[Stacomir-commits] r172 - in pkg/stacomir: . R inst/config man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Aug 20 19:08:38 CEST 2016
Author: briand
Date: 2016-08-20 19:08:38 +0200 (Sat, 20 Aug 2016)
New Revision: 172
Modified:
pkg/stacomir/DESCRIPTION
pkg/stacomir/NAMESPACE
pkg/stacomir/R/BilanConditionEnv.r
pkg/stacomir/R/BilanEspeces.r
pkg/stacomir/R/BilanFonctionnementDC.r
pkg/stacomir/R/BilanFonctionnementDF.r
pkg/stacomir/R/BilanMigration.r
pkg/stacomir/R/BilanMigrationConditionEnv.r
pkg/stacomir/R/BilanMigrationInterAnnuelle.r
pkg/stacomir/R/BilanMigrationMult.r
pkg/stacomir/R/BilanMigrationPar.r
pkg/stacomir/R/Bilan_carlot.r
pkg/stacomir/R/Bilan_poids_moyen.r
pkg/stacomir/R/Bilan_stades_pigm.r
pkg/stacomir/R/PasDeTempsJournalier.r
pkg/stacomir/R/PasdeTemps.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/RefPoidsMoyenPeche.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/R/Refperiode.r
pkg/stacomir/R/ReftextBox.r
pkg/stacomir/R/stacomi.r
pkg/stacomir/inst/config/generate_Roxygen2.R
pkg/stacomir/inst/config/stacomi_manual_launch.r
pkg/stacomir/man/BilanEspeces-class.Rd
pkg/stacomir/man/BilanFonctionnementDC-class.Rd
pkg/stacomir/man/BilanMigration-class.Rd
pkg/stacomir/man/BilanMigrationConditionEnv-class.Rd
pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
pkg/stacomir/man/BilanMigrationMult-class.Rd
pkg/stacomir/man/Bilan_carlot-class.Rd
pkg/stacomir/man/Bilan_poids_moyen-class.Rd
pkg/stacomir/man/Bilan_taille-class.Rd
pkg/stacomir/man/RefCheckBox-class.Rd
Log:
Adapting examples with \dontrun{} for all examples running through gWidgets (these cause the program to get stuck).
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/DESCRIPTION 2016-08-20 17:08:38 UTC (rev 172)
@@ -1,7 +1,7 @@
Package: stacomiR
Version: 0.5.0
Date: 2016-09-01
-Title: STACOMI migration control
+Title: Fish Migration Monitoring (stacomiR)
Authors at R: c(person("Cedric", "Briand", role = c("aut", "cre"), email = "cedric.briand at eptb-vilaine.fr"),
person("Marion", "Legrand", role = "aut", email="tableau-salt-loire at logrami.fr"))
Description: Graphical outputs and treatment for a database of fishway
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/NAMESPACE 2016-08-20 17:08:38 UTC (rev 172)
@@ -56,7 +56,6 @@
import(sqldf)
import(stacomirtools)
import(stringr)
-importFrom(RODBC,odbcClose)
importFrom(grDevices,X11)
importFrom(grDevices,gray)
importFrom(grDevices,rainbow)
Modified: pkg/stacomir/R/BilanConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanConditionEnv.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/BilanConditionEnv.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -27,10 +27,6 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @concept Bilan Object
-#' @examples
-#'
-#' showClass("BilanConditionEnv")
-#'
#' @export
setClass(Class="BilanConditionEnv",
representation=representation(
Modified: pkg/stacomir/R/BilanEspeces.r
===================================================================
--- pkg/stacomir/R/BilanEspeces.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/BilanEspeces.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -26,10 +26,6 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @concept Bilan Object
-#' @examples
-#'
-#' showClass("BilanEspeces")
-#'
#' @export
setClass(Class="BilanEspeces",
representation=
@@ -103,7 +99,6 @@
#' @return BilanEspeces with slots filled by user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
-#' @examples bilanEspeces=new("BilanEspeces")
setMethod("charge",signature=signature("BilanEspeces"),definition=function(object,...){
funout(get("msg",envir_stacomi)$BilanEspeces.7)
bilanEspeces<-object
@@ -247,7 +242,6 @@
#' Interface for BilanEspece class
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
-#' @examples interface_BilanEspeces()
interface_BilanEspeces=function(){
bilanEspeces=new("BilanEspeces")
assign("bilanEspeces",bilanEspeces,envir = .GlobalEnv)
Modified: pkg/stacomir/R/BilanFonctionnementDC.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDC.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/BilanFonctionnementDC.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -20,10 +20,6 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @concept Bilan Object
-#' @examples
-#'
-#' showClass("BilanFonctionnementDC")
-#'
#' @export
setClass(Class="BilanFonctionnementDC",
