[Stacomir-commits] r171 - / pkg/stacomir pkg/stacomir/R pkg/stacomir/examples/01_BilanMigrationMult pkg/stacomir/inst/config
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Aug 20 18:09:01 CEST 2016
Author: briand
Date: 2016-08-20 18:09:01 +0200 (Sat, 20 Aug 2016)
New Revision: 171
Removed:
branch0.5/
Modified:
pkg/stacomir/DESCRIPTION
pkg/stacomir/R/BilanEspeces.r
pkg/stacomir/R/BilanFonctionnementDC.r
pkg/stacomir/R/BilanMigration.r
pkg/stacomir/R/BilanMigrationConditionEnv.r
pkg/stacomir/R/BilanMigrationInterAnnuelle.r
pkg/stacomir/R/BilanMigrationMult.r
pkg/stacomir/R/Bilan_carlot.r
pkg/stacomir/R/Bilan_poids_moyen.r
pkg/stacomir/R/Bilan_taille.r
pkg/stacomir/R/RefCheckBox.r
pkg/stacomir/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R
pkg/stacomir/inst/config/generate_Roxygen2.R
Log:
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/DESCRIPTION 2016-08-20 16:09:01 UTC (rev 171)
@@ -6,7 +6,7 @@
person("Marion", "Legrand", role = "aut", email="tableau-salt-loire at logrami.fr"))
Description: Graphical outputs and treatment for a database of fishway
monitoring. It is a part of the STACOMI project developed in France by the ONEMA
- institute to centralize data obtained by fishway monitoring. Version 0.4.1 is
+ institute to centralize data obtained by fishway monitoring. Version 0.5.0 is
available in French English and Spanish.
License: GPL (>= 2)
Collate:
Modified: pkg/stacomir/R/BilanEspeces.r
===================================================================
--- pkg/stacomir/R/BilanEspeces.r 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/R/BilanEspeces.r 2016-08-20 16:09:01 UTC (rev 171)
@@ -25,7 +25,6 @@
#' \code{\linkS4class{BilanMigrationConditionEnv}}
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
-#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
#' @concept Bilan Object
#' @examples
#'
@@ -158,7 +157,7 @@
tableEspeces=bilanEspeces at data
if (nrow(tableEspeces)==0) funout(get("msg",envir_stacomi)$BilanEspeces.5,arret=TRUE)
tableEspeces$taxon_stades=paste(tableEspeces$tax_nom_latin,tableEspeces$std_libelle,sep="_")
- # je ne garde taxons_stades que pour les esp�ces pr�sentant plusieurs stades
+ # only keeping taxon stage for species with several stages
nbstades=tapply(tableEspeces$tax_nom_latin,tableEspeces$taxon_stades,function(X)(length(unique(X))))
if (length(nbstades[nbstades>1])>0){
les_multiples=names(nbstades[nbstades>1])
@@ -223,7 +222,6 @@
tableEspeces=bilanEspeces at data
if (nrow(tableEspeces)==0) funout(get("msg",envir_stacomi)$BilanEspeces.5,arret=TRUE)
tableEspeces$taxon_stades=paste(tableEspeces$tax_nom_latin,tableEspeces$std_libelle,sep="_")
- # je ne garde taxons_stades que pour les esp�ces pr�sentant plusieurs stades
nbstades=tapply(tableEspeces$tax_nom_latin,tableEspeces$taxon_stades,function(X)(length(unique(X))))
if (length(nbstades[nbstades>1])>0){
les_multiples=names(nbstades[nbstades>1])
Modified: pkg/stacomir/R/BilanFonctionnementDC.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDC.r 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/R/BilanFonctionnementDC.r 2016-08-20 16:09:01 UTC (rev 171)
@@ -19,7 +19,6 @@
#' \code{\linkS4class{BilanMigrationConditionEnv}}
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
-#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
#' @concept Bilan Object
#' @examples
#'
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/R/BilanMigration.r 2016-08-20 16:09:01 UTC (rev 171)
@@ -47,7 +47,6 @@
#' \code{\linkS4class{BilanMigrationConditionEnv}}
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
-#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
#' @concept Bilan Object
#' @examples
#'
Modified: pkg/stacomir/R/BilanMigrationConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanMigrationConditionEnv.r 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/R/BilanMigrationConditionEnv.r 2016-08-20 16:09:01 UTC (rev 171)
@@ -26,7 +26,6 @@
#' \code{\linkS4class{BilanMigrationConditionEnv}}
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
-#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
#' @concept Bilan Object
#' @examples
#'
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2016-08-20 16:09:01 UTC (rev 171)
@@ -28,7 +28,6 @@
#' \code{\linkS4class{BilanMigrationConditionEnv}}
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
-#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
#' @concept Bilan Object
#' @examples
#'
Modified: pkg/stacomir/R/BilanMigrationMult.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMult.r 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/R/BilanMigrationMult.r 2016-08-20 16:09:01 UTC (rev 171)
@@ -10,15 +10,16 @@
#' On each counting device, the migration is recorded. It can be either an instant recording (video control) or the use of traps,
#' Operations are monitoring operations during a period. For each operation, several species of fishes can be recorded (samples). In the case of migratory
#' fishes the stage of development is important as it may indicate generic migrations, to and fro, between the river and the sea.
