[Stacomir-commits] r396 - in pkg/stacomir: R inst/examples man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jun 16 22:48:18 CEST 2017
Author: briand
Date: 2017-06-16 22:48:18 +0200 (Fri, 16 Jun 2017)
New Revision: 396
Modified:
pkg/stacomir/R/BilanAgedemer.r
pkg/stacomir/R/BilanArgentee.r
pkg/stacomir/R/BilanConditionEnv.r
pkg/stacomir/R/BilanMigration.r
pkg/stacomir/R/BilanMigrationInterAnnuelle.r
pkg/stacomir/R/BilanMigrationMultConditionEnv.r
pkg/stacomir/R/Bilan_carlot.r
pkg/stacomir/R/Bilan_poids_moyen.r
pkg/stacomir/R/data.r
pkg/stacomir/inst/examples/bilanMigrationMultConditionEnv_example.R
pkg/stacomir/inst/examples/bilancarlot_example.R
pkg/stacomir/man/BilanConditionEnv-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/bMM_Arzal.Rd
pkg/stacomir/man/bM_Arzal.Rd
pkg/stacomir/man/bilPM.Rd
pkg/stacomir/man/bil_CE.Rd
pkg/stacomir/man/bilanOperation_bM.Rd
pkg/stacomir/man/bilan_adm.Rd
pkg/stacomir/man/bmC.Rd
pkg/stacomir/man/bmi.Rd
pkg/stacomir/man/bmi_vichy.Rd
pkg/stacomir/man/bmmCE.Rd
pkg/stacomir/man/calcmig.Rd
pkg/stacomir/man/calcule-BilanAgedemer-method.Rd
pkg/stacomir/man/calcule-BilanArgentee-method.Rd
pkg/stacomir/man/calcule-BilanMigration-method.Rd
pkg/stacomir/man/choice_c-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/fundat.Rd
pkg/stacomir/man/stacomiR-package.Rd
Log:
Edition of the manual
Modified: pkg/stacomir/R/BilanAgedemer.r
===================================================================
--- pkg/stacomir/R/BilanAgedemer.r 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/R/BilanAgedemer.r 2017-06-16 20:48:18 UTC (rev 396)
@@ -216,12 +216,17 @@
return(bilan_adm)
})
-#' Calcule method for BilanAgedemer, this method will split the data according to cut
+#' Split data according to the limits
+#' set in the limit1hm, and limit2hm arguments of the \link{BilanAgedemer-class}.
#'
+#' If no value are provided in the limit1hm slot, an error is returned, if
+#' no value is provided in the limit2hm slot a default upper value for salmon
+#' size is taken to ensure all salmon are either of age 1 or 2, but no age 3 are
+#' returned
#' @param object An object of class \code{\link{BilanAgedemer-class}}
#' @param silent Default FALSE, if TRUE the program should no display messages
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @return An object of class \link{BilanAgedemer-class}
+#' @return An object of class \link{BilanAgedemer-class} with calculated data in slot calcdata
#' @export
setMethod("calcule",signature=signature("BilanAgedemer"),definition=function(object,silent) {
#bilan_adm<-b_carlot
@@ -237,9 +242,7 @@
if (is.na(as.numeric(bilan_adm at limit2hm@label))) bilan_adm at limit2hm@label<-2000
lescoupes<-c(0,as.numeric(bilan_adm at limit1hm@label),as.numeric(bilan_adm at limit2hm@label),2001)
adm$age<-cut(x=adm$car_valeur_quantitatif,breaks=lescoupes,labels=FALSE)
- bilan_adm at calcdata[["data"]]<-adm
-
-
+ bilan_adm at calcdata[["data"]]<-adm
assign("bilan_adm",bilan_adm,envir_stacomi)
return(bilan_adm)
})
Modified: pkg/stacomir/R/BilanArgentee.r
===================================================================
--- pkg/stacomir/R/BilanArgentee.r 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/R/BilanArgentee.r 2017-06-16 20:48:18 UTC (rev 396)
@@ -190,20 +190,23 @@
return(bilanArg)
})
-#' Calcule method for BilanArgentee, this method will pass the data from long to wide format
-#' ( one line per individual) and calculate Durif silvering index and Pankhurst and Fulton's K.
