[Stacomir-commits] r222 - in pkg/stacomir: . R inst/examples inst/tests/testthat man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Sep 29 11:45:59 CEST 2016
Author: briand
Date: 2016-09-29 11:45:58 +0200 (Thu, 29 Sep 2016)
New Revision: 222
Added:
pkg/stacomir/man/bilanFonctionnementDC_bM.Rd
pkg/stacomir/man/bilanFonctionnementDF_bM.Rd
pkg/stacomir/man/bilanOperation_bM.Rd
Removed:
pkg/stacomir/R/RefPoidsMoyenPeche.r
pkg/stacomir/man/RefPoidsMoyenPeche-class.Rd
pkg/stacomir/man/charge-RefPoidsMoyenPeche-method.Rd
Modified:
pkg/stacomir/DESCRIPTION
pkg/stacomir/R/BilanFonctionnementDF.r
pkg/stacomir/R/BilanMigrationInterAnnuelle.r
pkg/stacomir/R/RefCheckBox.r
pkg/stacomir/R/RefDC.r
pkg/stacomir/R/RefDF.r
pkg/stacomir/R/RefListe.r
pkg/stacomir/R/RefMsg.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/R/ReftextBox.r
pkg/stacomir/R/data.r
pkg/stacomir/R/utilitaires.r
pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R
pkg/stacomir/inst/examples/bilanMigration_Arzal.R
pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
pkg/stacomir/man/BilanFonctionnementDF-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/Refpar-class.Rd
pkg/stacomir/man/Refparqual-class.Rd
pkg/stacomir/man/Refparquan-class.Rd
pkg/stacomir/man/Refperiode-class.Rd
pkg/stacomir/man/bilanFonctionnementDC.Rd
pkg/stacomir/man/bilanFonctionnementDF.Rd
pkg/stacomir/man/bilanOperation.Rd
pkg/stacomir/man/charge-RefCheckBox-method.Rd
pkg/stacomir/man/charge-RefChoix-method.Rd
pkg/stacomir/man/charge-RefDC-method.Rd
pkg/stacomir/man/charge-RefDF-method.Rd
pkg/stacomir/man/charge-RefListe-method.Rd
pkg/stacomir/man/charge-RefMsg-method.Rd
pkg/stacomir/man/charge-RefStationMesure-method.Rd
pkg/stacomir/man/charge-RefTaxon-method.Rd
pkg/stacomir/man/charge-RefTextBox-method.Rd
pkg/stacomir/man/charge-Refpar-method.Rd
pkg/stacomir/man/charge-Refparqual-method.Rd
pkg/stacomir/man/charge-Refparquan-method.Rd
pkg/stacomir/man/charge_avec_filtre-RefMsg-method.Rd
pkg/stacomir/man/charge_avec_filtre-RefTaxon-method.Rd
pkg/stacomir/man/charge_avec_filtre-Refpar-method.Rd
pkg/stacomir/man/choice-RefTaxon-method.Rd
pkg/stacomir/man/choice-Refpar-method.Rd
Log:
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/DESCRIPTION 2016-09-29 09:45:58 UTC (rev 222)
@@ -45,7 +45,6 @@
'Bilan_stades_pigm.r'
'Bilan_taille.r'
'RefMsg.r'
- 'RefPoidsMoyenPeche.r'
'Refperiode.r'
'data.r'
'fn_EcritBilanJournalier.r'
Modified: pkg/stacomir/R/BilanFonctionnementDF.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDF.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/BilanFonctionnementDF.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -12,7 +12,7 @@
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("BilanFonctionnementDF")}.
