[Stacomir-commits] r189 - in pkg/stacomir: . R examples/01_BilanMigrationMult examples/02_BilanMigration inst/config inst/tests/testthat man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Sep 4 22:06:20 CEST 2016
Author: briand
Date: 2016-09-04 22:06:19 +0200 (Sun, 04 Sep 2016)
New Revision: 189
Modified:
pkg/stacomir/NAMESPACE
pkg/stacomir/R/BilanMigration.r
pkg/stacomir/R/RefMsg.r
pkg/stacomir/R/fn_EcritBilanJournalier.r
pkg/stacomir/R/fn_EcritBilanMensuel.r
pkg/stacomir/R/fungraph.r
pkg/stacomir/R/funstat.r
pkg/stacomir/R/stacomi.r
pkg/stacomir/R/utilitaires.r
pkg/stacomir/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R
pkg/stacomir/examples/02_BilanMigration/bilanMigration_Arzal.R
pkg/stacomir/inst/config/generate_data.R
pkg/stacomir/inst/config/stacomi_manual_launch.r
pkg/stacomir/inst/tests/testthat/test-00stacomir.R
pkg/stacomir/inst/tests/testthat/test-01BilanMigrationMult.R
pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
pkg/stacomir/man/BilanMigration-class.Rd
pkg/stacomir/man/BilanMigrationMult-class.Rd
pkg/stacomir/man/createmessage-RefMsg-method.Rd
pkg/stacomir/man/husr.Rd
pkg/stacomir/man/plot-BilanMigration-ANY-method.Rd
pkg/stacomir/man/stacomi.Rd
Log:
Writing daily bilan and monthly bilan.
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/NAMESPACE 2016-09-04 20:06:19 UTC (rev 189)
@@ -48,6 +48,7 @@
exportMethods(supprime)
import(Hmisc)
import(RColorBrewer)
+import(RGtk2)
import(RODBC)
import(RPostgreSQL)
import(gWidgets)
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/R/BilanMigration.r 2016-09-04 20:06:19 UTC (rev 189)
@@ -264,7 +264,8 @@
#' \item{plot.type="multiple"}{Method to overlay graphs for BilanMigrationMult (multiple dc/taxa/stage in the same plot)}
#' }
#' @note When plotting the "standard" plot, the user will be prompted to "write" the daily migration and monthly migration in the database.
-#' these entries are necessary to run the Interannual Migration class.
+#' these entries are necessary to run the Interannual Migration class. If the stacomi has been launched with database_expected=FALSE,
+#' then no entry will be written to the database
#' @param x An object of class BilanMigrationMult
#' @param y From the formals but missing
#' @param plot.type One of "standard","step". Defaut to \code{standard} the standard BilanMigration with dc and operation displayed, can also be \code{step} or
@@ -346,7 +347,8 @@
###########################################""
# Writes the daily bilan in the database
#########################################
- fn_EcritBilanJournalier(bilanMigration)
+ database_expected<-get("database_expected",envir=envir_stacomi)
+ if (database_expected) fn_EcritBilanJournalier(bilanMigration,silent)
} # end is.null(data)
#§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§§
Modified: pkg/stacomir/R/RefMsg.r
===================================================================
--- pkg/stacomir/R/RefMsg.r 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/R/RefMsg.r 2016-09-04 20:06:19 UTC (rev 189)
@@ -49,15 +49,15 @@
#' createmessage method for RefMsg referential objects
#' @param ojbect An objet of class RefMsg
-#' @param pre_launch_test Default to TRUE, if FALSE, no database connection is expected and the messages will be loaded from msg dataset within the package
+#' @param database_expected Default to TRUE, if FALSE, no database connection is expected and the messages will be loaded from msg dataset within the package
