[Stacomir-commits] r369 - in pkg/stacomir: R inst/examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed May 17 17:03:26 CEST 2017
Author: legrand
Date: 2017-05-17 17:03:26 +0200 (Wed, 17 May 2017)
New Revision: 369
Modified:
pkg/stacomir/R/BilanAgedemer.r
pkg/stacomir/R/BilanConditionEnv.r
pkg/stacomir/R/BilanEspeces.r
pkg/stacomir/R/BilanMigration.r
pkg/stacomir/R/BilanMigrationCar.r
pkg/stacomir/R/BilanMigrationInterAnnuelle.r
pkg/stacomir/R/BilanMigrationMultConditionEnv.r
pkg/stacomir/R/BilanOperation.r
pkg/stacomir/R/Bilan_poids_moyen.r
pkg/stacomir/R/RefChoix.r
pkg/stacomir/R/RefCoe.r
pkg/stacomir/R/RefListe.r
pkg/stacomir/R/RefStades.r
pkg/stacomir/R/RefStationMesure.r
pkg/stacomir/R/ReftextBox.r
pkg/stacomir/inst/examples/bilanArgentee_example.R
pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R
Log:
Modified: pkg/stacomir/R/BilanAgedemer.r
===================================================================
--- pkg/stacomir/R/BilanAgedemer.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/BilanAgedemer.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -164,6 +164,8 @@
#' @param par Parameters chosen for the Bilan are mesured body size (1786), mesured fork length (1785),video size (C001) and number of year at sea (A124)
#' @param horodatedebut The starting date as a character, formats like \code{\%Y-\%m-\%d} or \code{\%d-\%m-\%Y} can be used as input
#' @param horodatefin The finishing date of the Bilan, for this class this will be used to calculate the number of daily steps.
+#' @param limit1hm Size limit of a salmon for an one sea winter fish
+#' @param limit2hm Size limit of a salmon for a two sea winter fish
#' @param silent Default FALSE, if TRUE the program should no display messages
#' @return An object of class \link{BilanAgedemer-class}
#' The choice_c method fills in the data slot for classes \link{RefDC-class}, \link{RefTaxon-class}, \link{RefStades-class}, \link{Refpar-class} and two slots of \link{RefHorodate-class} and then
@@ -463,6 +465,7 @@
#' supprime method for BilanMigrationInterannuelle class
#' @param object An object of class \link{BilanAgedemer-class}
+#' @param silent Default FALSE, if TRUE the program should no display messages
#' @return nothing
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
Modified: pkg/stacomir/R/BilanConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanConditionEnv.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/BilanConditionEnv.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -68,7 +68,7 @@
)
#' command line interface for BilanConditionEnv class
#' @param object An object of class \link{BilanConditionEnv-class}
-#' @param stationmesure A character, the code of the monitoring station, which records environmental parameters \link{choice_c,RefStationMesure-method}
+#' @param stationMesure A character, the code of the monitoring station, which records environmental parameters \link{choice_c,RefStationMesure-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 datefin The finishing date of the Bilan, for this class this will be used to calculate the number of daily steps.
#' @param silent Boolean default FALSE, if TRUE information messages not displayed.
Modified: pkg/stacomir/R/BilanEspeces.r
===================================================================
--- pkg/stacomir/R/BilanEspeces.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/BilanEspeces.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -23,14 +23,13 @@
#' @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{BilanMigrationMultConditionEnv}},
#' \code{\linkS4class{BilanMigrationInterAnnuelle}},
-#' \code{\linkS4class{BilanMigrationPar}}
+#' \code{\linkS4class{BilanMigrationCar}}
#' @family Bilan Objects
#' @keywords classes
#' @export
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/BilanMigration.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -575,7 +575,7 @@
#'
#' Daily values are needed to compare migrations from year to year, by the class \link{BilanMigrationInterAnnuelle-class}. They are added by
#' by this function.