+#' Calculate individual silver eel parameters.
#'
-#' @param object An object of class \code{\link{BilanArgentee-class}}
+#' This calcule method for BilanArgentee, will transform data from long (one line per size characteristic,
+#' size, weight, eye diameter, pectoral fin measurement, lateral line and constrast) to wide format (one
+#' line per silver eel). It will also calculate Durif silvering index and Pankhurst and Fulton's K.
+#'
+#' @param object An object of class \link{BilanArgentee-class}
#' @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
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
setMethod("calcule",signature=signature("BilanArgentee"),definition=function(object,silent) {
bilanArg<-object
if(nrow(bilanArg at data)==0) {
funout(gettext("No data of silver or yellow eel on the selected period",domain="R-stacomiR"), arret=TRUE)
}
- arg=bilanArg at data # on recupere le data.frame
-
-
+ arg=bilanArg at data
lesdc<-bilanArg at dc@dc_selectionne
parquant<-c("1786","A111","BBBB","CCCC","PECT")
parqual<-c("CONT","LINP")
Modified: pkg/stacomir/R/BilanConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanConditionEnv.r 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/R/BilanConditionEnv.r 2017-06-16 20:48:18 UTC (rev 396)
@@ -2,7 +2,7 @@
#' conditions...
#'
#' Annual overview of environmental conditions. This class enables to draw some plot, but will mostly used to build
-#' joined graphs crossing the information from \link{BilanMigrationMult-class} and \link{BilanMigrationConditionEnv-class}
+#' joined graphs crossing the information from \link{BilanMigrationMult-class} and \link{BilanMigrationMultConditionEnv-class}
#'
#' @include RefHorodate.r
#' @include RefStationMesure.r
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/R/BilanMigration.r 2017-06-16 20:48:18 UTC (rev 396)
@@ -196,17 +196,35 @@
})
-#' calcule method for BilanMigration
+#' Transforms migration per period to daily migrations, and performs the conversion from weights to number is data
+#' are stored as weights (glass eel).
#'
-#' does the calculation once data are filled by the connect method. It also performs conversion from weight to numbers
-#' in with the connect method
+#' 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{BilanMigration-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 Boolean, if TRUE, information messages are not displayed, only warnings and errors
#' @note The class BilanMigration does not handle escapement rates nor
#' 'devenir' i.e. the destination of the fishes.
-#' @return BilanMigration with calcdata slot filled.
+#' @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".
+#' 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
#' @export
setMethod("calcule",signature=signature("BilanMigration"),definition=function(object,negative=FALSE,silent=FALSE){
Modified: pkg/stacomir/R/BilanMigrationInterAnnuelle.r
===================================================================
--- pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/R/BilanMigrationInterAnnuelle.r 2017-06-16 20:48:18 UTC (rev 396)
@@ -344,6 +344,7 @@
#' @param silent Boolean, if TRUE, information messages are not displayed
#' @return An object of class \link{BilanMigrationInterAnnuelle-class}
#' The choice_c method fills in the data slot for classes \link{RefDC-class}, \link{RefTaxon-class}, \link{RefStades-class} and two slots of \link{RefAnnee-class}
+#' @aliases choice_c.bmi
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
setMethod("choice_c",signature=signature("BilanMigrationInterAnnuelle"),definition=function(object,
@@ -450,7 +451,7 @@
#' function called for bilamMigrationInterannelle objects renames columns
#' replaces nulls, and calculates reports with time period larger than day
#'
-#' @param dat a data frame
+#' @param dat a data frame with columns ("bjo_annee","bjo_jour","bjo_labelquantite","bjo_valeur")
#' @param annee The year to exclude from the historical series (it will be plotted against the historical series)
#' @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
Modified: pkg/stacomir/R/BilanMigrationMultConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMultConditionEnv.r 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/R/BilanMigrationMultConditionEnv.r 2017-06-16 20:48:18 UTC (rev 396)
@@ -1,7 +1,15 @@
#' Class "BilanMigrationMultConditionEnv"
#'
#' Enables to compute an annual overview of fish migration and environmental
-#' conditions in the same chart
+#' conditions in the same chart. Environmental conditions may trigger migration events, variation in flow
+#' or temperatures can be plotted along migration to check graphically for a possible relation. To enable this,
+#' environmental conditions are loaded from an "environmental monitoring station", which records environmental
+#' parameters and is attached to a migratory station in the database.
