[Stacomir-commits] r386 - in pkg/stacomir: R inst/examples inst/tests/testthat man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 8 11:22:43 CEST 2017
Author: briand
Date: 2017-06-08 11:22:43 +0200 (Thu, 08 Jun 2017)
New Revision: 386
Modified:
pkg/stacomir/R/BilanMigrationMultConditionEnv.r
pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
pkg/stacomir/inst/tests/testthat/test-00stacomir.R
pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
pkg/stacomir/inst/tests/testthat/test-06Bilan_MigrationInterAnnuelle.R
pkg/stacomir/inst/tests/testthat/test-09Bilan_MigrationAnnuelle.R
pkg/stacomir/inst/tests/testthat/test-11BilanMigrationMultConditionEnv.R
pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
Log:
modifications for check
Modified: pkg/stacomir/R/BilanMigrationMultConditionEnv.r
===================================================================
--- pkg/stacomir/R/BilanMigrationMultConditionEnv.r 2017-06-08 08:27:04 UTC (rev 385)
+++ pkg/stacomir/R/BilanMigrationMultConditionEnv.r 2017-06-08 09:22:43 UTC (rev 386)
@@ -82,7 +82,8 @@
taxons=taxons,
stades=stades,
datedebut=datedebut,
- datefin=datefin)
+ datefin=datefin,
+ silent=silent)
bmmCE at bilanConditionEnv=choice_c(bmmCE at bilanConditionEnv,
stationMesure=stationMesure,
datedebut=datedebut,
@@ -129,7 +130,7 @@
setMethod("calcule",signature=signature("BilanMigrationMultConditionEnv"),definition=function(object,silent=FALSE){
# silent=FALSE
bmmCE<-object
- bmmCE at bilanMigrationMult<-calcule(bmmCE at bilanMigrationMult)
+ bmmCE at bilanMigrationMult<-calcule(bmmCE at bilanMigrationMult,silent=silent)
if (!silent) funout(gettext("bmmCE object is stocked into envir_stacomi environment\n",domain="R-stacomiR"))
return(bmmCE)
})
Modified: pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R 2017-06-08 08:27:04 UTC (rev 385)
+++ pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R 2017-06-08 09:22:43 UTC (rev 386)
@@ -38,51 +38,51 @@
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)
- g+
- ggplot2::scale_fill_manual(values=viridis::viridis(22))+
- ggplot2::ggtitle("Saisonnalite de la migration aux Enfrenaux")
-}
+ if (requireNamespace("ggplot2", quietly = TRUE)&
+ requireNamespace("viridis", quietly = TRUE)){
+ g<-get("g",envir=envir_stacomi)
+ g+
+ ggplot2::scale_fill_manual(values=viridis::viridis(22))+
+ ggplot2::ggtitle("Saisonnalite de la migration aux Enfrenaux")
+ }
# the standard plot is showing daily values
-plot(bmi,plot.type="standard",silent=TRUE)
+ plot(bmi,plot.type="standard",silent=TRUE)
# Manual edition of the graph produced
-if (requireNamespace("ggplot2", quietly = TRUE)){
- g1<-get("g1",envir=envir_stacomi)
- g1<-g1+ggplot2::ggtitle("Les Enfrenaux")+
- ggplot2::scale_fill_manual(name="Source",
- values=c("purple","#0A0C01"),
- labels = c("historical set","2015 values"))+
- ggplot2::scale_colour_manual(name="Source", values="#B8EA00",
- labels = c("historical mean")) +
- ggplot2::ylab("Nombre d'anguilles")
- print(g1)
-}
-
+ if (requireNamespace("ggplot2", quietly = TRUE)){
+ g1<-get("g1",envir=envir_stacomi)
