[Stacomir-commits] r180 - in pkg/stacomir: . R man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Aug 25 17:05:18 CEST 2016
Author: briand
Date: 2016-08-25 17:05:18 +0200 (Thu, 25 Aug 2016)
New Revision: 180
Added:
pkg/stacomir/man/charge-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/msg.Rd
pkg/stacomir/man/plot-BilanMigrationPar-ANY-method.Rd
pkg/stacomir/man/supprime-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/vignettes/
pkg/stacomir/vignettes/images/
pkg/stacomir/vignettes/tables/
pkg/stacomir/vignettes/vignette_stacomi.Rnw
pkg/stacomir/vignettes/vignette_stacomi.aux
Removed:
pkg/stacomir/man/ceil.POSIXt.Rd
pkg/stacomir/man/choix-methods.Rd
pkg/stacomir/man/coerce-methods.Rd
pkg/stacomir/man/createmessage.Rd
pkg/stacomir/man/getvalue-methods.Rd
pkg/stacomir/man/monthDays.Rd
pkg/stacomir/man/plot-BilanMigrationPar-missing-method.Rd
pkg/stacomir/man/round.POSIXt.Rd
pkg/stacomir/man/trunc.POSIXt.Rd
Modified:
pkg/stacomir/NAMESPACE
pkg/stacomir/R/BilanConditionEnv.r
pkg/stacomir/R/BilanEspeces.r
pkg/stacomir/R/BilanFonctionnementDC.r
pkg/stacomir/R/BilanMigration.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/Bilan_taille.r
pkg/stacomir/R/PasdeTemps.r
pkg/stacomir/R/RefAnnee.r
pkg/stacomir/R/RefCheckBox.r
pkg/stacomir/R/RefChoix.r
pkg/stacomir/R/RefDC.r
pkg/stacomir/R/RefHorodate.r
pkg/stacomir/R/RefMsg.r
pkg/stacomir/R/RefStades.r
pkg/stacomir/R/RefTaxon.r
pkg/stacomir/R/data.r
pkg/stacomir/R/funstat.r
pkg/stacomir/R/funstatJournalier.r
pkg/stacomir/R/funtraitementdate.r
pkg/stacomir/R/interface_BilanMigration.r
pkg/stacomir/R/interface_BilanMigrationConditionEnv.r
pkg/stacomir/R/stacomi.r
pkg/stacomir/R/utilitaires.r
pkg/stacomir/man/BilanConditionEnv-class.Rd
pkg/stacomir/man/BilanEspeces-class.Rd
pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
pkg/stacomir/man/BilanMigrationMult-class.Rd
pkg/stacomir/man/BilanMigrationPar-class.Rd
pkg/stacomir/man/Bilan_poids_moyen-class.Rd
pkg/stacomir/man/Bilan_stades_pigm-class.Rd
pkg/stacomir/man/Bilan_taille-class.Rd
pkg/stacomir/man/RefMsg-class.Rd
pkg/stacomir/man/calcule-BilanMigration-method.Rd
pkg/stacomir/man/calcule-BilanMigrationMult-method.Rd
pkg/stacomir/man/calcule-BilanMigrationPar-method.Rd
pkg/stacomir/man/calcule-Bilan_carlot-method.Rd
pkg/stacomir/man/calcule-Bilan_taille-method.Rd
pkg/stacomir/man/charge-BilanConditionEnv-method.Rd
pkg/stacomir/man/charge-BilanEspeces-method.Rd
pkg/stacomir/man/charge-Bilan_carlot-method.Rd
pkg/stacomir/man/charge-Bilan_stades_pigm-method.Rd
pkg/stacomir/man/charge-Bilan_taille-method.Rd
pkg/stacomir/man/choice-RefDC-method.Rd
pkg/stacomir/man/choicemult-RefDC-method.Rd
pkg/stacomir/man/connect-BilanConditionEnv-method.Rd
pkg/stacomir/man/connect-BilanEspeces-method.Rd
pkg/stacomir/man/connect-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/connect-Bilan_taille-method.Rd
pkg/stacomir/man/createmessage-RefMsg-method.Rd
pkg/stacomir/man/envir_stacomi.Rd
