[Stacomir-commits] r397 - in pkg/stacomir: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jun 17 20:24:33 CEST 2017
Author: briand
Date: 2017-06-17 20:24:32 +0200 (Sat, 17 Jun 2017)
New Revision: 397
Modified:
pkg/stacomir/NAMESPACE
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/Bilan_carlot.r
pkg/stacomir/R/create_generic.r
pkg/stacomir/man/BilanAnnuels-class.Rd
pkg/stacomir/man/calcule-BilanArgentee-method.Rd
pkg/stacomir/man/calcule-BilanMigration-method.Rd
pkg/stacomir/man/calcule-BilanMigrationCar-method.Rd
pkg/stacomir/man/choice.Rd
pkg/stacomir/man/choice_c.Rd
pkg/stacomir/man/choicemult.Rd
pkg/stacomir/man/funbarchart1DF.Rd
pkg/stacomir/man/funbarchartDC.Rd
pkg/stacomir/man/funbarchartDF.Rd
pkg/stacomir/man/funboxDC.Rd
pkg/stacomir/man/funboxDF.Rd
pkg/stacomir/man/funboxplotBilan_carlot.Rd
pkg/stacomir/man/funchartDC.Rd
pkg/stacomir/man/funchartDF.Rd
pkg/stacomir/man/fundat.Rd
pkg/stacomir/man/fundensityBilan_carlot.Rd
pkg/stacomir/man/funplotBilanAgedemer.Rd
pkg/stacomir/man/funplotBilanArgentee.Rd
pkg/stacomir/man/funpointBilan_carlot.Rd
pkg/stacomir/man/funtableBilanAgedemer.Rd
pkg/stacomir/man/funtableBilanArgentee.Rd
pkg/stacomir/man/funtableBilan_carlot.Rd
pkg/stacomir/man/funtableDC.Rd
pkg/stacomir/man/funtableDF.Rd
pkg/stacomir/man/hTableBilanMigration.Rd
pkg/stacomir/man/hTableBilanMigrationMult.Rd
pkg/stacomir/man/hbarplotBilanAnnuels.Rd
pkg/stacomir/man/hbilanConditionEnvgraph.Rd
pkg/stacomir/man/hbilanMigrationMult_graph.Rd
pkg/stacomir/man/hbilanMigrationMultcalc.Rd
pkg/stacomir/man/hbilanMigrationMultgraph2.Rd
pkg/stacomir/man/hbilanMigrationMultgraph3.Rd
pkg/stacomir/man/hbilanMigrationcalc.Rd
pkg/stacomir/man/hbilanMigrationgraph.Rd
pkg/stacomir/man/hbilanMigrationgraph2.Rd
pkg/stacomir/man/hbilanMigrationwrite.Rd
pkg/stacomir/man/hbilespcalc.Rd
pkg/stacomir/man/hbmCcalc.Rd
pkg/stacomir/man/hbmCplotcrossed.Rd
pkg/stacomir/man/hbmCplotqual.Rd
pkg/stacomir/man/hbmCplotquan.Rd
pkg/stacomir/man/hbmCstat.Rd
pkg/stacomir/man/hbmmCEcalc.Rd
pkg/stacomir/man/hbmmCEgraph.Rd
pkg/stacomir/man/hgraphBilanMigrationInterAnnuelle.Rd
pkg/stacomir/man/hgraphBilanMigrationInterAnnuelle2.Rd
pkg/stacomir/man/hgraphBilanMigrationInterAnnuelle3.Rd
pkg/stacomir/man/hgraphBilanMigrationInterAnnuelle4.Rd
pkg/stacomir/man/hgraphBilanMigrationInterAnnuelle5.Rd
pkg/stacomir/man/hgraphBilanMigrationInterAnnuelle7.Rd
pkg/stacomir/man/houtBilanMigration.Rd
pkg/stacomir/man/houtBilanMigrationMult.Rd
pkg/stacomir/man/houtDC.Rd
pkg/stacomir/man/houtDF.Rd
pkg/stacomir/man/hplotBilanAnnuels.Rd
pkg/stacomir/man/hplotbilesp.Rd
pkg/stacomir/man/hsummaryBilanMigrationInterannuelle.Rd
pkg/stacomir/man/hsummarybilesp.Rd
pkg/stacomir/man/hxtableBilanAnnuels.Rd
Log:
setting all functions related with the gwidget graphical interface as
@internal to avoid those being printed in the help file
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/NAMESPACE 2017-06-17 18:24:32 UTC (rev 397)
@@ -1,7 +1,6 @@
# Generated by roxygen2: do not edit by hand
export(chargecsv)
-export(choice)
export(colortable)
export(f_stade_Durif)
export(fn_EcritBilanMensuel)
@@ -9,15 +8,9 @@
export(fun_bilanMigrationMult)
export(fun_bilanMigrationMult_Overlaps)
export(fun_char_spe)
-export(funboxplotBilan_carlot)
export(fundat)
-export(fundensityBilan_carlot)
export(funout)
-export(funplotBilanArgentee)
-export(funpointBilan_carlot)
export(funstat)
-export(funtableBilanArgentee)
-export(funtableBilan_carlot)
export(funtraitement_poids)
export(funtraitementdate)
export(mygtkProgressBar)
