[Stacomir-commits] r508 - / pkg/stacomir pkg/stacomir/inst/examples pkg/stacomir/inst/tests/testthat pkg/stacomir/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Sep 22 14:18:54 CEST 2018
Author: briand
Date: 2018-09-22 14:18:53 +0200 (Sat, 22 Sep 2018)
New Revision: 508
Removed:
pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
pkg/stacomir/vignettes/.Rhistory
stacomir0.5.3/
Modified:
pkg/stacomir/NEWS.md
pkg/stacomir/inst/tests/testthat/test-00-stacomir.R
pkg/stacomir/inst/tests/testthat/test-01-report_mig_mult.R
pkg/stacomir/vignettes/
Log:
Modified: pkg/stacomir/NEWS.md
===================================================================
--- pkg/stacomir/NEWS.md 2018-09-21 16:27:38 UTC (rev 507)
+++ pkg/stacomir/NEWS.md 2018-09-22 12:18:53 UTC (rev 508)
@@ -15,6 +15,7 @@
* Problem with ceilPOSIXt now named only ceil in package Hmisc. (@cedric #489)
+
# stacomiR 0.5.3.1
* added and edited readme.Rmd file (@cedric and @marion #447-#452)
Deleted: pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R 2018-09-21 16:27:38 UTC (rev 507)
+++ pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R 2018-09-22 12:18:53 UTC (rev 508)
@@ -1,144 +0,0 @@
-require(stacomiR)
-# launching stacomi without selecting the scheme or interface
-stacomi(gr_interface=FALSE,
- login_window=FALSE,
- database_expected=FALSE)
-# the following script will load the Arzal dataset if connected to iav schema
-\dontrun{
- # overriding user schema to point to Parc Marais Poitevin
- # (longest historical dataset available
- # in France for eel ...) this suppose you have access to the pmp schema...
- # a glimpse of the dataset is still available in the bmi dataset
- # loaded in the package...
- baseODBC<-get("baseODBC",envir=envir_stacomi)
- baseODBC[c(2,3)]<-rep("pmp",2)
- assign("baseODBC",baseODBC,envir_stacomi)
- sch<-get("sch",envir=envir_stacomi)
- assign("sch","pmp.",envir_stacomi)
- bmi<-new("BilanMigrationInterAnnuelle")
- bmi<-choice_c(bmi,
- dc=c(16),
- taxons=c("Anguilla anguilla"),
- stades=c("AGJ"),
- anneedebut="2007",
- anneefin="2012",
- silent=TRUE)
- bmi<-connect(bmi)
-}
-# load the dataset generated by previous lines
-data("bmi")
-# the first plot is of little interest, it allows to see what data
-# are available... simple lines
-# For irregular operations like those reported at the enfrenaux eel ladder....
-plot(bmi,plot.type="line",silent=TRUE)
-
-# a plot to show the seasonality, Here it has also to do with the monitoring period
-# the y unit has little sense in this graph
-plot(bmi,plot.type="density",silent=TRUE)
-
-bmi<-calcule(bmi,timesplit="semaine")
-
-#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")
-}
-# the standard plot is showing daily values
-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)
-}
-
-# 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")
-
-}
-# 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)
-# Comparison with historical values. Each year and 2 weeks values
-# is a point on the graph...
-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)){
- 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")
-
-}
-
-data("bmi_vichy")
-bmi_vichy<-calcule(bmi_vichy,timesplit="jour",silent=TRUE)
-#bmi_vichy at calcdata
-
-bmi_vichy<-calcule(bmi_vichy,timesplit="semaine",silent=TRUE)
-#bmi_vichy at calcdata
-
-bmi_vichy<-calcule(bmi_vichy,timesplit="jour_365")
-#bmi_vichy at calcdata
-
-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)
-assign("baseODBC",baseODBC,envir_stacomi)
-sch<-get("sch",envir=envir_stacomi)
-assign("sch","logrami.",envir_stacomi)
-bmi_des<-new("BilanMigrationInterAnnuelle") #descartes
-bmi_des<-choice_c(bmi_des,
- dc=c(23),
- taxons=c("Petromyzon marinus"),
- stades=c("5"),
- anneedebut="2007",
- anneefin="2014",
- silent=TRUE)
-bmi_des<-charge(bmi_des)
-bmi_des<-connect(bmi_des)
-bmi_des<-calcule(bmi_des,timesplit="semaine")
-plot(bmi_des,plot.type="seasonal",timesplit="semaine")
-plot(bmi_des,plot.type="seasonal",timesplit="jour")
-plot(bmi_des,plot.type="seasonal",timesplit="mois")
-}
-
-
-
Modified: pkg/stacomir/inst/tests/testthat/test-00-stacomir.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-00-stacomir.R 2018-09-21 16:27:38 UTC (rev 507)
+++ pkg/stacomir/inst/tests/testthat/test-00-stacomir.R 2018-09-22 12:18:53 UTC (rev 508)
@@ -183,9 +183,7 @@
req<-new("RequeteODBC")
baseODBC<-get("baseODBC", envir=envir_stacomi)
options(warn=-1)
- #warning : Coercing LHS to a list
- baseODBC["uid"]=relax::readline(prompt="Enter superuser name: ")
- baseODBC["pwd"]=relax::readline(prompt="Enter superuser password: ")
+ #warning : Coercing LHS to a list
options(warn=0)
req at baseODBC<-baseODBC
req at sql=paste(stringr::str_c("SELECT
Modified: pkg/stacomir/inst/tests/testthat/test-01-report_mig_mult.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-01-report_mig_mult.R 2018-09-21 16:27:38 UTC (rev 507)
+++ pkg/stacomir/inst/tests/testthat/test-01-report_mig_mult.R 2018-09-22 12:18:53 UTC (rev 508)
@@ -68,6 +68,9 @@
silent=TRUE)
options(warn = 0)
report_mig_mult<-charge(report_mig_mult,silent=TRUE)
+ expect_is(get("report_df",envir=envir_stacomi),"report_df")
+ expect_is(get("report_dc",envir=envir_stacomi),"report_dc")
+ expect_is(get("report_ope",envir=envir_stacomi),"report_ope")
rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
@@ -100,13 +103,13 @@
test_that("Test example 01_report_mig_mult",
{
# check if built with examples (Rtools install --example
- example_path<-file.path(.libPaths(),"stacomiR","R-ex","report_mig_mult-class.R")
+ example_path<-file.path(.libPaths()[1],"stacomiR","R-ex","report_mig_mult-class.R")
test<-file.access(example_path,0)
if (test[1]!=0) warnings("Package example dir not created ?") else
options(warn = -1)
source(example_path)
options(warn = 0)
- summary(r_mig_mult,silent=TRUE)
+ expect_output(summary(r_mig_mult,silent=FALSE))
rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
Property changes on: pkg/stacomir/vignettes
___________________________________________________________________
Modified: svn:ignore
- stacomir.pdf
*.synctex
*.tex
*.aux
*.md
*.out
+ *.aux
*.md
*.out
*.synctex
*.tex
.Rhistory
stacomir.pdf
Deleted: pkg/stacomir/vignettes/.Rhistory
===================================================================
More information about the Stacomir-commits
mailing list