pkg/stacomir/man/fun_weight_conversion.Rd
pkg/stacomir/man/funbarchartDC.Rd
pkg/stacomir/man/funboxDC.Rd
pkg/stacomir/man/fundensityBilan_carlot.Rd
pkg/stacomir/man/fungraph.Rd
pkg/stacomir/man/fungraphInteract_tail.Rd
pkg/stacomir/man/fungraph_civelle.Rd
pkg/stacomir/man/funout.Rd
pkg/stacomir/man/funstat.Rd
pkg/stacomir/man/funstatJournalier.Rd
pkg/stacomir/man/funtable.Rd
pkg/stacomir/man/funtableBilan_carlot.Rd
pkg/stacomir/man/funtableBilan_tail.Rd
pkg/stacomir/man/funtraitement_poids.Rd
pkg/stacomir/man/hBilanEspecescalc.Rd
pkg/stacomir/man/hTableBilanEspeces.Rd
pkg/stacomir/man/hTableBilanMigrationMult.Rd
pkg/stacomir/man/hbilanConditionEnvgraph.Rd
pkg/stacomir/man/hbilanMigrationConditionEnvcalc.Rd
pkg/stacomir/man/hbilanMigrationMult_graph.Rd
pkg/stacomir/man/hbilanMigrationMultcalc.Rd
pkg/stacomir/man/hbilanMigrationMultgraph2.Rd
pkg/stacomir/man/hbilanMigrationMultgraph3.Rd
pkg/stacomir/man/hbilanMigrationgraph.Rd
pkg/stacomir/man/houtBilanMigrationMult.Rd
pkg/stacomir/man/interface_BilanMigrationConditionEnv.Rd
pkg/stacomir/man/plot-BilanMigrationMult-ANY-method.Rd
pkg/stacomir/man/print-BilanMigrationMult-method.Rd
pkg/stacomir/man/stacomi.Rd
pkg/stacomir/man/stacomiR-package.Rd
pkg/stacomir/man/summary-BilanMigrationMult-method.Rd
Log:
package documentation
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2016-08-24 19:57:35 UTC (rev 179)
+++ pkg/stacomir/NAMESPACE 2016-08-25 15:05:18 UTC (rev 180)
@@ -4,7 +4,6 @@
export(fun_bilanMigrationMult)
export(fun_bilanMigrationMult_Overlaps)
export(fun_char_spe)
-export(fun_weight_conversion)
export(funbarchartDC)
export(funbarchartDF)
export(funboxDC)
@@ -13,9 +12,6 @@
export(fundensityBilan_carlot)
export(funout)
export(funpointBilan_carlot)
-export(funstat)
-export(funstatJournalier)
-export(funtable)
export(funtableBilan_carlot)
export(funtableDC)
export(funtableDF)
@@ -23,7 +19,6 @@
export(hBilanEspecescalc)
export(hCamembert)
export(hTableBilanEspeces)
-export(hbilanConditionEnvgraph)
export(hbilanMigrationConditionEnvcalc)
export(interface_BilanEspeces)
export(messages)
@@ -49,8 +44,8 @@
exportMethods(createmessage)
exportMethods(plot)
exportMethods(print)
-exportMethods(setRefHorodate)
exportMethods(summary)
+exportMethods(supprime)
import(Hmisc)
import(RColorBrewer)
import(RODBC)
@@ -100,6 +95,7 @@
importFrom(stats,predict)
importFrom(stats,sd)
importFrom(stats,xtabs)
+importFrom(utils,data)
importFrom(utils,globalVariables)
importFrom(utils,read.csv)
importFrom(utils,select.list)
Modified: pkg/stacomir/R/BilanConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanConditionEnv.r 2016-08-24 19:57:35 UTC (rev 179)
+++ pkg/stacomir/R/BilanConditionEnv.r 2016-08-25 15:05:18 UTC (rev 180)
@@ -1,6 +1,3 @@
-# Nom fichier : BilanConditionEnv (classe)
-# Date de creation : 24/06/2009 13:49:20
-# constructeur d'un bilan des conditions environnementales
#' class BilanConditionEnv simple output of one or several environmental
#' conditions...
