Package 'stacomiR'

barplot method for object report_annual-class

Description

barplot method for object report_annual-class

Usage

## S4 method for signature 'report_annual'
barplot(height, legend.text = NULL, ...)

Arguments

Value

No return value, called for side effects

Author(s)

Cedric Briand [email protected]

See Also

report_annual-class for examples

Description

Generic method for calculations

Usage

calcule(object, ...)

Arguments

Author(s)

cedric.briand

Description

Calcule method for report_ge_weight

Usage

## S4 method for signature 'report_ge_weight'
calcule(object, silent = FALSE)

Arguments

Value

An object of class report_ge_weight-class with @calcdata[["data"]] (essentially a selection of columns and renaming from @data) and coe daily coefficients extracted from the database @calcdata[["coe"]] and prepared for graphs

Author(s)

Cedric Briand [email protected]

Description

Merges the content of the list elements 'parqual' and 'parquan' in the data slot, and creates a single dataframe with one line per qualitative and quantitative pair. This methods allow to cross one quantity (e.g. length) with a qualitative parameter (e.g. sex).

Usage

## S4 method for signature 'report_mig_char'
calcule(object, silent = FALSE)

Arguments

Value

An object of class report_mig_char-class with slot @calcdata filled

Calculations for migration in the class report_mig_env-class

Description

Runs the calcule method in report_mig_mult-class

Usage

## S4 method for signature 'report_mig_env'
calcule(object, silent = FALSE)

Arguments

Value

report_mig_env-class with data in slot r_mig_env@report_mig_mult@calcdata

Description

Performs the calculation of seasonal coefficients for the plot(plot.type="seasonal") method. The numbers are split according to the period chosen, one of "day","week","month","2 weeks", French labels are also accepted as arguments. Once this is done, the seasonality of the migration is displayed using the day when the first fish was seen, then the days (or period) corresponding to 5, 50 , 95, and 100 percent of the migration. The duration of 90

Usage

## S4 method for signature 'report_mig_interannual'
calcule(object, silent = FALSE, timesplit = "mois")

Arguments

Value

An object of class report_mig_interannual-class with calcdata slot filled.

Note

The class report_mig_interannual does not handle escapement rates nor 'devenir' i.e. the destination of the fishes.

Author(s)

Marion Legrand

Description

The calculation must be launched once data are filled by the connect method. Currently the negative argument has no effect.

Usage

## S4 method for signature 'report_mig_mult'
calcule(object, negative = FALSE, silent = FALSE)

Arguments

Value

report_mig_mult with a list in slot calcdata. For each dc one will find a list with the following elements

method

In the case of instantaneous periods (video counting) the sum of daily values is done by the fun_report_mig_mult method and the value indicated in method is 'sum'. If any migration monitoring period is longer than a day, then the migration is split using the fun_report_mig_mult_overlaps function and the value indicated in the method is 'overlaps' as the latter method uses the overlap package to split migration period.

data

the calculated data. If weight are present, the columns display weight or numbers, the total number is 'Effectif_total' and corresponds to the addition of numbers and numbers converted from weight, the total weight is 'Poids_total'+'poids_depuis_effectifs' and corresponds to weighed glass eel plus glass eel number converted in weights. CALCULE corresponds to calulated number, MESURE to measured numbers, EXPERT to punctual expertise of migration (for instance measured in other path, or known migration of fishes passing the dam but not actually counted, PONCTUEL to fishes counted by visual identification but not by the counting apparatus (in case of technical problem for instance)

contient_poids

A boolean which indicates, in the case of glass eel, that the function fun_weight_conversion has been run to convert the weights to numbers using the weight to number coefficients in the database (see report_ge_weight).

negative

A parameter indicating if negative migration (downstream in the case of upstream migration devices) have been converted to positive numbers, not developed yet

Note

The class does not handle escapement rates, though structurally those are present in the database. If you want to use those you will have to do the calculation manually from the data in report_mig_mult@data.

Description

The calculation must be launched once data are filled by the connect method. Currently the negative argument has no effect.

Usage

## S4 method for signature 'report_mig'
calcule(object, negative = FALSE, silent = FALSE)

Arguments

Value

report_mig with calcdata slot filled. It is a list with one element per counting device containing

method

In the case of instantaneous periods (video counting) the sum of daily values is done by the fun_report_mig_mult method and the value indicated in method is "sum". If any migration monitoring period is longer than a day, then the migration is split using the fun_report_mig_mult_overlaps function and the value indicated in the method is "overlaps" as the latter method uses the overlap package to split migration period.

data

the calculated data.

contient_poids

A boolean which indicates, in the case of glass eel, that the function fun_weight_conversion has been run to convert the weights to numbers using the weight to number coefficients in the database (see report_ge_weight).

negative

A parameter indicating if negative migration (downstream in the case of upstream migration devices) have been converted to positive numbers, not developed yet

Note

The class report_mig does not handle escapement rates nor 'devenir' i.e. the destination of the fishes.

Description

In that class, most treatments are done in the query, this method checks that data are available and fills information for year, month, two weeks, week, doy

Usage

## S4 method for signature 'report_sample_char'
calcule(object, silent = FALSE)

Arguments

Value

An object of class report_sample_char-class with slot @data filled

Author(s)

Cedric Briand [email protected]

Split data according to the limits set in the limit1hm, and limit2hm arguments of the report_sea_age-class.

Description

If no value are provided in the limit1hm slot, an error is returned, if no value is provided in the limit2hm slot a default upper value for salmon size is taken to ensure all salmon are either of age 1 or 2, but no age 3 are returned

Usage

## S4 method for signature 'report_sea_age'
calcule(object, silent)

Arguments

Value

An object of class report_sea_age-class with calculated data in slot calcdata

Author(s)

Cedric Briand [email protected]

Description

This calcule method for report_silver_eel, will transform data from long (one line per size characteristic, size, weight, eye diameter, pectoral fin measurement, lateral line and constrast) to wide format (one line per silver eel). It will also calculate Durif silvering index and Pankhurst and Fulton's K.

Usage

## S4 method for signature 'report_silver_eel'
calcule(object, silent)

Arguments

Value

An object of class report_silver_eel-class with slot calcdata filled, as a list for each counting device

Author(s)

Cedric Briand [email protected]

Description

The number will be split according to the split argument passed to the class, e.g. per year or month or week. Data from different DC will be grouped. Counts are given per taxa, unless there are several stages, in which case the counts correspond to taxa + stage.

Usage

## S4 method for signature 'report_species'
calcule(object, silent = FALSE)

Arguments

Value

An object of class report_species-class with calcdata slot filled.

Description

Generic method to load referentials

Usage

charge(object, ...)

Arguments

Author(s)

cedric.briand

Description

Generic method to load additional data

Usage

charge_complement(object, ...)