+#'
#' Hence a Multiple Migration Bilan is built from several one or several counting devices (DC), one or several Taxa (Taxon), one or several stages
#' (stage). The migration can be also recorded not as numbers, but in the case of glass eels, as weight, which will be later transformed to number,
#' from daily conversion coefficients. The methods in this class test whether the counts are numbers or another type of quantity.
#' This class makes different calculations than BilanMigration, it does not handle escapement coefficients,
#' it uses quantities other than numbers if necessary (only used for glass eel in the connect method).
#' @slot dc An object of class \code{RefDC}
-#' @slot taxons An object of class \code{RefTaxon}
-#' @slot stades An object of class \code{RefStades}
-#' @slot pasDeTemps An object of class \code{PasDeTempsJournalier}
+#' @slot taxons An object of class \code{\link{RefTaxon}}
+#' @slot stades An object of class \code{\link{RefStades}}
+#' @slot pasDeTemps An object of class \code{\link{PasDeTempsJournalier}}
#' @slot data A data.frame containing raw data filled by the connect method
#' @slot calcdata A "list" of calculated daily data, one per dc, filled in by the calcule method
#' @slot coef_conversion A data.frame of daily weight to number conversion coefficients, filled in by the connect
Modified: pkg/stacomir/R/Bilan_carlot.r
===================================================================
--- pkg/stacomir/R/Bilan_carlot.r 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/R/Bilan_carlot.r 2016-08-20 16:09:01 UTC (rev 171)
@@ -20,8 +20,6 @@
#' \code{\linkS4class{BilanMigrationConditionEnv}}
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
-#' @references
-#' \url{http://w3.eptb-vilaine.fr:8080/tracstacomi/wiki/Recette\%20BilanLot}
#' @concept Bilan Object
#' @examples
#'
Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/R/Bilan_poids_moyen.r 2016-08-20 16:09:01 UTC (rev 171)
@@ -47,7 +47,6 @@
#' \code{\linkS4class{BilanMigrationConditionEnv}}
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
-#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
#' @concept Bilan Object
#' @examples
#'
Modified: pkg/stacomir/R/Bilan_taille.r
===================================================================
--- pkg/stacomir/R/Bilan_taille.r 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/R/Bilan_taille.r 2016-08-20 16:09:01 UTC (rev 171)
@@ -27,7 +27,6 @@
#' \code{\linkS4class{BilanMigrationConditionEnv}}
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
#' \code{\linkS4class{BilanMigrationPar}}
-#' @references \url{http://w3.eptb-vilaine.fr:8080/tracstacomi}
#' @concept Bilan Object
#' @examples
#'
Modified: pkg/stacomir/R/RefCheckBox.r
===================================================================
--- pkg/stacomir/R/RefCheckBox.r 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/R/RefCheckBox.r 2016-08-20 16:09:01 UTC (rev 171)
@@ -22,7 +22,6 @@
#' \code{\linkS4class{RefStades}}
#' \code{\linkS4class{RefStationMesure}}
#' \code{\linkS4class{RefTaxon}}
-#' @references ~put references to the literature/web site here ~
#' @family Referential objects
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
Modified: pkg/stacomir/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R
===================================================================
--- pkg/stacomir/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/examples/01_BilanMigrationMult/bilanMigrationMult_Arzal.R 2016-08-20 16:09:01 UTC (rev 171)
@@ -1,6 +1,6 @@
-#library(stacomiR)
-# launches the application in the command line
-stacomi(gr_interface=FALSE)
+library(stacomiR)
+
+stacomi(gr_interface=FALSE) ## launches the application in the command line
# here is the structure of the class
showClass("BilanMigrationMult")
data("bMM_Arzal")
Modified: pkg/stacomir/inst/config/generate_Roxygen2.R
===================================================================
--- pkg/stacomir/inst/config/generate_Roxygen2.R 2016-08-20 14:24:09 UTC (rev 170)
+++ pkg/stacomir/inst/config/generate_Roxygen2.R 2016-08-20 16:09:01 UTC (rev 171)
@@ -29,4 +29,4 @@
# or :
#vignette("roxygen2")
require(roxygen2)
-roxygen2::roxygenise("F:/workspace/stacomir/branch0.5/stacomir");warnings()[1:10]
\ No newline at end of file
+roxygen2::roxygenise("F:/workspace/stacomir/pkg/stacomir");warnings()[1:10]
\ No newline at end of file
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