Man pages for stacomiR
Fish Migration Monitoring

barplot-report_annual-methodbarplot method for object report_annual-class
calcmigA data frame containing the default connection arguments. The...
calculeGeneric method for calculations
calcule-report_ge_weight-methodCalcule method for report_ge_weight
calcule-report_mig_char-methodComputes data to a standard format for the summary and plot...
calcule-report_mig_env-methodCalculations for migration in the class report_mig_env-class
calcule-report_mig_interannual-methodcalcule method for report_mig_interannual
calcule-report_mig-methodTransforms migration per period to daily migrations, and...
calcule-report_mig_mult-method#' Transforms migration per period to daily migrations, and...
calcule-report_sample_char-methodCalculation for report_sample_char
calcule-report_sea_age-methodSplit data according to the limits set in the limit1hm, and...
calcule-report_silver_eel-methodCalculate individual silver eel parameters.
calcule-report_species-methodcalcule method for report_species
chargeGeneric method to load referentials
charge_complementGeneric method to load additional data
chargecomplement-methodsMethods for Function chargecomplement
charge_complement-ref_parqual-methodLoads an additional dataset this method is loaded to obtain...
chargecsvchargecsv loads the informations stored in c:/program...
charge-ref_checkbox-methodLoading method for ref_checkbox referential objects
charge-ref_choice-methodLoading method for Rechoice referential objects
charge-ref_coe-methodloads the coefficients for the period defined in class
charge-ref_dc-methodMethod to load the counting devices of the control station
charge-ref_df-methodLoading method for DF referential objects
charge-ref_env-methodLoading method for ref_env referential object
charge-ref_list-methodLoading method for refliste referential objects
charge-ref_par-methodLoading method for Repar referential objects
charge-ref_parqual-methodLoading method for Reparqual referential objects
charge-ref_parquan-methodLoading method for Reparquan referential objects
charge-ref_stage-methodLoading method for ref_stage referential objects
charge-ref_taxa-methodLoading method for ref_taxa referential objects
charge-ref_textbox-methodLoading method for ReTextBox referential objects
charge-ref_year-methodLoading method for ref_year referential objects
charge-report_annual-methodcharge method for report_annual class
charge-report_dc-methodcharge method for report_dc
charge-report_df-methodcharge method for report_df
charge-report_env-methodcharge method for report_env class
charge-report_ge_weight-methodcharge method for report_ge_weight class
charge-report_mig_char-methodcharge method for report_mig_char
charge-report_mig_env-methodcharge method for report_mig_env class
charge-report_mig_interannual-methodloading method for report_mig_interannual class
charge-report_mig-methodLoads additional data on migration control operations, df...
charge-report_mig_mult-methodcharge method for report_mig_mult
charge-report_ope-methodcharge method for report_ope
charge-report_sample_char-methodcharge method for report_sample_char class
charge-report_sea_age-methodLoads data and check that all choices in the graphical...
charge-report_silver_eel-methodcharge method for report_silver_eel class
charge-report_species-methodcharge method for report_species
charge_with_filterGeneric method to load referentials, with filters from the...
charge_with_filter-ref_par-methodLoading method for Repar referential objects searching only...
charge_with_filter-ref_parqual-methodLoading method for Reparqual referential objects searching...
charge_with_filter-ref_parquan-methodLoading method for Reparquan referential objects searching...
charge_with_filter-ref_stage-methodLoading method for ref_stage referential objects searching...
charge_with_filter-ref_taxa-methodLoading method for ref_taxa referential objects searching...
choiceGeneric method for choice (using the gwidget graphical...
choice_cGeneric method for manual choice using the command line
choice_c-ref_choice-methodChoice_c method for refchoix referential objects
choice_c-ref_dc-methodCommand line interface to select a counting device
choice_c-ref_df-methodCommand line interface to choose a fishway
choice_c-ref_env-methodCommand line interface to select a monitoring station
choice_c-ref_horodate-methodCommand line
choice_c-ref_list-methodChoice_c method for ref_list referential objects
choice_c-ref_par-methodCommand line interface to select a parameter
choice_c-ref_stage-methodchoice_c method for ref_stage
choice_c-ref_taxa-methodchoice_c method for ref_taxa
choice_c-ref_textbox-methodChoice_c method for ReTextBox referential objects
choice_c-ref_timestep_daily-methodchoice_c method for class ref_timestep_daily
choice_c-ref_year-methodchoice_c method for ref_year referential from the command...
