[Stacomir-commits] r214 - in pkg/stacomir: . R inst inst/examples inst/examples/01_BilanMigrationMult inst/tests/testthat man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Sep 23 21:32:44 CEST 2016
Author: briand
Date: 2016-09-23 21:32:43 +0200 (Fri, 23 Sep 2016)
New Revision: 214
Added:
pkg/stacomir/inst/examples/
pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R
pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R
pkg/stacomir/inst/examples/bilanMigration_Arzal.R
pkg/stacomir/man/funbarchart1DF.Rd
pkg/stacomir/man/funchartDF.Rd
pkg/stacomir/man/houtDF.Rd
pkg/stacomir/man/print-BilanFonctionnementDF-method.Rd
pkg/stacomir/man/split_per_day.Rd
pkg/stacomir/man/summary-BilanFonctionnementDF-method.Rd
Removed:
pkg/stacomir/examples/
pkg/stacomir/inst/examples/00_BilanMigration/
pkg/stacomir/inst/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R
Modified:
pkg/stacomir/NAMESPACE
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_poids_moyen.r
pkg/stacomir/R/Bilan_stades_pigm.r
pkg/stacomir/R/RefCheckBox.r
pkg/stacomir/R/RefChoix.r
pkg/stacomir/R/RefCoe.r
pkg/stacomir/R/fn_EcritBilanJournalier.r
pkg/stacomir/R/fn_EcritBilanMensuel.r
pkg/stacomir/R/funSousListeBilanMigrationPar.r
pkg/stacomir/R/interface_BilanFonctionnementDF.r
pkg/stacomir/R/stacomi.r
pkg/stacomir/R/utilitaires.r
pkg/stacomir/inst/tests/testthat/test-00stacomir.R
pkg/stacomir/man/BilanFonctionnementDF-class.Rd
pkg/stacomir/man/Bilan_stades_pigm-class.Rd
pkg/stacomir/man/calcule-BilanMigrationConditionEnv-method.Rd
pkg/stacomir/man/charge-BilanFonctionnementDC-method.Rd
pkg/stacomir/man/charge-BilanMigration-method.Rd
pkg/stacomir/man/charge-BilanMigrationMult-method.Rd
pkg/stacomir/man/charge-Bilan_poids_moyen-method.Rd
pkg/stacomir/man/charge-RefCheckBox-method.Rd
pkg/stacomir/man/charge-RefChoix-method.Rd
pkg/stacomir/man/charge-RefCoe-method.Rd
pkg/stacomir/man/fnstade.Rd
pkg/stacomir/man/funbarchartDF.Rd
pkg/stacomir/man/funboxDF.Rd
pkg/stacomir/man/fundist.Rd
pkg/stacomir/man/funtableDF.Rd
pkg/stacomir/man/msg.Rd
pkg/stacomir/man/summary-BilanMigrationMult-method.Rd
Log:
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/NAMESPACE 2016-09-23 19:32:43 UTC (rev 214)
@@ -7,15 +7,12 @@
export(fun_bilanMigrationMult)
export(fun_bilanMigrationMult_Overlaps)
export(fun_char_spe)
-export(funbarchartDF)
-export(funboxDF)
export(funboxplotBilan_carlot)
export(fundensityBilan_carlot)
export(funout)
export(funpointBilan_carlot)
export(funstat)
export(funtableBilan_carlot)
-export(funtableDF)
export(funtraitement_poids)
export(hBilanEspecescalc)
export(hCamembert)
@@ -24,6 +21,7 @@
export(interface_BilanEspeces)
export(messages)
export(mygtkProgressBar)
+export(split_per_day)
export(stacomi)
export(vector_to_listsql)
exportClasses(BilanConditionEnv)
@@ -49,7 +47,6 @@
exportMethods(print)
exportMethods(summary)
exportMethods(supprime)
-import(Hmisc)
import(RColorBrewer)
import(RGtk2)
import(RODBC)
Modified: pkg/stacomir/R/BilanFonctionnementDC.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDC.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/BilanFonctionnementDC.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -72,7 +72,6 @@
#' used by the graphical interface to retreive the objects of Referential classes
#' assigned to envir_stacomi
#' @param object 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
Modified: pkg/stacomir/R/BilanFonctionnementDF.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDF.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/BilanFonctionnementDF.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -25,7 +25,7 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
#' @concept Bilan Object
-#' @examples examples/03_BilanFonctionnementDF/bilanFonctionnementDF_example.R
+#' @examples inst/examples/bilanFonctionnementDF_example.R
#' @export
setClass(Class="BilanFonctionnementDF",
representation= representation(data="data.frame",
@@ -281,7 +281,7 @@
mypalette1<-c("#1B9E77","#AE017E","orange", RColorBrewer::brewer.pal(12,"Paired"))
# creation d'un graphique vide
if (is.null(title)) title<-""
- plot( graphdate(time.sequence),
+ plot(graphdate(time.sequence),
seq(0,1,length.out=length(time.sequence)),
xlim=c(debut,fin),
type= "n",
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/BilanMigration.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -26,7 +26,7 @@