Arguments

Author(s)

cedric.briand

Description

Loads an additional dataset this method is loaded to obtain the possible values of a qualitative parameter. Here data only contains one line

Usage

## S4 method for signature 'ref_parqual'
charge_complement(object)

Arguments

Value

An S4 object of class ref_parqual-class with the valqual slot filled

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 dc_selected=6
taxa_selected=2038
 stage_selected='AGJ'
 object=new('ref_parqual')
 object<-charge(object)
 charge_complement(object)

## End(Not run)

Description

Loading method for ref_par referential objects searching only those parameters existing for a DC, a Taxa, and a stage

Usage

## S4 method for signature 'ref_par'
charge_with_filter(object, dc_selected, taxa_selected, stage_selected)

Arguments

Value

An S4 object of class ref_par-class

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 object=new('ref_par')
charge_with_filter(object,dc_selected=6,taxa_selected=2038,stage_selected=c('AGJ','CIV'))

## End(Not run)

Description

Loading method for Reparqual referential objects searching only those parameters existing for a DC, a Taxon, and a stage

Usage

## S4 method for signature 'ref_parqual'
charge_with_filter(object, dc_selected, taxa_selected, stage_selected)

Arguments

Value

An S4 object of class ref_parqual-class

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 dc_selected=6
 taxa_selected=2038
 stage_selected='AGJ'
 object=new('ref_parqual')
 charge_with_filter(object,dc_selected,taxa_selected,stage_selected)

## End(Not run)

Description

Loading method for Reparquan referential objects searching only those parameters existing for a DC (counting device), a Taxon, and a stage

Usage

## S4 method for signature 'ref_parquan'
charge_with_filter(object, dc_selected, taxa_selected, stage_selected)

Arguments

Value

An S4 object of class ref_parquan-class with data loaded showing available parameters for one DC

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 dc_selected=6
taxa_selected=2038
 stage_selected='AGJ'
 object=new('ref_parquan')
 charge_with_filter(object,dc_selected,taxa_selected,stage_selected)

## End(Not run)

Description

Loading method for ref_stage referential objects searching only those stages existing for a DC and a Taxon

Usage

## S4 method for signature 'ref_stage'
charge_with_filter(object, dc_selected, taxa_selected)

Arguments

Value

An S4 object of class ref_stage-class listing all stages available for one DC and one taxon

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 dc_selected=6
taxa_selected=2038
 object=new('ref_stage')
 charge_with_filter(object,dc_selected,taxa_selected)

## End(Not run)

Description

Loading method for ref_taxa referential objects searching only taxa existing for a DC

Usage

## S4 method for signature 'ref_taxa'
charge_with_filter(object, dc_selected)

Arguments

Value

An S4 object of class ref_taxa-class with all taxa present on a DC (counting device)

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 dc_selected=6
 object=new('ref_taxa')
 charge_with_filter(object,dc_selected=dc_selected)
## End(Not run)

Description

Loading method for Refchoice referential objects

Usage

## S4 method for signature 'ref_choice'
charge(object, vecteur, label, selected)

Arguments

Value

An S4 object of class ref_choice-class

Author(s)

Cedric Briand [email protected]

See Also

Other referential objects: ref_choice-class, ref_coe-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Examples

## Not run: 
object=new('ref_choice')
charge(object,vecteur=c('oui','non'),label='essai',selected=as.integer(1))

## End(Not run)

Description

The slots datedebut and datefin have to be filled before using charge

Usage

## S4 method for signature 'ref_coe'
charge(object)

Arguments

Value

An object of class ref_coe-class

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
object<- new('ref_coe')
object@datedebut<-strptime('01/01/1996',format='%d/%m/%Y')
object@datefin<-strptime('01/01/1997',format='%d/%m/%Y')
charge(object) 

## End(Not run)

Description

Method to load the counting devices of the control station

Usage

## S4 method for signature 'ref_dc'
charge(object)

Arguments

Value

an object of class ref_dc with data loaded

Author(s)

Cedric Briand [email protected]

Description

Loading method for DF referential objects

Usage

## S4 method for signature 'ref_df'
charge(object)

Arguments

Value

An object of class ref_df with df loaded

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 object=new('ref_df')
charge(object)

## End(Not run)

Description

Loading method for ref_env referential object

Usage

## S4 method for signature 'ref_env'
charge(object)

Arguments

Value

An S4 object of class ref_env with data loaded from the database

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 object=new('ref_env')
 charge(object)

## End(Not run)

Description

Loading method for ref_list referential objects

Usage

## S4 method for signature 'ref_list'
charge(object, listechoice, label)

Arguments

Value

An S4 object of class ref_list-class

An S4 object of class ref_list-class

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 object=new('ref_list')
charge(object)

## End(Not run)

Description

Loading method for ref_par referential objects

Usage

## S4 method for signature 'ref_par'
charge(object)

Arguments

Value

An S4 object of class ref_par

An S4 object of class ref_par-class

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 object=new('ref_par')
charge(object)

## End(Not run)

Description

Loading method for Reparqual referential objects

Usage

## S4 method for signature 'ref_parqual'
charge(object)

Arguments

Value

An S4 object of class ref_parqual

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 object=new('ref_parqual')
 charge(object)

## End(Not run)

Description

Loading method for Reparquan referential objects

Usage

## S4 method for signature 'ref_parquan'
charge(object)

Arguments

Value

An S4 object of class ref_parquan-class with data loaded

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 object=new('ref_parquan')
 charge(object)

## End(Not run)

Description

Loading method for ref_stage referential objects

Usage

## S4 method for signature 'ref_stage'
charge(object)

Arguments

Value

An S4 object of class ref_stage-class with all stages available in the database

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 object=new('ref_stage')
 charge(object)

## End(Not run)

Description

Loading method for ref_taxa referential objects

Usage

## S4 method for signature 'ref_taxa'
charge(object)

Arguments

Value

An S4 object of class ref_taxa

An S4 object of class ref_taxa-class with all taxa loaded from the database

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 object=new('ref_taxa')
 charge(object)
## End(Not run)

Description

Loading method for ref_textbox referential objects

Usage

## S4 method for signature 'ref_textbox'
charge(object, title, label)

Arguments

Value

An S4 object of class ref_textbox-class

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 object=new('ref_textbox')
charge(object,title='un titre',label='20')

## End(Not run)

Description

Selects year available either in the bjo table if report_object==report_mig_interannual) or in the t_operation_ope table

Usage

## S4 method for signature 'ref_year'
charge(object, objectreport = "report_ge_weight")

Arguments

Value

object An object of class ref_year-class with slot data filled with the available years for the corresponding report

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
object=new("ref_year")
charge(object)
 validObject(annee)
showMethods("charge")

## End(Not run)

Description

#' Unique the other report classes where the charge method is only used by the graphical interface to collect and test objects in the environment envir_stacomi, and see if the right choices have been made in the graphical interface, this methods runs the charge,report_mig_mult-method and needs to be called from the command line (see examples)

Usage

## S4 method for signature 'report_mig_env'
charge(object, silent = FALSE)

Arguments

Value

An object of class report_mig_env-class with data set from values assigned in envir_stacomi environment

Author(s)

Cedric Briand [email protected]

Description

For the report_mig_mult class the charge method must be run to load data on migration control operations fishway operations, and counting devices operations as data from those are displayed in the main plots. For other classes the charge method is only used by the graphical interface (shiny)

Usage

## S4 method for signature 'report_mig_mult'
charge(object, silent = FALSE)

Arguments

Value

An object of class report_mig_mult-class with slots filled from values assigned in envir_stacomi environment

Author(s)

Cedric Briand [email protected]

Description

this method creates additional classes in envir_stacomi for later use in plot (operations, DF operation, DC operation). So unlike in most report classes where the charge method is only used by the graphical interface, it is necessary to run charge for report_mig.

Usage

## S4 method for signature 'report_mig'
charge(object, silent = FALSE)

Arguments

Value

An object of class report_mig-class with slots filled from values assigned in envir_stacomi environment

Author(s)

Cedric Briand [email protected]

Description

Choice_c method for ref_choice referential objects

Usage

## S4 method for signature 'ref_choice'
choice_c(object, selectedvalue)

Arguments

Value

An S4 object of class ref_choice-class

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
object=new('ref_list')
object<-charge(object,vecteur=c('1','2'),label='please choose')
object<-choice_c(object)

## End(Not run)

Description

the choice_c method is intended to have the same behaviour as choice (which creates a widget in the graphical interface) but from the command line. The parameters for dc are transformed to integer as the ref_dc only takes integer in the dc slots. The method also loads the stations and ouvrages (dams) associated with the counting device (dc). The values passed to the choice_c method are then checked with the setValidty method. Finally, if an objectreport is passed as a parameter, the method will do a charge_with_filter to select only the taxa present in the counting devices

Usage

## S4 method for signature 'ref_dc'
choice_c(object, dc)

Arguments

Value

An object of class ref_dc with dc selected

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
win=gwindow()
group=ggroup(container=win,horizontal=FALSE)
object=new('ref_dc')
object<-charge(object)
objectreport=new('report_mig_mult')
choice_c(object=object,objectreport=objectreport,dc=1)

## End(Not run)

Description

the choice_c method is intended to have the same behaviour as choice (which creates a widget in the graphical interface) but from the command line. The parameters for dF are transformed to integer as the ref_df only takes integer in the df slots. DF are third in hierarchy in the stacomi database Station>ouvrage>DF>DC>operation. This class is only used in the report_df class.