+#' This class enables both continuous output (temperature -flow) as well as discrete parameters (qualitative = moon
+#' phase, type of operation of a gate, opening of a gate...) which will be displayed on the graph. Values are scaled so that
+#' single plot can display migration numbers and environmental parameters. Environmental parameters when stored at a
+#' time scale lower that a day are averaged per day, unless they are qualitative parameters, in which case only the first
+#' event of the day is displayed on the annual plot.
#'
#' @include BilanMigrationMult.r
#' @include BilanConditionEnv.r
Modified: pkg/stacomir/R/Bilan_carlot.r
===================================================================
--- pkg/stacomir/R/Bilan_carlot.r 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/R/Bilan_carlot.r 2017-06-16 20:48:18 UTC (rev 396)
@@ -1,17 +1,18 @@
#' Class "Bilan_carlot"
#'
-#' Bilan_carlot Bilan class calls the content of the postgres view vue_lot_ope_car, it displays the
-#' results of a categorical variable, or quantitative variable attached for lot, for instance,
-#' it can be used to analyse size or sex
+#' The Bilan_carlot class is used to load and display sample characteristics, which can be either
+#' continuous or discrete variable, for instance, it can be used to analyse size or sex structure during
+#' a given period.
#'
-#' @note This class is displayed by interface_bilan_carlot
+#' @note This class is displayed by interface_bilan_carlot, in the database, the class calls the content
+#' of the view vue_lot_ope_car
#' @slot data A data frame
-#' @slot dc Object of class \link{RefDC-class}: the control devices
-#' @slot taxons Object of class \link{RefTaxon-class}: the speciess
-#' @slot stades Object of class \link{RefStades-class} : the stages of the fish
-#' @slot par Object of class \link{Refpar-class}: the parameters used
-#' @slot horodatedebut An object of class \code{RefHorodate-class}
-#' @slot horodatefin An object of class \code{RefHorodate-class}
+#' @slot dc An object of class \link{RefDC-class}: the control devices
+#' @slot taxons An object of class \link{RefTaxon-class}: the speciess
+#' @slot stades An object of class \link{RefStades-class} : the stages of the fish
+#' @slot par An object of class \link{Refpar-class}: the parameters used
+#' @slot horodatedebut An object of class \link{RefHorodate-class}
+#' @slot horodatefin An object of class \link{RefHorodate-class}
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("Bilan_carlot", ...)}
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
@@ -236,21 +237,21 @@
coord_flip()
print(g)
assign("g",g,envir_stacomi)
- if (!silent) funout(gettext("To obtain the graphical object, type : g<-get(\"g\",envir_stacomi), see http://trac.eptb-vilaine.fr:8066/tracstacomi/wiki/Recette%20BilanLot for help \n",domain="R-stacomiR"))
+ if (!silent) funout(gettext("To obtain the graphical object, type : g<-get(\"g\",envir_stacomi)\n",domain="R-stacomiR"))
} else if (plot.type==2){
g<-ggplot(bilan_carlot at data)
g<-g+geom_boxplot(aes(x=mois,y=car_valeur_quantitatif,fill=std_libelle))+
facet_grid(annee ~ .)
