[Stacomir-commits] r385 - in pkg/stacomir: data inst/config inst/examples man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 8 10:27:05 CEST 2017
Author: briand
Date: 2017-06-08 10:27:04 +0200 (Thu, 08 Jun 2017)
New Revision: 385
Modified:
pkg/stacomir/data/b_carlot.rda
pkg/stacomir/data/bilPM.rda
pkg/stacomir/data/bilan_adm.rda
pkg/stacomir/inst/config/generate_data.R
pkg/stacomir/inst/examples/bilanAgedemer_example.R
pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R
pkg/stacomir/inst/examples/bilan_poids_moyen_example.R
pkg/stacomir/inst/examples/bilancarlot_example.R
pkg/stacomir/man/BilanAgedemer-class.Rd
pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
pkg/stacomir/man/BilanMigrationMult-class.Rd
pkg/stacomir/man/Bilan_carlot-class.Rd
pkg/stacomir/man/Bilan_poids_moyen-class.Rd
Log:
changing CPU time to pass Rcheck
Modified: pkg/stacomir/data/b_carlot.rda
===================================================================
(Binary files differ)
Modified: pkg/stacomir/data/bilPM.rda
===================================================================
(Binary files differ)
Modified: pkg/stacomir/data/bilan_adm.rda
===================================================================
(Binary files differ)
Modified: pkg/stacomir/inst/config/generate_data.R
===================================================================
--- pkg/stacomir/inst/config/generate_data.R 2017-06-08 07:43:13 UTC (rev 384)
+++ pkg/stacomir/inst/config/generate_data.R 2017-06-08 08:27:04 UTC (rev 385)
@@ -243,6 +243,7 @@
b_carlot at data$std_libelle<-iconv(b_carlot at data$std_libelle,from="latin1",to="UTF8")
b_carlot at data$val_libelle<-iconv(b_carlot at data$val_libelle,from="latin1",to="UTF8")
b_carlot at data$par_nom<-iconv(b_carlot at data$par_nom,from="latin1",to="UTF8")
+b_carlot<-calcule(b_carlot)
setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(b_carlot,internal=FALSE,overwrite=TRUE)
@@ -411,6 +412,7 @@
bilPM at dc@data[,"type_df"]<-iconv(bilPM at dc@data[,"type_df"],from="latin1",to="UTF8")
bilPM at dc@data[,"type_dc"]<-iconv(bilPM at dc@data[,"type_dc"],from="latin1",to="UTF8")
bilPM at dc@data[,"dif_localisation"]<-iconv(bilPM at dc@data[,"dif_localisation"],from="latin1",to="UTF8")
+bilPM<-calcule(bilPM)
devtools::use_data(bilPM,internal=FALSE,overwrite=TRUE)
@@ -449,7 +451,7 @@
bilan_adm at taxons@data[,"tax_nom_commun"]<-iconv(bilan_adm at taxons@data[,"tax_nom_commun"],from="latin1",to="UTF8")
bilan_adm at par@data[,"par_nom"]<-iconv(bilan_adm at par@data[,"par_nom"],from="latin1",to="UTF8")
bilan_adm at stades@data[,"std_libelle"]<-iconv(bilan_adm at stades@data[,"std_libelle"],from="latin1",to="UTF8")
-
+bilan_adm<-calcule(bilan_adm)
devtools::use_data(bilan_adm,internal=FALSE,overwrite=TRUE)
Modified: pkg/stacomir/inst/examples/bilanAgedemer_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanAgedemer_example.R 2017-06-08 07:43:13 UTC (rev 384)
+++ pkg/stacomir/inst/examples/bilanAgedemer_example.R 2017-06-08 08:27:04 UTC (rev 385)
@@ -19,13 +19,14 @@
silent=FALSE
)
bilan_adm<-connect(bilan_adm)
+ bilan_adm<-calcule(bilan_adm)
}
# load the dataset generated by previous lines
# Salmons from the loire on two dams
data("bilan_adm")
# the calculation will fill the slot calcdata
-bilan_adm<-calcule(bilan_adm)
+