representation= representation(data="data.frame",
Modified: pkg/stacomir/R/BilanFonctionnementDF.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDF.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/BilanFonctionnementDF.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -21,10 +21,6 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @concept Bilan Object
-#' @examples
-#'
-#' showClass("BilanFonctionnementDF")
-#'
#' @export
setClass(Class="BilanFonctionnementDF",
representation= representation(data="data.frame",
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/BilanMigration.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -49,10 +49,6 @@
#' \code{\linkS4class{BilanMigrationPar}}
#' @concept Bilan Object
#' @examples
-#'
-#' showClass("BilanMigration")
-#' bilanMigration= new("BilanMigration")
-#'
#' @export
setClass(Class="BilanMigration",
representation=
Modified: pkg/stacomir/R/BilanMigrationConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanMigrationConditionEnv.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/BilanMigrationConditionEnv.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -27,10 +27,6 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @concept Bilan Object
-#' @examples
-#'
-#' showClass("BilanMigrationConditionEnv")
-#'
#' @export
setClass(Class="BilanMigrationConditionEnv",representation=
representation(
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -29,10 +29,6 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @concept Bilan Object
-#' @examples
-#'
-#' showClass("BilanMigrationConditionEnv")
-#'
#' @export
setClass(Class="BilanMigrationInterAnnuelle",representation=
representation(
Modified: pkg/stacomir/R/BilanMigrationMult.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMult.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/BilanMigrationMult.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -126,17 +126,6 @@
#' uses the choice_c methods of these object to "select" the data.
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
-#' @examples
-#' \dontrun{
-#' bilanMigrationMult=choice_c(bilanMigrationMult,
-#' dc=c(5,6,12),
-#' taxons=c("Anguilla anguilla"),
-#' stades=c("AGG","AGJ","CIV"),datedebut="2011-01-01",datefin="2011-12-31")
-#' bilanMigrationMult=calcule(bilanMigrationMult)
-#' hbilanMigrationMultgraph()
-#' hbilanMigrationMultgraph2()
-#' hbilanMigrationMultgraph3()
-#' }
setMethod("choice_c",signature=signature("BilanMigrationMult"),definition=function(object,dc,taxons,stades,datedebut,datefin,...){
bilanMigrationMult<-object
fonctionnementDC=new("BilanFonctionnementDC")
Modified: pkg/stacomir/R/BilanMigrationPar.r
===================================================================
--- pkg/stacomir/R/BilanMigrationPar.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/BilanMigrationPar.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -45,10 +45,6 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @concept Bilan Object
-#' @examples
-#'
-#' showClass("BilanMigrationPar")
-#'
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
setClass(Class="BilanMigrationPar",
representation=representation(parquan="Refparquan",
Modified: pkg/stacomir/R/Bilan_carlot.r
===================================================================
--- pkg/stacomir/R/Bilan_carlot.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/Bilan_carlot.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -22,10 +22,10 @@
#' \code{\linkS4class{BilanMigrationPar}}
#' @concept Bilan Object
#' @examples
-#'
+#' \donrun{
#' showClass("Bilan_carlot")
#' object=new("Bilan_carlot")
-#'
+#' }
#' @export
setClass(Class="Bilan_carlot",
representation= representation(
Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/Bilan_poids_moyen.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -49,10 +49,10 @@
#' \code{\linkS4class{BilanMigrationPar}}
#' @concept Bilan Object
#' @examples
-#'
+#' \donrun{
#' showClass("Bilan_poids_moyen")
#' object=new("Bilan_poids_moyen")
-#'
+#' }
#' @export
setClass(Class="Bilan_poids_moyen",
representation= representation(data="data.frame",
Modified: pkg/stacomir/R/Bilan_stades_pigm.r
===================================================================
--- pkg/stacomir/R/Bilan_stades_pigm.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/Bilan_stades_pigm.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -35,10 +35,8 @@
#' 995-1009.
