[Stacomir-commits] r179 - in pkg/stacomir: R inst/config
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Aug 24 21:57:35 CEST 2016
Author: briand
Date: 2016-08-24 21:57:35 +0200 (Wed, 24 Aug 2016)
New Revision: 179
Modified:
pkg/stacomir/R/BilanConditionEnv.r
pkg/stacomir/R/BilanEspeces.r
pkg/stacomir/R/BilanFonctionnementDC.r
pkg/stacomir/R/BilanMigration.r
pkg/stacomir/R/BilanMigrationConditionEnv.r
pkg/stacomir/R/BilanMigrationInterAnnuelle.r
pkg/stacomir/R/BilanMigrationMult.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/data.r
pkg/stacomir/R/fungraph.r
pkg/stacomir/R/fungraph_civelle.r
pkg/stacomir/R/fungraph_env.r
pkg/stacomir/R/funtable.r
pkg/stacomir/R/funtraitement_poids.r
pkg/stacomir/R/interface_BilanMigrationMult.r
pkg/stacomir/R/stacomi.r
pkg/stacomir/R/utilitaires.r
pkg/stacomir/inst/config/stacomi_manual_launch.r
Log:
Further changes, documentation .. for Rcheck
Modified: pkg/stacomir/R/BilanConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanConditionEnv.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/BilanConditionEnv.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -102,8 +102,8 @@
# 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
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
hbilanConditionEnvgraph = function(h,...)
Modified: pkg/stacomir/R/BilanEspeces.r
===================================================================
--- pkg/stacomir/R/BilanEspeces.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/BilanEspeces.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -85,8 +85,8 @@
#' handler du calcul du BilanEspeces
#' realise le calcul du bilan especes, l'ecrit dans l'environnement envir_stacomi
#' traite eventuellement les quantites de lots (si c'est des civelles)
-#' @param h
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
hBilanEspecescalc=function(h,...){
@@ -200,8 +200,8 @@
#' handler du calcul BilanEspeces : traitements
#' appelle les fonctions funstat et funtable pour faire le bilan des migrations
#' dans des fichiers csv
-#' @param h
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
hTableBilanEspeces=function(h,...) {
Modified: pkg/stacomir/R/BilanFonctionnementDC.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDC.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/BilanFonctionnementDC.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -97,8 +97,8 @@
# Compte tenu de la structure des donnees ce n'est pas si simple...
#' Function to create a barchart (lattice) corresponding to the periods
-#' @param h A handler
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @return assigns the data frame \code{periodeDC} allowing to build the lattice graph in the environment envir_stacomi
#'
#' @author cedric.briand
@@ -169,8 +169,8 @@
#' function used for some lattice graph
#'
-#' @param h A handler
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @export
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
funboxDC = function(h,...) {
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/BilanMigration.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -165,8 +165,8 @@
#' handler hBilanMigrationgraph
#' calls the fungraph for BilanMigration and allows the saving of daily and monthly counts in the database
#' @note pb if other than daily value, the time steps have been constrained to daily values for this plot
-#' @param h
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
hbilanMigrationgraph = function(h,...) {
if (exists("bilanMigration",envir_stacomi)) {
Modified: pkg/stacomir/R/BilanMigrationConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanMigrationConditionEnv.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/BilanMigrationConditionEnv.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -55,8 +55,8 @@
#' handler du graphique BilanMigrationConditionEnv
#' realise le calcul du bilan migration avec CE, l'ecrit dans l'environnement envir_stacomi
#' traite eventuellement les quantites de lots (si c'est des civelles)
-#' @param h
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