#' \code{\linkS4class{BilanMigrationInterAnnuelle}},
#' \code{\linkS4class{BilanMigrationPar}}
#' @concept Bilan Object
-#' @example examples/02_BilanMigration/bilanMigration_Arzal.R
+#' @example inst/examples/bilanMigration_Arzal.R
#' @export
setClass(Class="BilanMigration",
representation=
@@ -128,6 +128,7 @@
#'
#' fills also the data slot by the connect method
#' @param object An object of class \code{\link{BilanMigration-class}}
+#' @param silent Should the program be returning messages
#' @return An object of class \link{BilanMigration-class} with slots filled by user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
@@ -325,9 +326,9 @@
} else {
funout(get("msg",envir_stacomi)$BilanMigration.5,arret=TRUE)
}
- #§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§
+ ################################################################
# standard plot
- #§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§
+ ################################################################
if (plot.type=="standard"){
if (!silent) print("plot type standard")
if (!silent) funout(get("msg",envir_stacomi)$BilanMigration.9)
@@ -394,9 +395,9 @@
if (database_expected) fn_EcritBilanJournalier(bilanMigration,silent)
} # end is.null(data)
- #§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§
+ ################################################################
# step plot
- #§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§
+ ################################################################
} else if (plot.type=="step"){
taxon= as.character(bilanMigration at taxons@data$tax_nom_latin)
stade= as.character(bilanMigration at stades@data$std_libelle)
Modified: pkg/stacomir/R/BilanMigrationConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanMigrationConditionEnv.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/BilanMigrationConditionEnv.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -70,7 +70,7 @@
#' @param object An object of class \code{\link{BilanMigrationConditionEnv-class}}
#' @param ... additional parameters
-#' @return \code{\link{BilanMigrationEnv-class}}
+#' @return \code{\link{BilanMigrationConditionEnv-class}}
#' @export
setMethod("calcule",signature=signature("BilanMigrationConditionEnv"),definition=function(object,...){
# le chargement de bilanMigration utilise la methode calcule de BilanMigration
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -119,7 +119,7 @@
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
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="")
- invisible(capture_output(requete<-stacomirtools::connect(requete)))
+ invisible(utils::capture.output(requete<-stacomirtools::connect(requete)))
return(invisible(NULL))
}
Modified: pkg/stacomir/R/BilanMigrationMult.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMult.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/BilanMigrationMult.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -25,7 +25,7 @@
#' 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
+#' @example inst/examples/bilanMigrationMult_Arzal.R
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
setClass(Class="BilanMigrationMult",
representation=
@@ -64,9 +64,11 @@
#'
#' Used by the graphical interface to collect and test objects in the environment envir_stacomi,
#' fills also the data slot by the connect method
+#' @param object An object of class \link{BilanMigrationMult-class}
+#' @param silent Default FALSE, if TRUE the program should no display messages
#' @return BilanMigrationMult with slots filled by user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-setMethod("charge",signature=signature("BilanMigrationMult"),definition=function(object,...){
+setMethod("charge",signature=signature("BilanMigrationMult"),definition=function(object,silent=FALSE){
bilanMigrationMult<-object
if (exists("refDC",envir_stacomi)) {
bilanMigrationMult at dc<-get("refDC",envir_stacomi)
Modified: pkg/stacomir/R/BilanMigrationPar.r
===================================================================
--- pkg/stacomir/R/BilanMigrationPar.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/BilanMigrationPar.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -129,9 +129,6 @@
stopifnot(validObject(bilanMigrationPar, test=TRUE))
funout(get("msg",envir=envir_stacomi)$BilanMigrationPar.1)
- # save(bilanMigrationPar,file="EXAMPLES/devt.Rdata")
- #undebug(funSousListeBilanMigrationPar)
