stacomiR-package {stacomiR}R Documentation

Fish Migration Monitoring

Description

Graphical outputs and treatment for a database of fish pass monitoring. It is a part of the 'STACOMI' open source project developed in France by the French Office for Biodiversity (OFB) institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See <http://stacomir.r-forge.r-project.org/> for more information on 'STACOMI'.

Details

Package: stacomiR
Version: 0.5.4.4
Date: 2020-04-02
Title: Fish Migration Monitoring
Authors@R: c(person("Cedric", "Briand", role = c("aut", "cre"), email = "cedric.briand00@gmail.com"), person("Marion", "Legrand", role = "aut", email="tableau-salt-loire@logrami.fr"), person("Timothee", "Besse", role = "aut", email="tableau-ang-loire@logrami.fr"))
Description: Graphical outputs and treatment for a database of fish pass monitoring. It is a part of the 'STACOMI' open source project developed in France by the French Office for Biodiversity (OFB) institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See <http://stacomir.r-forge.r-project.org/> for more information on 'STACOMI'.
License: GPL (>= 2)
URL: http://stacomir.r-forge.r-project.org/
BugReports: https://github.com/MarionLegrandLogrami/stacomiR/issues
Collate: 'create_generic.R' 'data.R' 'fun_table_per_dis.R' 'fun_write_monthly.R' 'fungraph.R' 'fungraph_glasseel.R' 'funstat.R' 'funstat_daily.R' 'funtable.R' 'interface_report_annual.R' 'interface_report_dc.R' 'interface_report_df.R' 'interface_report_env.R' 'interface_report_ge_weight.R' 'interface_report_mig.R' 'interface_report_mig_char.R' 'interface_report_mig_env.R' 'interface_report_mig_interannual.R' 'interface_report_mig_mult.R' 'interface_report_sample_char.R' 'interface_report_sea_age.R' 'interface_report_silver_eel.R' 'interface_report_species.R' 'ref_checkbox.R' 'ref_choice.R' 'ref_coe.R' 'ref_dc.R' 'ref_df.R' 'ref_env.R' 'ref_horodate.R' 'ref_list.R' 'ref_par.R' 'ref_parqual.R' 'ref_parquan.R' 'ref_period.R' 'ref_stage.R' 'ref_taxa.R' 'ref_textbox.R' 'ref_timestep.R' 'ref_timestep_daily.R' 'ref_year.R' 'report_annual.R' 'report_dc.R' 'report_df.R' 'utilities.R' 'report_env.R' 'report_ge_weight.R' 'report_ope.R' 'report_mig.R' 'report_sample_char.R' 'report_mig_char.R' 'report_mig_mult.R' 'report_mig_env.R' 'report_mig_interannual.R' 'report_sea_age.R' 'report_silver_eel.R' 'report_species.R' 'setAs.R' 'stacomi.R'
LazyLoad: yes
LazyData: true
Depends: R (>= 3.5.0), methods, stacomirtools, RODBC
Imports: magrittr, intervals, RColorBrewer, stringr, gWidgets, gWidgetsRGtk2, RPostgreSQL, ggplot2, reshape2, sqldf, graphics, utils, stats, lattice, grDevices, Hmisc (>= 4.1-1), RGtk2, lubridate, dplyr, xtable, mgcv, rlang
Suggests: testthat, viridis, knitr, rmarkdown
Author: Cedric Briand [aut, cre], Marion Legrand [aut], Timothee Besse [aut]
Maintainer: Cedric Briand <cedric.briand00@gmail.com>
RoxygenNote: 6.1.0.9000
NeedsCompilation: no
VignetteBuilder: knitr
Repository: R-Forge
Repository/R-Forge/Project: stacomir
Repository/R-Forge/Revision: 563
Repository/R-Forge/DateTimeStamp: 2020-04-02 07:04:33
Date/Publication: 2020-04-02 07:04:33

Index of help topics:

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        Fish Migration Monitoring
stacomi_installed       Test that the program is installed.
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.

Further information is available in the following vignettes:

stacomir StacomiR- A package for fish migration monitoring (source)

To use the stacomiR package, simply load the library using library(stacomiR). Once done, type stacomi() in R terminal. The use of stacomi(gr_interface=FALSE) allows to launch stacomi without graphical interface from the command line. The program is currently translated to French, to switch to English or French type Sys.setenv(LANG = "en") Sys.setenv(LANG = "fr")

Author(s)

Cedric Briand [aut, cre], Marion Legrand [aut], Timothee Besse [aut] Maintainer: Cedric Briand <cedric.briand00@gmail.com>

See Also

stacomirtools

Examples

  #stacomi()

[Package stacomiR version 0.5.4.4 Index]