barplot,report_annual-method
                        barplot method for object report_annual-class
calcmig                 A data frame containing the default connection
                        arguments. The program will use a file
                        installed in c:/program files/stacomi but if
                        not found will switch to this default value
calcule                 Generic method for calculations
calcule,report_ge_weight-method
                        Calcule method for report_ge_weight
calcule,report_mig-method
                        Transforms migration per period to daily
                        migrations, and performs the conversion from
                        weights to number is data are stored as weights
                        (glass eel).
calcule,report_mig_char-method
                        Computes data to a standard format for the
                        summary and plot methods.
calcule,report_mig_env-method
                        Calculations for migration in the class
                        report_mig_env-class
calcule,report_mig_interannual-method
                        calcule method for report_mig_interannual
calcule,report_mig_mult-method
                        #' Transforms migration per period to daily
                        migrations, and performs the conversion from
                        weights to number is data are stored as weights
                        (glass eel). This calculation is performed in a
                        loop for all dc.
calcule,report_sample_char-method
                        Calculation for report_sample_char
calcule,report_sea_age-method
                        Split data according to the limits set in the
                        limit1hm, and limit2hm arguments of the
                        report_sea_age-class.
calcule,report_silver_eel-method
                        Calculate individual silver eel parameters.
calcule,report_species-method
                        calcule method for report_species
charge                  Generic method to load referentials
charge,ref_checkbox-method
                        Loading method for ref_checkbox referential
                        objects
charge,ref_choice-method
                        Loading method for Rechoice referential objects
charge,ref_coe-method   loads the coefficients for the period defined
                        in class
charge,ref_dc-method    Method to load the counting devices of the
                        control station
charge,ref_df-method    Loading method for DF referential objects
charge,ref_env-method   Loading method for ref_env referential object
charge,ref_list-method
                        Loading method for refliste referential objects
charge,ref_par-method   Loading method for Repar referential objects
charge,ref_parqual-method
                        Loading method for Reparqual referential
                        objects
charge,ref_parquan-method
                        Loading method for Reparquan referential
                        objects
charge,ref_stage-method
                        Loading method for ref_stage referential
                        objects
charge,ref_taxa-method
                        Loading method for ref_taxa referential objects
charge,ref_textbox-method
                        Loading method for ReTextBox referential
                        objects
charge,ref_year-method
                        Loading method for ref_year referential objects
charge,report_ge_weight-method
                        charge method for report_ge_weight class
charge,report_mig-method
                        Loads additional data on migration control
                        operations, df (fishway) dc (counting device).
charge,report_mig_env-method
                        charge method for report_mig_env class
charge,report_mig_mult-method
                        charge method for report_mig_mult
charge_complement       Generic method to load additional data
charge_complement,ref_parqual-method
                        Loads an additional dataset this method is
                        loaded to obtain the possible values of a
                        qualitative parameter. Here data only contains
                        one line
charge_with_filter,ref_par-method
                        Loading method for Repar referential objects
                        searching only those parameters existing for a
                        DC, a Taxa, and a stage
charge_with_filter,ref_parqual-method
                        Loading method for Reparqual referential
                        objects searching only those parameters
                        existing for a DC, a Taxon, and a stage
charge_with_filter,ref_parquan-method
                        Loading method for Reparquan referential
                        objects searching only those parameters
                        existing for a DC, a Taxon, and a stage
charge_with_filter,ref_stage-method
                        Loading method for ref_stage referential
                        objects searching only those stages existing
                        for a DC and a Taxon
charge_with_filter,ref_taxa-method
                        Loading method for ref_taxa referential objects
                        searching only taxa existing for a DC
chargecomplement-methods
                        Methods for Function chargecomplement
choice_c,ref_choice-method
                        Choice_c method for refchoix referential
                        objects
choice_c,ref_dc-method
                        Command line interface to select a counting
                        device
choice_c,ref_df-method
                        Command line interface to choose a fishway
choice_c,ref_env-method
                        Command line interface to select a monitoring
                        station
choice_c,ref_horodate-method
                        Command line
choice_c,ref_list-method
                        Choice_c method for ref_list referential
                        objects
choice_c,ref_par-method
                        Command line interface to select a parameter
choice_c,ref_stage-method
                        choice_c method for ref_stage
choice_c,ref_taxa-method
                        choice_c method for ref_taxa
choice_c,ref_textbox-method
                        Choice_c method for ReTextBox referential
                        objects
choice_c,ref_timestep_daily-method
                        choice_c method for class ref_timestep_daily
choice_c,ref_year-method
                        choice_c method for ref_year referential from