#' \url{http://www3.interscience.wiley.com/journal/118686679/abstract}
#' \url{http://www.eptb-vilaine.fr/site/index.php/publications-scientifiques/46-publications-migrateurs/60-dynamique-de-population-et-de-migration-des-civelles-en-estuaire-de-vilaine.}
-#' \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
#' @examples
-#'
-#' showClass("Bilan_stades_pigm")
+#' #' showClass("Bilan_stades_pigm")
#' @export
setClass(Class="Bilan_stades_pigm",
representation= representation(data="data.frame",
@@ -406,7 +404,7 @@
#' regular scale (phicum)
#' @seealso \code{\linkS4class{Bilan_stades_pigm}}
#' @examples
-#'
+#' \donrun{
#' Vparm<-list()
#' # below param for briand et al.,2005 pigmentation function in glass eel
#' Vparm$pigment_stage$p1<-0.267 # parameters for gamma functions describing changes from stage to stage
@@ -425,7 +423,7 @@
#' fundist(Vparm,seq(0,10, length.out=10000),graph=TRUE,lmax=0)
#' plot(seq(0,10, length.out=10000),pgamma(seq(0,10, length.out=10000),Vparm$pigment_stage[[1]]),col="pink")
#' points(seq(0,10, length.out=10000),pgamma(seq(0,10, length.out=10000),Vparm$pigment_stage[[2]]),col="firebrick")
-#'
+#' }
fundist=function(Vparm, phicum,graph=TRUE,lmax=1){
VB=fnstade(par1=Vparm$pigment_stage[[1]],VB=TRUE,phicum=phicum,neg=FALSE,lmax=lmax)
VBc=cumsum(VB$y)/sum(VB$y) # surface
Modified: pkg/stacomir/R/PasDeTempsJournalier.r
===================================================================
--- pkg/stacomir/R/PasDeTempsJournalier.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/PasDeTempsJournalier.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -37,10 +37,6 @@
#' @author cedric.briand"at"eptb-vilaine.fr
#' @seealso \code{\linkS4class{PasDeTemps}}
#' @keywords classes
-#' @examples
-#'
-#' showClass("PasDeTempsJournalier")
-#'
setClass(Class="PasDeTempsJournalier",contains="PasDeTemps",
prototype=(dureePas=86400)
)
@@ -109,7 +105,8 @@
#' \dontrun{
#' object=new("RefDC")
#' object<-charge(object)
-#' choice_c(object=object,datedebut="2012-01-01",datefin="2013-01-01")}
+#' choice_c(object=object,datedebut="2012-01-01",datefin="2013-01-01")
+#' }
setMethod("choice_c",signature=signature("PasDeTempsJournalier"),definition=function(object,datedebut,datefin) {
if (class(datedebut)=="character") {
if (grepl("/",datedebut)){
Modified: pkg/stacomir/R/PasdeTemps.r
===================================================================
--- pkg/stacomir/R/PasdeTemps.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/PasdeTemps.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -92,10 +92,6 @@
#' @author cedric.briand"at"eptb-vilaine.fr
#' @seealso \code{\linkS4class{PasDeTempsJournalier}}
#' @concept Bilan Object
-#' @examples
-#'
-#' showClass("PasDeTemps")
-#'
setClass(Class="PasDeTemps",representation=
representation(dateDebut="POSIXlt",dureePas="numeric",nbPas="numeric",noPasCourant="integer"),
validity=validite_PasDeTemps,
Modified: pkg/stacomir/R/RefAnnee.r
===================================================================
--- pkg/stacomir/R/RefAnnee.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefAnnee.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -40,10 +40,6 @@
#' @keywords classes
#' @family Referential objects
#' @author cedric.briand"at"eptb-vilaine.fr
-#' @examples
-#'
-#' showClass("RefAnnee")
-#'
setClass(Class="RefAnnee",representation=
representation(data="data.frame",annee_selectionnee="numeric"),
