[Stacomir-commits] r381 - in pkg/stacomir: . R data inst/config inst/examples man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jun 6 22:06:21 CEST 2017
Author: briand
Date: 2017-06-06 22:06:21 +0200 (Tue, 06 Jun 2017)
New Revision: 381
Added:
pkg/stacomir/man/choicemult-Refpar-method.Rd
pkg/stacomir/man/choicemult-Refparqual-method.Rd
Removed:
pkg/stacomir/vignettes/
Modified:
pkg/stacomir/DESCRIPTION
pkg/stacomir/R/BilanAgedemer.r
pkg/stacomir/R/BilanFonctionnementDC.r
pkg/stacomir/R/BilanFonctionnementDF.r
pkg/stacomir/R/BilanMigrationCar.r
pkg/stacomir/R/BilanMigrationInterAnnuelle.r
pkg/stacomir/R/BilanMigrationMult.r
pkg/stacomir/R/BilanMigrationMultConditionEnv.r
pkg/stacomir/R/BilanOperation.r
pkg/stacomir/R/Bilan_poids_moyen.r
pkg/stacomir/R/RefChoix.r
pkg/stacomir/R/RefDC.r
pkg/stacomir/R/RefHorodate.r
pkg/stacomir/R/RefStades.r
pkg/stacomir/R/RefStationMesure.r
pkg/stacomir/R/RefTaxon.r
pkg/stacomir/R/Refpar.r
pkg/stacomir/R/Refparqual.r
pkg/stacomir/R/funSousListeBilanMigrationPar.r
pkg/stacomir/R/fungraph.r
pkg/stacomir/R/utilitaires.r
pkg/stacomir/data/bilAM.rda
pkg/stacomir/data/bilan_adm.rda
pkg/stacomir/data/bmmCE.rda
pkg/stacomir/inst/config/generate_Roxygen2.R
pkg/stacomir/inst/config/generate_data.R
pkg/stacomir/inst/examples/bilanAgedemer_example.R
pkg/stacomir/inst/examples/bilanArgentee_example.R
pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R
pkg/stacomir/inst/examples/bilan_poids_moyen_example.R
pkg/stacomir/inst/examples/bilancarlot_example.R
pkg/stacomir/man/BilanAgedemer-class.Rd
pkg/stacomir/man/BilanArgentee-class.Rd
pkg/stacomir/man/BilanEspeces-class.Rd
pkg/stacomir/man/BilanMigrationCar-class.Rd
pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
pkg/stacomir/man/BilanMigrationMult-class.Rd
pkg/stacomir/man/BilanMigrationMultConditionEnv-class.Rd
pkg/stacomir/man/BilanOperation-class.Rd
pkg/stacomir/man/Bilan_carlot-class.Rd
pkg/stacomir/man/Bilan_poids_moyen-class.Rd
pkg/stacomir/man/calcule-BilanMigrationCar-method.Rd
pkg/stacomir/man/calcule-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/calcule-BilanMigrationMultConditionEnv-method.Rd
pkg/stacomir/man/choice-Refpar-method.Rd
pkg/stacomir/man/choice-Refparqual-method.Rd
pkg/stacomir/man/choice_c-BilanAgedemer-method.Rd
pkg/stacomir/man/choice_c-BilanConditionEnv-method.Rd
pkg/stacomir/man/choice_c-BilanMigrationCar-method.Rd
pkg/stacomir/man/choice_c-BilanMigrationMultConditionEnv-method.Rd
pkg/stacomir/man/choice_c-RefChoix-method.Rd
pkg/stacomir/man/choice_c-RefListe-method.Rd
pkg/stacomir/man/choice_c-RefStades-method.Rd
pkg/stacomir/man/choice_c-RefStationMesure-method.Rd
pkg/stacomir/man/choice_c-RefTextBox-method.Rd
pkg/stacomir/man/choicemult-RefChoix-method.Rd
pkg/stacomir/man/choicemult-RefHorodate-method.Rd
pkg/stacomir/man/colortable.Rd
pkg/stacomir/man/envir_stacomi.Rd
pkg/stacomir/man/fungraph.Rd
pkg/stacomir/man/funout.Rd
pkg/stacomir/man/funtraitementdate.Rd
pkg/stacomir/man/hbmmCEgraph.Rd
pkg/stacomir/man/model-Bilan_poids_moyen-method.Rd
pkg/stacomir/man/mygtkProgressBar.Rd
pkg/stacomir/man/plot-BilanMigrationCar-missing-method.Rd
pkg/stacomir/man/plot-BilanMigrationMult-missing-method.Rd
pkg/stacomir/man/supprime-BilanAgedemer-method.Rd
pkg/stacomir/man/supprime-RefCoe-method.Rd
pkg/stacomir/man/write_database-BilanMigration-method.Rd
pkg/stacomir/man/xtable-BilanMigrationCar-method.Rd
Log:
Changes to pass Rckeck, including assignin almost everything to envir_stacomi
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/DESCRIPTION 2017-06-06 20:06:21 UTC (rev 381)
@@ -6,9 +6,10 @@
person("Marion", "Legrand", role = "aut", email="tableau-salt-loire at logrami.fr"),
person("Timothee", "Besse", role = "aut", email="tableau-ang-loire at logrami.fr"))
Description: Graphical outputs and treatment for a database of fishway
- monitoring. It is a part of the STACOMI open source project developed in France
- by the French Agency for Biodiversity (AFB) institute to centralize data obtained by fishway monitoring.
