[Stacomir-commits] r600 - in pkg/stacomir: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Nov 12 09:07:58 CET 2021
Author: briand
Date: 2021-11-12 09:07:57 +0100 (Fri, 12 Nov 2021)
New Revision: 600
Modified:
pkg/stacomir/DESCRIPTION
pkg/stacomir/NAMESPACE
pkg/stacomir/man/report_dc-class.Rd
pkg/stacomir/man/report_df-class.Rd
pkg/stacomir/man/report_mig-class.Rd
pkg/stacomir/man/report_silver_eel-class.Rd
pkg/stacomir/man/report_species-class.Rd
pkg/stacomir/man/write_database-report_mig-method.Rd
Log:
updated description
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2021-11-12 07:55:26 UTC (rev 599)
+++ pkg/stacomir/DESCRIPTION 2021-11-12 08:07:57 UTC (rev 600)
@@ -89,13 +89,13 @@
xtable,
mgcv,
rlang,
- pool
+ pool,
+ withr
Suggests:
testthat,
viridis,
knitr,
- rmarkdown,
- withr
+ rmarkdown
Author: Cedric Briand [aut, cre],
Marion Legrand [aut],
Beaulaton Laurent [ctb],
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2021-11-12 07:55:26 UTC (rev 599)
+++ pkg/stacomir/NAMESPACE 2021-11-12 08:07:57 UTC (rev 600)
@@ -134,3 +134,4 @@
importFrom(utils,stack)
importFrom(utils,txtProgressBar)
importFrom(utils,write.table)
+importFrom(withr,defer)
Modified: pkg/stacomir/man/report_dc-class.Rd
===================================================================
--- pkg/stacomir/man/report_dc-class.Rd 2021-11-12 07:55:26 UTC (rev 599)
+++ pkg/stacomir/man/report_dc-class.Rd 2021-11-12 08:07:57 UTC (rev 600)
@@ -30,7 +30,8 @@
\examples{
-# this option allows to launch the program without the interface to display some of the program features.
+# this option allows to launch the program without the interface to display
+# some of the program features.
stacomi(database_expected=FALSE)
# An example that will work only if the database is present
# and the program installed and comprises the schema iav
Modified: pkg/stacomir/man/report_df-class.Rd
===================================================================
--- pkg/stacomir/man/report_df-class.Rd 2021-11-12 07:55:26 UTC (rev 599)
+++ pkg/stacomir/man/report_df-class.Rd 2021-11-12 08:07:57 UTC (rev 600)
@@ -41,9 +41,10 @@
database_expected=FALSE)
# An example that will work with the database installed only and schema iav in the database
# prompt for user and password but you can set appropriate options for host, port and dbname
-stacomi(
- database_expected=TRUE, sch='iav')
+
\dontrun{
+ stacomi(
+ database_expected=TRUE, sch='iav')
if (interactive()){
if (!exists("user")){
user <- readline(prompt="Enter user: ")
Modified: pkg/stacomir/man/report_mig-class.Rd
===================================================================
--- pkg/stacomir/man/report_mig-class.Rd 2021-11-12 07:55:26 UTC (rev 599)
+++ pkg/stacomir/man/report_mig-class.Rd 2021-11-12 08:07:57 UTC (rev 600)
@@ -39,7 +39,8 @@
\examples{
stacomi(database_expected=FALSE)
# If you have a working database
-# the following line of code will create the r_mig dataset from the iav (default) schema in the database
+# the following line of code will create the r_mig dataset from the iav (default)
+# schema in the database
\dontrun{
stacomi(database_expected=TRUE)
if (interactive()){
Modified: pkg/stacomir/man/report_silver_eel-class.Rd
===================================================================
--- pkg/stacomir/man/report_silver_eel-class.Rd 2021-11-12 07:55:26 UTC (rev 599)
+++ pkg/stacomir/man/report_silver_eel-class.Rd 2021-11-12 08:07:57 UTC (rev 600)
@@ -52,10 +52,12 @@
# the following script will load data from the two Anguillere monitored in the Somme
# If you have a working database
-# the following line of code will create the r_silver dataset from the "fd80." schema in the database
+# the following line of code will create the r_silver dataset
+# from the "fd80." schema in the database
\dontrun{
stacomi(database_expected=TRUE, sch="fd80.") # overrides the default option sch = 'iav'
- # prompt for user and password, you can set these in the options, including dbname and host
+ # prompt for user and password, you can set these in the options,
+ # including dbname and host
if (interactive()){
if (!exists("user")){
user <- readline(prompt="Enter user: ")
Modified: pkg/stacomir/man/report_species-class.Rd
===================================================================
--- pkg/stacomir/man/report_species-class.Rd 2021-11-12 07:55:26 UTC (rev 599)
+++ pkg/stacomir/man/report_species-class.Rd 2021-11-12 08:07:57 UTC (rev 600)
@@ -35,10 +35,11 @@
\examples{
# launching stacomi without selecting the scheme or interface
stacomi( database_expected=FALSE)
-# the following script will load data from the two Anguillere monitored in the Somme
-
+# the following script will load data
+# from the two Anguillere monitored in the Somme
# If you have a working database
-# the following line of code will create the bilesp dataset from the "iav." schema in the database
+# the following line of code will create the bilesp dataset from the "iav."
+# schema in the database
\dontrun{
bilesp<-new("report_species")
Modified: pkg/stacomir/man/write_database-report_mig-method.Rd
===================================================================
--- pkg/stacomir/man/write_database-report_mig-method.Rd 2021-11-12 07:55:26 UTC (rev 599)
+++ pkg/stacomir/man/write_database-report_mig-method.Rd 2021-11-12 08:07:57 UTC (rev 600)
@@ -3,7 +3,8 @@
\name{write_database,report_mig-method}
\alias{write_database,report_mig-method}
\alias{write_database.report_mig}
-\title{Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table}
+\title{handler h_report_migwrite
+Allows the saving of daily and monthly counts in the database}
\usage{
\S4method{write_database}{report_mig}(object, silent = TRUE, check_for_bjo = TRUE)
}
@@ -14,12 +15,19 @@
\item{check_for_bjo}{: do you want to check if data are already present in the bjo table, and delete them,
this param was added otherwise connect method when called from report_mig_interannual runs in loops}
+
+\item{h}{a handler}
+
+\item{...}{Additional parameters}
}
\description{
-Daily values are needed to compare migrations from year to year, by the class \link{report_mig_interannual-class}. They are added by
-by this function.
+handler h_report_migwrite
+Allows the saving of daily and monthly counts in the database
}
\note{
+these entries are necessary to run the Interannual Migration class.
+then no entry will be written to the database
+
the user is asked whether or not he wants to overwrite data only when silent is FALSE, if no
data are present in the database, the import is done anyway.
}
@@ -33,4 +41,35 @@
}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+
+Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
+\keyword{Command}
+\keyword{Daily}
+\keyword{They}
+\keyword{\link{report_mig_interannual-class}.}
+\keyword{added}
+\keyword{and}
+\keyword{are}
+\keyword{by}
+\keyword{class}
+\keyword{compare}
+\keyword{counts}
+\keyword{daily}
+\keyword{from}
+\keyword{function.}
+\keyword{internal}
+\keyword{line}
+\keyword{method}
+\keyword{migrations}
+\keyword{monthly}
+\keyword{needed}
+\keyword{t_bilanmigrationjournalier_bjo}
+\keyword{table}
+\keyword{the}
+\keyword{this}
+\keyword{to}
+\keyword{values}
+\keyword{write}
+\keyword{year}
+\keyword{year,}
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