[Stacomir-commits] r399 - in pkg/stacomir: R inst/config inst/examples man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jun 17 22:16:18 CEST 2017
Author: briand
Date: 2017-06-17 22:16:18 +0200 (Sat, 17 Jun 2017)
New Revision: 399
Modified:
pkg/stacomir/R/BilanAgedemer.r
pkg/stacomir/R/BilanAnnuels.r
pkg/stacomir/R/BilanArgentee.r
pkg/stacomir/R/BilanConditionEnv.r
pkg/stacomir/R/BilanEspeces.r
pkg/stacomir/R/BilanFonctionnementDC.r
pkg/stacomir/R/BilanFonctionnementDF.r
pkg/stacomir/R/BilanMigration.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_carlot.r
pkg/stacomir/R/Bilan_poids_moyen.r
pkg/stacomir/R/create_generic.r
pkg/stacomir/R/stacomi.r
pkg/stacomir/inst/config/generate_data.R
pkg/stacomir/inst/examples/bilanArgentee_example.R
pkg/stacomir/inst/examples/bilanEspeces_example.R
pkg/stacomir/inst/examples/bilanFonctionnementDC_example.R
pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R
pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
pkg/stacomir/inst/examples/bilanMigrationMultConditionEnv_example.R
pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R
pkg/stacomir/inst/examples/bilanMigration_Arzal.R
pkg/stacomir/inst/examples/bilancarlot_example.R
pkg/stacomir/man/BilanArgentee-class.Rd
pkg/stacomir/man/BilanFonctionnementDC-class.Rd
pkg/stacomir/man/BilanFonctionnementDF-class.Rd
pkg/stacomir/man/BilanMigration-class.Rd
pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
pkg/stacomir/man/BilanMigrationMult-class.Rd
pkg/stacomir/man/BilanMigrationMultConditionEnv-class.Rd
pkg/stacomir/man/Bilan_carlot-class.Rd
pkg/stacomir/man/Bilan_poids_moyen-class.Rd
pkg/stacomir/man/calcule-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/calcule-BilanMigrationMult-method.Rd
pkg/stacomir/man/calcule-BilanMigrationMultConditionEnv-method.Rd
pkg/stacomir/man/calcule-Bilan_carlot-method.Rd
pkg/stacomir/man/charge-BilanAgedemer-method.Rd
pkg/stacomir/man/charge-BilanAnnuels-method.Rd
pkg/stacomir/man/charge-BilanArgentee-method.Rd
pkg/stacomir/man/charge-BilanConditionEnv-method.Rd
pkg/stacomir/man/charge-BilanEspeces-method.Rd
pkg/stacomir/man/charge-BilanFonctionnementDC-method.Rd
pkg/stacomir/man/charge-BilanFonctionnementDF-method.Rd
pkg/stacomir/man/charge-BilanMigration-method.Rd
pkg/stacomir/man/charge-BilanMigrationCar-method.Rd
pkg/stacomir/man/charge-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/charge-BilanMigrationMult-method.Rd
pkg/stacomir/man/charge-BilanMigrationMultConditionEnv-method.Rd
pkg/stacomir/man/charge-BilanOperation-method.Rd
pkg/stacomir/man/charge-Bilan_carlot-method.Rd
pkg/stacomir/man/charge_avec_filtre.Rd
pkg/stacomir/man/hBilanConditionEnv.Rd
pkg/stacomir/man/hBilanEspeces.Rd
pkg/stacomir/man/hBilanMigration.Rd
pkg/stacomir/man/hBilanMigrationInterAnnuelle.Rd
pkg/stacomir/man/hBilanMigrationMult.Rd
pkg/stacomir/man/hBilanMigrationMultConditionEnv.Rd
pkg/stacomir/man/hBilanMigrationPar.Rd
pkg/stacomir/man/hBilan_carlot.Rd
pkg/stacomir/man/hDC.Rd
pkg/stacomir/man/hDF.Rd
pkg/stacomir/man/hDFDC.Rd
pkg/stacomir/man/hOPE.Rd
pkg/stacomir/man/hSt.Rd
pkg/stacomir/man/hTail.Rd
pkg/stacomir/man/hbilA.Rd
pkg/stacomir/man/hbilanagedemer.Rd
pkg/stacomir/man/hpds.Rd
pkg/stacomir/man/hsilver.Rd
pkg/stacomir/man/husr.Rd
pkg/stacomir/man/interface_graphique.Rd
Log:
removing most charge methods from documentation
Except when they are still necessary to the user
Modified: pkg/stacomir/R/BilanAgedemer.r
===================================================================
--- pkg/stacomir/R/BilanAgedemer.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanAgedemer.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -96,15 +96,18 @@
})
-#' charge method for BilanAgedemer class
+#' Loads data and check that all choices in the graphical interface have been made.
