report_sea_age-class: Class "report_sea_age"

In stacomiR: Fish Migration Monitoring

Class "report_sea_age"

Description

the report_sea_age class is used to dispatch adult salmons to age class according to their size and to basin dependent limits set by the user. Once checked with graphs and summary statistics, the results are to be written to the database.

Slots

data

A data frame with data generated from the database

calcdata

A list of dc with processed data. This lists consists of two elements

• (1) data A dataset with age set to be used by the plot and summary methods

• (2) tj_caracteristitiquelot_car A dataset to import into the database

dc

Object of class ref_dc-class: the control devices

taxa

Object of class ref_taxa-class: the species

stage

Object of class ref_stage-class : the stages of the fish

par

Object of class ref_par-class: the parameters used

horodatedebut

An object of class ref_horodate-class

horodatefin

An object of class ref_horodate-class

limit1hm

The size limit, in mm between 1 sea winter fishes and 2 sea winter fishes

limit2hm

The size limit, in mm between 2 sea winter fishes and 3 sea winter fishes

Objects from the Class

Objects can be created by calls of the form new("report_sea_age", ...)

Note

This class is displayed by interface_report_sea_age

Author(s)

Cedric Briand [e-mail]

See Also

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_silver_eel-class, report_species-class

Examples

require(stacomiR)
stacomi(
	database_expected=FALSE)
# If you have a working database
# the following line of code will create the r_seaa dataset 
# from the logrami schema in the database
## Not run: 
		stacomi(database_expected=TRUE, sch='logrami')	
		# overrides the default option sch = 'iav'
		# prompt for user and password, you can set these in the options,
	  # including dbname and host
		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						
		)	
  #create an instance of the class
  r_seaa<-new("report_sea_age")
  r_seaa<-choice_c(r_seaa,
	  dc=c(107,108,101),			
	  horodatedebut="2012-01-01",
	  horodatefin="2012-12-31",
	  limit1hm=675,
	  limit2hm=875,
	  silent=FALSE
  )
  r_seaa<-connect(r_seaa)
  r_seaa<-calcule(r_seaa)
  

## End(Not run)	
# load the dataset generated by previous lines
# Salmons from the loire on two dams
data("r_seaa")
# the calculation will fill the slot calcdata

# stages are in r_seaa@calcdata[["6"]][,"stage"] 
#look at data structure using str(r_seaa@calcdata[["6"]])

# plot data to confirm the split by limits is correct
plot(r_seaa, plot.type=1)

# if there are several dc, data it split by dc
plot(r_seaa, plot.type=2)
## Not run: 
# print a summary statistic, and save the output in a list for later use
  stats<-summary(r_seaa)
  
  
  write_database(r_seaa)

## End(Not run)

stacomiR documentation built on May 29, 2024, 10:41 a.m.