[Stacomir-commits] r155 - branch0.5/stacomir/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Aug 18 09:17:42 CEST 2016
Author: briand
Date: 2016-08-18 09:17:41 +0200 (Thu, 18 Aug 2016)
New Revision: 155
Modified:
branch0.5/stacomir/R/BilanConditionEnv.r
branch0.5/stacomir/R/BilanEspeces.r
branch0.5/stacomir/R/BilanFonctionnementDC.r
branch0.5/stacomir/R/BilanFonctionnementDF.r
branch0.5/stacomir/R/BilanMigration.r
branch0.5/stacomir/R/BilanMigrationConditionEnv.r
branch0.5/stacomir/R/BilanMigrationInterAnnuelle.r
branch0.5/stacomir/R/BilanMigrationMult.r
branch0.5/stacomir/R/BilanMigrationPar.r
branch0.5/stacomir/R/Bilan_carlot.r
branch0.5/stacomir/R/Bilan_poids_moyen.r
branch0.5/stacomir/R/Bilan_stades_pigm.r
branch0.5/stacomir/R/Bilan_taille.r
branch0.5/stacomir/R/PasdeTemps.r
branch0.5/stacomir/R/RefHorodate.r
branch0.5/stacomir/R/RefMsg.r
branch0.5/stacomir/R/interface_graphique.r
Log:
Modified: branch0.5/stacomir/R/BilanConditionEnv.r
===================================================================
--- branch0.5/stacomir/R/BilanConditionEnv.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/BilanConditionEnv.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -30,7 +30,7 @@
#' \code{\linkS4class{BilanMigrationConditionEnv}}
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
-#' @keywords classes dynamic
+#' @concept Bilan Object
#' @examples
#'
#' showClass("BilanConditionEnv")
Modified: branch0.5/stacomir/R/BilanEspeces.r
===================================================================
--- branch0.5/stacomir/R/BilanEspeces.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/BilanEspeces.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -28,7 +28,7 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
-#' @keywords classes dynamic
+#' @concept Bilan Object
#' @examples
#'
#' showClass("BilanEspeces")
Modified: branch0.5/stacomir/R/BilanFonctionnementDC.r
===================================================================
--- branch0.5/stacomir/R/BilanFonctionnementDC.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/BilanFonctionnementDC.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -23,7 +23,7 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
-#' @keywords classes dynamic
+#' @concept Bilan Object
#' @examples
#'
#' showClass("BilanFonctionnementDC")
Modified: branch0.5/stacomir/R/BilanFonctionnementDF.r
===================================================================
--- branch0.5/stacomir/R/BilanFonctionnementDF.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/BilanFonctionnementDF.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -20,8 +20,7 @@
#' \code{\linkS4class{BilanMigrationConditionEnv}}
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
-#' @references ~put references to the literature/web site here ~
-#' @keywords classes dynamic
+#' @concept Bilan Object
#' @examples
#'
#' showClass("BilanFonctionnementDF")
Modified: branch0.5/stacomir/R/BilanMigration.r
===================================================================
--- branch0.5/stacomir/R/BilanMigration.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/BilanMigration.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -51,6 +51,7 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
+#' @concept Bilan Object
#' @examples
#'
#' showClass("BilanMigration")
Modified: branch0.5/stacomir/R/BilanMigrationConditionEnv.r
===================================================================
--- branch0.5/stacomir/R/BilanMigrationConditionEnv.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/BilanMigrationConditionEnv.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -30,7 +30,7 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
-#' @keywords classes dynamic
+#' @concept Bilan Object
#' @examples
#'
#' showClass("BilanMigrationConditionEnv")
Modified: branch0.5/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- branch0.5/stacomir/R/BilanMigrationInterAnnuelle.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/BilanMigrationInterAnnuelle.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -8,40 +8,35 @@
#' @aliases BilanMigrationConditionEnv BilanMigrationConditionEnv-class
#' @include RefAnnee.r
#' @section Objects from the Class: Objects can be created by calls of the form
-#' \code{new("BilanMigrationConditionEnv",
-#' bilanMigration=new("BilanMigration"),
-#' bilanConditionEnv=new("BilanConditionEnv"))}. \describe{
-#' \item{list("bilanMigration")}{Object of class \code{"BilanMigration"} The
-#' migration overview }\item{:}{Object of class \code{"BilanMigration"} The
-#' migration overview } \item{list("bilanConditionEnv")}{Object of class
-#' \code{"BilanConditionEnv"} The environmental overview}\item{:}{Object of
-#' class \code{"BilanConditionEnv"} The environmental overview} }
+#' \code{new("BilanMigrationConditionEnv",
+#' bilanMigration=new("BilanMigration"),
+#' bilanConditionEnv=new("BilanConditionEnv"))}.