#'
-#' this method verifies that boxes have been clicked in the user interface and gets the objects pasted in
+#' It is not necessary to run this method if the choice_c method has been run.
+#' This method verifies that boxes have been clicked in the user interface and gets the objects pasted in
#' envir_stacomi
#' @param object An object of class \link{BilanAgedemer-class}
#' @param h a handler
#' @return An object of class \link{BilanAgedemer-class} with slots filled with user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @aliases charge.BilanAgedemer charge.bilanagedemer
#' @export
+#' @keywords internal
setMethod("charge",signature=signature("BilanAgedemer"),definition=function(object,h) {
if (exists("refDC",envir_stacomi)) {
object at dc<-get("refDC",envir_stacomi)
@@ -147,8 +150,7 @@
object at limit2hm<-get("limit2hm",envir_stacomi)
} else {
funout(gettext("you need to choose a value for limit2hm",domain="R-stacomiR"),arret=TRUE)
- }
-
+ }
return(object)
validObject(object)
assign("bilan_adm",object,envir_stacomi)
Modified: pkg/stacomir/R/BilanAnnuels.r
===================================================================
--- pkg/stacomir/R/BilanAnnuels.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanAnnuels.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -37,8 +37,12 @@
)
#' charge method for BilanAnnuels class
+#'
+#' Method used by the graphical interface to load data and check that all choices have
+#' been made by the user
#' @param object An object of class \link{BilanAnnuels-class}
#' @param silent Stops messages from being displayed if silent=TRUE, default FALSE
+#' @keywords internal
setMethod("charge",signature=signature("BilanAnnuels"),
definition=function(object,silent=FALSE){
bilA<-object
Modified: pkg/stacomir/R/BilanArgentee.r
===================================================================
--- pkg/stacomir/R/BilanArgentee.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanArgentee.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -92,13 +92,15 @@
#' charge method for BilanArgentee class
#'
#' this method verifies that boxes have been clicked in the user interface and gets the objects pasted in
-#' envir_stacomi
+#' envir_stacomi. It is not necessary to run this method when loading from the command line using the
+#' choice_c method
#' @param object An object of class \link{BilanArgentee-class}
#' @param h a handler
#' @return An object of class \link{BilanArgentee-class} with slots filled with user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
#' @return An object of the class
+#' @keywords internal
setMethod("charge",signature=signature("BilanArgentee"),definition=function(object,h) {
if (exists("refDC",envir_stacomi)) {
object at dc<-get("refDC",envir_stacomi)
@@ -120,13 +122,11 @@
} else {
funout(gettext("You need to choose a parameter, clic on validate\n",domain="R-stacomiR"),arret=TRUE)
}
- # rem pas tres satisfaisant car ce nom est choisi dans l'interface
if (exists("bilan_arg_date_debut",envir_stacomi)) {
object at horodatedebut@horodate<-get("bilan_arg_date_debut",envir_stacomi)
} else {
funout(gettext("You need to choose the starting date\n",domain="R-stacomiR"),arret=TRUE)
}
- # rem id
if (exists("bilan_arg_date_fin",envir_stacomi)) {
object at horodatefin@horodate<-get("bilan_arg_date_fin",envir_stacomi)
} else {
Modified: pkg/stacomir/R/BilanConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanConditionEnv.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanConditionEnv.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -101,6 +101,7 @@
#' @param silent Default FALSE, if TRUE the program should no display messages
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
+#' @keywords internal
setMethod("charge",signature=signature("BilanConditionEnv"),definition=function(object,silent) {
if (exists("refStationMesure",envir_stacomi)) {
Modified: pkg/stacomir/R/BilanEspeces.r
===================================================================
--- pkg/stacomir/R/BilanEspeces.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanEspeces.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -140,12 +140,16 @@
#' charge method for BilanEspeces
-#' verifies the content of objects and calls the connect method
+#'
+#' Verifies the content of objects when the graphical interface is used, it is not necessary
+#' to call the charge method if the choice_c method has been used
#' @param object An object of class \link{BilanEspeces-class}
#' @param silent Stops displaying the messages.
