI <a href="mailto:timothee.besse at logrami.fr">timothee.besse at logrami.fr</a><br/>
 Marion Legrand LOGRAMI <a href="mailto:marion.legrand at logrami.fr">marion.legrand at logrami.fr</a></p>
 
-<p><img src="stacomi.png"></p>
+<p><img src="images/stacomi.png"></p>
 
 </body>
 </html>

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