Modified: pkg/stacomir/R/BilanAgedemer.r
===================================================================
--- pkg/stacomir/R/BilanAgedemer.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/BilanAgedemer.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -442,6 +442,7 @@
#' @param h A handler, with action 1,2,3 or 4
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
funplotBilanAgedemer = function(h,...) {
bilan_adm<-get(x="bilan_adm",envir=envir_stacomi)
bilan_adm<-charge(bilan_adm)
@@ -459,6 +460,7 @@
#' @param h hanlder passed by the graphical interface
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
funtableBilanAgedemer = function(h,...) {
bilan_adm=charge(bilan_adm)
bilan_adm<-connect(bilan_adm)
Modified: pkg/stacomir/R/BilanAnnuels.r
===================================================================
--- pkg/stacomir/R/BilanAnnuels.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/BilanAnnuels.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -12,7 +12,7 @@
#' @slot anneedebut Object of class \code{\link{RefAnnee-class}}. RefAnnee allows to choose year of beginning
#' @slot anneefin Object of class \code{\link{RefAnnee-class}}
#' RefAnnee allows to choose last year of the Bilan
-#'
+#' @aliases calcule.BilanAnnuels calcule.bilanannuels
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @family Bilan Objects
#' @keywords classes
@@ -571,6 +571,7 @@
#' Barplot handler
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hbarplotBilanAnnuels = function(h,...)
{
bilA <- get("bilanAnnuels",envir=envir_stacomi)
@@ -582,6 +583,7 @@
#' plot handler
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hplotBilanAnnuels = function(h,...)
{
bilA <- get("bilanAnnuels",envir=envir_stacomi)
@@ -594,6 +596,7 @@
#' xtable handler
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hxtableBilanAnnuels = function(h,...)
{
bilA <- get("bilanAnnuels",envir=envir_stacomi)
Modified: pkg/stacomir/R/BilanArgentee.r
===================================================================
--- pkg/stacomir/R/BilanArgentee.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/BilanArgentee.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -200,6 +200,7 @@
#' @param silent Boolean, if TRUE, information messages are not displayed, only warnings and errors
#' @return An object of class \link{BilanArgentee-class} with slot calcdata filled, as a list
#' for each counting device
+#' @aliases calcule.BilanArgentee calcule.bilanargentee
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
setMethod("calcule",signature=signature("BilanArgentee"),definition=function(object,silent) {
bilanArg<-object
@@ -693,7 +694,7 @@
#' @param h A handler, with action 1,2,3 or 4
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
+#' @keywords internal
funplotBilanArgentee = function(h,...) {
bilanArg<-get(x="bilan_arg",envir=envir_stacomi)
bilanArg<-charge(bilanArg)
@@ -711,7 +712,7 @@
#' @param h hanlder passed by the graphical interface
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
+#' @keywords internal
funtableBilanArgentee = function(h,...) {
bilanArg=charge(bilanArg)
bilanArg<-connect(bilanArg)
Modified: pkg/stacomir/R/BilanConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanConditionEnv.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/BilanConditionEnv.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -128,6 +128,7 @@
#' @param h a handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hbilanConditionEnvgraph = function(h,...)
