[Stacomir-commits] r224 - in pkg/stacomir: R inst/config inst/examples inst/tests/testthat man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Oct 1 09:43:01 CEST 2016
Author: briand
Date: 2016-10-01 09:43:01 +0200 (Sat, 01 Oct 2016)
New Revision: 224
Modified:
pkg/stacomir/R/BilanFonctionnementDF.r
pkg/stacomir/R/RefAnnee.r
pkg/stacomir/R/RefCheckBox.r
pkg/stacomir/R/RefChoix.r
pkg/stacomir/R/RefCoe.r
pkg/stacomir/R/RefDC.r
pkg/stacomir/R/RefDF.r
pkg/stacomir/R/RefHorodate.r
pkg/stacomir/R/RefListe.r
pkg/stacomir/R/RefMsg.r
pkg/stacomir/R/RefStades.r
pkg/stacomir/R/RefStationMesure.r
pkg/stacomir/R/RefTaxon.r
pkg/stacomir/R/Refpar.r
pkg/stacomir/R/Refparqual.r
pkg/stacomir/R/Refparquan.r
pkg/stacomir/inst/config/stacomi_manual_launch.r
pkg/stacomir/inst/config/testthat.R
pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R
pkg/stacomir/inst/examples/bilanMigration_Arzal.R
pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
pkg/stacomir/inst/tests/testthat/test-03BilanFonctionnementDF.R
pkg/stacomir/man/BilanMigration-class.Rd
pkg/stacomir/man/BilanMigrationMult-class.Rd
pkg/stacomir/man/RefAnnee-class.Rd
pkg/stacomir/man/RefCheckBox-class.Rd
pkg/stacomir/man/RefChoix-class.Rd
pkg/stacomir/man/RefCoe-class.Rd
pkg/stacomir/man/RefDC-class.Rd
pkg/stacomir/man/RefDF-class.Rd
pkg/stacomir/man/RefHorodate-class.Rd
pkg/stacomir/man/RefListe-class.Rd
pkg/stacomir/man/RefStades-class.Rd
pkg/stacomir/man/RefStationMesure-class.Rd
pkg/stacomir/man/RefTaxon-class.Rd
pkg/stacomir/man/Refpar-class.Rd
pkg/stacomir/man/Refparqual-class.Rd
pkg/stacomir/man/Refparquan-class.Rd
pkg/stacomir/man/Refperiode-class.Rd
pkg/stacomir/man/charge-RefChoix-method.Rd
pkg/stacomir/man/charge-RefMsg-method.Rd
pkg/stacomir/man/charge_avec_filtre-RefMsg-method.Rd
Log:
Finalizing test for bilanFonctionnementDF-class
Modified: pkg/stacomir/R/BilanFonctionnementDF.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDF.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/BilanFonctionnementDF.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -134,7 +134,7 @@
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
setMethod("choice_c",signature=signature("BilanFonctionnementDF"),definition=function(object,df,horodatedebut,horodatefin,silent=FALSE){
- # bilanFonctionnementDF<-BfDF;df=2;horodatedebut="2013-01-01";horodatefin="2013-12-31"
+ # bilanFonctionnementDF<-bfDF;df=2;horodatedebut="2013-01-01";horodatefin="2013-12-31";silent=TRUE
bilanFonctionnementDF<-object
assign("bilanFonctionnementDF",bilanFonctionnementDF,envir=envir_stacomi)
if (!silent) funout(get("msg",envir=envir_stacomi)$interface_BilanFonctionnementDC.1)
@@ -144,11 +144,11 @@
bilanFonctionnementDF at horodatedebut<-choice_c(object=bilanFonctionnementDF at horodatedebut,
nomassign="bilanFonctionnementDF_date_debut",
funoutlabel=get("msg",envir=envir_stacomi)$interface_Bilan_lot.5,
- horodate=horodatedebut, silent)
+ horodate=horodatedebut, silent=silent)
bilanFonctionnementDF at horodatefin<-choice_c(bilanFonctionnementDF at horodatefin,
nomassign="bilanFonctionnementDF_date_fin",
funoutlabel=get("msg",envir=envir_stacomi)$interface_Bilan_lot.6,
- horodate=horodatefin,silent)
+ horodate=horodatefin,silent=silent)
assign("bilanFonctionnementDF",bilanFonctionnementDF,envir=envir_stacomi)
return(bilanFonctionnementDF)
})
@@ -559,14 +559,14 @@
sommes<-tapply(duree,t_periodefonctdispositif_per$per_tar_code,sum)
perc<-round(100*sommes/as.numeric(sum(duree)))
sommes<-round(sommes,2)
- funout(get("msg",envir=envir_stacomi)$FonctionnementDF.12)
+ funout(get("msg",envir=envir_stacomi)$BilanFonctionnementDF.12)
funout(paste(get("msg",envir=envir_stacomi)$BilanFonctionnementDF.11,
" :",
sommes,"(",perc,"%)",sep=""))
sommes<-tapply(duree,t_periodefonctdispositif_per$per_etat_fonctionnement,sum)
perc<-round(100*sommes/as.numeric(sum(duree)))
sommes<-round(sommes,2)
- funout(get("msg",envir=envir_stacomi)$FonctionnementDF.13)
+ funout(get("msg",envir=envir_stacomi)$BilanFonctionnementDF.13)
funout(paste(rev(get("msg",envir=envir_stacomi)$BilanFonctionnementDC.11),