Usage

## S4 method for signature 'ref_df'
choice_c(object, df)

Arguments

Value

An object of class ref_df with df selected

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
win=gwindow()
group=ggroup(container=win,horizontal=FALSE)
object=new('ref_df')
object<-charge(object)
objectreport=new('report_mig_mult')
choice_c(object=object,objectreport=objectreport,dc=1)

## End(Not run)

Description

the choice_c method is intended to have the same behaviour as choice (which creates a widget in the graphical interface) but from the command line.

Usage

## S4 method for signature 'ref_env'
choice_c(object, stationMesure)

Arguments

Value

an object of class ref_env-class with the monitoring station selected

Author(s)

Cedric Briand [email protected]

Description

Choice_c method for ref_horodate

Usage

## S4 method for signature 'ref_horodate'
choice_c(
  object,
  nomassign = "horodate",
  funoutlabel = "nous avons le choix dans la date\n",
  horodate,
  silent = FALSE
)

Arguments

Value

An object of class ref_horodate-class with slot horodate set, and assigns an object of class POSIXt with name nomassign in envir_stacomi

Description

Choice_c method for ref_list referential objects

Usage

## S4 method for signature 'ref_list'
choice_c(object, selectedvalue)

Arguments

Value

An S4 object of class ref_list-class

Note

the choice method assigns an object of class refList named ref_list in the environment envir_stacomi

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
object=new('ref_list')
object<-charge(object,vecteur=c('1','2'),label='please choose')
object<-choice_c(object)

## End(Not run)

Description

Command line interface to select a parameter

Usage

## S4 method for signature 'ref_par'
choice_c(object, par, silent = FALSE)

Arguments

Value

An object of class ref_par-class

Author(s)

Cedric Briand [email protected]

Description

the choice_c method is intended to have the same behaviour as choice (which creates a widget in the graphical interface) but from the command line. The values passed to the choice_c method for stage is the code. Any numeric value will be discarded

Usage

## S4 method for signature 'ref_stage'
choice_c(object, stage, silent = FALSE)

Arguments

Value

An S4 object of class ref_stage-class with the stage selected in the data slot

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
object=new('ref_stage')
object<-charge(object)

## End(Not run)

Description

the choice_cc method is intended to have the same behaviour as choice (which creates a widget in the graphical interface) but from the command line. The values passed to the choice_c method for taxa can be either numeric (2038 = Anguilla anguilla) or character.

Usage

## S4 method for signature 'ref_taxa'
choice_c(object, taxa)

Arguments

Value

An S4 object of class ref_taxa-class with data filtered according to the taxa

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
object=new('ref_taxa')
object<-charge(object)
objectreport=new('report_mig_mult')
choice_c(object=object,'Anguilla anguilla')

## End(Not run)

Description

Choice_c method for ref_textbox referential objects

Usage

## S4 method for signature 'ref_textbox'
choice_c(object, value, nomassign = "ref_textbox")

Arguments

Value

An S4 object of class ref_textbox-class label selected

Author(s)

Cedric Briand [email protected]

Description

the choice_c method is intended to have the same behaviour as choice (which creates a widget in the graphical interface) but from the command line.

Usage

## S4 method for signature 'ref_timestep_daily'
choice_c(object, datedebut, datefin)

Arguments

Value

An S4 object of class ref_timestep_daily-class with date selected

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
 object=new('ref_dc')
 object<-charge(object)
 choice_c(object=object,datedebut='2012-01-01',datefin='2013-01-01')

## End(Not run)

Description

The choice_c method will issue a warning if the year is not present in the database Allows the selection of year and the assignment in environment envir_stacomi

Usage

## S4 method for signature 'ref_year'
choice_c(
  object,
  annee,
  nomassign = "ref_year",
  funoutlabel = gettext("Year selected\n", domain = "R-stacomiR"),
  silent = FALSE
)

Arguments

Value

object An object of class ref_year-class with year selected

Author(s)

Cedric Briand [email protected]

Examples

## Not run: 
object=new("ref_year")
object<-charge(object)
win=gwindow(title="test ref_year")
group=ggroup(container=win,horizontal=FALSE)
choice(object,nomassign="ref_year",funoutlabel="essai",titleFrame="essai ref_year",preselect=1)
dispose(win)

## End(Not run)

command line interface for report_annual-class

Description

The choice_c method fills in the data slot for classes ref_dc-class, ref_taxa-class, ref_stage-class and two slots of ref_year-class

Usage

## S4 method for signature 'report_annual'
choice_c(object, dc, taxa, stage, start_year, end_year, silent = FALSE)

Arguments

Value

An object of class report_annual-class with data selected

Author(s)

Cedric Briand [email protected]

Description

The choice_c method fills in the data slot for ref_dc, and then uses the choice_c methods of these object to "select" the data.

Usage

## S4 method for signature 'report_dc'
choice_c(object, dc, horodatedebut, horodatefin, silent = FALSE)

Arguments

Value

An object of class ref_dc-class with data selected

Author(s)

Cedric Briand [email protected]

Description

The choice_c method fills in the data slot for ref_df, and then uses the choice_c methods of these object to "select" the data.

Usage

## S4 method for signature 'report_df'
choice_c(object, df, horodatedebut, horodatefin, silent = FALSE)

Arguments

Value

An object of class ref_df-class with data selected

Author(s)

Cedric Briand [email protected]

Description

The choice_c method fills in the data slot for ref_env-class by runnning the charge method of this object. It then runs the choice method on this object. It also applies the choice method for objects of class ref_horodate-class

Usage

## S4 method for signature 'report_env'
choice_c(object, stationMesure, datedebut, datefin, silent = FALSE)

Arguments

Value

An object of class report_env-class with data selected

Author(s)

Cedric Briand [email protected]

command line interface for report_ge_weight-class

Description

command line interface for report_ge_weight-class

Usage

## S4 method for signature 'report_ge_weight'
choice_c(object, dc, start_year, end_year, selectedvalue, silent = FALSE)

Arguments

Value

An object of class report_ge_weight-class with data selected The choice_c method fills in the data slot for classes ref_dc-class ref_year-class ref_coe-class ref_list-class

Author(s)

Cedric Briand [email protected]

Description

command line interface for report_mig_char class

Usage

## S4 method for signature 'report_mig_char'
choice_c(
  object,
  dc,
  taxa,
  stage,
  parquan = NULL,
  parqual = NULL,
  horodatedebut,
  horodatefin,
  echantillon = c("with", "without"),
  silent = FALSE
)

Arguments

Value

An object of class report_sea_age-class The choice_c method fills in the data slot for classes ref_dc-class, ref_taxa-class, ref_stage-class, ref_par-class and two slots of ref_horodate-class and then uses the choice_c methods of these object to select the data.