- Version 0.5.2 is available in French and English.
+ monitoring. It is a part of the STACOMI open source project developed in
+ France by the French Agency for Biodiversity (AFB) institute to centralize
+ data obtained by fishway monitoring. Version 0.5.2 is available in French and
+ English.
License: GPL (>= 2)
Collate:
'create_generic.r'
Modified: pkg/stacomir/R/BilanAgedemer.r
===================================================================
--- pkg/stacomir/R/BilanAgedemer.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/BilanAgedemer.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -34,7 +34,7 @@
#' @family Bilan Objects
#' @keywords classes
#' @example inst/examples/bilanAgedemer_example.R
-#' @aliases BilanAgedemer bilA bilanagedemer bilanAgedeMer BilanAgeDeMer bilan_adm
+#' @aliases BilanAgedemer bilanagedemer bilanAgedeMer BilanAgeDeMer
#' @export
setClass(Class="BilanAgedemer",
representation= representation(
Modified: pkg/stacomir/R/BilanFonctionnementDC.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDC.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/BilanFonctionnementDC.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -191,6 +191,7 @@
mygtkProgressBar(
title=gettext("time in hours",domain="R-stacomiR"),
progress_text=gettext("Working of the counting device",domain="R-stacomiR"))
+ progress_bar<-get("progress_bar",envir=envir_stacomi)
# this function assigns
z=0 # compteur tableau t_periodefonctdispositif_per_mois
for(j in 1:nrow(t_periodefonctdispositif_per)){
Modified: pkg/stacomir/R/BilanFonctionnementDF.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDF.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/BilanFonctionnementDF.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -197,6 +197,7 @@
mygtkProgressBar(
title=gettext("computing ...",domain="R-stacomiR"),
progress_text=gettext("Progress %",domain="R-stacomiR"))
+ progress_bar<-get("progress_bar",envir=envir_stacomi)
# this function assigns
z=0 # compteur tableau t_periodefonctdispositif_per_mois
for(j in 1:nrow(t_periodefonctdispositif_per)){
Modified: pkg/stacomir/R/BilanMigrationCar.r
===================================================================
--- pkg/stacomir/R/BilanMigrationCar.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/BilanMigrationCar.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -18,18 +18,18 @@
#' \code{new("BilanMigrationCar", ...)}. they are loaded by the interface
#' using interface_BilanMigrationCar function.
#' @slot calcdata A "list" of calculated data, filled in by the calcule method
+#' @slot data A \code{data.frame} inherited from \link{Bilan_carlot-class}
+#' @slot dc an object of class \link{RefDC-class} inherited from \link{Bilan_carlot-class}
+#' @slot taxons An object of class \link{RefTaxon-class} inherited from \link{Bilan_carlot-class}
+#' @slot stades An object of class \link{RefStades-class} inherited from \link{Bilan_carlot-class}
+#' @slot horodatedebut An object of class \link{RefHorodate-class} inherited from \link{Bilan_carlot-class}
+#' @slot horodatefin An object of class \link{RefHorodate-class} inherited from \link{Bilan_carlot-class}
+#' @slot par An object of class \link{Refpar-class} inherited from \link{Bilan_carlot-class}
+#' @slot echantillon An object of class \link{RefChoix-class}, vector of choice
#' @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 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}
-#' @slot stades An object of class \link{RefStades-class} inherited from \link{BilanMigration-class}
-#' @slot pasDeTemps An object of class \link{PasDeTempsJournalier-class} inherited from \link{BilanMigration-class}
-#' @slot data A \code{data.frame} inherited from \link{BilanMigration-class}, stores the results
-#' @slot time.sequence An object of class "POSIXct" inherited from \link{BilanMigration-class}
#' @family Bilan Objects
-#' @aliases BilanMigrationMult bilanMigrationMult
+#' @aliases BilanMigrationCar bilanMigrationCar
#' @note program : default two parameter choice, checking box "none" will allow the program to ignore the parameter
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @concept Bilan Object
@@ -406,7 +406,6 @@
#'
#'
#' @param x An object of class BilanMigrationCar
-#' @param y not used there
#' @param plot.type One of "qual", "quant" "crossed" default to qual
#' @param color_parm A named vector for the colors of either parameters (if plot.type=quant) or levels for
#' parameters (if plot.type=qual).