# stages are in bilan_adm at calcdata[["6"]][,"stage"]
#look at data structure using str(bilan_adm at calcdata[["6"]])
Modified: pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R 2017-06-08 07:43:13 UTC (rev 384)
+++ pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R 2017-06-08 08:27:04 UTC (rev 385)
@@ -37,7 +37,7 @@
# the y unit has little sense in this graph
plot(bmi,plot.type="density",silent=TRUE)
#install.packages("viridis")
-
+\dontrun{
if (requireNamespace("ggplot2", quietly = TRUE)&
requireNamespace("viridis", quietly = TRUE)){
g<-get("g",envir=envir_stacomi)
@@ -83,7 +83,6 @@
ggplot2::ggtitle("Historical trend at Les Enfrenaux Eel trap")
}
-\dontrun{
# available arguments for timesplit are "quinzaine" and "mois" and "semaine"
# with the silent=TRUE argument, it's always the latest year that is selected
plot(bmi,plot.type="barchart",timesplit="quinzaine",silent=TRUE)
Modified: pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R 2017-06-08 07:43:13 UTC (rev 384)
+++ pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R 2017-06-08 08:27:04 UTC (rev 385)
@@ -51,8 +51,8 @@
"#A66F24","#012746","#6C3E00","#DC7ED8","#8AA123"),
color_ope=c("#5589B5","#FFDB6E","#FF996E","#1C4D76"),
silent=TRUE)
-}
+
#cumulated migration at the station (all stages and DC grouped)
plot(bMM_Arzal,plot.type="step",silent=TRUE)
@@ -64,6 +64,5 @@
plot(bMM_Arzal,plot.type="multiple",silent=TRUE)
# data will be written in the data directory specified in
# the stacomi/calcmig.csv file
-\dontrun{
- summary(bMM_Arzal,silent=TRUE)
+summary(bMM_Arzal,silent=TRUE)
}
Modified: pkg/stacomir/inst/examples/bilan_poids_moyen_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilan_poids_moyen_example.R 2017-06-08 07:43:13 UTC (rev 384)
+++ pkg/stacomir/inst/examples/bilan_poids_moyen_example.R 2017-06-08 08:27:04 UTC (rev 385)
@@ -22,11 +22,12 @@
selectedvalue=">1",
silent=FALSE)
bilPM<-connect(bilPM)
+ bilPM<-calcule(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
@@ -34,6 +35,8 @@
# 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)
+\dontrun{
# First model with nls, see Guerault and Desaunay (1993)
model(bilPM,model.type="seasonal")
model(bilPM,model.type="seasonal1")
+}
Modified: pkg/stacomir/inst/examples/bilancarlot_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilancarlot_example.R 2017-06-08 07:43:13 UTC (rev 384)
+++ pkg/stacomir/inst/examples/bilancarlot_example.R 2017-06-08 08:27:04 UTC (rev 385)
@@ -21,11 +21,12 @@
silent=FALSE)
# two warning produced, ignored if silent=TRUE
b_carlot<-connect(b_carlot)
+ b_carlot<-calcule(b_carlot,silent=TRUE)
}
# load the dataset generated by previous lines
data("b_carlot")
-b_carlot<-calcule(b_carlot,silent=TRUE)
+
# A "violin" plot
plot(b_carlot,plot.type="1",silent=TRUE)
# get the plot from envir_stacomi to change labels for name
@@ -42,6 +43,7 @@
plot(b_carlot,plot.type="3",silent=TRUE)
\dontrun{
+
#####################################
# an example graph created manually from data
#####################################
Modified: pkg/stacomir/man/BilanAgedemer-class.Rd
===================================================================
--- pkg/stacomir/man/BilanAgedemer-class.Rd 2017-06-08 07:43:13 UTC (rev 384)
+++ pkg/stacomir/man/BilanAgedemer-class.Rd 2017-06-08 08:27:04 UTC (rev 385)
@@ -69,13 +69,14 @@
silent=FALSE
)
bilan_adm<-connect(bilan_adm)
