[Stacomir-commits] r192 - in pkg/stacomir: . R inst/tests/testthat man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Sep 5 21:24:01 CEST 2016
Author: briand
Date: 2016-09-05 21:24:01 +0200 (Mon, 05 Sep 2016)
New Revision: 192
Removed:
pkg/stacomir/vignettes/vignette_stacomi.aux
Modified:
pkg/stacomir/NAMESPACE
pkg/stacomir/R/BilanMigration.r
pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
pkg/stacomir/man/BilanMigration-class.Rd
pkg/stacomir/man/fn_EcritBilanJournalier.Rd
pkg/stacomir/man/fn_EcritBilanMensuel.Rd
pkg/stacomir/man/plot-BilanMigration-ANY-method.Rd
Log:
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2016-09-05 19:23:41 UTC (rev 191)
+++ pkg/stacomir/NAMESPACE 2016-09-05 19:24:01 UTC (rev 192)
@@ -13,6 +13,7 @@
export(fundensityBilan_carlot)
export(funout)
export(funpointBilan_carlot)
+export(funstat)
export(funtableBilan_carlot)
export(funtableDF)
export(funtraitement_poids)
Modified: pkg/stacomir/R/BilanMigration.r
===================================================================
--- pkg/stacomir/R/BilanMigration.r 2016-09-05 19:23:41 UTC (rev 191)
+++ pkg/stacomir/R/BilanMigration.r 2016-09-05 19:24:01 UTC (rev 192)
@@ -357,7 +357,7 @@
} else if (plot.type=="step"){
taxon= as.character(bilanMigration at taxons@data$tax_nom_latin)
stade= as.character(bilanMigration at stades@data$std_libelle)
- DC=as.numeric(bilanMigration at dc@dc_selectionne)
+ dc=as.numeric(bilanMigration at dc@dc_selectionne)
if (bilanMigration at pasDeTemps@stepDuration==86400 & bilanMigration at pasDeTemps@stepDuration==86400) {
grdata<-bilanMigration at calcdata[[stringr::str_c("dc_",dc)]][["data"]]
grdata<-funtraitementdate(grdata,
Modified: pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R 2016-09-05 19:23:41 UTC (rev 191)
+++ pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R 2016-09-05 19:24:01 UTC (rev 192)
@@ -60,5 +60,18 @@
test_that("Test writing an example to the database",
{
-
+ stacomi(gr_interface=FALSE,
+ login_window=FALSE,
+ database_expected=TRUE)
+ # overriding user schema
+ baseODBC<-get("baseODBC",envir=envir_stacomi)
+ baseODBC[c(2,3)]<-rep("iav",2)
+ assign("baseODBC",baseODBC,envir_stacomi)
+ sch<-get("sch",envir=envir_stacomi) # "iav."
+ assign("sch","iav.",envir_stacomi)
+ # this chunk is not launched from examples but loads the bM_Arzal dataset if connection works
+ data("bM_Arzal")
+ bM_Arzal<-calcule(bM_Arzal)
+ fn_EcritBilanJournalier(bilanMigration=bM_Arzal,silent=FALSE)
+ rm("envir_stacomi",envir =.GlobalEnv)
})
\ No newline at end of file
Modified: pkg/stacomir/man/BilanMigration-class.Rd
===================================================================
--- pkg/stacomir/man/BilanMigration-class.Rd 2016-09-05 19:23:41 UTC (rev 191)
+++ pkg/stacomir/man/BilanMigration-class.Rd 2016-09-05 19:24:01 UTC (rev 192)
@@ -64,6 +64,8 @@
bM_Arzal<-calcule(bM_Arzal)
#Individual plot for all DC (standard), taxon and stage where data present
#silent argument to stop all messages
+# this will also write daily and monthly migration balance to the database,
+# but only if stacomi has been run with argument : database_expected=FALSE
plot(bM_Arzal,plot.type="standard",silent=TRUE)
#cumulated migration at the station (all stages and DC grouped)
Modified: pkg/stacomir/man/fn_EcritBilanJournalier.Rd
===================================================================
--- pkg/stacomir/man/fn_EcritBilanJournalier.Rd 2016-09-05 19:23:41 UTC (rev 191)
+++ pkg/stacomir/man/fn_EcritBilanJournalier.Rd 2016-09-05 19:24:01 UTC (rev 192)
@@ -5,10 +5,12 @@