#' @slot data A data frame
-#' @slot dc An object of class \code{RefDC-class}
+#' @slot df An object of class \code{RefDF-class}
#' @slot horodatedebut An object of class \code{RefHorodate-class}
#' @slot horodatefin An object of class \code{RefHorodate-class}
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -113,7 +113,7 @@
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
requete at select=stringr::str_c("DELETE from ",get("sch",envir=envir_stacomi),"t_bilanmigrationjournalier_bjo ")
requete at where=paste("WHERE bjo_annee IN (",paste(les_annees,collapse=","),") AND bjo_tax_code='",tax,"' AND bjo_std_code='",std,"' AND bjo_dis_identifiant=",dic,sep="")
- invisible(capture_output(requete<-stacomirtools::connect(requete)))
+ invisible(utils::capture.output(requete<-stacomirtools::connect(requete)))
requete=new("RequeteODBCwhere")
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
Modified: pkg/stacomir/R/RefCheckBox.r
===================================================================
--- pkg/stacomir/R/RefCheckBox.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/RefCheckBox.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -28,11 +28,11 @@
prototype=prototype(title="liste de choice",labels="choice",checked=FALSE))
#' Loading method for ReCheckBox referential objects
-#' @param object An object of class \link{ReCheckBox-class}
+#' @param object An object of class \link{RefCheckBox-class}
#' @param title Title of the frame
#' @param labels Labels for checked
#' @param checked Vector of boolean indicating if refCheckBox are checked
-#' @return An object of class \link{ReCheckBox-class}
+#' @return An object of class \link{RefCheckBox-class}
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
#' \dontrun{
Modified: pkg/stacomir/R/RefDC.r
===================================================================
--- pkg/stacomir/R/RefDC.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/RefDC.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -51,6 +51,7 @@
#' Method to load the counting devices of the control station
+#' @slot object An object of class \link{RefDC-class}
#' @return Object of class RefDC
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
setMethod("charge",signature=signature("RefDC"),definition=function(object) {
Modified: pkg/stacomir/R/RefDF.r
===================================================================
--- pkg/stacomir/R/RefDF.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/RefDF.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -8,7 +8,7 @@
#' \code{new("RefDF", df_selectionne=integer(), ouvrage=integer(),
#' data=data.frame())}.
#'
-#'
+
#' @slot df_selectionne Object of class \code{"integer"} The identifier of the fishway
#' @slot ouvrage Object of class \code{"integer"} The attached dam
#' @slot data Object of class \code{"data.frame"} Data concerning the fishway
@@ -50,7 +50,7 @@
}
)
#' Loading method for DF referential objects
-#'
+#' @slot object An object of class \link{RefDF-class}
#' @return An object of class RefDF
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
Modified: pkg/stacomir/R/RefListe.r
===================================================================
--- pkg/stacomir/R/RefListe.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/RefListe.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -28,6 +28,9 @@
#' Loading method for Refliste referential objects
#' @return An object of class RefListe
+#' @slot object An object of class \link{RefListe-class}
+#' @slot vecteur A character vector
+#' @slot label A label for Refliste
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
#' \dontrun{
Modified: pkg/stacomir/R/RefMsg.r
===================================================================
--- pkg/stacomir/R/RefMsg.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/RefMsg.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -9,6 +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}
#' @family Referential objects
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
@@ -28,6 +29,8 @@
#' 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 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}
#' @examples
Deleted: pkg/stacomir/R/RefPoidsMoyenPeche.r
===================================================================
--- pkg/stacomir/R/RefPoidsMoyenPeche.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/RefPoidsMoyenPeche.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -1,70 +0,0 @@
-#' Class "RefPoidsMoyenPeche"
-#'
-#' Class which enables to load bunches of elver of experimental fishings
-#'
-#'
-#' @section Objects from the Class: Objects can be created by calls of the form
-#' \code{new("RefPoidsMoyenPeche",
-#' data=data.frame(),datedebut="POSIXlt",datefin="POSIXlt")}. \describe{
-#' \item{list("data")}{Object of class \code{"data.frame"} ~
-#' Datas}\item{:}{Object of class \code{"data.frame"} ~ Datas}
-#' \item{list("datedebut")}{Object of class \code{"POSIXlt"} ~ Starting
-#' year}\item{:}{Object of class \code{"POSIXlt"} ~ Starting year}
-#' \item{list("datefin")}{Object of class \code{"POSIXlt"} ~ Ending
-#' year}\item{:}{Object of class \code{"POSIXlt"} ~ Ending year} }
-#' @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="RefPoidsMoyenPeche",representation=
- representation(data="data.frame",datedebut="POSIXlt",datefin="POSIXlt"),
- prototype=prototype(data=data.frame()))
-# pour test
-# object= new("RefPoidsMoyenPeche")
-
-
-
-#' Charge method for RefPoidsMoyenPeche
-#'
-#' @return An object of class \code{\linkS4class{RefPoidsMoyenPeche}}