#' @return BilanEspeces with slots filled by user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @aliases charge.bilanespeces charge.BilanEspeces
#' @export
+#' @keywords internal
setMethod("charge",signature=signature("BilanEspeces"),definition=function(object, silent=FALSE){
if (!silent) funout(gettext("Checking objects and launching query\n",domain="R-stacomiR"))
bilesp<-object
Modified: pkg/stacomir/R/BilanFonctionnementDC.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDC.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanFonctionnementDC.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -71,11 +71,8 @@
#' @param object An object of class \link{BilanFonctionnementDC-class}
#' @param silent boolean, default FALSE, if TRUE messages are not displayed.
#' @return An object of class \link{BilanFonctionnementDC-class}
-#'
-#' @author cedric.briand
+#' @keywords internal
setMethod("charge",signature=signature("BilanFonctionnementDC"),definition=function(object,silent=FALSE) {
-# construit une requete ODBCwheredate
- # chargement des donnees dans l'environnement de la fonction
if (exists("refDC",envir_stacomi)) {
object at dc<-get("refDC",envir_stacomi)
} else {
Modified: pkg/stacomir/R/BilanFonctionnementDF.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDF.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanFonctionnementDF.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -82,8 +82,7 @@
#' @param object An object of class \link{BilanFonctionnementDF-class}
#' @param silent Keeps program silent
#' @return An object of class \link{BilanFonctionnementDF-class}
-#'
-#' @author cedric.briand
+#' @keywords internal
setMethod("charge",signature=signature("BilanFonctionnementDF"),definition=function(object,silent=FALSE) {
# object<-BfDF
if (exists("refDF",envir=envir_stacomi)) {
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanMigration.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -3,7 +3,7 @@
#' This class performs a migration summary. A migration monitoring operation can correspond to a single
#' horodate (in the case of some video monitoring operation) or comprise a period which does not necessarily
#' span a full day. The daily migration is calculated by splitting the operation between days, and the migration is either
-#' grouped or split according to the lenth of the different time spans.#'
+#' grouped or split according to the lenth of the different time spans.
#' @include RefTaxon.r
#' @include RefStades.r
#' @include PasDeTempsJournalier.r
@@ -120,10 +120,11 @@
return(bilanMigration)
})
-#' charge method for BilanMigration
+#' Loads additional data on migration control operations, df (fishway) dc (counting device).
#'
#' this method creates additional classes in envir_stacomi for later use in plot (operations,
-#' DF operation, DC operation.
+#' DF operation, DC operation). So unlike in most Bilan classes where the charge method is only
+#' used by the graphical interface, it is necessary to run charge for BilanMigration.
#' @param object An object of class \code{\link{BilanMigration-class}}
#' @param silent Should the program be returning messages
#' @return An object of class \link{BilanMigration-class} with slots filled by user choice
Modified: pkg/stacomir/R/BilanMigrationCar.r
===================================================================
--- pkg/stacomir/R/BilanMigrationCar.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanMigrationCar.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -131,11 +131,13 @@
#' charge method for BilanMigrationCar
#'
#' Used by the graphical interface to collect and test objects in the environment envir_stacomi,
-#' fills also the data slot by the connect method
+#' fills also the data slot by the connect method. It is not necessary to run the charge method
+#' if the choice is made from the command line using the choice_c method.