                        the command line
choice_c,report_annual-method
                        command line interface for report_annual-class
choice_c,report_dc-method
                        command line interface for report_dc class
choice_c,report_df-method
                        command line interface for report_df class
choice_c,report_env-method
                        command line interface for report_env class
choice_c,report_ge_weight-method
                        command line interface for
                        report_ge_weight-class
choice_c,report_mig-method
                        command line interface for report_mig class
choice_c,report_mig_char-method
                        command line interface for report_mig_char
                        class
choice_c,report_mig_env-method
                        command line interface for report_env class
choice_c,report_mig_interannual-method
                        command line interface for
                        report_mig_interannual class
choice_c,report_mig_mult-method
                        command line interface for report_mig_mult
                        class
choice_c,report_sample_char-method
                        command line interface for report_sample_char
                        class
choice_c,report_sea_age-method
                        command line interface for report_sea_age class
choice_c,report_silver_eel-method
                        command line interface for report_silver_eel
                        class
choice_c,report_species-method
                        command line interface for report_species-class
choicemult,ref_dc-method
                        choicemult, selection method for ref_dc
                        allowing to select several DC
choicemult,ref_taxa-method
                        Multiple Choice method for reftaxa referential
                        objects, the graphical interface is built to
                        allow for multiple choices. See load for method
                        in the command line.
coef_durif              Silvering index coefficients from Caroline
                        Durif (2009) to predict silvering stage from
                        morphological parameters
colortable              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).
connect,report_annual-method
                        connect method for report_annual class this
                        method performs the sum over the year attention
                        this function does not count subsamples.
connect,report_dc-method
                        connect method for report_dc
connect,report_df-method
                        connect method for report_df
connect,report_env-method
                        connect method for report_env class
connect,report_ge_weight-method
                        connect method for report_Poids_moyen
connect,report_mig-method
                        connect method for report_mig
connect,report_mig_char-method
                        connect method for report_mig_char
connect,report_mig_env-method
                        connect method for report_mig_env class
connect,report_mig_interannual-method
                        connect method for report_mig_interannual
connect,report_mig_mult-method
                        connect method for report_mig_mult
connect,report_ope-method
                        connect method for report_ope
connect,report_sample_char-method
                        connect method for report_sample_char
connect,report_sea_age-method
                        connect method for report_sea_age
connect,report_silver_eel-method
                        connect method for report_silver_eel
connect,report_species-method
                        connect method for report_species
createmessage           Generic method to forward outputs
current_end_date,ref_timestep-method
                        Gets the ending date of a time step for an
                        object of class ref_timestep-class
envir_stacomi           Environment where most objects from the package
                        are stored and then loaded by the charge method
fun_aggreg_for_plot     returns a table where all components within the
                        list calcdata are aggregated and formatted for
                        plot
fun_char_spe            function used to remove special non utf8
                        character which cause the gtk interface to
                        crash
fun_date_extraction     This function extracts temporal characteristics
                        from a dataframe
fun_report_mig_interannual
                        statistics per time period
fun_report_mig_mult     Calculate daily migration by simple repartition
fun_report_mig_mult_overlaps
                        Function to calculate daily migration using
                        overlaps functions
fun_stage_durif         Function to calculate the stages from Durif
fun_table_per_dis       functions called in DF and DC
fun_weight_conversion   returns a table where weights and number are
                        calculated from number and weights respectively
                        performs a query to collect the conversion
                        coefficients
fun_write_monthly       This writes monthly data in
                        t_reportmensuel_mens table
funbarchart1DC          Handler for barchart for report_df class from
                        the graphical interface
fungraph                Function for report_mig graphs including
                        numbers DF DC operations
fungraph_glasseel       Graph function for glass eel migration. Differs
                        from fungraph as it does not draw the ggplot
                        graph for month
funstat                 Function to calculate statistics per month
funstat_daily           function to create daily statistics
funtable                function to print and save statistics in .csv
                        and .html formats for report_mig and
                        report_mig_mult class
getdbname               Retrieves the dbname from a connection using
                        "baseODBC"
getnocurrent_step       Generic method to get current time step
getvalue                Generic method getvalue
getvalue,ref_period-method
                        Returns the POSIXt value of a given name
graphdate               function used for some lattice graphs with
                        dates
graphe-methods          Methods for Function graphe
model                   Generic for prediction
model,report_ge_weight-method
                        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.