validity=validite_Annee,
@@ -55,10 +51,13 @@
#' @param object An object of class RefAnnee
#' @return object An object of class RefAnnee with slot data filled with the selected value
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @examples object=new("RefAnnee")
+#' @examples
+#' \dontrun{
+#' object=new("RefAnnee")
#' charge(object)
#' validObject( annee)
#' showMethods("charge")
+#' }
setMethod("charge",signature=signature("RefAnnee"),definition=function(object){
requete=new("RequeteODBC")
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
@@ -78,12 +77,15 @@
#' @param funoutlabel The label that appears in funout
#' @param titleFrame Title for the frame
#' @param preselect The number of the year selected in the gdroplist (integer)
-#' @examples object=new("RefAnnee")
+#' @examples
+#' \dontrun{
+#' object=new("RefAnnee")
#' object<-charge(object)
#' win=gwindow(title="test refAnnee")
#' group=ggroup(container=win,horizontal=FALSE)
#' choice(object,nomassign="refAnnee",funoutlabel="essai",titleFrame="essai RefAnnee",preselect=1)
#' dispose(win)
+#' }
setMethod("choice",
signature=signature("RefAnnee"),definition=function(object,
nomassign="refAnnee",
Modified: pkg/stacomir/R/RefCheckBox.r
===================================================================
--- pkg/stacomir/R/RefCheckBox.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefCheckBox.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -24,9 +24,6 @@
#' \code{\linkS4class{RefTaxon}}
#' @family Referential objects
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @examples
-#'
-#' showClass("RefCheckBox")
setClass(Class="RefCheckBox",representation= representation(title="character",labels="character",checked="logical"),
prototype=prototype(title="liste de choice",labels="choice",checked=FALSE))
@@ -34,8 +31,10 @@
#' @return An S4 object of class RefCheckBox
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("RefCheckBox")
#' charge(object,title="essai",labels=c("par1","par2","par3"),checked=c(TRUE,TRUE,TRUE))
+#' }
setMethod("charge",signature=signature("RefCheckBox"),definition=function(object,title,labels,checked) {
if (length(labels) != length(checked)) stop ("les longeur de 'labels' et 'checked' sont differentes")
object at title=title
@@ -46,12 +45,14 @@
#' Choice method for ReCheckBox referential objects
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("RefCheckBox")
#' object<- charge(object,title="essai",labels=c("par1","par2","par3"),checked=c(TRUE,TRUE,TRUE))
#' win=gwindow(title="test RefCheckBox")
#' group=ggroup(container=win,horizontal=FALSE)
#' choice(object)
#' dispose(win)
+#' '}
setMethod("choice",signature=signature("RefCheckBox"),definition=function(object) {
hlist=function(h,...){
i=h$action
Modified: pkg/stacomir/R/RefChoix.r
===================================================================
--- pkg/stacomir/R/RefChoix.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefChoix.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -26,10 +26,6 @@
#' \code{\linkS4class{RefStationMesure}}
#' \code{\linkS4class{RefTaxon}}
#' @family Referential objects
-#' @examples
-#'
-#' showClass("RefChoix")
-#'
setClass(Class="RefChoix",representation= representation(listechoice="character",label="character",selected="integer"))
#' Loading method for Rechoice referential objects
@@ -41,9 +37,11 @@
#' @param vecteur A vector of name, see example code.