print(g)
assign("g",g,envir_stacomi)
- if (!silent) funout(gettext("To obtain the graphical object, type : g<-get(\"g\",envir_stacomi), see http://trac.eptb-vilaine.fr:8066/tracstacomi/wiki/Recette%20BilanLot for help \n",domain="R-stacomiR"))
+ if (!silent) funout(gettext("To obtain the graphical object, type : g<-get(\"g\",envir_stacomi)\n",domain="R-stacomiR"))
}else if (plot.type==3){
g<-ggplot(bilan_carlot at data)
g<-g+geom_point(aes(x=ope_date_debut,y=car_valeur_quantitatif))
print(g)
assign("g",g,envir_stacomi)
- if (!silent) funout(gettext("To obtain the graphical object, type : g<-get(\"g\",envir_stacomi), see http://trac.eptb-vilaine.fr:8066/tracstacomi/wiki/Recette%20BilanLot for help \n",domain="R-stacomiR"))
+ if (!silent) funout(gettext("To obtain the graphical object, type : g<-get(\"g\",envir_stacomi)\n",domain="R-stacomiR"))
}
return(invisible(NULL))
})
Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/R/Bilan_poids_moyen.r 2017-06-16 20:48:18 UTC (rev 396)
@@ -1,12 +1,20 @@
#' Class "Bilan_poids_moyen"
#'
-#' Bilan_poids_moyen class The objective is to calculate mean weight of glass
-#' eel which are counted from weight measurements and to reintegrate weight to
-#' number coefficients
+#' 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
+#' need to be converted to numbers. The glass eel weight may follow a seasonal pattern. It's the case for Anguilla anguilla
+#' glass eel in the Bay of Biscay. Weights can be modelled using sine wave curves, or more complex gam models.
+#' This class has a model method to try those models, which can also be used to extact coefficients manually
+#' to manually test more complex models.
+#' Some plots are provided to display the coefficients stored in the database, and the model results. A parameter provided in
+#' the graphical interface or in the command line (slot liste) takes values "1", ">1", "tous" wich mean respectively use
+#' only individual sample of glass eels, or use "group weights" which can be more close to the real weight of glass eel
+#' during counts as glass eel are not completely drained from their water during handling to preserve their muccus. The list choice
+#' "tous" means that both individual and group weights are selected.
#' @include RefCoe.r
-#' @note We have also tools available to import glass eel measurement from
-#' experimental fishing in the estuary For the charge method dates for the
+#' @note In this class some tools are avalaible to import glass eel measurement from
+#' experimental fishing in the estuary. For the charge method dates for the
#' request are from august to august (a glass eel season)
#' @slot data A \code{"data.frame"} data for bilan lot
#' @slot calcdata A list containing two processed data frames, data and coe
Modified: pkg/stacomir/R/data.r
===================================================================
--- pkg/stacomir/R/data.r 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/R/data.r 2017-06-16 20:48:18 UTC (rev 396)
@@ -9,9 +9,10 @@
#' Anguilla migration at the Arzal station (BilanMigrationMult-class)
#'
-#' This data corresponds to the data collected from three fishways
-#' and correspond to the migration station at Arzal in 2011 for all
-#' stages of eel (Anguilla anguilla)
+#' This data corresponds to data collected from three fishways
+#' and correspond to the migration station at Arzal (Vilaine estuary, France) in 2011 for
+#' three continental stages of eel (Anguilla anguilla) : glass eel, yellow eel
+#' and silver eel.
#'
#' @format An object of class bilanMigrationMult with slots:
#' \describe{
@@ -41,9 +42,9 @@
"bMM_Arzal"
-#' Video counting of thin lipped mullet (Liza ramada) in 2015 on the Vilaine (France)
+#' Video counting of thin lipped mullet (Liza ramada) in 2015 in the Vilaine (France)
#'
-#' This data corresponds to the data collected at the vertical slot fishway
+#' This dataset corresponds to the data collected at the vertical slot fishway
#' in 2015, video recording of the thin lipped mullet Liza ramada migration
#'
#' @format An object of class bilanMigration with 8 slots:
@@ -128,9 +129,9 @@
#' @keywords data
"bilanOperation"
-#' dataframe containing the default connection arguments
-#' the program will use a file installed in c:/program files/stacomi but
-#' if not found will switch to the default
+#' A data frame containing the default connection arguments.