+ g1<-g1+ggplot2::ggtitle("Les Enfrenaux")+
+ ggplot2::scale_fill_manual(name="Source",
+ values=c("purple","#0A0C01"),
+ labels = c("historical set","2015 values"))+
+ ggplot2::scale_colour_manual(name="Source", values="#B8EA00",
+ labels = c("historical mean")) +
+ ggplot2::ylab("Nombre d'anguilles")
+ print(g1)
+ }
+
# Another graph from scratch
-if (requireNamespace("ggplot2", quietly = TRUE)&
- requireNamespace("viridis", quietly = TRUE)){
-dat<-funtraitementdate(bmi at data, # tableau de donnees a importer
- "bjo_jour", # nom de la colonne
- annee=FALSE,
- mois=TRUE,
- semaine =TRUE,
- jour_mois=FALSE)
- # sum per month
-res<-dplyr::select(dat,bjo_valeur,bjo_annee,semaine)
-res<-dplyr::group_by(res,bjo_annee,semaine)
-res<-dplyr::summarize(res,effectif=sum(bjo_valeur))
-ggplot2::ggplot(res, ggplot2::aes(x = semaine, y = bjo_annee,fill=effectif)) +
- ggplot2::geom_tile(colour="black") + ggplot2::coord_fixed() +
- viridis::scale_fill_viridis(begin=0,option="D") + ggplot2::theme_bw()+
- ggplot2::theme(panel.background= ggplot2::element_rect(fill = "#9360A9"),
- panel.grid.major=ggplot2::element_line(colour="#C1DB39"),
- panel.grid.minor=ggplot2::element_line(colour="#7DD632"))+
- ggplot2::ylab("year")+ggplot2::xlab("week")+
- ggplot2::ggtitle("Historical trend at Les Enfrenaux Eel trap")
-
-}
+ if (requireNamespace("ggplot2", quietly = TRUE)&
+ requireNamespace("viridis", quietly = TRUE)){
+ dat<-funtraitementdate(bmi at data, # tableau de donnees a importer
+ "bjo_jour", # nom de la colonne
+ annee=FALSE,
+ mois=TRUE,
+ semaine =TRUE,
+ jour_mois=FALSE)
+ # sum per month
+ res<-dplyr::select(dat,bjo_valeur,bjo_annee,semaine)
+ res<-dplyr::group_by(res,bjo_annee,semaine)
+ res<-dplyr::summarize(res,effectif=sum(bjo_valeur))
+ ggplot2::ggplot(res, ggplot2::aes(x = semaine, y = bjo_annee,fill=effectif)) +
+ ggplot2::geom_tile(colour="black") + ggplot2::coord_fixed() +
+ viridis::scale_fill_viridis(begin=0,option="D") + ggplot2::theme_bw()+
+ ggplot2::theme(panel.background= ggplot2::element_rect(fill = "#9360A9"),
+ panel.grid.major=ggplot2::element_line(colour="#C1DB39"),
+ panel.grid.minor=ggplot2::element_line(colour="#7DD632"))+
+ ggplot2::ylab("year")+ggplot2::xlab("week")+
+ ggplot2::ggtitle("Historical trend at Les Enfrenaux Eel trap")
+
+ }
# 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)
@@ -96,26 +96,26 @@
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")
+ at les Enfrenaux eel trap")
}
-data("bmi_vichy")
+ data("bmi_vichy")
# statistics for seaonal migration, daily values
-bmi_vichy<-calcule(bmi_vichy,timesplit="jour",silent=TRUE)
+ bmi_vichy<-calcule(bmi_vichy,timesplit="jour",silent=TRUE)
#bmi_vichy at calcdata #check this to see the results
# statistics for seaonal migration, weekly values
-bmi_vichy<-calcule(bmi_vichy,timesplit="semaine",silent=TRUE)
+ bmi_vichy<-calcule(bmi_vichy,timesplit="semaine",silent=TRUE)
#bmi_vichy at calcdata
-
-
+
+
# the plot method also runs calcule
-plot(bmi_vichy,plot.type="seasonal",timesplit="semaine",silent=TRUE)