" :",
sommes,"(",perc,"%)",sep=""))
Modified: pkg/stacomir/R/RefAnnee.r
===================================================================
--- pkg/stacomir/R/RefAnnee.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/RefAnnee.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -33,7 +33,6 @@
#' \code{\linkS4class{Refpar}}
#' \code{\linkS4class{Refparqual}}
#' \code{\linkS4class{Refparquan}}
-#' \code{\linkS4class{RefPoidsMoyenPeche}}
#' \code{\linkS4class{RefStades}}
#' \code{\linkS4class{RefStationMesure}}
#' \code{\linkS4class{RefTaxon}}
Modified: pkg/stacomir/R/RefCheckBox.r
===================================================================
--- pkg/stacomir/R/RefCheckBox.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/RefCheckBox.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -7,21 +7,6 @@
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("RefCheckBox", ...)}.
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @seealso Other referential classes
-#' \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}}
-#' \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}}
-#' \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}}
-#' \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}}
-#' \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}}
-#' \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}}
-#' \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
#' @family Referential objects
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
setClass(Class="RefCheckBox",representation= representation(title="character",labels="character",checked="logical"),
Modified: pkg/stacomir/R/RefChoix.r
===================================================================
--- pkg/stacomir/R/RefChoix.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/RefChoix.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -10,21 +10,6 @@
#' @slot label A character, title of the box giving the possible choices
#' @slot selected An \code{Integer} the initial selected value (as an index), first=1 used in gradio
#' @author cedric.briand"at"eptb-vilaine.fr
-#' @seealso Other referential classes
-#' \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}}
-#' \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}}
-#' \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}}
-#' \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}}
-#' \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}}
-#' \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}}
-#' \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
#' @family Referential objects
setClass(Class="RefChoix",representation= representation(listechoice="character",label="character",selected="integer"))
Modified: pkg/stacomir/R/RefCoe.r
===================================================================
--- pkg/stacomir/R/RefCoe.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/RefCoe.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -16,21 +16,6 @@
#' @slot datefin A "POSIXlt"
#' @author cedric.briand"at"eptb-vilaine.fr
#' @family Referential objects
-#' @seealso Other referential classes
-#' \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}}
-#' \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}}
-#' \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}}
-#' \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}}
-#' \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}}
-#' \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}}
-#' \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
#' @keywords classes
setClass(Class="RefCoe",representation=
representation(data="data.frame",datedebut="POSIXlt",datefin="POSIXlt"),
Modified: pkg/stacomir/R/RefDC.r
===================================================================
--- pkg/stacomir/R/RefDC.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/RefDC.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -14,14 +14,6 @@
#' \code{new("RefDC", dc_selectionne=integer(), ouvrage=integer(),
#' data=data.frame())}.