#' @return An S4 object of class RefMsg
#' @note When coming from the database, doublequotes are now escaped with an antislash (/"), those at the beginning and end are left as doublequotes,
#' the others are single quote when they are to be pasted within the text as code example. The remainder "c("a","b","c") are rebuilt into vectors by the function
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
#' @keywords internal
-setMethod("createmessage",signature=signature("RefMsg"),definition=function(object,pre_launch_test) {
- if (pre_launch_test){
+setMethod("createmessage",signature=signature("RefMsg"),definition=function(object,database_expected) {
+ if (database_expected){
#object=new("RefMsg")
object<-charge(object)
object<-charge_avec_filtre(object,lang=get("lang",envir=envir_stacomi))
@@ -114,7 +114,7 @@
}
msg<-create_vector(msg)
assign("msg",msg,envir=envir_stacomi)
- } else { # !pre_launch_test
+ } else { # !database_expected
utils::data("msg")
assign("msg",msg,envir=envir_stacomi)
}
Modified: pkg/stacomir/R/fn_EcritBilanJournalier.r
===================================================================
--- pkg/stacomir/R/fn_EcritBilanJournalier.r 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/R/fn_EcritBilanJournalier.r 2016-09-04 20:06:19 UTC (rev 189)
@@ -5,28 +5,40 @@
#' the function fn_EcritBilanJournalier
#'
#' @param bilanMigration an object of class \code{\linkS4class{BilanMigration}}
+#' @param silent : TRUE to avoid messages
#' @note the user is asked whether or not he wants to overwrite data, if no
#' data are present in the database, the import is done anyway
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @examples
+#' \dontrun{
+#' stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
+#' data("bM_Arzal")
+#' bM_Arzal<-calcule(bM_Arzal)
+#' fn_EcritBilanJournalier(bilanMigration=bM_Arzal,silent=FALSE)
+#' }
#' @export
-fn_EcritBilanJournalier<-function(bilanMigration){
+fn_EcritBilanJournalier<-function(bilanMigration,silent){
# voir essai_table_bilanJournalier.sql pour le format du tableau
# je cherche les colonnes que je ne veux pas retenir
- data=bilanMigration at data
- jour_dans_lannee_non_nuls=strftime(bilanMigration at time.sequence,'%Y-%m-%d %H:%M:%S')[data$Effectif_total!=0]
+ if (class(bilanMigration)!="BilanMigration") stop("the bilanMigration should be of class BilanMigration")
+ if (class(silent)!="logical") stop("the silent argument should be a logical")
+ dc=as.numeric(bilanMigration at dc@dc_selectionne)[1]
+ data=bilanMigration at calcdata[[stringr::str_c("dc_",dc)]][["data"]]
+ jour_dans_lannee_non_nuls=data$debut_pas
data=data[data$Effectif_total!=0,]
- col_a_retirer=match(c("No.pas","type_de_quantite"),colnames(data))
+ col_a_retirer=match(c("No.pas","type_de_quantite","debut_pas","fin_pas"),colnames(data))
data=data[,-col_a_retirer]
- data$"Taux_d_echappement"[data$Taux_d_echappement==-1]<-NA
+ data$taux_d_echappement[data$taux_d_echappement==-1]<-NA
data$coe_valeur_coefficient[data$"coe_valeur_coefficient"==1]<-NA
- peuventpaszero=match(c("Taux_d_echappement","coe_valeur_coefficient"),colnames(data))
+ peuventpaszero=match(c("taux_d_echappement","coe_valeur_coefficient"),colnames(data))
data[,-peuventpaszero][data[,-peuventpaszero]==0]<-NA
- t_bilanmigrationjournalier_bjo=cbind(bilanMigration at dc@dc_selectionne,
+ t_bilanmigrationjournalier_bjo=cbind(