-#' @param bilanMigration an object of class \code{\linkS4class{BilanMigration}}
+#' @param object an object of class \code{\linkS4class{BilanMigration}}
#' @param silent : TRUE to avoid messages
#' @param dbname : the name of the database, defaults to "bd_contmig_nat"
#' @param check_for_bjo : do you want to check if data are already present in the bjo table, and delete them,
Modified: pkg/stacomir/R/BilanMigrationCar.r
===================================================================
--- pkg/stacomir/R/BilanMigrationCar.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/BilanMigrationCar.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -67,7 +67,8 @@
#' @param taxons '2220=Salmo salar',
#' these should match the ref.tr_taxon_tax referential table in the stacomi database, see \link{choice_c,RefTaxon-method}
#' @param stades TODO
-#' @param car Sample TODO
+#' @param parquan quantitative parameter
+#' @param parqual qualitative parameter
#' @param horodatedebut The starting date as a character, formats like \code{\%Y-\%m-\%d} or \code{\%d-\%m-\%Y} can be used as input
#' @param horodatefin The finishing date of the Bilan, for this class this will be used to calculate the number of daily steps.
#' @param echantillon Default TRUE,
@@ -318,8 +319,9 @@
#' calcule methode
#'
-#'
-#'@param object An object of class \code{\link{BilanMigrationCar-class}}
+#' @param object An object of class \code{\link{BilanMigrationCar-class}}
+#' @param silent Boolean default FALSE, if TRUE information messages not displayed
+
setMethod("calcule",signature=signature("BilanMigrationCar"),definition=function(object,silent=FALSE){
bmC<-object
qual<-bmC at data[["parqual"]]
@@ -399,7 +401,7 @@
#' @param x An object of class BilanMigrationCar
#' @param y not used there
#' @param plot.type One of "qual", "quant" "crossed" default to qual
-#' @param color A named vector for the colors of either parameters (if plot.type=quant) or levels for
+#' @param color_parm A named vector for the colors of either parameters (if plot.type=quant) or levels for
#' parameters (if plot.type=qual).
#' @param silent Boolean default FALSE, if TRUE information messages not displayed
#' @param ... Additional parameters
@@ -504,8 +506,7 @@
#' @param caption, see xtable
#' @param label, see xtable
#' @param align, see xtable, overidden if NULL
-#' @param digits default 0
-#' @param display see xtable
+#' @param ... Additional parameters
#' @export
setMethod("xtable",signature=signature("BilanMigrationCar"),definition=function(x,caption=NULL, label=NULL,align=NULL,...){
bmC<-x
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -379,7 +379,7 @@
#' calcule method for BilanMigrationInterannuelle
#'
-#' @param object An object of class \code{\link{BilanMigrationInterannuelle-class}}
+#' @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
Modified: pkg/stacomir/R/BilanMigrationMultConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMultConditionEnv.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/BilanMigrationMultConditionEnv.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -57,7 +57,11 @@
)
#' command line interface for BilanConditionEnv class
#' @param object An object of class \link{BilanConditionEnv-class}
-#' @param stationmesure A character, the code of the monitoring station, which records environmental parameters \link{choice_c,RefStationMesure-method}
+#' @param dc A numeric or integer, the code of the dc, coerced to integer,see \link{choice_c,RefDC-method}
+#' @param taxons '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 'AGJ=Anguille jaune', 'AGG=Anguille argentee', 'CIV=civelle'
+#' @param stationMesure A character, the code of the monitoring station, which records environmental parameters \link{choice_c,RefStationMesure-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 datefin The finishing date of the Bilan, for this class this will be used to calculate the number of daily steps.
#' @param silent Boolean default FALSE, if TRUE information messages not displayed.