choice_c-report_annual-methodcommand line interface for report_annual-class
choice_c-report_dc-methodcommand line interface for report_dc class
choice_c-report_df-methodcommand line interface for report_df class
choice_c-report_env-methodcommand line interface for report_env class
choice_c-report_ge_weight-methodcommand line interface for report_ge_weight-class
choice_c-report_mig_char-methodcommand line interface for report_mig_char class
choice_c-report_mig_env-methodcommand line interface for report_env class
choice_c-report_mig_interannual-methodcommand line interface for report_mig_interannual class
choice_c-report_mig-methodcommand line interface for report_mig class
choice_c-report_mig_mult-methodcommand line interface for report_mig_mult class
choice_c-report_sample_char-methodcommand line interface for report_sample_char class
choice_c-report_sea_age-methodcommand line interface for report_sea_age class
choice_c-report_silver_eel-methodcommand line interface for report_silver_eel class
choice_c-report_species-methodcommand line interface for report_species-class
choicemultGeneric method for multiple choice (using the gwidget...
choicemult-ref_choice-methodMultiple Choice method for ref_choice referential objects, to...
choicemult-ref_dc-methodchoicemult, selection method for ref_dc allowing to select...
choicemult-ref_horodate-methodMultiple Choice method for ref_horodate referential objects,...
choicemult-ref_par-methodMultiple Choice method for ref_par referential objects,...
choicemult-ref_parqual-methodMultiple Choice method for ref_parqual referential objects...
choicemult-ref_stage-methodMultiple Choice method for ref_stage referential objects
choicemult-ref_taxa-methodMultiple Choice method for reftaxa referential objects, the...
choicemult-ref_timestep-methodGraphical interface for multiple choice method for PasdeTemps...
choice-ref_checkbox-methodChoice method for ref_checkbox referential objects
choice-ref_choice-methodChoice method for Rechoice referential objects
choice-ref_dc-methodGraphical method to choose a fishway through the interface
choice-ref_df-methodGraphical method to choose a fishway through the interface
choice-ref_env-methodChoice method for ref_env referential object
choice-ref_horodate-methodGraphical interface
choice-ref_list-methodChoice method for ref_list referential objects
choice-ref_par-methodChoice method for ref_par referential objects
choice-ref_parqual-methodChoice method for ref_parqual referential objects, internal...
choice-ref_stage-methodChoice method for ref_stage referential objects
choice-ref_taxa-methodChoice method for reftaxa referential objects with only one...
choice-ref_textbox-methodChoice method for ReTextBox referential objects
choice-ref_timestep_daily-methodMethod to select timesteps from the graphical interface
choice-ref_timestep-methodMethod to select timesteps from the graphical interface
choice-ref_year-methodchoice method for ref_year referential
coef_durifSilvering index coefficients from Caroline Durif (2009) to...
colortableBuilds a table with colors to merge with a dataframe for...
connect-report_annual-methodconnect method for report_annual class this method performs...
connect-report_dc-methodconnect method for report_dc
connect-report_df-methodconnect method for report_df
connect-report_env-methodconnect method for report_env class
connect-report_ge_weight-methodconnect method for report_Poids_moyen
connect-report_mig_char-methodconnect method for report_mig_char
connect-report_mig_env-methodconnect method for report_mig_env class
connect-report_mig_interannual-methodconnect method for report_mig_interannual
connect-report_mig-methodconnect method for report_mig
connect-report_mig_mult-methodconnect method for report_mig_mult
connect-report_ope-methodconnect method for report_ope
connect-report_sample_char-methodconnect method for report_sample_char
connect-report_sea_age-methodconnect method for report_sea_age
connect-report_silver_eel-methodconnect method for report_silver_eel
connect-report_species-methodconnect method for report_species
createmessageGeneric method to forward outputs
current_end_dateGeneric method for getting the ending date for current time...
current_end_date-ref_timestep-methodGets the ending date of a time step for an object of class...
currentstart_dateGeneric method for getting the beginning date for current...
currentstart_date-ref_timestep-methodGets the starting date of a time step for an object of class...
end_dateGeneric method for getting the final date
end_date-ref_timestep-methodGets the final horodate for an object of class...
envir_stacomiEnvironment where most objects from the package are stored...
fun_aggreg_for_plotreturns a table where all components within the list calcdata...
funbarchart1DCHandler for barchart for report_df class from the graphical...