plot,report_annual,missing-method
                        Plot method for report_annual
plot,report_dc,ANY-method
                        Different plots for report_dc
plot,report_df,ANY-method
                        Different plots for report_df
plot,report_env,missing-method
                        Plot method for report_env
plot,report_ge_weight,missing-method
                        Plot method for report_ge_weight'
plot,report_mig,ANY-method
                        Plots of various type for report_mig.
plot,report_mig_char,missing-method
                        plot method for report_mig_char
plot,report_mig_env,missing-method
                        Plot method for report_mig_env
plot,report_mig_interannual,missing-method
                        Plot method for report_mig_interannual
plot,report_mig_mult,missing-method
                        Plots of various type for report_mig_mult
plot,report_sample_char,missing-method
                        Plots of various type for reportcarlot
plot,report_sea_age,missing-method
                        Plots of various type for report_sea_age
plot,report_silver_eel,missing-method
                        Plots of various type for report_silver_eel
plot,report_species,missing-method
                        Plot method for report_species
print,report_dc-method
                        Method to print the command line of the object
print,report_df-method
                        Method to print the command line of the object
print,report_mig-method
                        Method to print the command line of the object
print,report_mig_mult-method
                        Method to print the command line of the object
print,report_sample_char-method
                        Method to print the command line of the object
print,report_sea_age-method
                        Method to print the command line of the object
print,report_silver_eel-method
                        Method to print the command line of the object
progress_bar            Progress bar using a gtkdialog, the progress
                        bar is assigned in envir_stacomi This progress
                        bar has a button to close.
quitte                  function used to clean the objects within the
                        group and the graphs and also elements
                        remaining in the envir_stacomi environment
r_ann                   Annual migration of yellow and silver eel for
                        three fishways / counting devices at the Arzal
                        dam (data from 1995 to 2016)
r_ann_adour             Annual migration of salmon in the Adour and
                        tributaries
r_dc                    Counting Device (DC) operation from 2000 to
                        2015 at the Arzal dam (Vilaine, France)
r_df                    Overview of the fishway operation at Arzal in
                        (Vilaine France).
r_env                   An object of class report_env with data loaded
r_gew                   Wet weight of glass eel from the trapping
                        ladder (Arzal, Vilaine France)
r_mig                   Video counting of thin lipped mullet (Liza
                        ramada) in 2015 in the Vilaine (France)
r_mig_char              Qualitative and quantitative parameters
                        describing Salmon migration at Decize (Loire)
r_mig_dc                Counting device operation for the video
                        recording (Arzal dam, Vilaine, France).
r_mig_df                Fishway operation for the vertical slot fishway
                        (Arzal dam, Vilaine, France).
r_mig_env               An object of class report_mig_env with data
                        loaded
r_mig_interannual       Daily glass eel and elver migration from 1984
                        to 2016 in the Sevre Niortaise
r_mig_interannual_vichy
                        Seasonality of salmon migration at the Vichy
                        counting station (Loire)
r_mig_mult              Anguilla migration at the Arzal station
                        (report_mig_mult-class)
r_mig_mult_dc           Counting device operation for three different
                        counting device in Arzal (Vilaine, France)
r_mig_mult_df           Fishway operation at the Arzal Dam (Vilaine
                        France) (3 Fishways in 2011)
r_mig_mult_ope          Counting operations for three different
                        counting device in Arzal (Vilaine, France)
r_mig_ope               An object of class report_ope-class with data
                        loaded
r_sample_char           Size of yellow and glass eel at the Arzal dam
                        (Vilaine, France) in the fishway and main eel
                        trapping ladder.