{
bilanConditionEnv<-get("bilanConditionEnv",envir=envir_stacomi)
Modified: pkg/stacomir/R/BilanEspeces.r
===================================================================
--- pkg/stacomir/R/BilanEspeces.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/BilanEspeces.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -126,6 +126,7 @@
#' @param h a handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hbilespcalc=function(h,...){
if (exists("bilesp",envir_stacomi)) {
bilesp<-get("bilesp",envir_stacomi)
@@ -178,6 +179,7 @@
#' handler for plot internal use
#' @param h Handler
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hplotbilesp = function(h) {
bilesp<-get("bilesp",envir_stacomi)
plot(bilesp,plot.type=h$action)
@@ -296,6 +298,7 @@
#' handler for summary BilanEspeces, internal use
#' @param h a handler
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hsummarybilesp=function(h) {
if (exists("bilesp",envir_stacomi)) {
bilesp<-get("bilesp",envir_stacomi)
Modified: pkg/stacomir/R/BilanFonctionnementDC.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDC.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/BilanFonctionnementDC.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -433,7 +433,7 @@
#' @param h a handler
#' @param ... Additional parameters
#' @return assigns the data frame \code{periodeDC} allowing to build the lattice graph in the environment envir_stacomi
-#'
+#' @keywords internal
#' @author cedric.briand
funbarchartDC = function(h,...) {
bilanFonctionnementDC=charge(bilanFonctionnementDC)
@@ -467,6 +467,7 @@
#' @param h a handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
funboxDC = function(h,...) {
bilanFonctionnementDC=charge(bilanFonctionnementDC)
bilanFonctionnementDC=connect(bilanFonctionnementDC)
@@ -481,6 +482,7 @@
#' @param h handler
#' @param ... additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
funchartDC = function(h,...) {
bilanFonctionnementDC<-get("bilanFonctionnementDC",envir=envir_stacomi)
bilanFonctionnementDC=charge(bilanFonctionnementDC)
@@ -497,6 +499,7 @@
#' @param h a handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
houtDC = function(h,...) {
bilanFonctionnementDC<-get("bilanFonctionnementDC",envir=envir_stacomi)
bilanFonctionnementDC<-charge(bilanFonctionnementDC)
@@ -529,6 +532,7 @@
#' @param h Handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
funtableDC = function(h,...) {
bilanFonctionnementDC<-get("bilanFonctionnementDC",envir=envir_stacomi)
bilanFonctionnementDC=charge(bilanFonctionnementDC)
Modified: pkg/stacomir/R/BilanFonctionnementDF.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDF.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/BilanFonctionnementDF.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -410,6 +410,7 @@
#' @param h handler
#' @param ... additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
funbarchartDF = function(h,...) {
bilanFonctionnementDF<-get("bilanFonctionnementDF",envir=envir_stacomi)
bilanFonctionnementDF=charge(bilanFonctionnementDF)
@@ -426,7 +427,7 @@
#' @note The program cuts periods which overlap between two month
#' @param h handler
#' @param ... additional parameters
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
funbarchart1DF = function(h,...) {
bilanFonctionnementDF<-get("bilanFonctionnementDF",envir=envir_stacomi)
bilanFonctionnementDF=charge(bilanFonctionnementDF)
@@ -440,7 +441,7 @@
#' graphical interface handler
#' @param h handler
#' @param ... additional parameters
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
funboxDF = function(h,...) {
bilanFonctionnementDF<-get("bilanFonctionnementDF",envir=envir_stacomi)
bilanFonctionnementDF=charge(bilanFonctionnementDF)
