[Stacomir-commits] r184 - in pkg/stacomir: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Aug 27 13:27:39 CEST 2016
Author: briand
Date: 2016-08-27 13:27:39 +0200 (Sat, 27 Aug 2016)
New Revision: 184
Added:
pkg/stacomir/man/choice_c-BilanMigration-method.Rd
pkg/stacomir/man/mygtkProgressBar.Rd
Modified:
pkg/stacomir/NAMESPACE
pkg/stacomir/R/BilanMigration.r
pkg/stacomir/R/utilitaires.r
pkg/stacomir/man/BilanMigration-class.Rd
pkg/stacomir/man/BilanMigrationMult-class.Rd
pkg/stacomir/man/BilanMigrationPar-class.Rd
pkg/stacomir/man/Bilan_poids_moyen-class.Rd
pkg/stacomir/man/Bilan_taille-class.Rd
pkg/stacomir/man/calcule-BilanMigrationPar-method.Rd
pkg/stacomir/man/calcule-Bilan_carlot-method.Rd
pkg/stacomir/man/calcule-Bilan_taille-method.Rd
pkg/stacomir/man/charge-Bilan_stades_pigm-method.Rd
pkg/stacomir/man/charge-Bilan_taille-method.Rd
pkg/stacomir/man/connect-Bilan_taille-method.Rd
Log:
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/NAMESPACE 2016-08-27 11:27:39 UTC (rev 184)
@@ -19,6 +19,7 @@
export(hbilanMigrationConditionEnvcalc)
export(interface_BilanEspeces)
export(messages)
+export(mygtkProgressBar)
export(stacomi)
export(vector_to_listsql)
exportClasses(BilanConditionEnv)
@@ -96,7 +97,5 @@
importFrom(utils,globalVariables)
importFrom(utils,read.csv)
importFrom(utils,select.list)
-importFrom(utils,setWinProgressBar)
importFrom(utils,stack)
-importFrom(utils,winProgressBar)
importFrom(utils,write.table)
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/R/BilanMigration.r 2016-08-27 11:27:39 UTC (rev 184)
@@ -66,10 +66,10 @@
#' @param taxons Either a species name in latin or the SANDRE code for species (ie 2038=Anguilla anguilla),
#' these should match the ref.tr_taxon_tax referential table in the stacomi database, see \link{choice_c-RefTaxon-method}
#' @param stades A stage code matching the ref.tr_stadedeveloppement_std table in the stacomi database see \link{choice_c-RefStades-method}
-#' @param datedebut The starting date as a character, formats like \code{%Y-%m-%d} or \code{%d-%m-%Y} can be used as input
+#' @param datedebut The starting date as a character, formats like \code{\%Y-\%m-\%d} or \code{\%d-\%m-\%Y} can be used as input
#' @param datefin The finishing date of the Bilan, for this class this will be used to calculate the number of daily steps.
#' The choice_c method fills in the data slot for RefDC, RefTaxon, RefStades, and RefPasDeTempsJournalier and then
-#' uses the choice_c methods of these object to "select" the data.
+#' uses the choice_c methods of these object to select the data.