+ bilanMigration at dc@dc_selectionne,
bilanMigration at taxons@data$tax_code,
bilanMigration at stades@data$std_code,
- unique(strftime(as.POSIXlt(bilanMigration at time.sequence),"%Y")),
- rep(jour_dans_lannee_non_nuls,ncol(data)),
- utils::stack(data),
+ unique(strftime(as.POSIXlt(bilanMigration at time.sequence),"%Y")), # une valeur
+ rep(as.character(jour_dans_lannee_non_nuls),ncol(data[,c("MESURE","CALCULE","EXPERT","PONCTUEL","Effectif_total","taux_d_echappement","coe_valeur_coefficient")])),
+ utils::stack(data[,c("MESURE","CALCULE","EXPERT","PONCTUEL","Effectif_total","taux_d_echappement","coe_valeur_coefficient")]),
format(Sys.time(), "%Y-%m-%d %H:%M:%S"),
substr(toupper(get("sch",envir=envir_stacomi)),1,nchar(toupper(get("sch",envir=envir_stacomi)))-1)
)
@@ -76,8 +88,8 @@
} # end for
funout(paste(get("msg",envir=envir_stacomi)$fn_EcritBilanJournalier.5,"\n"))
# si l'utilisateur accepte de remplacer les valeurs
- dispose(progres)
odbcClose(requete at connection)
+ gtkWidgetDestroy(progres)
# ecriture egalement du bilan mensuel
taxon= as.character(bilanMigration at taxons@data$tax_nom_latin)
stade= as.character(bilanMigration at stades@data$std_libelle)
@@ -126,13 +138,13 @@
"('",paste(t_bilanmigrationjournalier_bjo[i,],collapse="','"),"');",sep="")
requete<-stacomirtools::connect(requete)
} # end for
- dispose(progres)
RODBC::odbcClose(requete at connection)
funout(paste(get("msg",envir=envir_stacomi)$fn_EcritBilanJournalier.5,"\n"))
taxon= as.character(bilanMigration at taxons@data$tax_nom_latin)
stade= as.character(bilanMigration at stades@data$std_libelle)
DC=as.numeric(bilanMigration at dc@dc_selectionne)
- resum=funstat(tableau=bilanMigration at data,time.sequence=bilanMigration at time.sequence,taxon,stade,DC)
+ tableau<-bilanMigration at calcdata[[stringr::str_c("dc_",DC)]][["data"]]
+ resum=funstat(tableau=tableau,time.sequence=tableau$debut_pas,taxon,stade,DC,silent=silent)
fn_EcritBilanMensuel(bilanMigration,resum)
} # end else
} # end function
Modified: pkg/stacomir/R/fn_EcritBilanMensuel.r
===================================================================
--- pkg/stacomir/R/fn_EcritBilanMensuel.r 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/R/fn_EcritBilanMensuel.r 2016-09-04 20:06:19 UTC (rev 189)
@@ -1,6 +1,7 @@
#' This writes monthly data in t_bilanmensuel_mens table
#'
-#' Launched by fun_EcritBilanJournalier
+#' @note This function is launched by fun_EcritBilanJournalier, the resum
+#' dataset is created by the \link{funstat} function
#'
#'
#' @param bilanMigration an object of class \code{\linkS4class{BilanMigration}}
@@ -8,14 +9,15 @@
#' @export
fn_EcritBilanMensuel<-function(bilanMigration,resum){
# voir essai_table_bilanmensuel.sql pour le format du tableau
+ # below not the most elegant way to do it but efficient
+
t_bilanmigrationmensuel_bme=stacomirtools::killfactor(
cbind(bilanMigration at dc@dc_selectionne,
bilanMigration at taxons@data$tax_code,
bilanMigration at stades@data$std_code,
- unique(strftime(as.POSIXlt(bilanMigration at time.sequence),"%Y")),
- rep(rownames(resum),12),
- # stack re-ordonne les tab de donnees !
- stack(resum,select=c(1:13)),
+ unique(strftime(as.POSIXlt(bilanMigration at time.sequence),"%Y")), # une valeur
+ rep(rownames(resum),(ncol(resum)-2)), # nb of month except columns bilan and label
+ stack(resum,select=c(2:(ncol(resum)-1))),# stack re-ordonne les tab de donnees !
