[Stacomir-commits] r585 - in pkg: stacomir stacomir/R stacomir/data stacomir/inst stacomir/man stacomir/man/figures stacomir/tests stacomirtools
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 9 11:05:16 CET 2021
Author: briand
Date: 2021-11-09 11:05:16 +0100 (Tue, 09 Nov 2021)
New Revision: 585
Added:
pkg/stacomir/man/figures/
pkg/stacomir/man/figures/README-rmmmult-1.pdf
pkg/stacomir/man/figures/README-rmmmult-1.png
pkg/stacomir/man/figures/README-rmmstandard-1.png
pkg/stacomir/man/figures/README-rmmstd-1.pdf
pkg/stacomir/man/figures/README-rmmstd-1.png
pkg/stacomir/man/figures/README-silver-1.pdf
pkg/stacomir/man/figures/README-silver-1.png
Removed:
pkg/stacomir/R/interface_report_annual.R
pkg/stacomir/R/interface_report_dc.R
pkg/stacomir/R/interface_report_df.R
pkg/stacomir/R/interface_report_env.R
pkg/stacomir/R/interface_report_ge_weight.R
pkg/stacomir/R/interface_report_mig.R
pkg/stacomir/R/interface_report_mig_char.R
pkg/stacomir/R/interface_report_mig_env.R
pkg/stacomir/R/interface_report_mig_interannual.R
pkg/stacomir/R/interface_report_mig_mult.R
pkg/stacomir/R/interface_report_sample_char.R
pkg/stacomir/R/interface_report_sea_age.R
pkg/stacomir/R/interface_report_silver_eel.R
pkg/stacomir/R/interface_report_species.R
pkg/stacomir/R/ref_checkbox.R
pkg/stacomir/data/calcmig.csv
pkg/stacomir/data/calcmig.rda
pkg/stacomir/inst/doc/
pkg/stacomir/man/figures/
pkg/stacomir/tests/testthat.R
Modified:
pkg/stacomir/NEWS.md
pkg/stacomir/R/ref_par.R
pkg/stacomir/R/report_annual.R
pkg/stacomir/R/report_dc.R
pkg/stacomir/R/report_df.R
pkg/stacomir/R/report_mig.R
pkg/stacomir/R/report_mig_env.R
pkg/stacomir/R/report_mig_mult.R
pkg/stacomir/R/report_sample_char.R
pkg/stacomir/R/report_silver_eel.R
pkg/stacomir/R/report_species.R
pkg/stacomir/man/calcule-report_mig_env-method.Rd
pkg/stacomir/man/calcule-report_species-method.Rd
pkg/stacomir/man/choice_c-ref_par-method.Rd
pkg/stacomir/man/funbarchart1DF.Rd
pkg/stacomir/man/funbarchartDC.Rd
pkg/stacomir/man/funboxDF.Rd
pkg/stacomir/man/funboxplotreport_sample_char.Rd
pkg/stacomir/man/funchartDF.Rd
pkg/stacomir/man/fundensityreport_sample_char.Rd
pkg/stacomir/man/funplotreport_silver_eel.Rd
pkg/stacomir/man/funpointreport_sample_char.Rd
pkg/stacomir/man/funtableDC.Rd
pkg/stacomir/man/funtableDF.Rd
pkg/stacomir/man/plot-report_mig_env-missing-method.Rd
pkg/stacomir/man/print-report_dc-method.Rd
pkg/stacomir/man/print-report_df-method.Rd
pkg/stacomir/man/write_database-report_mig-method.Rd
pkg/stacomirtools/NEWS.md
Log:
check passing on local machine
Modified: pkg/stacomir/NEWS.md
===================================================================
--- pkg/stacomir/NEWS.md 2021-11-08 10:49:07 UTC (rev 584)
+++ pkg/stacomir/NEWS.md 2021-11-09 10:05:16 UTC (rev 585)
@@ -1,12 +1,17 @@
-# stacomiR 0.5.4.XXX
+# stacomiR 0.6.0
-## Minor improvement and bug fix
+* adapted to stacomirtools new connection and connection options (using pool and DBI instead of RODC)
+* removed all dependency to gwidgetRGTK2 so in practise there is no longer a graphical interface, the shiny package is due soon.