#' @author cedric.briand"at"eptb-vilaine.fr
-#' @seealso Other referential classes \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}} \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}} \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}} \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}} \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}} \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}} \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
#' @keywords classes
#' @family Referential objects
setClass(Class="RefDC",representation=
Modified: pkg/stacomir/R/RefDF.r
===================================================================
--- pkg/stacomir/R/RefDF.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/RefDF.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -13,21 +13,6 @@
#' @slot ouvrage Object of class \code{"integer"} The attached dam
#' @slot data Object of class \code{"data.frame"} Data concerning the fishway
#' @author cedric.briand"at"eptb-vilaine.fr
-#' @seealso Other referential classes
-#' \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}}
-#' \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}}
-#' \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}}
-#' \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}}
-#' \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}}
-#' \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}}
-#' \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
#' @family Referential objects
setClass(Class="RefDF",representation=
representation(df_selectionne="integer",ouvrage="integer",data="data.frame") )
Modified: pkg/stacomir/R/RefHorodate.r
===================================================================
--- pkg/stacomir/R/RefHorodate.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/RefHorodate.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -19,14 +19,6 @@
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("RefHorodate", \dots{})}.
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @seealso Other referential classes \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}} \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}} \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}} \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}} \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}} \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}} \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
#' @family Referential objects
setClass(Class="RefHorodate",representation=
representation(horodate="POSIXt"),
@@ -157,6 +149,9 @@
if (is.na(.horodate)){
.horodate=strptime(horodate, format="%d-%m-%Y")
}
+ } else {
+ stop("Formatting problem, the character vector you are trying to pass as horodate could not
+be parsed. Check example or documentation")
}
} else if (class(horodate)=="Date"){
Modified: pkg/stacomir/R/RefListe.r
===================================================================
--- pkg/stacomir/R/RefListe.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/RefListe.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -13,14 +13,7 @@
#' of class \code{"character"}} \item{list("label")}{Object of class
#' \code{"character"}}\item{:}{Object of class \code{"character"}} }
#' @author cedric.briand"at"eptb-vilaine.fr
-#' @seealso Other referential classes \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}} \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}} \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}} \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}} \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}} \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}} \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
+
#' @keywords classes
#' @family Referential objects
setClass(Class="RefListe",representation= representation(listechoice="character",label="character"))
Modified: pkg/stacomir/R/RefMsg.r
===================================================================
--- pkg/stacomir/R/RefMsg.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/RefMsg.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -9,7 +9,7 @@
#'
#' loads the common table ts_messager_msr
#' @return An S4 object of class RefMsg
-#' @param object An object of class \link {RefMsg-class}
+#' @param object An object of class \link{RefMsg-class}
#' @family Referential objects
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
@@ -29,7 +29,7 @@
#' Loading method for RefMsg referential objects
#'
#' searching ref.ts_messagerlang_mrl for the lines corresponding to lang
-#' @param object An object of class \link{refMsg-class}
+#' @param object An object of class \link{RefMsg-class}
#' @param lang A language, either "French" or "English" or "Spanish"
#' @return An S4 object of class RefMsg
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
Modified: pkg/stacomir/R/RefStades.r
===================================================================
--- pkg/stacomir/R/RefStades.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/RefStades.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -10,14 +10,6 @@
#' available in the database}\item{:}{Object of class \code{"data.frame"} ~ The
#' phases available in the database} }
#' @author cedric.briand"at"eptb-vilaine.fr
-#' @seealso Other referential classes \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}} \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}} \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}} \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}} \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}} \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}} \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
#' @keywords classes
#' @family Referential objects
setClass(Class="RefStades",representation=representation(data="data.frame") )
Modified: pkg/stacomir/R/RefStationMesure.r
===================================================================
--- pkg/stacomir/R/RefStationMesure.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/RefStationMesure.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -10,21 +10,6 @@
#' @slot dataframe Data concerning the
#' measure station
#' @author cedric.briand"at"eptb-vilaine.fr
-#' @seealso Other referential classes
-#' \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}}
-#' \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}}
-#' \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}}
-#' \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}}
-#' \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}}
-#' \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}}
-#' \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
#' @keywords classes
setClass (Class="RefStationMesure",
representation=representation(data="data.frame"),
Modified: pkg/stacomir/R/RefTaxon.r
===================================================================
--- pkg/stacomir/R/RefTaxon.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/RefTaxon.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -7,22 +7,10 @@
#' \code{new("RefTaxon", ...)}.