#' @param object An object of class \link{BilanMigrationCar-class}
#' @param silent Default FALSE, if TRUE the program should not display messages
#' @return \link{BilanMigrationCar-class} with slots filled by user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
setMethod("charge",signature=signature("BilanMigrationCar"),definition=function(object,silent=FALSE){
bmC<-object
if (exists("bmC_date_debut",envir_stacomi)) {
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -294,6 +294,7 @@
#' @return An object of class \link{BilanMigrationInterAnnuelle-class}
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
+#' @keywords internal
setMethod("charge",signature=signature("BilanMigrationInterAnnuelle"),
definition=function(object,silent=FALSE)
{
@@ -386,12 +387,19 @@
#' calcule method for BilanMigrationInterannuelle
#'
+#' Performs the calculation of seasonal coefficients for the plot(plot.type="seasonal") method. The numbers
+#' are split according to the period chosen, one of "day","week","month","2 weeks", french labels are also
+#' accepted as arguments. Once this is done, the seasonality of the migration is displayed using the day when the
+#' first fish was seen, then the days (or period) corresponding to 5, 50 , 95, and 100 percent of the migration.
+#' The duration of 90% of the migraton between Q5 and Q95 is also of interest.
+#'
#' @param object An object of class \code{\link{BilanMigrationInterAnnuelle-class}}
#' @param silent Boolean, if TRUE, information messages are not displayed, only warnings and errors
#' @param timesplit One of "day","week","month","2 weeks", "jour","semaine","quinzaine","mois"
#' @note The class BilanMigration does not handle escapement rates nor
#' 'devenir' i.e. the destination of the fishes.
#' @return BilanMigration with calcdata slot filled.
+#' @author Marion Legrand
#' @export
setMethod("calcule",signature=signature("BilanMigrationInterAnnuelle"),definition=function(object,silent=FALSE,timesplit="mois"){
bilanMigrationInterAnnuelle<-object
Modified: pkg/stacomir/R/BilanMigrationMult.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMult.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanMigrationMult.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -65,8 +65,11 @@
#' charge method for BilanMigrationMult
#'
-#' Used by the graphical interface to collect and test objects in the environment envir_stacomi,
-#' fills also the data slot by the connect method
+#' Unique the other Bilan classes where the charge method is only used by the graphical interface
+#' to collect and test objects in the environment envir_stacomi, and see if the right choices have
+#' been made in the graphical interface, this method is used to load data on migration control operations
+#' fishway operations, and counting devices operations as data from those are displayed in the main plots.
+#'
#' @param object An object of class \link{BilanMigrationMult-class}
#' @param silent Default FALSE, if TRUE the program should no display messages
#' @return BilanMigrationMult with slots filled by user choice
@@ -171,17 +174,29 @@
return(bilanMigrationMult)
})
-#' calcule method for BilanMigrationMult
+#' #' Transforms migration per period to daily migrations, and performs the conversion from weights to number is data
+#' are stored as weights (glass eel). This calculation is performed in a loop for all dc.
#'
-#' does the calculation once data are filled.
+#' The calculation must be launched once data are filled by the connect method. Currently the negative argument
+#' has no effect.
#'
-#' @param object An object of class \code{\link{BilanMigrationMult-class}}
+#' @param object An object of class \link{BilanMigrationMult-class}
#' @param negative a boolean indicating if a separate sum must be done for positive and negative values, if true, positive and negative counts return
#' different rows
#' @param silent Default FALSE, should messages be stopped
-#' @note The class BilanMigrationMult does not handle escapement rates. Use class BilanMigration if you want to handle them. The class does not handler
-#' 'devenir' i.e. the destination of the fishes.
-#' @return BilanMigrationMult with a list in calcdata, one for each triplet (dc/taxa/stage) with data
+#' @note The class does not handle escapement rates, though structurally those are present in the database. If you
+#' want to use those you will have to do the calculation manually from the data in \code{BilanMigrationMult at data}
+#' @return BilanMigrationMult with a list in slot calcdata. For each dc one will find a list with the following elements
+#' \describe{
+#' \item{method}{In the case of instantaneous periods (video counting) the sum of daily values is done by the \link{fun_bilanMigrationMult} method and the value indicated in method is "sum".