-#'
-#' @author cedric.briand
-#' @export
-setMethod("charge",signature=signature("RefPoidsMoyenPeche"),definition=function(object){
- baseODBCmortciv<-get("baseODBCmortciv",envir=envir_stacomi)
- requete=new("RequeteODBCwheredate")
- requete at datedebut=object at datedebut
- requete at datefin=object at datefin
- requete at colonnedebut="datedebutpeche"
- requete at colonnefin="datefinpeche"
- requete at baseODBC<-baseODBCmortciv
- requete at select="SELECT lot_identifiant,
- datedebutpeche AS ope_date_debut ,
- datefinpeche AS ope_date_fin,
- lot_effectif,
- car_valeur_quantitatif as poids,
- (car_valeur_quantitatif/lot_effectif) AS poids_moyen,
- (datefinpeche-datedebutpeche)/2 AS time.sequence,
- datedebutpeche+(datefinpeche-datedebutpeche)/2 AS datemoy,
- date_part('year', datedebutpeche) AS annee,
- date_part('month',datedebutpeche) AS mois
- FROM vue_ope_lot_poids"
- requete at and=""
- requete<-stacomirtools::connect(requete)
- object at data<-requete at query
- return(object)
- })
Modified: pkg/stacomir/R/RefStationMesure.r
===================================================================
--- pkg/stacomir/R/RefStationMesure.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/RefStationMesure.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -33,6 +33,7 @@
#' Loading method for RefStationMesure referential object
#' @return An S4 object of class RefStationMesure
+#' @param object An object of class \link{RefStationMesure-class}
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
#' \dontrun{
Modified: pkg/stacomir/R/RefTaxon.r
===================================================================
--- pkg/stacomir/R/RefTaxon.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/RefTaxon.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -27,6 +27,7 @@
#'
#' @return An S4 object of class RefTaxon
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @param object An object of class \link{RefTaxon-class}
#' @examples \dontrun{
#' object=new("RefTaxon")
#' charge(object)}
@@ -39,7 +40,9 @@
return(object)
})
-#' Loading method for RefTaxon referential objects searching only those stages existing for a DC and a Taxon
+#' Loading method for RefTaxon referential objects searching only taxa existing for a DC
+#' @param object An object of class \link{RefTaxon-class}
+#' @param dc_selectionne A counting device selected, only taxa attached to this dc are selected
#' @return An S4 object of class RefTaxon
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
@@ -65,6 +68,9 @@
#' Choice method for Reftaxon referential objects with only one taxa selected
+#' @param object An object of class \link{RefTaxon-class}
+#' @param objectBilan An object Bilan which includes the \link{RefTaxon-class}, default NULL
+#' @param is.enabled Sets if the frame is enabled at launch, defaut TRUE
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples \dontrun{
#' object=new("RefTaxon")
@@ -74,7 +80,11 @@
#' bilanMigration<-new(BilanMigration)
#' choice(object,objectBilan=bilanMigration)
#' }
-setMethod("choice",signature=signature("RefTaxon"),definition=function(object,objectBilan=NULL,is.enabled=TRUE) {
+setMethod("choice",signature=signature("RefTaxon"),
+ definition=function(
+ object,
+ objectBilan=NULL,
+ is.enabled=TRUE) {
if (nrow(object at data) > 0){
htax=function(h,...){
taxons=svalue(choice)
Modified: pkg/stacomir/R/Refpar.r
===================================================================
--- pkg/stacomir/R/Refpar.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/Refpar.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -28,6 +28,7 @@
setClass(Class="Refpar",representation= representation(data="data.frame"))
#' Loading method for Repar referential objects
+#' @param object An object of class \link{Refpar-class}
#' @return An S4 object of class Refpar
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
@@ -44,7 +45,11 @@
object at data<-requete at query
return(object)
})
-#' Loading method for Repar referential objects searching only those parameters existing for a DC, a Taxon, and a stade
+#' Loading method for Repar referential objects searching only those parameters existing for a DC, a Taxa, and a stage
+#' @param object An object of class \link{Refpar-class}
+#' @param dc_selectionne A counting device selected for the bilan
+#' @param taxon_selectionne The taxa selected for the bilan
+#' @param stade_selectionne The stage selected for the bilan
#' @return An S4 object of class Refpar
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
@@ -52,7 +57,9 @@
#' object=new("Refpar")
#' charge_avec_filtre(object,dc_selectionne=6,taxon_selectionne=2038,stade_selectionne="CIV")
#' }
-setMethod("charge_avec_filtre",signature=signature("Refpar"),definition=function(object,dc_selectionne,taxon_selectionne,stade_selectionne) {
+setMethod("charge_avec_filtre",signature=signature("Refpar"),definition=function(object,dc_selectionne,
+ taxon_selectionne,
+ stade_selectionne) {
requete=new("RequeteODBCwhere")
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
requete at select=paste("SELECT DISTINCT ON (par_code) par_code, par_nom",
@@ -71,8 +78,13 @@
return(object)
})
#' Choice method for Refpar referential objects
+#' @param object An object of class \link{Refpar-class}
+#' @param label The label that will be displayed in the message frame or as output text
+#' @param nomassign The assignment name in envir_stacomi
+#' @param frameassign The name of the frame used for assignement in .GlobalEnv
+#' @param is.enabled Default TRUE.
