[Stacomir-commits] r276 - in pkg/stacomir: R inst/examples inst/po/fr/LC_MESSAGES man po
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Feb 2 22:02:22 CET 2017
Author: briand
Date: 2017-02-02 22:02:22 +0100 (Thu, 02 Feb 2017)
New Revision: 276
Added:
pkg/stacomir/man/hreg.Rd
pkg/stacomir/man/supprime-RefCoe-method.Rd
Modified:
pkg/stacomir/R/Bilan_poids_moyen.r
pkg/stacomir/R/RefCoe.r
pkg/stacomir/R/data.r
pkg/stacomir/inst/examples/bilanAgedemer_example.R
pkg/stacomir/inst/examples/bilan_poids_moyen_example.R
pkg/stacomir/inst/po/fr/LC_MESSAGES/R-stacomiR.mo
pkg/stacomir/man/BilanAgedemer-class.Rd
pkg/stacomir/man/Bilan_poids_moyen-class.Rd
pkg/stacomir/man/bilPM.Rd
pkg/stacomir/man/choice-RefAnnee-method.Rd
pkg/stacomir/man/choice-RefStationMesure-method.Rd
pkg/stacomir/man/choice-Refparqual-method.Rd
pkg/stacomir/man/choice_c-RefAnnee-method.Rd
pkg/stacomir/man/choice_c-RefStades-method.Rd
pkg/stacomir/man/coef_Durif.Rd
pkg/stacomir/po/R-stacomiR_fr_FR.mo
pkg/stacomir/po/R-stacomiR_fr_FR.po
Log:
developed a method to delete coefficients from the database
Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/R/Bilan_poids_moyen.r 2017-02-02 21:02:22 UTC (rev 276)
@@ -364,7 +364,7 @@
}
print(result)
p<-ggplot(don)+ geom_jitter(aes(x=doy,y=w),col="aquamarine4")+facet_wrap(~season )+
- geom_line(aes(x=doy,y=pred_weight),data=predatafull)+
+ geom_line(aes(x=doy,y=pred_weight),data=predata)+
#geom_line(aes(x=doy,y=pred_weight),color="green",size=1,data=predatafull[predatafull$doy==50,])+
theme_minimal()+
theme(panel.border = element_blank(),
@@ -536,8 +536,9 @@
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @export
setMethod("write_database",signature=signature("Bilan_poids_moyen"),definition=function(object,silent,dbname="bd_contmig_nat",host="localhost",port=5432){
- object<-bilPM
+ bilPM<-object
if (!"import_coe"%in% names(bilPM at calcdata)) funout(gettext("Attention, you must fit a model before trying to write the predictions in the database",domain="R-stacomiR"),arret=TRUE)
+ supprime(bilPM,tax=2038,std="CIV")
import_coe<-bilPM at calcdata$import_coe
baseODBC<-get("baseODBC",envir=envir_stacomi)
sql<-stringr::str_c("INSERT INTO ",get("sch",envir=envir_stacomi),"tj_coefficientconversion_coe (",
@@ -553,4 +554,7 @@
host=host,
port=port)
))
- })
\ No newline at end of file
+ })
+
+
+
Modified: pkg/stacomir/R/RefCoe.r
===================================================================
--- pkg/stacomir/R/RefCoe.r 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/R/RefCoe.r 2017-02-02 21:02:22 UTC (rev 276)
@@ -49,4 +49,33 @@
requete<-connect(requete)
object at data<-requete at query
return(object)
- })
\ No newline at end of file
+ })
+
+
+#' supprime method for "RefCoe" class
+#' @param object An object of class \link{RefCoe-class}
+#' @return nothing
+#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @export
+
+setMethod("supprime",signature=signature("RefCoe"),
+ definition=function(object,tax,std,silent=FALSE)
+ {
+ #object<-bilPM at coe;tax=2038;std="CIV"
+ # getting the data to import
+
+ # here I assume that dc_selectionne will be unique (no bilan with several dc)
+ #
+ requete=new("RequeteODBCwheredate")
+ requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
+ requete at datedebut<-object at datedebut
+ requete at datefin<-object at datefin
+ requete at colonnedebut<-"coe_date_debut"
+ requete at colonnefin<-"coe_date_fin"
+ requete at select=stringr::str_c("DELETE from ",get("sch",envir=envir_stacomi),"tj_coefficientconversion_coe ")
+ requete at and=" and coe_tax_code='2038' and coe_std_code='CIV' and coe_qte_code='1'"
