[Stacomir-commits] r458 - in pkg/stacomir: . R man

Fri Sep 1 11:21:28 CEST 2017

Author: briand
Date: 2017-09-01 11:21:27 +0200 (Fri, 01 Sep 2017)
New Revision: 458

Modified:
   pkg/stacomir/DESCRIPTION
   pkg/stacomir/NAMESPACE
   pkg/stacomir/R/report_mig_char.R
   pkg/stacomir/man/calcule-report_mig_mult-method.Rd
   pkg/stacomir/man/choice_c-report_mig_char-method.Rd
   pkg/stacomir/man/envir_stacomi.Rd
   pkg/stacomir/man/fun_report_mig_mult.Rd
   pkg/stacomir/man/stacomi.Rd
Log:


Modified: pkg/stacomir/DESCRIPTION
===================================================================

--- pkg/stacomir/DESCRIPTION	2017-08-31 17:46:34 UTC (rev 457)
+++ pkg/stacomir/DESCRIPTION	2017-09-01 09:21:27 UTC (rev 458)
@@ -1,6 +1,6 @@
 Package: stacomiR
 Version: 0.5.3
-Date: 2017-06-24
+Date: 2017-08-31
 Title: Fish Migration Monitoring
 Authors at R: c(person("Cedric", "Briand", role = c("aut", "cre"), email = "cedric.briand00 at gmail.com"),
 	      person("Marion", "Legrand", role = "aut", email="tableau-salt-loire at logrami.fr"),

Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE	2017-08-31 17:46:34 UTC (rev 457)
+++ pkg/stacomir/NAMESPACE	2017-09-01 09:21:27 UTC (rev 458)
@@ -2,6 +2,7 @@
 
 export(chargecsv)
 export(colortable)
+export(envir_stacomi)
 export(fun_aggreg_for_plot)
 export(fun_char_spe)
 export(fun_date_extraction)
@@ -16,7 +17,6 @@
 export(split_per_day)
 export(stacomi)
 export(vector_to_listsql)
-export(envir_stacomi)
 exportClasses(report_annual)
 exportClasses(report_dc)
 exportClasses(report_df)

Modified: pkg/stacomir/R/report_mig_char.R
===================================================================
--- pkg/stacomir/R/report_mig_char.R	2017-08-31 17:46:34 UTC (rev 457)
+++ pkg/stacomir/R/report_mig_char.R	2017-09-01 09:21:27 UTC (rev 458)
@@ -203,7 +203,6 @@
 #' @param object An object of class \link{report_mig_char-class}
 #' @param silent Boolean default FALSE, if TRUE information messages not displayed
 #' @return report_mig_char with slot @data filled from the database
-#' @note 
 #' @aliases connect.report_mig_char
 #' @export
 setMethod("connect",signature=signature("report_mig_char"),definition=function(object,silent=FALSE){

Modified: pkg/stacomir/man/calcule-report_mig_mult-method.Rd
===================================================================
--- pkg/stacomir/man/calcule-report_mig_mult-method.Rd	2017-08-31 17:46:34 UTC (rev 457)
+++ pkg/stacomir/man/calcule-report_mig_mult-method.Rd	2017-09-01 09:21:27 UTC (rev 458)
@@ -24,7 +24,11 @@
 \item{method}{In the case of instantaneous periods (video counting) the sum of daily values is done by the \link{fun_report_mig_mult} method and the value indicated in method is "sum".
  If any migration monitoring period is longer than a day, then the migration is split using the \link{fun_report_mig_mult_overlaps} function and the value indicated in the 
 method is "overlaps" as the latter method uses the overlap package to split migration period.}
-\item{data}{the calculated data.}
+\item{data}{the calculated data. If weight are present, the columns display weight or numbers, the total number is 
+"Effectif_total" and corresponds to the addition of numbers and numbers converted from weight,
+the total weight is "Poids_total"+"poids_depuis_effectifs" and corresponds to weighed glass eel plus glass eel number converted in weights.
+CALCULE corresponds to calulated number, MESURE to measured numbers, EXPERT to punctual expertise of migration (for instance measured in other path, or known migration
+of fishes passing the dam but not actually counted, PONCTUEL to fishes counted by visual identification but not by the counting apparatus (in case of technical problem for instance)}
 \item{contient_poids}{A boolean which indicates, in the case of glass eel, that the function \link{fun_weight_conversion} has been run to convert the weights to numbers using the weight
 to number coefficients in the database (see link{report_ge_weight}).}
 \item{negative}{A parameter indicating if negative migration (downstream in the case of upstream migration devices) have been converted to positive numbers,