#' @note the choice method assigns an object of class Refpar named refpar in the environment envir_stacomi
-#' @note this method choice is also on sons objects Refparquan, hence the parameters,however it was redefined in refparqual
+#' @note this method choice is also on daughter classes Refparquan, hence the parameters, however it was redefined in refparqual
#' @note to load the possible values of qualitative parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
@@ -83,7 +95,11 @@
#' object<-charge(object)
#' choice(object)
#' }
-setMethod("choice",signature=signature("Refpar"),definition=function(object,label="Choix d'une caracteristique de lot",nomassign="refpar",frameassign="frame_par",is.enabled=TRUE) {
+setMethod("choice",signature=signature("Refpar"),definition=function(object,
+ label="Choix d'une caracteristique de lot",
+ nomassign="refpar",
+ frameassign="frame_par",
+ is.enabled=TRUE) {
if (nrow(object at data) > 0){
hcar=function(h,...){
carchoisi=svalue(choice)
Modified: pkg/stacomir/R/Refparqual.r
===================================================================
--- pkg/stacomir/R/Refparqual.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/Refparqual.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -30,6 +30,7 @@
setClass(Class="Refparqual",representation= representation(valqual="data.frame"),contains="Refpar")
#' Loading method for Reparqual referential objects
+#' @param object An object of class \link{Refparqual-class}
#' @return An S4 object of class Refparqual
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
Modified: pkg/stacomir/R/Refparquan.r
===================================================================
--- pkg/stacomir/R/Refparquan.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/Refparquan.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -25,6 +25,7 @@
setClass(Class="Refparquan",contains="Refpar")
#' Loading method for Reparquan referential objects
+#' @param object An object of class \link{Refparquan-class}
#' @return An S4 object of class Refparquan
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
Modified: pkg/stacomir/R/ReftextBox.r
===================================================================
--- pkg/stacomir/R/ReftextBox.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/ReftextBox.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -8,6 +8,9 @@
setClass(Class="RefTextBox",representation= representation(title="character",label="character"))
#' Loading method for ReTextBox referential objects
+#' @param object An object of class \link{RefTextBox-class}
+#' @param title A title for the frame
+#' @param label A label for the TextBox
#' @return An S4 object of class RefTextBox
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
Modified: pkg/stacomir/R/data.r
===================================================================
--- pkg/stacomir/R/data.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/data.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -81,7 +81,7 @@
#' An object of class \link{BilanFonctionnementDF-class} with data loaded
#'
#' This dataset corresponds to the data collected at three different fishways
-#' it is loaded along with \link{bM_Arzal}
+#' it is loaded along with \link{bMM_Arzal}
#' @format An object of class BilanFonctionnementDF
#' @keywords data
"bilanFonctionnementDF"
@@ -90,7 +90,7 @@
#' An object of class \link{BilanFonctionnementDC-class} with data loaded
#'
#' This dataset corresponds to the data collected at three different control devices