@@ -456,7 +457,7 @@
#' Handler fonction to plot calendar like graph, internal use
#' @param h handler
#' @param ... additional parameters
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
funchartDF = function(h,...) {
bilanFonctionnementDF<-get("bilanFonctionnementDF",envir=envir_stacomi)
bilanFonctionnementDF=charge(bilanFonctionnementDF)
@@ -472,7 +473,7 @@
#' Table output for BilanFonctionnementDF class
#' @param h handler
#' @param ... additional parameters
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
funtableDF = function(h,...) {
bilanFonctionnementDF<-get("bilanFonctionnementDF",envir=envir_stacomi)
bilanFonctionnementDF=charge(bilanFonctionnementDF)
@@ -487,7 +488,7 @@
#' handler to print the command line
#' @param h a handler
#' @param ... Additional parameters
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
houtDF = function(h,...) {
bilanFonctionnementDF<-get("bilanFonctionnementDF",envir=envir_stacomi)
bilanFonctionnementDF<-charge(bilanFonctionnementDF)
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/BilanMigration.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -64,6 +64,7 @@
#' @param h handler
#' @param ... additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hbilanMigrationcalc=function(h,...){
bilanMigration<-get("bilanMigration",envir=envir_stacomi)
bilanMigration<-charge(bilanMigration)
@@ -209,23 +210,15 @@
#' 'devenir' i.e. the destination of the fishes.
#' @return BilanMigration with calcdata slot filled. It is a list with one element per counting device containing
#' \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".
+#' \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.bilanmigration
+#' 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.bilanmigration calcule.BilanMigration
#' @export
setMethod("calcule",signature=signature("BilanMigration"),definition=function(object,negative=FALSE,silent=FALSE){
#bilanMigration<-bM_Arzal
@@ -316,6 +309,7 @@
#' @param h a handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
houtBilanMigration=function(h=null,...) {
if (exists("refStades",envir_stacomi)) {
bilanMigration<-get("bilanMigration",envir_stacomi)
@@ -507,6 +501,7 @@
#' @param h handler
#' @param ... additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hbilanMigrationgraph = function(h,...) {
if (exists("bilanMigration",envir_stacomi)) {
bilanMigration<-get("bilanMigration",envir_stacomi)
@@ -523,6 +518,7 @@
#' @param h handler
#' @param ... additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hbilanMigrationgraph2 = function(h,...) {
if (exists("bilanMigration",envir_stacomi)) {
bilanMigration<-get("bilanMigration",envir_stacomi)
@@ -538,6 +534,7 @@
#' @param h Handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hTableBilanMigration=function(h,...) {
if (exists("bilanMigration",envir_stacomi))
{
@@ -577,6 +574,7 @@
#' @param h a handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hbilanMigrationwrite = function(h,...) {
if (exists("bilanMigration",envir_stacomi)) {
bilanMigration<-get("bilanMigration",envir_stacomi)
Modified: pkg/stacomir/R/BilanMigrationCar.r
===================================================================
--- pkg/stacomir/R/BilanMigrationCar.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/BilanMigrationCar.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -275,6 +275,7 @@
#' handler for bilanmigrationpar
#' @param h handler
#' @param ... Additional parameters
+#' @keywords internal
hbmCcalc=function(h,...){
bmC<-get("bmC",envir=envir_stacomi)
bmC<-charge(bmC)
@@ -323,11 +324,15 @@
return(bmC)
})
-#' calcule methode
+#' Computes data to a standard format for the summary and plot methods.