#'
@@ -11,6 +8,11 @@
#' @include RefStationMesure.r
#' @include create_generic.r
#' @include utilitaires.r
+#' @slot horodate \link{RefHorodate-class}
+#' @slot stationMesure \link{RefStationMesure-class}
+#' @slot data \code{data.frame}
+#' @slot datedebut A \link[base]{-.POSIXt} value
+#' @slot datefin A \link[base]{-.POSIXt} value
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("BilanConditionEnv", horodate=new("Horodate"),
#' stationMesure=new("RefStationMesure"), data=data.frame(),
@@ -43,11 +45,13 @@
#' connect method for BilanConditionEnv class
+#' @param object An objet of class \link{BilanConditionEnv-class}
+#' @param h A handler
#' @return an object of BilanConditionEnv class
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
setMethod("connect",signature=signature("BilanConditionEnv"),
- definition=function(object,h,..) {
+ definition=function(object,h) {
# construit une requete ODBCwheredate
requete=new("RequeteODBCwheredate")
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
@@ -75,6 +79,8 @@
)
#' charge method for BilanCondtionEnv class
+#' @param object An objet of class \link{BilanConditionEnv-class}
+#' @param h A handler
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
setMethod("charge",signature=signature("BilanConditionEnv"),definition=function(object,h) {
@@ -100,12 +106,11 @@
return(object)
})
-# affiche un graphe si des CE sont dans la base pendant la periode selectionnee
+
#' hbilanConditionEnvgraph function called by handler which displays a graphe if environmental conditons are in the database during the selected period
#' @param h a handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
hbilanConditionEnvgraph = function(h,...)
{
# chargement des conditions environnementales
@@ -162,7 +167,7 @@
return (lesGraphes)
}
-# affichage de stats
+
hbilanConditionEnvstat = function(h,...)
{
bilanConditionEnv=charge(bilanConditionEnv)
Modified: pkg/stacomir/R/BilanEspeces.r
===================================================================
--- pkg/stacomir/R/BilanEspeces.r 2016-08-24 19:57:35 UTC (rev 179)
+++ pkg/stacomir/R/BilanEspeces.r 2016-08-25 15:05:18 UTC (rev 180)
@@ -8,22 +8,29 @@
#' this class is used to make the assessment of all species, and their number,
#' per month it writes either an histogram or a pie chart of number per
#' year/week/month
-#'
-#'
+#' @slot dc an object of class \link{RefDC-class} inherited from \link{BilanMigration-class}
+#' @slot horodate \link{RefHorodate-class}
+#' @slot datedebut A \link[base]{-.POSIXt} value
+#' @slot datefin A \link[base]{-.POSIXt} value
+#' @slot data \code{data.frame}
+#' @slot liste Object of class \code{\link{RefListe}} RefListe referential
+#' class choose within a list
+
#' @include RefDC.r
#' @include RefListe.r
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("BilanEspeces", ...)}.
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @seealso Other Bilan Classes \code{\linkS4class{Bilan_carlot}}
-#' \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}}
+#' @seealso Other Bilan Classes
+#' \code{\linkS4class{Bilan_carlot}},
+#' \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}}
#' @concept Bilan Object
#' @export
@@ -50,6 +57,7 @@
)
#' connect method for BilanEspeces
+#' @param object An object of class \link{BilanEspeces-class}
#' @return bilanEspeces instance with request corresponding to the user choices
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
@@ -96,10 +104,11 @@
#' charge method for BilanEspeces
#' verifies the content of objects and calls the connect method
+#' @param object An object of class \link{BilanEspeces-class}
#' @return BilanEspeces with slots filled by user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
-setMethod("charge",signature=signature("BilanEspeces"),definition=function(object,...){
+setMethod("charge",signature=signature("BilanEspeces"),definition=function(object){
funout(get("msg",envir_stacomi)$BilanEspeces.7)
bilanEspeces<-object
if (exists("refDC",envir_stacomi)) {
Modified: pkg/stacomir/R/BilanFonctionnementDC.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDC.r 2016-08-24 19:57:35 UTC (rev 179)
+++ pkg/stacomir/R/BilanFonctionnementDC.r 2016-08-25 15:05:18 UTC (rev 180)
@@ -4,20 +4,22 @@
#' The counting device is not always working. It may me stopped either
#' following a monitoring protocol, or due to misfunction of the device, this
#' class allows to draw graphics allowing an overview of the device operation
-#'
-#'
+#' @slot data A data frame
+#' @slot dc An object of class \code{RefDC-class}
+#' @slot horodate An object of class \code{RefHorodate-class}
+#' @slot requete An object of class \code{RequeteODBCwheredate-class}
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("BilanFonctionnementDC", ...)}.