-#' it is loaded along with \link{bM_Arzal}
+#' it is loaded along with \link{bMM_Arzal}
#' @format An object of class BilanFonctionnementDC
#' @keywords data
"bilanFonctionnementDC"
@@ -98,7 +98,7 @@
#' An object of class \link{BilanOperation-class} with data loaded
#'
#' This dataset corresponds to the data collected at three different control devices
-#' it is loaded along with \link{bM_Arzal}
+#' it is loaded along with \link{bMM_Arzal}
#' @format An object of class BilanOperation
#' @keywords data
"bilanOperation"
@@ -140,5 +140,28 @@
#' @keywords data
"bfDF"
+#' An object of class \link{BilanFonctionnementDF-class} with data loaded
+#'
+#' This dataset corresponds to the data collected at three different fishways
+#' it is loaded along with \link{bM_Arzal}
+#' @format An object of class BilanFonctionnementDF
+#' @keywords data
+"bilanFonctionnementDF_bM"
+#' An object of class \link{BilanFonctionnementDC-class} with data loaded
+#'
+#' This dataset corresponds to the data collected at three different control devices
+#' it is loaded along with \link{bM_Arzal}
+#' @format An object of class BilanFonctionnementDC
+#' @keywords data
+"bilanFonctionnementDC_bM"
+
+#' An object of class \link{BilanOperation-class} with data loaded
+#'
+#' This dataset corresponds to the data collected at three different control devices
+#' it is loaded along with \link{bM_Arzal}
+#' @format An object of class BilanOperation
+#' @keywords data
+"bilanOperation_bM"
+
Modified: pkg/stacomir/R/utilitaires.r
===================================================================
--- pkg/stacomir/R/utilitaires.r 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/R/utilitaires.r 2016-09-29 09:45:58 UTC (rev 222)
@@ -291,7 +291,7 @@
data[match(data2$newid,data$newid),]<-data2
# now get the sequence of days righly set by adding the number of days to xmin and xmax
data3<-data%>%filter(n0>0)%>%group_by(id)%>%mutate(xmin=xmin+ as.difftime(rank(newid)-1, units="days"),
- xmax=xmax+as.difftime(rank(newid)-1, unit="days"))
+ xmax=xmax+as.difftime(rank(newid)-1, units="days"))
data[match(data3$newid,data$newid),]<-data3
data<-as.data.frame(data)
return(data)
Modified: pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R 2016-09-29 09:45:58 UTC (rev 222)
@@ -19,10 +19,13 @@
}
data("bfDF")
+ plot(bfDF,plot.type="4")
+ # the following examples work but take a while to compute
+ \dontrun{
plot(bfDF,plot.type="1")
plot(bfDF,plot.type="2",title="A nice title")
- plot(bfDF,plot.type="3",title="A nice title")
- plot(bfDF,plot.type="4")
+ plot(bfDF,plot.type="3",title="A nice title")
+ }
Modified: pkg/stacomir/inst/examples/bilanMigration_Arzal.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigration_Arzal.R 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/inst/examples/bilanMigration_Arzal.R 2016-09-29 09:45:58 UTC (rev 222)
@@ -45,4 +45,7 @@
plot(bM_Arzal,plot.type="step")
# data will be written in the data directory specified in the stacomi/calcmig.csv file
+
+\dontrun{
summary(bM_Arzal,silent=TRUE)
+}
\ No newline at end of file
Modified: pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R 2016-09-29 09:45:58 UTC (rev 222)
@@ -60,6 +60,24 @@
})
+test_that("Summary method works",
+ {
+ stacomi(gr_interface=FALSE,
+ login_window=FALSE,
+ database_expected=TRUE)
+ # overriding user schema
+ baseODBC<-get("baseODBC",envir=envir_stacomi)
+ baseODBC[c(2,3)]<-rep("iav",2)
+ assign("baseODBC",baseODBC,envir_stacomi)
+ sch<-get("sch",envir=envir_stacomi) # "iav."
