[Stacomir-commits] r613 - in pkg/stacomir: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Nov 22 20:14:28 CET 2021
Author: briand
Date: 2021-11-22 20:14:28 +0100 (Mon, 22 Nov 2021)
New Revision: 613
Removed:
pkg/stacomir/R/fun_dailystats.R
pkg/stacomir/man/fun_dailystats.Rd
pkg/stacomir/man/setref_horodate-ref_horodate-method.Rd
Modified:
pkg/stacomir/DESCRIPTION
Log:
preparing for release 0.6.0.1
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2021-11-22 16:53:13 UTC (rev 612)
+++ pkg/stacomir/DESCRIPTION 2021-11-22 19:14:28 UTC (rev 613)
@@ -1,106 +1,106 @@
-Package: stacomiR
-Version: 0.6.0
-Date: 2021-11-16
-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"),
- person("Beaulaton", "Laurent", role = "ctb", email = "laurent.beaulaton at ofb.gouv.fr"),
- person("Boulenger", "Clarisse", role = "ctb", email = "Clarisse.Boulenger at ofb.gouv.fr"),
- person("Lafage", "Denis", role = "ctb", email = "denis.lafage at logrami.fr"),
- person("Grall", "Sebastien", role = "ctb", email = "seinormigr.grall at gmail.com"))
-Description: Graphical outputs and treatment for a database of fish pass
- monitoring. It is a part of the 'STACOMI' open source project developed in
- France by the French Office for Biodiversity institute to centralize
- data obtained by fish pass monitoring. This version is available in French and
- English. See <http://stacomir.r-forge.r-project.org/> for more information on
- 'STACOMI'.
-License: GPL (>= 2)
-URL: http://stacomir.r-forge.r-project.org/
-BugReports: https://github.com/MarionLegrandLogrami/stacomiR/issues
-Collate:
- 'create_generic.R'
- 'data.R'
- 'fun_table_per_dis.R'
- 'fun_write_monthly.R'
- 'fungraph.R'
- 'fungraph_glasseel.R'
- 'funstat.R'
- 'funtable.R'
- 'ref_choice.R'
- 'ref_coe.R'
- 'ref_dc.R'
- 'ref_df.R'
- 'ref_env.R'
- 'ref_horodate.R'
- 'ref_list.R'
- 'ref_par.R'
- 'ref_parqual.R'
- 'ref_parquan.R'
- 'ref_period.R'
- 'ref_stage.R'
- 'ref_taxa.R'
- 'ref_textbox.R'
- 'ref_timestep.R'
- 'ref_timestep_daily.R'
- 'ref_year.R'
- 'report_annual.R'
- 'report_dc.R'
- 'report_df.R'
- 'utilities.R'
- 'report_env.R'
- 'report_ge_weight.R'
- 'report_ope.R'
- 'report_mig.R'
- 'report_sample_char.R'
- 'report_mig_char.R'
- 'report_mig_mult.R'
- 'report_mig_env.R'
- 'report_mig_interannual.R'
- 'report_sea_age.R'
- 'report_silver_eel.R'
- 'report_species.R'
- 'setAs.R'
- 'stacomi.R'
- 'stacomiR-package.R'
-LazyLoad: yes
-LazyData: true
-Depends:
- R (>= 4.0.0),
- methods,
- stacomirtools (>= 0.6.0)
-Imports:
- magrittr,
- intervals,
- RColorBrewer,
- stringr,
- RPostgres,
- ggplot2,
- reshape2,
- graphics,
- utils,
- stats,
- lattice,
- grDevices,
- Hmisc (>= 4.1-1),
- lubridate,
- dplyr,
- xtable,
- mgcv,
- rlang,
- pool,
- withr
-Suggests:
- testthat,
- viridis,
- knitr,
- rmarkdown
-Author: Cedric Briand [aut, cre],
- Marion Legrand [aut],
- Beaulaton Laurent [ctb],
- Boulenger Clarisse [ctb],
- Lafage Denis [ctb],
- Grall Sebastien [ctb]
-Maintainer: Cedric Briand <cedric.briand00 at gmail.com>
-RoxygenNote: 7.1.2
-NeedsCompilation: no
-VignetteBuilder: knitr
+Package: stacomiR
+Version: 0.6.0
+Date: 2021-11-16
+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"),
+ person("Beaulaton", "Laurent", role = "ctb", email = "laurent.beaulaton at ofb.gouv.fr"),
+ person("Boulenger", "Clarisse", role = "ctb", email = "Clarisse.Boulenger at ofb.gouv.fr"),
+ person("Lafage", "Denis", role = "ctb", email = "denis.lafage at logrami.fr"),
+ person("Grall", "Sebastien", role = "ctb", email = "seinormigr.grall at gmail.com"))
+Description: Graphical outputs and treatment for a database of fish pass
+ monitoring. It is a part of the 'STACOMI' open source project developed in
+ France by the French Office for Biodiversity institute to centralize
+ data obtained by fish pass monitoring. This version is available in French and
+ English. See <http://stacomir.r-forge.r-project.org/> for more information on
+ 'STACOMI'.