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
setMethod("choice_c",signature=signature("BilanMigration"),definition=function(object,dc,taxons,stades,datedebut,datefin){
Modified: pkg/stacomir/R/utilitaires.r
===================================================================
--- pkg/stacomir/R/utilitaires.r 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/R/utilitaires.r 2016-08-27 11:27:39 UTC (rev 184)
@@ -203,8 +203,7 @@
#' @param width Width of the progress bar
#' @param height Height of the progress bar
#' @param pulse Do you want the widget to pulse
-#' @returnType
-#' @return
+#' @return nothing but progress_bar and dialog gwidgets are assigned to .globalEnv
#'
#' @author cedric.briand
#' @examples
@@ -237,6 +236,7 @@
progress_bar$setText(progress_text)
if (pulse) gtkProgressBarPulse(progress_bar)
dialog$showAll()
+ return(invisible(NULL))
}
Modified: pkg/stacomir/man/BilanMigration-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigration-class.Rd 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/man/BilanMigration-class.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -20,7 +20,12 @@
constrained to daily value and 365 days}
\item{\code{data}}{Object of class \code{data.frame}}
+
+\item{\code{time.sequence}}{Object of class \code{POSIXct} : a time sequence of days generated by the calcule method}
}}
+\note{
+TODO discuss the lenght of the bilan and how it is used to "write" in the database
+}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
Modified: pkg/stacomir/man/BilanMigrationMult-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationMult-class.Rd 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/man/BilanMigrationMult-class.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -27,7 +27,7 @@
\item{\code{coef_conversion}}{A data.frame of daily weight to number conversion coefficients, filled in by the connect
method if any weight are found in the data slot.}
-\item{\code{time}}{sequence A POSIXt time sequence}
+\item{\code{time.sequence}}{A POSIXt time sequence}
}}
\note{
A Migration Bilan comes from a migration monitoring : the fishes are monitored in a section of river, this section is
Modified: pkg/stacomir/man/BilanMigrationPar-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationPar-class.Rd 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/man/BilanMigrationPar-class.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -52,17 +52,17 @@
}
\seealso{
Other Bilan Class
-\code{\linkS4class{Bilan_carlot}},
-\code{\linkS4class{Bilan_poids_moyen}},
-\code{\linkS4class{Bilan_stades_pigm}},
-\code{\linkS4class{Bilan_taille}},
+\code{\linkS4class{Bilan_carlot}},
+\code{\linkS4class{Bilan_poids_moyen}},
+\code{\linkS4class{Bilan_stades_pigm}},
+\code{\linkS4class{Bilan_taille}},
\code{\linkS4class{BilanConditionEnv}},
-\code{\linkS4class{BilanEspeces}},
-\code{\linkS4class{BilanFonctionnementDC}},
-\code{\linkS4class{BilanFonctionnementDF}},
-\code{\linkS4class{BilanMigration}},
-\code{\linkS4class{BilanMigrationConditionEnv}},
-\code{\linkS4class{BilanMigrationInterAnnuelle}},
+\code{\linkS4class{BilanEspeces}},
+\code{\linkS4class{BilanFonctionnementDC}},
+\code{\linkS4class{BilanFonctionnementDF}},
+\code{\linkS4class{BilanMigration}},
+\code{\linkS4class{BilanMigrationConditionEnv}},
+\code{\linkS4class{BilanMigrationInterAnnuelle}},
\code{\linkS4class{BilanMigrationPar}}
}
\concept{
Modified: pkg/stacomir/man/Bilan_poids_moyen-class.Rd
===================================================================
--- pkg/stacomir/man/Bilan_poids_moyen-class.Rd 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/man/Bilan_poids_moyen-class.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -22,10 +22,10 @@
\item{\code{anneefin}}{Object of class \code{\link{RefAnnee-class}}
refAnnee allows to choose last year of the Bilan}
-\item{\code{coe}}{Object of class \code{\link{RefCoe}} class loading coefficient
+\item{\code{coe}}{Object of class \code{\link{RefCoe-class}} class loading coefficient
of conversion between quantity (weights or volumes of glass eel) and numbers}
-\item{\code{liste}}{Object of class \code{\link{RefListe}} RefListe referential
+\item{\code{liste}}{Object of class \code{\link{RefListe-class}} RefListe referential