+#' If any migration monitoring period is longer than a day, then the migration is split using the \link{fun_bilanMigrationMult_Overlaps} function and the value indicated in the
+#' method is "overlaps" as the latter method uses the overlap package to split migration period.}
+#' \item{data}{the calculated data.}
+#' \item{contient_poids}{A boolean which indicates, in the case of glass eel, that the function \link{fun_weight_conversion} has been run to convert the weights to numbers using the weight
+#' to number coefficients in the database (see link{Bilan_poids_moyen}).}
+#' \item{negative}{A parameter indicating if negative migration (downstream in the case of upstream migration devices) have been converted to positive numbers,
+#' not developped yet}}
+#' @aliases calcule.bilanmigrationMult calcule.BilanMigrationMult
#' @export
setMethod("calcule",signature=signature("BilanMigrationMult"),definition=function(object,negative=FALSE,silent=FALSE){
# bilanMigrationMult<-bMM_Arzal
Modified: pkg/stacomir/R/BilanMigrationMultConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMultConditionEnv.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanMigrationMultConditionEnv.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -100,6 +100,11 @@
return(bmmCE)
})
#' charge method for BilanMigrationMultConditionEnv class
+#'
+#' #' Unique the other Bilan classes where the charge method is only used by the graphical interface
+#' to collect and test objects in the environment envir_stacomi, and see if the right choices have
+#' been made in the graphical interface, this methods runs the \link{charge,BilanMigrationMult-method}
+#' and needs to be called from the command line (see examples)
#' @param object An object of class \link{BilanMigrationMultConditionEnv-class}
#' @param silent Should the function remain silent (boolean)
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
@@ -131,11 +136,12 @@
return(invisible(NULL))
}
-#' Calculation for the BilanMigrationMultConditionEnv
+#' Calculations for migration in the class \link{BilanMigrationMultConditionEnv-class}
#'
-#' @param object An object of class \code{\link{BilanMigrationMultConditionEnv-class}}
+#' Runs the calcule method in \link{BilanMigrationMult-class}
+#' @param object An object of class \link{BilanMigrationMultConditionEnv-class}
#' @param silent Boolean default FALSE, if TRUE information messages not displayed
-#' @return \code{\link{BilanMigrationMultConditionEnv-class}}
+#' @return \link{BilanMigrationMultConditionEnv-class} with data in slot bmmCE at bilanMigrationMult@calcdata
#' @export
setMethod("calcule",signature=signature("BilanMigrationMultConditionEnv"),definition=function(object,silent=FALSE){
# silent=FALSE
Modified: pkg/stacomir/R/BilanOperation.r
===================================================================
--- pkg/stacomir/R/BilanOperation.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/BilanOperation.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -72,6 +72,7 @@
#' @return An object of class \link{BilanOperation-class}
#'
#' @author cedric.briand
+#' @keywords internal
setMethod("charge",signature=signature("BilanOperation"),definition=function(object,silent=FALSE) {
# object<-bilanOperation
if (exists("refDC",envir=envir_stacomi)) {
Modified: pkg/stacomir/R/Bilan_carlot.r
===================================================================
--- pkg/stacomir/R/Bilan_carlot.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/Bilan_carlot.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -76,6 +76,7 @@
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
#' @return An object of the class
+#' @keywords internal
setMethod("charge",signature=signature("Bilan_carlot"),definition=function(object,h) {
if (exists("refDC",envir_stacomi)) {
object at dc<-get("refDC",envir_stacomi)
@@ -156,15 +157,17 @@
funoutlabel=gettext("Beginning date has been chosen\n",domain="R-stacomiR"),
horodate=horodatedebut,
silent=silent)
- bilanFonctionnementDC at horodatefin<-choice_c(bilanFonctionnementDC at horodatefin,
+ bilan_carlot at horodatefin<-choice_c(bilan_carlot at horodatefin,
nomassign="bilan_carlot_date_fin",
funoutlabel=gettext("Ending date has been chosen\n",domain="R-stacomiR"),
horodate=horodatefin,
silent=silent)
return(bilan_carlot)
})
-#' Calcule method for Bilan_carlot
+
+#' Calculation for Bilan_carlot
#'
+#' In that class, most treatments are done in the query, this method checks that data are available and fills information for year, month, two weeks, week, doy
#' @param object An object of class \code{\link{Bilan_carlot-class}}
#' @param silent Boolean, if TRUE, information messages are not displayed, only warnings and errors
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/Bilan_poids_moyen.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -1,5 +1,4 @@
-
-#' Class "Bilan_poids_moyen"
+#' Trend of wet weight in glass eel
#'
#' In trapping ladders, glass eel are seldom counted, as they are too tiny to handle and too numerous to count.