hbilanMigrationConditionEnvcalc=function(h,...){
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -295,7 +295,7 @@
} else {
# si nul on remplace par jour pour generer le script en dessous
timesplit="jour"
- jour2000=as.Date(trunc.POSIXt(seq.POSIXt(from=strptime("2000-01-01",format='%Y-%m-%d'),
+ jour2000=as.Date(Hmisc::trunc.POSIXt(seq.POSIXt(from=strptime("2000-01-01",format='%Y-%m-%d'),
to=strptime("2000-12-31",format='%Y-%m-%d'), by="day"), digits='days'))
for (j in unique(dat$annee)){
# les jours qui n'ont pas de bilan journalier pour ce jour sont rajoutes avec zero
@@ -430,8 +430,8 @@
ymin="mintab",ymax="maxtab"),fill="grey60",alpha=0.5,size=0.5)
g <- g+geom_crossbar(stat="identity",aes_string(ymin="valeur",ymax="valeur",col="comp"),fatten=2)
#g <- g+scale_x_date(name=paste("mois"),breaks="month",minor_breaks=getvalue(new("Refperiode"),label=date_format("%b"),timesplit))
- #lim=as.POSIXct(c(trunc.POSIXt((min(tmp[tmp$com!="0",timesplit])),"month")-delai,
- # ceil.POSIXt((max(tmp[tmp$com!="0",timesplit])),"month")+delai))
+ #lim=as.POSIXct(c(Hmisc::trunc.POSIXt((min(tmp[tmp$com!="0",timesplit])),"month")-delai,
+ # Hmisc::ceil.POSIXt((max(tmp[tmp$com!="0",timesplit])),"month")+delai))
# pb the limit truncs the value
g <- g+ylab("effectif")
cols <- c("max" = "blue","min" = "red",">=moy" = "darkgreen", "<moy" = "darkorange","0"="grey10")
@@ -550,7 +550,7 @@
g <- g+scale_x_datetime(name=paste("mois"),breaks="month",
minor_breaks=getvalue(new("Refperiode"),timesplit),
labels=date_format("%b"),
- limits=as.POSIXct(c(trunc.POSIXt((min(dat[dat$valeur!=0,timesplit])),"month"),ceil.POSIXt((max(dat[dat$valeur!="0",timesplit])),"month"))))
+ limits=as.POSIXct(c(Hmisc::trunc.POSIXt((min(dat[dat$valeur!=0,timesplit])),"month"),Hmisc::ceil.POSIXt((max(dat[dat$valeur!="0",timesplit])),"month"))))
g <- g+scale_y_continuous(name="Somme des pourcentages annuels de migration par quinzaine")
cols <- grDevices::rainbow(length(levels(dat$annee)))
g <- g+scale_fill_manual(name="annee",values=cols)
Modified: pkg/stacomir/R/BilanMigrationMult.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMult.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/BilanMigrationMult.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -292,8 +292,8 @@
#' handler for graphe method in BilanMigrationMult class
#'
#' internal use
-#' @param h handler
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
hbilanMigrationMult_graph=function(h=null,...){
if (exists("bilanMigrationMult",envir_stacomi)) {
@@ -374,6 +374,7 @@
if (bilanMigrationMult at calcdata[[stringr::str_c("dc_",dc)]][["contient_poids"]]&
taxon=="Anguilla anguilla"&
stade=="civelle") {
+
#----------------------------------
# bilan migration avec poids (civelles
#-----------------------------------------
@@ -386,6 +387,7 @@
dc=dc,
...)
} else {
+
#----------------------------------
# bilan migration standard
#-----------------------------------------
@@ -516,8 +518,8 @@
#' handler for calculations
#'
#' internal use for graphical interface
-#' @param h
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @seealso BilanMigrationMult
hbilanMigrationMultcalc=function(h=null,...){
@@ -530,8 +532,8 @@
#' handler du calcul hBilanMigrationgraph2
#'
#' cumuls de migration au cours du temps
-#' @param h
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
hbilanMigrationMultgraph2 = function(h=null,...) {
if (exists("bilanMigrationMult",envir_stacomi)) {
@@ -546,8 +548,8 @@
#' hanler
#'
#' internal use
-#' @param h
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
hbilanMigrationMultgraph3 = function(h=null,...) {
if (exists("bilanMigrationMult",envir_stacomi)) {
@@ -565,8 +567,8 @@
#' handler function
#'
#' internal use
-#' @param h
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
hTableBilanMigrationMult=function(h=null,...) {
funout("Tableau de sortie \n")
@@ -585,7 +587,7 @@
#' calls functions funstat and funtable to create migration overviews
#' and generate csv and html output in the user data directory
#'
-#' @param ...