- # debug(funSousListeBilanMigrationPar)
if (bilanMigrationPar at parquan@data$par_nom=="aucune" & bilanMigrationPar at parqual@data$par_nom=="aucune") {
funout(get("msg",envir=envir_stacomi)$BilanMigrationPar.2,arret=TRUE)}
res<-funSousListeBilanMigrationPar(bilanMigrationPar=bilanMigrationPar)
Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/Bilan_poids_moyen.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -100,11 +100,11 @@
# Cette methode permet de verifier que les boites ont ete cliquees et va chercher les
# objects qui sont colles dans l'environnement envir_stacomi de l'interface
#' charge method for Bilan_poids_moyen class
-#' @param h a handler
+#' @param object An object of class \link{Bilan_poids_moyen-class}
#' @return Bilan_poids_moyen with slots filled with user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
-setMethod("charge",signature=signature("Bilan_poids_moyen"),definition=function(object,h) {
+setMethod("charge",signature=signature("Bilan_poids_moyen"),definition=function(object) {
if (exists("refliste",envir_stacomi)) {
object at liste<-get("refliste",envir_stacomi)
} else {
Modified: pkg/stacomir/R/Bilan_stades_pigm.r
===================================================================
--- pkg/stacomir/R/Bilan_stades_pigm.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/Bilan_stades_pigm.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -53,7 +53,7 @@
#' glass eel Anguilla anguilla pigmentation development. J Fish Biol, 67,
#' 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://www.eptb-vilaine.fr/site/index.php/les-migrateurs/documents/publications-scientifiques/46-publications-migrateurs/60-dynamique-de-population-et-de-migration-des-civelles-en-estuaire-de-vilaine}
#' @examples
#' #' showClass("Bilan_stades_pigm")
#' @export
@@ -351,7 +351,7 @@
#' glass eel Anguilla anguilla pigmentation development. J Fish Biol, 67,
#' 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://www.eptb-vilaine.fr/site/index.php/les-migrateurs/documents/publications-scientifiques/46-publications-migrateurs/60-dynamique-de-population-et-de-migration-des-civelles-en-estuaire-de-vilaine}
fnstade<-function(par1, par2=NULL,phicum,phidates,VB=FALSE,neg=TRUE,lmax=1){
if (neg){
phidates=as.numeric(as.POSIXct(strptime(phidates,format="%Y-%m-%d")))
@@ -426,8 +426,9 @@
#' @examples
#' \dontrun{
#' 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
+#' #below param for briand et al.,2005 pigmentation function in glass eel
+#' #parameters for gamma functions describing changes from stage to stage
+#' Vparm$pigment_stage$p1<-0.267
#' Vparm$pigment_stage$p2<-0.835
#' Vparm$pigment_stage$p3<-1.56
#' Vparm$pigment_stage$p4<-3.682
@@ -441,8 +442,10 @@
#' fundist(Vparm,seq(0,10, length.out=10000),graph=FALSE,lmax=1)
#' fundist(Vparm,seq(0,10, length.out=10000),graph=TRUE,lmax=1)
#' 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")
+#' 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)
@@ -738,7 +741,7 @@
}
if (graphstades) {
# stades cumules calcul necessaire pour points et graphique time.sequences
- # le graphique ne supporte pas plusieurs echantillons a la même date d'ou le choice
+ # le graphique ne supporte pas plusieurs echantillons a la meme date d'ou le choice
graphics::par("mar"=c(2, 4, 3, 2)+ 0.1)
surface(dates,tablestades,couleur=grDevices::gray(5:1/6),ordre=c(1,2,3,4,5),
Modified: pkg/stacomir/R/RefCheckBox.r
===================================================================
--- pkg/stacomir/R/RefCheckBox.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/RefCheckBox.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -28,7 +28,11 @@
prototype=prototype(title="liste de choice",labels="choice",checked=FALSE))
#' Loading method for ReCheckBox referential objects
-#' @return An S4 object of class RefCheckBox
+#' @param object An object of class \link{ReCheckBox-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}
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
#' \dontrun{
Modified: pkg/stacomir/R/RefChoix.r
===================================================================
--- pkg/stacomir/R/RefChoix.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/RefChoix.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -35,6 +35,7 @@
#' @return An S4 object of class RefChoix
#' @param object An object of class RefChoix
#' @param vecteur A vector of name, see example code.
