[Stacomir-commits] r295 - in pkg/stacomir: R man

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

Author: briand
Date: 2017-02-27 16:12:31 +0100 (Mon, 27 Feb 2017)
New Revision: 295

Modified:
   pkg/stacomir/R/BilanMigration.r
   pkg/stacomir/R/BilanMigrationMult.r
   pkg/stacomir/man/BilanMigration-class.Rd
   pkg/stacomir/man/BilanMigrationMult-class.Rd
Log:
bug when writing to the database after having checked that data have changed (BilanMigrationInterannuelle)

Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r	2017-02-12 20:44:58 UTC (rev 294)
+++ pkg/stacomir/R/BilanMigration.r	2017-02-27 15:12:31 UTC (rev 295)
@@ -18,6 +18,7 @@
 #' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
 #' @family Bilan Objects
 #' @keywords classes
+#' @aliases BilanMigration bilanMigration
 #' @example inst/examples/bilanMigration_Arzal.R
 #' @export 
 setClass(Class="BilanMigration",
@@ -580,6 +581,7 @@
 #' @export
 setMethod("write_database",signature=signature("BilanMigration"),definition=function(object,silent=TRUE,dbname="bd_contmig_nat",host="localhost",port=5432,check_for_bjo=TRUE){
 			# dbname="bd_contmig_nat";host="localhost";silent=FALSE;port=5432
+			# object=bM
 			bilanMigration<-object
 			if (class(bilanMigration)!="BilanMigration") stop("the bilanMigration should be of class BilanMigration")
 			if (class(silent)!="logical") stop("the silent argument should be a logical")
@@ -590,7 +592,11 @@
 			col_a_retirer=match(c("No.pas","type_de_quantite","debut_pas","fin_pas"),colnames(data))
 			data=data[,-col_a_retirer]
 			data$taux_d_echappement[data$taux_d_echappement==-1]<-NA 
+			# bug 27/02/2017 for some reasons crashes with arzal and coef_valeur_coefficient
+			# and didn't crash for logrami or smatah
+			if (!is.null(data$coe_valeur_coefficient)){
 			data$coe_valeur_coefficient[data$"coe_valeur_coefficient"==1]<-NA 
+		    }else {data$coe_valeur_coefficient<-NA}
 			peuventpaszero=match(c("taux_d_echappement","coe_valeur_coefficient"),colnames(data))
 			data[,-peuventpaszero][data[,-peuventpaszero]==0]<-NA
 			annee<-as.numeric(unique(strftime(as.POSIXlt(bilanMigration at time.sequence),"%Y"))[1])

Modified: pkg/stacomir/R/BilanMigrationMult.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMult.r	2017-02-12 20:44:58 UTC (rev 294)
+++ pkg/stacomir/R/BilanMigrationMult.r	2017-02-27 15:12:31 UTC (rev 295)
@@ -25,6 +25,7 @@
 #' method if any weight are found in the data slot.
 #' @slot time.sequence A POSIXt time sequence
 #' @family Bilan Objects
+#' @aliases BilanMigrationMult bilanMigrationMult
 #' @keywords classes
 #' @export
 #' @example inst/examples/bilanMigrationMult_Arzal.R

Modified: pkg/stacomir/man/BilanMigration-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigration-class.Rd	2017-02-12 20:44:58 UTC (rev 294)
+++ pkg/stacomir/man/BilanMigration-class.Rd	2017-02-27 15:12:31 UTC (rev 295)
@@ -2,7 +2,9 @@
 % Please edit documentation in R/BilanMigration.r
 \docType{class}
 \name{BilanMigration-class}
+\alias{BilanMigration}
 \alias{BilanMigration-class}
+\alias{bilanMigration}
 \title{Migration report for one DC, one species and one stage}
 \description{
 Migration report for one DC, one species and one stage

Modified: pkg/stacomir/man/BilanMigrationMult-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationMult-class.Rd	2017-02-12 20:44:58 UTC (rev 294)
+++ pkg/stacomir/man/BilanMigrationMult-class.Rd	2017-02-27 15:12:31 UTC (rev 295)
@@ -2,7 +2,9 @@
 % Please edit documentation in R/BilanMigrationMult.r
 \docType{class}
 \name{BilanMigrationMult-class}
+\alias{BilanMigrationMult}
 \alias{BilanMigrationMult-class}
+\alias{bilanMigrationMult}
 \title{Migration reports for multiple DC / species / stages}
 \description{
 Migration counts for several Fish counting devices (DC), several taxa and several stages.