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
setMethod("summary",signature=signature(object="BilanMigrationMult"),definition=function(object,...){
@@ -641,8 +643,8 @@
})
#' handler to print the command line
-#' @param h
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
houtBilanMigrationMult=function(h=null,...) {
if (exists("refStades",envir_stacomi)) {
Modified: pkg/stacomir/R/Bilan_carlot.r
===================================================================
--- pkg/stacomir/R/Bilan_carlot.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/Bilan_carlot.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -166,8 +166,8 @@
#' fundensityBilan_carlot uses ggplot2 to draw density plots
#'
#' assigns an object g in envir_stacomi for eventual modification of the plot
-#' @param h
-#' @param ...
+#' @param h A handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
fundensityBilan_carlot = function(h,...) {
@@ -224,7 +224,7 @@
#'
#' funtableBilan_carlot shows a table of results in gdf
#' @param h hanlder passed by the graphical interface
-#' @param ...
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
funtableBilan_carlot = function(h,...) {
Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/Bilan_poids_moyen.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -185,7 +185,7 @@
# graphique des poids moyens en fonction du milieu de l'operation de contrele)
# la date est la date moyenne du lot
-# fonction handler appellees
+
hgra=function(h,...){
p<-qplot(x=date,y=poids_moyen,data=don)
print(p)
Modified: pkg/stacomir/R/Bilan_stades_pigm.r
===================================================================
--- pkg/stacomir/R/Bilan_stades_pigm.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/Bilan_stades_pigm.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -699,9 +699,9 @@
border=NA)
curvsum=curvsum-curv[[strdates[j]]][[k]]$y
}
- segments( x0=as.numeric(as.POSIXct(trunc.POSIXt(dates[j],digits="day"))),
+ segments( x0=as.numeric(as.POSIXct(Hmisc::trunc.POSIXt(dates[j],digits="day"))),
y0=nrow(tablestades)+1,
- x1=as.numeric(as.POSIXct(trunc.POSIXt(dates[j],digits="day"))),
+ x1=as.numeric(as.POSIXct(Hmisc::trunc.POSIXt(dates[j],digits="day"))),
y1=nrow(tablestades)-j+1,
lty=3,
col="gray")
Modified: pkg/stacomir/R/Bilan_taille.r
===================================================================
--- pkg/stacomir/R/Bilan_taille.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/Bilan_taille.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -170,8 +170,8 @@
calcule(h$action)
}
#' Calcule method for BilanTaille
-#' @param h
-#' @param ...
+#' @param h A handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
setMethod("calcule",signature=signature("Bilan_taille"),definition=function(object) {
bilan_taille<-object
@@ -211,7 +211,7 @@
#' fungraphInteract_tail uses the ggplot2usr interface to build the graphes
#' @param h a handler
-#' @param ...
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
fungraphInteract_tail = function(h,...) {
if(!exists(x="bilan_taille",envir=envir_stacomi)) {
@@ -234,8 +234,8 @@
#
#' function used to display a table of the data
-#' @param h
-#' @param ...