#' The usuall operation is to weight them, or to use a bucket to measure their volume. These weights or volumes will later
Modified: pkg/stacomir/R/create_generic.r
===================================================================
--- pkg/stacomir/R/create_generic.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/create_generic.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -26,6 +26,7 @@
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
+#' @keywords internal
setGeneric("charge_avec_filtre",def=function(object,...) standardGeneric("charge_avec_filtre"))
#setGeneric("connect",def=function(object,...) standardGeneric("connect")) # package stacomirtools
#setGeneric("plot",def=function(x,y,...) standardGeneric("plot"))
Modified: pkg/stacomir/R/stacomi.r
===================================================================
--- pkg/stacomir/R/stacomi.r 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/R/stacomi.r 2017-06-17 20:16:18 UTC (rev 399)
@@ -3,6 +3,7 @@
#'
#' @param h A handler
#' @param ... Other parameters
+#' @keywords internal
hDF=function(h,...){
funout(gettext("Calculation of the operating fishway\n",domain="R-stacomiR"),wash=TRUE)
eval(interface_BilanFonctionnementDF(),envir = envir_stacomi)
@@ -10,6 +11,7 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hDC=function(h,...){
funout(gettext("Calculation of the operating counting device\n",domain="R-stacomiR"),wash=TRUE)
eval(interface_BilanFonctionnementDC(),envir = envir_stacomi)
@@ -17,13 +19,15 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hOPE=function(h,...){
# TODO a developper
funout(text=gettext("Summary of the operations of a device ... to do\n",domain="R-stacomiR"),wash=TRUE)
}
-#' handler function used by the main interface#'
+#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hDFDC=function(h,...){
# TODO developper cette fonction
funout(gettext("Summary between the operating fishway and the counting device ... to do\n",domain="R-stacomiR"),wash=TRUE)
@@ -31,6 +35,7 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hBilanMigration=function(h,...){
funout(gettext("Migration summary (for a species and a stage)\n",domain="R-stacomiR"),wash=TRUE)
eval(interface_BilanMigration(),envir = envir_stacomi)
@@ -38,6 +43,7 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hBilanMigrationMult=function(h,...){
funout(gettext("For help, contact Cedric Briand - 0033 29 99 08 844 - cedric.briand at eptb-vilaine.fr, or mail stacomi at googlegroups.com.\n",domain="R-stacomiR"),wash=TRUE)
eval(interface_BilanMigrationMult(),envir = envir_stacomi)
@@ -45,6 +51,7 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hBilanMigrationInterAnnuelle=function(h,...){
funout(gettext("Summary of interannual migration\n",domain="R-stacomiR"),wash=TRUE)
eval(interface_BilanMigrationInterAnnuelle(),envir = envir_stacomi)
@@ -52,6 +59,7 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hBilanMigrationMultConditionEnv=function(h,...){
funout(gettext("Summary of migration environnemental conditions\n",domain="R-stacomiR"),wash=TRUE)
eval(interface_BilanMigrationMultConditionEnv(),envir = envir_stacomi)
@@ -59,6 +67,7 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hBilanMigrationPar=function(h,...){
funout(gettext("Summary of migration with parameters\n",domain="R-stacomiR"),wash=TRUE)
eval(interface_BilanMigrationPar(),envir = envir_stacomi)
@@ -66,6 +75,7 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hBilanConditionEnv=function(h,...){
funout(gettext("Summary of the environnemental conditions\n",domain="R-stacomiR"),wash=TRUE)
eval(interface_ConditionEnv(),envir = envir_stacomi)