+License: GPL (>= 2)
+URL: http://stacomir.r-forge.r-project.org/
+BugReports: https://github.com/MarionLegrandLogrami/stacomiR/issues
+Collate:
+ 'create_generic.R'
+ 'data.R'
+ 'fun_table_per_dis.R'
+ 'fun_write_monthly.R'
+ 'fungraph.R'
+ 'fungraph_glasseel.R'
+ 'funstat.R'
+ 'funtable.R'
+ 'ref_choice.R'
+ 'ref_coe.R'
+ 'ref_dc.R'
+ 'ref_df.R'
+ 'ref_env.R'
+ 'ref_horodate.R'
+ 'ref_list.R'
+ 'ref_par.R'
+ 'ref_parqual.R'
+ 'ref_parquan.R'
+ 'ref_period.R'
+ 'ref_stage.R'
+ 'ref_taxa.R'
+ 'ref_textbox.R'
+ 'ref_timestep.R'
+ 'ref_timestep_daily.R'
+ 'ref_year.R'
+ 'report_annual.R'
+ 'report_dc.R'
+ 'report_df.R'
+ 'utilities.R'
+ 'report_env.R'
+ 'report_ge_weight.R'
+ 'report_ope.R'
+ 'report_mig.R'
+ 'report_sample_char.R'
+ 'report_mig_char.R'
+ 'report_mig_mult.R'
+ 'report_mig_env.R'
+ 'report_mig_interannual.R'
+ 'report_sea_age.R'
+ 'report_silver_eel.R'
+ 'report_species.R'
+ 'setAs.R'
+ 'stacomi.R'
+ 'stacomiR-package.R'
+LazyLoad: yes
+LazyData: true
+Depends:
+ R (>= 4.0.0),
+ methods,
+ stacomirtools (>= 0.6.0)
+Imports:
+ magrittr,
+ intervals,
+ RColorBrewer,
+ stringr,
+ RPostgres,
+ ggplot2,
+ reshape2,
+ graphics,
+ utils,
+ stats,
+ lattice,
+ grDevices,
+ Hmisc (>= 4.1-1),
+ lubridate,
+ dplyr,
+ xtable,
+ mgcv,
+ rlang,
+ pool,
+ withr
+Suggests:
+ testthat,
+ viridis,
+ knitr,
+ rmarkdown
+Author: Cedric Briand [aut, cre],
+ Marion Legrand [aut],
+ Beaulaton Laurent [ctb],
+ Boulenger Clarisse [ctb],
+ Lafage Denis [ctb],
+ Grall Sebastien [ctb]
+Maintainer: Cedric Briand <cedric.briand00 at gmail.com>
+RoxygenNote: 7.1.2
+NeedsCompilation: no
+VignetteBuilder: knitr
Deleted: pkg/stacomir/R/fun_dailystats.R
===================================================================
--- pkg/stacomir/R/fun_dailystats.R 2021-11-22 16:53:13 UTC (rev 612)
+++ pkg/stacomir/R/fun_dailystats.R 2021-11-22 19:14:28 UTC (rev 613)
@@ -1,47 +0,0 @@
-#' function to create daily statistics
-#' @param tableau A table
-#' @param time.sequence Time sequence from report_mig and report_mig_mult
-#' @param taxa A taxa
-#' @param stage A stage
-#' @param DC A counting device
-#' @author Cedric Briand \email{cedric.briand'at'eptb-vilaine.fr}
-#' @note to be used in shiny
-fun_dailystats = function(tableau, time.sequence, taxa, stage, DC) {
- mois = months(time.sequence)
- moislab = unique(mois)
- annee = unique(strftime(as.POSIXlt(time.sequence), "%Y"))
- somme = tapply(tableau$Effectif_total, mois, sum, na.rm = TRUE) # sums
- moyennes_journalieres = tapply(tableau$Effectif_total, mois, mean, na.rm = TRUE) # means
- ecarts_types = tapply(tableau$Effectif_total, mois, stats::sd, na.rm = TRUE) # std. deviations
- nombre = as.integer(tapply(tableau$Effectif_total, mois, function(x) sum(!is.na(x)))) # counts
- resum = rbind(nombre, somme, moyennes_journalieres, ecarts_types)
-
- if (taxa == "Anguilla anguilla" & stage == "civelle") {
- poids_depuis_effectif = tapply(tableau$poids_depuis_effectif, mois, sum,