+#' @param h a handler
+#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
funtableBilan_tail = function(h,...) {
bilan_taille=charge(bilan_taille)
Modified: pkg/stacomir/R/PasdeTemps.r
===================================================================
--- pkg/stacomir/R/PasdeTemps.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/PasdeTemps.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -1,17 +1,3 @@
-# Nom fichier : PasdeTemps (classe)
-# Projet : controle migrateur
-# Organisme : IAV
-# Auteur : Cedric Briand
-# Contact : cedric.briand"at"eptb-vilaine.fr
-# Date de creation : 31/03/2008 17:21:25
-# Compatibilite :
-# Etat : developpement
-# Description calcul et affichage des pas de temps (classe object)
-#**********************************************************************
-#*
-
-
-
UNE_SECONDE = as.difftime(c("0:0:1")) ;
UNE_MINUTE = 60 * UNE_SECONDE ;
DIX_MINUTES = 10 * UNE_MINUTE ;
@@ -95,7 +81,7 @@
setClass(Class="PasDeTemps",representation=
representation(dateDebut="POSIXlt",stepDuration="numeric",nbStep="numeric",noPasCourant="integer"),
validity=validite_PasDeTemps,
- prototype=prototype(dateDebut=as.POSIXlt(trunc.POSIXt(Sys.time(),"year")),
+ prototype=prototype(dateDebut=as.POSIXlt(Hmisc::trunc.POSIXt(Sys.time(),"year")),
stepDuration=as.numeric(86400),
nbStep=as.numeric(1),
noPasCourant=as.integer(0) ) )
@@ -177,7 +163,7 @@
CurrentDateDebut=object at dateDebut+ object at stepDuration*object at noPasCourant
# bug cht heure
if (object at stepDuration==86400) {
- CurrentDateDebut=round.POSIXt(CurrentDateDebut,"days")
+ CurrentDateDebut=Hmisc::round.POSIXt(CurrentDateDebut,"days")
}
return(CurrentDateDebut)
})
@@ -191,7 +177,7 @@
CurrentDateFin=object at dateDebut+ object at stepDuration*(object at noPasCourant+as.integer(1))
# bug cht heure
if (object at stepDuration==86400) {
- CurrentDateFin=round.POSIXt(CurrentDateFin,"days")
+ CurrentDateFin=Hmisc::round.POSIXt(CurrentDateFin,"days")
}
return(CurrentDateFin)
})
Modified: pkg/stacomir/R/data.r
===================================================================
--- pkg/stacomir/R/data.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/data.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -29,4 +29,19 @@
#' \item{time.sequence}{A time sequence generated for the bilan, used internally by the object}
#' }
#' @keywords data
-"bMM_Arzal"
\ No newline at end of file
+"bMM_Arzal"
+
+#' Messages
+#'
+#' In english
+#'
+#'
+#' @keywords data
+"msg"
+
+#' Working environment for stacomiR created when launching stacomi()
+#'
+#' This is where the graphical interface stores its objects
+#' try \code{ls{envir=envir_stacomi)}
+#' @keywords environment
+"envir_stacomi"
\ No newline at end of file
Modified: pkg/stacomir/R/fungraph.r
===================================================================
--- pkg/stacomir/R/fungraph.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/fungraph.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -5,12 +5,15 @@
#'
#' @usage fungraph(bilanMigration, tableau, time.sequence, taxon, stade, dc,...)
#' @param bilanMigration An object of class \code{\linkS4class{BilanMigration}}
-#' @param table=tableau A data frame with the results
+#' @param table=tableau A data frame with the with the following columns : No.pas,debut_pas,fin_pas,
+#' ope_dic_identifiant,lot_tax_code,lot_std_code,type_de_quantite,MESURE,CALCULE,
+#' EXPERT,PONCTUEL,Effectif_total,taux_d_echappement,coe_valeur_coefficient
+#' @note this function is intended to be called from the plot method in BilanMigrationMult and BilanMigration
#' @param time.sequence A vector POSIXt
#' @param taxon The species
#' @param stade The stage
#' @param dc The DC
-#' @param ... other parameters passed but not used
+#' @param ... other parameters passed from the plot method to the matplot function
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
fungraph=function(bilanMigration,tableau,time.sequence,taxon,stade,dc=NULL,...){
#mat <- matrix(1:6,3,2)
Modified: pkg/stacomir/R/fungraph_civelle.r
===================================================================
--- pkg/stacomir/R/fungraph_civelle.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/fungraph_civelle.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -11,7 +11,8 @@
#' @param time.sequence a vector POSIXt
#' @param taxon the species
#' @param stade the stage
-#' @param dc the dc, default to null, only necessary for \code{\linkS4class{BilanMigrationMult}}
+#' @param dc the counting device, default to null, only necessary for \code{\linkS4class{BilanMigrationMult}}
+#' @param ... additional parameters passed from the plot method to plot
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
fungraph_civelle=function(bilanMigration,table,time.sequence,taxon,stade,dc=null,...){
# calcul des variables
Modified: pkg/stacomir/R/fungraph_env.r
===================================================================
--- pkg/stacomir/R/fungraph_env.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/fungraph_env.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -1,11 +1,3 @@
-# Nom fichier : fungraph_env.R
-
-
-
-
-
-
-
#' Function for class BilanMigrationEnv drawing both the response of
#' environment variables...