@@ -513,9 +512,15 @@
#' @param caption, see xtable
#' @param label, see xtable
#' @param align, see xtable, overidden if NULL
+#' @param digits, see xtable
+#' @param display see xtable
+#' @param auto see xtable
#' @param ... Additional parameters
#' @export
-setMethod("xtable",signature=signature("BilanMigrationCar"),definition=function(x,caption=NULL, label=NULL,align=NULL,...){
+setMethod("xtable",signature=signature("BilanMigrationCar"),definition=function(x,
+ caption=NULL,
+ label=NULL,
+ align=NULL,...){
bmC<-x
dat=bmC at data
dc=stringr::str_c(bmC at dc@dc_selectionne,collapse=" ")
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -3,7 +3,7 @@
#' When daily bilan are written in the t_bilanjournalier_bjo table by the
#' \link{BilanMigration-class} they can be used by this class to display
#' interannual comparisons of migration. Different charts are produced with different
-#' period grouping. See \link{fn_EcritBilanJournalier} for details about the writing to the
+#' period grouping. See \link{write_database,BilanMigration-method} for details about the writing to the
#' t_bilanjournalier_bjo table.
#'
#' @include RefAnnee.r
Modified: pkg/stacomir/R/BilanMigrationMult.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMult.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/BilanMigrationMult.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -376,7 +376,6 @@
#' \item{plot.type="multiple"}{Method to overlay graphs for BilanMigrationMult (multiple dc/taxa/stage in the same plot)}
#' }
#' @param x An object of class BilanMigrationMult
-#' @param y From the formals but missing
#' @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 silent Stops most messages from being displayed
Modified: pkg/stacomir/R/BilanMigrationMultConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMultConditionEnv.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/BilanMigrationMultConditionEnv.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -12,7 +12,7 @@
#' @author cedric.briand"at"eptb-vilaine.fr marion.legrand"at"logrami.fr
#' @family Bilan Objects
#' @keywords classes
-#' @aliases BilanMigrationMultConditionEnv bilanmigrationmultconditionenv bmmCE
+#' @aliases BilanMigrationMultConditionEnv bilanmigrationmultconditionenv
#' @keywords classes
#' @example inst/examples/bilanMigrationMultConditionEnv_example.R
#' @export
@@ -138,7 +138,7 @@
#' internal method for graphical interface
#' @param h A handler
-hbmmCEgraph = function(h=null,...){
+hbmmCEgraph = function(h=null){
bmmCE<-get("bmmCE",envir_stacomi)
bmmCE<-plot(bmmCE)
return(invisible(NULL))
Modified: pkg/stacomir/R/BilanOperation.r
===================================================================
--- pkg/stacomir/R/BilanOperation.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/BilanOperation.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -19,7 +19,7 @@
#' \code{\linkS4class{BilanMigrationCar}}
#' @concept Bilan Object
#' @keywords classes
-#' @aliases BilanOperation bilanoperation bilanOperation
+#' @aliases BilanOperation
#' @export
setClass(Class="BilanOperation",
representation= representation(data="data.frame",
Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/Bilan_poids_moyen.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -288,7 +288,6 @@
#' @param object An object of class \link{Bilan_poids_moyen-class}
#' @param model.type default "seasonal", "seasonal1","seasonal2","manual".