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @seealso Other Bilan Class \code{\linkS4class{Bilan_carlot}}
-#' \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{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}}
#' @concept Bilan Object
#' @export
@@ -38,7 +40,8 @@
#' connect method for BilanFonctionnementDC
#'
#' loads the working periods and type of arrest or disfunction of the DC
-#' @return An object of class \code{BilanFonctionnementDC}
+#' @param objet An object of class \link{BilanFonctionnementDC-class}
+#' @return An object of class \link{BilanFonctionnementDC-class}
#'
#' @author cedric.briand
setMethod("connect",signature=signature("BilanFonctionnementDC"),definition=function(object,h) {
@@ -68,7 +71,9 @@
#'
#' used by the graphical interface to retreive the objects of Referential classes
#' assigned to envir_stacomi
-#' @return An object of class \code{BilanFonctionnementDC}
+#' @param objet An object of class \link{BilanFonctionnementDC-class}
+#' @param h A handler passed from the graphical interface
+#' @return An object of class \link{BilanFonctionnementDC-class}
#'
#' @author cedric.briand
setMethod("charge",signature=signature("BilanFonctionnementDC"),definition=function(object,h) {
@@ -102,7 +107,6 @@
#' @return assigns the data frame \code{periodeDC} allowing to build the lattice graph in the environment envir_stacomi
#'
#' @author cedric.briand
-#' @export
funbarchartDC = function(h,...) {
fonctionnementDC=charge(fonctionnementDC)
@@ -171,7 +175,6 @@
#'
#' @param h a handler
#' @param ... Additional parameters
-#' @export
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
funboxDC = function(h,...) {
fonctionnementDC=charge(fonctionnementDC)
@@ -293,7 +296,6 @@
#' FuntableDC create a table output for BilanFonctionnementDC class
#' @param h a handler
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
funtableDC = function(h,...) {
fonctionnementDC=charge(fonctionnementDC)
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2016-08-24 19:57:35 UTC (rev 179)
+++ pkg/stacomir/R/BilanMigration.r 2016-08-25 15:05:18 UTC (rev 180)
@@ -87,10 +87,11 @@
#' calcule method for BilanMigration
+#' @param object An object of class \code{\link{BilanMigration-class}}
#' @return BilanMigration with slots filled by user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
-setMethod("calcule",signature=signature("BilanMigration"),definition=function(object,...){
+setMethod("calcule",signature=signature("BilanMigration"),definition=function(object){
bilanMigration<-object
#pour l'instant ne lancer que si les fenetre sont fermees
# funout("lancement updateplot \n")
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2016-08-24 19:57:35 UTC (rev 179)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2016-08-25 15:05:18 UTC (rev 180)
@@ -9,24 +9,26 @@
#' \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} }
+#' @slot dc Object of class \code{\link{RefDC-class}}, the counting device
+#' @slot data Object of class \code{"data.frame"} data for bilan lot
+#' @slot taxons An object of class \code{\link{RefTaxon-class}}
+#' @slot stades An object of class \code{\link{RefStades-class}}
+#' @slot anneedebut Object of class \code{\link{RefAnnee-class}}. refAnnee allows to choose year of beginning
+#' @slot anneefin Object of class \code{\link{RefAnnee-class}}
+#' refAnnee allows to choose last year of the Bilan
+#'
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @seealso Other Bilan Class \code{\linkS4class{Bilan_carlot}}
-#' \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}}
+#' @seealso Other Bilan Class \code{\linkS4class{Bilan_carlot}},
+#' \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}}
#' @concept Bilan Object
#' @export
@@ -49,11 +51,12 @@
)
#' connect method for BilanMigrationInterannuelle class
+#' @param object An object of class \link{BilanMigrationInterAnnuelle-class}
#' @return bilanMigrationInterannuelle an instantianted object with values filled with user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
setMethod("connect",signature=signature("BilanMigrationInterAnnuelle"),
- definition=function(object,...)
+ definition=function(object)
{
# tableau contenant toutes les annees
les_annees = (object at anneeDebut@annee_selectionnee):(object at anneeFin@annee_selectionnee)
@@ -89,10 +92,14 @@
}
)
-# supprime les enregistrements de la base pour l'annee courante
-# object<-bmi
+#' supprime method for BilanMigrationInterannuelle class
+#' @param object An object of class \link{BilanMigrationInterAnnuelle-class}
+#' @return nothing
+#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @export
+
setMethod("supprime",signature=signature("BilanMigrationInterAnnuelle"),
- definition=function(object,...)