#' @slot data A \code{"data.frame"} of species available in the database
#' @author cedric.briand"at"eptb-vilaine.fr
-#' @seealso Other referential classes
-#' \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}}
-#' \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}}
-#' \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}}
-#' \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}}
-#' \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}}
-#' \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}}
-#' \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
+#' @family Referential objects
setClass(Class="RefTaxon",representation= representation(data="data.frame" ))
+
+
#' Loading method for RefTaxon referential objects
#'
#' @return An S4 object of class RefTaxon
Modified: pkg/stacomir/R/Refpar.r
===================================================================
--- pkg/stacomir/R/Refpar.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/Refpar.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -14,14 +14,6 @@
#' database}\item{:}{Object of class \code{"data.frame"} ~ All the parameters
#' stored in the database} }
#' @author cedric.briand"at"eptb-vilaine.fr
-#' @seealso Other referential classes \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}} \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}} \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}} \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}} \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}} \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}} \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
#' @keywords classes
#' @slot data="data.frame" the list of parameters
#' @family Referential objects
Modified: pkg/stacomir/R/Refparqual.r
===================================================================
--- pkg/stacomir/R/Refparqual.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/Refparqual.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -16,14 +16,6 @@
#' parameters }\item{:}{Object of class \code{"data.frame"} Qualitatives
#' parameters } }
#' @author cedric.briand"at"eptb-vilaine.fr
-#' @seealso Other referential classes \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}} \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}} \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}} \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}} \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}} \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}} \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
#' @slot valqual="data.frame" the list of qualitative parameters
#' @include Refpar.r
#' @family Referential objects
Modified: pkg/stacomir/R/Refparquan.r
===================================================================
--- pkg/stacomir/R/Refparquan.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/R/Refparquan.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -11,14 +11,6 @@
#' parameters }\item{:}{Object of class \code{"data.frame"} ~ Quantitative
#' parameters } }
#' @author cedric.briand"at"eptb-vilaine.fr
-#' @seealso Other referential classes \code{\linkS4class{RefAnnee}}
-#' \code{\linkS4class{RefCheckBox}} \code{\linkS4class{RefChoix}}
-#' \code{\linkS4class{RefCoe}} \code{\linkS4class{RefDC}}
-#' \code{\linkS4class{RefDF}} \code{\linkS4class{RefListe}}
-#' \code{\linkS4class{Refpar}} \code{\linkS4class{Refparqual}}
-#' \code{\linkS4class{Refparquan}} \code{\linkS4class{RefPoidsMoyenPeche}}
-#' \code{\linkS4class{RefStades}} \code{\linkS4class{RefStationMesure}}