#' @param silent Default FALSE, if TRUE the program should no display messages
-#' @usage model(object,model.type=c("seasonal","seasonal1","seasonal2","manual"),silent=FALSE)
#' @details
#' Depending on model.type several models are produced
#' \itemize{
Modified: pkg/stacomir/R/RefChoix.r
===================================================================
--- pkg/stacomir/R/RefChoix.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/RefChoix.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -112,13 +112,15 @@
svalue(notebook)<-svalue(notebook)+1
}
}
-
+ group<-get("group",envir=envir_stacomi)
if (!exists("notebook",envir=envir_stacomi)){
notebook <- gnotebook(container=group)
} else {
notebook<-get("notebook",envir=envir_stacomi)
}
- groupchoice<-ggroup(container=notebook, label=gettext("options",domain="R-stacomiR"),horizontal=FALSE)
+ groupchoice<-ggroup(container=notebook,
+ label=gettext("options",domain="R-stacomiR"),
+ horizontal=FALSE)
glabel(object at label,container=groupchoice)
list_libelle=fun_char_spe(object at listechoice)
choice=gradio(items=list_libelle,
Modified: pkg/stacomir/R/RefDC.r
===================================================================
--- pkg/stacomir/R/RefDC.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/RefDC.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -115,11 +115,26 @@
# pas non plus d'appel pour les bilanArgentee dont les slots taxon, stade ,et par sont fixes
if("RefTaxon"%in%as.character(getSlots(class(objectBilan)))&class(objectBilan)!="BilanArgentee"&class(objectBilan)!="BilanAgedemer"){
objectBilan at taxons<<-charge_avec_filtre(object=objectBilan at taxons,dc_selectionne=get("refDC",object,envir_stacomi)@dc_selectionne)
- if (exists("frame_tax")) delete(group,frame_tax)
- if (exists("frame_std")) delete(group,frame_std)
- if (exists("frame_par")) delete(group,frame_par)
- if (exists("frame_parquan")) delete(group,frame_parquan)
- if (exists("frame_parqual")) delete(group,frame_parqual)
+ if (exists("frame_tax",envir=envir_stacomi)) {
+ frame_tax<-get("frame_tax",envir=envir_stacomi)
+ delete(group,frame_tax)
+ }
+ if (exists("frame_std",envir=envir_stacomi)) {
+ frame_std<-get("frame_std",envir=envir_stacomi)
+ delete(group,frame_std)
+ }
+ if (exists("frame_par",envir=envir_stacomi)) {
+ frame_par<-get("frame_par",envir=envir_stacomi)
+ delete(group,frame_par)
+ }
+ if (exists("frame_parquan",envir=envir_stacomi)) {
+ frame_parquan<-get("frame_parquan",envir=envir_stacomi)
+ delete(group,frame_parquan)
+ }
+ if (exists("frame_parqual",envir=envir_stacomi)) {
+ frame_parqual<-get("frame_parqual",envir=envir_stacomi)
+ delete(group,frame_parqual)
+ }
choice(objectBilan at taxons,objectBilan,is.enabled=TRUE)
funout(gettext("Select taxa for this counting device (for all periods)\n",domain="R-stacomiR"))
}
Modified: pkg/stacomir/R/RefHorodate.r
===================================================================
--- pkg/stacomir/R/RefHorodate.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/RefHorodate.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -173,36 +173,42 @@
#' @param label the name to write in the frame
#' @param nomassign the name with which the frame will be assigned to envir_stacomi
#' @param funoutlabel the sentence to write when the choice has been made
+#' @param decal Default year will be current year, use -1 to set the default value in the interface to the year before
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
setMethod("choicemult",signature=signature("RefHorodate"),definition=function(object,
label="date",
nomassign="horodate",
funoutlabel="nous avons le choix dans la date\n",
decal=0
- ) {
- hhoro=function(h,...){
- object=setRefHorodate(object,svalue(horodate))
- assign(nomassign,object at horodate,envir_stacomi)
- funout(gettext("Horodate selected\n",domain="R-stacomiR"))
- # changing tab of notebook to next tab
- if (svalue(notebook)<length(notebook)){
- svalue(notebook)<-svalue(notebook)+1
- }
+ ) {
+ hhoro=function(h,...){
+ object=setRefHorodate(object,svalue(horodate))
+ assign(nomassign,object at horodate,envir_stacomi)
+ funout(gettext("Horodate selected\n",domain="R-stacomiR"))
+ # changing tab of notebook to next tab
+ if (svalue(notebook)<length(notebook)){
+ svalue(notebook)<-svalue(notebook)+1
}
- if (decal!=0){
- # Returns the first horodate of a year shifted by decal
- # @param horodate The horodate to shift (class POSIXt)