+ definition=function(object)
{
# recuperation des annees taxons et stades concernes
les_annees = (object at anneeDebut@annee_selectionnee):(object at anneeFin@annee_selectionnee)
@@ -109,12 +116,18 @@
requete at select=stringr::str_c("DELETE from ",get("sch",envir=envir_stacomi),"t_bilanmigrationmensuel_bme ")
requete at where=paste("WHERE bme_annee IN (",paste(les_annees,collapse=","),") AND bme_tax_code='",tax,"' AND bme_std_code='",std,"' AND bme_dis_identifiant=",dic,sep="")
requete<-stacomirtools::connect(requete)
+ return(invisible(NULL))
}
+
)
-# object = bilanMigrationInterAnnuelle
+#' loading method for BilanMigrationInterannuelle class
+#' @param object An object of class \link{BilanMigrationInterAnnuelle-class}
+#' @return An object of class \link{BilanMigrationInterAnnuelle-class}
+#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @export
setMethod("charge",signature=signature("BilanMigrationInterAnnuelle"),
- definition=function(object,...)
+ definition=function(object)
{
if (exists("refDC",envir_stacomi)) {
object at dc<-get("refDC",envir_stacomi)
Modified: pkg/stacomir/R/BilanMigrationMult.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMult.r 2016-08-24 19:57:35 UTC (rev 179)
+++ pkg/stacomir/R/BilanMigrationMult.r 2016-08-25 15:05:18 UTC (rev 180)
@@ -16,14 +16,15 @@
#' from daily conversion coefficients. The methods in this class test whether the counts are numbers or another type of quantity.
#' This class makes different calculations than BilanMigration, it does not handle escapement coefficients,
#' it uses quantities other than numbers if necessary (only used for glass eel in the connect method).
-#' @slot dc An object of class \code{RefDC}
-#' @slot taxons An object of class \code{\link{RefTaxon}}
-#' @slot stades An object of class \code{\link{RefStades}}
-#' @slot pasDeTemps An object of class \code{\link{PasDeTempsJournalier}}
+#' @slot dc An object of class \code{RefDC-class}
+#' @slot taxons An object of class \code{\link{RefTaxon-class}}
+#' @slot stades An object of class \code{\link{RefStades-class}}
+#' @slot pasDeTemps An object of class \code{\link{PasDeTempsJournalier-class}}
#' @slot data A data.frame containing raw data filled by the connect method
#' @slot calcdata A "list" of calculated daily data, one per dc, filled in by the calcule method
#' @slot coef_conversion A data.frame of daily weight to number conversion coefficients, filled in by the connect
#' method if any weight are found in the data slot.
+#' @slot time sequence A POSIXt time sequence
#' @export
#' @example examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
@@ -148,13 +149,14 @@
#'
#' does the calculation once data are filled
#' in with the connect method
+#' @param object An object of class \code{\link{BilanMigrationMult-class}}
#' @param negative a boolean indicating if a separate sum must be done for positive and negative values, if true, positive and negative counts return
#' different rows
#' @note The class BilanMigrationMult does not handle escapement rates. Use class BilanMigration if you want to handle them. The class does not handler
#' 'devenir' i.e. the destination of the fishes.
#' @return BilanMigrationMult with slots filled by user choice
#' @export
-setMethod("calcule",signature=signature("BilanMigrationMult"),definition=function(object,negative=FALSE,...){
+setMethod("calcule",signature=signature("BilanMigrationMult"),definition=function(object,negative=FALSE){
bilanMigrationMult<-object
bilanMigrationMult=connect(bilanMigrationMult)
@@ -313,10 +315,9 @@
#' \item{plot.type="step"}{creates Cumulated graphs for BilanMigrationMult. Data are summed per day for different dc taxa and stages}