+#' The program will use a file installed in c:/program files/stacomi but
+#' if not found will switch to this default value
"calcmig"
#' Overview of the fishway operation at Arzal in (Vilaine France).
@@ -217,8 +218,9 @@
#' An object of class \link{BilanOperation-class} with data loaded
#'
-#' This dataset corresponds to the data collected at three different control devices
-#' it is loaded along with \link{bM_Arzal}
+#' This dataset corresponds to the data collected at the vertical slot fishway in Arzal (Vilaine river
+#' estuary, France). The operation of the fishway is dependent on tide and is recorded every 10 minutes. This dataset has
+#' to be loaded along with \link{bM_Arzal} to demonstrate the use of the \link{BilanMigration-class}
#' @format An object of class BilanOperation
#' @keywords data
"bilanOperation_bM"
@@ -239,7 +241,7 @@
#' operational at the same location and provides one of the longest series of eel migration.
#' For this reason,
#' the dataset has been loaded as an example for the BilanMigrationInterAnnuelle-class. It has been
-#' kindly given by the parc du Marais Poitevin.
+#' kindly provided by the parc du Marais Poitevin.
#' @format An object of class \link{BilanMigrationInterAnnuelle-class} with data loaded.
#' @keywords data
"bmi"
@@ -284,9 +286,9 @@
#' \url{http://fishlarvae.org/common/SiteMedia/durif\%20et\%20al\%202009b.pdf}
"coef_Durif"
-#' Wet weight of glass eel from the trapping ladder.
+#' Wet weight of glass eel from the trapping ladder (Arzal, Vilaine France)
#'
-#' The years selected are 2009 to 2012,
+#' Data correspond to glass eel collected in the VIlaine at the trapping ladder (Arzal, France). The years selected are 2009 to 2012,
#' the query used in the \link{Bilan_poids_moyen-class} loads from 2008-08-01 to 2012-08-01
#' Glass eel are too numerous to be counted. They are weighted and in the stacomi database,
#' a table with daily coefficients (in N glass eel/g) to transform weight into number.
@@ -295,7 +297,7 @@
#' the seasonal evolution of wet weight.
"bilPM"
-#' An object of class BilanMigrationInterAnnuelle with data loaded
+#' Seasonality of salmon migration at the Vichy counting station (Loire)
#'
#' This data corresponds to the data collected at the Vichy fishway
#' between 1997 and 2012, video recording of the Salmo salar upstream migration.
@@ -328,9 +330,9 @@
#' An object of class BilanAgedemer with data loaded
#'
-#' This data corresponds to the data collected at Vichy (left and right bank fishways) and Decize-Saint
-#' Leger des Vignes fishways (respectively on the Allier and Loire river) in 2012 on the size structure of Salmo salar.
-#' This dataset has been kindly provided by Loire Grands Migrateurs.
+#' This dataset corresponds to the data collected at Vichy (left and right bank fishways) and Decize-Saint
+#' Leger des Vignes fishways (respectively on the Allier and Loire river, France) in 2012 on the size structure of Salmo salar.
+#' It has been kindly provided by the Loire Grands Migrateurs (LOGRAMI) association.
#'
#' @format An object of class \link{BilanAgedemer-class} with 8 slots:
#' \describe{
@@ -370,7 +372,7 @@
#' An object of class BilanConditionEnv with data loaded
#'
-#' The dataset corresponds to the dayly temperature at Gabion station during the year 2008. This environmental station is used to
+#' The dataset corresponds to the daily temperatures and moon phases in Arzal (Vilaine estuary, France). This environmental station is used to
#' analyse conditions in which fish migrated at Arzal dam
#'
#' @format An object of class \link{BilanConditionEnv-class} with data slot loaded:
@@ -393,14 +395,12 @@
"bil_CE"
-#' An object of class BilanMigrationCar with data loaded
+#' Qualitative and quantitative parameters describing Salmon migration at Decize (Loire)
#'
#' The dataset corresponds to the caracteristics (qualitative and quantitative) of salmo salar migrating
-#' at Decize (Loire river) and Vichy (Allier river) counting device in 2012.
