[Stacomir-commits] r234 - in pkg/stacomir: inst/config inst/examples man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 16 10:07:59 CET 2016
Author: briand
Date: 2016-11-16 10:07:59 +0100 (Wed, 16 Nov 2016)
New Revision: 234
Modified:
pkg/stacomir/inst/config/generate_Roxygen2.R
pkg/stacomir/inst/examples/bilancarlot_example.R
pkg/stacomir/man/BilanArgentee-class.Rd
pkg/stacomir/man/Bilan_carlot-class.Rd
pkg/stacomir/man/bilanArg.Rd
pkg/stacomir/man/envir_stacomi.Rd
pkg/stacomir/man/msg.Rd
pkg/stacomir/man/plot-BilanArgentee-missing-method.Rd
pkg/stacomir/man/plot-Bilan_carlot-missing-method.Rd
Log:
Modified: pkg/stacomir/inst/config/generate_Roxygen2.R
===================================================================
--- pkg/stacomir/inst/config/generate_Roxygen2.R 2016-11-15 18:17:55 UTC (rev 233)
+++ pkg/stacomir/inst/config/generate_Roxygen2.R 2016-11-16 09:07:59 UTC (rev 234)
@@ -2,33 +2,35 @@
install.packages("roxygen2")
install.packages("Rd2roxygen") # reverse documentation
-####################"
-# reversing documentation
-######################"
-require(Rd2roxygen)
-setwd("F:/workspace/stacomir/branch0.5/")
-Rd2roxygen(pkg="stacomir")
-#########"
-# pour les classes S4
-##########
-files<-list.files("F:/workspace/stacomir/branch0.5/stacomir/man")
-files<-files[grep("class",files)]
-for (i in 1:length(files)){
-parse_and_save(stringr::str_c("F:/workspace/stacomir/branch0.5/stacomir/man/",files[i]),
- gsub(".rd","",stringr::str_c("F:/temp/",files[i])))
-}
-#########################""
-# Building documentation
-######################
-#use either :
-require(devtools)
-document("F:/workspace/stacomir/branch0.5/stacomir")
-# or :
-#vignette("roxygen2")
-setwd("F:/workspace/stacomir/pkg/stacomir")
-data("bMM_Arzal")
-data("bM_Arzal")
-data("msg")
-envir_stacomi <- new.env(parent = emptyenv())
+#####################"
+## reversing documentation
+#######################"
+#require(Rd2roxygen)
+#setwd("F:/workspace/stacomir/branch0.5/")
+#Rd2roxygen(pkg="stacomir")
+##########"
+## pour les classes S4
+###########
+#files<-list.files("F:/workspace/stacomir/branch0.5/stacomir/man")
+#files<-files[grep("class",files)]
+#for (i in 1:length(files)){
+#parse_and_save(stringr::str_c("F:/workspace/stacomir/branch0.5/stacomir/man/",files[i]),
+# gsub(".rd","",stringr::str_c("F:/temp/",files[i])))
+#}
+##########################""
+## Building documentation
+#######################
+##use either :
+#require(devtools)
+#document("F:/workspace/stacomir/branch0.5/stacomir")
+## or :
+##vignette("roxygen2")
+#setwd("F:/workspace/stacomir/pkg/stacomir")
+#data("bMM_Arzal")
+#data("bM_Arzal")
+#data("msg")
+#envir_stacomi <- new.env(parent = emptyenv())
+#
+
require(roxygen2)
roxygen2::roxygenise("F:/workspace/stacomir/pkg/stacomir");warnings()[1:10]
\ No newline at end of file
Modified: pkg/stacomir/inst/examples/bilancarlot_example.R
===================================================================
--- pkg/stacomir/inst/examples/bilancarlot_example.R 2016-11-15 18:17:55 UTC (rev 233)
+++ pkg/stacomir/inst/examples/bilancarlot_example.R 2016-11-16 09:07:59 UTC (rev 234)
@@ -50,6 +50,7 @@
b_carlot at data$std_libelle[b_carlot at data$std_libelle=="civelle"]<-"Glass eel (ramp)"
# creating a boxplot with custom output : an example
# again if you use require(ggplot2) the :: argument is not needed
+\dontrun{
if (requireNamespace("ggplot2", quietly = TRUE)){
g<-ggplot2::ggplot(b_carlot at data)+
ggplot2::geom_boxplot(ggplot2::aes(x=annee,
@@ -63,6 +64,7 @@
ggplot2::theme_bw()
print(g)
}
+}