+#' \describe{
+#' \item{list("bilanMigration")}{Object of class \code{"BilanMigration"} The
+#' migration overview }\item{:}{Object of class \code{"BilanMigration"} The
+#' migration overview } \item{list("bilanConditionEnv")}{Object of class
+#' \code{"BilanConditionEnv"} The environmental overview}\item{:}{Object of
+#' class \code{"BilanConditionEnv"} The environmental overview} }
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @seealso Other Bilan Class \code{\linkS4class{Bilan_lot}}
-#' \code{\linkS4class{Bilan_poids_moyen}}
-#' \code{\linkS4class{Bilan_stades_pigm}} \code{\linkS4class{Bilan_taille}}
-#' \code{\linkS4class{BilanConditionEnv}} \code{\linkS4class{BilanEspeces}}
-#' \code{\linkS4class{BilanFonctionnementDC}}
-#' \code{\linkS4class{BilanFonctionnementDF}}
-#' \code{\linkS4class{BilanMigration}}
-#' \code{\linkS4class{BilanMigrationConditionEnv}}
-#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
-#' \code{\linkS4class{BilanMigrationPar}}
+#' \code{\linkS4class{Bilan_poids_moyen}}
+#' \code{\linkS4class{Bilan_stades_pigm}}
+#' \code{\linkS4class{Bilan_taille}}
+#' \code{\linkS4class{BilanConditionEnv}}
+#' \code{\linkS4class{BilanEspeces}}
+#' \code{\linkS4class{BilanFonctionnementDC}}
+#' \code{\linkS4class{BilanFonctionnementDF}}
+#' \code{\linkS4class{BilanMigration}}
+#' \code{\linkS4class{BilanMigrationConditionEnv}}
+#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
+#' \code{\linkS4class{BilanMigrationPar}}
#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
-#' @keywords classes dynamic
+#' @concept Bilan Object
#' @examples
#'
#' showClass("BilanMigrationConditionEnv")
#'
#' @export
-
-
-
-
-
-
-
-
setClass(Class="BilanMigrationInterAnnuelle",representation=
representation(
dc="RefDC",
Modified: branch0.5/stacomir/R/BilanMigrationMult.r
===================================================================
--- branch0.5/stacomir/R/BilanMigrationMult.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/BilanMigrationMult.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -270,7 +270,7 @@
" FROM ",sch,"t_operation_ope",
" JOIN ",sch,"t_lot_lot on lot_ope_identifiant=ope_identifiant")
# removing character marks
- req at select<-str_replace_all(req at select,"[\r\n\t]" , "")
+ req at select<-stringr::str_replace_all(req at select,"[\r\n\t]" , "")
# the where clause is returned by ODBCWheredate
req at and=stringr::str_c(" AND ope_dic_identifiant in",dc,
" AND lot_tax_code in ",tax,
Modified: branch0.5/stacomir/R/BilanMigrationPar.r
===================================================================
--- branch0.5/stacomir/R/BilanMigrationPar.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/BilanMigrationPar.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -44,6 +44,7 @@
#' \code{\linkS4class{BilanMigrationConditionEnv}}
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
+#' @concept Bilan Object
#' @examples
#'
#' showClass("BilanMigrationPar")
Modified: branch0.5/stacomir/R/Bilan_carlot.r
===================================================================
--- branch0.5/stacomir/R/Bilan_carlot.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/Bilan_carlot.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -22,6 +22,7 @@
#' \code{\linkS4class{BilanMigrationPar}}
#' @references
#' \url{http://w3.eptb-vilaine.fr:8080/tracstacomi/wiki/Recette\%20BilanLot}
+#' @concept Bilan Object
#' @examples
#'
#' showClass("Bilan_carlot")
Modified: branch0.5/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- branch0.5/stacomir/R/Bilan_poids_moyen.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/Bilan_poids_moyen.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -39,8 +39,10 @@