#'
+#' Merges the content of the list elements "parqual" and "parquan" in the data slot, and creates
+#' a single dataframe with one line per qualitative and quantitative pair. This methods allow to
+#' cross one quantity (e.g. length) with a qualitative parameter (e.g. sex).
+#'
#' @param object An object of class \code{\link{BilanMigrationCar-class}}
#' @param silent Boolean default FALSE, if TRUE information messages not displayed
-
+#TODO create a dataframe with only one line per fish for all parameters
setMethod("calcule",signature=signature("BilanMigrationCar"),definition=function(object,silent=FALSE){
bmC<-object
qual<-bmC at data[["parqual"]]
@@ -355,6 +360,7 @@
#'
#' @param h handler
#' @param ... Additional parameters
+#' @keywords internal
hbmCplotquan = function(h,...) {
if (exists("bmC",envir_stacomi)) {
bmC<-get("bmC",envir_stacomi)
@@ -367,6 +373,7 @@
#'
#' @param h handler
#' @param ... Additional parameters
+#' @keywords internal
hbmCplotqual=function(h,...){
if (exists("bmC",envir_stacomi)) {
bmC<-get("bmC",envir_stacomi)
@@ -379,6 +386,7 @@
#'
#' @param h handler
#' @param ... Additional parameters
+#' @keywords internal
hbmCplotcrossed=function(h,...){
if (exists("bmC",envir_stacomi)) {
bmC<-get("bmC",envir_stacomi)
@@ -392,6 +400,7 @@
#'
#' @param h handler
#' @param ... Additional parameters
+#' @keywords internal
hbmCstat=function(h){
if (exists("bmC",envir_stacomi)) {
bmC<-get("bmC",envir_stacomi)
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -456,7 +456,6 @@
#' @param timesplit "week" "2 week" "month" as provided to seq.POSIXT, default NULL
#' @return a data frame with mean, max, and min calculated for each timesplit
#' @export
-#' @seealso \code{\linkS4class{Bilan_poids_moyen}}
fundat=function(dat,annee=NULL,timesplit=NULL)
{
@@ -961,6 +960,7 @@
#' Plot of all interannual from top to bottom
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hgraphBilanMigrationInterAnnuelle = function(h,...)
{
bilanMigrationInterAnnuelle <- get("bilanMigrationInterAnnuelle",envir=envir_stacomi)
@@ -973,6 +973,7 @@
#'Plot of daily migrations
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hgraphBilanMigrationInterAnnuelle2 = function(h,...)
{
bilanMigrationInterAnnuelle <- get("bilanMigrationInterAnnuelle",envir=envir_stacomi)
@@ -992,6 +993,7 @@
#' can be highlighted against the others
#' @param h handler
#' @param ... additional parameters
+#' @keywords internal
hgraphBilanMigrationInterAnnuelle3 = function(h,...)
{
bilanMigrationInterAnnuelle <- get("bilanMigrationInterAnnuelle",envir=envir_stacomi)
@@ -1008,6 +1010,7 @@
#' This function plots comparisions for periods of 1 week, 2 weeks, month
#' @param h A handler
#' @param ... Additional parameters
+#' @keywords internal
hgraphBilanMigrationInterAnnuelle4 = function(h,...)
{
timesplit=h$action # timesplit="quinzaine" timesplit="semaine" timesplit="mois"
@@ -1024,6 +1027,7 @@
#' This function plots comparisions for periods of 1 week, 2 weeks, month
#' @param h A handler
#' @param ... Additional parameters
+#' @keywords internal
hgraphBilanMigrationInterAnnuelle5 = function(h,...)
{
timesplit=h$action # timesplit="quinzaine" # timesplit="mois"
@@ -1039,6 +1043,7 @@
#' 2 weeks period then centered and reduced
#' @param h A handler
#' @param ... Additional parameters
+#' @keywords internal
hgraphBilanMigrationInterAnnuelle7 = function(h,...)