#' @param selected An integer indicating which object is selected at launch
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' #' @examples
-#' object=new("RefChoix")
+#' @examples
+#' \dontrun{
+#' object=new("RefChoix")
#' charge(object,vecteur=c("oui","non"),label="essai",selected=as.integer(1))
+#' }
setMethod("charge",signature=signature("RefChoix"),definition=function(object,vecteur,label,selected) {
object at listechoice=vecteur
object at label=label
Modified: pkg/stacomir/R/RefCoe.r
===================================================================
--- pkg/stacomir/R/RefCoe.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefCoe.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -32,10 +32,6 @@
#' \code{\linkS4class{RefStationMesure}}
#' \code{\linkS4class{RefTaxon}}
#' @keywords classes
-#' @examples
-#'
-#' showClass("RefCoe")
-#'
setClass(Class="RefCoe",representation=
representation(data="data.frame",datedebut="POSIXlt",datefin="POSIXlt"),
prototype=prototype(data=data.frame()))
@@ -46,10 +42,13 @@
#' The slots datedebut and datefin have to be filled before using charge
#' @return Object of class RefCoe
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @examples object<- new("RefCoe")
+#' @examples
+#' \dontrun{
+#' object<- new("RefCoe")
#' object at datedebut<-strptime("01/01/1996",format="%d/%m/%Y")
#' object at datefin<-strptime("01/01/1997",format="%d/%m/%Y")
#' charge(object)
+#' }
setMethod("charge",signature=signature("RefCoe"),definition=function(object){
requete=new("RequeteODBCwheredate")
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
Modified: pkg/stacomir/R/RefDC.r
===================================================================
--- pkg/stacomir/R/RefDC.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefDC.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -24,10 +24,6 @@
#' \code{\linkS4class{RefTaxon}}
#' @keywords classes
#' @family Referential objects
-#' @examples
-#'
-#' showClass("RefDC")
-#'
setClass(Class="RefDC",representation=
representation(dc_selectionne="integer",ouvrage="integer",station="character",data="data.frame") ,
prototype=prototype(dc_selectionne=integer(),ouvrage=integer(),station=character(),data=data.frame())
Modified: pkg/stacomir/R/RefDF.r
===================================================================
--- pkg/stacomir/R/RefDF.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefDF.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -28,10 +28,6 @@
#' \code{\linkS4class{RefStationMesure}}
#' \code{\linkS4class{RefTaxon}}
#' @family Referential objects
-#' @examples
-#'
-#' showClass("RefDF")
-#'
setClass(Class="RefDF",representation=
representation(df_selectionne="integer",ouvrage="integer",data="data.frame") )
Modified: pkg/stacomir/R/RefHorodate.r
===================================================================
--- pkg/stacomir/R/RefHorodate.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefHorodate.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -28,9 +28,6 @@
#' \code{\linkS4class{RefStades}} \code{\linkS4class{RefStationMesure}}
#' \code{\linkS4class{RefTaxon}}
#' @family Referential objects
-#' @examples
-#' showClass("RefHorodate")
-#'
setClass(Class="RefHorodate",representation=
representation(horodate="POSIXt"),
validity=validite_RefHorodate,
Modified: pkg/stacomir/R/RefListe.r
===================================================================
--- pkg/stacomir/R/RefListe.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefListe.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -23,10 +23,6 @@
#' \code{\linkS4class{RefTaxon}}
#' @keywords classes
#' @family Referential objects
-#' @examples
-#'
-#' showClass("RefListe")
-#'
