report_species-class {stacomiR} | R Documentation |
This class is used to make the assessment of all species, and their number. It is intended as a simple way to check what fishes are present (taxa + development stage). Unlike the report_annual, it is not restricted to chosen taxa or stages but gives counts for all species present. The taxa is reported unless a taxa has several case, in which case the different stages for the taxa will be reported Using the split arguments the calc method of the class will count numbers, subsamples are not accounted for in the Overview. The split argument currently takes values year or month. The class is intended to be used over long periods e.g years. The plot method writes either an histogram or a pie chart of number per year/week/month.
dc
an object of class ref_dc-class
anneedebut
Object of class ref_year-class
anneefin
Object of class ref_year-class
data
data.frame
calcdata
data.frame
with data processed by the calc method
split
Object of class ref_list-class
ref_list referential class choose within a list
Cedric Briand cedric.briand"at"eptb-vilaine.fr
Other report Objects: report_annual-class
,
report_dc-class
,
report_df-class
,
report_env-class
,
report_ge_weight-class
,
report_mig-class
,
report_mig_char-class
,
report_mig_env-class
,
report_mig_interannual-class
,
report_mig_mult-class
,
report_sample_char-class
,
report_sea_age-class
,
report_silver_eel-class
require(stacomiR) stacomi(gr_interface=FALSE, login_window=FALSE, database_expected=FALSE) ## Not run: bilesp<-new("report_species") # split is one of "none", "year", "week", "month bilesp<-choice_c(bilesp, dc=c(5,6,12), split="year", anneedebut="2008", anneefin="2012", silent=FALSE) #bilesp<-charge(bilesp) this is used by the graphical interface bilesp<-connect(bilesp) bilesp<-calcule(bilesp) plot(bilesp,plot.type="pie",silent=FALSE) plot(bilesp,plot.type="barplot",silent=FALSE) bilesp<-choice_c(bilesp, dc=c(5,6,12), split="month", anneedebut="2015", anneefin="2016", silent=FALSE) bilesp<-charge(bilesp) bilesp<-connect(bilesp) plot(bilesp,plot.type="pie",silent=FALSE) plot(bilesp,plot.type="barplot",silent=FALSE) #length(unique(bilesp@calcdata$taxa_stage)) # 15 # here creating a vector of length 15 with nice blending colours color<-c(mycolorrampblue(5), mycolorrampyellow(5), mycolorrampred(5)) plot(bilesp,plot.type="barplot",color=color,silent=TRUE) summary(bilesp) ## End(Not run)