-#' \code{\linkS4class{RefTaxon}}
#' @keywords classes
#' @family Referential objects
#' @include Refpar.r
Modified: pkg/stacomir/inst/config/stacomi_manual_launch.r
===================================================================
--- pkg/stacomir/inst/config/stacomi_manual_launch.r 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/inst/config/stacomi_manual_launch.r 2016-10-01 07:43:01 UTC (rev 224)
@@ -53,7 +53,6 @@
source("RefChoix.r")
source("ReftextBox.r")
source("RefCheckBox.r")
-source("RefPoidsMoyenPeche.r")
source("RefStationMesure.r")
source("Refperiode.r")
source("RefHorodate.r")
Modified: pkg/stacomir/inst/config/testthat.R
===================================================================
--- pkg/stacomir/inst/config/testthat.R 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/inst/config/testthat.R 2016-10-01 07:43:01 UTC (rev 224)
@@ -14,4 +14,5 @@
test_file("F:/workspace/stacomir/pkg/stacomir/inst/tests/testthat/test-01BilanMigrationMult.R")
-test_file("F:/workspace/stacomir/pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R")
\ No newline at end of file
+test_file("F:/workspace/stacomir/pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R")
+test_file("F:/workspace/stacomir/pkg/stacomir/inst/tests/testthat/test-03BilanFonctionnementDF.R")
\ No newline at end of file
Modified: pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R 2016-10-01 07:43:01 UTC (rev 224)
@@ -14,7 +14,8 @@
dc=c(5,6,12),
taxons=c("Anguilla anguilla"),
stades=c("AGG","AGJ","CIV"),datedebut="2011-01-01",datefin="2011-12-31")
- bMM_Arzal<-charge(bMM_Arzal) # launching charge will also load classes associated with the bilan
+ bMM_Arzal<-charge(bMM_Arzal)
+ # launching charge will also load classes associated with the bilan
# e.g. BilanOperation, BilanFonctionnementDF, BilanFonctionnementDC
bMM_Arzal<-connect(bMM_Arzal)
}
@@ -22,8 +23,8 @@
data("bMM_Arzal")
# The following re-create the object at the time of loading
-# All three classes were created by the charge and connect method of BilanMigrationMult
-# in the previous example
+# All three classes were created by the charge and connect
+# method of BilanMigrationMult in the previous example
data("bilanOperation")
assign("bilanOperation",bilanOperation,envir=envir_stacomi)
data("bilanFonctionnementDF")
@@ -50,7 +51,8 @@
#same for spanish.
# combined plot for ggplot2
plot(bMM_Arzal,plot.type="multiple")
-# data will be written in the data directory specified in the stacomi/calcmig.csv file
+# data will be written in the data directory specified in
+# the stacomi/calcmig.csv file
\dontrun{
-summary(bMM_Arzal,silent=TRUE)
+ summary(bMM_Arzal,silent=TRUE)
}
Modified: pkg/stacomir/inst/examples/bilanMigration_Arzal.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigration_Arzal.R 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/inst/examples/bilanMigration_Arzal.R 2016-10-01 07:43:01 UTC (rev 224)
@@ -25,7 +25,8 @@
# use the following to get the raw data loaded by the connect method
# not shown there as the database and program might not be installed
-# All three classes were created by the charge and connect method of BilanMigrationMult
+# All three classes were created by the charge and connect method
+# of BilanMigrationMult
# in the previous example
data("bilanOperation_bM")
assign("bilanOperation",bilanOperation_bM,envir=envir_stacomi)
@@ -44,7 +45,8 @@
#cumulated migration at the station (all stages and DC grouped)
plot(bM_Arzal,plot.type="step")
-# data will be written in the data directory specified in the stacomi/calcmig.csv file