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @seealso Other Bilan Classes \code{\linkS4class{Bilan_lot}}
#' \code{\linkS4class{Bilan_poids_moyen}}
-#' \code{\linkS4class{Bilan_stades_pigm}} \code{\linkS4class{Bilan_taille}}
-#' \code{\linkS4class{BilanConditionEnv}} \code{\linkS4class{BilanEspeces}}
+#' \code{\linkS4class{Bilan_stades_pigm}}
+#' \code{\linkS4class{Bilan_taille}}
+#' \code{\linkS4class{BilanConditionEnv}}
+#' \code{\linkS4class{BilanEspeces}}
#' \code{\linkS4class{BilanFonctionnementDC}}
#' \code{\linkS4class{BilanFonctionnementDF}}
#' \code{\linkS4class{BilanMigration}}
@@ -48,7 +50,7 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
-#' @keywords classes dynamic
+#' @concept Bilan Object
#' @examples
#'
#' showClass("Bilan_poids_moyen")
Modified: branch0.5/stacomir/R/Bilan_stades_pigm.r
===================================================================
--- branch0.5/stacomir/R/Bilan_stades_pigm.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/Bilan_stades_pigm.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -200,12 +200,13 @@
return(list("tablestades"=tablestades,"dates"=dates))
}
-#' Charge : method used by the graphical interface to buid object from values
+#' Charge method for BilanStadePigm
+#'
+#' method used by the graphical interface to build object from values
#' stored in envir_stacomi
#'
#' @return Bilan_stades_pigm with slots filled with user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-
setMethod("charge",signature=signature("Bilan_stades_pigm"),definition=function(object,h) {
if (exists("refDC",envir_stacomi)) {
object at dc<-get("refDC",envir_stacomi)
@@ -250,18 +251,11 @@
object<-connect(object)
return(object)
})
-# Methode permettant l'affichage d'un graphique en lattice (barchart) du fonctionnement mensuel du dispositif
-# Compte tenu de la structure des donnees ce n'est pas si simple...
-
-
-
#' plots polygons
#'
-#' plots polygons
#'
-#'
#' @param xmat a matrix of x values of the polygons
#' @param ymat a matrix where the number of rows is of the same length as xmat
#' @param ordre the order in which the polygons will be drawn
@@ -290,8 +284,7 @@
#' Function to calculate pigmentation times.
#'
-#'
-#'
+#'
#' @param parm parameters of the model
#' @param datatempsal data.frame containing temperatures and salinities
#' @return list("dates"=duree,"phi_jour"=phi_jour)
Modified: branch0.5/stacomir/R/Bilan_taille.r
===================================================================
--- branch0.5/stacomir/R/Bilan_taille.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/Bilan_taille.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -31,7 +31,7 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
-#' @keywords classes dynamic
+#' @concept Bilan Object
#' @examples
#'
#' showClass("Bilan_taille")
Modified: branch0.5/stacomir/R/PasdeTemps.r
===================================================================
--- branch0.5/stacomir/R/PasdeTemps.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/PasdeTemps.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -69,7 +69,7 @@
if (!rep4) retValue=paste(retValue,"length(object at noPasCourant) !=1")
return(ifelse(rep1 & rep2 & rep3 & rep4,TRUE,retValue))
}
-#definition de la classe
+
#' Class "PasDeTemps"
#'
#' Describes a time step
@@ -101,7 +101,7 @@
#' current step } }
#' @author cedric.briand"at"eptb-vilaine.fr
#' @seealso \code{\linkS4class{PasDeTempsJournalier}}
-#' @keywords classes
+#' @concept Bilan Object
#' @examples
#'
#' showClass("PasDeTemps")
Modified: branch0.5/stacomir/R/RefHorodate.r
===================================================================
--- branch0.5/stacomir/R/RefHorodate.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/RefHorodate.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -50,8 +50,7 @@
