[Stacomir-commits] r289 - in pkg/stacomir: R data

[noreply at r-forge.r-project.org]

Author: briand
Date: 2017-02-12 18:00:26 +0100 (Sun, 12 Feb 2017)
New Revision: 289

Modified:
   pkg/stacomir/R/BilanMigrationInterAnnuelle.r
   pkg/stacomir/R/Refperiode.r
   pkg/stacomir/data/bmi_vichy.rda
Log:


Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r	2017-02-06 16:32:31 UTC (rev 288)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r	2017-02-12 17:00:26 UTC (rev 289)
@@ -73,6 +73,8 @@
 			# object<-bmi 
 			# object<-bmi_cha
 			# object<-bmi_des
+			# object<-bmi_vichy
+			# require(dplyr); require(ggplot2)
 			#---------------------------------------------------------------------------------------
 			# this function will be run several times if missing data or mismatching data are found
 			# later in the script (hence the encapsulation)
@@ -84,7 +86,7 @@
 				dic= object at dc@dc_selectionne
 				requete=new("RequeteODBCwhere")
 				requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
-				requete at where=paste("WHERE bjo_annee IN ",vector_to_listsql(les_annees)," AND bjo_tax_code='",tax,"' AND bjo_std_code='",std,"' AND bjo_dis_identifiant=",dic,sep="")
+				requete at where=paste("WHERE bjo_annee IN ",vector_to_listsql(les_annees)," AND bjo_tax_code='",tax,"' AND bjo_std_code='",std,"' AND bjo_dis_identifiant in",vector_to_listsql(dic),sep="")
 				requete at select=paste("SELECT * FROM ",get("sch",envir=envir_stacomi),"t_bilanmigrationjournalier_bjo",sep="")
 				requete at order_by=" ORDER BY bjo_jour "
 				requete<-stacomirtools::connect(requete)
@@ -133,6 +135,7 @@
 					if (any(is.na(compared_numbers$effectif_bjo))){
 						index_missing_years<-which(is.na(compared_numbers$effectif_bjo))
 						missing_years<-compared_numbers$annee[index_missing_years]
+						if (! silent & length(dic)>1) funout(gettextf("DC with missing values : %s ",dic[i],domain="R-StacomiR"))
 						if (! silent) funout(gettextf("Years with no value : %s ",stringr::str_c(missing_years,collapse="; "),domain="R-StacomiR"))
 						if (! silent) funout(gettextf("Some years are missing in the t_bilanjournalier_bjo table, loading them now !",domain="R-StacomiR"))
 						
@@ -142,7 +145,7 @@
 							bM=new("BilanMigration")
 							funout(gettextf("Running Bilanmigraton for year %s",Y,domain="R-StacomiR"))
 							bM=choice_c(bM,
-									dc=dic,
+									dc=dic[i],
 									taxons=object at taxons@data$tax_nom_latin,
 									stades=object at stades@data$std_code,
 									datedebut=stringr::str_c(Y,"-01-01"),
@@ -182,9 +185,10 @@
 						reload_years_with_error=function(h,...){	
 							bM=new("BilanMigration")
 							for (Y in differing_years){
+								# Y=differing_years[1]
 								funout(gettextf("Running Bilanmigraton to correct data for year %s",Y))
 								bM=choice_c(bM,
-										dc=dic,
+										dc=dic[i],
 										taxons=object at taxons@data$tax_nom_latin,
 										stades=object at stades@data$std_code,
 										datedebut=stringr::str_c(Y,"-01-01"),
@@ -386,6 +390,8 @@
 			taxon<-bilanMigrationInterAnnuelle at taxons@data$tax_code
 			stade<-bilanMigrationInterAnnuelle at stades@data$std_code
 			if(length(unique(bilanMigrationInterAnnuelle at dc@station))!=1) stop("You have more than one station in the Bilan, the dc from the Bilan should belong to the same station")
+			if(nrow(bilanMigrationInterAnnuelle at data)==0) stop("No rows in bilanMigrationInterannuelle at data, nothing to run calculations on")
+			
 			datadic<-bilanMigrationInterAnnuelle at data[
 					bilanMigrationInterAnnuelle at data$bjo_labelquantite=="Effectif_total",]
 			datadic<-funtraitementdate(datadic, nom_coldt = "bjo_jour", jour_an = TRUE, quinzaine = TRUE)
@@ -870,7 +876,7 @@
 					
 				} else if (plot.type=="seasonal"){
 					if (! silent) funout("Seasonal graph to show the phenology of migration")
-					#bilanMigrationInterAnnuelle<-bmi_vichy;silent=FALSE;timesplit="semaine";require(ggplot2)
+					#bilanMigrationInterAnnuelle<-bmi_vichy;silent=FALSE;timesplit="mois";require(ggplot2)
 					bilanMigrationInterAnnuelle<-calcule(bilanMigrationInterAnnuelle,timesplit=timesplit)
 					#if (!silent& nrow(bilanMigrationInterAnnuelle at calcdata)==0) stop("You should run calculation before plotting seasonal data")
 					dat3<-bilanMigrationInterAnnuelle at calcdata
@@ -890,7 +896,7 @@
 									},"semaine"={
 										as.Date(paste(year,"-",dat[,col[i]],"-",6,sep=""),"%Y-%U-%w")
 									},"mois"={
-										as.Date(paste(year,"-",dat[,col[i]],"-",1,sep=""),"%Y-%m")
+										as.Date(paste(year,"-",dat[,col[i]],"-",1,sep=""),"%Y-%m-%d")
 									},stop(stringr::str_c("Internal error, timesplit ",timesplit_," not working for seasonal plot"))									
 							)
 						}

Modified: pkg/stacomir/R/Refperiode.r
===================================================================
--- pkg/stacomir/R/Refperiode.r	2017-02-06 16:32:31 UTC (rev 288)
+++ pkg/stacomir/R/Refperiode.r	2017-02-12 17:00:26 UTC (rev 289)
@@ -28,6 +28,7 @@
 #' \dontrun{
 #'  getvalue(new("Refperiode"),"quinzaine")
 #' }
+#' @export
 setMethod("getvalue",signature=signature("Refperiode"), definition=function(object,id)
   {return(as.character(object at data[object at data$id==id,"pgval"]))
   } ) 
\ No newline at end of file

Modified: pkg/stacomir/data/bmi_vichy.rda
===================================================================
(Binary files differ)