@@ -73,6 +83,7 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hBilan_carlot=function(h,...){
funout(gettext("Summary of samples characteristics (size, weight...) by calling the view vue_lot_ope\n",domain="R-stacomiR"),wash=TRUE)
eval(interface_Bilan_carlot(),envir = envir_stacomi)
@@ -80,6 +91,7 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hTail=function(h,...){
funout(gettext("Lengths summary\n",domain="R-stacomiR"),wash=TRUE)
#eval(interface_BilanTaille(),envir = envir_stacomi)
@@ -87,6 +99,7 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hpds=function(h,...){
eval(interface_BilanPoidsMoyen(),envir = envir_stacomi)
funout(gettext("Summary of average weight for the calculation of the relation between length and number.\n",domain="R-stacomiR"),wash=TRUE)
@@ -94,6 +107,7 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hSt=function(h,...){
funout(gettext("Not adapted yet to version 0.5.2",domain="R-stacomiR"))
#funout(gettext("Calculation of the pigmentary stages\n",domain="R-stacomiR"),wash=TRUE)
@@ -102,18 +116,21 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hbilA=function(h,...){
eval(interface_BilanAnnuels(),envir = envir_stacomi)
}
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hsilver=function(h,...){
eval(interface_BilanArgentee(),envir = envir_stacomi)
}
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hBilanEspeces=function(h,...){
funout(gettext("Species summary of the counting device\n",domain="R-stacomiR"),wash=TRUE)
eval(interface_BilanEspeces(),envir = envir_stacomi)
@@ -121,6 +138,7 @@
#' handler function used by the main interface
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hbilanagedemer=function(h,...){
funout(gettext("Age calculation from size limit \n",domain="R-stacomiR"),wash=TRUE)
eval(interface_BilanAgedemer(),envir = envir_stacomi)
@@ -133,6 +151,7 @@
#' @param h A handler
#' @param ... Other arguments
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
husr=function(h,...){
baseODBC<-get("baseODBC",envir=envir_stacomi)
# assigned when passing through stacomi
@@ -394,6 +413,7 @@
#' interface to stacomi. To be able to run, some widgets (win, grouptotal, group...)
#' are assigned in the user environment \code{.GlobalEnv}.
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
interface_graphique=function(){
if (exists("ggroupboutonsbas")) rm(list=c("ggroupboutonsbas"),envir=envir_stacomi)
if (exists("group")) rm(list=c("group"),envir=envir_stacomi)
Modified: pkg/stacomir/inst/config/generate_data.R
===================================================================
--- pkg/stacomir/inst/config/generate_data.R 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/inst/config/generate_data.R 2017-06-17 20:16:18 UTC (rev 399)
@@ -273,7 +273,7 @@
anneefin=2015,
silent=TRUE)
# this will just test that the object is valid... not really a necessary step for this class
-bmi<-charge(bmi,silent=TRUE)
+#bmi<-charge(bmi,silent=TRUE)
bmi<-connect(bmi,silent=TRUE)
@@ -480,7 +480,7 @@
anneedebut="1997",
anneefin="2012",
silent=FALSE)
-bmi_vichy<-charge(bmi_vichy)
+#bmi_vichy<-charge(bmi_vichy)
bmi_vichy<-connect(bmi_vichy)
bmi_vichy at dc@data[,"ouv_libelle"]<-iconv(bmi_vichy at dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
bmi_vichy at dc@data[,"dis_commentaires"]<-iconv(bmi_vichy at dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
Modified: pkg/stacomir/inst/examples/bilanArgentee_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanArgentee_example.R 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/inst/examples/bilanArgentee_example.R 2017-06-17 20:16:18 UTC (rev 399)
@@ -18,8 +18,7 @@
