Fish Migration Monitoring

Documentation for package ‘stacomiR’ version 0.5.3.1

DESCRIPTION file.

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B C E F G M P Q R S V W X

stacomiR-package

package Fish Migration Monitoring (stacomiR)- Stations de Controle des Migrations

-- B --

barplot-method	barplot method for object report_annual-class
barplot.report_annual	barplot method for object report_annual-class

-- C --

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-method	Calcule method for report_ge_weight
calcule-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-method	Computes data to a standard format for the summary and plot methods.
calcule-method	Calculations for migration in the class report_mig_env-class
calcule-method	calcule method for report_mig_interannual
calcule-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-method	Calculation for report_sample_char
calcule-method	Split data according to the limits set in the limit1hm, and limit2hm arguments of the report_sea_age-class.
calcule-method	Calculate individual silver eel parameters.
calcule-method	calcule method for report_species
calcule.report_ge_weight	Calcule method for report_ge_weight
calcule.report_mig	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	Computes data to a standard format for the summary and plot methods.
calcule.report_mig_env	Calculations for migration in the class report_mig_env-class
calcule.report_mig_interannual	calcule method for report_mig_interannual
calcule.report_mig_mult	#' 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	Calculation for report_sample_char
calcule.report_sea_age	Split data according to the limits set in the limit1hm, and limit2hm arguments of the report_sea_age-class.
calcule.report_silver_eel	Calculate individual silver eel parameters.
calcule.report_species	calcule method for report_species
charge	Generic method to load referentials
charge-method	Loading method for ref_checkbox referential objects
charge-method	Loading method for Rechoice referential objects
charge-method	loads the coefficients for the period defined in class
charge-method	Method to load the counting devices of the control station
charge-method	Loading method for DF referential objects
charge-method	Loading method for ref_env referential object
charge-method	Loading method for refliste referential objects
charge-method	Loading method for Repar referential objects
charge-method	Loading method for Reparqual referential objects
charge-method	Loading method for Reparquan referential objects
charge-method	Loading method for ref_stage referential objects
charge-method	Loading method for ref_taxa referential objects
charge-method	Loading method for ReTextBox referential objects
charge-method	Loading method for ref_year referential objects
charge-method	charge method for report_ge_weight class
charge-method	Loads additional data on migration control operations, df (fishway) dc (counting device).
charge-method	charge method for report_mig_env class
charge-method	charge method for report_mig_mult
charge.report_ge_weight	charge method for report_ge_weight class
charge.report_mig	Loads additional data on migration control operations, df (fishway) dc (counting device).
charge.report_mig_env	charge method for report_mig_env class
charge.report_mig_mult	charge method for report_mig_mult
chargecomplement	Methods for Function chargecomplement
chargecomplement-method	Methods for Function chargecomplement
chargecomplement-methods	Methods for Function chargecomplement
charge_complement	Generic method to load additional data
charge_complement-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-method	Loading method for Repar referential objects searching only those parameters existing for a DC, a Taxa, and a stage
charge_with_filter-method	Loading method for Reparqual referential objects searching only those parameters existing for a DC, a Taxon, and a stage
charge_with_filter-method	Loading method for Reparquan referential objects searching only those parameters existing for a DC, a Taxon, and a stage
charge_with_filter-method	Loading method for ref_stage referential objects searching only those stages existing for a DC and a Taxon
charge_with_filter-method	Loading method for ref_taxa referential objects searching only taxa existing for a DC
choicemult-method	choicemult, selection method for ref_dc allowing to select several DC
choicemult-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.
choice_c-method	Choice_c method for refchoix referential objects
choice_c-method	Command line interface to select a counting device
choice_c-method	Command line interface to choose a fishway
choice_c-method	Command line interface to select a monitoring station
choice_c-method	Command line
choice_c-method	Choice_c method for ref_list referential objects
choice_c-method	Command line interface to select a parameter
choice_c-method	choice_c method for ref_stage
choice_c-method	choice_c method for ref_taxa
choice_c-method	Choice_c method for ReTextBox referential objects
choice_c-method	choice_c method for class ref_timestep_daily
choice_c-method	choice_c method for ref_year referential from the command line
choice_c-method	command line interface for report_annual-class
choice_c-method	command line interface for report_dc class
choice_c-method	command line interface for report_df class
choice_c-method	command line interface for report_env class
choice_c-method	command line interface for report_ge_weight-class
choice_c-method	command line interface for report_mig class
choice_c-method	command line interface for report_mig_char class
choice_c-method	command line interface for report_env class
choice_c-method	command line interface for report_mig_interannual class
choice_c-method	command line interface for report_mig_mult class
choice_c-method	command line interface for report_sample_char class
choice_c-method	command line interface for report_sea_age class
choice_c-method	command line interface for report_silver_eel class
choice_c-method	command line interface for report_species-class
choice_c.report_annual	command line interface for report_annual-class
choice_c.report_dc	command line interface for report_dc class
choice_c.report_df	command line interface for report_df class
choice_c.report_ge_weight	command line interface for report_ge_weight-class
choice_c.report_mig	command line interface for report_mig class
choice_c.report_mig_char	command line interface for report_mig_char class
choice_c.report_mig_env	command line interface for report_env class
choice_c.report_mig_interannual	command line interface for report_mig_interannual class
choice_c.report_mig_mult	command line interface for report_mig_mult class
choice_c.report_sample_char	command line interface for report_sample_char class
choice_c.report_sea_age	command line interface for report_sea_age class
choice_c.report_silver_eel	command line interface for report_silver_eel class
choice_c.report_species	command line interface for report_species-class
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-method	connect method for report_annual class this method performs the sum over the year attention this function does not count subsamples.
connect-method	connect method for report_dc
connect-method	connect method for report_df
connect-method	connect method for report_env class
connect-method	connect method for report_Poids_moyen
connect-method	connect method for report_mig
connect-method	connect method for report_mig_char
connect-method	connect method for report_mig_env class
connect-method	connect method for report_mig_interannual
connect-method	connect method for report_mig_mult
connect-method	connect method for report_ope
connect-method	connect method for report_sample_char
connect-method	connect method for report_sea_age
connect-method	connect method for report_silver_eel
connect-method	connect method for report_species
connect.report_annual	connect method for report_annual class this method performs the sum over the year attention this function does not count subsamples.
connect.report_dc	connect method for report_dc
connect.report_df	connect method for report_df
connect.report_env	connect method for report_env class
connect.report_ge_weight	connect method for report_Poids_moyen
connect.report_mig	connect method for report_mig
connect.report_mig_char	connect method for report_mig_char
connect.report_mig_interannual	connect method for report_mig_interannual
connect.report_mig_mult	connect method for report_mig_mult
connect.report_ope	connect method for report_ope
connect.report_sample_char	connect method for report_sample_char
connect.report_sea_age	connect method for report_sea_age
connect.report_silver_eel	connect method for report_silver_eel
connect.report_species	connect method for report_species
createmessage	Generic method to forward outputs
current_end_date-method	Gets the ending date of a time step for an object of class ref_timestep-class

