[Stacomir-commits] r601 - in pkg/stacomir: R man

Fri Nov 12 09:14:00 CET 2021

Author: briand
Date: 2021-11-12 09:14:00 +0100 (Fri, 12 Nov 2021)
New Revision: 601

Removed:
   pkg/stacomir/R/NAMESPACE
Modified:
   pkg/stacomir/R/report_mig.R
   pkg/stacomir/R/stacomi.R
   pkg/stacomir/man/write_database-report_mig-method.Rd
Log:
checks changes

Deleted: pkg/stacomir/R/NAMESPACE
===================================================================

--- pkg/stacomir/R/NAMESPACE	2021-11-12 08:07:57 UTC (rev 600)
+++ pkg/stacomir/R/NAMESPACE	2021-11-12 08:14:00 UTC (rev 601)
@@ -1,137 +0,0 @@
-# Generated by roxygen2: do not edit by hand
-
-export(calcule)
-export(charge)
-export(charge_complement)
-export(charge_with_filter)
-export(choice_c)
-export(colortable)
-export(createmessage)
-export(envir_stacomi)
-export(fun_aggreg_for_plot)
-export(fun_date_extraction)
-export(fun_report_mig_interannual)
-export(fun_report_mig_mult)
-export(fun_report_mig_mult_overlaps)
-export(fun_stage_durif)
-export(fun_write_monthly)
-export(funstat)
-export(getvalue)
-export(model)
-export(setasqualitative)
-export(split_per_day)
-export(stacomi)
-export(supprime)
-export(vector_to_listsql)
-export(write_database)
-exportClasses(report_annual)
-exportClasses(report_dc)
-exportClasses(report_df)
-exportClasses(report_env)
-exportClasses(report_ge_weight)
-exportClasses(report_mig)
-exportClasses(report_mig_char)
-exportClasses(report_mig_env)
-exportClasses(report_mig_interannual)
-exportClasses(report_mig_mult)
-exportClasses(report_ope)
-exportClasses(report_sample_char)
-exportClasses(report_sea_age)
-exportClasses(report_silver_eel)
-exportClasses(report_species)
-exportMethods(barplot)
-exportMethods(choice_c)
-exportMethods(plot)
-exportMethods(print)
-exportMethods(summary)
-exportMethods(supprime)
-exportMethods(write_database)
-exportMethods(xtable)
-import(RColorBrewer)
-import(RPostgreSQL)
-import(ggplot2)
-import(methods)
-import(stacomirtools)
-import(stringr)
-import(xtable)
-importFrom(Hmisc,capitalize)
-importFrom(Hmisc,wtd.quantile)
-importFrom(dplyr,desc)
-importFrom(dplyr,do)
-importFrom(dplyr,filter)
-importFrom(dplyr,first)
-importFrom(dplyr,group_by)
-importFrom(dplyr,min_rank)
-importFrom(dplyr,mutate)
-importFrom(dplyr,rename)
-importFrom(dplyr,select)
-importFrom(dplyr,summarize)
-importFrom(dplyr,ungroup)
-importFrom(grDevices,adjustcolor)
-importFrom(grDevices,dev.new)
-importFrom(grDevices,gray)
-importFrom(grDevices,gray.colors)
-importFrom(grDevices,rainbow)
-importFrom(graphics,abline)
-importFrom(graphics,arrows)
-importFrom(graphics,axis)
-importFrom(graphics,axis.Date)
-importFrom(graphics,hist)
-importFrom(graphics,layout)
-importFrom(graphics,legend)
-importFrom(graphics,matplot)
-importFrom(graphics,mtext)
-importFrom(graphics,par)
-importFrom(graphics,points)
-importFrom(graphics,polygon)
-importFrom(graphics,rect)
-importFrom(graphics,segments)
-importFrom(graphics,text)
-importFrom(grid,gpar)
-importFrom(grid,grid.layout)
-importFrom(grid,grid.newpage)
-importFrom(grid,pushViewport)
-importFrom(grid,viewport)
-importFrom(intervals,"closed<-")
-importFrom(intervals,Intervals)
-importFrom(intervals,interval_overlap)
-importFrom(lattice,barchart)
-importFrom(lattice,simpleKey)
-importFrom(lattice,trellis.par.get)
-importFrom(lattice,trellis.par.set)
-importFrom(lubridate,"%m+%")
-importFrom(lubridate,floor_date)
-importFrom(lubridate,isoweek)
-importFrom(lubridate,round_date)
-importFrom(lubridate,years)
-importFrom(magrittr,"%>%")
-importFrom(mgcv,gam)
-importFrom(pool,dbExecute)
-importFrom(pool,dbGetQuery)
-importFrom(pool,dbWriteTable)
-importFrom(pool,poolClose)
-importFrom(reshape2,dcast)
-importFrom(reshape2,melt)
-importFrom(stats,AIC)
-importFrom(stats,as.formula)
-importFrom(stats,coef)
-importFrom(stats,coefficients)
-importFrom(stats,complete.cases)
-importFrom(stats,ftable)
-importFrom(stats,na.fail)
-importFrom(stats,nls)
-importFrom(stats,pbeta)
-importFrom(stats,predict)
-importFrom(stats,sd)
-importFrom(stats,update)
-importFrom(stats,xtabs)
-importFrom(utils,data)
-importFrom(utils,globalVariables)
-importFrom(utils,menu)
-importFrom(utils,read.csv)
-importFrom(utils,select.list)
-importFrom(utils,setTxtProgressBar)
-importFrom(utils,stack)
-importFrom(utils,txtProgressBar)
-importFrom(utils,write.table)
-importFrom(withr,defer)