#' \item{plot.type="multiple"}{Method to overlay graphs for BilanMigrationMult (multiple dc/taxa/stage in the same plot)}
#' }
-#' @usage plot(x,y,plot.type=c("standard","step","multiple"))
#' @param x An object of class BilanMigrationMult
#' @param y From the formals but missing
-#' @param plot.type Defaut to \code{standard} the standard BilanMigration with dc and operation displayed, can also be \code{step} or
+#' @param plot.type One of "standard","step","multiple". Defaut to \code{standard} the standard BilanMigration with dc and operation displayed, can also be \code{step} or
#' \code{multiple}
#' @param ... Additional arguments, see \code{plot}, \code{plot.default} and \code{par}
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
@@ -495,17 +496,17 @@
if (length(unique(grdata$taxon))==1){
p<-ggplot(grdata,aes(x=debut_pas,y=effectif_total,fill=stade))+
geom_bar(position="stack", stat="identity")+
- facet_grid(DC~.,scale="free_y")+
+ facet_grid(DC~.,scales="free_y")+
scale_fill_brewer(palette="Set2")
} else if (length(unique(grdata$stade))==1){
p<-ggplot(grdata,aes(x=debut_pas,y=effectif_total,fill=taxon))+
geom_bar(position="stack", stat="identity")+
- facet_grid(DC~.,scale="free_y")+
+ facet_grid(DC~.,scales="free_y")+
scale_fill_brewer(palette="Set2")
} else {
p<-ggplot(grdata,aes(x=debut_pas,y=effectif_total,fill=stade))+
geom_bar(position="stack", stat="identity")+
- facet_grid(DC+taxon~.,scale="free_y")+
+ facet_grid(DC+taxon~.,scales="free_y")+
scale_fill_brewer(palette="Set2")
}
@@ -586,8 +587,8 @@
#' summary for bilanMigrationMult
#' calls functions funstat and funtable to create migration overviews
#' and generate csv and html output in the user data directory
-#'
-#' @param ... Additional parameters
+#' @param object An object of class \code{\link{BilanMigrationMult-class}}
+#' @param ... Additional parameters (not used there)
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
setMethod("summary",signature=signature(object="BilanMigrationMult"),definition=function(object,...){
@@ -658,6 +659,8 @@
}
#' Method to print the command line of the object
+#' @param x An object of class BilanMigrationMult
+#' @param ... Additional parameters passed to print
#' @return NULL
#' @author cedric.briand
#' @docType methods
@@ -671,8 +674,8 @@
"datedebut=",shQuote(strftime(x at pasDeTemps@dateDebut,format="%d/%m/%Y")),
",datefin=",shQuote(strftime(DateFin(x at pasDeTemps),format="%d/%m/%Y")),")")
# removing backslashes
- funout(stringr::str_c(sortie1,sortie2))
- return(NULL)
+ funout(stringr::str_c(sortie1,sortie2),...)
+ return(invisible(NULL))
})
#' Function to calculate daily migration using overlaps functions
@@ -874,11 +877,10 @@
#' returns a table where weights and number are calculated from number and weights respectively
#' performs a query to collect the conversion coefficients
-#' @param tableau
-#' @param time.sequence
+#' @param tableau Table issued from BilanMigration
+#' @param time.sequence Time sequence from BilanMigration
#' @return tableau, the data frame
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
fun_weight_conversion=function(tableau,time.sequence) {
funout(paste("dc=",unique(tableau$ope_dic_identifiant),get("msg",envir=envir_stacomi)$funtraitement_poids.1))
nr<-table(tableau$type_de_quantite)[1]
Modified: pkg/stacomir/R/BilanMigrationPar.r
===================================================================
--- pkg/stacomir/R/BilanMigrationPar.r 2016-08-24 19:57:35 UTC (rev 179)
+++ pkg/stacomir/R/BilanMigrationPar.r 2016-08-25 15:05:18 UTC (rev 180)
@@ -21,7 +21,7 @@
#' using interface_BilanMigrationPar function.