-#'
-#' the dataset has been loaded as an example for the BilanMigrationCar-class. It has been
-#' kindly given by Loire Grands Migrateurs.
-#' @format An object of class \link{BilanConditionEnv-class} with data slot loaded:
+#' at Decize (Loire river) and Vichy (Allier river) counting device in 2012. It has been loaded as
+#' an example for the BilanMigrationCar-class and kindly provided by Loire Grands Migrateurs (LOGRAMI).
+#' @format An object of class \link{BilanMigrationCar-class} with data slot loaded:
#' \describe{
#' \item{calcdata}{slot to be filled with the calcule method}
#' \item{data}{ A list of 2 elements
@@ -412,9 +412,9 @@
#' \item{dc}{the \code{RefDC} : the control devices selected}
#' \item{taxons}{the \code{RefTaxon} : Salmo salar selected}
#' \item{stades}{the \code{RefStades} : the stages selected}
-#' \item{par}{Object of class \link{Refpar-class}: the parameters used}
-#' \item{horodatedebut}{object of class \code{RefHorodate-class} : the start date selected}
-#' \item{horodatefin}{object of class \code{RefHorodate-class} : the end date selected}
+#' \item{par}{an object of class \link{Refpar-class}: the parameters used}
+#' \item{horodatedebut}{an object of class \code{RefHorodate-class} : the start date selected}
+#' \item{horodatefin}{an object of class \code{RefHorodate-class} : the end date selected}
#' }
#' @keywords data
"bmC"
@@ -424,7 +424,7 @@
#' An object of class BilanMigrationMultConditionEnv with data loaded
#'
#' The dataset correspond to data loaded for the Arzal dam (Vilaine) in 2008, two quantitative
-#' parameters (temperature and tide coefficient and a qualitative parameter moon phase are loaded.
+#' parameters (temperature and tide coefficient) and a qualitative parameter (moon phase) are loaded.
#' @format An object of class \link{BilanConditionEnv-class} with data slot loaded:
#' \describe{
#' \item{bilanMigrationMult}{An object of class \link{BilanMigrationMult-class}}
Modified: pkg/stacomir/inst/examples/bilanMigrationMultConditionEnv_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationMultConditionEnv_example.R 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/inst/examples/bilanMigrationMultConditionEnv_example.R 2017-06-16 20:48:18 UTC (rev 396)
@@ -2,6 +2,8 @@
stacomi(gr_interface=FALSE,
login_window=FALSE,
database_expected=FALSE)
+# the following will load the data provided the user has access to the database
+# with data in the iav example scheme.
\dontrun{
bmmCE<-new("BilanMigrationMultConditionEnv")
bmmCE<-choice_c(bmmCE,
@@ -19,6 +21,7 @@
data("bmmCE")
bmmCE<-calcule(bmmCE,silent=TRUE)
+# An example of plot with custom colors.