{
bilanMigrationInterAnnuelle <- get("bilanMigrationInterAnnuelle",envir=envir_stacomi)
@@ -1053,6 +1058,7 @@
#'Summary handler internal method
#' @param h A handler
#' @param ... Additional parameters
+#' @keywords internal
hsummaryBilanMigrationInterannuelle<-function(h,...){
bilanMigrationInterAnnuelle <- get("bilanMigrationInterAnnuelle",envir=envir_stacomi)
bilanMigrationInterAnnuelle <- charge(bilanMigrationInterAnnuelle)
Modified: pkg/stacomir/R/BilanMigrationMult.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMult.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/BilanMigrationMult.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -356,6 +356,7 @@
#' @param h a handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hbilanMigrationMult_graph=function(h=null,...){
if (exists("bilanMigrationMult",envir_stacomi)) {
bilanMigrationMult<-get("bilanMigrationMult",envir_stacomi)
@@ -597,7 +598,7 @@
#' @param h a handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @seealso BilanMigrationMult
+#' @keywords internal
hbilanMigrationMultcalc=function(h=null,...){
bilanMigrationMult<-get("bilanMigrationMult",envir=envir_stacomi)
bilanMigrationMult<-charge(bilanMigrationMult)
@@ -611,7 +612,7 @@
#' cumuls de migration au cours du temps
#' @param h a handler
#' @param ... Additional parameters
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hbilanMigrationMultgraph2 = function(h=null,...) {
if (exists("bilanMigrationMult",envir_stacomi)) {
bilanMigrationMult<-get("bilanMigrationMult",envir_stacomi)
@@ -627,7 +628,7 @@
#' internal use
#' @param h a handler
#' @param ... Additional parameters
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hbilanMigrationMultgraph3 = function(h=null,...) {
if (exists("bilanMigrationMult",envir_stacomi)) {
bilanMigrationMult<-get("bilanMigrationMult",envir_stacomi)
@@ -641,12 +642,12 @@
#'
#'
-#' handler function
+#' handler function table
#'
#' internal use
#' @param h a handler
#' @param ... Additional parameters
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hTableBilanMigrationMult=function(h=null,...) {
if (exists("bilanMigrationMult",envir_stacomi))
{
@@ -725,6 +726,7 @@
})
#' handler to print the command line
+#' @keywords internal
#' @param h a handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
Modified: pkg/stacomir/R/BilanMigrationMultConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMultConditionEnv.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/BilanMigrationMultConditionEnv.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -119,6 +119,7 @@
#' @param h a handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @keywords internal
hbmmCEcalc=function(h=null,...){
bmmCE<-get("bmmCE",envir_stacomi)
bmmCE<-charge(bmmCE)
@@ -148,6 +149,7 @@
#' internal method for graphical interface
#' @param h A handler
+#' @keywords internal
hbmmCEgraph = function(h=null){
bmmCE<-get("bmmCE",envir_stacomi)
bmmCE<-plot(bmmCE)
Modified: pkg/stacomir/R/Bilan_carlot.r
===================================================================
--- pkg/stacomir/R/Bilan_carlot.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/Bilan_carlot.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -294,7 +294,7 @@
#' @param h A handler
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
+#' @keywords internal
fundensityBilan_carlot = function(h,...) {
bilan_carlot<-get("bilan_carlot",envir=envir_stacomi)
bilan_carlot<-charge(bilan_carlot)
@@ -309,7 +309,7 @@
#' @param h A handler passed by the graphical interface
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
+#' @keywords internal
funboxplotBilan_carlot = function(h,...) {
bilan_carlot<-get("bilan_carlot",envir=envir_stacomi)
bilan_carlot<-charge(bilan_carlot)
@@ -325,7 +325,7 @@
#' @param h handler passed by the graphical interface