class choose within a list, here the choice is wether subsamples or not. Subsamples
in the stacomi database are samples with a non null value for parent sample. Migration
counts are never made on subsamples but those can be integrated to calculate mean weights.}
Modified: pkg/stacomir/man/Bilan_taille-class.Rd
===================================================================
--- pkg/stacomir/man/Bilan_taille-class.Rd 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/man/Bilan_taille-class.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -21,8 +21,10 @@
\section{Slots}{
\describe{
-\item{\code{dc}}{an object of class \link{RefDC-class}}
+\item{\code{data}}{A data frame}
+\item{\code{dc}}{An object of class \link{RefDC-class}}
+
\item{\code{taxons}}{An object of class \link{RefTaxon-class}}
\item{\code{stades}}{An object of class \link{RefStades-class} inherited from \link{BilanMigration-class}}
@@ -51,15 +53,15 @@
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
\seealso{
-Other Bilan Classes \code{\linkS4class{Bilan_carlot}},
-\code{\linkS4class{Bilan_poids_moyen}},
-\code{\linkS4class{Bilan_stades_pigm}}, \code{\linkS4class{Bilan_taille}},
-\code{\linkS4class{BilanConditionEnv}}, \code{\linkS4class{BilanEspeces}},
-\code{\linkS4class{BilanFonctionnementDC}},
-\code{\linkS4class{BilanFonctionnementDF}},
-\code{\linkS4class{BilanMigration}},
-\code{\linkS4class{BilanMigrationConditionEnv}},
-\code{\linkS4class{BilanMigrationInterAnnuelle}},
+Other Bilan Classes \code{\linkS4class{Bilan_carlot}},
+\code{\linkS4class{Bilan_poids_moyen}},
+\code{\linkS4class{Bilan_stades_pigm}}, \code{\linkS4class{Bilan_taille}},
+\code{\linkS4class{BilanConditionEnv}}, \code{\linkS4class{BilanEspeces}},
+\code{\linkS4class{BilanFonctionnementDC}},
+\code{\linkS4class{BilanFonctionnementDF}},
+\code{\linkS4class{BilanMigration}},
+\code{\linkS4class{BilanMigrationConditionEnv}},
+\code{\linkS4class{BilanMigrationInterAnnuelle}},
\code{\linkS4class{BilanMigrationPar}}
}
\concept{
Modified: pkg/stacomir/man/calcule-BilanMigrationPar-method.Rd
===================================================================
--- pkg/stacomir/man/calcule-BilanMigrationPar-method.Rd 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/man/calcule-BilanMigrationPar-method.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -8,7 +8,7 @@
\S4method{calcule}{BilanMigrationPar}(object)
}
\arguments{
-\item{object}{An object of class \code{\link{BilanMigrationPar}}}
+\item{object}{An object of class \code{\link{BilanMigrationPar-class}}}
}
\description{
calcule methode
Modified: pkg/stacomir/man/calcule-Bilan_carlot-method.Rd
===================================================================
--- pkg/stacomir/man/calcule-Bilan_carlot-method.Rd 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/man/calcule-Bilan_carlot-method.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -8,7 +8,7 @@
\S4method{calcule}{Bilan_carlot}(object, h)
}
\arguments{
-\item{object}{An object of class \code{\link{Bilan_carlot}}}
+\item{object}{An object of class \code{\link{Bilan_carlot-class}}}
\item{h}{a handler}
}
Modified: pkg/stacomir/man/calcule-Bilan_taille-method.Rd
===================================================================
--- pkg/stacomir/man/calcule-Bilan_taille-method.Rd 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/man/calcule-Bilan_taille-method.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -8,7 +8,7 @@
\S4method{calcule}{Bilan_taille}(object)
}
\arguments{
-\item{object}{An object of class \code{\link{Bilan_taille}}}
+\item{object}{An object of class \code{\link{Bilan_taille-class}}}
}
\description{
Calcule method for BilanTaille
Modified: pkg/stacomir/man/charge-Bilan_stades_pigm-method.Rd
===================================================================
--- pkg/stacomir/man/charge-Bilan_stades_pigm-method.Rd 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/man/charge-Bilan_stades_pigm-method.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -8,7 +8,7 @@
\S4method{charge}{Bilan_stades_pigm}(object, h)
}
\arguments{
-\item{object}{An object of class \code{\link{Bilan_carlot}}}
+\item{object}{An object of class \code{\link{Bilan_stades_pigm-class}}}