+ invisible(utils::capture.output(requete<-stacomirtools::connect(requete)))
+ if (!silent) funout(gettextf("%s rows deleted from table tj_coefficientconversion_coe",nrow(object at data),domain="R-stacomiR"))
+ return(invisible(NULL))
+ })
+
Modified: pkg/stacomir/R/data.r
===================================================================
--- pkg/stacomir/R/data.r 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/R/data.r 2017-02-02 21:02:22 UTC (rev 276)
@@ -243,6 +243,7 @@
"bilanArg"
#' Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters
+#'
#' Classification scores are calculated by multiplying the metrics
#' BL = body length, W = weight, MD = mean eye diameter (Dv+Dh)/2, and FL length of the pectoral fin,
#' with each parameter p as S=Constant+BL*p(bl)+W*p(W)... The stage chosen is the one achieving the
@@ -253,7 +254,9 @@
#' \url{http://fishlarvae.org/common/SiteMedia/durif\%20et\%20al\%202009b.pdf}
"coef_Durif"
-#' Wet weight of glass eel from the trapping ladder. The years selected are 2009 to 2012,
+#' Wet weight of glass eel from the trapping ladder.
+#'
+#' 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.
Modified: pkg/stacomir/inst/examples/bilanAgedemer_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanAgedemer_example.R 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/inst/examples/bilanAgedemer_example.R 2017-02-02 21:02:22 UTC (rev 276)
@@ -2,7 +2,7 @@
# launching stacomi without selecting the scheme or interface
stacomi(gr_interface=FALSE,
login_window=FALSE,
- database_expected=TRUE)
+ database_expected=FALSE)
# the following script will load data from the two Anguillere monitored in the Somme
\dontrun{
@@ -31,14 +31,8 @@
# stages are in bilan_adm at calcdata[["6"]][,"stage"]
#look at data structure using str(bilan_adm at calcdata[["6"]])
-# standard plot as drawn by Laurent Beaulaton (Analyse des données d'argenture acquises en France)
-# showing Durif's stage according to size and eye diameter
+# plot data to confirm the split by limits is correct
plot(bilan_adm, plot.type=1)
-
# print a summary statistic, and save the output in a list for later use
stats<-summary(bilan_adm)
-
-object=new("RefMsg")
-msgfr<-charge_avec_filtre(object,lang='French')
-str(msgfr)
\ No newline at end of file
Modified: pkg/stacomir/inst/examples/bilan_poids_moyen_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilan_poids_moyen_example.R 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/inst/examples/bilan_poids_moyen_example.R 2017-02-02 21:02:22 UTC (rev 276)
@@ -28,17 +28,14 @@
# the calculation will fill the slot calcdata
bilPM<-calcule(bilPM)
+# A ggplot showing the trend in weight
plot(bilPM, plot.type=1)
-
-#
+# A plot showing both the data and the trend as recorded in the database
plot(bilPM, plot.type=2)
-
-# plot showing fulton's coefficient, and size weight graphs
-# inspired from Acou et al., 2009
-# Differential Production and Condition Indices of Premigrant
-# Eels in Two Small Atlantic Coastal Catchments
-# of France
+# Same as plot.type=1 but with size according to size of the sample,
+# usefull for wet weights where weight are recorded on a number of glass eel
plot(bilPM, plot.type=3)
-# get a list of summary data and print output to screen
-plot(bilPM, plot.type=4)
+# First model with nls, see Guerault and Desaunay (1993)
+model(bilPM,model.type="seasonal")
+model(bilPM,model.type="seasonal1")
\ No newline at end of file
Modified: pkg/stacomir/inst/po/fr/LC_MESSAGES/R-stacomiR.mo
===================================================================