Author(s)

Cedric Briand [email protected]

Description

command line interface for report_env class

Usage

## S4 method for signature 'report_mig_env'
choice_c(
  object,
  dc,
  taxa,
  stage,
  stationMesure,
  datedebut,
  datefin,
  silent = FALSE
)

Arguments

Value

An object of class report_env-class with data selected

Author(s)

Cedric Briand [email protected]

Description

command line interface for report_mig_interannual class

Usage

## S4 method for signature 'report_mig_interannual'
choice_c(object, dc, taxa, stage, start_year, end_year, silent = FALSE)

Arguments

Value

An object of class report_mig_interannual-class with data selected The choice_c method fills in the data slot for classes ref_dc-class, ref_taxa-class, ref_stage-class and two slots of ref_year-class

Author(s)

Cedric Briand [email protected]

Description

The choice_c method fills in the data slot for ref_dc, ref_taxa, ref_stage and then uses the choice_c methods of these object to 'select' the data.

Usage

## S4 method for signature 'report_mig_mult'
choice_c(object, dc, taxa, stage, datedebut, datefin, silent = FALSE)

Arguments

Value

An object of class report_mig_mult-class with data selected

Author(s)

Cedric Briand [email protected]

Description

The choice_c method fills in the data slot for ref_dc, ref_taxa, ref_stage, and refref_timestep_daily and then uses the choice_c methods of these object to select the data.

Usage

## S4 method for signature 'report_mig'
choice_c(object, dc, taxa, stage, datedebut, datefin)

Arguments

Value

An object of class report_mig-class with data selected

Author(s)

Cedric Briand [email protected]

Description

#' The choice_c method fills in the data slot for classes ref_dc-class, ref_taxa-class, ref_stage-class, ref_par-class and two slots of ref_horodate-class and then uses the choice_c methods of these object to select the data.

Usage

## S4 method for signature 'report_sample_char'
choice_c(
  object,
  dc,
  taxa,
  stage,
  par,
  horodatedebut,
  horodatefin,
  silent = FALSE
)

Arguments

Value

An object of class report_mig-class with data selected

Author(s)

Cedric Briand [email protected]

Description

#' The choice_c method fills in the data slot for classes ref_dc-class, ref_taxa-class, ref_stage-class, ref_par-class and two slots of ref_horodate-class and then uses the choice_c methods of these object to select the data.

Usage

## S4 method for signature 'report_sea_age'
choice_c(
  object,
  dc,
  taxa = 2220,
  stage = c("5", "11", "BEC", "BER", "IND"),
  par = c("1786", "1785", "C001", "A124"),
  horodatedebut,
  horodatefin,
  limit1hm,
  limit2hm,
  silent = FALSE
)

Arguments

Value

An object of class report_sea_age-class

Author(s)

Cedric Briand [email protected]

Description

#' The choice_c method fills in the data slot for classes ref_dc-class, ref_taxa-class, ref_stage-class, ref_par-class and two slots of ref_horodate-class and then uses the choice_c methods of these object to select the data.

Usage

## S4 method for signature 'report_silver_eel'
choice_c(
  object,
  dc,
  taxa = 2038,
  stage = "AGG",
  par = c("1786", "CCCC", "BBBB", "CONT", "LINP", "A111", "PECT"),
  horodatedebut,
  horodatefin,
  silent = FALSE
)

Arguments

Value

An object of class report_mig-class

Author(s)

Cedric Briand [email protected]

command line interface for report_species-class

Description

command line interface for report_species-class

Usage

## S4 method for signature 'report_species'
choice_c(
  object,
  dc,
  taxa = "all",
  split = "none",
  start_year,
  end_year,
  silent = FALSE
)

Arguments

Value

An object of class report_species-class with data selected

Author(s)

Cedric Briand [email protected]

Description

Classification scores are calculated by multiplying the metrics BL = body length, W = weight, MD = mean eye diameter (Dv+Dh)/2, and FL length of the pectoral fin, with each parameter p as S=Constant+BL*p(bl)+W*p(W)... The stage chosen is the one achieving the highest score

Usage

coef_durif

Format

An object of class matrix (inherits from array) with 5 rows and 6 columns.

References

Durif, C.M., Guibert, A., and Elie, P. 2009. Morphological discrimination of the silvering stages of the European eel. In American Fisheries Society Symposium. pp. 103-111. https://fishlarvae.org/common/SiteMedia/durif%20et%20al%202009b.pdf

Description

Builds a table with colors to merge with a dataframe for later use in ggplot. An initial check will be done on the name of the color vector. A data frame is built. It contains a column color which is a factor. The factor order match the order of the vector (not the alphabetical order of the colors).

Usage

colortable(
  color = NULL,
  vec,
  palette = "Set2",
  color_function = c("brewer.pal", "gray.colors", "random")
)

Arguments

Value

A dataframe with two columns, the vector (name) and the color (color) as a reordered factor

Author(s)

Cedric Briand [email protected]

Description

connect method for report_annual class this method performs the sum over the year attention this function does not count subsamples.

Usage

## S4 method for signature 'report_annual'
connect(object, silent = FALSE)

Arguments

Value

An instantiated object with values filled with user choice

An object of class report_annual-class including a dataframe with column effectif, comprising the sum of report_mig counts

Author(s)

Cedric Briand [email protected]

Description

loads the working periods and type of arrest or disfunction of the DC

Usage

## S4 method for signature 'report_dc'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_dc-class with slot data filled from the database

Author(s)

cedric.briand

Description

connect method for report_df

Usage

## S4 method for signature 'report_df'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_df with slot data filled from the database

Author(s)

cedric.briand

Description

connect method for report_env class

Usage

## S4 method for signature 'report_env'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_env-class with slot data filled from the database

Author(s)

Cedric Briand [email protected]

Description

The connect method adapts queries according to user choices, mean weight w is calculated as car_valeur_quantitatif/lot_effectif. These coefficients are stored in the database, and the connect method loads them from the table using the ref_coe-class

Usage

## S4 method for signature 'report_ge_weight'
connect(object, silent = TRUE)

Arguments

Value

An object of class report_ge_weight-class with slots data and coe filled from the database

Note

dates for the request are from august to august (a glass eel season)

Author(s)

Cedric Briand [email protected]

Description

uses the report_mig_mult method

Usage

## S4 method for signature 'report_mig_char'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_mig_char-class with list in @data$parquan and @data$parqual filled in from the database

Description

connect method for report_mig_env class

Usage

## S4 method for signature 'report_mig_env'
connect(object, silent = FALSE)

Arguments

Value

an object of report_mig_env class

Author(s)

Cedric Briand [email protected]

Description

This method will check if the data in the t_reportjournalier_bjo table has no missing data, if missing the program will load missing data. As a second step, the program will check if the numbers in the table t_reportjournalier_bjo differ from those in the database, and propose to re-run the report_mig (which has a write_database methode to write daily reports) for those years.

Usage

## S4 method for signature 'report_mig_interannual'
connect(object, silent = FALSE, check = TRUE)

Arguments

Value

report_mig_interannual an instantiated object with values filled with user choice

Note

We expect different results between daily reports from the t_reportjournalier_bjo table and the annual sums from report_annual for glass eels as those may have been weighted and not only counted. The t_reportjournalier_bjo table used by report_mig_interannual contains the sum of glass eel numbers converted from weights and those directly counted. The report_annual does not.