+ assign("sch","iav.",envir_stacomi)
+ # 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)
+ rm("envir_stacomi",envir =.GlobalEnv)
+ })
+
test_that("Test writing an example to the database",
{
stacomi(gr_interface=FALSE,
Modified: pkg/stacomir/man/BilanFonctionnementDF-class.Rd
===================================================================
--- pkg/stacomir/man/BilanFonctionnementDF-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/BilanFonctionnementDF-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -18,7 +18,7 @@
\describe{
\item{\code{data}}{A data frame}
-\item{\code{dc}}{An object of class \code{RefDC-class}}
+\item{\code{df}}{An object of class \code{RefDF-class}}
\item{\code{horodatedebut}}{An object of class \code{RefHorodate-class}}
@@ -50,10 +50,13 @@
}
data("bfDF")
+ plot(bfDF,plot.type="4")
+ # the following examples work but take a while to compute
+ \dontrun{
plot(bfDF,plot.type="1")
plot(bfDF,plot.type="2",title="A nice title")
- plot(bfDF,plot.type="3",title="A nice title")
- plot(bfDF,plot.type="4")
+ plot(bfDF,plot.type="3",title="A nice title")
+ }
Modified: pkg/stacomir/man/RefAnnee-class.Rd
===================================================================
--- pkg/stacomir/man/RefAnnee-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/RefAnnee-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -43,7 +43,6 @@
\code{\link{RefDC-class}}, \code{\link{RefDF-class}},
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
- \code{\link{RefPoidsMoyenPeche-class}},
\code{\link{RefStades-class}},
\code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
Modified: pkg/stacomir/man/RefCheckBox-class.Rd
===================================================================
--- pkg/stacomir/man/RefCheckBox-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/RefCheckBox-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -47,7 +47,6 @@
\code{\link{RefDC-class}}, \code{\link{RefDF-class}},
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
- \code{\link{RefPoidsMoyenPeche-class}},
\code{\link{RefStades-class}},
\code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
Modified: pkg/stacomir/man/RefChoix-class.Rd
===================================================================
--- pkg/stacomir/man/RefChoix-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/RefChoix-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -48,7 +48,6 @@
\code{\link{RefDF-class}},
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
- \code{\link{RefPoidsMoyenPeche-class}},
\code{\link{RefStades-class}},
\code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
Modified: pkg/stacomir/man/RefCoe-class.Rd
===================================================================
--- pkg/stacomir/man/RefCoe-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/RefCoe-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -52,7 +52,6 @@
\code{\link{RefDF-class}},
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
- \code{\link{RefPoidsMoyenPeche-class}},
\code{\link{RefStades-class}},
\code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
Modified: pkg/stacomir/man/RefDC-class.Rd
===================================================================
--- pkg/stacomir/man/RefDC-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/RefDC-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -43,7 +43,6 @@
\code{\link{RefDF-class}},
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
- \code{\link{RefPoidsMoyenPeche-class}},
\code{\link{RefStades-class}},
\code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
Modified: pkg/stacomir/man/RefDF-class.Rd
===================================================================
--- pkg/stacomir/man/RefDF-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/RefDF-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -46,7 +46,6 @@
\code{\link{RefDC-class}},
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
- \code{\link{RefPoidsMoyenPeche-class}},
\code{\link{RefStades-class}},
\code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
Modified: pkg/stacomir/man/RefHorodate-class.Rd
===================================================================
--- pkg/stacomir/man/RefHorodate-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/RefHorodate-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -34,7 +34,6 @@
\code{\link{RefChoix-class}}, \code{\link{RefCoe-class}},
\code{\link{RefDC-class}}, \code{\link{RefDF-class}},
\code{\link{RefListe-class}},
- \code{\link{RefPoidsMoyenPeche-class}},
\code{\link{RefStades-class}},
\code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
Modified: pkg/stacomir/man/RefListe-class.Rd
===================================================================
--- pkg/stacomir/man/RefListe-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/RefListe-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -39,7 +39,6 @@
\code{\link{RefChoix-class}}, \code{\link{RefCoe-class}},
\code{\link{RefDC-class}}, \code{\link{RefDF-class}},
\code{\link{RefHorodate-class}},
- \code{\link{RefPoidsMoyenPeche-class}},
\code{\link{RefStades-class}},
\code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
Deleted: pkg/stacomir/man/RefPoidsMoyenPeche-class.Rd
===================================================================