(Binary files differ)
Modified: pkg/stacomir/man/BilanAgedemer-class.Rd
===================================================================
--- pkg/stacomir/man/BilanAgedemer-class.Rd 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/man/BilanAgedemer-class.Rd 2017-02-02 21:02:22 UTC (rev 276)
@@ -48,7 +48,7 @@
# launching stacomi without selecting the scheme or interface
stacomi(gr_interface=FALSE,
login_window=FALSE,
- database_expected=TRUE)
+ database_expected=FALSE)
# the following script will load data from the two Anguillere monitored in the Somme
\dontrun{
@@ -77,17 +77,11 @@
# stages are in bilan_adm at calcdata[["6"]][,"stage"]
#look at data structure using str(bilan_adm at calcdata[["6"]])
-# standard plot as drawn by Laurent Beaulaton (Analyse des données d'argenture acquises en France)
-# showing Durif's stage according to size and eye diameter
+# plot data to confirm the split by limits is correct
plot(bilan_adm, plot.type=1)
-
# print a summary statistic, and save the output in a list for later use
stats<-summary(bilan_adm)
-
-object=new("RefMsg")
-msgfr<-charge_avec_filtre(object,lang='French')
-str(msgfr)
}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
Modified: pkg/stacomir/man/Bilan_poids_moyen-class.Rd
===================================================================
--- pkg/stacomir/man/Bilan_poids_moyen-class.Rd 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/man/Bilan_poids_moyen-class.Rd 2017-02-02 21:02:22 UTC (rev 276)
@@ -37,11 +37,48 @@
request are from august to august (a glass eel season)
}
\examples{
- \dontrun{
-showClass("Bilan_poids_moyen")
-object=new("Bilan_poids_moyen")
+require(stacomiR)
+# launching stacomi without selecting the scheme or interface
+stacomi(gr_interface=FALSE,
+ login_window=FALSE,
+ database_expected=TRUE)
+# the following script will load data from the two Anguillere monitored in the Somme
+
+\dontrun{
+ #create an instance of the class
+ bilPM<-new("Bilan_poids_moyen")
+ baseODBC<-get("baseODBC",envir=envir_stacomi)
+ baseODBC[c(2,3)]<-rep("iav",2)
+ assign("baseODBC",baseODBC,envir_stacomi)
+ sch<-get("sch",envir=envir_stacomi)
+ assign("sch","iav.",envir_stacomi)
+ bilPM at liste<-charge(object=bilPM at liste,listechoice=c("=1",">1","tous"),label="")
+ # here I'm using weights when number are larger than 1 ie wet weight
+ bilPM<-choice_c(bilPM,
+ dc=c(6),
+ anneedebut="2009",
+ anneefin="2015",
+ selectedvalue=">1",
+ silent=FALSE)
+ bilPM<-connect(bilPM)
+}
+# load the dataset generated by previous lines
+data("bilPM")
+# the calculation will fill the slot calcdata
+bilPM<-calcule(bilPM)
+
+# A ggplot showing the trend in weight
+plot(bilPM, plot.type=1)
+# A plot showing both the data and the trend as recorded in the database
+plot(bilPM, plot.type=2)
+# Same as plot.type=1 but with size according to size of the sample,
+# usefull for wet weights where weight are recorded on a number of glass eel
+plot(bilPM, plot.type=3)
+
+# First model with nls, see Guerault and Desaunay (1993)
+model(bilPM,model.type="seasonal")
+model(bilPM,model.type="seasonal1")
}
-}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
Modified: pkg/stacomir/man/bilPM.Rd
===================================================================
--- pkg/stacomir/man/bilPM.Rd 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/man/bilPM.Rd 2017-02-02 21:02:22 UTC (rev 276)
@@ -3,19 +3,13 @@
\docType{data}
\name{bilPM}
\alias{bilPM}
-\title{Wet weight of glass eel from the trapping ladder. 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.