- # @param decal number of year to shift
- # @return A POSIXt
- shiftyear<-function(horodate,decal){
- anneeprec=as.numeric(strftime(horodate,"%Y"))+decal
- return(strptime(paste(anneeprec,"-01-01",sep=""),format="%Y-%m-%d"))
- }
- object at horodate<-shiftyear(object at horodate,decal)
+ }
+ if (decal!=0){
+ # Returns the first horodate of a year shifted by decal
+ # @param horodate The horodate to shift (class POSIXt)
+ # @param decal number of year to shift
+ # @return A POSIXt
+ shiftyear<-function(horodate,decal){
+ anneeprec=as.numeric(strftime(horodate,"%Y"))+decal
+ return(strptime(paste(anneeprec,"-01-01",sep=""),format="%Y-%m-%d"))
}
- if (!exists("notebook",envir_stacomi)) notebook <- gnotebook(container=group) else
- notebook<-get("notebook",envir=envir_stacomi)
- grouphorodate<-ggroup(container=notebook, label=label,horizontal=FALSE)
- horodate<-gedit(getRefHorodate(object),container=grouphorodate,handler=hhoro,width=20)
- gbutton("OK", container=grouphorodate,handler=hhoro,icon="execute")
+ object at horodate<-shiftyear(object at horodate,decal)
+ }
+
+ if (!exists("notebook",envir_stacomi)){
+ group<-get("group",envir_stacomi)
+ notebook <- gnotebook(container=group)}
+ else {
+ notebook<-get("notebook",envir=envir_stacomi)
+ }
+ grouphorodate<-ggroup(container=notebook, label=label,horizontal=FALSE)
+ horodate<-gedit(getRefHorodate(object),container=grouphorodate,handler=hhoro,width=20)
+ gbutton("OK", container=grouphorodate,handler=hhoro,icon="execute")
})
\ No newline at end of file
Modified: pkg/stacomir/R/RefStades.r
===================================================================
--- pkg/stacomir/R/RefStades.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/RefStades.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -94,7 +94,10 @@
dc_selectionne=get("refDC",envir_stacomi)@dc_selectionne,
taxon_selectionne=get("refTaxon",envir_stacomi)@data$tax_code,
stade_selectionne=get("refStades",envir_stacomi)@data$std_code)
- if (exists("frame_par")) delete(group,frame_par)
+
+ if (exists("frame_par",envir_stacomi)){
+ delete(group,get("frame_par",envir_stacomi))
+ }
choice(objectBilan at par,is.enabled=TRUE)
}
#il y a bien un object parqual dans l'object Bilan
@@ -104,7 +107,9 @@
taxon_selectionne=get("refTaxon",envir_stacomi)@data$tax_code,
stade_selectionne=get("refStades",envir_stacomi)@data$std_code)
- if (exists("frame_parqual")) delete(group,frame_parqual)
+ if (exists("frame_parqual",envir_stacomi)) {
+ delete(group,get("frame_parqual",envir_stacomi))
+ }
choice(objectBilan at parqual,label=gettext("Qualitative feature",domain="R-stacomiR"),
nomassign="refparqual",
frameassign="frame_parqual",is.enabled=TRUE)
@@ -123,7 +128,10 @@
is.na(objectBilan at parquan@data$par_code)|objectBilan at parquan@data$par_code=="C001",] # aucune
}
}
- if (exists("frame_parquan")) delete(group,frame_parquan)
+ if (exists("frame_parquan",envir_stacomi)){
+ delete(group,get("frame_parquan",envir_stacomi))
+
+ }
choice(objectBilan at parquan,label=gettext("Quantitative feature",domain="R-stacomiR"),
nomassign="refparquan",
frameassign="frame_parquan",is.enabled=TRUE)
@@ -233,8 +241,13 @@
}
# below the widget structure [=> within (=> type
# group(ggroup)[notebook(notebook)[groupstd(ggroup&tab)[[framestdsource(gframe)[tbsourcestd(gtable)],framestddest(gframe)[tbdeststd(gtable)]],OKbutton]]
- if (!exists("notebook",envir=envir_stacomi)) notebook <- gnotebook(container=group) else
- notebook<-get("notebook",envir=envir_stacomi)
+
+ if (!exists("notebook",envir=envir_stacomi)) {
+ group<-get("group",envir_stacomi)
+ notebook <- gnotebook(container=group)
+ } else {
+ notebook<-get("notebook",envir=envir_stacomi)
+ }
std_libelle=fun_char_spe(object at data$std_libelle)
groupstd<-ggroup()
assign("goupstd",groupstd,envir=envir_stacomi)
Modified: pkg/stacomir/R/RefStationMesure.r
===================================================================
--- pkg/stacomir/R/RefStationMesure.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/RefStationMesure.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -44,7 +44,6 @@
#' @param object An object of class \link{RefStationMesure-class}
#' @param is.enabled A boolean parameter, if TRUE the frame is enabled when first displayed
#' @param title The title of the frame, defaut to "Monitoring stations selection"
-#' @param stationMesure A character, the code of the monitoring station, which records environmental parameters \link{choice_c,RefStationMesure-method}