\item{h}{A handler}
}
Modified: pkg/stacomir/man/charge-Bilan_taille-method.Rd
===================================================================
--- pkg/stacomir/man/charge-Bilan_taille-method.Rd 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/man/charge-Bilan_taille-method.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -8,7 +8,7 @@
\S4method{charge}{Bilan_taille}(object)
}
\arguments{
-\item{object}{An object of class \code{\link{Bilan_taille}}}
+\item{object}{An object of class \code{\link{Bilan_taille-class}}}
}
\description{
charge method for Bilan_taille
Added: pkg/stacomir/man/choice_c-BilanMigration-method.Rd
===================================================================
--- pkg/stacomir/man/choice_c-BilanMigration-method.Rd (rev 0)
+++ pkg/stacomir/man/choice_c-BilanMigration-method.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/BilanMigration.r
+\docType{methods}
+\name{choice_c,BilanMigration-method}
+\alias{choice_c,BilanMigration-method}
+\title{command line interface for BilanMigration class}
+\usage{
+\S4method{choice_c}{BilanMigration}(object, dc, taxons, stades, datedebut,
+ datefin)
+}
+\arguments{
+\item{object}{An object of class \link{BilanMigration-class}}
+
+\item{dc}{A numeric or integer, the code of the dc, coerced to integer,see \link{choice_c-RefDC-method}}
+
+\item{taxons}{Either a species name in latin or the SANDRE code for species (ie 2038=Anguilla anguilla),
+these should match the ref.tr_taxon_tax referential table in the stacomi database, see \link{choice_c-RefTaxon-method}}
+
+\item{stades}{A stage code matching the ref.tr_stadedeveloppement_std table in the stacomi database see \link{choice_c-RefStades-method}}
+
+\item{datedebut}{The starting date as a character, formats like \code{\%Y-\%m-\%d} or \code{\%d-\%m-\%Y} can be used as input}
+
+\item{datefin}{The finishing date of the Bilan, for this class this will be used to calculate the number of daily steps.
+The choice_c method fills in the data slot for RefDC, RefTaxon, RefStades, and RefPasDeTempsJournalier and then
+uses the choice_c methods of these object to select the data.}
+}
+\description{
+command line interface for BilanMigration class
+}
+\author{
+Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+}
+
Modified: pkg/stacomir/man/connect-Bilan_taille-method.Rd
===================================================================
--- pkg/stacomir/man/connect-Bilan_taille-method.Rd 2016-08-27 10:12:04 UTC (rev 183)
+++ pkg/stacomir/man/connect-Bilan_taille-method.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -8,7 +8,7 @@
\S4method{connect}{Bilan_taille}(object, h)
}
\arguments{
-\item{object}{An object of class \code{\link{Bilan_taille}}}
+\item{object}{An object of class \code{\link{Bilan_taille-class}}}
\item{...}{Additional parameters}
}
Added: pkg/stacomir/man/mygtkProgressBar.Rd
===================================================================
--- pkg/stacomir/man/mygtkProgressBar.Rd (rev 0)
+++ pkg/stacomir/man/mygtkProgressBar.Rd 2016-08-27 11:27:39 UTC (rev 184)
@@ -0,0 +1,43 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utilitaires.r
+\name{mygtkProgressBar}
+\alias{mygtkProgressBar}
+\title{Progress bar using a gtkdialog, the progress bar is assigned in .GlobalEnv
+This progress bar has a button to close. Use}
+\usage{
+mygtkProgressBar(title, progress_text, width = 400, height = 50,
+ pulse = TRUE)
+}
+\arguments{
+\item{title}{THe title of the bar}
+
+\item{progress_text}{The text to display for progression}
+
+\item{width}{Width of the progress bar}
+
+\item{height}{Height of the progress bar}
+
+\item{pulse}{Do you want the widget to pulse}
+}
+\value{
+nothing but progress_bar and dialog gwidgets are assigned to .globalEnv
+}
+\description{
+Progress bar using a gtkdialog, the progress bar is assigned in .GlobalEnv
+This progress bar has a button to close. Use
+}
+\examples{
+\dontrun{
+mygtkProgressBar("Trial","progress text")
+fraction_progressed=seq(0,1,length.out=50)
+for(i in fraction_progressed) {
+ Sys.sleep(0.1)
+ progress_bar$setFraction(i)
+}
+dispose(dialog)
+}
+}
+\author{
+cedric.briand
+}
+
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