Modified: pkg/stacomir/man/choice_c-report_mig_char-method.Rd
===================================================================
--- pkg/stacomir/man/choice_c-report_mig_char-method.Rd	2017-08-31 17:46:34 UTC (rev 457)
+++ pkg/stacomir/man/choice_c-report_mig_char-method.Rd	2017-09-01 09:21:27 UTC (rev 458)
@@ -28,7 +28,8 @@
 
 \item{horodatefin}{The finishing date of the report, for this class this will be used to calculate the number of daily steps.}
 
-\item{echantillon}{Default TRUE,}
+\item{echantillon}{Default "with" can be "without" (values "avec" and "sans") are accepted, checking without modifies the query
+in the connect method so that subsamples are not allowed,}
 
 \item{silent}{Default FALSE, if TRUE the program should no display messages}
 }

Modified: pkg/stacomir/man/envir_stacomi.Rd
===================================================================
--- pkg/stacomir/man/envir_stacomi.Rd	2017-08-31 17:46:34 UTC (rev 457)
+++ pkg/stacomir/man/envir_stacomi.Rd	2017-09-01 09:21:27 UTC (rev 458)
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/create_generic.R, R/data.R
+% Please edit documentation in R/create_generic.R, R/data.R, R/stacomi.R
 \docType{data}
 \name{envir_stacomi}
 \alias{envir_stacomi}
@@ -10,6 +10,8 @@
 envir_stacomi
 
 envir_stacomi
+
+envir_stacomi
 }
 \description{
 envir_stacomi \code{envir_stacomi <- new.env(parent = baseenv())} is the
@@ -17,6 +19,9 @@
 
 This is where the graphical interface stores its objects
 try \code{ls(envir=envir_stacomi)}
+
+This is where the graphical interface stores its objects
+try \code{ls(envir=envir_stacomi)}
 }
 \author{
 Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}

Modified: pkg/stacomir/man/fun_report_mig_mult.Rd
===================================================================
--- pkg/stacomir/man/fun_report_mig_mult.Rd	2017-08-31 17:46:34 UTC (rev 457)
+++ pkg/stacomir/man/fun_report_mig_mult.Rd	2017-09-01 09:21:27 UTC (rev 458)
@@ -16,7 +16,9 @@
 \value{
 A data.frame with number summed over over the time.sequence. 
 The function returns the same output than \link{fun_report_mig_mult_overlaps}
-but is intended to work faster
+but is intended to work faster. In the data.frame, the total number is 
+"Effectif_total" and corresponds to the addition of numbers and numbers converted from weight,
+the total weight is "Poids_total"+"poids_depuis_effectifs" and corresponds to weighed glass eel plus glass eel number converted in weights.
 }
 \description{
 Function to calculate daily migration from migration monitoring whose length is less than one day,

Modified: pkg/stacomir/man/stacomi.Rd
===================================================================
--- pkg/stacomir/man/stacomi.Rd	2017-08-31 17:46:34 UTC (rev 457)
+++ pkg/stacomir/man/stacomi.Rd	2017-09-01 09:21:27 UTC (rev 458)
@@ -36,6 +36,7 @@
 			through the command line.}
  }
 When \code{database_expected=FALSE} a connection to the database is not expected. Therefore test are run by calling examples object stored in Rdata.
+To change the language use Sys.setenv(LANG = "fr") or Sys.setenv(LANG = "en")
 }
 \examples{
 
@@ -50,6 +51,7 @@
 }  
 #launch stacomi without connection to the database
 stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
+
 }
 \author{
 Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}

