# NOT RUN {
require(stacomiR)
# launching stacomi without selecting the scheme or interface
stacomi(gr_interface=FALSE,
login_window=FALSE,
database_expected=FALSE)
# the following script will load the Arzal dataset
#if connected to iav schema
# }
# NOT RUN {
#create an instance of the class
r_sample_char<-new("report_sample_char")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
r_sample_char<-choice_c(r_sample_char,
dc=c(5,6),
taxa=c("Anguilla anguilla"),
stage=c("AGJ","CIV"),
par=c(1785,1786,1787,"C001"),
horodatedebut="2013-01-01",
horodatefin="2013-12-31",
silent=FALSE)
# two warning produced, ignored if silent=TRUE
r_sample_char<-connect(r_sample_char)
r_sample_char<-calcule(r_sample_char,silent=TRUE)
# }
# NOT RUN {
# load the dataset generated by previous lines
data("r_sample_char")
# A "violin" plot
plot(r_sample_char,plot.type="1",silent=TRUE)
# get the plot from envir_stacomi to change labels for name
# if you use require(ggplot2) the :: argument is not needed
# e.g. write require(ggplot2);g<-get("g",envir=envir_stacomi)
# g+xlab("size")+ylab("year")
if (requireNamespace("ggplot2", quietly = TRUE)){
g<-get("g",envir=envir_stacomi)
g+ggplot2::xlab("size")+ggplot2::ylab("year")
}
# A boxplot per month
plot(r_sample_char,plot.type="2",silent=TRUE)
# A xyplot
plot(r_sample_char,plot.type="3",silent=TRUE)
# }
# NOT RUN {
#####################################
# an example graph created manually from data
#####################################
# two variables one on DC, one on stage
# passing dc information to the stage variable
r_sample_char@data$std_libelle[r_sample_char@data$ope_dic_identifiant==5]<-
"Yellow eel (vert. slot fishway)"
r_sample_char@data$std_libelle[r_sample_char@data$std_libelle=="Anguille jaune"]<-
"Yellow eel (ramp)"
r_sample_char@data$std_libelle[r_sample_char@data$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
if (requireNamespace("ggplot2", quietly = TRUE)){
g<-ggplot2::ggplot(r_sample_char@data)+
ggplot2::geom_boxplot(ggplot2::aes(x=annee,
y =car_valeur_quantitatif,
fill = std_libelle))+
ggplot2::xlab("size")+ggplot2::ylab("year")+
ggplot2::scale_fill_manual("stage & fishway",
values=c("Yellow eel (vert. slot fishway)"="blue",
"Yellow eel (ramp)"="turquoise3",
"Glass eel (ramp)"="Cyan"))+
ggplot2::theme_bw()
print(g)
}
# get a simple summary using Hmisc::describe
summary(r_sample_char)
# get the command line to create the object using choice_c
# when the graphical interface has been used
print(r_sample_char)
# }
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