Author(s)

Cedric Briand [email protected]

Description

this method loads data from the database for report_mig but also fills the table of conversion coefficient, if the taxa is eel. It also calls connect method for report_df-class, report_dc-class and report_ope-class associated with the report and used by the fungraph and fungraph_glasseel functions. As a side effect it assigns objects report_dc-class, report_df-class and report_ope-class in environment envir_stacomi

Usage

## S4 method for signature 'report_mig_mult'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_mig_mult-class with slot @data filled from the database

Description

uses the report_mig_mult method

Usage

## S4 method for signature 'report_mig'
connect(object, silent = FALSE)

Arguments

Value

report_mig with slot @data filled from the database

Description

connect method for report_ope

Usage

## S4 method for signature 'report_ope'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_ope-class with slot data @data filled

Author(s)

cedric.briand

Description

connect method for report_sample_char

Usage

## S4 method for signature 'report_sample_char'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_sample_char-class with slot data @data filled

Author(s)

Cedric Briand [email protected]

Description

connect method for report_sea_age

Usage

## S4 method for signature 'report_sea_age'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_sea_age-class with slot data @data filled

Author(s)

Cedric Briand [email protected]

Description

connect method for report_silver_eel

Usage

## S4 method for signature 'report_silver_eel'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_silver_eel-class with slot data @data filled

Author(s)

Cedric Briand [email protected]

Description

connect method for report_species

Usage

## S4 method for signature 'report_species'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_species-class with data slot filled with slot data @data filled

Author(s)

Cedric Briand [email protected]

Description

envir_stacomi envir_stacomi <- new.env(parent = baseenv()) is the environment where most object created by the interface are stored

This is where the graphical interface stores its objects try ls(envir=envir_stacomi)

This is where the graphical interface stores its objects try ls(envir=envir_stacomi)

Usage

envir_stacomi

envir_stacomi

envir_stacomi

Format

An object of class environment of length 0.

An object of class environment of length 0.

An object of class environment of length 0.

Author(s)

Cedric Briand [email protected]

Description

Each time a report mig runs, it can write its content in the t_bilanmigrationjournalier_bjo table which stores the results of the report_mig with one value per day

Usage

fn_connect_report_mig_interannual(years, taxa, stage, dc)

Arguments

Value

a data frame with the content of table t_bilanmigrationjournalier_bjo in the database

Description

Calculates a data.frame where all components within the list calcdata are aggregated and formatted for plot

Usage

fun_aggreg_for_plot(object)

Arguments

Value

A data.frame

Author(s)

Cedric Briand [email protected]

Description

function used to remove special non utf8 character which cause the gtk interface to crash

Usage

fun_char_spe(text)

Arguments

Value

text

Author(s)

Cedric Briand [email protected]

Description

This function extracts temporal characteristics from a dataframe

Usage

fun_date_extraction(
  data,
  nom_coldt,
  annee = TRUE,
  mois = TRUE,
  quinzaine = FALSE,
  semaine = TRUE,
  semaine_std = FALSE,
  jour_an = FALSE,
  jour_mois = TRUE,
  heure = FALSE
)

Arguments

Value

The dataframe with date column filled

Author(s)

Cedric Briand [email protected]

Description

statistics per time period

Usage

fun_report_mig_interannual(dat, year = NULL, timesplit = NULL)

Arguments

Value

a data frame with mean, max, and min calculated for each timesplit

Description

Function to calculate daily migration from migration monitoring whose length is less than one day, typically video recording whose period are instant events.

Usage

fun_report_mig_mult(time.sequence, datasub, negative = FALSE)

Arguments

Value

A data.frame with number summed over over the time.sequence. The function returns the same output than fun_report_mig_mult_overlaps but is intended to work faster. In the data.frame, the total number is 'Effectif_total' and corresponds to the addition of numbers and numbers converted from weight, the total weight is 'Poids_total'+'poids_depuis_effectifs' and corresponds to weighed glass eel plus glass eel number converted in weights.

Author(s)

Cedric Briand [email protected]

Description

Function to calculate daily migration from migration monitoring whose length is more than one day, this calculation relies on the (false) assumption that migration is evenly spread over time.

Usage

fun_report_mig_mult_overlaps(time.sequence, datasub, negative = FALSE)

Arguments

Value

A data.frame with daily migrations

Author(s)

Cedric Briand [email protected]

See Also

calcule,report_mig_mult-method

Description

Creates a list of available schemas in the db

Usage

fun_schema()

Value

A table with of data providers with org_code, the user of each schema, and org_description the description of the schema

Description

Function to calculate the stages from Durif

Usage

fun_stage_durif(data)

Arguments

Value

A data.frame with durif stages per individual

Author(s)

Laurent Beaulaton [email protected]

Description

functions called in DF and DC

Usage

fun_table_per_dis(
  typeperiode,
  tempsdebut,
  tempsfin,
  libelle,
  color,
  date = TRUE
)

Arguments

Value

A list

Note

returns either POSIXt or date if date=TRUE

Author(s)

Cedric Briand [email protected]

Description

returns a table where weights and number are calculated from number and weights respectively performs a query to collect the conversion coefficients

Usage

fun_weight_conversion(tableau, time.sequence, silent)

Arguments

Value

tableau, the data frame with weight converted to numbers

Author(s)

Cedric Briand [email protected]

Description

This writes monthly data in t_reportmensuel_mens table

Usage

fun_write_monthly(report_mig, resum, silent)

Arguments

Value

No return value, called for side effects

Note

This function is launched by fun_write_daily, the resum dataset is created by the funstat function

Description

This graph is for species other than glass eel

Usage

fungraph(
  report_mig,
  tableau,
  time.sequence,
  taxa,
  stage,
  dc = NULL,
  silent,
  color = NULL,
  color_ope = NULL,
  ...
)

Arguments

Value

No return value, called for side effects

Note

this function is intended to be called from the plot method in report_mig_mult and report_mig

Author(s)

Cedric Briand [email protected]

Description

This graph will also plot numbers and bars according to whether the glass eel have been counted through weight or numbers

Usage

fungraph_glasseel(
  report_mig,
  table,
  time.sequence,
  taxa,
  stage,
  dc = null,
  silent,
  color = NULL,
  color_ope = NULL,
  ...
)

Arguments

Value

No return value, called for side effects

Author(s)

Cedric Briand [email protected]

Description

Function to calculate statistics per month

Usage

funstat(tableau, time.sequence, taxa, stage, DC, silent)

Arguments

Value

No return value, called for side effects

Note

this function is intended to be called from within the summary method

Author(s)

Cedric Briand [email protected]

Description

function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class

Usage

funtable(tableau, time.sequence, taxa, stage, DC, resum, silent)

Arguments

Value

No return value, called for side effects

Note

this function is intended to be called from within the summary method

Author(s)

Cedric Briand [email protected]

Description

Generic method getvalue

Usage

getvalue(object, ...)

Arguments

Author(s)

cedric.briand

Description

function used for some lattice graphs with dates

Usage

graphdate(vectordate)

Arguments

Value

vectordate (without class)

Author(s)

Cedric Briand [email protected]

Description

Generic for prediction

Usage

model(object, ...)

Arguments

Author(s)

cedric.briand

Description

model method for report_ge_weight' this method uses samples collected over the season to model the variation in weight of glass eel or yellow eels.

Usage

## S4 method for signature 'report_ge_weight'
model(object, model.type = "seasonal", silent = FALSE)

Arguments

Details

Depending on model.type several models are produced

model.type='seasonal'.

The simplest model uses a seasonal variation, it is fitted with a sine wave curve allowing a cyclic variation w ~ a*cos(2*pi*(d'-T)/365)+b with a period T. The modified day d' used is this model is set at 1 the 1st of august doy = d' + d0; d0 = 212, doy=julian days

model.type='seasonal1'.

A time component is introduced in the model, which allows for a long term variation along with the seasonal variation. This long term variation is is fitted with a gam, the time variable is set at zero at the beginning of the first day of observed values. The seasonal variation is modeled on the same modified julian time as model.type='seasonal' but here we use a cyclic cubic spline cc, which allows to return at the value of d0=0 at d=365. This model was considered as the best to model size variations by Diaz & Briand in prep. but using a large set of values over years.

model.type='seasonal2'.

The seasonal trend in the previous model is now modelled with a sine curve similar to the sine curve used in seasonal. The formula for this is $sin(\omega vt) + cos(\omega vt)$, where vt is the time index variable $\omega$ is a constant that describes how the index variable relates to the full period (here, $2\pi/365=0.0172$). The model is written as following $w~cos(0.0172*doy)+sin(0.0172*doy)+s(time).$

model.type='manual'.