format(Sys.time(), "%Y-%m-%d %H:%M:%S"),
substr(toupper(get("sch",envir=envir_stacomi)),1,nchar(toupper(get("sch",envir=envir_stacomi)))-1)
)
Modified: pkg/stacomir/R/fungraph.r
===================================================================
--- pkg/stacomir/R/fungraph.r 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/R/fungraph.r 2016-09-04 20:06:19 UTC (rev 189)
@@ -355,7 +355,6 @@
graphics::par("mar"=c(4, 4, 1, 2) + 0.1)
tableau$mois=factor(months(tableau$debut_pas,abbreviate=TRUE),
levels=unique(months(tableau$debut_pas,abbreviate=TRUE)))
-
tableaum<-reshape2::melt(data=tableau[,c("MESURE","CALCULE","EXPERT","PONCTUEL","mois")],
id.vars=c("mois"),
measure.vars=c("MESURE","CALCULE","EXPERT","PONCTUEL"),
Modified: pkg/stacomir/R/funstat.r
===================================================================
--- pkg/stacomir/R/funstat.r 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/R/funstat.r 2016-09-04 20:06:19 UTC (rev 189)
@@ -9,8 +9,9 @@
#' @param DC The counting device
#' @param silent Message displayed or not
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @export
funstat=function(tableau,time.sequence,taxon,stade,DC,silent){
- funout(get("msg",envir=envir_stacomi)$funstat.1)
+ if (!silent) funout(get("msg",envir=envir_stacomi)$funstat.1)
mois=strftime(as.POSIXlt(time.sequence),"%m")
moislab=unique(mois)
annee=unique(strftime(as.POSIXlt(time.sequence),"%Y"))
Modified: pkg/stacomir/R/stacomi.r
===================================================================
--- pkg/stacomir/R/stacomi.r 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/R/stacomi.r 2016-09-04 20:06:19 UTC (rev 189)
@@ -87,7 +87,7 @@
#' Internal function, tests the connection and if it works loads the stacomi interface
-#' @note \code{gr_interface} is copied by stacomi into envir_stacomi. Same for \code{pre_launch_test}
+#' @note \code{gr_interface} is copied by stacomi into envir_stacomi. Same for \code{database_expected}
#'
#' @param h A handler
#' @param ... Other arguments
@@ -96,10 +96,10 @@
baseODBC<-get("baseODBC",envir=envir_stacomi)
# assigned when passing through stacomi
gr_interface<-get("gr_interface",envir_stacomi) # logical true or false
- pre_launch_test<-get("pre_launch_test",envir_stacomi) # logical true or false
+ database_expected<-get("database_expected",envir_stacomi) # logical true or false
login_window<-get("login_window",envir_stacomi) # logical true or false
# test de la connection
- if (login_window & gr_interface&pre_launch_test){
+ if (login_window & gr_interface&database_expected){
baseODBC[2]<-svalue(usrname)
baseODBC[3]<-svalue(usrpwd)
assign("sch",paste(baseODBC[2],".",sep=""),envir=envir_stacomi)
@@ -112,7 +112,7 @@
# we dispose loginwindow
- if (pre_launch_test){
+ if (database_expected){
con=new("ConnectionODBC")
con at baseODBC=get("baseODBC",envir=envir_stacomi)
e=expression(con<-connect(con))
@@ -129,7 +129,7 @@
#############################
# second test to check that the database is working well
############################
- if (pre_launch_test){
+ if (database_expected){
if (test) { # il existe un lien ODBC mais qui pointe peut etre ailleurs
requete=new("RequeteODBC")
requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
@@ -181,7 +181,7 @@
handler=hgmessage)
} # end else test (else == the test didn't pass, we have to change the name and password
} else {
- # here : pre_launch_test=FALSE
+ # here : database_expected=FALSE
# we don't want to check the connection at all...
if (gr_interface){
interface_graphique()
@@ -213,26 +213,27 @@
#' the program will skip the login window and use calcmig values for user (\code{uid}) and password(\code{pwd}) as a default.}
#' \item{tests for connection}{ Test for the existence of a calcmig.csv file, and then the existence of the file
#' \code{usr.tr_taxon_tax} where usr is the username extracted from calcmig. These tests are only done if
-#' \code{pre_launch_test=TRUE}. If the test don't pass, then the user is prompted for a "login window" even if argument
+#' \code{database_expected=TRUE}. If the test don't pass, then the user is prompted for a "login window" even if argument
#' \code{login_window} was set to \code{FALSE} at launch.}
#' \item{graphical interface}{ When either, previous tests have been run successfully, or the value for
-#' \code{pre_launch_test=FALSE} the program will launch. If \code{graphical_interface} is \code{TRUE}, the program will use
+#' \code{database_expected=FALSE} the program will launch. If \code{graphical_interface} is \code{TRUE}, the program will use
#' a graphical interface \code{\link{interface_graphique}} to build the graphical interface, otherwise the program is expected to run
#' through the command line.}
#' }
-#' When \code{pre_launch_test=FALSE} a connection to the database is not expected. Therefore test are run by calling examples object stored in Rdata.
+#' When \code{database_expected=FALSE} a connection to the database is not expected. Therefore test are run by calling examples object stored in Rdata.
#' And also messages are downloaded from the database in several languages. These are loaded from the data directory of the package instead, and
#' are only avalaible in english.
