Man pages for stacomiR
Fish Migration Monitoring

barplot-report_annual-methodbarplot method for object report_annual-class
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
charge_complement-ref_parqual-methodLoads an additional dataset this method is loaded to obtain...
charge-ref_choice-methodLoading method for Refchoice 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 ref_list referential objects
charge-ref_par-methodLoading method for ref_par 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 ref_textbox 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_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 'ref_par referential' objects searching...
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...
choice_cGeneric method for manual choice using the command line
choice_c-ref_choice-methodChoice_c method for ref_choice 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-methodChoice_c method for ref_horodate
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 ref_textbox 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
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-methodhandler for calculations 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
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_plotCalculates a data.frame where all components within the list...
funbarchart1DFInternal use barchart for report_df class from the graphical...
funbarchartDCFunction to create a barchart (lattice) corresponding to the...
funbarchartDFInternal use, function used in the graphical interface to...
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...
funchartDFFunction 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 displays text and will be used to convey...
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
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
fun_weight_conversionreturns a table where weights and number are calculated from...
fun_write_monthlyThis writes monthly data in t_reportmensuel_mens table
get_orgthis function gets the name of the stucture as it is set in...
get_schemathis function gets the schema from envir stacomi and throws...
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
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-methodh_report_envgraph Internal method
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-methodhandler for plot
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-methodhandler to print the command line
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
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_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-methodhandler for report_mig_char
split_per_dayCreate a dataframe suitable for charts per 24h and day
stacomistacomi Main launcher for program stacomi
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
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, deletes...
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-methodMethod 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 Nov. 22, 2021, 9:06 a.m.