@@ -119,6 +123,7 @@
#' Calculation for the BilanMigrationMultConditionEnv
#'
#' @param object An object of class \code{\link{BilanMigrationMultConditionEnv-class}}
+#' @param silent Boolean default FALSE, if TRUE information messages not displayed
#' @return \code{\link{BilanMigrationMultConditionEnv-class}}
#' @export
setMethod("calcule",signature=signature("BilanMigrationMultConditionEnv"),definition=function(object,silent){
Modified: pkg/stacomir/R/BilanOperation.r
===================================================================
--- pkg/stacomir/R/BilanOperation.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/BilanOperation.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -9,16 +9,14 @@
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @seealso Other Bilan Class \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{BilanMigrationMultConditionEnv}}
#' \code{\linkS4class{BilanMigrationInterAnnuelle}}
-#' \code{\linkS4class{BilanMigrationPar}}
+#' \code{\linkS4class{BilanMigrationCar}}
#' @concept Bilan Object
#' @keywords classes
#' @aliases BilanOperation bilanoperation bilanOperation
Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/Bilan_poids_moyen.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -285,7 +285,7 @@
#' model method for Bilan_poids_moyen'
#' this method uses samples collected over the season to model the variation in weight of
#' glass eel or yellow eels.
-#' @param object An object of class \link{Bilan_pois_moyen-class}
+#' @param object An object of class \link{Bilan_poids_moyen-class}
#' @param model.type default "seasonal", "seasonal1","seasonal2","manual".
#' @param silent Default FALSE, if TRUE the program should no display messages
#' @usage model(object,model.type=c("seasonal","seasonal1","seasonal2","manual"),silent=FALSE)
Modified: pkg/stacomir/R/RefChoix.r
===================================================================
--- pkg/stacomir/R/RefChoix.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/RefChoix.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -69,6 +69,7 @@
#' Choice_c method for Refchoix referential objects
#' @param object An object of class \link{RefListe-class}
+#' @param selectedvalue TODO
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
#' \dontrun{
@@ -95,6 +96,7 @@
#' Multiple Choice method for RefChoix referential objects, to put together with notebook widgets
#' @param object An object of class \link{RefChoix-class}
+#' @param selected_value TODO
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
setMethod("choicemult",signature=signature("RefChoix"),definition=function(object,
selected_value
Modified: pkg/stacomir/R/RefCoe.r
===================================================================
--- pkg/stacomir/R/RefCoe.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/RefCoe.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -55,6 +55,9 @@
#' supprime method for "RefCoe" class
#' @param object An object of class \link{RefCoe-class}
+#' @param tax '2038=Anguilla anguilla'
+#' @param std 'CIV=civelle'
+#' @param silent Default FALSE, if TRUE the program should no display messages
#' @return nothing
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
Modified: pkg/stacomir/R/RefListe.r
===================================================================
--- pkg/stacomir/R/RefListe.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/RefListe.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -66,6 +66,7 @@
#' Choice_c method for RefListe referential objects
#' @param object An object of class \link{RefListe-class}
+#' @param selectedvalue TODO
#' @note the choice method assigns an object of class refList named refListe in the environment envir_stacomi
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
Modified: pkg/stacomir/R/RefStades.r
===================================================================
--- pkg/stacomir/R/RefStades.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/RefStades.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -279,6 +279,7 @@
#' for stades is the code. Any numeric value will be discarded
#' @param object An object of class \link{RefStades-class}
#' @param stades the vector of stages chosen
+#' @param silent Boolean, if TRUE, information messages are not displayed
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
#' \dontrun{
Modified: pkg/stacomir/R/RefStationMesure.r
===================================================================
--- pkg/stacomir/R/RefStationMesure.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/RefStationMesure.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -44,6 +44,7 @@
#' @param object An object of class \link{RefStationMesure-class}
#' @param is.enabled A boolean parameter, if TRUE the frame is enabled when first displayed
#' @param title The title of the frame, defaut to "Monitoring stations selection"
+#' @param stationMesure A character, the code of the monitoring station, which records environmental parameters \link{choice_c,RefStationMesure-method}
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @examples
#' \dontrun{
@@ -87,7 +88,7 @@
#' the choice_c method is intented to have the same behaviour as choice (which creates a
#' widget in the graphical interface) but from the command line.