+* added code of conduct
+* rewrote unit tests
+# stacomiR 0.5.4.4 (not released on CRAN)
+
+
* added import to package `rlang`
* Change to adapt to new dplyr format `dplyr:n()` instead of `n()` see dplyr breaking change in version 1.0.0
-
# stacomiR 0.5.4.3
Deleted: pkg/stacomir/R/interface_report_annual.R
===================================================================
--- pkg/stacomir/R/interface_report_annual.R 2021-11-08 10:49:07 UTC (rev 584)
+++ pkg/stacomir/R/interface_report_annual.R 2021-11-09 10:05:16 UTC (rev 585)
@@ -1,61 +0,0 @@
-#deprecated0.6
-##' interface for report_annual class
-##' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-##' @keywords internal
-#interface_report_annual = function()
-#{
-# quitte() # vidange de l'interface
-# report_annual=new("report_annual")
-# assign("report_annual",report_annual,envir=envir_stacomi)
-# objectreport="report_annual"
-# # the following name is created by the interface
-# # as I can't get the name from within the function (deparse(substitute(objectreport)) does not return
-# # "report_mig_mult" see ref_dc choice_c method)
-# # so this will allow to assign "report_mig_mult" in envir_stacomi while using other class
-# # like ref_dc
-# assign("objectreport",objectreport,envir=envir_stacomi)
-# report_annual at dc=charge(report_annual at dc)
-# report_annual at taxa=charge(report_annual at taxa)
-# report_annual at stage=charge(report_annual at stage)
-# report_annual at anneedebut=charge(report_annual at anneedebut,objectreport="report_annual")
-# report_annual at anneefin=charge(report_annual at anneefin,objectreport="report_annual")
-#
-#
-# group <- gWidgets::ggroup(horizontal=FALSE) # doit toujours s'appeller group
-# assign("group",group,envir = envir_stacomi)
-# ggroupboutons<-get("ggroupboutons",envir=envir_stacomi)
-# add(ggroupboutons,group)
-# notebook <- gnotebook(container=group)
-# assign("notebook",notebook,envir=envir_stacomi)
-# size(notebook)<-c(400,300)
-# # pour preselectionner une date on lui fournit l'indice de la date dans le ref_year. indice = 11 pour 2005
-#
-# choice(report_annual at anneedebut,
-# nomassign="anneedebut",
-# funoutlabel=gettext("The year of beginning has been chosen\n",domain="R-stacomiR"),
-# titleFrame=gettext("First year",domain="R-stacomiR"),
-# preselect=which(report_annual at anneedebut@data==min(report_annual at anneedebut@data)))
-# choice(report_annual at anneefin,
-# nomassign="anneefin",
-# funoutlabel=gettext("The last year has been chosen\n",domain="R-stacomiR"),
-# titleFrame=gettext("Last year",domain="R-stacomiR"),
-# preselect=which(report_annual at anneefin@data==max(report_annual at anneefin@data)))
-# choicemult(report_annual at dc,objectreport=report_annual,is.enabled=TRUE)
-# svalue(notebook)<-1
-#
-# ggroupboutonsbas = gWidgets::ggroup(horizontal=FALSE)
-# assign("ggroupboutonsbas",ggroupboutonsbas,envir=envir_stacomi)
-# gWidgets::add(ggroupboutons,ggroupboutonsbas)
-#
-# toolbarlist = list(
-# aGraph=gWidgets::gaction(label="barplot",icon="barplot",handler=hbarplotreport_annual,tooltip=gettext("Migration of all the years in the same graphic",domain="R-stacomiR")),
-# aGraph2=gWidgets::gaction(label="plot",icon="plot",handler=hplotreport_annual,tooltip=gettext("Migration of all the years in the same graphic",domain="R-stacomiR")),
-# a_table=gWidgets::gaction(handler=hxtablereport_annual, icon="dataframe", label="xtable", tooltip="xtable"),
-# aQuit=gWidgets::gaction(label="fermer",icon="close", handler=quitte,tooltip=gettext("Exit",domain="R-stacomiR"))
-# )
-#
-# add(ggroupboutonsbas, gtoolbar(toolbarlist))
-# gWidgets::addSpring(group)
-#
-#
-#}
\ No newline at end of file
Deleted: pkg/stacomir/R/interface_report_dc.R
===================================================================
--- pkg/stacomir/R/interface_report_dc.R 2021-11-08 10:49:07 UTC (rev 584)
+++ pkg/stacomir/R/interface_report_dc.R 2021-11-09 10:05:16 UTC (rev 585)
@@ -1,68 +0,0 @@
-#deprecated0.6
-##' interface for report_dc class
-##' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-##' @keywords internal
-#interface_report_dc = function()
-#{
-# quitte()
-# report_dc=new("report_dc")
-# assign("report_dc",report_dc,envir=envir_stacomi)
-#
-# funout(gettext("Loading of the list for fishways and choice of the time step\n",domain="R-stacomiR"))
-# report_dc at dc=charge(report_dc at dc)
-#
-# group <- gWidgets::ggroup(horizontal=FALSE) # doit toujours s'appeller group
-#
-# assign("group",group,envir = envir_stacomi)
-# ggroupboutons<-get("ggroupboutons",envir=envir_stacomi)
-# gWidgets::add(ggroupboutons,group)