# get a simple summary using Hmisc::describe
summary(b_carlot)
# get the command line to create the object using choice_c
Modified: pkg/stacomir/man/BilanArgentee-class.Rd
===================================================================
--- pkg/stacomir/man/BilanArgentee-class.Rd 2016-11-15 18:17:55 UTC (rev 233)
+++ pkg/stacomir/man/BilanArgentee-class.Rd 2016-11-16 09:07:59 UTC (rev 234)
@@ -12,11 +12,15 @@
\describe{
\item{\code{data}}{A data frame with data generated from the database}
-\item{\code{calcdata}}{A list of dc with processed data. Each dc contains three elements,
-"quant" A matrix with quantitative data, one column per quantitative parm and one line per sample,
-"qual" a matrix with qualitative parameters with one column per qualitative parm and one line per sample, this matrix also contains calculated durif stages, "other"
-A data frame with columns lot_identifiant,ope_identifiant,ope_dic_identifiant,ope_date_debut,ope_date_fin,dev_code (destination code of fish),
-dev_libelle (text for destination of fish) containing data pertaining to the sample and the control operation.}
+\item{\code{calcdata}}{A list of dc with processed data. Each dc contains a data frame with
+\itemize{
+\item (1) qualitative data on body contrast (CONT), presence of punctuation on the lateral line (LINP)
+\item (2) quantitative data "BL" Body length,"W" weight,"Dv" vertical eye diameter,"Dh" horizontal eye diameter,"FL" pectoral fin length
+\item (3) calculated durif stages, Pankhurst's index
+\item (4) other columns containing data pertaining to the sample and the control operation: lot_identifiant,ope_identifiant,
+ope_dic_identifiant,ope_date_debut,ope_date_fin,dev_code (destination code of fish),
+dev_libelle (text for destination of fish)
+}}
\item{\code{dc}}{Object of class \link{RefDC-class}: the control devices}
@@ -90,6 +94,7 @@
b_carlot at data$std_libelle[b_carlot at data$std_libelle=="civelle"]<-"Glass eel (ramp)"
# creating a boxplot with custom output : an example
# again if you use require(ggplot2) the :: argument is not needed
+\dontrun{
if (requireNamespace("ggplot2", quietly = TRUE)){
g<-ggplot2::ggplot(b_carlot at data)+
ggplot2::geom_boxplot(ggplot2::aes(x=annee,
@@ -103,6 +108,7 @@
ggplot2::theme_bw()
print(g)
}
+}
# get a simple summary using Hmisc::describe
summary(b_carlot)
# get the command line to create the object using choice_c
Modified: pkg/stacomir/man/Bilan_carlot-class.Rd
===================================================================
--- pkg/stacomir/man/Bilan_carlot-class.Rd 2016-11-15 18:17:55 UTC (rev 233)
+++ pkg/stacomir/man/Bilan_carlot-class.Rd 2016-11-16 09:07:59 UTC (rev 234)
@@ -86,6 +86,7 @@
b_carlot at data$std_libelle[b_carlot at data$std_libelle=="civelle"]<-"Glass eel (ramp)"
# creating a boxplot with custom output : an example
# again if you use require(ggplot2) the :: argument is not needed
+\dontrun{
if (requireNamespace("ggplot2", quietly = TRUE)){
g<-ggplot2::ggplot(b_carlot at data)+
ggplot2::geom_boxplot(ggplot2::aes(x=annee,
@@ -99,6 +100,7 @@
ggplot2::theme_bw()
print(g)
}
+}
# get a simple summary using Hmisc::describe
summary(b_carlot)
# get the command line to create the object using choice_c
Modified: pkg/stacomir/man/bilanArg.Rd
===================================================================
--- pkg/stacomir/man/bilanArg.Rd 2016-11-15 18:17:55 UTC (rev 233)
+++ pkg/stacomir/man/bilanArg.Rd 2016-11-16 09:07:59 UTC (rev 234)
@@ -9,8 +9,8 @@
bilanArg
}
\description{
-The dataset corresponds to the silver eel traps ("anguillères) for 2015-2016.