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
#' \dontrun{
Modified: pkg/stacomir/R/RefTaxon.r
===================================================================
--- pkg/stacomir/R/RefTaxon.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/RefTaxon.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -81,10 +81,18 @@
funout(gettext("Taxon selected\n",domain="R-stacomiR"))
if (!is.null(objectBilan)) {
objectBilan at stades<<-charge_avec_filtre(object=objectBilan at stades,dc_selectionne=get("refDC",envir_stacomi)@dc_selectionne,taxon_selectionne=get("refTaxon",envir_stacomi)@data$tax_code)
- if (exists("frame_std")) delete(group,frame_std)
- if (exists("frame_par")) delete(group,frame_par)
- if (exists("frame_parquan")) delete(group,frame_parquan)
- if (exists("frame_parqual")) delete(group,frame_parqual)
+ if (exists("frame_std",envir_stacomi)){
+ delete(group,get("frame_std",envir_stacomi))
+ }
+ if (exists("frame_par")) {
+ delete(group,get("frame_par",envir_stacomi))
+ }
+ if (exists("frame_parquan")) {
+ delete(group,get("frame_parquan",envir_stacomi))
+ }
+ if (exists("frame_parqual")) {
+ delete(group,get("frame_parqual",envir_stacomi))
+ }
choice(objectBilan at stades,objectBilan,is.enabled=TRUE)
}
}
@@ -148,8 +156,12 @@
}
# below the widget structure [=> within (=> type
# group(ggroup)[notebook(notebook)[grouptaxon(ggroup&tab)[[frametaxonsource(gframe)[tbsourcetaxon(gtable)],frametaxondest(gframe)[tbdtaxondest(gtable)]],OKbutton]]
- if (!exists("notebook",envir=envir_stacomi)) notebook <- gnotebook(container=group) else
- notebook<-get("notebook",envir=envir_stacomi)
+ if (!exists("notebook",envir_stacomi)){
+ group<-get("group",envir_stacomi)
+ notebook <- gnotebook(container=group)}
+ else {
+ notebook<-get("notebook",envir=envir_stacomi)
+ }
tax_libelle=fun_char_spe(object at data$tax_nom_latin)
grouptaxon<-ggroup()
assign("grouptaxon",grouptaxon,envir_stacomi)
Modified: pkg/stacomir/R/Refpar.r
===================================================================
--- pkg/stacomir/R/Refpar.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/Refpar.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -166,10 +166,12 @@
})
-#' Multiple Choice method for Refpar referential objects
+#' Multiple Choice method for Refpar referential objects, internal use
#'
#' @param object An object of class \link{Refpar-class}
#' @param objectBilan An object Bilan which includes the \link{Refpar-class}, default NULL
+#' @param label The name for the frame
+#' @param nomassign The name by which the widget will be assigned in envir_stacomi
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
#' \dontrun{
@@ -181,7 +183,8 @@
#' objectBilan=bilan_taille # for other test
#' choicemult(object,objectBilan=bilanMigrationCar)
#' }
-setMethod("choicemult",signature=signature("Refpar"),definition=function(object,objectBilan=NULL,
+setMethod("choicemult",signature=signature("Refpar"),definition=function(object,
+ objectBilan=NULL,
label=gettext("Sample characteristic",domain="R-stacomiR"),
nomassign="refpar") {
@@ -210,8 +213,12 @@
}
# below the widget structure [=> within (=> type
# group(ggroup)[notebook(notebook)[groupstd(ggroup&tab)[[framestdsource(gframe)[tbsourcestd(gtable)],framestddest(gframe)[tbdeststd(gtable)]],OKbutton]]
- if (!exists("notebook",envir=envir_stacomi)) notebook <- gnotebook(container=group) else
- notebook<-get("notebook",envir=envir_stacomi)
+ if (!exists("notebook",envir_stacomi)){
+ group<-get("group",envir_stacomi)
+ notebook <- gnotebook(container=group)}
+ else {
+ notebook<-get("notebook",envir=envir_stacomi)
+ }
car_libelle=fun_char_spe(object at data$par_nom)
car_libelle[nchar(car_libelle)>30]<-paste(substr(car_libelle[nchar(car_libelle)>30],1,30),".",sep="")
grouppar<-ggroup()
Modified: pkg/stacomir/R/Refparqual.r
===================================================================
--- pkg/stacomir/R/Refparqual.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/Refparqual.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -155,11 +155,11 @@
hpar=function(h,...){
parm=tbdestpar[,][tbdestpar[,]!=""]
if (length(parm)>0){
- object at par_selectionne<-object at data[car_libelle%in%parm ,"par_code"]
- # below the line that changes from the Refpar
- object<-charge_complement(object)
- assign(nomassign,object,envir_stacomi)
- funout(gettext("Parameter selected\n",domain="R-stacomiR"))