#'
Modified: pkg/stacomir/R/funtable.r
===================================================================
--- pkg/stacomir/R/funtable.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/funtable.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -1,12 +1,14 @@
-#' function to print and save statistics in .csv and .html formats
-#' @param tableau
-#' @param time.sequence
-#' @param taxon
-#' @param stade
-#' @param DC
-#' @param resum
+#' function to print and save statistics in .csv and .html formats for BilanMigration and BilanMigrationMult class
+#' @param tableau A table with the following columns : No.pas,debut_pas,fin_pas,
+#' ope_dic_identifiant,lot_tax_code,lot_std_code,type_de_quantite,MESURE,CALCULE,
+#' EXPERT,PONCTUEL,Effectif_total,taux_d_echappement,coe_valeur_coefficient
+#' @note this function is intended to be called from within the summary method
+#' @param time.sequence Passed from BilanMigration or BilanMigrationMult
+#' @param taxon Taxa
+#' @param stade The Stage
+#' @param DC The counting device
+#' @param resum A summary table generated by funstat
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
funtable=function(tableau,time.sequence,taxon,stade,DC,resum){
annee=unique(strftime(as.POSIXlt(time.sequence),"%Y"))
path1=file.path(path.expand(get("datawd",envir=envir_stacomi)),paste(DC,"_",taxon,"_",stade,"_",annee,".csv",sep=""),fsep ="/")
Modified: pkg/stacomir/R/funtraitement_poids.r
===================================================================
--- pkg/stacomir/R/funtraitement_poids.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/funtraitement_poids.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -1,17 +1,7 @@
-# Nom fichier : funtraitement_poids
-# Projet : calmig/prog/fonctions
-# Organisme : IAV/CSP
-# Auteur : Cedric Briand
-# Contact : cedric.briand"at"eptb-vilaine.fr
-# Date de creation : 17 mai 2004
-# Compatibilite : R 2.8.0
-# Etat : OK
-# Description tansformation des donnees de poids en nombre
-
#' 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 A table passed BilanMigration
+#' @param time.sequence Time sequence passed from BilanMigration
#' @return tableau
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
Modified: pkg/stacomir/R/interface_BilanMigrationMult.r
===================================================================
--- pkg/stacomir/R/interface_BilanMigrationMult.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/interface_BilanMigrationMult.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -37,7 +37,7 @@
# getStockIcons()
toolbarlist = list(
Calc=gWidgets::gaction(handler=hbilanMigrationMultcalc, action=bilanMigrationMult, icon="new", label="calcul", tooltip=get("msg",envir=envir_stacomi)$interface_BilanMigration.2),
- Graph=gWidgets::gaction(handler=hbilanMigrationMult_graphe, icon="graph", label="graph", tooltip=get("msg",envir=envir_stacomi)$interface_BilanMigration.3),
+ Graph=gWidgets::gaction(handler=hbilanMigrationMult_graph, icon="graph", label="graph", tooltip=get("msg",envir=envir_stacomi)$interface_BilanMigration.3),
Graph2=gWidgets::gaction(handler=hbilanMigrationMultgraph2, icon="graph2", label="grcum", tooltip=get("msg",envir=envir_stacomi)$interface_BilanMigration.4),
Graph3=gWidgets::gaction(handler=hbilanMigrationMultgraph3, icon="gWidgetsRGtk2-barplot", label="gr(tous)", tooltip=get("msg",envir=envir_stacomi)$interface_BilanMigration.3),
Stat=gWidgets::gaction(handler=hTableBilanMigrationMult, icon="dataframe", label="stat", tooltip=get("msg",envir=envir_stacomi)$interface_BilanMigration.5),
Modified: pkg/stacomir/R/stacomi.r