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
+#' @keywords internal
funpointBilan_carlot = function(h,...) {
bilan_carlot<-get("bilan_carlot",envir=envir_stacomi)
bilan_carlot<-charge(bilan_carlot)
@@ -340,7 +340,7 @@
#' @param h hanlder passed by the graphical interface
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
+#' @keywords internal
funtableBilan_carlot = function(h,...) {
bilan_carlot<-get("bilan_carlot",envir=envir_stacomi)
bilan_carlot=charge(bilan_carlot)
Modified: pkg/stacomir/R/create_generic.r
===================================================================
--- pkg/stacomir/R/create_generic.r 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/R/create_generic.r 2017-06-17 18:24:32 UTC (rev 397)
@@ -3,17 +3,19 @@
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
-#' @export
+#' @keywords internal
setGeneric("choice",def=function(object,...) standardGeneric("choice"))
-#' Generic method for multiple choice (using the gwidget graphical interface)
+#' Generic method for multiple choice (using the gwidget notebook for multiple choice)
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
+#' @keywords internal
setGeneric("choicemult",def=function(object,...) standardGeneric("choicemult"))
-#' Generic method for manual choice
+#' Generic method for manual choice using the command line
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
+#' @keywords internal
setGeneric("choice_c",def=function(object,...) standardGeneric("choice_c"))
#' Generic method to load referentials
#' @param object Object
Modified: pkg/stacomir/man/BilanAnnuels-class.Rd
===================================================================
--- pkg/stacomir/man/BilanAnnuels-class.Rd 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/man/BilanAnnuels-class.Rd 2017-06-17 18:24:32 UTC (rev 397)
@@ -3,6 +3,8 @@
\docType{class}
\name{BilanAnnuels-class}
\alias{BilanAnnuels-class}
+\alias{calcule.BilanAnnuels}
+\alias{calcule.bilanannuels}
\title{Class "BilanAnnuels"}
\description{
This class displays annual migration counts, for several counting device, taxa or stages.
Modified: pkg/stacomir/man/calcule-BilanArgentee-method.Rd
===================================================================
--- pkg/stacomir/man/calcule-BilanArgentee-method.Rd 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/man/calcule-BilanArgentee-method.Rd 2017-06-17 18:24:32 UTC (rev 397)
@@ -3,6 +3,8 @@
\docType{methods}
\name{calcule,BilanArgentee-method}
\alias{calcule,BilanArgentee-method}
+\alias{calcule.BilanArgentee}
+\alias{calcule.bilanargentee}
\title{Calculate individual silver eel parameters.}
\usage{
\S4method{calcule}{BilanArgentee}(object, silent)
Modified: pkg/stacomir/man/calcule-BilanMigration-method.Rd
===================================================================
--- pkg/stacomir/man/calcule-BilanMigration-method.Rd 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/man/calcule-BilanMigration-method.Rd 2017-06-17 18:24:32 UTC (rev 397)
@@ -3,6 +3,7 @@
\docType{methods}
\name{calcule,BilanMigration-method}
\alias{calcule,BilanMigration-method}
+\alias{calcule.BilanMigration}
\alias{calcule.bilanmigration}
\title{Transforms migration per period to daily migrations, and performs the conversion from weights to number is data
are stored as weights (glass eel).}
@@ -20,23 +21,15 @@
\value{
BilanMigration with calcdata slot filled. It is a list with one element per counting device containing
\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".
+\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.
+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}}
}
-\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
-}
-}
-}
\description{
The calculation must be launched once data are filled by the connect method. Currently the negative argument
has no effect.