+ bilan_adm<-calcule(bilan_adm)
}
# load the dataset generated by previous lines
# Salmons from the loire on two dams
data("bilan_adm")
# the calculation will fill the slot calcdata
-bilan_adm<-calcule(bilan_adm)
+
# stages are in bilan_adm at calcdata[["6"]][,"stage"]
#look at data structure using str(bilan_adm at calcdata[["6"]])
Modified: pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd 2017-06-08 07:43:13 UTC (rev 384)
+++ pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd 2017-06-08 08:27:04 UTC (rev 385)
@@ -69,7 +69,7 @@
# the y unit has little sense in this graph
plot(bmi,plot.type="density",silent=TRUE)
#install.packages("viridis")
-
+\dontrun{
if (requireNamespace("ggplot2", quietly = TRUE)&
requireNamespace("viridis", quietly = TRUE)){
g<-get("g",envir=envir_stacomi)
@@ -115,7 +115,6 @@
ggplot2::ggtitle("Historical trend at Les Enfrenaux Eel trap")
}
-\dontrun{
# available arguments for timesplit are "quinzaine" and "mois" and "semaine"
# with the silent=TRUE argument, it's always the latest year that is selected
plot(bmi,plot.type="barchart",timesplit="quinzaine",silent=TRUE)
Modified: pkg/stacomir/man/BilanMigrationMult-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationMult-class.Rd 2017-06-08 07:43:13 UTC (rev 384)
+++ pkg/stacomir/man/BilanMigrationMult-class.Rd 2017-06-08 08:27:04 UTC (rev 385)
@@ -98,8 +98,8 @@
"#A66F24","#012746","#6C3E00","#DC7ED8","#8AA123"),
color_ope=c("#5589B5","#FFDB6E","#FF996E","#1C4D76"),
silent=TRUE)
-}
+
#cumulated migration at the station (all stages and DC grouped)
plot(bMM_Arzal,plot.type="step",silent=TRUE)
@@ -111,8 +111,7 @@
plot(bMM_Arzal,plot.type="multiple",silent=TRUE)
# data will be written in the data directory specified in
# the stacomi/calcmig.csv file
-\dontrun{
- summary(bMM_Arzal,silent=TRUE)
+summary(bMM_Arzal,silent=TRUE)
}
}
\author{
Modified: pkg/stacomir/man/Bilan_carlot-class.Rd
===================================================================
--- pkg/stacomir/man/Bilan_carlot-class.Rd 2017-06-08 07:43:13 UTC (rev 384)
+++ pkg/stacomir/man/Bilan_carlot-class.Rd 2017-06-08 08:27:04 UTC (rev 385)
@@ -57,11 +57,12 @@
silent=FALSE)
# two warning produced, ignored if silent=TRUE
b_carlot<-connect(b_carlot)
+ b_carlot<-calcule(b_carlot,silent=TRUE)
}
# load the dataset generated by previous lines
data("b_carlot")
-b_carlot<-calcule(b_carlot,silent=TRUE)
+
# A "violin" plot
plot(b_carlot,plot.type="1",silent=TRUE)
# get the plot from envir_stacomi to change labels for name
@@ -78,6 +79,7 @@
plot(b_carlot,plot.type="3",silent=TRUE)
\dontrun{
+
#####################################
# an example graph created manually from data
#####################################
Modified: pkg/stacomir/man/Bilan_poids_moyen-class.Rd
===================================================================
--- pkg/stacomir/man/Bilan_poids_moyen-class.Rd 2017-06-08 07:43:13 UTC (rev 384)
+++ pkg/stacomir/man/Bilan_poids_moyen-class.Rd 2017-06-08 08:27:04 UTC (rev 385)
@@ -61,11 +61,12 @@
selectedvalue=">1",
silent=FALSE)
bilPM<-connect(bilPM)
+ bilPM<-calcule(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
@@ -73,10 +74,12 @@
# 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)
+\dontrun{
# 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}
}
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