-- E --

envir_stacomi

Environment where most objects from the package are stored and then loaded by the charge method

-- F --

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
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

-- G --

getdbname	Retrieves the dbname from a connection using "baseODBC"
getnocurrent_step	Generic method to get current time step
getvalue	Generic method getvalue
getvalue-method	Returns the POSIXt value of a given name
graphdate	function used for some lattice graphs with dates
graphe	Methods for Function graphe
graphe-method	Methods for Function graphe
graphe-methods	Methods for Function graphe

-- M --

model	Generic for prediction
model-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.
model.report_ge_weight	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.

-- P --

plot-method	Plot method for report_annual
plot-method	Different plots for report_dc
plot-method	Different plots for report_df
plot-method	Plot method for report_env
plot-method	Plot method for report_ge_weight'
plot-method	Plots of various type for report_mig.
plot-method	plot method for report_mig_char
plot-method	Plot method for report_mig_env
plot-method	Plot method for report_mig_interannual
plot-method	Plots of various type for report_mig_mult
plot-method	Plots of various type for reportcarlot
plot-method	Plots of various type for report_sea_age
plot-method	Plots of various type for report_silver_eel
plot-method	Plot method for report_species
plot.reportreport_species	Plot method for report_species
plot.report_annual	Plot method for report_annual
plot.report_dc	Different plots for report_dc
plot.report_df	Different plots for report_df
plot.report_env	Plot method for report_env
plot.report_ge_weight	Plot method for report_ge_weight'
plot.report_mig	Plots of various type for report_mig.
plot.report_mig_char	plot method for report_mig_char
plot.report_mig_env	Plot method for report_mig_env
plot.report_mig_interannual	Plot method for report_mig_interannual
plot.report_mig_mult	Plots of various type for report_mig_mult
plot.report_sample_char	Plots of various type for reportcarlot
plot.report_sea_age	Plots of various type for report_sea_age
plot.report_silver_eel	Plots of various type for report_silver_eel
print-method	Method to print the command line of the object
print-method	Method to print the command line of the object
print-method	Method to print the command line of the object
print-method	Method to print the command line of the object
print-method	Method to print the command line of the object
print-method	Method to print the command line of the object
print-method	Method to print the command line of the object
print.report_dc	Method to print the command line of the object
print.report_df	Method to print the command line of the object
print.report_mig	Method to print the command line of the object
print.report_mig_mult	Method to print the command line of the object
print.report_sample_char	Method to print the command line of the object
print.report_sea_age	Method to print the command line of the object
print.report_silver_eel	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.