+#' @param label Labels for the choices
#' @param selected An integer indicating which object is selected at launch
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
Modified: pkg/stacomir/R/RefCoe.r
===================================================================
--- pkg/stacomir/R/RefCoe.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/RefCoe.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -40,6 +40,7 @@
#'
#'
#' The slots datedebut and datefin have to be filled before using charge
+#' @param object An object of class \link{RefCoe-class}
#' @return Object of class RefCoe
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
Modified: pkg/stacomir/R/fn_EcritBilanJournalier.r
===================================================================
--- pkg/stacomir/R/fn_EcritBilanJournalier.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/fn_EcritBilanJournalier.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -71,7 +71,6 @@
zz=i/nrow(t_bilanmigrationjournalier_bjo)
progress_bar$setFraction(zz)
progress_bar$setText(sprintf("%d%% progression",round(100*zz)))
- # TODO verifier si nécessaire ci dessous
RGtk2::gtkMainIterationDo(FALSE)
# utils::setWinProgressBar(progres,
# zz,
@@ -86,7 +85,7 @@
"bjo_dis_identifiant,bjo_tax_code,bjo_std_code,bjo_annee,bjo_jour,bjo_valeur,bjo_labelquantite,bjo_horodateexport,bjo_org_code)",
" VALUES " ,"('",paste(t_bilanmigrationjournalier_bjo[i,],collapse="','"),"');",sep="")
# to avoid printing character use of invisible (capture_output(
- invisible(capture_output(stacomirtools::connect(requete)))
+ invisible(utils::capture.output(stacomirtools::connect(requete)))
} # end for
if (!silent){
@@ -146,7 +145,7 @@
"bjo_dis_identifiant,bjo_tax_code,bjo_std_code,bjo_annee,bjo_jour,bjo_valeur,bjo_labelquantite,bjo_horodateexport,bjo_org_code)",
" VALUES " ,
"('",paste(t_bilanmigrationjournalier_bjo[i,],collapse="','"),"');",sep="")
- invisible(capture_output(stacomirtools::connect(requete)))
+ invisible(utils::capture.output(stacomirtools::connect(requete)))
} # end for
if (!silent) funout(paste(get("msg",envir=envir_stacomi)$fn_EcritBilanJournalier.5,"\n"))
taxon= as.character(bilanMigration at taxons@data$tax_nom_latin)
Modified: pkg/stacomir/R/fn_EcritBilanMensuel.r
===================================================================
--- pkg/stacomir/R/fn_EcritBilanMensuel.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/fn_EcritBilanMensuel.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -36,7 +36,7 @@
requete at sql=paste("INSERT INTO ",get("sch",envir=envir_stacomi),"t_bilanMigrationMensuel_bme (",
"bme_dis_identifiant,bme_tax_code,bme_std_code,bme_annee,bme_labelquantite,bme_valeur,bme_mois,bme_horodateexport,bme_org_code)",
" VALUES ('",paste(t_bilanmigrationmensuel_bme[i,],collapse="','"),"');",sep="")
- invisible(capture_output(stacomirtools::connect(requete)))
+ invisible(utils::capture.output(stacomirtools::connect(requete)))
} # end for
if (!silent) funout(paste(get("msg",envir=envir_stacomi)$fn_EcritBilanMensuel.1,"\n"))
} # end function
Modified: pkg/stacomir/R/funSousListeBilanMigrationPar.r
===================================================================
--- pkg/stacomir/R/funSousListeBilanMigrationPar.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/funSousListeBilanMigrationPar.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -10,18 +10,11 @@
# Notes de devt Dans les requetes recuperer valeurs quan ou valeur qual ou l'interrogation croisee (trois cas differents)
#
#**********************************************************************
-#*
-#* Modifications :
-# load(file="EXAMPLES/devt.Rdata")
-#@param bilanMigrationPar