-# choice(report_dc at dc)
-# choice(report_dc at horodatedebut,
-# label=gettext("Start",domain="R-stacomiR"),
-# nomassign="report_dc_date_debut",
-# funoutlabel=gettext("Beginning date has been chosen\n",domain="R-stacomiR"),
-# decal=-2)
-# choice(report_dc at horodatefin,
-# label=gettext("End",domain="R-stacomiR"),
-# nomassign="report_dc_date_fin",
-# funoutlabel=gettext("Ending date has been chosen\n",domain="R-stacomiR"),
-# decal=-1)
-#
-# #toolbarlist$Calc$handler = connect(report_dc)
-# #toolbarlist$Calc$icon = "dataframe"
-# #getStockIcons(toolkit=guiToolkit())
-#
-# bar_chart=gWidgets::gaction(label="barchart",
-# icon="barplot",
-# handler=funbarchartDC,
-# tooltip=gettext("Monthly graph",domain="R-stacomiR"))
-# bar_chart1=gWidgets::gaction(label="barchart_fct",
-# icon="barplot",
-# handler=funbarchart1DC,
-# tooltip=gettext("Another monthly graph",domain="R-stacomiR"))
-# a_box=gWidgets::gaction(label=gettext("box"),
-# icon="graph2",
-# handler=funboxDC,
-# tooltip=gettext("Boxplot",domain="R-stacomiR"))
-# a_table=gWidgets::gaction(label=gettext("table",domain="R-stacomiR"),
-# icon="dataframe",
-# handler=funtableDC,
-# tooltip=gettext("Table",domain="R-stacomiR"))
-# aQuit=gWidgets::gaction(label="Quitter",
-# icon="close",
-# handler=quitte,
-# tooltip=gettext("Exit",domain="R-stacomiR"))
-# aOut=gWidgets::gaction(label=gettext("code"),
-# handler=houtDC,
-# icon="gtk-info",
-# tooltip=gettext("code",domain="R-stacomiR"))
-# toolbarlist <- list(
-# barchart=bar_chart,
-# barchart1=bar_chart1,
-# box= a_box,
-# table=a_table,
-# out=aOut,
-# Quit = aQuit)
-# add(group, gmenu(toolbarlist))
-# gWidgets::addSpring(group)
-#}
\ No newline at end of file
Deleted: pkg/stacomir/R/interface_report_df.R
===================================================================
--- pkg/stacomir/R/interface_report_df.R 2021-11-08 10:49:07 UTC (rev 584)
+++ pkg/stacomir/R/interface_report_df.R 2021-11-09 10:05:16 UTC (rev 585)
@@ -1,50 +0,0 @@
-#deprecated0.6
-##' interface for report_df class
-##' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-##' @keywords internal
-#interface_report_df = function()
-#{
-# quitte()
-#
-# report_df=new("report_df")
-# assign("report_df",report_df,envir=envir_stacomi)
-# funout(gettext("Loading of the list for fishways and choice of the time step\n",domain="R-stacomiR"))
-# report_df at df=charge(report_df at df)
-# group <- gWidgets::ggroup(horizontal=FALSE) # doit toujours s'appeller group
-# assign("group",group,envir=envir_stacomi)
-# ggroupboutons<-get("ggroupboutons",envir=envir_stacomi)
-# gWidgets::add(ggroupboutons,group)
-#
-# choice(report_df at df)
-# # here decale =-1 or -2 will make the report for the year preceeding the current date
-# choice(report_df at horodatedebut,
-# label=gettext("start",domain="R-stacomiR"),
-# nomassign="report_df_date_debut",
-# funoutlabel=gettext("The beginning date has been chosen\n",domain="R-stacomiR"),
-# decal=-2)
-# choice(report_df at horodatefin,
-# label=gettext("End",domain="R-stacomiR"),
-# nomassign="report_df_date_fin",
-# funoutlabel=gettext("The ending date has been chosen\n",domain="R-stacomiR"),
-# decal=-1)
-#
-# bar_chart=gWidgets::gaction(label="barchart_typefct",icon="barplot",handler=funbarchartDF,tooltip=gettext("Monthly graph",domain="R-stacomiR"))
-# bar_chart1=gWidgets::gaction(label="barchart_fct",icon="barplot",handler=funbarchart1DF,tooltip=gettext("Monthly graph",domain="R-stacomiR"))
-# a_box=gWidgets::gaction(label="box",icon="graph2",handler=funboxDF,tooltip=gettext("Boxplot",domain="R-stacomiR"))
-# aChart=gWidgets::gaction(label="chart",icon="graph",handler=funchartDF,tooltip=gettext("Calendar",domain="R-stacomiR"))
-# a_table=gWidgets::gaction(label="table",icon="dataframe",handler=funtableDF,tooltip=gettext("Table",domain="R-stacomiR"))
-# aOut=gWidgets::gaction(label="code",handler=houtDF, icon="gtk-info", tooltip=gettext("Code",domain="R-stacomiR"))
-# aQuit=gWidgets::gaction(label="Close",icon="close", handler=quitte,tooltip=gettext("Exit",domain="R-stacomiR"))
-#
-# toolbarlist <- list(
-# barchart=bar_chart,
-# barchart1=bar_chart1,
-# box= a_box,
-# chart=aChart,
-# table=a_table,
-# out=aOut,
-# Quit = aQuit)
-#
-# add(group, gmenu(toolbarlist))
-# gWidgets::addSpring(group)
-#}
\ No newline at end of file
Deleted: pkg/stacomir/R/interface_report_env.R
===================================================================
--- pkg/stacomir/R/interface_report_env.R 2021-11-08 10:49:07 UTC (rev 584)
+++ pkg/stacomir/R/interface_report_env.R 2021-11-09 10:05:16 UTC (rev 585)
@@ -1,39 +0,0 @@
-#deprecated0.6