\title{fn_EcritBilanJournier writes the daily migration in the
t_bilanmigrationjournalier_bjo table}
\usage{
-fn_EcritBilanJournalier(bilanMigration)
+fn_EcritBilanJournalier(bilanMigration, silent)
}
\arguments{
\item{bilanMigration}{an object of class \code{\linkS4class{BilanMigration}}}
+
+\item{silent}{: TRUE to avoid messages}
}
\description{
Daily values are needed to compare migrations from year to year, by the class \link{BilanMigrationInterAnnuelle-class}. They are added by
@@ -18,6 +20,14 @@
the user is asked whether or not he wants to overwrite data, if no
data are present in the database, the import is done anyway
}
+\examples{
+\dontrun{
+stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
+data("bM_Arzal")
+bM_Arzal<-calcule(bM_Arzal)
+fn_EcritBilanJournalier(bilanMigration=bM_Arzal,silent=FALSE)
+}
+}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
Modified: pkg/stacomir/man/fn_EcritBilanMensuel.Rd
===================================================================
--- pkg/stacomir/man/fn_EcritBilanMensuel.Rd 2016-09-05 19:23:41 UTC (rev 191)
+++ pkg/stacomir/man/fn_EcritBilanMensuel.Rd 2016-09-05 19:24:01 UTC (rev 192)
@@ -12,6 +12,10 @@
\item{resum}{data frame with summary per month}
}
\description{
-Launched by fun_EcritBilanJournalier
+This writes monthly data in t_bilanmensuel_mens table
}
+\note{
+This function is launched by fun_EcritBilanJournalier, the resum
+dataset is created by the \link{funstat} function
+}
Modified: pkg/stacomir/man/plot-BilanMigration-ANY-method.Rd
===================================================================
--- pkg/stacomir/man/plot-BilanMigration-ANY-method.Rd 2016-09-05 19:23:41 UTC (rev 191)
+++ pkg/stacomir/man/plot-BilanMigration-ANY-method.Rd 2016-09-05 19:24:01 UTC (rev 192)
@@ -28,7 +28,8 @@
}
\note{
When plotting the "standard" plot, the user will be prompted to "write" the daily migration and monthly migration in the database.
-these entries are necessary to run the Interannual Migration class.
+these entries are necessary to run the Interannual Migration class. If the stacomi has been launched with database_expected=FALSE,
+then no entry will be written to the database
}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
Deleted: pkg/stacomir/vignettes/vignette_stacomi.aux
===================================================================
--- pkg/stacomir/vignettes/vignette_stacomi.aux 2016-09-05 19:23:41 UTC (rev 191)
+++ pkg/stacomir/vignettes/vignette_stacomi.aux 2016-09-05 19:24:01 UTC (rev 192)
@@ -1,27 +0,0 @@
-\relax
-\providecommand\hyper at newdestlabel[2]{}
-\bibstyle{jss}
-\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
-\HyperFirstAtBeginDocument{\ifx\hyper at anchor\@undefined
-\global\let\oldcontentsline\contentsline
-\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
-\global\let\oldnewlabel\newlabel
-\gdef\newlabel#1#2{\newlabelxx{#1}#2}
-\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
-\AtEndDocument{\ifx\hyper at anchor\@undefined
-\let\contentsline\oldcontentsline
-\let\newlabel\oldnewlabel
-\fi}
-\fi}
-\global\let\hyper at last\relax
-\gdef\HyperFirstAtBeginDocument#1{#1}
-\providecommand\HyField at AuxAddToFields[1]{}
-\providecommand\HyField at AuxAddToCoFields[2]{}
-\catcode `:\active
-\catcode `;\active
-\catcode `!\active
-\catcode `?\active
-\select at language{french}
-\@writefile{toc}{\select at language{french}}
-\@writefile{lof}{\select at language{french}}
-\@writefile{lot}{\select at language{french}}
More information about the Stacomir-commits
mailing list