-The weight is called a "wet weight" as we don't wan't to drain any of the mucus in glass eel
-when weighting them. Samples of 50 to 200 glass eel are weighted and then counted to provide an idea of
-the seasonal evolution of wet weight.}
+\title{Wet weight of glass eel from the trapping ladder.}
\format{An object of class \code{Bilan_poids_moyen} of length 1.}
\usage{
bilPM
}
\description{
-Wet weight of glass eel from the trapping ladder. The years selected are 2009 to 2012,
+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.
Modified: pkg/stacomir/man/choice-RefAnnee-method.Rd
===================================================================
--- pkg/stacomir/man/choice-RefAnnee-method.Rd 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/man/choice-RefAnnee-method.Rd 2017-02-02 21:02:22 UTC (rev 276)
@@ -6,8 +6,8 @@
\title{choice method for RefAnnee referential}
\usage{
\S4method{choice}{RefAnnee}(object, nomassign = "refAnnee",
- funoutlabel = gettext("Year selected\\n"),
- titleFrame = gettext("Year choice"), preselect = 1)
+ funoutlabel = gettext("Year selected\\n", domain = "R-stacomiR"),
+ titleFrame = gettext("Year choice", domain = "R-stacomiR"), preselect = 1)
}
\arguments{
\item{object}{An object of class \link{RefAnnee-class}}
Modified: pkg/stacomir/man/choice-RefStationMesure-method.Rd
===================================================================
--- pkg/stacomir/man/choice-RefStationMesure-method.Rd 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/man/choice-RefStationMesure-method.Rd 2017-02-02 21:02:22 UTC (rev 276)
@@ -6,7 +6,7 @@
\title{Choice method for RefStationMesure referential object}
\usage{
\S4method{choice}{RefStationMesure}(object, is.enabled = TRUE,
- title = gettext("Monitoring stations selection"))
+ title = gettext("Monitoring stations selection", domain = "R-stacomiR"))
}
\arguments{
\item{object}{An object of class \link{RefStationMesure-class}}
Modified: pkg/stacomir/man/choice-Refparqual-method.Rd
===================================================================
--- pkg/stacomir/man/choice-Refparqual-method.Rd 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/man/choice-Refparqual-method.Rd 2017-02-02 21:02:22 UTC (rev 276)
@@ -6,7 +6,7 @@
\title{Choice method for Refparqual referential objects, internal use}
\usage{
\S4method{choice}{Refparqual}(object,
- label = "Choix d'une caracteristique qualitative de lot",
+ label = gettext("Choice of a sample characteristic", domain = "R-stacomiR"),
nomassign = "refpar", frameassign = "frame_par", is.enabled = TRUE)
}
\arguments{
Modified: pkg/stacomir/man/choice_c-RefAnnee-method.Rd
===================================================================
--- pkg/stacomir/man/choice_c-RefAnnee-method.Rd 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/man/choice_c-RefAnnee-method.Rd 2017-02-02 21:02:22 UTC (rev 276)
@@ -6,7 +6,8 @@
\title{choice method for RefAnnee referential from the command line}
\usage{
\S4method{choice_c}{RefAnnee}(object, annee, nomassign = "refAnnee",
- funoutlabel = gettext("Year selected\\n"), silent = FALSE)
+ funoutlabel = gettext("Year selected\\n", domain = "R-stacomiR"),
+ silent = FALSE)
}
\arguments{
\item{object}{An object of class \link{RefAnnee-class}}
Modified: pkg/stacomir/man/choice_c-RefStades-method.Rd
===================================================================
--- pkg/stacomir/man/choice_c-RefStades-method.Rd 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/man/choice_c-RefStades-method.Rd 2017-02-02 21:02:22 UTC (rev 276)
@@ -5,7 +5,7 @@
\alias{choice_c,RefStades-method}