-plot(bmi_vichy,plot.type="seasonal",timesplit="mois",silent=TRUE)
-plot(bmi_vichy,plot.type="seasonal",timesplit="jour",silent=TRUE)
-
-
-
+ plot(bmi_vichy,plot.type="seasonal",timesplit="semaine",silent=TRUE)
+ plot(bmi_vichy,plot.type="seasonal",timesplit="mois",silent=TRUE)
+ plot(bmi_vichy,plot.type="seasonal",timesplit="jour",silent=TRUE)
+
+
+
# A test with lampreys in the Descarte DF (Vienne)
baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("logrami",2)
@@ -129,7 +129,7 @@
stades=c("5"),
anneedebut="2007",
anneefin="2014",
- silent=FALSE)
+ silent=TRUE)
bmi_des<-charge(bmi_des)
bmi_des<-connect(bmi_des)
bmi_des<-calcule(bmi_des,timesplit="semaine")
Modified: pkg/stacomir/inst/tests/testthat/test-00stacomir.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2017-06-08 08:27:04 UTC (rev 385)
+++ pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2017-06-08 09:22:43 UTC (rev 386)
@@ -77,6 +77,7 @@
require(stacomiR)
stacomi(gr_interface=TRUE,login_window=TRUE,database_expected=TRUE)
expect_true(exists("envir_stacomi"))
+ dispose(get("logw",envir_stacomi))
rm("envir_stacomi",envir =.GlobalEnv)
})
Modified: pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R 2017-06-08 08:27:04 UTC (rev 385)
+++ pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R 2017-06-08 09:22:43 UTC (rev 386)
@@ -7,8 +7,7 @@
baseODBC[c(2,3)]<-rep("iav",2)
assign("baseODBC",baseODBC,envir_stacomi)
sch<-get("sch",envir=envir_stacomi) # "iav."
- assign("sch","iav.",envir_stacomi)
-
+ assign("sch","iav.",envir_stacomi)
bilanMigration<-new("BilanMigration")
options(warn = -1)
bilanMigration<-choice_c(bilanMigration,
Modified: pkg/stacomir/inst/tests/testthat/test-06Bilan_MigrationInterAnnuelle.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-06Bilan_MigrationInterAnnuelle.R 2017-06-08 08:27:04 UTC (rev 385)
+++ pkg/stacomir/inst/tests/testthat/test-06Bilan_MigrationInterAnnuelle.R 2017-06-08 09:22:43 UTC (rev 386)
@@ -157,7 +157,8 @@
taxons=bmM at taxons@data$tax_code,
stades=bmM at stades@data$std_code,
datedebut=as.character(bmM at pasDeTemps@dateDebut),
- datefin=as.character(as.POSIXlt(DateFin(bmM at pasDeTemps))))
+ datefin=as.character(as.POSIXlt(DateFin(bmM at pasDeTemps))),
+ silent=TRUE)
bmM<-charge(bmM,silent=TRUE)
bmM<-connect(bmM,silent=TRUE)
bmM<-calcule(bmM,silent=TRUE)
Modified: pkg/stacomir/inst/tests/testthat/test-09Bilan_MigrationAnnuelle.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-09Bilan_MigrationAnnuelle.R 2017-06-08 08:27:04 UTC (rev 385)
+++ pkg/stacomir/inst/tests/testthat/test-09Bilan_MigrationAnnuelle.R 2017-06-08 09:22:43 UTC (rev 386)
@@ -41,8 +41,10 @@
anneedebut="1996",
anneefin="2015",
silent=TRUE)
- bilA<-connect(bilA,silent=TRUE)
+ bilA<-connect(bilA,silent=TRUE)
+ dev.new()
plot(bilA,silent=TRUE)
+ dev.new()
barplot(bilA)
rm("envir_stacomi",envir =.GlobalEnv)
})
@@ -81,7 +83,9 @@
format.args = list(big.mark = " ", decimal.mark = ",")
))
# barplot transforms the data, further arguments can be passed as to barplot
+ dev.new()
barplot(bilA)
+ dev.new()
barplot(bilA,