+# data will be written in the data directory specified in the stacomi/calcmig.csv
+#file
\dontrun{
summary(bM_Arzal,silent=TRUE)
Modified: pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R 2016-10-01 07:43:01 UTC (rev 224)
@@ -74,7 +74,7 @@
# this chunk is not launched from examples but loads the bM_Arzal dataset if connection works
data("bM_Arzal")
bM_Arzal<-calcule(bM_Arzal,silent=TRUE)
- summary(bM_Arzal)
+ summary(bM_Arzal,silent=TRUE)
rm("envir_stacomi",envir =.GlobalEnv)
})
Modified: pkg/stacomir/inst/tests/testthat/test-03BilanFonctionnementDF.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-03BilanFonctionnementDF.R 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/inst/tests/testthat/test-03BilanFonctionnementDF.R 2016-10-01 07:43:01 UTC (rev 224)
@@ -21,10 +21,11 @@
the RefDF slot,nrow(bfDF at df@data)")
expect_s4_class(bfDF,
"BilanFonctionnementDF")
- expect_failure(BfDF<-choice_c(bfDF,
+ expect_error(BfDF<-choice_c(bfDF,
2,
horodatedebut="2013 01 011",
- horodatefin="2013-12-31"))
+ horodatefin="2013-12-31",
+ silent=TRUE))
})
@@ -45,7 +46,8 @@
horodatefin="2013-12-31",
silent=TRUE)
bfDF<-charge(bfDF,silent=TRUE)
- expect_equals(nrow(bfDF at data),5)
+ bfDF<-connect(bfDF,silent=TRUE)
+ expect_equal(nrow(bfDF at data),5)
})
@@ -66,7 +68,7 @@
stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
data(bfDF)
bfDF<-bfDF
- expect_output(summary(bfDF))
+ expect_output(summary(bfDF,silent=FALSE),"summary")
})
Modified: pkg/stacomir/man/BilanMigration-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigration-class.Rd 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/man/BilanMigration-class.Rd 2016-10-01 07:43:01 UTC (rev 224)
@@ -60,7 +60,8 @@
# use the following to get the raw data loaded by the connect method
# not shown there as the database and program might not be installed
-# All three classes were created by the charge and connect method of BilanMigrationMult
+# All three classes were created by the charge and connect method
+# of BilanMigrationMult
# in the previous example
data("bilanOperation_bM")
assign("bilanOperation",bilanOperation_bM,envir=envir_stacomi)
@@ -79,7 +80,8 @@
#cumulated migration at the station (all stages and DC grouped)
plot(bM_Arzal,plot.type="step")
-# data will be written in the data directory specified in the stacomi/calcmig.csv file
+# data will be written in the data directory specified in the stacomi/calcmig.csv
+#file
\dontrun{
summary(bM_Arzal,silent=TRUE)
Modified: pkg/stacomir/man/BilanMigrationMult-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationMult-class.Rd 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/man/BilanMigrationMult-class.Rd 2016-10-01 07:43:01 UTC (rev 224)
@@ -59,7 +59,8 @@
dc=c(5,6,12),
taxons=c("Anguilla anguilla"),
stades=c("AGG","AGJ","CIV"),datedebut="2011-01-01",datefin="2011-12-31")
- bMM_Arzal<-charge(bMM_Arzal) # launching charge will also load classes associated with the bilan
+ bMM_Arzal<-charge(bMM_Arzal)
+ # launching charge will also load classes associated with the bilan
# e.g. BilanOperation, BilanFonctionnementDF, BilanFonctionnementDC
bMM_Arzal<-connect(bMM_Arzal)
}
@@ -67,8 +68,8 @@
data("bMM_Arzal")
# The following re-create the object at the time of loading
-# All three classes were created by the charge and connect method of BilanMigrationMult
-# in the previous example
+# All three classes were created by the charge and connect
+# method of BilanMigrationMult in the previous example
data("bilanOperation")
assign("bilanOperation",bilanOperation,envir=envir_stacomi)
data("bilanFonctionnementDF")
@@ -95,9 +96,10 @@
#same for spanish.