plot(bmmCE,
color_station=c("temp_gabion"="red","coef_maree"="blue","phases_lune"="pink"),
color_dc=c("5"="yellow","6"="orange","12"="purple")
Modified: pkg/stacomir/inst/examples/bilancarlot_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilancarlot_example.R 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/inst/examples/bilancarlot_example.R 2017-06-16 20:48:18 UTC (rev 396)
@@ -20,6 +20,7 @@
horodatefin="2013-12-31",
silent=FALSE)
# two warning produced, ignored if silent=TRUE
+ b_carlot<-charge(b_carlot) # don't forget this step otherwise dates are not loaded
b_carlot<-connect(b_carlot)
b_carlot<-calcule(b_carlot,silent=TRUE)
Modified: pkg/stacomir/man/BilanConditionEnv-class.Rd
===================================================================
--- pkg/stacomir/man/BilanConditionEnv-class.Rd 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/man/BilanConditionEnv-class.Rd 2017-06-16 20:48:18 UTC (rev 396)
@@ -9,7 +9,7 @@
conditions...}
\description{
Annual overview of environmental conditions. This class enables to draw some plot, but will mostly used to build
-joined graphs crossing the information from \link{BilanMigrationMult-class} and \link{BilanMigrationConditionEnv-class}
+joined graphs crossing the information from \link{BilanMigrationMult-class} and \link{BilanMigrationMultConditionEnv-class}
}
\section{Slots}{
Modified: pkg/stacomir/man/BilanMigrationMultConditionEnv-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationMultConditionEnv-class.Rd 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/man/BilanMigrationMultConditionEnv-class.Rd 2017-06-16 20:48:18 UTC (rev 396)
@@ -8,7 +8,15 @@
\title{Class "BilanMigrationMultConditionEnv"}
\description{
Enables to compute an annual overview of fish migration and environmental
-conditions in the same chart
+conditions in the same chart. Environmental conditions may trigger migration events, variation in flow
+or temperatures can be plotted along migration to check graphically for a possible relation. To enable this,
+environmental conditions are loaded from an "environmental monitoring station", which records environmental
+parameters and is attached to a migratory station in the database.
+This class enables both continuous output (temperature -flow) as well as discrete parameters (qualitative = moon
+phase, type of operation of a gate, opening of a gate...) which will be displayed on the graph. Values are scaled so that
+single plot can display migration numbers and environmental parameters. Environmental parameters when stored at a
+time scale lower that a day are averaged per day, unless they are qualitative parameters, in which case only the first
+event of the day is displayed on the annual plot.
}
\section{Slots}{
@@ -22,6 +30,8 @@
stacomi(gr_interface=FALSE,
login_window=FALSE,
database_expected=FALSE)
+# the following will load the data provided the user has access to the database
+# with data in the iav example scheme.
\dontrun{
bmmCE<-new("BilanMigrationMultConditionEnv")
bmmCE<-choice_c(bmmCE,
@@ -39,6 +49,7 @@
data("bmmCE")
bmmCE<-calcule(bmmCE,silent=TRUE)
+# An example of plot with custom colors.
plot(bmmCE,
color_station=c("temp_gabion"="red","coef_maree"="blue","phases_lune"="pink"),
color_dc=c("5"="yellow","6"="orange","12"="purple")
Modified: pkg/stacomir/man/Bilan_carlot-class.Rd
===================================================================
--- pkg/stacomir/man/Bilan_carlot-class.Rd 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/man/Bilan_carlot-class.Rd 2017-06-16 20:48:18 UTC (rev 396)
@@ -5,29 +5,30 @@
\alias{Bilan_carlot-class}
\title{Class "Bilan_carlot"}
\description{
-Bilan_carlot Bilan class calls the content of the postgres view vue_lot_ope_car, it displays the
-results of a categorical variable, or quantitative variable attached for lot, for instance,
-it can be used to analyse size or sex
+The Bilan_carlot class is used to load and display sample characteristics, which can be either
+continuous or discrete variable, for instance, it can be used to analyse size or sex structure during
+a given period.