-#@return une liste de deux dataframe
-
-
#' funSousListeBilanMigrationPar
#'
#' see \code{funSousListeBilanMigration} This function is similar to
Modified: pkg/stacomir/R/interface_BilanFonctionnementDF.r
===================================================================
--- pkg/stacomir/R/interface_BilanFonctionnementDF.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/interface_BilanFonctionnementDF.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -43,7 +43,6 @@
Quit = aQuit)
add(group, gmenu(toolbarlist))
- add(group,gbutton(text = "graph", handler = function(h,...){X11()}))
gWidgets::addSpring(group)
dev.new()
}
\ No newline at end of file
Modified: pkg/stacomir/R/stacomi.r
===================================================================
--- pkg/stacomir/R/stacomi.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/stacomi.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -144,7 +144,7 @@
con=new("ConnectionODBC")
con at baseODBC=get("baseODBC",envir=envir_stacomi)
e=expression(con<-connect(con))
- con=tryCatch(eval(e),error=get("msg",envir=envir_stacomi)$interface_graphique_log.7) #finally=odbcClose(con at connection)clause inutile car si �a plante la connection n'est pas ouverte
+ con=tryCatch(eval(e),error=get("msg",envir=envir_stacomi)$interface_graphique_log.7)
test<-con at etat==get("msg",envir=envir_stacomi)$ConnectionODBC.6
odbcCloseAll()
}
@@ -268,7 +268,6 @@
#' @import methods
#' @import stacomirtools
#' @import RODBC
-#' @import Hmisc
#' @import RGtk2
#' @import dplyr
#' @importFrom intervals Intervals
@@ -296,7 +295,6 @@
#' @importFrom lubridate round_date
#' @importFrom lubridate floor_date
#' @importFrom lubridate %m+%
-#' @importFrom lubridate %d+%
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
#'
@@ -316,7 +314,7 @@
# first loading of connection and odbc info using chargexml()
envir_stacomi <- new.env(parent = emptyenv())
assign("envir_stacomi",envir_stacomi,.GlobalEnv)
- # trois variables passées à interface graphique via envir_stacomi :
+ # trois variables passees a interface graphique via envir_stacomi :
assign("gr_interface",gr_interface,envir=envir_stacomi)
assign("database_expected",database_expected,envir=envir_stacomi)
assign("login_window",login_window,envir=envir_stacomi)
@@ -452,8 +450,8 @@
menubarlist[[msg$interface_graphique_menu.3]]$lang$handler = hlang
menubarlist[[msg$interface_graphique_menu.3]]$lang$icon="dialog-info"
gWidgets::add(win, gmenu(menubarlist))
- ggrouptotal<- gWidgets::ggroup(horizontal=FALSE) # celui ci empile les autres de haut en bas
- # gsortie est au dessus de la fenêtre
+ ggrouptotal<- gWidgets::ggroup(horizontal=FALSE) # this one stacks from bottom to up
+ # gsortie is above the window
assign("ggrouptotal",ggrouptotal,envir=.GlobalEnv)
gWidgets::add(win,ggrouptotal)
@@ -485,8 +483,12 @@
"quantite_EXPERT","quantite_MESURE","quantite_PONCTUEL","libelle","null","type",
'val_libelle','lot_effectif','bilan_stades_pigm','ope_date_debut','p','g','poids_moyen',
'taxon_stades,"jour',"valeur","mintab","maxtab","moyenne","jour","total_annuel",
- "taxon_stades","time.sequence","sum","variable"))
+ "taxon_stades","time.sequence","sum","variable","duree","Hdeb","Hfin","per_tar_code"))
+# variable used by dplyr
+utils::globalVariables(c("n0","newid","xmin","xmax"))
+
+
# Assignation in global environment for the use of gWidget interface (there is no way arround this)
utils::globalVariables(c("win","group","nbligne","ggrouptotal","ggrouptotal1","gSortie",
"col.sortie","ggroupboutons","ggroupboutonsbas","groupdate","groupdc","graphes",
Modified: pkg/stacomir/R/utilitaires.r
===================================================================