horodatedebut="2010-09-01",
horodatefin="2016-10-04",
silent=FALSE)
- bilanArg<-connect(bilanArg)
-
+ bilanArg<-connect(bilanArg)
}
# load the dataset generated by previous lines
data("bilanArg")
Modified: pkg/stacomir/inst/examples/bilanEspeces_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanEspeces_example.R 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/inst/examples/bilanEspeces_example.R 2017-06-17 20:16:18 UTC (rev 399)
@@ -11,7 +11,7 @@
anneedebut="2008",
anneefin="2012",
silent=FALSE)
- bilesp<-charge(bilesp)
+ #bilesp<-charge(bilesp) this is used by the graphical interface
bilesp<-connect(bilesp)
bilesp<-calcule(bilesp)
plot(bilesp,plot.type="pie",silent=FALSE)
Modified: pkg/stacomir/inst/examples/bilanFonctionnementDC_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanFonctionnementDC_example.R 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/inst/examples/bilanFonctionnementDC_example.R 2017-06-17 20:16:18 UTC (rev 399)
@@ -16,7 +16,6 @@
Sys.setenv(TZ='GMT')
# This dataset formating is GMT. If this option is not set
# the dataset is tranformed from timestamp to date
- bfDC<-charge(bfDC)
bfDC<-connect(bfDC)
# this dataset has been loaded by the previous lines
###########################################################
Modified: pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R 2017-06-17 20:16:18 UTC (rev 399)
@@ -14,7 +14,6 @@
# the times at Arzal are recorded continuously
# they are converted to date when a time appears while the hour is changing
# hence the following
- bfDF<-charge(bfDF)
bfDF<-connect(bfDF)
}
Modified: pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R 2017-06-17 20:16:18 UTC (rev 399)
@@ -24,7 +24,6 @@
anneedebut="1990",
anneefin="2015",
silent=TRUE)
- bmi<-charge(bmi,silent=TRUE)
bmi<-connect(bmi,silent=TRUE)
}
#############otherwise use this ######################
@@ -156,7 +155,6 @@
anneedebut="2007",
anneefin="2014",
silent=TRUE)
-bmi_des<-charge(bmi_des)
bmi_des<-connect(bmi_des)
bmi_des<-calcule(bmi_des,timesplit="semaine")
plot(bmi_des,plot.type="seasonal",timesplit="semaine")
Modified: pkg/stacomir/inst/examples/bilanMigrationMultConditionEnv_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationMultConditionEnv_example.R 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/inst/examples/bilanMigrationMultConditionEnv_example.R 2017-06-17 20:16:18 UTC (rev 399)
@@ -14,7 +14,7 @@
datedebut="2008-01-01",
datefin="2008-12-31",
silent=FALSE)
- bmmCE<-charge(bmmCE)
+ bmmCE<-charge(bmmCE) # this is necessary to load operations, DF and DC
bmmCE<-connect(bmmCE)
}
Modified: pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R 2017-06-17 20:16:18 UTC (rev 399)
@@ -15,7 +15,7 @@
dc=c(5,6,12),
taxons=c("Anguilla anguilla"),
stades=c("AGG","AGJ","CIV"),datedebut="2011-01-01",datefin="2011-12-31")
- bMM_Arzal<-charge(bMM_Arzal)
+ bMM_Arzal<-charge(bMM_Arzal)
# launching charge will also load classes associated with the bilan
# e.g. BilanOperation, BilanFonctionnementDF, BilanFonctionnementDC
bMM_Arzal<-connect(bMM_Arzal)
Modified: pkg/stacomir/inst/examples/bilanMigration_Arzal.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigration_Arzal.R 2017-06-17 18:26:49 UTC (rev 398)
+++ pkg/stacomir/inst/examples/bilanMigration_Arzal.R 2017-06-17 20:16:18 UTC (rev 399)
@@ -17,6 +17,8 @@
datedebut="2015-01-01",
datefin="2015-12-31")
bM_Arzal<-charge(bM_Arzal)
+ # launching charge will also load classes associated with the bilan
+ # e.g. BilanOperation, BilanFonctionnementDF, BilanFonctionnementDC
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 399
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