-##' Interface for class conditionEnv
-##' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-##' @keywords internal
-#interface_report_env = function()
-#{
-# quitte()
-# report_env=new("report_env")
-# funout(gettext("Loading of the monitoring stations\n",domain="R-stacomiR"))
-# report_env at stationMesure=charge(report_env at stationMesure)
-# assign("report_env",report_env,envir=envir_stacomi)
-#
-# group <- gWidgets::ggroup(horizontal=FALSE) # doit toujours s'appeller group
-#
-# assign("group",group,envir = envir_stacomi)
-# ggroupboutons<-get("ggroupboutons",envir=envir_stacomi)
-# gWidgets::add(ggroupboutons,group)
-# choice(report_env at horodatedebut,label=gettext("Begginning",domain="R-stacomiR"),
-# nomassign="report_env_date_debut",
-# funoutlabel=gettext("Beginning date has been chosen\n",domain="R-stacomiR"),
-# decal=-2)
-# choice(report_env at horodatefin,
-# label=gettext("End",domain="R-stacomiR"),
-# nomassign="report_env_date_fin",
-# funoutlabel=gettext("Ending date has been chosen\n",domain="R-stacomiR"),
-# decal=-1)
-# choice(report_env at stationMesure)
-#
-# ggroupboutonsbas = gWidgets::ggroup(horizontal=FALSE)
-# gWidgets::add(ggroupboutons,ggroupboutonsbas)
-# assign("ggroupboutonsbas",ggroupboutonsbas, envir=envir_stacomi)
-#
-# toolbarlist = list(
-# Graph=gWidgets::gaction(handler=h_report_envgraph , icon = "graph",label="graph",tooltip=gettext("Summary graphic",domain="R-stacomiR")),
-# annuler=gWidgets::gaction(handler= quitte,icon = "close",label=gettext("Exit",domain="R-stacomiR"),domain="R-stacomiR"))
-# gWidgets::add(ggroupboutonsbas, gtoolbar(toolbarlist))
-# gWidgets::addSpring(group)
-# dev.new()
-#}
\ No newline at end of file
Deleted: pkg/stacomir/R/interface_report_ge_weight.R
===================================================================
--- pkg/stacomir/R/interface_report_ge_weight.R 2021-11-08 10:49:07 UTC (rev 584)
+++ pkg/stacomir/R/interface_report_ge_weight.R 2021-11-09 10:05:16 UTC (rev 585)
@@ -1,67 +0,0 @@
-#deprecated0.6
-##' interface for report_ge_weight class
-##' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-##' @keywords internal
-#interface_report_ge_weight = function()
-#{
-# quitte() # erase the interface
-# r_gew=new("report_ge_weight")
-# assign("report_ge_weight",r_gew,envir = envir_stacomi)
-# r_gew at dc=charge(r_gew at dc)
-# r_gew at anneedebut=charge(r_gew at anneedebut)
-# r_gew at anneefin=charge(r_gew at anneefin)
-# r_gew at liste=charge(object=r_gew at liste,listechoice=c("=1",">1",gettext("all",domain="R-stacomiR")),label=gettext("choice of number in sample (one, several, both)",domain="R-stacomiR"))
-# # choice of number type
-# group <- gWidgets::ggroup(horizontal=FALSE) # must always be named group
-# assign("group",group,envir = envir_stacomi)
-# ggroupboutons<-get("ggroupboutons",envir=envir_stacomi)
-# gWidgets::add(ggroupboutons,group)
-# gl=glabel(text=gettext("Mean weight report",domain="R-stacomiR"),container=group)
-#
-# ### first toobar
-# gWidgets::addSpring(group)
-# choice(r_gew at liste)
-# choice(r_gew at dc,objectreport=NULL,is.enabled=TRUE)
-# choice(r_gew at anneedebut,
-# nomassign="ref_yearDebut",
-# titleFrame=gettext("Beginning year",domain="R-stacomiR")) #annee debut
-# choice(r_gew at anneefin,
-# nomassign="ref_yearFin",
-# titleFrame=gettext("Ending year",domain="R-stacomiR"))#annee fin
-# aCalc=gWidgets::gaction(label=gettext("load",domain="R-stacomiR"),
-# icon="lines",
-# handler=hcalc,
-# tooltip=gettext("load",domain="R-stacomiR"))
-# a_table=gWidgets::gaction(label="table",
-# icon="dataframe",
-# handler=funtablereport_ge_weight,
-# tooltip=gettext("table",domain="R-stacomiR"))
-# aQuit=gWidgets::gaction(
-# label=gettext("exit",domain="R-stacomiR"),
-# icon="close",
-# handler=quitte,
-# tooltip=gettext("exit",domain="R-stacomiR"))
-# toolbarlist <- list(barchart=aCalc,table=a_table,Quit = aQuit)
-# add(group, gmenu(toolbarlist))
-#
-# ### second toobar
-# aGra=gWidgets::gaction(label=gettext("Gra",domain="R-stacomiR"),icon="lines",handler=hplot,action="1",
-# tooltip=gettext("plot.type='1', plot of mean weight of glass eel against the mean date of operation",domain="R-stacomiR"))
-# aCoe=gWidgets::gaction(label=gettext("Coe",domain="R-stacomiR"),icon="newplot",handler=hplot,action="2",
-# tooltip=gettext("plot.type=2, standard plot of current coefficent",domain="R-stacomiR"))
-# aSize=gWidgets::gaction(label=gettext("Leng",domain="R-stacomiR"),icon="gWidgetsRGtk2-bubbles",handler=hplot,action="3",
-# tooltip=gettext("plot.type=3, same as 1 but size of the bubble according to number",domain="R-stacomiR"))