+ object at par_selectionne<-object at data[car_libelle%in%parm ,"par_code"]
+ # below the line that changes from the Refpar
+ object<-charge_complement(object)
+ assign(nomassign,object,envir_stacomi)
+ funout(gettext("Parameter selected\n",domain="R-stacomiR"))
} else {
funout(gettext("No Parameter selected\n",domain="R-stacomiR"))
}
@@ -175,8 +175,12 @@
}
# below the widget structure [=> within (=> type
# group(ggroup)[notebook(notebook)[groupstd(ggroup&tab)[[framestdsource(gframe)[tbsourcestd(gtable)],framestddest(gframe)[tbdeststd(gtable)]],OKbutton]]
- if (!exists("notebook",envir=envir_stacomi)) notebook <- gnotebook(container=group) else
+ if (!exists("notebook",envir_stacomi)){
+ group<-get("group",envir_stacomi)
+ notebook <- gnotebook(container=group)}
+ else {
notebook<-get("notebook",envir=envir_stacomi)
+ }
car_libelle=fun_char_spe(object at data$par_nom)
car_libelle[nchar(car_libelle)>30]<-paste(substr(car_libelle[nchar(car_libelle)>30],1,30),".",sep="")
grouppar<-ggroup()
Modified: pkg/stacomir/R/funSousListeBilanMigrationPar.r
===================================================================
--- pkg/stacomir/R/funSousListeBilanMigrationPar.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/funSousListeBilanMigrationPar.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -20,6 +20,7 @@
req at baseODBC<-get("baseODBC", envir=envir_stacomi)
mygtkProgressBar(title="cumul val. quant. par pas de temps",
progress_text=gettext("Progress %",domain="R-stacomiR"))
+ progress_bar<-get("progress_bar",envir_stacomi)
##############################
on.exit(dispose(progres))
Modified: pkg/stacomir/R/fungraph.r
===================================================================
--- pkg/stacomir/R/fungraph.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/fungraph.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -3,7 +3,6 @@
#' This graph is for species other than glass eel
#'
#'
-#' @usage fungraph(bilanMigration, tableau, time.sequence, taxon, stade, dc=NULL,silent,...)
#' @param bilanMigration An object of class \code{\linkS4class{BilanMigration}}
#' @param 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,
Modified: pkg/stacomir/R/utilitaires.r
===================================================================
--- pkg/stacomir/R/utilitaires.r 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/R/utilitaires.r 2017-06-06 20:06:21 UTC (rev 381)
@@ -217,10 +217,10 @@
}
-#' Progress bar using a gtkdialog, the progress bar is assigned in .GlobalEnv
+#' Progress bar using a gtkdialog, the progress bar is assigned in envir_stacomi
#' This progress bar has a button to close.
-#' @note The name of the progress bar is \code{progres}, it will be assigned in .GlobalEnv,
-#' it contains a progress bar widget named progress bar, also assigned in .GLobalEnv. See example for use.
+#' @note The name of the progress bar is \code{progres}, it will be assigned in envir_stacomi,
+#' it contains a progress bar widget named progress bar, also assigned in envir_stacomi See example for use.
#' @param title The title of the bar
#' @param progress_text The text to display for progression
#' @param width Width of the progress bar
@@ -233,7 +233,8 @@
#' \dontrun{
#' mygtkProgressBar(title="Trial",progress_text="progress text")
#' fraction_progressed=seq(0,1,length.out=50)
-#' for(i in fraction_progressed) {
+#' progress_bar<-get("progress_bar",envir_stacomi)
+#' for(i in fraction_progressed){
#' Sys.sleep(0.1)
#' progress_bar$setText(sprintf("%d%% progression",round(100*i)))
#' progress_bar$setFraction(i)
@@ -327,6 +328,7 @@
#' @param mois logical, add column with month
#' @param quinzaine logical, add column with 15 days
#' @param semaine logical, add column with weeks
+#' @param semaine_std logical, add column with standard weeks (using isoweek from lubridate)
#' @param jour_an logical, add column with day of year
#' @param jour_mois logical, add column with day of month
#' @param heure logical, add column with hour
Modified: pkg/stacomir/data/bilAM.rda
===================================================================
(Binary files differ)
Modified: pkg/stacomir/data/bilan_adm.rda
===================================================================
(Binary files differ)
Modified: pkg/stacomir/data/bmmCE.rda
===================================================================
(Binary files differ)
Modified: pkg/stacomir/inst/config/generate_Roxygen2.R