# combined plot for ggplot2
plot(bMM_Arzal,plot.type="multiple")
-# data will be written in the data directory specified in the stacomi/calcmig.csv file
+# data will be written in the data directory specified in
+# the stacomi/calcmig.csv file
\dontrun{
-summary(bMM_Arzal,silent=TRUE)
+ summary(bMM_Arzal,silent=TRUE)
}
}
\author{
Modified: pkg/stacomir/man/RefAnnee-class.Rd
===================================================================
--- pkg/stacomir/man/RefAnnee-class.Rd 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/man/RefAnnee-class.Rd 2016-10-01 07:43:01 UTC (rev 224)
@@ -33,7 +33,6 @@
\code{\linkS4class{Refpar}}
\code{\linkS4class{Refparqual}}
\code{\linkS4class{Refparquan}}
-\code{\linkS4class{RefPoidsMoyenPeche}}
\code{\linkS4class{RefStades}}
\code{\linkS4class{RefStationMesure}}
\code{\linkS4class{RefTaxon}}
@@ -44,7 +43,7 @@
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
\code{\link{RefStades-class}},
- \code{\link{Refpar-class}},
+ \code{\link{RefTaxon-class}}, \code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
Modified: pkg/stacomir/man/RefCheckBox-class.Rd
===================================================================
--- pkg/stacomir/man/RefCheckBox-class.Rd 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/man/RefCheckBox-class.Rd 2016-10-01 07:43:01 UTC (rev 224)
@@ -26,29 +26,13 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other referential classes
-\code{\linkS4class{RefAnnee}}
-\code{\linkS4class{RefCheckBox}}
-\code{\linkS4class{RefChoix}}
-\code{\linkS4class{RefCoe}}
-\code{\linkS4class{RefDC}}
-\code{\linkS4class{RefDF}}
-\code{\linkS4class{RefListe}}
-\code{\linkS4class{Refpar}}
-\code{\linkS4class{Refparqual}}
-\code{\linkS4class{Refparquan}}
-\code{\linkS4class{RefPoidsMoyenPeche}}
-\code{\linkS4class{RefStades}}
-\code{\linkS4class{RefStationMesure}}
-\code{\linkS4class{RefTaxon}}
-
Other Referential.objects: \code{\link{RefAnnee-class}},
\code{\link{RefChoix-class}}, \code{\link{RefCoe-class}},
\code{\link{RefDC-class}}, \code{\link{RefDF-class}},
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
\code{\link{RefStades-class}},
- \code{\link{Refpar-class}},
+ \code{\link{RefTaxon-class}}, \code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
Modified: pkg/stacomir/man/RefChoix-class.Rd
===================================================================
--- pkg/stacomir/man/RefChoix-class.Rd 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/man/RefChoix-class.Rd 2016-10-01 07:43:01 UTC (rev 224)
@@ -26,22 +26,6 @@
cedric.briand"at"eptb-vilaine.fr
}
\seealso{
-Other referential classes
-\code{\linkS4class{RefAnnee}}
-\code{\linkS4class{RefCheckBox}}
-\code{\linkS4class{RefChoix}}
-\code{\linkS4class{RefCoe}}
-\code{\linkS4class{RefDC}}
-\code{\linkS4class{RefDF}}
-\code{\linkS4class{RefListe}}
-\code{\linkS4class{Refpar}}
-\code{\linkS4class{Refparqual}}
-\code{\linkS4class{Refparquan}}
-\code{\linkS4class{RefPoidsMoyenPeche}}
-\code{\linkS4class{RefStades}}
-\code{\linkS4class{RefStationMesure}}
-\code{\linkS4class{RefTaxon}}
-
Other Referential.objects: \code{\link{RefAnnee-class}},
\code{\link{RefCheckBox-class}},
\code{\link{RefCoe-class}}, \code{\link{RefDC-class}},
@@ -49,7 +33,7 @@
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
\code{\link{RefStades-class}},
- \code{\link{Refpar-class}},
+ \code{\link{RefTaxon-class}}, \code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