--- pkg/stacomir/R/utilitaires.r 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/R/utilitaires.r 2016-09-23 19:32:43 UTC (rev 214)
@@ -51,10 +51,10 @@
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
fun_char_spe<-function(text){
- text=gsub("\u00e9","e",text) #é
- text=gsub("\u00e8","e",text) #è
- text=gsub("\u00ea","e",text) #ê
- text=gsub("\u00e0","a",text) #à
+ text=gsub("\u00e9","e",text)
+ text=gsub("\u00e8","e",text)
+ text=gsub("\u00ea","e",text)
+ text=gsub("\u00e0","a",text)
return(text)}
@@ -252,17 +252,19 @@
#' @return A data frame with four new columns, Hmin (hour min), Hmax (hmax), xmin (day) and xmax (next day),
#' and new rows
#' @author cedric.briand
-#' @example
-#' datatemp<-structure(list(per_dis_identifiant = c(1L, 1L, 1L), per_date_debut = structure(c(1420056600,
-#' 1420071000, 1420081200), class = c("POSIXct", "POSIXt"), tzone = ""),
-#' per_date_fin = structure(c(1420071000, 1420081200, 1421000000
-#' ), class = c("POSIXct", "POSIXt"), tzone = ""), per_commentaires = c("fonct calcul",
-#' "fonct calcul", "fonct calcul"), per_etat_fonctionnement = c(1L,
-#' 0L, 0L), per_tar_code = 1:3, libelle = c("Fonc normal", "Arr ponctuel",
-#' "Arr maint")), .Names = c("per_dis_identifiant", "per_date_debut",
-#' "per_date_fin", "per_commentaires", "per_etat_fonctionnement",
-#' "per_tar_code", "libelle"), row.names = c(NA, 3L), class = "data.frame")
-#'newdf<-split_per_day(data=datatemp,horodatedebut="per_date_debut",horodatefin="per_date_fin")
+#' @examples
+#' datatemp<-structure(list(per_dis_identifiant = c(1L, 1L, 1L),
+#' per_date_debut = structure(c(1420056600,
+#' 1420071000, 1420081200), class = c("POSIXct", "POSIXt"), tzone = ""),
+#' per_date_fin = structure(c(1420071000, 1420081200, 1421000000
+#' ), class = c("POSIXct", "POSIXt"), tzone = ""), per_commentaires = c("fonct calcul",
+#' "fonct calcul", "fonct calcul"), per_etat_fonctionnement = c(1L,
+#' 0L, 0L), per_tar_code = 1:3, libelle = c("Fonc normal", "Arr ponctuel",
+#' "Arr maint")), .Names = c("per_dis_identifiant", "per_date_debut",
+#' "per_date_fin", "per_commentaires", "per_etat_fonctionnement",
+#' "per_tar_code", "libelle"), row.names = c(NA, 3L), class = "data.frame")
+#'newdf<-split_per_day(data=datatemp,horodatedebut="per_date_debut",
+#' horodatefin="per_date_fin")
#' @export
split_per_day<-function(data,horodatedebut,horodatefin){
if(!horodatedebut%in%colnames(data)) stop("horodatedebut not in column names for data")
@@ -288,7 +290,7 @@
#replacing rows in data
data[match(data2$newid,data$newid),]<-data2
# now get the sequence of days righly set by adding the number of days to xmin and xmax
- data3<-data%>%filter(n0>0)%>%group_by(id)%>%mutate(xmin=xmin+ as.difftime(rank(newid)-1, unit="days"),
+ data3<-data%>%filter(n0>0)%>%group_by(id)%>%mutate(xmin=xmin+ as.difftime(rank(newid)-1, units="days"),
xmax=xmax+as.difftime(rank(newid)-1, unit="days"))
data[match(data3$newid,data$newid),]<-data3
data<-as.data.frame(data)
Deleted: pkg/stacomir/inst/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R
===================================================================
--- pkg/stacomir/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R 2016-09-01 18:46:49 UTC (rev 187)
+++ pkg/stacomir/inst/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R 2016-09-23 19:32:43 UTC (rev 214)
@@ -1,41 +0,0 @@
-library(stacomiR)
-
-stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
-## launches the application in the command line
-## here an example of loading
-## not run as the program is possibly not installed
-## this example generates the bMM_Arzal dataset
-\dontrun{
- stacomi(gr_interface=FALSE,
- login_window=FALSE,
- pre_launch_test=FALSE)