The dataset don (the raw data), coe (the coefficients already present in the database, and newcoe the dataset to make the predictions from, are written to the environment envir_stacomi. please see example for further description on how to fit your own model, build the table of coefficients, and write it to the database.

Value

An object of class report_ge_weight-class with @calcdata[["import_coe"]] filled.

Author(s)

Cedric Briand [email protected]

Description

Plot method for report_annual

Usage

## S4 method for signature 'report_annual,missing'
plot(x, plot.type = "point", silent = FALSE)

Arguments

Value

No return value, called for side effects

Author(s)

Cedric Briand [email protected]

See Also

report_mig_interannual-class for examples

Description

plot.type=1

A barplot of the operation time per month

plot.type=2

Barchat giving the time per type of operation

plot.type=2

Rectangle plots drawn along a line

plot.type=4

Plots per day drawn over the period to show the operation of a df, days in x, hours in y

Usage

## S4 method for signature 'report_dc,missing'
plot(
  x,
  plot.type = 1,
  silent = FALSE,
  main = NULL,
  color_type_oper = c(`Fonc normal` = "#76BEBE", `Arr ponctuel` = "#FF6700", `Arr maint`
    = "#9E0142", Dysfonc = "#EE1874", `Non connu` = "#999999"),
  color_etat = c(`TRUE` = "#0F313A", `FALSE` = "#CEB99A")
)

Arguments

Value

Nothing but prints the different plots.

Note

The program cuts periods which overlap between two month. The splitting of different periods into month is assigned to the envir_stacomi environment.

Author(s)

Cedric Briand [email protected]

Description

plot.type=1

A barplot of the operation time per month

plot.type=2

Barchat giving the time per type of operation

plot.type=2

Rectangle plots drawn along a line

plot.type=4

Plots per day drawn over the period to show the operation of a df, days in x, hours in y

Usage

## S4 method for signature 'report_df,missing'
plot(
  x,
  plot.type = 1,
  silent = FALSE,
  main = NULL,
  color_type_oper = c(`Fonc normal` = "#1B9E77", `Arr ponctuel` = "#E6AB02", `Arr maint`
    = "#9E0142", Dysfonc = "#E41A1C", `Non connu` = "#999999"),
  color_etat = c(`TRUE` = "chartreuse3", `FALSE` = "orangered3")
)

Arguments

Value

Nothing but prints the different plots.

Note

The program cuts periods which overlap between two month. The splitting of different periods into month is assigned to the envir_stacomi environment.

Author(s)

Cedric Briand [email protected]

Description

Plot method for report_env

Usage

## S4 method for signature 'report_env,missing'
plot(x, silent = FALSE)

Arguments

Value

Nothing, called for its side effect of plotting data

Author(s)

Cedric Briand [email protected]

Description

Plot method for report_ge_weight'

Usage

## S4 method for signature 'report_ge_weight,missing'
plot(x, plot.type = 1, silent = FALSE)

Arguments

Value

Nothing, called for its side effect of plotting data

Note

the model method provides plots for the fitted models

Author(s)

Cedric Briand [email protected]

Description

plot method for report_mig_char

Usage

## S4 method for signature 'report_mig_char,missing'
plot(x, color_parm = NULL, plot.type = "qual", silent = FALSE, ...)

Arguments

Value

Nothing, called for its side effect of plotting data

Author(s)

Cedric Briand [email protected]

Description

Plot method for report_mig_env

Usage

## S4 method for signature 'report_mig_env,missing'
plot(x, color_station = NULL, color_dc = NULL, silent = FALSE)

Arguments

Value

Nothing, called for its side effect of plotting

Author(s)

Cedric Briand [email protected]

Description

Several of these plots are scaled against the same year,i.e.the comparison is based on year 2000, meaning that day 1 would correspond to the first date of 2000, which is also a saturday, the last day of the week.

Usage

## S4 method for signature 'report_mig_interannual,missing'
plot(
  x,
  plot.type = "standard",
  timesplit = "month",
  year_choice = NULL,
  alpha = 1,
  silent = FALSE
)

Arguments

Value

Nothing, called for its side effect of plotting

Author(s)

Cedric Briand [email protected]

Description

plot.type='standard'

calls fungraph and fungraph_glasseel functions to plot as many 'report_mig' as needed, the function will test for the existence of data for one dc, one taxa, and one stage

plot.type='step'

creates Cumulated graphs for report_mig_mult. Data are summed per day for different dc taxa and stages

plot.type='multiple'

Method to overlay graphs for report_mig_mult (multiple dc/taxa/stage in the same plot)

Usage

## S4 method for signature 'report_mig_mult,missing'
plot(
  x,
  plot.type = "standard",
  color = NULL,
  color_ope = NULL,
  silent = FALSE,
  ...
)

Arguments

Value

Nothing, called for its side effect of plotting

Author(s)

Cedric Briand [email protected]

Description

plot.type="standard"

calls fungraph and fungraph_glasseel functions to plot as many "report_mig" as needed, the function will test for the existence of data for one dc, one taxa, and one stage

plot.type="step"

creates Cumulated graphs for report_mig_mult. Data are summed per day for different dc taxa and stages

plot.type="multiple"

Method to overlay graphs for report_mig_mult (multiple dc/taxa/stage in the same plot)

Usage

## S4 method for signature 'report_mig,ANY'
plot(
  x,
  y,
  plot.type = "standard",
  color = NULL,
  color_ope = NULL,
  silent = FALSE,
  ...
)

Arguments

Value

Nothing, called for its side effect

Author(s)

Cedric Briand [email protected]

Description

Plots of various type for reportcarlot

Usage

## S4 method for signature 'report_sample_char,missing'
plot(x, plot.type = "1", silent = FALSE)

Arguments

Value

Nothing, called for its side effect, plotting

Author(s)

Cedric Briand [email protected]

Description

Plots of various type for report_sea_age

Usage

## S4 method for signature 'report_sea_age,missing'
plot(x, plot.type = "1", silent = FALSE)

Arguments

Value

Nothing, called for its side effect of plotting

Author(s)

Cedric Briand [email protected]

Description

Plots of various type for report_silver_eel

Usage

## S4 method for signature 'report_silver_eel,missing'
plot(x, plot.type = c("1", "2", "3", "4"), silent = FALSE)

Arguments

Value

A lattice xy.plot if plot.type =1, a lattice barchart if plot.type=2, nothing but plots a series of graphs in a single plot if plot.type=3, a lattice cloud object if plot.type=4

Author(s)

Cedric Briand [email protected]

Description

Plot method for report_species

Usage

## S4 method for signature 'report_species,missing'
plot(x, plot.type = "pie", color = NULL, silent = FALSE)

Arguments

Value

Nothing, called for producing plots

Author(s)

Cedric Briand [email protected]

Description

Method to print the command line of the object.

Usage

## S4 method for signature 'report_dc'
print(x, ...)

Arguments

Value

Nothing, called for its side effect

Author(s)

cedric.briand

Description

Method to print the command line of the object

Usage

## S4 method for signature 'report_df'
print(x, ...)

Arguments

Value

Nothing, called for its side effect of printing data

Author(s)

cedric.briand

Description

Method to print the command line of the object

Usage

## S4 method for signature 'report_mig_mult'
print(x, ...)

Arguments

Author(s)

cedric.briand

Description

Method to print the command line of the object

Usage

## S4 method for signature 'report_mig'
print(x, ...)

Arguments

Author(s)

cedric.briand

Description

Method to print the command line of the object

Usage

## S4 method for signature 'report_sample_char'
print(x, ...)

Arguments

Author(s)

cedric.briand

Description

Method to print the command line of the object

Usage

## S4 method for signature 'report_sea_age'
print(x, ...)

Arguments

Author(s)

cedric.briand

Description

Method to print the command line of the object

Usage

## S4 method for signature 'report_silver_eel'
print(x, ...)

Arguments

Value

NULL, prints data in the console

Author(s)

cedric.briand

Description

The dataset corresponds to the three fishways located on the Arzal dam, filled with annual data

Usage

r_ann

Format

An object of class report_annual-class with data slot loaded.