Modified: pkg/stacomir/man/RefCoe-class.Rd
===================================================================
--- pkg/stacomir/man/RefCoe-class.Rd 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/man/RefCoe-class.Rd 2016-10-01 07:43:01 UTC (rev 224)
@@ -30,22 +30,6 @@
cedric.briand"at"eptb-vilaine.fr
}
\seealso{
-Other referential classes
-\code{\linkS4class{RefAnnee}}
-\code{\linkS4class{RefCheckBox}}
-\code{\linkS4class{RefChoix}}
-\code{\linkS4class{RefCoe}}
-\code{\linkS4class{RefDC}}
-\code{\linkS4class{RefDF}}
-\code{\linkS4class{RefListe}}
-\code{\linkS4class{Refpar}}
-\code{\linkS4class{Refparqual}}
-\code{\linkS4class{Refparquan}}
-\code{\linkS4class{RefPoidsMoyenPeche}}
-\code{\linkS4class{RefStades}}
-\code{\linkS4class{RefStationMesure}}
-\code{\linkS4class{RefTaxon}}
-
Other Referential.objects: \code{\link{RefAnnee-class}},
\code{\link{RefCheckBox-class}},
\code{\link{RefChoix-class}}, \code{\link{RefDC-class}},
@@ -53,7 +37,7 @@
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
\code{\link{RefStades-class}},
- \code{\link{Refpar-class}},
+ \code{\link{RefTaxon-class}}, \code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
Modified: pkg/stacomir/man/RefDC-class.Rd
===================================================================
--- pkg/stacomir/man/RefDC-class.Rd 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/man/RefDC-class.Rd 2016-10-01 07:43:01 UTC (rev 224)
@@ -28,15 +28,6 @@
cedric.briand"at"eptb-vilaine.fr
}
\seealso{
-Other referential classes \code{\linkS4class{RefAnnee}}
-\code{\linkS4class{RefCheckBox}} \code{\linkS4class{RefChoix}}
-\code{\linkS4class{RefCoe}} \code{\linkS4class{RefDC}}
-\code{\linkS4class{RefDF}} \code{\linkS4class{RefListe}}
-\code{\linkS4class{Refpar}} \code{\linkS4class{Refparqual}}
-\code{\linkS4class{Refparquan}} \code{\linkS4class{RefPoidsMoyenPeche}}
-\code{\linkS4class{RefStades}} \code{\linkS4class{RefStationMesure}}
-\code{\linkS4class{RefTaxon}}
-
Other Referential.objects: \code{\link{RefAnnee-class}},
\code{\link{RefCheckBox-class}},
\code{\link{RefChoix-class}}, \code{\link{RefCoe-class}},
@@ -44,7 +35,7 @@
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
\code{\link{RefStades-class}},
- \code{\link{Refpar-class}},
+ \code{\link{RefTaxon-class}}, \code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
Modified: pkg/stacomir/man/RefDF-class.Rd
===================================================================
--- pkg/stacomir/man/RefDF-class.Rd 2016-09-29 09:47:49 UTC (rev 223)
+++ pkg/stacomir/man/RefDF-class.Rd 2016-10-01 07:43:01 UTC (rev 224)
@@ -24,22 +24,6 @@
cedric.briand"at"eptb-vilaine.fr
}
\seealso{
-Other referential classes
-\code{\linkS4class{RefAnnee}}
-\code{\linkS4class{RefCheckBox}}
-\code{\linkS4class{RefChoix}}
-\code{\linkS4class{RefCoe}}
-\code{\linkS4class{RefDC}}
-\code{\linkS4class{RefDF}}
-\code{\linkS4class{RefListe}}
-\code{\linkS4class{Refpar}}
-\code{\linkS4class{Refparqual}}
-\code{\linkS4class{Refparquan}}
-\code{\linkS4class{RefPoidsMoyenPeche}}
-\code{\linkS4class{RefStades}}
-\code{\linkS4class{RefStationMesure}}
-\code{\linkS4class{RefTaxon}}
-
Other Referential.objects: \code{\link{RefAnnee-class}},
\code{\link{RefCheckBox-class}},
\code{\link{RefChoix-class}}, \code{\link{RefCoe-class}},
@@ -47,7 +31,7 @@
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 224
More information about the Stacomir-commits
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