setClass(Class="RefListe",representation= representation(listechoice="character",label="character"))
@@ -34,8 +30,10 @@
#' @return An object of class RefListe
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("RefListe")
#' charge(object)
+#' }
setMethod("charge",signature=signature("RefListe"),definition=function(object,vecteur,label) {
object at listechoice=vecteur
object at label=label
@@ -45,11 +43,13 @@
#' @note the choice method assigns an object of class refList named refListe in the environment envir_stacomi
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("RefListe")
#' win=gwindow()
#' group=ggroup(container=win,horizontal=FALSE)
#' object<-charge(object)
#' choice(object)
+#' }
setMethod("choice",signature=signature("RefListe"),definition=function(object,is.enabled=TRUE) {
hlist=function(h,...){
valeurchoisie=svalue(choice)
Modified: pkg/stacomir/R/RefMsg.r
===================================================================
--- pkg/stacomir/R/RefMsg.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefMsg.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -21,8 +21,10 @@
#' @family Referential objects
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("RefMsg")
#' charge(object)
+#' }
setMethod("charge",signature=signature("RefMsg"),definition=function(object) {
req=new("RequeteODBC")
req at baseODBC<-get("baseODBC",envir=envir_stacomi)
@@ -38,8 +40,10 @@
#' @return An S4 object of class RefMsg
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("RefMsg")
#' charge_avec_filtre(object,lang='French')
+#' }
#' @export
setMethod("charge_avec_filtre",signature=signature("RefMsg"),definition=function(object,lang) {
requete=new("RequeteODBCwhere")
Modified: pkg/stacomir/R/RefPoidsMoyenPeche.r
===================================================================
--- pkg/stacomir/R/RefPoidsMoyenPeche.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefPoidsMoyenPeche.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -23,10 +23,6 @@
#' \code{\linkS4class{RefTaxon}}
#' @keywords classes
#' @family Referential objects
-#' @examples
-#'
-#' showClass("RefPoidsMoyenPeche")
-#'
setClass(Class="RefPoidsMoyenPeche",representation=
representation(data="data.frame",datedebut="POSIXlt",datefin="POSIXlt"),
prototype=prototype(data=data.frame()))
Modified: pkg/stacomir/R/RefStades.r
===================================================================
--- pkg/stacomir/R/RefStades.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefStades.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -21,18 +21,16 @@
#' \code{\linkS4class{RefTaxon}}
#' @keywords classes
#' @family Referential objects
-#' @examples
-#'
-#' showClass("RefStades")
-#'
setClass(Class="RefStades",representation=representation(data="data.frame") )
#' Loading method for RefStades referential objects
#' @return An S4 object of class RefStades
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("RefStades")
#' charge(object)
+#' }
setMethod("charge",signature=signature("RefStades"),definition=function(object) {
req=new("RequeteODBC")
req at baseODBC<-get("baseODBC",envir=envir_stacomi)
@@ -45,10 +43,12 @@
#' @return An S4 object of class RefStades
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' dc_selectionne=6
#' taxon_selectionne=2038
#' object=new("RefStades")
#' charge_avec_filtre(object,dc_selectionne,taxon_selectionne)
+#' }
setMethod("charge_avec_filtre",signature=signature("RefStades"),definition=function(object,dc_selectionne,taxon_selectionne) {
requete=new("RequeteODBCwhere")
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
@@ -70,13 +70,15 @@
#' @note the method tests if the load is called from within a "bilan" object, and loads par, parqual, or parquan objects accordingly