\title{choice_c method for RefStades}
\usage{
-\S4method{choice_c}{RefStades}(object, stades)
+\S4method{choice_c}{RefStades}(object, stades, silent = FALSE)
}
\arguments{
\item{object}{An object of class \link{RefStades-class}}
Modified: pkg/stacomir/man/coef_Durif.Rd
===================================================================
--- pkg/stacomir/man/coef_Durif.Rd 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/man/coef_Durif.Rd 2017-02-02 21:02:22 UTC (rev 276)
@@ -3,17 +3,12 @@
\docType{data}
\name{coef_Durif}
\alias{coef_Durif}
-\title{Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters
-Classification scores are calculated by multiplying the metrics
-BL = body length, W = weight, MD = mean eye diameter (Dv+Dh)/2, and FL length of the pectoral fin,
-with each parameter p as S=Constant+BL*p(bl)+W*p(W)... The stage chosen is the one achieving the
-highest score}
+\title{Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters}
\format{An object of class \code{matrix} with 5 rows and 6 columns.}
\usage{
coef_Durif
}
\description{
-Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters
Classification scores are calculated by multiplying the metrics
BL = body length, W = weight, MD = mean eye diameter (Dv+Dh)/2, and FL length of the pectoral fin,
with each parameter p as S=Constant+BL*p(bl)+W*p(W)... The stage chosen is the one achieving the
Added: pkg/stacomir/man/hreg.Rd
===================================================================
--- pkg/stacomir/man/hreg.Rd (rev 0)
+++ pkg/stacomir/man/hreg.Rd 2017-02-02 21:02:22 UTC (rev 276)
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Bilan_poids_moyen.r
+\name{hreg}
+\alias{hreg}
+\title{Internal handler for reg, class \code{\link{Bilan_poids_moyen-class}}.}
+\usage{
+hreg(h, ...)
+}
+\arguments{
+\item{h}{handler}
+
+\item{\dots}{additional arguments passed to the function}
+}
+\description{
+Internal handler for reg, class \code{\link{Bilan_poids_moyen-class}}.
+}
+
Added: pkg/stacomir/man/supprime-RefCoe-method.Rd
===================================================================
--- pkg/stacomir/man/supprime-RefCoe-method.Rd (rev 0)
+++ pkg/stacomir/man/supprime-RefCoe-method.Rd 2017-02-02 21:02:22 UTC (rev 276)
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/RefCoe.r
+\docType{methods}
+\name{supprime,RefCoe-method}
+\alias{supprime,RefCoe-method}
+\title{supprime method for "RefCoe" class}
+\usage{
+\S4method{supprime}{RefCoe}(object, tax, std, silent = FALSE)
+}
+\arguments{
+\item{object}{An object of class \link{RefCoe-class}}
+}
+\value{
+nothing
+}
+\description{
+supprime method for "RefCoe" class
+}
+\author{
+Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+}
+
Modified: pkg/stacomir/po/R-stacomiR_fr_FR.mo
===================================================================
(Binary files differ)
Modified: pkg/stacomir/po/R-stacomiR_fr_FR.po
===================================================================
--- pkg/stacomir/po/R-stacomiR_fr_FR.po 2017-02-02 12:09:10 UTC (rev 275)
+++ pkg/stacomir/po/R-stacomiR_fr_FR.po 2017-02-02 21:02:22 UTC (rev 276)
@@ -2,7 +2,7 @@
msgstr ""
"Project-Id-Version: stacomiR 0.5.0\n"
"POT-Creation-Date: 2017-02-02 12:54+0100\n"
-"PO-Revision-Date: 2017-02-02 13:06+0100\n"
+"PO-Revision-Date: 2017-02-02 13:21+0100\n"
"Last-Translator: \n"
"Language-Team: \n"
"Language: fr_FR\n"
@@ -1542,7 +1542,7 @@
msgstr "Station"
msgid "Counting Device"
-msgstr "Dispositif de Franchissement"
+msgstr "Dispositif de Comptage"
msgid "Operation (TODO)"
msgstr "Opération (TODO)"
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