- na.rm = TRUE)
- poids_mesure = tapply(tableau$Poids_total, mois, sum, na.rm = TRUE)
- Poids_total = poids_depuis_effectif + poids_mesure
- resum = rbind(nombre, somme, moyennes_journalieres, ecarts_types, poids_depuis_effectif,
- poids_mesure, Poids_total)
- }
-
- resum = resum[, moislab]
- resum = data.frame(resum)
- resum["somme", "report"] = round(sum(tableau$Effectif_total, na.rm = TRUE), 2)
- resum["moyennes_journalieres", "report"] = round(mean(tableau$Effectif_total,
- na.rm = TRUE), 2)
- resum["ecarts_types", "report"] = round(stats::sd(tableau$Effectif_total, na.rm = TRUE),
- 2)
- if (taxa == "Anguilla anguilla" & stage == "civelle") {
- resum["poids_depuis_effectif", "report"] = round(sum(tableau$poids_depuis_effectif,
- na.rm = TRUE), 2)
- resum["poids_mesure", "report"] = round(sum(tableau$Poids_total, na.rm = TRUE),
- 2)
- resum["Poids_total", "report"] = round(sum(Poids_total, na.rm = TRUE), 2)
- }
- resum = cbind(label = paste("DC", DC, taxa, stage, annee, sep = "_"), resum)
- funout(paste(DC, taxa, stage, annee, "\n"))
-
- print(resum["somme", ])
- return(resum)
-}
Deleted: pkg/stacomir/man/fun_dailystats.Rd
===================================================================
--- pkg/stacomir/man/fun_dailystats.Rd 2021-11-22 16:53:13 UTC (rev 612)
+++ pkg/stacomir/man/fun_dailystats.Rd 2021-11-22 19:14:28 UTC (rev 613)
@@ -1,28 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fun_dailystats.R
-\name{fun_dailystats}
-\alias{fun_dailystats}
-\title{function to create daily statistics}
-\usage{
-fun_dailystats(tableau, time.sequence, taxa, stage, DC)
-}
-\arguments{
-\item{tableau}{A table}
-
-\item{time.sequence}{Time sequence from report_mig and report_mig_mult}
-
-\item{taxa}{A taxa}
-
-\item{stage}{A stage}
-
-\item{DC}{A counting device}
-}
-\description{
-function to create daily statistics
-}
-\note{
-to be used in shiny
-}
-\author{
-Cedric Briand \email{cedric.briand'at'eptb-vilaine.fr}
-}
Deleted: pkg/stacomir/man/setref_horodate-ref_horodate-method.Rd
===================================================================
--- pkg/stacomir/man/setref_horodate-ref_horodate-method.Rd 2021-11-22 16:53:13 UTC (rev 612)
+++ pkg/stacomir/man/setref_horodate-ref_horodate-method.Rd 2021-11-22 19:14:28 UTC (rev 613)
@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ref_horodate.R
-\name{setref_horodate,ref_horodate-method}
-\alias{setref_horodate,ref_horodate-method}
-\title{Method to set the Horodate}
-\usage{
-\S4method{setref_horodate}{ref_horodate}(object, string)
-}
-\arguments{
-\item{object}{An object of class \link{ref_horodate-class}}
-
-\item{string}{A string representing an horodate in the format "\%Y-\%m-\%d \%H:\%M:\%S"}
-}
-\value{
-An Object of class "ref_horodate"
-}
-\description{
-Method to set the Horodate
-}
-\author{
-cedric.briand
-}
-\keyword{internal}
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