Modified: pkg/stacomir/R/report_mig.R
===================================================================
--- pkg/stacomir/R/report_mig.R	2021-11-12 08:07:57 UTC (rev 600)
+++ pkg/stacomir/R/report_mig.R	2021-11-12 08:14:00 UTC (rev 601)
@@ -693,33 +693,8 @@
 
 
 
-#deprecated0.6
-##' 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
-##' @param h a handler
-##' @param ... Additional parameters
-##' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-##' @keywords internal
-#h_report_migwrite = function(h,...) {
-#  if (exists("report_mig",envir_stacomi)) {
-#	report_mig<-get("report_mig",envir_stacomi)
-#  } else {
-#	funout(gettext("You need to launch computation first, clic on calc\n",domain="R-stacomiR"),arret=TRUE)
-#  }
-#  # ecriture du report journalier, ecrit aussi le report mensuel
-#  database_expected<-get("database_expected",envir=envir_stacomi)
-#  if (database_expected) {
-#	write_database(report_mig,silent=FALSE)
-#  }	else {
-#	funout(gettext("no report written to database : database_expected argument=FALSE",domain="R-stacomiR"))
-#  }
-#
-#}
 
-#' Command line method to write the daily and monthly counts to the
-#' t_bilanmigrationjournalier_bjo table
+#' Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table
 #'
 #' 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.

Modified: pkg/stacomir/R/stacomi.R
===================================================================
--- pkg/stacomir/R/stacomi.R	2021-11-12 08:07:57 UTC (rev 600)
+++ pkg/stacomir/R/stacomi.R	2021-11-12 08:14:00 UTC (rev 601)
@@ -37,10 +37,11 @@
 			test <- FALSE
 		} else {
 			test <- TRUE
+			pool::poolClose(con at connection)		
 		}
 		
-		pool::poolClose(con at connection)		
 		
+		
 		# second test to check that the database is working OK		
 		
 		if (test) {

Modified: pkg/stacomir/man/write_database-report_mig-method.Rd
===================================================================
--- pkg/stacomir/man/write_database-report_mig-method.Rd	2021-11-12 08:07:57 UTC (rev 600)
+++ pkg/stacomir/man/write_database-report_mig-method.Rd	2021-11-12 08:14:00 UTC (rev 601)
@@ -3,8 +3,7 @@
 \name{write_database,report_mig-method}
 \alias{write_database,report_mig-method}
 \alias{write_database.report_mig}
-\title{handler h_report_migwrite
-Allows the saving of daily and monthly counts in the database}
+\title{Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table}
 \usage{
 \S4method{write_database}{report_mig}(object, silent = TRUE, check_for_bjo = TRUE)
 }
@@ -15,19 +14,12 @@
 
 \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{
-handler h_report_migwrite
-Allows the saving of daily and monthly counts in the database
+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.
 }
 \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.
 }
@@ -41,35 +33,4 @@
 }
 \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,}