#'
#' @param gr_interface Boolean, if \code{TRUE} the program will launch the graphical interface
#' @param login_window Boolean, if \code{TRUE} a login window will be displayed asking the user to specify
#' user name.
-#' @param pre_launch_test Boolean, if \code{TRUE} pre launch tests will be run to test the connection validity
-#' @usage stacomi(gr_interface=TRUE,login_window=TRUE,pre_launch_test=TRUE)
+#' @param database_expected Boolean, if \code{TRUE} pre launch tests will be run to test the connection validity
+#' @usage stacomi(gr_interface=TRUE,login_window=TRUE,database_expected=TRUE)
#' @import stringr
#' @import RColorBrewer
#' @import gWidgets
#' @import gWidgetsRGtk2
+#' @import RGtk2
#' @import ggplot2
#' @import RPostgreSQL
#' @import sqldf
@@ -240,6 +241,7 @@
#' @import stacomirtools
#' @import RODBC
#' @import Hmisc
+#' @import RGtk2
#' @importFrom intervals Intervals
#' @importFrom intervals closed<-
#' @importFrom intervals interval_overlap
@@ -273,15 +275,15 @@
#' stacomi(login_window=FALSE)
#' }
#' #launch stacomi without connection to the database
-#' stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
+#' stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
#' @export
-stacomi=function(gr_interface=TRUE,login_window=TRUE,pre_launch_test=TRUE){
+stacomi=function(gr_interface=TRUE,login_window=TRUE,database_expected=TRUE){
# first loading of connection and odbc info using chargexml()
envir_stacomi <- new.env(parent = emptyenv())
assign("envir_stacomi",envir_stacomi,.GlobalEnv)
# trois variables passées à interface graphique via envir_stacomi :
assign("gr_interface",gr_interface,envir=envir_stacomi)
- assign("pre_launch_test",pre_launch_test,envir=envir_stacomi)
+ assign("database_expected",database_expected,envir=envir_stacomi)
assign("login_window",login_window,envir=envir_stacomi)
# the first messages are necessary for the first access to the database, they are in French
msg<-messages()
@@ -300,7 +302,7 @@
assign("sch",paste(baseODBC[2],".",sep=""),envir=envir_stacomi)
refMsg=new("RefMsg")
- createmessage(refMsg,pre_launch_test)
+ createmessage(refMsg,database_expected)
msg=get("msg",envir=envir_stacomi)
#libraries()
@@ -311,7 +313,7 @@
sqldf.RPostgreSQL.port = sqldf.options["sqldf.port"])
# loginWindow, will call the husr handler
# user login
- if (gr_interface&login_window&pre_launch_test){
+ if (gr_interface&login_window&database_expected){
logw <- gWidgets::gwindow(msg$interface_graphique_log.1,
name="log",
parent=c(0,0),
Modified: pkg/stacomir/R/utilitaires.r
===================================================================
--- pkg/stacomir/R/utilitaires.r 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/R/utilitaires.r 2016-09-04 20:06:19 UTC (rev 189)
@@ -219,7 +219,7 @@
#'dispose(progres)
#' }
mygtkProgressBar<-function(title,progress_text,width=400,height=50,pulse=TRUE){
- .dialog <- RGtk2::gtkDialog(title=title, NULL, NULL,
+ .dialog <- gWidgetsRGtk2::gtkDialog(title=title, NULL, NULL,
"gtk-close", RGtk2::GtkResponseType["none"],
show = FALSE)
assign("progres",.dialog,envir=envir_stacomi)
Modified: pkg/stacomir/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R
===================================================================
--- pkg/stacomir/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R 2016-09-04 20:06:19 UTC (rev 189)
@@ -1,6 +1,6 @@
library(stacomiR)
-stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
+stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
## launches the application in the command line
## here an example of loading
## not run as the program is possibly not installed
@@ -8,7 +8,7 @@
\dontrun{
stacomi(gr_interface=FALSE,
login_window=FALSE,
- pre_launch_test=FALSE)
+ database_expected=FALSE)
bMM_Arzal=new("BilanMigrationMult")
bMM_Arzal=choice_c(bMM_Arzal,
dc=c(5,6,12),
Modified: pkg/stacomir/examples/02_BilanMigration/bilanMigration_Arzal.R
===================================================================
--- pkg/stacomir/examples/02_BilanMigration/bilanMigration_Arzal.R 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/examples/02_BilanMigration/bilanMigration_Arzal.R 2016-09-04 20:06:19 UTC (rev 189)
@@ -1,6 +1,6 @@