--- pkg/stacomir/man/RefPoidsMoyenPeche-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/RefPoidsMoyenPeche-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -1,56 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RefPoidsMoyenPeche.r
-\docType{class}
-\name{RefPoidsMoyenPeche-class}
-\alias{RefPoidsMoyenPeche-class}
-\title{Class "RefPoidsMoyenPeche"}
-\description{
-Class which enables to load bunches of elver of experimental fishings
-}
-\section{Objects from the Class}{
- Objects can be created by calls of the form
-\code{new("RefPoidsMoyenPeche",
-data=data.frame(),datedebut="POSIXlt",datefin="POSIXlt")}. \describe{
-\item{list("data")}{Object of class \code{"data.frame"} ~
-Datas}\item{:}{Object of class \code{"data.frame"} ~ Datas}
-\item{list("datedebut")}{Object of class \code{"POSIXlt"} ~ Starting
-year}\item{:}{Object of class \code{"POSIXlt"} ~ Starting year}
-\item{list("datefin")}{Object of class \code{"POSIXlt"} ~ Ending
-year}\item{:}{Object of class \code{"POSIXlt"} ~ Ending year} }
-}
-\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}}
-
-Other Referential.objects: \code{\link{RefAnnee-class}},
- \code{\link{RefCheckBox-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{Refparqual-class}},
- \code{\link{Refparquan-class}},
- \code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
-}
-\keyword{classes}
-
Modified: pkg/stacomir/man/RefStades-class.Rd
===================================================================
--- pkg/stacomir/man/RefStades-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/RefStades-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -32,9 +32,7 @@
\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{RefPoidsMoyenPeche-class}},
- \code{\link{Refpar-class}},
+ \code{\link{RefListe-class}}, \code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
Modified: pkg/stacomir/man/Refpar-class.Rd
===================================================================
--- pkg/stacomir/man/Refpar-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/Refpar-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -38,7 +38,6 @@
\code{\link{RefDC-class}}, \code{\link{RefDF-class}},
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
- \code{\link{RefPoidsMoyenPeche-class}},
\code{\link{RefStades-class}},
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
Modified: pkg/stacomir/man/Refparqual-class.Rd
===================================================================
--- pkg/stacomir/man/Refparqual-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/Refparqual-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -41,7 +41,6 @@
\code{\link{RefDC-class}}, \code{\link{RefDF-class}},
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
- \code{\link{RefPoidsMoyenPeche-class}},
\code{\link{RefStades-class}},
\code{\link{Refpar-class}},
\code{\link{Refparquan-class}},
Modified: pkg/stacomir/man/Refparquan-class.Rd
===================================================================
--- pkg/stacomir/man/Refparquan-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/Refparquan-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -34,7 +34,6 @@
\code{\link{RefDC-class}}, \code{\link{RefDF-class}},
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
- \code{\link{RefPoidsMoyenPeche-class}},
\code{\link{RefStades-class}},
\code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
Modified: pkg/stacomir/man/Refperiode-class.Rd
===================================================================
--- pkg/stacomir/man/Refperiode-class.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/Refperiode-class.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -26,7 +26,6 @@
\code{\link{RefDC-class}}, \code{\link{RefDF-class}},
\code{\link{RefHorodate-class}},
\code{\link{RefListe-class}},
- \code{\link{RefPoidsMoyenPeche-class}},
\code{\link{RefStades-class}},
\code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
Modified: pkg/stacomir/man/bilanFonctionnementDC.Rd
===================================================================
--- pkg/stacomir/man/bilanFonctionnementDC.Rd 2016-09-28 11:32:30 UTC (rev 221)
+++ pkg/stacomir/man/bilanFonctionnementDC.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -10,7 +10,7 @@
}
\description{
This dataset corresponds to the data collected at three different control devices
-it is loaded along with \link{bM_Arzal}
+it is loaded along with \link{bMM_Arzal}
}
\keyword{data}
Added: pkg/stacomir/man/bilanFonctionnementDC_bM.Rd
===================================================================
--- pkg/stacomir/man/bilanFonctionnementDC_bM.Rd (rev 0)
+++ pkg/stacomir/man/bilanFonctionnementDC_bM.Rd 2016-09-29 09:45:58 UTC (rev 222)
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.r
+\docType{data}
+\name{bilanFonctionnementDC_bM}
+\alias{bilanFonctionnementDC_bM}
+\title{An object of class \link{BilanFonctionnementDC-class} with data loaded}
+\format{An object of class BilanFonctionnementDC}
+\usage{
+bilanFonctionnementDC_bM
+}
+\description{
+This dataset corresponds to the data collected at three different control devices
+it is loaded along with \link{bM_Arzal}
+}
+\keyword{data}
+
Modified: pkg/stacomir/man/bilanFonctionnementDF.Rd
===================================================================
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 222
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