}
\section{Slots}{
\describe{
\item{\code{data}}{A data frame}
-\item{\code{dc}}{Object of class \link{RefDC-class}: the control devices}
+\item{\code{dc}}{An object of class \link{RefDC-class}: the control devices}
-\item{\code{taxons}}{Object of class \link{RefTaxon-class}: the speciess}
+\item{\code{taxons}}{An object of class \link{RefTaxon-class}: the speciess}
-\item{\code{stades}}{Object of class \link{RefStades-class} : the stages of the fish}
+\item{\code{stades}}{An object of class \link{RefStades-class} : the stages of the fish}
-\item{\code{par}}{Object of class \link{Refpar-class}: the parameters used}
+\item{\code{par}}{An object of class \link{Refpar-class}: the parameters used}
-\item{\code{horodatedebut}}{An object of class \code{RefHorodate-class}}
+\item{\code{horodatedebut}}{An object of class \link{RefHorodate-class}}
-\item{\code{horodatefin}}{An object of class \code{RefHorodate-class}}
+\item{\code{horodatefin}}{An object of class \link{RefHorodate-class}}
}}
\note{
-This class is displayed by interface_bilan_carlot
+This class is displayed by interface_bilan_carlot, in the database, the class calls the content
+of the view vue_lot_ope_car
}
\section{Objects from the Class}{
Objects can be created by calls of the form
@@ -56,6 +57,7 @@
horodatefin="2013-12-31",
silent=FALSE)
# two warning produced, ignored if silent=TRUE
+ b_carlot<-charge(b_carlot) # don't forget this step otherwise dates are not loaded
b_carlot<-connect(b_carlot)
b_carlot<-calcule(b_carlot,silent=TRUE)
Modified: pkg/stacomir/man/Bilan_poids_moyen-class.Rd
===================================================================
--- pkg/stacomir/man/Bilan_poids_moyen-class.Rd 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/man/Bilan_poids_moyen-class.Rd 2017-06-16 20:48:18 UTC (rev 396)
@@ -5,9 +5,17 @@
\alias{Bilan_poids_moyen-class}
\title{Class "Bilan_poids_moyen"}
\description{
-Bilan_poids_moyen class The objective is to calculate mean weight of glass
-eel which are counted from weight measurements and to reintegrate weight to
-number coefficients
+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
+need to be converted to numbers. The glass eel weight may follow a seasonal pattern. It's the case for Anguilla anguilla
+glass eel in the Bay of Biscay. Weights can be modelled using sine wave curves, or more complex gam models.
+This class has a model method to try those models, which can also be used to extact coefficients manually
+to manually test more complex models.
+Some plots are provided to display the coefficients stored in the database, and the model results. A parameter provided in
+the graphical interface or in the command line (slot liste) takes values "1", ">1", "tous" wich mean respectively use
+only individual sample of glass eels, or use "group weights" which can be more close to the real weight of glass eel
+during counts as glass eel are not completely drained from their water during handling to preserve their muccus. The list choice
+"tous" means that both individual and group weights are selected.
}
\section{Slots}{
@@ -32,8 +40,8 @@
counts are never made on subsamples but those can be integrated to calculate mean weights.}
}}
\note{
-We have also tools available to import glass eel measurement from
-experimental fishing in the estuary For the charge method dates for the
+In this class some tools are avalaible to import glass eel measurement from
+experimental fishing in the estuary. For the charge method dates for the
request are from august to august (a glass eel season)
}
\examples{
Modified: pkg/stacomir/man/bMM_Arzal.Rd
===================================================================
--- pkg/stacomir/man/bMM_Arzal.Rd 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/man/bMM_Arzal.Rd 2017-06-16 20:48:18 UTC (rev 396)
@@ -32,9 +32,10 @@
bMM_Arzal
}
\description{
-This data corresponds to the data collected from three fishways
-and correspond to the migration station at Arzal in 2011 for all
-stages of eel (Anguilla anguilla)
+This data corresponds to data collected from three fishways
+and correspond to the migration station at Arzal (Vilaine estuary, France) in 2011 for
+three continental stages of eel (Anguilla anguilla) : glass eel, yellow eel
+and silver eel.
}
\keyword{data}
Modified: pkg/stacomir/man/bM_Arzal.Rd
===================================================================
--- pkg/stacomir/man/bM_Arzal.Rd 2017-06-11 20:35:32 UTC (rev 395)
+++ pkg/stacomir/man/bM_Arzal.Rd 2017-06-16 20:48:18 UTC (rev 396)
@@ -3,7 +3,7 @@
\docType{data}
\name{bM_Arzal}
\alias{bM_Arzal}
-\title{Video counting of thin lipped mullet (Liza ramada) in 2015 on the Vilaine (France)}
+\title{Video counting of thin lipped mullet (Liza ramada) in 2015 in the Vilaine (France)}
\format{An object of class bilanMigration with 8 slots:
\describe{
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 396
More information about the Stacomir-commits
mailing list