funbarchart1DFHandler for barchart for report_df class from the graphical...
funbarchartDCFunction to create a barchart (lattice) corresponding to the...
funbarchartDFHandler for barchart for report_df class from the graphical...
funboxDCfunction used for some lattice graph
funboxDFInternal use, rectangles to describe the DF work for...
funboxplotreport_sample_charBoxplots for ggplot2
fun_char_spefunction used to remove special non utf8 character which...
funchartDCHandler function to plot calendar like graph, internal use
funchartDFHandler function to plot calendar like graph, internal use
fun_date_extractionThis function extracts temporal characteristics from a...
fundensityreport_sample_charfundensityreport_sample_char uses ggplot2 to draw density...
fungraphFunction for report_mig graphs including numbers DF DC...
fungraph_glasseelGraph function for glass eel migration. Differs from fungraph...
funoutthis function uses gfile, edits a text with info and changing...
funplotreport_sea_agefunplotreport_sea_age
funplotreport_silver_eelfunplotreport_silver_eel
funpointreport_sample_charPoint graph from ggplot
fun_report_mig_interannualstatistics per time period
fun_report_mig_multCalculate daily migration by simple repartition
fun_report_mig_mult_overlapsFunction to calculate daily migration using overlaps...
fun_stage_durifFunction to calculate the stages from Durif
funstatFunction to calculate statistics per month
funstat_dailyfunction to create daily statistics
funtablefunction to print and save statistics in .csv and .html...
funtableDCFuntableDC create a table output for report_dc class
funtableDFTable output for report_df class
fun_table_per_disfunctions called in DF and DC
funtablereport_ge_weightInternal handler for reg, class 'report_ge_weight-class'.
funtablereport_sample_chartable function
funtablereport_sea_agetable function
funtablereport_silver_eeltable function
fun_weight_conversionreturns a table where weights and number are calculated from...
fun_write_monthlyThis writes monthly data in t_reportmensuel_mens table
getdateDebutGeneric method the get starting date
getdateDebut-ref_timestep-methodReturns the starting date as character
getdbnameRetrieves the dbname from a connection using "baseODBC"
getnocurrent_stepGeneric method to get current time step
getnocurrent_step-ref_timestep-methodGets the current time step of an object of class...
get_step_labelGeneric method to get the string value of time step
get_step_label-ref_timestep-methodGets the string value of time step
getvalueGeneric method getvalue
getvalue-ref_period-methodReturns the POSIXt value of a given name
get_yearGeneric method to get the years
get_year-ref_timestep-methodGets the year or a vector of years corresponding to the...
graphdatefunction used for some lattice graphs with dates
graphe-methodsMethods for Function graphe
hbarplotreport_annualBarplot handler
hbilespcalchandler for calculation
hbmCcalchandler for report_mig_char
hbmCplotcrossedhandler for plot
hbmCplotqualhandler for plot
hbmCplotquanhandler for plot
hbmCstatThis handler calls the generic method stat
hbmmCEcalcInternal handler function
hbmmCEgraphinternal method for graphical interface
hcalcInternal handler for reg, class 'report_ge_weight-class'.
hexpInternal handler for reg, class 'report_ge_weight-class'.
hgraph_report_mig_interannualPlot of all interannual from top to bottom
hgraph_report_mig_interannual2Plot of daily migrations
hgraph_report_mig_interannual3Step plot with different years displayed on the same graph....
hgraph_report_mig_interannual4Plot comparing the migration to the migration computed for...
hgraph_report_mig_interannual5Function displaying comparison similar to...
hgraph_report_mig_interannual7This function creates a cumulated area plot to highlight...
houtDChandler to print the command line
houtDFhandler to print the command line
houtreport_mighandler to print the command line
houtreport_mig_multhandler to print the command line
hplotInternal handler for reg, class 'report_ge_weight-class'.
hplotbilesphandler for plot internal use
hplotreport_annualplot handler
hregInternal handler for reg, class 'report_ge_weight-class'.