library(stacomiR)
-stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
+stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
## launches the application in the command line
## here an example of loading
## not run as the program is possibly not installed
@@ -8,7 +8,7 @@
\dontrun{
stacomi(gr_interface=FALSE,
login_window=FALSE,
- pre_launch_test=FALSE)
+ database_expected=FALSE)
bM_Arzal=new("BilanMigration")
bM_Arzal=choice_c(bM_Arzal,
dc=5,
@@ -30,6 +30,8 @@
bM_Arzal<-calcule(bM_Arzal)
#Individual plot for all DC (standard), taxon and stage where data present
#silent argument to stop all messages
+# this will also write daily and monthly migration balance to the database,
+# but only if stacomi has been run with argument : database_expected=FALSE
plot(bM_Arzal,plot.type="standard",silent=TRUE)
#cumulated migration at the station (all stages and DC grouped)
Modified: pkg/stacomir/inst/config/generate_data.R
===================================================================
--- pkg/stacomir/inst/config/generate_data.R 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/inst/config/generate_data.R 2016-09-04 20:06:19 UTC (rev 189)
@@ -6,7 +6,7 @@
source ("F:/workspace/stacomir/pkg/stacomir/inst/config/stacomi_manual_launch.r")
assign("lang","English",envir=envir_stacomi)
refMsg=new("RefMsg")
-createmessage(refMsg,pre_launch_test=TRUE)
+createmessage(refMsg,database_expected=TRUE)
msg=get("msg",envir=envir_stacomi)
devtools::use_data(msg,internal=FALSE,overwrite=TRUE)
@@ -42,7 +42,7 @@
stacomi(gr_interface=FALSE,
login_window=FALSE,
- pre_launch_test=FALSE)
+ database_expected=FALSE)
bM_Arzal=new("BilanMigration")
bM_Arzal=choice_c(bM_Arzal,
dc=5,
Modified: pkg/stacomir/inst/config/stacomi_manual_launch.r
===================================================================
--- pkg/stacomir/inst/config/stacomi_manual_launch.r 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/inst/config/stacomi_manual_launch.r 2016-09-04 20:06:19 UTC (rev 189)
@@ -100,6 +100,6 @@
# interface_BilanEspeces dans BilanEspeces
setwd("F:/workspace/stacomir/pkg/stacomir")
data("msg")
- stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
+ stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
Modified: pkg/stacomir/inst/tests/testthat/test-00stacomir.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2016-09-04 20:06:19 UTC (rev 189)
@@ -76,7 +76,7 @@
test_that("Test that working environment is created",{
require(stacomiR)
- stacomi(gr_interface=TRUE,login_window=TRUE,pre_launch_test=TRUE)
+ stacomi(gr_interface=TRUE,login_window=TRUE,database_expected=TRUE)
expect_true(exists("envir_stacomi"))
dispose(logw)
rm("envir_stacomi",envir =.GlobalEnv)
@@ -84,15 +84,15 @@
test_that("Test that gWidget loginwindow is loaded ",{
require(stacomiR)
- stacomi(gr_interface=TRUE,login_window=TRUE,pre_launch_test=TRUE)
+ stacomi(gr_interface=TRUE,login_window=TRUE,database_expected=TRUE)
expect_true(exists("logw"))
dispose(logw)
rm("envir_stacomi",envir =.GlobalEnv)
})
-test_that("Test that gWidget gr_interface is loaded, without pre_launch_test, nor login window",{
+test_that("Test that gWidget gr_interface is loaded, without database_expected, nor login window",{
require(stacomiR)
- stacomi(gr_interface=TRUE,login_window=FALSE,pre_launch_test=FALSE)
+ stacomi(gr_interface=TRUE,login_window=FALSE,database_expected=FALSE)
expect_true(exists("win"))
dispose(win)
rm("envir_stacomi",envir =.GlobalEnv)
@@ -100,7 +100,7 @@
test_that("gWidget gr_interface is loaded, with pre launch_test, but without login window",{
require(stacomiR)
- stacomi(gr_interface=TRUE,login_window=FALSE,pre_launch_test=TRUE)
+ stacomi(gr_interface=TRUE,login_window=FALSE,database_expected=TRUE)
expect_true(exists("win"))
dispose(win)
rm("envir_stacomi",envir =.GlobalEnv)
@@ -127,7 +127,7 @@
object<-createmessage(object,TRUE)
msgbase<-get("msg",envir=envir_stacomi)
require(stacomiR)
- stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
+ stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
msg<-get("msg",envir=envir_stacomi)
# objects should have the same length but different languages
expect_identical(length(msg),length(msgbase))