- bMM_Arzal=new("BilanMigrationMult")
- bMM_Arzal=choice_c(bMM_Arzal,
- dc=c(5,6,12),
- taxons=c("Anguilla anguilla"),
- stades=c("AGG","AGJ","CIV"),datedebut="2011-01-01",datefin="2011-12-31")
- bMM_Arzal<-connect(bMM_Arzal)
-}
-
-
-data("bMM_Arzal")
-# use the following to get the raw data loaded by the connect method
-# not shown there as the database and program might not be installed
-
-#bMM_Arzal<-connect(bMM_Arzal)
-#str(bMM_Arzal at data)
-# calculations
-bMM_Arzal<-calcule(bMM_Arzal,silent=TRUE)
-#Individual plot for all DC, taxon and stage where data present
-#Silent=TRUE to turn off messages
-plot(bMM_Arzal,plot.type="standard",silent=TRUE)
-
-#cumulated migration at the station (all stages and DC grouped)
-plot(bMM_Arzal,plot.type="step")
-#some plots are a mixture of french and english
-#changing the reference table names to english should shift all to english.
-#same for spanish.
-# combined plot for ggplot2
-plot(bMM_Arzal,plot.type="multiple")
-# data will be written in the data directory specified in the stacomi/calcmig.csv file
-summary(bMM_Arzal,silent=TRUE)
Copied: pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R (from rev 213, pkg/stacomir/examples/03_BilanFonctionnementDF/bilanFonctionnementDF_example.R)
===================================================================
--- pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R (rev 0)
+++ pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R 2016-09-23 19:32:43 UTC (rev 214)
@@ -0,0 +1,26 @@
+require(stacomiR)
+stacomi(gr_interface=FALSE,
+ login_window=FALSE,
+ database_expected=FALSE)
+## An example that will work with the database installed only
+\dontrun{
+ bfDF=new("BilanFonctionnementDF")
+ bfDF<-choice_c(bfDF,
+ 1,
+ horodatedebut="2015-01-01",
+ horodatefin="2015-12-31",
+ silent=TRUE)
+ # the times at Arzal are recorded continuously
+ # they are converted to date when a time appears while the hour is changing
+ # hence the following
+ Sys.setenv(TZ='GMT')
+ bfDF<-charge(bfDF)
+ 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")
+}
+
+
+
+
Copied: pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R (from rev 207, pkg/stacomir/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R)
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R (rev 0)
+++ pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R 2016-09-23 19:32:43 UTC (rev 214)
@@ -0,0 +1,45 @@
+library(stacomiR)
+
+stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
+## launches the application in the command line
+## here an example of loading
+## not run as the program is possibly not installed
+## this example generates the bMM_Arzal dataset
+\dontrun{
+ stacomi(gr_interface=FALSE,
+ login_window=FALSE,
+ database_expected=FALSE)
+ bMM_Arzal=new("BilanMigrationMult")
+ bMM_Arzal=choice_c(bMM_Arzal,
+ dc=c(5,6,12),
+ taxons=c("Anguilla anguilla"),
+ stades=c("AGG","AGJ","CIV"),datedebut="2011-01-01",datefin="2011-12-31")
+ bMM_Arzal<-connect(bMM_Arzal)
+}
+
+
+data("bMM_Arzal")
+# use the following to get the raw data loaded by the connect method
+# not shown there as the database and program might not be installed
+
+#bMM_Arzal<-connect(bMM_Arzal)
+#str(bMM_Arzal at data)
+# calculations
+bMM_Arzal<-calcule(bMM_Arzal,silent=TRUE)
+#Individual plot for all DC, taxon and stage where data present
+#Silent=TRUE to turn off messages
+# not run because of multiple graphical devices
+\dontrun{
+plot(bMM_Arzal,plot.type="standard",silent=TRUE)
+}
+#cumulated migration at the station (all stages and DC grouped)
+
+plot(bMM_Arzal,plot.type="step")
+
+#some plots are a mixture of french and english
+#changing the reference table names to english should shift all to english.