-This dataset has been kindly provided by the Fédération de Pêche de la Somme,
+The dataset corresponds to the silver eel traps ("anguilleres) for 2015-2016.
+This dataset has been kindly provided by the Federation de Peche de la Somme,
given the upstream location of the trap, all individuals are female
}
\keyword{data}
Modified: pkg/stacomir/man/envir_stacomi.Rd
===================================================================
--- pkg/stacomir/man/envir_stacomi.Rd 2016-11-15 18:17:55 UTC (rev 233)
+++ pkg/stacomir/man/envir_stacomi.Rd 2016-11-16 09:07:59 UTC (rev 234)
@@ -5,7 +5,7 @@
\alias{envir_stacomi}
\title{Environment where most objects from the package are stored and then loaded
by the charge method}
-\format{An object of class \code{environment} of length 0.}
+\format{An object of class \code{environment} of length 11.}
\usage{
envir_stacomi
Modified: pkg/stacomir/man/msg.Rd
===================================================================
--- pkg/stacomir/man/msg.Rd 2016-11-15 18:17:55 UTC (rev 233)
+++ pkg/stacomir/man/msg.Rd 2016-11-16 09:07:59 UTC (rev 234)
@@ -4,7 +4,7 @@
\name{msg}
\alias{msg}
\title{Messages}
-\format{An object of class \code{list} of length 352.}
+\format{An object of class \code{list} of length 353.}
\usage{
msg
}
Modified: pkg/stacomir/man/plot-BilanArgentee-missing-method.Rd
===================================================================
--- pkg/stacomir/man/plot-BilanArgentee-missing-method.Rd 2016-11-15 18:17:55 UTC (rev 233)
+++ pkg/stacomir/man/plot-BilanArgentee-missing-method.Rd 2016-11-16 09:07:59 UTC (rev 234)
@@ -6,7 +6,7 @@
\alias{plot.BilanArgentee}
\alias{plot.b_carlot}
\alias{plot.bilanArg}
-\title{Plots of various type for BilanMigration, and performs writing to the database of daily values.}
+\title{Plots of various type for BilanArgentee}
\usage{
\S4method{plot}{BilanArgentee,missing}(x, plot.type = "1", silent = FALSE)
}
Modified: pkg/stacomir/man/plot-Bilan_carlot-missing-method.Rd
===================================================================
--- pkg/stacomir/man/plot-Bilan_carlot-missing-method.Rd 2016-11-15 18:17:55 UTC (rev 233)
+++ pkg/stacomir/man/plot-Bilan_carlot-missing-method.Rd 2016-11-16 09:07:59 UTC (rev 234)
@@ -11,7 +11,7 @@
\S4method{plot}{Bilan_carlot,missing}(x, plot.type = "1", silent = FALSE)
}
\arguments{
-\item{x}{An object of class BilanMigrationMult}
+\item{x}{An object of class Bilan_carlot}
\item{plot.type}{One of "1","violin plot". Defaut to \code{1} , can also be \code{2} boxplot or
\code{3} points.}
@@ -21,18 +21,8 @@
\item{...}{Additional arguments, see \code{plot}, \code{plot.default} and \code{par}}
}
\description{
-\itemize{
- \item{plot.type="standard"}{calls \code{\link{fungraph}} and \code{\link{fungraph_civelle}} functions to plot as many "bilanmigration"
- as needed, the function will test for the existence of data for one dc, one taxa, and one stage}
- \item{plot.type="step"}{creates Cumulated graphs for BilanMigrationMult. Data are summed per day for different dc taxa and stages}
- \item{plot.type="multiple"}{Method to overlay graphs for BilanMigrationMult (multiple dc/taxa/stage in the same plot)}
+Plots of various type for BilanMigration, and performs writing to the database of daily values.
}
-}
-\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. 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}
}
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