Modified: pkg/stacomir/inst/tests/testthat/test-01BilanMigrationMult.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-01BilanMigrationMult.R 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/inst/tests/testthat/test-01BilanMigrationMult.R 2016-09-04 20:06:19 UTC (rev 189)
@@ -1,7 +1,7 @@
context("BilanMigrationMult")
test_that("Test an instance of bilanMigrationMult",{
require(stacomiR)
- stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
+ stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
bilanMigrationMult<-new("BilanMigrationMult")
options(warn = 2)
bilanMigrationMult<-choice_c(bilanMigrationMult,
@@ -16,7 +16,7 @@
## This test check that the code above works with numeric and a different formating for date
test_that("Test another instance of bilanMigrationMult",{
require(stacomiR)
- stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
+ stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
bilanMigrationMult<-new("BilanMigrationMult")
options(warn = 2)
bilanMigrationMult<-choice_c(bilanMigrationMult,
@@ -31,7 +31,7 @@
test_that("Tests one instance with error (dc does not exist)",
{
require(stacomiR)
- stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
+ stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
bilanMigrationMult<-new("BilanMigrationMult")
options(warn = 2)
expect_error(choice_c(bilanMigrationMult,
@@ -45,7 +45,7 @@
test_that("Tests one instance with error (dc does not exist)",
{
require(stacomiR)
- stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
+ stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
bilanMigrationMult<-new("BilanMigrationMult")
options(warn = 2)
expect_error(choice_c(bilanMigrationMult,
Modified: pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R 2016-09-04 20:06:19 UTC (rev 189)
@@ -1,7 +1,7 @@
context("BilanMigration")
test_that("Test an instance of bilanMigration",{
require(stacomiR)
- stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
+ stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
# overriding user schema to point to iav
baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("iav",2)
@@ -26,7 +26,7 @@
test_that("Test connect method",{
stacomi(gr_interface=FALSE,
login_window=FALSE,
- pre_launch_test=FALSE)
+ database_expected=FALSE)
# overriding user schema
baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("iav",2)
Modified: pkg/stacomir/man/BilanMigration-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigration-class.Rd 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/man/BilanMigration-class.Rd 2016-09-04 20:06:19 UTC (rev 189)
@@ -34,7 +34,7 @@
\examples{
library(stacomiR)
-stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
+stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
## launches the application in the command line
## here an example of loading
## not run as the program is possibly not installed
@@ -42,7 +42,7 @@
\dontrun{
stacomi(gr_interface=FALSE,
login_window=FALSE,
- pre_launch_test=FALSE)
+ database_expected=FALSE)
bM_Arzal=new("BilanMigration")
bM_Arzal=choice_c(bM_Arzal,
dc=5,
Modified: pkg/stacomir/man/BilanMigrationMult-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationMult-class.Rd 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/man/BilanMigrationMult-class.Rd 2016-09-04 20:06:19 UTC (rev 189)
@@ -45,7 +45,7 @@
\examples{
library(stacomiR)
-stacomi(gr_interface=FALSE,login_window=FALSE,pre_launch_test=FALSE)
+stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
## launches the application in the command line
## here an example of loading
## not run as the program is possibly not installed
@@ -53,7 +53,7 @@
\dontrun{
stacomi(gr_interface=FALSE,
login_window=FALSE,
- pre_launch_test=FALSE)
+ database_expected=FALSE)
bMM_Arzal=new("BilanMigrationMult")
bMM_Arzal=choice_c(bMM_Arzal,
dc=c(5,6,12),
Modified: pkg/stacomir/man/createmessage-RefMsg-method.Rd
===================================================================
--- pkg/stacomir/man/createmessage-RefMsg-method.Rd 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/man/createmessage-RefMsg-method.Rd 2016-09-04 20:06:19 UTC (rev 189)
@@ -5,10 +5,10 @@
\alias{createmessage,RefMsg-method}
\title{createmessage method for RefMsg referential objects}