-# aReg=gWidgets::gaction(label=gettext("seasonal",domain="R-stacomiR"),icon="function",handler=hreg,action="seasonal",
-# tooltip=gettext("model.type='seasonal', sine wave curve for a cyclic variation fitted with nls",domain="R-stacomiR"))
-# aReg1=gWidgets::gaction(label=gettext("seasonal1",domain="R-stacomiR"),icon="function1",handler=hreg,action="seasonal1",
-# tooltip=gettext("model.type='seasonal1', long term variation along with seasonal variation fitted with gam",domain="R-stacomiR"))
-# aReg2=gWidgets::gaction(label=gettext("seasonal2",domain="R-stacomiR"),icon="function",handler=hreg,action="seasonal2",
-# tooltip=gettext("model.type='seasonal2', long term variation + seasonal component fitted with sine curve",domain="R-stacomiR"))
-# aExp=gWidgets::gaction(label=gettext("export",domain="R-stacomiR"),icon="gtk-harddisk",handler=hexp)
-# toolbarlistgraph <- gmenu(list(gra=aGra,coe=aCoe,size=aSize))
-# assign("toolbarlistgraph",toolbarlistgraph,envir_stacomi)
-# toolbarlistgraph1<-gmenu(list(reg=aReg,reg1=aReg1,reg2=aReg2,exp=aExp))
-# assign("toolbarlistgraph1",toolbarlistgraph1,envir_stacomi)
-# add(group,toolbarlistgraph)
-# add(group,toolbarlistgraph1)
-#}
\ No newline at end of file
Deleted: pkg/stacomir/R/interface_report_mig.R
===================================================================
--- pkg/stacomir/R/interface_report_mig.R 2021-11-08 10:49:07 UTC (rev 584)
+++ pkg/stacomir/R/interface_report_mig.R 2021-11-09 10:05:16 UTC (rev 585)
@@ -1,50 +0,0 @@
-#deprecated0.6
-##' Interface for report_mig class, internal use, this function is called
-##' by a handler in the main graphical interface
-##' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-##' @keywords internal
-#interface_report_mig=function(){
-# # the quitte() method removes everything assigned in envir_stacomi by report classes
-# quitte()
-# # classes used along with report_mig by functions fungraph and fungraphcivelle
-# # they are loaded there to be used later by methods "load" and "connect" of report_mig
-# # so that connections to the database are not used later in examples (they are surrounded
-# # by dontrun{}
-# report_dc=new("report_dc")
-# assign("report_dc",report_dc,envir = envir_stacomi)
-# report_df=new("report_df")
-# assign("report_df",report_df,envir = envir_stacomi)
-# report_ope=new("report_ope")
-# assign("report_ope",report_ope, envir=envir_stacomi)
-# report_mig=new("report_mig")
-# assign("report_mig",report_mig,envir = envir_stacomi)
-# # see report_mig_mult for explaination
-# # this is used internally by ref_dc
-# objectreport="report_mig"
-# assign("objectreport",objectreport,envir=envir_stacomi)
-# funout(gettext("Loading of the lists for taxa, stages and counting devices\n",domain="R-stacomiR"))
-# report_mig at taxa=charge(report_mig at taxa)
-# report_mig at stage=charge(report_mig at stage)
-# report_mig at dc=charge(report_mig at dc)
-# group <- gWidgets::ggroup(horizontal=FALSE) # doit toujours s'appeller group
-# assign("group",group,envir = envir_stacomi)
-# ggroupboutons<-get("ggroupboutons",envir=envir_stacomi)
-# add(ggroupboutons,group)
-# choice(report_mig at timestep)
-# choice(object=report_mig at dc,objectreport=report_mig,is.enabled=TRUE)
-# ggroupboutonsbas = gWidgets::ggroup(horizontal=FALSE)
-# assign("ggroupboutonsbas",ggroupboutonsbas,envir=envir_stacomi)
-# gWidgets::add(ggroupboutons,ggroupboutonsbas)
-# toolbarlist = list(
-# Calc=gWidgets::gaction(handler=h_report_migcalc, action=report_mig, icon="new", label=gettext("calculate",domain="R-stacomiR"), tooltip=gettext("Calculation of numbers by time step",domain="R-stacomiR")),
-# Graph=gWidgets::gaction(handler=h_report_miggraph, icon="graph", label=gettext("graph",domain="R-stacomiR"), tooltip=gettext("Balance graphic",domain="R-stacomiR")),
-# Graph2=gWidgets::gaction(handler=h_report_miggraph2, icon="graph2", label=gettext("grcum",domain="R-stacomiR"), tooltip=gettext("Cumulative graphic",domain="R-stacomiR")),
-# Stat=gWidgets::gaction(handler=hTablereport_mig, icon="dataframe", label=gettext("stat",domain="R-stacomiR"), tooltip=gettext("Balance sheet in .csv",domain="R-stacomiR")),
-# write=gWidgets::gaction(handler=h_report_migwrite, icon="gtk-harddisk", label=gettext("write",domain="R-stacomiR"), tooltip=gettext("Writing daily summary in the database",domain="R-stacomiR")),
-# Out=gWidgets::gaction(handler=houtreport_mig, icon="gtk-info", label=gettext("code",domain="R-stacomiR"), tooltip=gettext("Code",domain="R-stacomiR")),
-# annuler=gWidgets::gaction(handler= quitte,icon = "close",label=gettext("quit",domain="R-stacomiR"))