===================================================================
--- pkg/stacomir/inst/config/generate_Roxygen2.R 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/inst/config/generate_Roxygen2.R 2017-06-06 20:06:21 UTC (rev 381)
@@ -24,10 +24,10 @@
##use either :
require(devtools)
# uncomment lines in stacomi to run the program (calcmig and envir_stacomi necessary)
-document("F:/workspace/stacomir/pkg/stacomir")
+document("C:/workspace/stacomir/pkg/stacomir")
## or :
##vignette("roxygen2")
-setwd("F:/workspace/stacomir/pkg/stacomir")
+setwd("C:/workspace/stacomir/pkg/stacomir")
#data("bMM_Arzal")
#data("bM_Arzal")
envir_stacomi <- new.env(parent = emptyenv())
@@ -37,7 +37,7 @@
require(roxygen2)
#Pour Cédric
-roxygen2::roxygenise("F:/workspace/stacomir/pkg/stacomir");warnings()[1:10]
+roxygen2::roxygenise("C:/workspace/stacomir/pkg/stacomir");warnings()[1:10]
#Pour Marion
#roxygen2::roxygenise("C:/Users/logrami/workspace/stacomir/pkg/stacomir");warnings()[1:10]
Modified: pkg/stacomir/inst/config/generate_data.R
===================================================================
--- pkg/stacomir/inst/config/generate_data.R 2017-06-05 20:09:53 UTC (rev 380)
+++ pkg/stacomir/inst/config/generate_data.R 2017-06-06 20:06:21 UTC (rev 381)
@@ -16,14 +16,14 @@
##################################
filecsv<-"C:/Program Files/stacomi/calcmig.csv"
calcmig<-utils::read.csv(filecsv,header=TRUE,sep=";")
-setwd("F:/workspace/stacomir/pkg/stacomir")
+setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(calcmig,internal=FALSE,overwrite=TRUE)
#################################
# generates a dataset with Durif coefficients
# source Laurent Beaulaton
##################################
-setwd("F:/workspace/stacomir/pkg/stacomir")
+setwd("C:/workspace/stacomir/pkg/stacomir")
coef_Durif = matrix(NA, nrow=5, ncol=6)
colnames(coef_Durif) = c("I", "FII", "FIII", "FIV", "FV", "MII")
rownames(coef_Durif) = c("Constant", "BL", "W", "MD", "FL")
@@ -59,7 +59,7 @@
bMM_Arzal at dc@data[,"dif_localisation"]<-iconv(bMM_Arzal at dc@data[,"dif_localisation"],from="latin1",to="UTF8")
bMM_Arzal at taxons@data[,"tax_nom_commun"]<-iconv(bMM_Arzal at taxons@data[,"tax_nom_commun"],from="latin1",to="UTF8")
bMM_Arzal at stades@data[,"std_libelle"]<-iconv(bMM_Arzal at stades@data[,"std_libelle"],from="latin1",to="UTF8")
-setwd("F:/workspace/stacomir/pkg/stacomir")
+setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(bMM_Arzal,internal=FALSE,overwrite=TRUE)
bilanOperation<-get("bilanOperation",envir=envir_stacomi)
bilanOperation at data$ope_commentaires<-iconv(bilanOperation at data$ope_commentaires,from="latin1",to="UTF8")
@@ -118,7 +118,7 @@
bM_Arzal at dc@data[,"dif_localisation"]<-iconv(bM_Arzal at dc@data[,"dif_localisation"],from="latin1",to="UTF8")
bM_Arzal at taxons@data[,"tax_nom_commun"]<-iconv(bM_Arzal at taxons@data[,"tax_nom_commun"],from="latin1",to="UTF8")
bM_Arzal at stades@data[,"std_libelle"]<-iconv(bM_Arzal at stades@data[,"std_libelle"],from="latin1",to="UTF8")
-setwd("F:/workspace/stacomir/pkg/stacomir")
+setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(bM_Arzal,internal=FALSE,overwrite=TRUE)
@@ -175,14 +175,14 @@
bfDF at data$per_commentaires<-iconv(bfDF at data$per_commentaires,from="latin1",to="UTF8")
#plot(bfDF,plot.type="1")
#plot(bfDF,plot.type="2",title="A nice title")
-setwd("F:/workspace/stacomir/pkg/stacomir")
+setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(bfDF,internal=FALSE,overwrite=TRUE)
#################################
# generates dataset for BilanFonctionnementDC
##################################
-setwd("F:/workspace/stacomir/pkg/stacomir")
+setwd("C:/workspace/stacomir/pkg/stacomir")
require(stacomiR)
stacomi(gr_interface=FALSE,
login_window=FALSE,
@@ -204,13 +204,13 @@
bfDC at data$per_commentaires<-iconv(bfDC at data$per_commentaires,from="latin1",to="UTF8")
#plot(bfDC,plot.type="1")
#plot(bfDC,plot.type="2",title="A nice title")
-setwd("F:/workspace/stacomir/pkg/stacomir")
+setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(bfDC,internal=FALSE,overwrite=TRUE)
#################################
# generates dataset for Bilan_carlot
##################################
-setwd("F:/workspace/stacomir/pkg/stacomir")
+setwd("C:/workspace/stacomir/pkg/stacomir")
require(stacomiR)
stacomi(gr_interface=FALSE,
login_window=FALSE,
@@ -243,13 +243,13 @@
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 381
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