+#same for spanish.
+# combined plot for ggplot2
+plot(bMM_Arzal,plot.type="multiple")
+# data will be written in the data directory specified in the stacomi/calcmig.csv file
+summary(bMM_Arzal,silent=TRUE)
Copied: pkg/stacomir/inst/examples/bilanMigration_Arzal.R (from rev 206, pkg/stacomir/examples/02_BilanMigration/bilanMigration_Arzal.R)
===================================================================
--- pkg/stacomir/inst/examples/bilanMigration_Arzal.R (rev 0)
+++ pkg/stacomir/inst/examples/bilanMigration_Arzal.R 2016-09-23 19:32:43 UTC (rev 214)
@@ -0,0 +1,41 @@
+library(stacomiR)
+
+stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
+## launches the application in the command line
+## here an example of loading
+## not run as the program is possibly not installed
+## this example generates the bM_Arzal dataset
+\dontrun{
+ stacomi(gr_interface=FALSE,
+ login_window=FALSE,
+ database_expected=FALSE)
+ bM_Arzal=new("BilanMigration")
+ bM_Arzal=choice_c(bM_Arzal,
+ dc=5,
+ taxons=c("Liza ramada"),
+ stades=c("IND"),
+ datedebut="2015-01-01",
+ datefin="2015-12-31")
+ bM_Arzal<-connect(bM_Arzal)
+}
+
+
+data("bM_Arzal")
+# use the following to get the raw data loaded by the connect method
+# not shown there as the database and program might not be installed
+
+#bM_Arzal<-connect(bM_Arzal)
+#str(bM_Arzal at data)
+# calculations
+bM_Arzal<-calcule(bM_Arzal,silent=TRUE)
+#Individual plot for all DC (standard), taxon and stage where data present
+#silent argument to stop all messages
+# this will also write daily and monthly migration balance to the database,
+# but only if stacomi has been run with argument : database_expected=FALSE
+plot(bM_Arzal,plot.type="standard",silent=TRUE)
+
+#cumulated migration at the station (all stages and DC grouped)
+plot(bM_Arzal,plot.type="step")
+
+# data will be written in the data directory specified in the stacomi/calcmig.csv file
+summary(bM_Arzal,silent=TRUE)
Modified: pkg/stacomir/inst/tests/testthat/test-00stacomir.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2016-09-21 09:51:22 UTC (rev 213)
+++ pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2016-09-23 19:32:43 UTC (rev 214)
@@ -196,15 +196,15 @@
baseODBC$uid=readline(prompt="Enter superuser name: ")
baseODBC$pwd=readline(prompt="Enter superuser password: ")
req at baseODBC<-baseODBC
- req at sql=paste("SELECT
- distinct on (tc.constraint_name) tc.constraint_name, tc.table_name
+ req at sql=paste(stringr::str_c("SELECT
+ distinct on (tc.constraint_name) tc.constraint_name, tc.table_name
FROM
information_schema.table_constraints AS tc
JOIN information_schema.key_column_usage AS kcu
ON tc.constraint_name = kcu.constraint_name
JOIN information_schema.constraint_column_usage AS ccu
ON ccu.constraint_name = tc.constraint_name
- WHERE constraint_type = 'FOREIGN KEY';")
+ WHERE constraint_type = 'FOREIGN KEY' and tc.constraint_schema='",gsub("\\.","",get("sch",envir=envir_stacomi)),"';"))
req<-stacomirtools::connect(req)
result<-req at query
fk<-structure(list(constraint_name = c("c_fk_act_lot_identifiant",
@@ -223,25 +223,23 @@
"c_fk_lot_std_code", "c_fk_lot_tax_code", "c_fk_maa_mal_id",
"c_fk_mac_valeurqualitatifdefaut", "c_fk_mae_mao_id", "c_fk_mae_stm_identifiant",
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 214
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