h_report_dchandler function used by the main interface
h_report_dfhandler function used by the main interface
h_report_dfdchandler function used by the main interface
h_report_envhandler function used by the main interface
h_report_envgraphh_report_envgraph Internal method
h_report_ge_weighthandler function used by the main interface
h_report_mighandler function used by the main interface
h_report_mig_annualhandler function used by the main interface
h_report_migcalchandler for calculations report_mig
h_report_mig_charhandler function used by the main interface
h_report_mig_envhandler function used by the main interface
h_report_miggraphhandler for h_report_miggraph
h_report_miggraph2handler for h_report_miggraph2
h_report_mig_interannualhandler function used by the main interface
h_report_mig_multhandler function used by the main interface
h_report_mig_multcalchandler for calculations
h_report_mig_mult_graphhandler for plot method in report_mig_mult class
h_report_mig_multgraph2handler du calcul h_report_miggraph2
h_report_mig_multgraph3handler
h_report_migwritehandler h_report_migwrite Allows the saving of daily and...
h_report_opehandler function used by the main interface
h_report_pigment_stageshandler function used by the main interface
h_report_sample_charhandler function used by the main interface
h_report_sea_agehandler function used by the main interface
h_report_silverhandler function used by the main interface
h_report_sizehandler function used by the main interface
h_report_specieshandler function used by the main interface
hsummarybilesphandler for summary report_species, internal use
hsummaryreport_migInterannuelleSummary handler internal method
hTablereport_mighandler for summary function, internal use calls functions...
hTablereport_mig_multhandler function table
hxtablereport_annualxtable handler
interface_graphiqueProgram launch, this function launches the GwidgetRgtk...
interface_report_annualinterface for report_annual class
interface_report_dcinterface for report_dc class
interface_report_dfinterface for report_df class
interface_report_envInterface for class conditionEnv
interface_report_ge_weightinterface for report_ge_weight class
interface_report_migInterface for report_mig class, internal use, this function...
interface_report_mig_charinterface for report_migPar class
interface_report_mig_envinterface for report_migConditionEnv class
interface_report_mig_interannualinterface for report_mig_interannual class
interface_report_mig_multgraphical interface for report_mig_mult class
interface_report_sample_charAn interface that calls the object to build the user...
interface_report_sea_ageAn interface that calls the object to build the user...
interface_report_silver_eelAn interface that calls the object to build the user...
interface_report_speciesInterface for report_species class
load_stacomiInternal function, tests the connection and if it works loads...
modelGeneric for prediction
model-report_ge_weight-methodmodel method for report_ge_weight' this method uses samples...
plot-report_annual-missing-methodPlot method for report_annual
plot-report_dc-ANY-methodDifferent plots for report_dc
plot-report_df-ANY-methodDifferent plots for report_df
plot-report_env-missing-methodPlot method for report_env
plot-report_ge_weight-missing-methodPlot method for report_ge_weight'
plot-report_mig-ANY-methodPlots of various type for report_mig.
plot-report_mig_char-missing-methodplot method for report_mig_char
plot-report_mig_env-missing-methodPlot method for report_mig_env
plot-report_mig_interannual-missing-methodPlot method for report_mig_interannual
plot-report_mig_mult-missing-methodPlots of various type for report_mig_mult
plot-report_sample_char-missing-methodPlots of various type for reportcarlot
plot-report_sea_age-missing-methodPlots of various type for report_sea_age
plot-report_silver_eel-missing-methodPlots of various type for report_silver_eel
plot-report_species-missing-methodPlot method for report_species
print-report_dc-methodMethod to print the command line of the object
print-report_df-methodMethod to print the command line of the object
print-report_mig-methodMethod to print the command line of the object
print-report_mig_mult-methodMethod to print the command line of the object
print-report_sample_char-methodMethod to print the command line of the object
print-report_sea_age-methodMethod to print the command line of the object
print-report_silver_eel-methodMethod to print the command line of the object
progress_barProgress bar using a gtkdialog, the progress bar is assigned...
quittefunction used to clean the objects within the group and the...
r_annAnnual migration of yellow and silver eel for three fishways...
r_ann_adourAnnual migration of salmon in the Adour and tributaries
r_dcCounting Device (DC) operation from 2000 to 2015 at the Arzal...
r_dfOverview of the fishway operation at Arzal in (Vilaine...
ref_checkbox-classref_checkbox referencial class
ref_choice-classClass "ref_choice"
ref_coe-classClass "ref_coe"
ref_dc-classClass "ref_dc"
ref_df-classClass "ref_df"
ref_env-classClass "ref_env"
ref_horodate-classClass ref_horodate
ref_list-classClass "ref_list"
ref_par-classClass "ref_par"
ref_parqual-classClass "ref_parqual"
ref_parquan-classClass "ref_parquan"
ref_period-classClass "ref_period" referential class
ref_stage-classClass "ref_stage"
ref_taxa-classClass "ref_taxa"
ref_textbox-classref_textbox referencial class
ref_timestepChar-classClass "ref_timestepChar"
ref_timestep-classClass "ref_timestep"
ref_timestep_daily-classClass "ref_timestep_daily"
ref_year-classYear reference class
r_envAn object of class report_env with data loaded
report_annual-classClass "report_annual"
report_dc-classClass "report_dc" report du fonctionnement du dispositif de...
