stacomiR (version 0.6.1)

report_mig_env-class: Class "report_mig_env"

Description

Enables to compute an annual overview of fish migration and environmental conditions in the same chart. Environmental conditions may trigger migration events, variation in flow or temperatures can be plotted along migration to check graphically for a possible relation. To enable this, environmental conditions are loaded from an "environmental monitoring station", which records environmental parameters and is attached to a migratory station in the database. This class enables both continuous output (temperature -flow) as well as discrete parameters (qualitative = moon phase, type of operation of a gate, opening of a gate...) which will be displayed on the graph. Values are scaled so that single plot can display migration numbers and environmental parameters. Environmental parameters when stored at a time scale lower that a day are averaged per day, unless they are qualitative parameters, in which case only the first event of the day is displayed on the annual plot.

Slots

report_mig_mult

report_mig_mult-class

report_env

report_env-class

Author

[e-mail] [e-mail]

Cedric Briand

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_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

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_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

Examples

require(stacomiR)
stacomi(
	database_expected=FALSE)
# the following will load the data provided the user has access to the database
# with data in the iav example scheme.
# prompt for user and password but you can set appropriate options for host, port and dbname
if (FALSE) {
	stacomi(
			database_expected=TRUE)	
	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_mig_env<-new("report_mig_env")
  r_mig_env<-choice_c(r_mig_env,
	  dc=c(5,6,12),
	  taxa=c("Anguilla anguilla"),
	  stage=c("AGJ","AGG","CIV"),
	  stationMesure=c("temp_gabion","coef_maree","phases_lune"),
	  datedebut="2008-01-01",
	  datefin="2008-12-31",
	  silent=FALSE)	
  r_mig_env<-charge(r_mig_env) # this is necessary to load operations, DF and DC
  r_mig_env<-connect(r_mig_env)
  r_mig_env<-calcule(r_mig_env,silent=TRUE)
}	

data("r_mig_env")
# An example of plot with custom colors.
plot(r_mig_env,
	color_station=c("temp_gabion"="red","coef_maree"="blue","phases_lune"="pink"),
 	color_dc=c("5"="yellow","6"="orange","12"="purple")
)