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("RefStades")
#' win=gwindow()
#' group=ggroup(container=win,horizontal=FALSE)
#' object<-charge(object)
#' bilanMigrationPar=new(BilanMigrationPar)
-#' # objectBilan=bilan_taille # pour autre test
+#' objectBilan=bilan_taille # for another test
#' choice(object,objectBilan=bilanMigrationPar)
+#' }
setMethod("choice",signature=signature("RefStades"),definition=function(object,objectBilan=NULL,is.enabled=TRUE) {
if (nrow(object at data) > 0){
hstd=function(h,...){
@@ -130,13 +132,15 @@
#' @note the method tests if the load is called from within a "bilan" object, and loads par, parqual, or parquan objects accordingly
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("RefStades")
#' win=gwindow()
#' group=ggroup(container=win,horizontal=FALSE)
#' object<-charge(object)
#' bilanMigrationPar=new(BilanMigrationPar)
-#' # objectBilan=bilan_taille # for other test
-#' choicemult(object,objectBilan=bilanMigrationPar)
+#' objectBilan=bilan_taille # for other test
+#' choicemult(object,objectBilan=bilanMigrationPar)
+#' }
setMethod("choicemult",signature=signature("RefStades"),definition=function(object,objectBilan=NULL,is.enabled=TRUE) {
if (nrow(object at data) > 0){
@@ -256,10 +260,12 @@
#' @param stades the vector of stages chosen
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#'object=new("RefTaxon")
#'object<-charge(object)
#'objectBilan=new("BilanMigrationMult")
#' choice_c(object=object,objectBilan=objectBilan,"Anguilla anguilla")
+#' }
setMethod("choice_c",signature=signature("RefStades"),definition=function(object,stades) {
if (is.null(stades)) {
Modified: pkg/stacomir/R/RefStationMesure.r
===================================================================
--- pkg/stacomir/R/RefStationMesure.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefStationMesure.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -26,9 +26,6 @@
#' \code{\linkS4class{RefStationMesure}}
#' \code{\linkS4class{RefTaxon}}
#' @keywords classes
-#' @examples
-#'
-#' showClass("RefStationMesure")
setClass (Class="RefStationMesure",
representation=representation(data="data.frame"),
prototype=prototype(data=data.frame())
@@ -38,8 +35,10 @@
#' @return An S4 object of class RefStationMesure
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("RefStationMesure")
#' charge(object)
+#' }
setMethod("charge",
signature=signature("RefStationMesure"),
definition=function(object)
@@ -58,11 +57,13 @@
#' Choice method for RefStationMesure referential object
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("RefStationMesure")
#' win=gwindow()
#' group=ggroup(container=win,horizontal=FALSE)
#' object<-charge(object)
#' choice(object)
+#' }
setMethod("choice",signature=signature("RefStationMesure"),definition=function(object,is.enabled=TRUE,title=get("msg",envir=envir_stacomi)$RefStationMesure.3) {
if (nrow(object at data) > 0){
hSTM=function(h,...){
Modified: pkg/stacomir/R/RefTaxon.r
===================================================================
--- pkg/stacomir/R/RefTaxon.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/RefTaxon.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -22,10 +22,6 @@
#' \code{\linkS4class{RefStades}}
#' \code{\linkS4class{RefStationMesure}}
#' \code{\linkS4class{RefTaxon}}
-#' @keywords classes
-#' @examples
-#'
-#' showClass("RefTaxon")
setClass(Class="RefTaxon",representation= representation(data="data.frame" ))
#' Loading method for RefTaxon referential objects
#'
@@ -106,13 +102,15 @@
#' Multiple Choice method for Reftaxon referential objects, the graphical interface is built to allow
#' for multiple choices. See load for method in the command line.