#' @slot parquan An object of class \link{Refparquan-class}, quantitative parameter
#' @slot parqual An object of class \link{Refparqual-class}, quanlitative parameter
-#' @slot echantillon An object of class \link{RefChoix-class}", vector of choice
+#' @slot echantillon An object of class \link{RefChoix-class}, vector of choice
#' @slot valeurs_possibles A \code{data.frame} choice among possible choice of a qualitative parameter (discrete)
#' @slot dc an object of class \link{RefDC-class} inherited from \link{BilanMigration-class}
#' @slot taxons An object of class \link{RefTaxon-class} inherited from \link{BilanMigration-class}
@@ -32,20 +32,19 @@
#' @note program : default two parameter choice, checking box "aucun" will allow the program to ignore the parameter
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @seealso Other Bilan Class
-#' \code{\linkS4class{Bilan_carlot}}
-#' \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{Bilan_carlot}},
+#' \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}}
#' @concept Bilan Object
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
setClass(Class="BilanMigrationPar",
representation=representation(parquan="Refparquan",
parqual="Refparqual",
@@ -81,8 +80,8 @@
#' calcule methode
#'
#'
-#'@param object "BilanMigrationPar"
-setMethod("calcule",signature=signature("BilanMigrationPar"),definition=function(object,...){
+#'@param object An object of class \code{\link{BilanMigrationPar}}
+setMethod("calcule",signature=signature("BilanMigrationPar"),definition=function(object){
bilanMigrationPar<-object
if (exists("refDC",envir_stacomi)) {
bilanMigrationPar at dc<-get("refDC",envir_stacomi)
@@ -196,11 +195,12 @@
}
#' plot method for BilanMigrationPar
-#' @usage plot(x,plot.type=c("barplot","xyplot","summary"))
+#'
+#'
#' @param x An object of class BilanMigrationPar
-#' @param plot.type =barplot, 2=xyplot, 3=summary table
+#' @param plot.type One of "barplot", "xyplot", "summary table"
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-setMethod("plot",signature=signature(x="BilanMigrationPar",y="missing"),definition=function(x,y,plot.type="barplot",...){
+setMethod("plot",signature=signature(x="BilanMigrationPar",y="ANY"),definition=function(x,y,plot.type="barplot",...){
###########################
bilanMigrationPar<-x # ne pas passer dessus en debug manuel
##########################
@@ -220,14 +220,15 @@
stop("normalement ce cas est impossible")
# ce cas est impossible
}
- mb=stacomirtools::chnames(mb,"value","sommes")
+ mb=stacomirtools::chnames(mb,"value","sum")
mb=funtraitementdate(data=mb,nom_coldt="Date")
# transformation du tableau de donnees
if (plot.type=="barplot") {
g<-ggplot(mb)
- g<-g+geom_bar(aes(x=mois,y=sommes,fill=variable),stat='identity',stack=TRUE)
+ g<-g+geom_bar(aes(x=mois,y=sum,fill=variable),stat='identity',
+ stack=TRUE)
assign("g",g,envir_stacomi)
funout(get("msg",envir=envir_stacomi)$BilanMigrationPar.6)
print(g)
@@ -235,14 +236,14 @@
if (plot.type=="xyplot") {
g<-ggplot(mb)
- g<-g+geom_point(aes(x=Date,y=sommes,col=variable),stat='identity',stack=TRUE)
+ g<-g+geom_point(aes(x=Date,y=sum,col=variable),stat='identity',stack=TRUE)
assign("g",g,envir_stacomi)
funout(get("msg",envir=envir_stacomi)$BilanMigrationPar.6)
print(g)
} #end plot.type="xyplot"
#TODO create summary method
if (plot.type=="summary") {
- table=round(tapply(mb$somme,list(mb$mois,mb$variable),sum),1)
+ table=round(tapply(mb$sum,list(mb$mois,mb$variable),sum),1)
table=as.data.frame(table)
table[,"total"]<-rowSums(table)
gdf(table, container=TRUE)
Modified: pkg/stacomir/R/Bilan_carlot.r
===================================================================
--- pkg/stacomir/R/Bilan_carlot.r 2016-08-24 19:57:35 UTC (rev 179)
+++ pkg/stacomir/R/Bilan_carlot.r 2016-08-25 15:05:18 UTC (rev 180)
@@ -48,7 +48,8 @@
#' connect method for Bilan_carlot
#'
-#' @return An object of class bilan_lot Bilan_carlot
+#' @return An object of class \link{Bilan_carlot-class}
+#' @param object An object of class \link{Bilan_carlot-class}
#' @param h a handler
#' @param ... additional parameters passed to the method
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
@@ -76,6 +77,8 @@
#'
#' this method verifies that boxes have been clicked in the user interface and gets the objects pasted in
#' envir_stacomi
+#' @param object An object of class \code{\link{Bilan_carlot}}
+#' @param h a handler
#' @return Bilan_carlot with slots filled with user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
@@ -120,9 +123,8 @@
#' Calcule method for Bilan_carlot
#'
-#'
-#' @param h A handler
-#' @param ... Additional parameters