-# )
-# gWidgets::add(ggroupboutonsbas, gtoolbar(toolbarlist))
-# gWidgets::addSpring(group)
-# dev.new()
-#}
\ No newline at end of file
Deleted: pkg/stacomir/R/interface_report_mig_char.R
===================================================================
--- pkg/stacomir/R/interface_report_mig_char.R 2021-11-08 10:49:07 UTC (rev 584)
+++ pkg/stacomir/R/interface_report_mig_char.R 2021-11-09 10:05:16 UTC (rev 585)
@@ -1,83 +0,0 @@
-#deprecated0.6
-##' interface for report_migPar class
-##' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-##' @keywords internal
-#interface_report_mig_char = function()
-#{
-# quitte()
-#
-# r_mig_char=new("report_mig_char")
-# assign("r_mig_char",r_mig_char,envir=envir_stacomi)
-#
-# report_dc=new("report_dc")
-# assign("report_dc",report_dc,envir=envir_stacomi)
-#
-# objectreport="r_mig_char"
-# # the following name is created by the interface
-# # as I can't get the name from within the function (deparse(substitute(objectreport)) does not return
-# # "report_mig_mult" see ref_dc choice_c method)
-# # so this will allow to assign "report_mig_mult" in envir_stacomi while using other class
-# # like ref_dc
-# assign("objectreport",objectreport,envir=envir_stacomi)
-# funout(gettext("Loading of the lists for taxa, stages, counting devices, qualitative and quantitative parameters\n",domain="R-stacomiR"))
-# r_mig_char at taxa=charge(r_mig_char at taxa)
-# r_mig_char at stage=charge(r_mig_char at stage)
-# r_mig_char at dc=charge(r_mig_char at dc)
-# r_mig_char at parquan=charge(r_mig_char at parquan)
-# r_mig_char at parqual=charge(r_mig_char at parqual)
-# # below, the first element must be the element where samples are accepted (currently with)
-# # this is how it will be evaluated in the connect method, as I can't base myself on the value
-# # which will change with language
-# r_mig_char at echantillon=charge(r_mig_char at echantillon,
-# vecteur=gettext("with","without",domain="R-stacomiR"),
-# label=gettext("Choice of batch type, inclusion of samples ?",domain="R-stacomiR"),
-# selected=as.integer(1))
-# #######################
-# # Interface Graphique
-# ##########################
-# group <- gWidgets::ggroup(horizontal=TRUE) # doit toujours s'appeller group
-# assign("group",group,envir = envir_stacomi)
-# notebook <- gnotebook(container=group)
-# assign("notebook",notebook,envir=envir_stacomi)
-# size(notebook)<-c(400,600)
-#
-#
-# choicemult(r_mig_char at horodatedebut,nomassign="bmC_date_debut",label=gettext("from",domain="R-stacomiR"),decal=-1)
-# choicemult(r_mig_char at horodatefin,,nomassign="bmC_date_fin",label=gettext("to",domain="R-stacomiR"),decal=0)
-# choicemult(r_mig_char at echantillon)
-# choicemult(r_mig_char at dc,objectreport=r_mig_char,is.enabled=TRUE)
-# svalue(notebook)<-1
-# ggroupboutons<-get("ggroupboutons",envir=envir_stacomi)
-# gWidgets::add(ggroupboutons,group)
-# # ggroupboutons is attached to the original frame
-# ggroupboutonsbas = gWidgets::ggroup(horizontal=FALSE)
-# gWidgets::add(ggroupboutons,ggroupboutonsbas)
-# assign("ggroupboutonsbas",ggroupboutonsbas, envir=envir_stacomi)
-# toolbarlist = list(
-# Calc=gWidgets::gaction(handler = hbmCcalc,
-# icon = "new",
-# label=gettext("calculation"),
-# tooltip=gettext("calculation",domain="R-stacomiR")),
-# Graph=gWidgets::gaction(handler = hbmCplotquan,
-# icon = "graph",
-# label="gr quan",
-# tooltip=gettext("Plot for qualitative parm",domain="R-stacomiR")),
-# Graph2=gWidgets::gaction(handler = hbmCplotqual,
-# icon = "graph2",
-# label="gr qual",
-# tooltip=gettext("plot for quantitative parm",domain="R-stacomiR")),
-# Graph3=gWidgets::gaction(handler = hbmCplotcrossed,
-# icon = "graph2",
-# label="gr crossed",
-# tooltip=gettext("Crossed graph for qualitative and quantitative parameter",domain="R-stacomiR")),
-# Stat =gWidgets::gaction(handler= hbmCstat,
-# icon = "matrix",
-# label="stat",
-# tooltip=gettext("Summary",domain="R-stacomiR")),
-# annuler=gWidgets::gaction(handler= quitte,
-# icon = "close",
-# label=gettext("Exit",domain="R-stacomiR")))
-# gWidgets::add(ggroupboutonsbas, gtoolbar(toolbarlist))
-# gWidgets::addSpring(group)
-# assign("r_mig_char",r_mig_char,envir=envir_stacomi)
-#}
\ No newline at end of file
Deleted: pkg/stacomir/R/interface_report_mig_env.R
===================================================================
--- pkg/stacomir/R/interface_report_mig_env.R 2021-11-08 10:49:07 UTC (rev 584)
+++ pkg/stacomir/R/interface_report_mig_env.R 2021-11-09 10:05:16 UTC (rev 585)
@@ -1,69 +0,0 @@
-#deprecated0.6
-##' interface for report_migConditionEnv class