===================================================================
--- pkg/stacomir/R/stacomi.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/stacomi.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -280,7 +280,8 @@
#' @export
stacomi=function(gr_interface=TRUE,login_window=TRUE,pre_launch_test=TRUE){
# first loading of connection and odbc info using chargexml()
- envir_stacomi <<- new.env(parent = emptyenv())
+ envir_stacomi <- new.env(parent = emptyenv())
+ assign("envir_stacomi",envir_stacomi,.GlobalEnv)
assign("gr_interface",gr_interface,envir=envir_stacomi)
assign("pre_launch_test",pre_launch_test,envir=envir_stacomi)
assign("login_window",login_window,envir=envir_stacomi)
@@ -454,9 +455,11 @@
"col.sortie","ggroupboutons","ggroupboutonsbas","groupdate","groupdc","graphes",
"frame_annee","frame_check","frame_choice","frame_par","frame_parqual","frame_parquan",
"frame_std","frame_tax","frame_annee","frame_check","frame_choice",
- "logw","bilan_stades_pigm","usrname","usrpwd","notebook"))
+ "logw","bilan_stades_pigm","usrname","usrpwd","notebook","values","ind"))
# Progressbar
utils::globalVariables(c("progres"))
+# environment
+utils::globalVariables(c("envir_stacomi"))
# reoxygenize fails if data are not loaded
#setwd("F:/workspace/stacomir/branch0.5/stacomir")
#data("bMM_Arzal")
Modified: pkg/stacomir/R/utilitaires.r
===================================================================
--- pkg/stacomir/R/utilitaires.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/R/utilitaires.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -1,189 +1,3 @@
-# Nom fichier : utilitaires.R
-# Projet : stacomiR
-
-
-#############################################
-# functions copied from Hmisc
-#############################################
-
-
-
-
-
-
-#' monthDays function imported from depuis Hmisc that cannot be loaded for
-#' reasons of compatibility with xtable
-#'
-#' monthDays function imported from depuis Hmisc
-#'
-#'
-#' @param time A POSIXt or Date object describing the month or year in question
-#' @author Charles Dupont
-monthDays<-
- function (time)
-{
- time <- as.POSIXlt(time)
- time$mday[] <- time$sec[] <- time$min <- time$hour <- 0
- time$mon <- time$mon + 1
- return(as.POSIXlt(as.POSIXct(time))$mday)
-}
-#' round.POSIXT function imported from Hmisc that cannot be loaded
-#' @param x
-#' @param digits
-#' @return a rounded time value
-#' @author Charles Dupont
-round.POSIXt<-function (x, digits = c("secs", "mins", "hours", "days", "months",
- "years"),...)
-{
- if (is.numeric(digits) && digits == 0) digits <- "secs"
- units <- match.arg(digits)
- month.length <- monthDays(x)
- x <- as.POSIXlt(x)
- if (length(x$sec) > 0)
- switch(units, secs = {
- x$sec <- x$sec
- }, mins = {
- x$sec <- x$sec + 30
- }, hours = {
- x$sec <- 0
- x$min <- x$min + 30
- }, days = {
- x$sec <- 0
- x$min <- 0
- x$hour <- x$hour + 12
- isdst <- x$isdst <- -1
- }, months = {
- x$sec <- 0
- x$min <- 0
- x$hour <- 0
- x$mday <- x$mday + trunc(monthDays(x)/2)
- isdst <- x$isdst <- -1
- }, years = {
- x$sec <- 0
- x$min <- 0
- x$hour <- 0
- x$mday <- 0
- x$mon <- x$mon + 6
- isdst <- x$isdst <- -1
- })
- return(trunc(as.POSIXct(x), digits = units))
-}
-
-
-
-
-#' trunc.POSIXt function copied from Hmisc that cannot be
-#' loaded in Rforge
-#'
-#'
-#' @param x Date to be floored, ceilinged, truncated, or rounded
-#' @param digits Unit to that is is rounded up or down to, called digit for
-#' compatibility with round or trunc generic method
-#' @param \dots Further arguments to be passed to or from other methods
-#' @return An object of class POSIXlt.