args.legend=list(x="topleft",bty = "n"),
col=c("#CA003E","#1A9266","#E10168","#005327","#FF9194"))
@@ -96,6 +100,8 @@
col=RColorBrewer::brewer.pal(9,"Spectral"),
beside=TRUE)
}
+ dev.new()
plot(bilAM,silent=TRUE)
+ graphics.off()
})
Modified: pkg/stacomir/inst/tests/testthat/test-11BilanMigrationMultConditionEnv.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-11BilanMigrationMultConditionEnv.R 2017-06-08 08:27:04 UTC (rev 385)
+++ pkg/stacomir/inst/tests/testthat/test-11BilanMigrationMultConditionEnv.R 2017-06-08 09:22:43 UTC (rev 386)
@@ -35,10 +35,10 @@
bmmCE<-charge(bmmCE,silent=TRUE)
bmmCE<-connect(bmmCE,silent=TRUE)
bmmCE<-calcule(bmmCE,silent=TRUE)
- suppressWarnings(plot(bmmCE))
+ suppressWarnings(plot(bmmCE,silent=TRUE))
suppressWarnings(plot(bmmCE,
color_station=c("temp_gabion"="red","coef_maree"="blue","phases_lune"="pink"),
- color_dc=c("5"="yellow","6"="orange","12"="purple")))
+ color_dc=c("5"="yellow","6"="orange","12"="purple"),silent=TRUE))
rm("envir_stacomi",envir =.GlobalEnv)
})
Modified: pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd 2017-06-08 08:27:04 UTC (rev 385)
+++ pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd 2017-06-08 09:22:43 UTC (rev 386)
@@ -70,51 +70,51 @@
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)
- g+
- ggplot2::scale_fill_manual(values=viridis::viridis(22))+
- ggplot2::ggtitle("Saisonnalite de la migration aux Enfrenaux")
-}
+ if (requireNamespace("ggplot2", quietly = TRUE)&
+ requireNamespace("viridis", quietly = TRUE)){
+ g<-get("g",envir=envir_stacomi)
+ g+
+ ggplot2::scale_fill_manual(values=viridis::viridis(22))+
+ ggplot2::ggtitle("Saisonnalite de la migration aux Enfrenaux")
+ }
# the standard plot is showing daily values
-plot(bmi,plot.type="standard",silent=TRUE)
+ plot(bmi,plot.type="standard",silent=TRUE)
# Manual edition of the graph produced
-if (requireNamespace("ggplot2", quietly = TRUE)){
- g1<-get("g1",envir=envir_stacomi)
- g1<-g1+ggplot2::ggtitle("Les Enfrenaux")+
- ggplot2::scale_fill_manual(name="Source",
- values=c("purple","#0A0C01"),
- labels = c("historical set","2015 values"))+
- ggplot2::scale_colour_manual(name="Source", values="#B8EA00",
- labels = c("historical mean")) +
- ggplot2::ylab("Nombre d'anguilles")
- print(g1)
-}
-
+ if (requireNamespace("ggplot2", quietly = TRUE)){
+ g1<-get("g1",envir=envir_stacomi)
+ g1<-g1+ggplot2::ggtitle("Les Enfrenaux")+
+ ggplot2::scale_fill_manual(name="Source",
+ values=c("purple","#0A0C01"),
+ labels = c("historical set","2015 values"))+
+ ggplot2::scale_colour_manual(name="Source", values="#B8EA00",
+ labels = c("historical mean")) +
+ ggplot2::ylab("Nombre d'anguilles")
+ print(g1)
+ }
+
# Another graph from scratch
-if (requireNamespace("ggplot2", quietly = TRUE)&
- requireNamespace("viridis", quietly = TRUE)){
-dat<-funtraitementdate(bmi at data, # tableau de donnees a importer
- "bjo_jour", # nom de la colonne
- annee=FALSE,
- mois=TRUE,
- semaine =TRUE,
- jour_mois=FALSE)
- # sum per month
-res<-dplyr::select(dat,bjo_valeur,bjo_annee,semaine)