-##' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-##' @keywords internal
-#interface_report_mig_env = function()
-#{
-# quitte()
-# r_mig_env=new("report_mig_env")
-# assign("r_mig_env",r_mig_env,envir=envir_stacomi)
-# funout(gettext("Loading of the lists for taxa, stages, counting devices and monitoring stations\n",domain="R-stacomiR"))
-# r_mig_env at report_env@stationMesure=charge(r_mig_env at report_env@stationMesure)
-# #(destroys everything in envir_stacomi except stuff required at to level)
-# objectreport="report_mig_mult"
-# # the following name is created by the interface
-# # as I can't get the name from within the function (deparse(substitute(objectreport)) does not return
-# # "report_mig_mult" see ref_dc choice_c method)
-# # so this will allow to assign "report_mig_mult" in envir_stacomi while using other class
-# # like ref_dc
-# assign("objectreport",objectreport,envir=envir_stacomi)
-# r_mig_env at report_mig_mult=new("report_mig_mult")
-# assign("report_mig_mult",r_mig_env at report_mig_mult,envir = envir_stacomi)
-# report_dc=new("report_dc")
-# assign("report_dc",report_dc,envir = envir_stacomi)
-# report_df=new("report_df")
-# assign("report_df",report_df,envir = envir_stacomi)
-# report_ope=new("report_ope")
-# assign("report_ope",report_ope, envir=envir_stacomi)
-# report_mig=new("report_mig")
-# assign("report_mig",report_mig,envir = envir_stacomi)
-#
-#
-# r_mig_env at report_mig_mult@taxa=charge(r_mig_env at report_mig_mult@taxa)
-# r_mig_env at report_mig_mult@stage=charge(r_mig_env at report_mig_mult@stage)
-# r_mig_env at report_mig_mult@dc=charge(r_mig_env at report_mig_mult@dc)
-# group = ggroup(horizontal=TRUE) # doit toujours s'appeller group
-# assign("group",group,envir = envir_stacomi)
-# choice(r_mig_env at report_env@stationMesure)
-# notebook <- gnotebook(container=group)
-# assign("notebook",notebook,envir=envir_stacomi)
-# size(notebook)<-c(400,300)
-# ggroupboutons<-get("ggroupboutons",envir=envir_stacomi)
-# add(ggroupboutons,group)
-#
-# choicemult(r_mig_env at report_mig_mult@timestep)
-# choicemult(r_mig_env at report_mig_mult@dc,objectreport=r_mig_env at report_mig_mult,is.enabled=TRUE)
-# svalue(notebook)<-1
-# ggroupboutonsbas = gWidgets::ggroup(horizontal=FALSE)
-# assign("ggroupboutonsbas",ggroupboutonsbas,envir=envir_stacomi)
-# gWidgets::add(ggroupboutons,ggroupboutonsbas)
-#
-# toolbarlist = list(
-# Calc=gWidgets::gaction(handler = hbmmCEcalc,
-# icon = "new",
-# label="calcul",
-# tooltip=gettext("Calculation of environnemental conditions by time step",domain="R-stacomiR")),
-# Graph=gWidgets::gaction(handler = hbmmCEgraph,
-# icon = "graph",
-# label="graph",
-# tooltip=gettext("Balance graphic",domain="R-stacomiR")),
-# annuler=gWidgets::gaction(handler= quitte,
-# icon = "close",
-# label="quitter"))
-# assign("toolbarlist",toolbarlist,envir=envir_stacomi)
-# enabled(toolbarlist[["Graph"]])<-FALSE
-# gWidgets::add(ggroupboutonsbas, gtoolbar(toolbarlist))
-# assign("ggroupboutonsbas",ggroupboutonsbas,envir=envir_stacomi)
-# gWidgets::addSpring(group)
-# return(invisible(NULL))
-#}
\ No newline at end of file
Deleted: pkg/stacomir/R/interface_report_mig_interannual.R
===================================================================
--- pkg/stacomir/R/interface_report_mig_interannual.R 2021-11-08 10:49:07 UTC (rev 584)
+++ pkg/stacomir/R/interface_report_mig_interannual.R 2021-11-09 10:05:16 UTC (rev 585)
@@ -1,106 +0,0 @@
-#deprecated0.6
-##' interface for report_mig_interannual class
-##' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-##' @keywords internal
-#interface_report_mig_interannual = function()
-#{
-# quitte() # vidange de l'interface
-# report_mig_interannual=new("report_mig_interannual")
-# assign("report_mig_interannual",report_mig_interannual,envir=envir_stacomi)
-# funout(gettext("Loading of the existing daily summaries\n",domain="R-stacomiR"))
-# report_mig_interannual at start_year=charge(report_mig_interannual at start_year)
-# report_mig_interannual at end_year=charge(report_mig_interannual at end_year)
-# report_mig_interannual at dc=charge(report_mig_interannual at dc)
-# report_mig_interannual at taxa=charge(report_mig_interannual at taxa)
-# report_mig_interannual at stage=charge(report_mig_interannual at stage)
-#
-# group <- gWidgets::ggroup(horizontal=FALSE) # doit toujours s'appeller group
-# assign("group",group,envir = envir_stacomi)
-# ggroupboutons<-get("ggroupboutons",envir=envir_stacomi)
-# add(ggroupboutons,group)
-#
-# # pour preselectionner une date on lui fournit l'indice de la date dans le ref_year. indice = 11 pour 2005