Modified: pkg/stacomir/man/calcule-BilanMigrationCar-method.Rd
===================================================================
--- pkg/stacomir/man/calcule-BilanMigrationCar-method.Rd 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/man/calcule-BilanMigrationCar-method.Rd 2017-06-17 18:24:32 UTC (rev 397)
@@ -3,7 +3,7 @@
\docType{methods}
\name{calcule,BilanMigrationCar-method}
\alias{calcule,BilanMigrationCar-method}
-\title{calcule methode}
+\title{Computes data to a standard format for the summary and plot methods.}
\usage{
\S4method{calcule}{BilanMigrationCar}(object, silent = FALSE)
}
@@ -13,6 +13,8 @@
\item{silent}{Boolean default FALSE, if TRUE information messages not displayed}
}
\description{
-calcule methode
+Merges the content of the list elements "parqual" and "parquan" in the data slot, and creates
+a single dataframe with one line per qualitative and quantitative pair. This methods allow to
+cross one quantity (e.g. length) with a qualitative parameter (e.g. sex).
}
Modified: pkg/stacomir/man/choice.Rd
===================================================================
--- pkg/stacomir/man/choice.Rd 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/man/choice.Rd 2017-06-17 18:24:32 UTC (rev 397)
@@ -17,4 +17,5 @@
\author{
cedric.briand
}
+\keyword{internal}
Modified: pkg/stacomir/man/choice_c.Rd
===================================================================
--- pkg/stacomir/man/choice_c.Rd 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/man/choice_c.Rd 2017-06-17 18:24:32 UTC (rev 397)
@@ -2,7 +2,7 @@
% Please edit documentation in R/create_generic.r
\name{choice_c}
\alias{choice_c}
-\title{Generic method for manual choice}
+\title{Generic method for manual choice using the command line}
\usage{
choice_c(object, ...)
}
@@ -12,9 +12,10 @@
\item{...}{Additional parms}
}
\description{
-Generic method for manual choice
+Generic method for manual choice using the command line
}
\author{
cedric.briand
}
+\keyword{internal}
Modified: pkg/stacomir/man/choicemult.Rd
===================================================================
--- pkg/stacomir/man/choicemult.Rd 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/man/choicemult.Rd 2017-06-17 18:24:32 UTC (rev 397)
@@ -2,7 +2,7 @@
% Please edit documentation in R/create_generic.r
\name{choicemult}
\alias{choicemult}
-\title{Generic method for multiple choice (using the gwidget graphical interface)}
+\title{Generic method for multiple choice (using the gwidget notebook for multiple choice)}
\usage{
choicemult(object, ...)
}
@@ -12,9 +12,10 @@
\item{...}{Additional parms}
}
\description{
-Generic method for multiple choice (using the gwidget graphical interface)
+Generic method for multiple choice (using the gwidget notebook for multiple choice)
}
\author{
cedric.briand
}
+\keyword{internal}
Modified: pkg/stacomir/man/funbarchart1DF.Rd
===================================================================
--- pkg/stacomir/man/funbarchart1DF.Rd 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/man/funbarchart1DF.Rd 2017-06-17 18:24:32 UTC (rev 397)
@@ -17,7 +17,5 @@
\note{
The program cuts periods which overlap between two month
}
-\author{
-Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-}
+\keyword{internal}
Modified: pkg/stacomir/man/funbarchartDC.Rd
===================================================================
--- pkg/stacomir/man/funbarchartDC.Rd 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/man/funbarchartDC.Rd 2017-06-17 18:24:32 UTC (rev 397)
@@ -20,4 +20,5 @@
\author{
cedric.briand
}
+\keyword{internal}
Modified: pkg/stacomir/man/funbarchartDF.Rd
===================================================================
--- pkg/stacomir/man/funbarchartDF.Rd 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/man/funbarchartDF.Rd 2017-06-17 18:24:32 UTC (rev 397)
@@ -20,4 +20,5 @@
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
+\keyword{internal}
Modified: pkg/stacomir/man/funboxDC.Rd
===================================================================
--- pkg/stacomir/man/funboxDC.Rd 2017-06-16 20:48:18 UTC (rev 396)
+++ pkg/stacomir/man/funboxDC.Rd 2017-06-17 18:24:32 UTC (rev 397)
@@ -17,4 +17,5 @@
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
+\keyword{internal}
Modified: pkg/stacomir/man/funboxDF.Rd
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 397
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