report_annual-class | 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
start_year
Object of class ref_year-class
. ref_year allows to choose year of beginning
end_year
Object of class ref_year-class
ref_year allows to choose last year of the report
Cedric Briand cedric.briand@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
# launching stacomi without database for demo stacomi(database_expected=FALSE) # the following piece of script will load the Arzal dataset and connected to iav postgres schema # it requires a working database # prompt for user and password but you can set appropriate options for host, port and dbname ## Not run: stacomi(database_expected=TRUE, sch='iav') if (interactive()){ if (!exists("user")){ user <- readline(prompt="Enter user: ") password <- readline(prompt="Enter password: ") } } options( stacomiR.dbname = "bd_contmig_nat", stacomiR.host ="localhost", stacomiR.port = "5432", stacomiR.user = user, stacomiR.user = password ) r_ann<-new("report_annual") r_ann<-choice_c(r_ann, dc=c(5,6,12), taxa=c("Anguilla anguilla"), stage=c("AGJ","AGG"), start_year="1996", end_year="2015", silent=FALSE) r_ann<-connect(r_ann) ## End(Not run) # 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_selected,collapse="+"),"_", paste(r_ann@taxa@taxa_selected,collapse="+"),"_", paste(r_ann@stage@stage_selected,collapse="+"),"_", r_ann@start_year@year_selected,":", r_ann@end_year@year_selected,".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_selected] 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)
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