#' @param object an object of class RefStationMesure
-#' @param stationmesure a character vector of the monitoring station code (corresponds to stm_libelle in the tj_stationmesure_stm table)
+#' @param stationMesure a character vector of the monitoring station code (corresponds to stm_libelle in the tj_stationmesure_stm table)
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
setMethod("choice_c",signature=signature("RefStationMesure"),definition=function(object,stationMesure) {
if (class(stationMesure)!="character") {
Modified: pkg/stacomir/R/ReftextBox.r
===================================================================
--- pkg/stacomir/R/ReftextBox.r 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/R/ReftextBox.r 2017-05-17 15:03:26 UTC (rev 369)
@@ -61,6 +61,7 @@
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @param object An object of class \link{RefTextBox-class}
#' @param value The value to set
+#' @param nomassign The name with which the object will be assigned in envir_stacomi
setMethod("choice_c",signature=signature("RefTextBox"),definition=function(object,value,nomassign="refTextBox") {
object at label<-value
assign(nomassign,object,envir_stacomi)
Modified: pkg/stacomir/inst/examples/bilanArgentee_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanArgentee_example.R 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/inst/examples/bilanArgentee_example.R 2017-05-17 15:03:26 UTC (rev 369)
@@ -28,7 +28,7 @@
# stages are in bilanArg at calcdata[["6"]][,"stage"]
#look at data structure using str(bilanArg at calcdata[["6"]])
-# standard plot as drawn by Laurent Beaulaton (Analyse des données d'argenture acquises en France)
+# standard plot as drawn by Laurent Beaulaton (Analyse des donnees d'argenture acquises en France)
# showing Durif's stage according to size and eye diameter
plot(bilanArg, plot.type=1)
Modified: pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R 2017-05-17 15:03:26 UTC (rev 369)
@@ -42,7 +42,7 @@
requireNamespace("viridis", quietly = TRUE)){
g<-get("g",envir=envir_stacomi)
g+ggplot2::scale_fill_manual(values=viridis::viridis(22))+
- ggplot2::ggtitle(iconv("Saisonalité de la migration aux Enfrenaux","UTF8"))
+ ggplot2::ggtitle("Saisonnalite de la migration aux Enfrenaux")
}
# the standard plot is showing daily values
plot(bmi,plot.type="standard",silent=TRUE)
@@ -90,7 +90,8 @@
plot(bmi,plot.type="pointrange",timesplit="mois",silent=TRUE)
plot(bmi,plot.type="step",silent=TRUE)
- if (requireNamespace("ggplot2", quietly = TRUE)&requireNamespace("viridis", quietly = TRUE)){
+ if (requireNamespace("ggplot2", quietly = TRUE)&
+ requireNamespace("viridis", quietly = TRUE)){
g<-get("g",envir=envir_stacomi) + ggplot2::theme_minimal()
g+viridis::scale_color_viridis(discrete=TRUE)+
ggplot2::ggtitle("Cumulated migration step plot at les Enfrenaux eel trap")
Modified: pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R 2017-05-16 19:14:20 UTC (rev 368)
+++ pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R 2017-05-17 15:03:26 UTC (rev 369)
@@ -46,7 +46,8 @@
# for yellow eel and other taxa
# stopped, 1...5 types of operation, ponctuel, expert, calcule,mesure,working,
plot(bMM_Arzal,plot.type="standard",
- color=c("#DEF76B","#B950B5","#9ABDDA","#781A74","#BF9D6E","#FFC26E","#A66F24","#012746","#6C3E00","#DC7ED8","#8AA123"),
+ color=c("#DEF76B","#B950B5","#9ABDDA","#781A74","#BF9D6E","#FFC26E",
+ "#A66F24","#012746","#6C3E00","#DC7ED8","#8AA123"),
color_ope=c("#5589B5","#FFDB6E","#FF996E","#1C4D76"),
silent=TRUE)
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