-res<-dplyr::group_by(res,bjo_annee,semaine)
-res<-dplyr::summarize(res,effectif=sum(bjo_valeur))
-ggplot2::ggplot(res, ggplot2::aes(x = semaine, y = bjo_annee,fill=effectif)) +
- ggplot2::geom_tile(colour="black") + ggplot2::coord_fixed() +
- viridis::scale_fill_viridis(begin=0,option="D") + ggplot2::theme_bw()+
- ggplot2::theme(panel.background= ggplot2::element_rect(fill = "#9360A9"),
- panel.grid.major=ggplot2::element_line(colour="#C1DB39"),
- panel.grid.minor=ggplot2::element_line(colour="#7DD632"))+
- ggplot2::ylab("year")+ggplot2::xlab("week")+
- ggplot2::ggtitle("Historical trend at Les Enfrenaux Eel trap")
-
-}
+ if (requireNamespace("ggplot2", quietly = TRUE)&
+ requireNamespace("viridis", quietly = TRUE)){
+ dat<-funtraitementdate(bmi at data, # tableau de donnees a importer
+ "bjo_jour", # nom de la colonne
+ annee=FALSE,
+ mois=TRUE,
+ semaine =TRUE,
+ jour_mois=FALSE)
+ # sum per month
+ res<-dplyr::select(dat,bjo_valeur,bjo_annee,semaine)
+ res<-dplyr::group_by(res,bjo_annee,semaine)
+ res<-dplyr::summarize(res,effectif=sum(bjo_valeur))
+ ggplot2::ggplot(res, ggplot2::aes(x = semaine, y = bjo_annee,fill=effectif)) +
+ ggplot2::geom_tile(colour="black") + ggplot2::coord_fixed() +
+ viridis::scale_fill_viridis(begin=0,option="D") + ggplot2::theme_bw()+
+ ggplot2::theme(panel.background= ggplot2::element_rect(fill = "#9360A9"),
+ panel.grid.major=ggplot2::element_line(colour="#C1DB39"),
+ panel.grid.minor=ggplot2::element_line(colour="#7DD632"))+
+ ggplot2::ylab("year")+ggplot2::xlab("week")+
+ ggplot2::ggtitle("Historical trend at Les Enfrenaux Eel trap")
+
+ }
# 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)
@@ -128,26 +128,26 @@
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")
+ at les Enfrenaux eel trap")
}
-data("bmi_vichy")
+ data("bmi_vichy")
# statistics for seaonal migration, daily values
-bmi_vichy<-calcule(bmi_vichy,timesplit="jour",silent=TRUE)
+ bmi_vichy<-calcule(bmi_vichy,timesplit="jour",silent=TRUE)
#bmi_vichy at calcdata #check this to see the results
# statistics for seaonal migration, weekly values
-bmi_vichy<-calcule(bmi_vichy,timesplit="semaine",silent=TRUE)
+ bmi_vichy<-calcule(bmi_vichy,timesplit="semaine",silent=TRUE)
#bmi_vichy at calcdata
-
-
+
+
# the plot method also runs calcule
-plot(bmi_vichy,plot.type="seasonal",timesplit="semaine",silent=TRUE)
-plot(bmi_vichy,plot.type="seasonal",timesplit="mois",silent=TRUE)
-plot(bmi_vichy,plot.type="seasonal",timesplit="jour",silent=TRUE)
-
-
-
+ plot(bmi_vichy,plot.type="seasonal",timesplit="semaine",silent=TRUE)
+ plot(bmi_vichy,plot.type="seasonal",timesplit="mois",silent=TRUE)
+ plot(bmi_vichy,plot.type="seasonal",timesplit="jour",silent=TRUE)
+
+
+
# A test with lampreys in the Descarte DF (Vienne)
baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("logrami",2)
@@ -161,7 +161,7 @@
stades=c("5"),
anneedebut="2007",
anneefin="2014",
- silent=FALSE)
+ silent=TRUE)
bmi_des<-charge(bmi_des)
bmi_des<-connect(bmi_des)
bmi_des<-calcule(bmi_des,timesplit="semaine")
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