Description

The dataset corresponds to the fishways DC=33:40 of the Adour for adult migrant salmons from 1996 to 2005 (annual counts). It has been kindly provided as an example set by the Migradour association.

Usage

r_ann_adour

Format

An object of class report_annual-class with data slot loaded.

Description

This data corresponds to the data collected at the vertical slot fishway camera from 2000 to 2015. It represents an object of class report_dc-class with data loaded

Usage

r_dc

Format

An object of class report_dc with 4 slots:

data

A dataframe with 544 obs. of 7 variables

per_dis_identifiant

The number of the DC

per_date_debut

Starting time a POSIXct

per_date_fin

Ending time a POSIXct

ope_dic_identifiant

DC id

per_commentaires

A comment

per_etat_fonctionnement

Integer 1= working, 0 not working

per_tar_code

The type of operation ('1'=normal operation, '2'=Device stopped in normal operation (e.g. the trap is disactivated for the duration of the fish sorting and counting by operators), '3'='Stopped for maintenance or other problem', '4'='Works but not fully operational, i.e. the camera is not working properly because of high turbidity...', '5'='Not known')

libelle

label corresponding to per_tar_code

df

the ref_dc object with 3 slots filled with data corresponding to the iav postgres schema

horodatedebut

the ref_horodate with horodate set for starting date

horodatefin

the ref_horodate with horodate set for ending date

Description

This dataset corresponds to the data collected at the vertical slot fishway in 2015, the fishway is working daily with a cycle depending on tide. This dataset is used to show an example of detailed output for an object of class report_df-class with data loaded

Usage

r_df

Format

An object of class report_df with 4 slots:

data

A dataframe with 4261 obs. of 7 variables

per_dis_identifiant

The number of the DF

per_date_debut

Starting time a POSIXct

per_date_fin

Ending time a POSIXct

ope_dic_identifiant

DF id

per_commentaires

A comment

per_etat_fonctionnement

Integer 1= working, 0 not working

per_tar_code

The type of operation ('1'=normal operation, '2'=Device stopped in normal operation (ie lift ascending, high tide...), '3'='Stopped for maintenance or other problem', '4'='Works but not fully operational,i.e.flow problem, flood, clogged with debris...', '5'='Not known')

libelle

label corresponding to per_tar_code

df

the ref_df object with 3 slots filled with data corresponding to the iav postgres schema

horodatedebut

the ref_horodate with horodate set for starting date

horodatefin

the ref_horodate with horodate set for ending date

'

Description

The dataset corresponds to the daily temperatures and moon phases in Arzal (Vilaine estuary, France). This environmental station is used to analyze conditions in which fish migrated at Arzal dam

Usage

r_env

Format

An object of class report_env-class with data slot loaded:

stationMesure

the ref_env object with 5 slots filled with data corresponding to the iav postgres schema

horodatedebut

object of class ref_horodate-class : the start date selected

horodatefin

object of class ref_horodate-class : the end date selected

data

A dataframe with 723 rows and 6 variables

env_date_debut

start date

env_date_fin

end date

env_methode_obtention

method of data collection, measured, calculated...

env_val_identifiant

the value of the parameter if qualitative

env_valeur_quantitatif

the value of the parameter if quantitative

env_stm_identifiant

station id

Description

Data correspond to glass eel collected in the Vilaine at the trapping ladder (Arzal, France). The years selected are 2009 to 2012, the query used in the report_ge_weight-class loads from 2008-08-01 to 2012-08-01 Glass eel are too numerous to be counted. They are weighted and in the stacomi database, a table with daily coefficients (in N glass eel/g) to transform weight into number. The weight is called a 'wet weight' as we don't wan't to drain any of the mucus in glass eel when weighting them. Samples of 50 to 200 glass eel are weighted and then counted to provide an idea of the seasonal evolution of wet weight.

Usage

r_gew

Format

An object of class report_ge_weight of length 1.

Description

This dataset corresponds to the data collected at the vertical slot fishway in 2012, video recording marine lamprey migration

Usage

r_mig

Format

An object of class report_mig with 8 slots:

dc

the ref_dc object with 4 slots filled with data corresponding to the iav postgres schema

taxa

the ref_taxa the taxa selected

stage

the ref_stage the stage selected

timestep

the ref_timestep_daily calculated for all 2015

data

A dataframe with 10304 rows and 11 variables

ope_identifiant

operation id

lot_identifiant

sample id

lot_identifiant

sample id

ope_dic_identifiant

dc id

lot_tax_code

species id

lot_std_code

stage id

value

the value

type_de_quantite

either effectif (number) or poids (weights)

lot_dev_code

destination of the fishes

lot_methode_obtention

method of data collection, measured, calculated...

coef_conversion

A data frame with 0 observations : no quantity are reported for video recording of mullets, only numbers

time.sequence

A time sequence generated for the report, used internally

Description

The dataset corresponds to the characteristics (qualitative and quantitative) of salmo salar migrating at Decize (Loire river) and Vichy (Allier river) counting device in 2012. It has been loaded as an example for the report_mig_char-class and kindly provided by Loire Grands Migrateurs (LOGRAMI).

Usage

r_mig_char

Format

An object of class report_mig_char-class with data slot loaded:

calcdata

slot to be filled with the calcule method

data

A list of 2 elements

parqual

values of all the qualitative parameters

parquan

values of all the quantitative parameters

dc

the ref_dc : the control devices selected

taxa

the ref_taxa : Salmo salar selected

stage

the ref_stage : the stages selected

par

an object of class ref_par-class: the parameters used

horodatedebut

an object of class ref_horodate-class : the start date selected

horodatefin

an object of class ref_horodate-class : the end date selected

Description

This dataset corresponds to the data collected in the vertical slot fishway for the video recording operation. It is loaded along with r_mig to demonstrate the use of the report_mig-class when the database is not loaded

Usage

r_mig_dc

Format

An object of class report_dc-class

Description

This dataset corresponds to the data collected at in the vertical slot fishway it is loaded along with r_mig and used to demonstrate the report_mig-class when the database is not installed.

Usage

r_mig_df

Format

An object of class report_df-class

Description

The dataset correspond to data loaded for the Arzal dam (Vilaine) in 2008, two quantitative parameters (temperature and tide coefficient) and a qualitative parameter (moon phase) are loaded.

Usage

r_mig_env

Format

An object of class report_env-class with data slot loaded:

report_mig_mult

An object of class report_mig_mult-class

report_env

An object of class report_env-class

#'

Description

The first eel trapping ladder in France was built by Antoine Legault and the team from Rennes in the Sevre Niortaise, Marais Poitevin. Also refurbished several times since 1984 it has been operational at the same location and provides one of the longest series of eel migration. For this reason, the dataset has been loaded as an example for the report_mig_interannual-class. It has been kindly provided by the parc du Marais Poitevin. The stage corresponds to small eels (elvers) less than 150 mmm stage name 'PANG'

Usage

r_mig_interannual

Format

An object of class report_mig_interannual-class with data loaded.

Description

This data corresponds to the data collected at the Vichy fishway between 1997 and 2012, video recording of the Salmo salar upstream migration. This dataset has been kindly provided by Loire Grands Migrateurs.