-#
-# choice(report_mig_interannual at start_year,
-# nomassign="start_year",
-# funoutlabel=gettext("The year of beginning has been chosen\n",domain="R-stacomiR"),
-# titleFrame=gettext("Beginning year",domain="R-stacomiR"),
-# preselect=which(report_mig_interannual at start_year@data==min(report_mig_interannual at start_year@data)))
-# choice(report_mig_interannual at end_year,
-# nomassign="end_year",
-# funoutlabel=gettext("The last year has been chosen\n",domain="R-stacomiR"),
-# titleFrame=gettext("Ending year",domain="R-stacomiR"),
-# preselect=which(report_mig_interannual at start_year@data==max(report_mig_interannual at end_year@data)))
-# choice(report_mig_interannual at dc,objectreport=report_mig_interannual,is.enabled=TRUE)
-#
-# # dans l'ordre
-# # dans le handler, modifier le contenu de l'object fils si il existe
-# # supprimer les widgets fils si ils existent (appel de la methode delete)
-# # appeller la methode choice pour l'affichage du fils si il existe
-# ### premiere toobar
-#
-# ggroupboutonsbas = gWidgets::ggroup(horizontal=FALSE)
-# assign("ggroupboutonsbas",ggroupboutonsbas,envir=envir_stacomi)
-# gWidgets::add(ggroupboutons,ggroupboutonsbas)
-#
-# toolbarlist1 = list(
-# aGraph=gWidgets::gaction(label="all",
-# icon="lines",
-# handler=hgraph_report_mig_interannual,
-# tooltip=gettext("Migration of all the years in the same graphic",domain="R-stacomiR")),
-# aGraph7=gWidgets::gaction(label="cum15",
-# icon="curve",
-# handler=hgraph_report_mig_interannual7,
-# tooltip=gettext("Migration of all the years in the same graphic, cumulated",domain="R-stacomiR")),
-# aGraph3=gWidgets::gaction(label="step",
-# icon="graph2",
-# handler=hgraph_report_mig_interannual3,
-# tooltip=gettext("cumulated migrations %",domain="R-stacomiR")),
-# aSummary=gWidgets::gaction(handler=hsummaryreport_migInterannuelle,
-# icon="dataframe",
-# label="stat",
-# tooltip="summary"),
-# aQuit=gWidgets::gaction(label="fermer",
-# icon="close",
-# handler=quitte,
-# tooltip=gettext("Exit",domain="R-stacomiR"))
-# )
-# toolbarlist2=list(
-# aGraph2=gWidgets::gaction(label=gettext("day",domain="R-stacomiR"),
-# icon="hist",handler=hgraph_report_mig_interannual2,
-# tooltip=gettext("Daily migration",domain="R-stacomiR")),
-# aGraph4=gWidgets::gaction(label=gettext("week",domain="R-stacomiR"),
-# icon="hist",handler=hgraph_report_mig_interannual4,
-# action="semaine",
-# tooltip=gettext("weekly migration",domain="R-stacomiR")),
-# aGraph5=gWidgets::gaction(label=gettext("fortnight",domain="R-stacomiR"),
-# icon="hist",
-# handler=hgraph_report_mig_interannual4,
-# action="quinzaine",
-# tooltip=gettext("Fortnight Migration",domain="R-stacomiR")),
-# aGraph6=gWidgets::gaction(label=gettext("month",domain="R-stacomiR"),
-# icon="hist",handler=hgraph_report_mig_interannual4,
-# action="mois",
-# tooltip=gettext("Monthly migration",domain="R-stacomiR"))
-# )
-# toolbarlist3=list(
-# aGraph1=gWidgets::gaction(label=gettext("week",domain="R-stacomiR"),
-# icon="gWidgetsRGtk2-points",handler=hgraph_report_mig_interannual5,
-# action="semaine",
-# tooltip=gettext("weekly migration",domain="R-stacomiR")),
-# aGraph2=gWidgets::gaction(label=gettext("fortnight",domain="R-stacomiR"),
-# icon="gWidgetsRGtk2-points",
-# handler=hgraph_report_mig_interannual5,
-# action="quinzaine",
-# tooltip=gettext("Fortnight migration",domain="R-stacomiR")),
-# aGraph3=gWidgets::gaction(label=gettext("month",domain="R-stacomiR"),
-# icon="gWidgetsRGtk2-points",handler=hgraph_report_mig_interannual5,
-# action="mois",
-# tooltip=gettext("Monthly migration",domain="R-stacomiR"))
-# )
-# add(ggroupboutonsbas, gtoolbar(toolbarlist1))
-# add(ggroupboutonsbas, gtoolbar(toolbarlist2))
-# add(ggroupboutonsbas, gtoolbar(toolbarlist3))
-# gWidgets::addSpring(group)
-# dev.new()
-#}
\ No newline at end of file
Deleted: pkg/stacomir/R/interface_report_mig_mult.R
===================================================================
--- pkg/stacomir/R/interface_report_mig_mult.R 2021-11-08 10:49:07 UTC (rev 584)
+++ pkg/stacomir/R/interface_report_mig_mult.R 2021-11-09 10:05:16 UTC (rev 585)
@@ -1,74 +0,0 @@
-#deprecated0.6
-##' graphical interface for report_mig_mult class
-##'
-##' launches the graphical interface after the main gwidget dialog has been launched
-##' This function is called from a handler in the main graphical interface
-##' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-##' @keywords internal
-#interface_report_mig_mult=function(){
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 585
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