-- Q --

quitte

function used to clean the objects within the group and the graphs and also elements remaining in the envir_stacomi environment

-- R --

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 "report_annual"
report_annual-class	Class "report_annual"
report_dc	Class "report_dc" report du fonctionnement du dispositif de comptage
report_dc-class	Class "report_dc" report du fonctionnement du dispositif de comptage
report_df	Report on fishway operation
report_df-class	Report on fishway operation
report_env	class report_env simple output of one or several environmental conditions...
report_env-class	class report_env simple output of one or several environmental conditions...
report_ge_weight	Trend of wet weight in glass eel
report_ge_weight-class	Trend of wet weight in glass eel
report_mig	Migration report for one DC, one species and one stage
report_mig-class	Migration report for one DC, one species and one stage
report_mig_char	Migration report along with quantitative and qualitative characteristics
report_mig_char-class	Migration report along with quantitative and qualitative characteristics
report_mig_env	Class "report_mig_env"
report_mig_env-class	Class "report_mig_env"
report_mig_interannual	Class "report_mig_interannual"
report_mig_interannual-class	Class "report_mig_interannual"
report_mig_mult	Migration reports for multiple DC / species / stages
report_mig_mult-class	Migration reports for multiple DC / species / stages
report_ope	Report on operations
report_ope-class	Report on operations
report_sample_char	Class "report_sample_char"
report_sample_char-class	Class "report_sample_char"
report_sea_age	Class "report_sea_age"
report_sea_age-class	Class "report_sea_age"
report_silver_eel	Class "report_silver_eel"
report_silver_eel-class	Class "report_silver_eel"
report_species	Counts of number per taxa/stages
report_species-class	Counts of number per taxa/stages
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

-- S --

setasqualitative	Generic method to transform quantitative par into a qualitative one
setasqualitative-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
summary-method	summary for report_dc, write csv and html output, and prints summary statistics
summary-method	summary for report_df, write csv and html output, and prints summary statistics
summary-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-method	summary for report_mig_char
summary-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-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-method	summary for report_sample_char
summary-method	summary for report_sea_age
summary-method	summary for report_silver_eel
summary-method	summary for report_species generate csv and html output in the user data directory
summary.report_dc	summary for report_dc, write csv and html output, and prints summary statistics
summary.report_df	summary for report_df, write csv and html output, and prints summary statistics
summary.report_mig	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	summary for report_mig_char
summary.report_mig_env	connect method for report_mig_env class
summary.report_mig_interannual	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	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	summary for report_sample_char
summary.report_sea_age	summary for report_sea_age
summary.report_silver_eel	summary for report_silver_eel
summary.report_species	summary for report_species generate csv and html output in the user data directory
supprime	Generic method to delete entires from the database
supprime-method	supprime method for "ref_coe" class
supprime-method	supprime method for report_mig_interannual class
supprime-method	supprime method for report_mig_interannual class
supprime.report_mig_interannual	supprime method for report_mig_interannual class
supprime.report_sea_age	supprime method for report_mig_interannual class

-- V --

vector_to_listsql

Transforms a vector into a string called within an sql command e.g. c('A','B','C') => in ('A','B','C')

-- W --

write_database	Generic method write_database
write_database-method	Function to write data to the stacomi database for report_ge_weight-class
write_database-method	Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table
write_database-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
write_database.report_ge_weight	Function to write data to the stacomi database for report_ge_weight-class
write_database.report_mig	Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table
write_database.report_sea_age	Command line method to write the characteristic "sea age" (car_par_code='A124') into the tj_caracteristiquelot_car table in the user's scheme

-- X --

xtable-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-method	xtable function for report_mig_char-class create an xtable objet to be later used by the print.xtable method.
xtable.report_annual	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	xtable function for report_mig_char-class create an xtable objet to be later used by the print.xtable method.