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @examples
+#' @examples
+#' \dontrun{
#' object=new("RefTaxon")
#' win=gwindow()
#' group=ggroup(container=win,horizontal=FALSE)
#' object<-charge(object)
#' bilanMigration=new(BilanMigration)
#' choicemult(object,objectBilan=bilanMigration)
+#' }
setMethod("choicemult",signature=signature("RefTaxon"),definition=function(object,objectBilan=NULL,is.enabled=TRUE) {
if (nrow(object at data) > 0){
htax=function(h,...){
@@ -204,10 +202,12 @@
#' @param taxons The vector of taxon, can be either code (numeric) or latin name
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("RefTaxon")
#' object<-charge(object)
#' objectBilan=new("BilanMigrationMult")
#' choice_c(object=object,objectBilan=objectBilan,"Anguilla anguilla")
+#' }
setMethod("choice_c",signature=signature("RefTaxon"),definition=function(object,taxons) {
if (is.null(taxons)) {
funout(get("msg",envir=envir_stacomi)$RefTaxon.5,arret=TRUE)
Modified: pkg/stacomir/R/Refpar.r
===================================================================
--- pkg/stacomir/R/Refpar.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/Refpar.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -25,21 +25,16 @@
#' @keywords classes
#' @slot data="data.frame" the list of parameters
#' @family Referential objects
-
-#' @examples
-#'
-#' showClass("Refpar")
-#'
-
-#' @examples object=new("Refpar")
setClass(Class="Refpar",representation= representation(data="data.frame"))
#' Loading method for Repar referential objects
#' @return An S4 object of class Refpar
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("Refpar")
#' charge(object)
+#' }
setMethod("charge",signature=signature("Refpar"),definition=function(object) {
requete=new("RequeteODBC")
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
@@ -53,8 +48,10 @@
#' @return An S4 object of class Refpar
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' 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) {
requete=new("RequeteODBCwhere")
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
@@ -79,11 +76,13 @@
#' @note to load the possible values of qualitative parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("Refpar")
-#' win=gwindow()
-#' group=ggroup(container=win,horizontal=FALSE)
-#' object<-charge(object)
-#' choice(object)
+#' win=gwindow()
+#' group=ggroup(container=win,horizontal=FALSE)
+#' 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) {
if (nrow(object at data) > 0){
hcar=function(h,...){
Modified: pkg/stacomir/R/Refparqual.r
===================================================================
--- pkg/stacomir/R/Refparqual.r 2016-08-20 16:09:01 UTC (rev 171)
+++ pkg/stacomir/R/Refparqual.r 2016-08-20 17:08:38 UTC (rev 172)
@@ -27,17 +27,16 @@
#' @slot valqual="data.frame" the list of qualitative parameters
#' @include Refpar.r
#' @family Referential objects
-#' @examples
-#'
-#' showClass("Refparqual")
setClass(Class="Refparqual",representation= representation(valqual="data.frame"),contains="Refpar")
#' Loading method for Reparqual referential objects
#' @return An S4 object of class Refparqual
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("Refparqual")
#' charge(object)
+#' }
setMethod("charge",signature=signature("Refparqual"),definition=function(object) {
requete=new("RequeteODBC")
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
@@ -53,11 +52,13 @@
#' @return An S4 object of class Refparqual
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' dc_selectionne=6
#' taxon_selectionne=2038
#' stade_selectionne="AGJ"
#' object=new("Refparqual")
#' charge_avec_filtre(object,dc_selectionne,taxon_selectionne,stade_selectionne)
+#' }
setMethod("charge_avec_filtre",signature=signature("Refparqual"),definition=function(object,dc_selectionne,taxon_selectionne,stade_selectionne) {
requete=new("RequeteODBCwhere")
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
@@ -85,12 +86,14 @@
#' @return An S4 object of class Refparqual with the valqual slot filled
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' dc_selectionne=6
#' taxon_selectionne=2038
#' stade_selectionne="AGJ"
#' object=new("Refparqual")
#' object<-charge(object)
-#' charge_complement(object)
+#' charge_complement(object)
+#' }
setMethod("charge_complement",signature=signature("Refparqual"),definition=function(object) {
if (nrow(object at data)!=1) funout(paste(get("msg",envir=envir_stacomi)$Refparqual.1,nrow(object at data)),arret=TRUE)
requete=new("RequeteODBC")
@@ -112,11 +115,13 @@
#' to load the possible values of qualitative parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
+#' \dontrun{
#' object=new("Refparqual")
#' win=gwindow()
#' group=ggroup(container=win,horizontal=FALSE)
#' object<-charge(object)
#' choice(object)
+#' }
setMethod("choice",signature=signature("Refparqual"),definition=function(object,label="Choix d'une caracteristique qualitative de lot",nomassign="refpar",frameassign="frame_par",is.enabled=TRUE) {
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 172
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