Loading method for ref_par referential objects
Loading method for DF referential objects
Generic method for calculations
Loading method for ref_env referential object
charge,ref_parqual-method
Loading method for Reparqual referential objects
calcule,report_species-method
calcule method for report_species
Loading method for Refchoice referential objects
Method to load the counting devices of the control station
loads the coefficients for the period defined in class
charge method for report_dc
Loading method for ref_year referential objects
Loads additional data on migration control operations, df (fishway) dc (counting device).
charge method for report_env class
charge method for report_df
charge,report_annual-method
charge method for report_annual class
Loading method for ref_list referential objects
charge method for report_ope
Loading method for ref_stage referential objects
charge,ref_parquan-method
Loading method for Reparquan referential objects
Generic method to load referentials
charge,report_mig_interannual-method
loading method for report_mig_interannual class
charge,report_sample_char-method
charge method for report_sample_char class
charge,report_species-method
charge method for report_species
charge,report_mig_char-method
charge method for report_mig_char
charge_with_filter,ref_par-method
Loading method for ref_par 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,report_mig_env-method
charge method for report_mig_env class
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
Command line interface to select a parameter
Command line interface to select a counting device
charge,report_silver_eel-method
charge method for report_silver_eel class
choice_c,ref_choice-method
Choice_c method for ref_choice referential objects
Loading method for ref_taxa referential objects
charge,ref_textbox-method
Loading method for ref_textbox referential objects
charge,report_mig_mult-method
charge method for report_mig_mult
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_parquan-method
Loading method for Reparquan referential objects searching only those parameters existing for a DC (counting device), a Taxon, and a stage
choice_c,ref_stage-method
choice_c method for ref_stage
charge,report_sea_age-method
Loads data and check that all choices in the graphical interface have been made.
Command line interface to select a monitoring station
choice_c,report_mig_interannual-method
command line interface for report_mig_interannual class
Command line interface to choose a fishway
charge_with_filter,ref_taxa-method
Loading method for ref_taxa referential objects searching only taxa existing for a DC
choice_c,report_mig_char-method
command line interface for report_mig_char class
connect method for report_dc
choice_c,ref_timestep_daily-method
choice_c method for class ref_timestep_daily
choice_c,report_annual-method
command line interface for report_annual-class
choice_c method for ref_year referential from the command line
choice_c,report_dc-method
command line interface for report_dc class
connect method for report_df
connect,report_mig_env-method
connect method for report_mig_env class
connect,report_mig_interannual-method
connect method for report_mig_interannual
Generic method for manual choice using the command line
Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters
choice_c,report_mig_env-method
command line interface for report_env class
connect,report_species-method
connect method for report_species
connect,report_silver_eel-method
connect method for report_silver_eel
connect,report_mig_mult-method
connect method for report_mig_mult
connect,report_ope-method
connect method for report_ope
choice_c,report_env-method
command line interface for report_env class
choice_c,report_silver_eel-method
command line interface for report_silver_eel class
Choice_c method for ref_list referential objects
choice_c,ref_horodate-method
Choice_c method for ref_horodate
choice_c,report_sea_age-method
command line interface for report_sea_age class
choice_c method for ref_taxa
choice_c,report_ge_weight-method
command line interface for report_ge_weight-class
choice_c,report_sample_char-method
command line interface for report_sample_char class
choice_c,report_mig-method
command line interface for report_mig class
choice_c,report_df-method
command line interface for report_df class
Generic method to load referentials, with filters from the parent object in the database
choice_c,ref_textbox-method
Choice_c method for ref_textbox referential objects
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).