#' Method to set the Horodate
#'
-#' @return An Object of class "RefHorodate"
-#'
+#' @return An Object of class "RefHorodate"
#' @author cedric.briand
#' @docType methods
#' @export
Modified: branch0.5/stacomir/R/RefMsg.r
===================================================================
--- branch0.5/stacomir/R/RefMsg.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/RefMsg.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -40,7 +40,7 @@
#' @examples
#' object=new("RefMsg")
#' charge_avec_filtre(object,lang='French')
-#' @exportMethod
+#' @export
setMethod("charge_avec_filtre",signature=signature("RefMsg"),definition=function(object,lang) {
requete=new("RequeteODBCwhere")
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
@@ -59,8 +59,8 @@
#' @note When coming from the database, " are now /", those at the beginning and end are turned into ", the others are single quote when they are to be pasted within the text as code example. The remainder "c("a","b","c") are rebuilt into vectors by the function
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
-#' object=new("RefMsg")
setMethod("createmessage",signature=signature("RefMsg"),definition=function(object) {
+ #object=new("RefMsg")
object<-charge(object)
object<-charge_avec_filtre(object,lang=get("lang",envir=envir_stacomi))
if (nrow(object at messager)!=nrow(object at messagerlang)) stop("internal error, check messager and messagerlang length, they should match")
Modified: branch0.5/stacomir/R/interface_graphique.r
===================================================================
--- branch0.5/stacomir/R/interface_graphique.r 2016-08-16 14:51:55 UTC (rev 154)
+++ branch0.5/stacomir/R/interface_graphique.r 2016-08-18 07:17:41 UTC (rev 155)
@@ -186,32 +186,34 @@
#' window
#'
#' @param gr_interface Will be used to launch the program as graphical
+#' interface or in command line
#' @import stringr
-#' @import intervals intervals
-#' @import intervals closed<-
-#' @import intervals interval_overlap
+#' @importFrom intervals Intervals
+#' @importFrom intervals closed<-
+#' @importFrom intervals interval_overlap
#' @import RColorBrewer
-#' @import package gWidgets
-#' @import package gWidgetsRGtk2
-#' @import package ggplot2
+#' @import gWidgets
+#' @import gWidgetsRGtk2
+#' @import ggplot2
#' @importFrom methods as
#' @importFrom methods new
#' @importFrom methods slot
-#' @importFrom methods slot<-
+#' @importFrom methods "slot<-"
#' @importFrom grid viewport
#' @importFrom grid pushViewport
#' @importFrom grid grid.newpage
#' @importFrom grid grid.layout
#' @importFrom utils winProgressBar
-#' @importFrom utils setwinProgressBar
+#' @importFrom utils setWinProgressBar
#' @importFrom utils read.csv
#' @importFrom utils stack
+#' @importFrom utils globalVariables
#' @importFrom RODBC odbcClose
#' @importFrom stats ftable
#' @importFrom stats xtabs
-#' @import package RPostgreSQL
-#' @import package sqldf
-#' @importFrom dplyr dcast
+#' @import RPostgreSQL
+#' @import sqldf
+#' @importFrom reshape2 dcast
#' @importFrom reshape2 melt
#' @importFrom lattice barchart
#' @importFrom lattice trellis.par.get
@@ -223,7 +225,6 @@
#' @importFrom graphics legend
#' @importFrom graphics text
#' @importFrom graphics axis
-#' interface or in command line
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
stacomi=function(gr_interface=TRUE){
# first loading of connection and odbc info using chargexml()
@@ -381,4 +382,5 @@
add(ggrouptotal1,ggroupboutons,expand=FALSE)
}
-
+# http://stackoverflow.com/questions/9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-notes-when
+utils::globalVariables(c("quinzaine", "mois","val_quant","duree"))
\ No newline at end of file
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