Usage

r_mig_interannual_vichy

Format

An object of class report_mig_interannual-class with 7 slots:

dc

the ref_dc object with 4 slots filled with data corresponding to the iav postgres schema

taxa

the ref_taxa the taxa selected

stage

the ref_stage the stage selected

start_year

the ref_timestep_daily calculated for all 2015

end_year

the ref_timestep_daily calculated for all 2015

data

A dataframe with 7138 rows and 10 variables

bjo_identifiant

sample id

bjo_dis_identifiant

dc id

bjo_tax_code

species id

bjo_std_code

stage id

bjo_annee

year

bjo_jour

date

bjo_labelquantite

method of data collection, measured, calculated...

bjo_horodateexport

date with special format for export

bjo_org_code

organisme provided the data

Description

This data corresponds to data collected from three fishways and correspond to the migration station at Arzal (Vilaine estuary, France) in 2011 for three continental stages of eel (Anguilla anguilla) : glass eel, yellow eel and silver eel.

Usage

r_mig_mult

Format

An object of class report_mig_mult with slots:

dc

the ref_dc object filled with data

taxa

the ref_taxa object filled in with data corresponding to dc

stage

the ref_stage object filled in with data corresponding to dc, and taxa

timestep

the ref_timestep_daily calculated for all 2011

data

A dataframe with 400 rows and 11 variables

ope_identifiant

operation id

lot_identifiant

sample id

lot_identifiant

sample id

ope_dic_identifiant

dc id

lot_tax_code

species id

lot_std_code

stage id

value

the value

type_de_quantite

either effectif (number) or poids (weights)

lot_dev_code

destination of the fishes

lot_methode_obtention

method of data collection, measured, calculated...

calcdata

slot to be filled with the calcule method

coef_conversion

A data frame with 364 observations with daily coefficients to convert from weight to numbers

time.sequence

A time sequence generated for the report, used internally by the object

Description

This dataset corresponds to data collected at three different control devices. This object is of class report_dc-class with data loaded it is loaded along with r_mig_mult and used in demonstration for the report_mig_mult-class

Usage

r_mig_mult_dc

Format

An object of class report_dc with 4 slots

data

A dataframe with 25 rows and 7 variables

per_dis_identifiant

the df or dc unique id

per_date_debut

the starting date of the counting device operation POSIXct

per_date_fin

the ending date of the counting device operation POSIXct

per_commentaires

comments on the counting device operation

per_etat_fonctionnement

Boolean, is the counting device working ?

lot_std_code

stage id

per_tar_code

The type of operation for the DC, 1 normal operation, 2 device stopped in normal operation (the stop is considered as normal, e.g. you don't monitor video if a cage has been placed to trap fishes), 3 stopped for maintenance or other problem, 4 the DC is working but not well (escapement in a tank, high turbidity preventing video counting...), 5 unknown operation.

libelle

The label for the type or operation

dc

the ref_dc the DC with 4 slots

dc_selected

the selected device

ouvrage

the dam

station

the monitoring station, a section of river

data

A dataset of all dc present in the database with 10 observations

horodatedebut

the beginning date, a ref_horodate-class

horodatefin

the ending date, a ref_horodate-class

Description

This dataset corresponds to the data collected at three different fishways it is loaded along with r_mig_mult and used in demonstration for the report_mig_mult-class

Usage

r_mig_mult_df

Format

An object of class report_df report_df-class

Description

This dataset corresponds to the data collected at three different control devices It is an object of class report_ope-class with data loaded. it is loaded along with r_mig_mult

Usage

r_mig_mult_ope

Format

An object of class report_ope

An object of class report_ope-class with data loaded

Description

This dataset corresponds to the data collected at the vertical slot fishway in Arzal (Vilaine river estuary, France). The operation of the fishway is dependent on tide and is recorded every 10 minutes. This dataset has to be loaded along with r_mig to demonstrate the use of the report_mig-class

Usage

r_mig_ope

Format

An object of class report_ope

Description

This dataset corresponds to the data collected at two different control devices at the Arzal control station (see example in report_sample_char-class), all body size parameters (total size, size converted from pixel in video control) are used in example

Usage

r_sample_char

Format

An object of class report_sample_char-class

Description

This dataset corresponds to the data collected at Vichy (left and right bank fishways) and Decize-Saint Leger des Vignes fishways (respectively on the Allier and Loire river, France) in 2012 on the size structure of Salmo salar. It has been kindly provided by the Loire Grands Migrateurs (LOGRAMI) association.

Usage

r_seaa

Format

An object of class report_sea_age-class with 8 slots:

dc

the ref_dc : the control devices selected

taxa

the ref_taxa : Salmo salar selected

stage

the ref_stage : the stages selected

par

Object of class ref_par-class: the parameters used

horodatedebut

object of class ref_horodate-class : the start date selected

horodatefin

object of class ref_horodate-class : the end date selected

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

data

A dataframe with 898 rows and 20 variables

ope_identifiant

operation id

lot_identifiant

sample id

ope_dic_identifiant

dc id

ope_date_debut

start date

ope_date_fin

end date

lot_effectif

number of fishes

lot_tax_code

species id

lot_std_code

stages id

tax_nom_latin

species latin names

std_libelle

stages names

dev_code

destination of the fishes id

dev_libelle

destination of the fishes names

par_nom

parameter name

car_par_code

parameter id

car_methode_obtention

method of data collection, measured, calculated...

car_valeur_quantitatif

the value of the parameter

Description

The dataset corresponds to the silver eel traps ('anguilleres) for 2015-2016. This dataset has been kindly provided by the Federation de Peche de la Somme, given the upstream location of the trap, most individuals are female

Usage

r_silver

Format

An object of class report_silver_eel-class with data slot loaded.

Description

ref_choice referential class allows to choose within several values with radiobuttons interface

Slots

listechoice

A character vector giving possible choices

label

A character, title of the box giving the possible choices

selected

An Integer the initial selected value (as an index), first=1 used in gradio

Objects from the Class

Objects can be created by calls of the form new('ref_choice', listechoice=character() ,label=character() ,selected=integer()).

Author(s)

[email protected]

See Also

Other referential objects: charge,ref_choice-method, ref_coe-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Description

Enables to load conversion coefficients quantity-number. This class only exists to load the data with its method charge. It is not used directly as component of the graphical interface, as the year is already loaded in the different report objects

Slots

data

A data.frame

datedebut

A 'POSIXlt'

datefin

A 'POSIXlt'

Objects from the Class

Objects can be created by calls of the form new('ref_coe').

Note

Class loading coefficient of conversion between quantity (weights or volumes of glass eel) and numbers between a starting and finishing date

Author(s)

[email protected]

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Description

Description of a control device.

Slots

dc_selected

Object of class 'integer', The selected device

ouvrage

Object of class 'integer', the attached dam

station

Object of class 'character', the attached migration monitoring station, this is necessary to join the table of escapements calculated at the station level.

data

Object of class 'data.frame' data pertaining to the control device

Objects from the Class

Objects can be created by calls of the form new('ref_dc', dc_selected=integer(), ouvrage=integer(), data=data.frame()).

Author(s)

[email protected]

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Description

Representation of a fishway, contains description data of all fishways from the database along with the selected fishways (df) (integer) Objects from the Class: Objects can be created by calls of the form new('ref_df', df_selected=integer(), ouvrage=integer(), data=data.frame()).

Arguments

Author(s)

[email protected]

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_dc-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Description

Enables to load measure stations and to select one of them

Slots

dataframe

Data concerning the measure station

env_selected

The selected measure station

Objects from the Class

Objects can be created by calls of the form new('ref_env', ...).

Author(s)

[email protected]

Description

choice of date with method to show current and previous year

Slots

horodate

a "POSIXt"

Objects from the Class

Objects can be created by calls of the form new("ref_horodate", ...{}).

Author(s)

Cedric Briand [email protected]

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_dc-class, ref_df-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Description

Class enabling to load the list of parameters and select one of them

Slots

data

A data.frame

par_selected

A character vector corresponding to par_code

data='data.frame'

the list of parameters

Objects from the Class

Objects can be created by calls of the form

Author(s)

[email protected]

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class