+#' @param object An object of class \code{\link{Bilan_carlot}}
+#' @param h a handler
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
setMethod("calcule",signature=signature("Bilan_carlot"),definition=function(object,h) {
bilan_lot<-object
Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r 2016-08-24 19:57:35 UTC (rev 179)
+++ pkg/stacomir/R/Bilan_poids_moyen.r 2016-08-25 15:05:18 UTC (rev 180)
@@ -9,33 +9,25 @@
#' Bilan_poids_moyen class The objective is to calculate mean weight of glass
#' eel which are counted from weight measurements and to reintegrate weight to
#' number coefficients
-#'
-#'
+#' #'
#' @include RefCoe.r
#' @note We have also tools available to import glass eel measurement from
#' experimental fishing in the estuary For the charge method dates for the
#' request are from august to august (a glass eel season)
-#' @section Slots: \describe{ \item{list("data")}{Object of class
-#' \code{"data.frame"} data for bilan lot }\item{:}{Object of class
-#' \code{"data.frame"} data for bilan lot } \item{list("dc")}{Object of class
-#' \code{"RefDC"} refDC an instantiation of the counting device
-#' class}\item{:}{Object of class \code{"RefDC"} refDC an instantiation of the
-#' counting device class} \item{list("anneedebut")}{Object of class
-#' \code{"RefAnnee"} refAnnee allows to choose year of beginning
-#' }\item{:}{Object of class \code{"RefAnnee"} refAnnee allows to choose year
-#' of beginning } \item{list("anneefin")}{Object of class \code{"RefAnnee"}
-#' refAnnee allows to choose year of ending }\item{:}{Object of class
-#' \code{"RefAnnee"} refAnnee allows to choose year of ending }
-#' \item{list("coe")}{Object of class \code{"RefCoe"} class loading coefficient
+#' @slot data Object of class \code{"data.frame"} data for bilan lot
+#' @slot dc Object of class \code{\link{RefDC-class}}, the counting device
+#' @slot anneedebut Object of class \code{\link{RefAnnee-class}}. refAnnee allows to choose year of beginning
+#' @slot anneefin Object of class \code{\link{RefAnnee-class}}
+#' refAnnee allows to choose last year of the Bilan
+#' @slot coe Object of class \code{\link{RefCoe}} class loading coefficient
#' of conversion between quantity (weights or volumes of glass eel) and numbers
-#' }\item{:}{Object of class \code{"RefCoe"} class loading coefficient of
-#' conversion between quantity (weights or volumes of glass eel) and numbers }
-#' \item{list("liste")}{Object of class \code{"RefListe"} RefListe referential
-#' class choose within a list, here do you want subsamples or not
-#' }\item{:}{Object of class \code{"RefListe"} RefListe referential class
-#' choose within a list, here do you want subsamples or not } }
+#' @slot liste Object of class \code{\link{RefListe}} RefListe referential
+#' class choose within a list, here the choice is wether subsamples or not. Subsamples
+#' in the stacomi database are samples with a non null value for parent sample. Migration
+#' counts are never made on subsamples but those can be integrated to calculate mean weights.
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @seealso Other Bilan Classes \code{\linkS4class{Bilan_carlot}}
+#' @seealso
+#' Other Bilan Classes \code{\linkS4class{Bilan_carlot}}
#' \code{\linkS4class{Bilan_poids_moyen}}
#' \code{\linkS4class{Bilan_stades_pigm}}
#' \code{\linkS4class{Bilan_taille}}
Modified: pkg/stacomir/R/Bilan_stades_pigm.r
===================================================================
--- pkg/stacomir/R/Bilan_stades_pigm.r 2016-08-24 19:57:35 UTC (rev 179)
+++ pkg/stacomir/R/Bilan_stades_pigm.r 2016-08-25 15:05:18 UTC (rev 180)
@@ -8,6 +8,25 @@
#' modeled with gamma functions which use a pigment time calculated from daily
#' temperatures and salinities. The temperatures has a major influence on the
#' glass eel pigment stage evolution.
+#' @slot data (please_describe)
+#' @slot datatempsal (please_describe)
+#' @slot tablestades (please_describe)
+#' @slot phi (please_describe)
+#' @slot dates (please_describe)
+#' @slot Vparm default values for parm from Briand 2005 \code{list(pigment_stage=list("p1"=0.267,"p2"=0.835,"p3"=1.560,"p4"=3.682),
+#' pigmentation=list("teta"=30,"sigma"=40,"sigma2"=-5,"p5"=4.566,
+#' "p6"=8.141,"p7"=0.071,"p8"=0.426))}
+#' @slot dc (please_describe)
+#' @slot stationMesure (please_describe)
+#' @slot horodate (please_describe)
+#' @slot datedebut (please_describe)
+#' @slot datefin (please_describe)
+#' @slot lmax (please_describe)
+#' @slot options (please_describe)
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 180
More information about the Stacomir-commits
mailing list