report_df-classReport on fishway operation
report_env-classclass report_env simple output of one or several...
report_ge_weight-classTrend of wet weight in glass eel
report_mig_char-classMigration report along with quantitative and qualitative...
report_mig-classMigration report for one DC, one species and one stage
report_mig_env-classClass "report_mig_env"
report_mig_interannual-classClass "report_mig_interannual"
report_mig_mult-classMigration reports for multiple DC / species / stages
report_ope-classReport on operations
report_sample_char-classClass "report_sample_char"
report_sea_age-classClass "report_sea_age"
report_silver_eel-classClass "report_silver_eel"
report_species-classCounts of number per taxa/stages
r_gewWet weight of glass eel from the trapping ladder (Arzal,...
r_migVideo counting of thin lipped mullet (Liza ramada) in 2015 in...
r_mig_charQualitative and quantitative parameters describing Salmon...
r_mig_dcCounting device operation for the video recording (Arzal dam,...
r_mig_dfFishway operation for the vertical slot fishway (Arzal dam,...
r_mig_envAn object of class report_mig_env with data loaded
r_mig_interannualDaily glass eel and elver migration from 1984 to 2016 in the...
r_mig_interannual_vichySeasonality of salmon migration at the Vichy counting station...
r_mig_multAnguilla migration at the Arzal station...
r_mig_mult_dcCounting device operation for three different counting device...
r_mig_mult_dfFishway operation at the Arzal Dam (Vilaine France) (3...
r_mig_mult_opeCounting operations for three different counting device in...
r_mig_opeAn object of class report_ope-class with data loaded
r_sample_charSize of yellow and glass eel at the Arzal dam (Vilaine,...
r_seaaAn object of class report_sea_age with data loaded
r_silverSilver eel migration in the Somme
setasqualitativeGeneric method to transform quantitative par into a...
setasqualitative-report_mig_char-methodTurns a quantitative parameter into qualitative
setref_horodate-ref_horodate-methodMethod to set the Horodate
set_starting_dateGeneric method to set the starting date
set_starting_date-ref_timestep-methodSets starting date from a character
split_per_dayCreate a dataframe suitable for charts per 24h and day
stacomiFunction that loads the loginwindow, tests connection, and...
stacomiR-packagepackage Fish Migration Monitoring (stacomiR)- Stations de...
summary-report_dc-methodsummary for report_dc, write csv and html output, and prints...
summary-report_df-methodsummary for report_df, write csv and html output, and prints...
summary-report_mig_char-methodsummary for report_mig_char
summary-report_mig_interannual-methodsummary for report_mig_interannual provides summary...
summary-report_mig-methodsummary for report_mig calls functions funstat and funtable...
summary-report_mig_mult-methodsummary for report_mig_mult calls functions funstat and...
summary-report_sample_char-methodsummary for report_sample_char
summary-report_sea_age-methodsummary for report_sea_age
summary-report_silver_eel-methodsummary for report_silver_eel
summary-report_species-methodsummary for report_species generate csv and html output in...
supprimeGeneric method to delete entires from the database
supprime-ref_coe-methodsupprime method for "ref_coe" class
supprime-report_mig_interannual-methodsupprime method for report_mig_interannual class
supprime-report_sea_age-methodsupprime method for report_mig_interannual class
validity_ref_horodateValidity check for ref_horodate
validity_yearValidity check for ref_year
vector_to_listsqlTransforms a vector into a string called within an sql...
write_databaseGeneric method write_database
write_database-report_ge_weight-methodFunction to write data to the stacomi database for...
write_database-report_mig-methodCommand line method to write the daily and monthly counts to...
write_database-report_sea_age-methodCommand line method to write the characteristic "sea age"...
xtable-report_annual-methodxtable function for report_annual-class create an xtable...
xtable-report_mig_char-methodxtable function for report_mig_char-class create an xtable...
stacomiR documentation built on Sept. 4, 2017, 3:03 p.m.