-#' @author Charles Dupont
-trunc.POSIXt<-function (x, digits = c("secs", "mins", "hours", "days", "months",
- "years"), ...)
-{
- #UseMethod("trunc.POSIXt")
- units <- match.arg(digits)
- x <- as.POSIXlt(x)
- isdst <- x$isdst
- if (length(x$sec) > 0)
- switch(units, secs = {
- x$sec <- trunc(x$sec)
- }, mins = {
- x$sec <- 0
- }, hours = {
- x$sec <- 0
- x$min <- 0
- }, days = {
- x$sec <- 0
- x$min <- 0
- x$hour <- 0
- isdst <- x$isdst <- -1
- }, months = {
- x$sec <- 0
- x$min <- 0
- x$hour <- 0
- x$mday <- 1
- isdst <- x$isdst <- -1
- }, years = {
- x$sec <- 0
- x$min <- 0
- x$hour <- 0
- x$mday <- 1
- x$mon <- 0
- isdst <- x$isdst <- -1
- })
- x <- as.POSIXlt(as.POSIXct(x))
- if (isdst == -1) {
- x$isdst <- -1
- }
- return(x)
-}
-#' ceil.POSIXT function imported from depuis Hmisc that cannot be loaded
-#'
-#'
-#' @param x A POSIXt
-#' @param digits
-#' @return a truncated time value
-#' @author Charles Dupont
-ceil.POSIXt<-function (x, digits = c("secs", "mins", "hours", "days", "months",
- "years"), ...)
-{
- units <- match.arg(digits)
- x <- as.POSIXlt(x)
- isdst <- x$isdst
- if (length(x$sec) > 0 && x != trunc.POSIXt(x, digits = units)) {
- switch(units, secs = {
- x$sec <- ceiling(x$sec)
- }, mins = {
- x$sec <- 0
- x$min <- x$min + 1
- }, hours = {
- x$sec <- 0
- x$min <- 0
- x$hour <- x$hour + 1
- }, days = {
- x$sec <- 0
- x$min <- 0
- x$hour <- 0
- x$mday <- x$mday + 1
- isdst <- x$isdst <- -1
- }, months = {
- x$sec <- 0
- x$min <- 0
- x$hour <- 0
- x$mday <- 1
- x$mon <- x$mon + 1
- isdst <- x$isdst <- -1
- }, years = {
- x$sec <- 0
- x$min <- 0
- x$hour <- 0
- x$mday <- 1
- x$mon <- 0
- x$year <- x$year + 1
- isdst <- x$isdst <- -1
- })
- x <- as.POSIXlt(as.POSIXct(x))
- if (isdst == -1) {
- x$isdst <- -1
- }
- }
- return(x)
-}
-
-###########################################
-# functions used by the graphical interface
-#############################################
-
-
-
-
-
-
#' function used to clean the objects whithin the group and the graphes and
#' also elements remaining in the envir_stacomi environment
#'
Modified: pkg/stacomir/inst/config/stacomi_manual_launch.r
===================================================================
--- pkg/stacomir/inst/config/stacomi_manual_launch.r 2016-08-24 18:53:15 UTC (rev 178)
+++ pkg/stacomir/inst/config/stacomi_manual_launch.r 2016-08-24 19:57:35 UTC (rev 179)
@@ -1,20 +1,7 @@
-# Nom fichier : stacomi
-# Projet : controle migrateur
-# Organisme : IAV/ONEMA
-# Auteur : Cedric Briand
-# Contact : cedric.briand"at"eptb-vilaine.fr
-# Date de creation : 11/04/2006 15:51:44
-# Compatibilite : PostgreSQL 8.4
-# R 2.10.1
-# Etat : fonctionne
-# Description interface principale, fonction de lancement
-# chargement des librairies
-#**********************************************************************
-# initiation des parametres en fonctions des utilisateurs
+
rm(list=ls(all=TRUE))
-# les donnees sont stockees dans un fichier xml stocke dans le repertoire par defaut,
-# ce fichier peut etre edite pour modifier des parametres
+
## lancement du programme proprement dit
# if (exists("group")) {rm(group)}
# if (exists("graphes")) {rm(graphes) }
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