report_annual-class {stacomiR} | R Documentation |
This class displays annual migration counts, for several counting device, taxa or stages.
dc
Object of class ref_dc-class
, the counting device, multiple values allowed
data
Object of class "data.frame"
data for report lot
taxa
An object of class ref_taxa-class
, multiple values allowed
stage
An object of class ref_stage-class
, multiple values allowed
anneedebut
Object of class ref_year-class
. ref_year allows to choose year of beginning
anneefin
Object of class ref_year-class
ref_year allows to choose last year of the report
Cedric Briand cedric.briand"at"eptb-vilaine.fr
Other report Objects: 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
,
report_species-class
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 baseODBC<-get("baseODBC",envir=envir_stacomi) baseODBC[c(2,3)]<-rep("iav",2) assign("baseODBC",baseODBC,envir_stacomi) sch<-rlang::env_get(envir_stacomi, "sch") assign("sch","iav.",envir_stacomi) r_ann<-new("report_annual") r_ann<-choice_c(r_ann, dc=c(5,6,12), taxa=c("Anguilla anguilla"), stage=c("AGJ","AGG"), anneedebut="1996", anneefin="2015", silent=FALSE) r_ann<-connect(r_ann) # the following dataset has been generated by the previous code data(r_ann) xtr_ann<-stacomiR::xtable(r_ann, dc_name=c("Passe bassins","Piege anguille RG","Piege anguille RD"), tax_name="Anguille", std_name=c("Arg.","Jaun.")) # below not run but one can create a file as following ## Not run: path=file.path(path.expand(get("datawd",envir=envir_stacomi)), paste(paste(r_ann@dc@dc_selectionne,collapse="+"),"_", paste(r_ann@taxa@data$tax_code,collapse="+"),"_", paste(r_ann@stage@data$std_code,collapse="+"),"_", r_ann@anneedebut@annee_selectionnee,":", r_ann@anneefin@annee_selectionnee,".html",sep=""),fsep ="/") # here you can add an argument file=path print(xtr_ann,type="html") # the following uses the "addtorow" argument which creates nice column headings, # format.args creates a thousand separator # again this will need to be saved in a file using the file argument print(xtr_ann, add.to.row=get("addtorow",envir_stacomi), include.rownames = TRUE, include.colnames = FALSE, format.args = list(big.mark = " ", decimal.mark = ",") ) # barplot transforms the data, further arguments can be passed as to barplot barplot(r_ann) barplot(r_ann, args.legend=list(x="topleft",bty = "n"), col=c("#CA003E","#1A9266","#E10168","#005327","#FF9194")) # An example with custom arguments for legend.text (overriding plot defauts) data(r_ann_adour) if (requireNamespace("RColorBrewer", quietly = TRUE)){ lesdc<-r_ann_adour@dc@data$dc_code[r_ann_adour@dc@data$dc%in%r_ann_adour@dc@dc_selectionne] barplot(r_ann_adour, legend.text=lesdc, args.legend=list(x="topleft",bty = "n"), col=RColorBrewer::brewer.pal(9,"Spectral"), beside=TRUE) } plot(r_ann_adour) ## End(Not run)