r_seaa                  An object of class report_sea_age with data
                        loaded
r_silver                Silver eel migration in the Somme
ref_checkbox-class      ref_checkbox referencial class
ref_choice-class        Class "ref_choice"
ref_coe-class           Class "ref_coe"
ref_dc-class            Class "ref_dc"
ref_df-class            Class "ref_df"
ref_env-class           Class "ref_env"
ref_horodate-class      Class ref_horodate
ref_par-class           Class "ref_par"
ref_parqual-class       Class "ref_parqual"
ref_parquan-class       Class "ref_parquan"
ref_period-class        Class "ref_period" referential class
ref_stage-class         Class "ref_stage"
ref_taxa-class          Class "ref_taxa"
ref_textbox-class       ref_textbox referencial class
ref_timestep-class      Class "ref_timestep"
ref_timestepChar-class
                        Class "ref_timestepChar"
ref_timestep_daily-class
                        Class "ref_timestep_daily"
ref_year-class          Year reference class
report_annual-class     Class "report_annual"
report_dc-class         Class "report_dc" report du fonctionnement du
                        dispositif de comptage
report_df-class         Report on fishway operation
report_env-class        class report_env simple output of one or
                        several environmental conditions...
report_ge_weight-class
                        Trend of wet weight in glass eel
report_mig-class        Migration report for one DC, one species and
                        one stage
report_mig_char-class   Migration report along with quantitative and
                        qualitative characteristics
report_mig_env-class    Class "report_mig_env"
report_mig_interannual-class
                        Class "report_mig_interannual"
report_mig_mult-class   Migration reports for multiple DC / species /
                        stages
report_ope-class        Report on operations
report_sample_char-class
                        Class "report_sample_char"
report_sea_age-class    Class "report_sea_age"
report_silver_eel-class
                        Class "report_silver_eel"
report_species-class    Counts of number per taxa/stages
setasqualitative        Generic method to transform quantitative par
                        into a qualitative one
setasqualitative,report_mig_char-method
                        Turns a quantitative parameter into qualitative
split_per_day           Create a dataframe suitable for charts per 24h
                        and day
stacomi                 Function that loads the loginwindow, tests
                        connection, and then destroys the window
stacomiR-package        package Fish Migration Monitoring (stacomiR)-
                        Stations de Controle des Migrations
summary,report_dc-method
                        summary for report_dc, write csv and html
                        output, and prints summary statistics
summary,report_df-method
                        summary for report_df, write csv and html
                        output, and prints summary statistics
summary,report_mig-method
                        summary for report_mig calls functions funstat
                        and funtable to create migration overviews and
                        generate csv and html output in the user data
                        directory
summary,report_mig_char-method
                        summary for report_mig_char
summary,report_mig_interannual-method
                        summary for report_mig_interannual provides
                        summary statistics for the latest year (if
                        silent=TRUE), or the year selected in the
                        interface, if silent=FALSE. Mean, min and max
                        are historical statistics with the selected
                        year excluded from the historical dataset.
summary,report_mig_mult-method
                        summary for report_mig_mult calls functions
                        funstat and funtable to create migration
                        overviews and generate csv and html output in
                        the user data directory
summary,report_sample_char-method
                        summary for report_sample_char
summary,report_sea_age-method
                        summary for report_sea_age
summary,report_silver_eel-method
                        summary for report_silver_eel
summary,report_species-method
                        summary for report_species generate csv and
                        html output in the user data directory
supprime                Generic method to delete entires from the
                        database
supprime,ref_coe-method
                        supprime method for "ref_coe" class
supprime,report_mig_interannual-method
                        supprime method for report_mig_interannual
                        class
supprime,report_sea_age-method
                        supprime method for report_mig_interannual
                        class
vector_to_listsql       Transforms a vector into a string called within
                        an sql command e.g. c('A','B','C') => in
                        ('A','B','C')
write_database          Generic method write_database
write_database,report_ge_weight-method
                        Function to write data to the stacomi database
                        for report_ge_weight-class
write_database,report_mig-method
                        Command line method to write the daily and
                        monthly counts to the
                        t_bilanmigrationjournalier_bjo table
write_database,report_sea_age-method
                        Command line method to write the characteristic
                        "sea age" (car_par_code='A124') into the
                        tj_caracteristiquelot_car table in the user's
                        scheme
xtable,report_annual-method
                        xtable function for report_annual-class create
                        an xtable objet but also assigns an
                        add.to.column argument in envir_stacomi, for
                        later use by the print.xtable method.
xtable,report_mig_char-method
                        xtable function for report_mig_char-class
                        create an xtable objet to be later used by the
                        print.xtable method.