\usage{
-\S4method{createmessage}{RefMsg}(object, pre_launch_test)
+\S4method{createmessage}{RefMsg}(object, database_expected)
}
\arguments{
-\item{pre_launch_test}{Default to TRUE, if FALSE, no database connection is expected and the messages will be loaded from msg dataset within the package}
+\item{database_expected}{Default to TRUE, if FALSE, no database connection is expected and the messages will be loaded from msg dataset within the package}
\item{ojbect}{An objet of class RefMsg}
}
Modified: pkg/stacomir/man/husr.Rd
===================================================================
--- pkg/stacomir/man/husr.Rd 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/man/husr.Rd 2016-09-04 20:06:19 UTC (rev 189)
@@ -15,7 +15,7 @@
Internal function, tests the connection and if it works loads the stacomi interface
}
\note{
-\code{gr_interface} is copied by stacomi into envir_stacomi. Same for \code{pre_launch_test}
+\code{gr_interface} is copied by stacomi into envir_stacomi. Same for \code{database_expected}
}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
Modified: pkg/stacomir/man/plot-BilanMigration-ANY-method.Rd
===================================================================
--- pkg/stacomir/man/plot-BilanMigration-ANY-method.Rd 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/man/plot-BilanMigration-ANY-method.Rd 2016-09-04 20:06:19 UTC (rev 189)
@@ -3,7 +3,7 @@
\docType{methods}
\name{plot,BilanMigration,ANY-method}
\alias{plot,BilanMigration,ANY-method}
-\title{Plots of various type for BilanMigration}
+\title{Plots of various type for BilanMigration, and performs writing to the database of daily values.}
\usage{
\S4method{plot}{BilanMigration,ANY}(x, y, plot.type = "standard",
silent = FALSE, ...)
@@ -26,6 +26,10 @@
\item{plot.type="multiple"}{Method to overlay graphs for BilanMigrationMult (multiple dc/taxa/stage in the same plot)}
}
}
+\note{
+When plotting the "standard" plot, the user will be prompted to "write" the daily migration and monthly migration in the database.
+these entries are necessary to run the Interannual Migration class.
+}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
Modified: pkg/stacomir/man/stacomi.Rd
===================================================================
--- pkg/stacomir/man/stacomi.Rd 2016-09-01 19:39:15 UTC (rev 188)
+++ pkg/stacomir/man/stacomi.Rd 2016-09-04 20:06:19 UTC (rev 189)
@@ -5,7 +5,7 @@
\title{Function that loads the loginwindow, tests connection, and then destroys the
window}
\usage{
-stacomi(gr_interface=TRUE,login_window=TRUE,pre_launch_test=TRUE)
+stacomi(gr_interface=TRUE,login_window=TRUE,database_expected=TRUE)
}
\arguments{
\item{gr_interface}{Boolean, if \code{TRUE} the program will launch the graphical interface}
@@ -13,7 +13,7 @@
\item{login_window}{Boolean, if \code{TRUE} a login window will be displayed asking the user to specify
user name.}
-\item{pre_launch_test}{Boolean, if \code{TRUE} pre launch tests will be run to test the connection validity}
+\item{database_expected}{Boolean, if \code{TRUE} pre launch tests will be run to test the connection validity}
}
\description{
Function that loads the loginwindow, tests connection, and then destroys the
@@ -28,14 +28,14 @@
the program will skip the login window and use calcmig values for user (\code{uid}) and password(\code{pwd}) as a default.}
\item{tests for connection}{ Test for the existence of a calcmig.csv file, and then the existence of the file
\code{usr.tr_taxon_tax} where usr is the username extracted from calcmig. These tests are only done if
- \code{pre_launch_test=TRUE}. If the test don't pass, then the user is prompted for a "login window" even if argument
+ \code{database_expected=TRUE}. If the test don't pass, then the user is prompted for a "login window" even if argument
\code{login_window} was set to \code{FALSE} at launch.}
\item{graphical interface}{ When either, previous tests have been run successfully, or the value for
- \code{pre_launch_test=FALSE} the program will launch. If \code{graphical_interface} is \code{TRUE}, the program will use
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 189
More information about the Stacomir-commits
mailing list