choice_c,report_species-method
command line interface for report_species-class
fn_connect_report_mig_interannual
Get table content for table t_bilanmigrationjournalier_bjo in report_mig_interannual
Environment where most objects from the package are stored and then loaded
by the charge method
Calculate daily migration by simple repartition
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_env-method
connect method for report_env class
choice_c,report_mig_mult-method
command line used to build report_mig_mult class
fun_report_mig_mult_overlaps
Function to calculate daily migration using overlaps functions
funplotreport_silver_eel
connect,report_ge_weight-method
connect method for report_Poids_moyen
This writes monthly data in t_reportmensuel_mens table
Internal use barchart for report_df class from the graphical interface
Function to plot calendar like graph, internal use
Function for report_mig graphs including numbers DF DC operations
Generic for prediction
connect,report_mig-method
connect method for report_mig
plot,report_annual,missing-method
Plot method for report_annual
plot,report_mig_mult,missing-method
Plots of various type for report_mig_mult
Calculates a data.frame where all components within the list calcdata are aggregated
and formatted for plot
connect,report_sample_char-method
connect method for report_sample_char
connect,report_mig_char-method
connect method for report_mig_char
Function to calculate statistics per month
end_date,ref_timestep-method
Gets the final horodate for an object of class ref_timestep-class
Generic method for getting the final date
connect,report_sea_age-method
connect method for report_sea_age
plot,report_sample_char,missing-method
Plots of various type for reportcarlot
function used to remove special non utf8 character which cause the gtk
interface to crash
Creates a list of available schemas in the db
plot,report_mig_env,missing-method
Plot method for report_mig_env
An object of class report_mig_env with data loaded
Internal use, function used in the graphical interface to create a barchart for report_df class
function used for some lattice graphs with dates
Generic method getvalue
Function to calculate the stages from Durif
Internal use, rectangles to describe the DF work for report_df class,
print,report_mig_mult-method
Method to print the command line of the object
plot,report_mig_interannual,missing-method
Plot method for report_mig_interannual
print,report_sample_char-method
Method to print the command line of the object
this function gets the name of the stucture as it is set in the database
plot,report_dc,missing-method
Different plots for report_dc
Graph function for glass eel migration. Differs from fungraph as it does not
draw the ggplot graph for month
plot,report_df,missing-method
Different plots for report_df
Generic method to get the years
this function displays text and will be used to convey stacomiR message in shiny
get_year,ref_timestep-method
Gets the year or a vector of years corresponding to the timestep ("ref_timestep") object
Method to print the command line of the object
Method to print the command line of the object
Class 'ref_df'
Video counting of Marine lamprey (Petromyzon marinus) in 2012 in the Vilaine (France)
Silver eel migration in the Somme
this function gets the schema from envir stacomi and throws warning
Anguilla migration at the Arzal station (report_mig_mult-class)
Qualitative and quantitative parameters describing Salmon migration at Decize (Loire)
Daily glass eel and elver migration from 1984 to 2016 in the Sevre Niortaise
Seasonality of salmon migration at the Vichy counting station (Loire)
Counting device operation for three different counting device in Arzal (Vilaine, France)
Counting device operation for the video recording (Arzal dam, Vilaine, France).
Fishway operation for the vertical slot fishway (Arzal dam, Vilaine, France).
Class 'ref_choice'
Class 'ref_env'
returns a table where weights and number are calculated from number and weights respectively
performs a query to collect the conversion coefficients
This function extracts temporal characteristics from a dataframe
fun_report_mig_interannual
statistics per time period
functions called in DF and DC
function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class
Table output for report_df class
Internal function, tests the connection and if it works loads the stacomi interface
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_env,missing-method
Plot method for report_env
Class "ref_timestep"
Class 'ref_coe'
Annual migration of yellow and silver eel for three fishways / counting devices at the
Arzal dam (data from 1995 to 2016)
Class "ref_timestepChar"
Class 'ref_dc'
plot,report_mig,ANY-method
Plots of various type for report_mig.
plot,report_ge_weight,missing-method
Plot method for report_ge_weight'
An object of class report_env with data loaded
Class 'ref_parquan'
Fishway operation at the Arzal Dam (Vilaine France) (3 Fishways in 2011)
Annual migration of salmon in the Adour and tributaries
Wet weight of glass eel from the trapping ladder (Arzal, Vilaine France)
print,report_sea_age-method
Method to print the command line of the object
plot,report_silver_eel,missing-method
Plots of various type for report_silver_eel
plot,report_sea_age,missing-method
Plots of various type for report_sea_age
print,report_silver_eel-method
Method to print the command line of the object
Class 'ref_par'
Counts of number per taxa/stages
setasqualitative,report_mig_char-method
Turns a continuous parameter into discrete values
Class 'ref_stage'
Class "report_annual"
Class "report_dc" report du fonctionnement du dispositif de
comptage
Class ref_horodate
summary for report_df, write csv and html output, and prints summary statistics
An object of class report_ope-class with data loaded
Migration report for one DC, one species and one stage
Counting operations for three different counting device in Arzal (Vilaine, France)
Trend of wet weight in glass eel
Report on fishway operation
Class "report_silver_eel"
class report_env simple output of one or several environmental
conditions...
Class 'ref_parqual'
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
Year reference class
Class 'ref_list'
Class 'ref_timestep_daily'
report_mig_interannual-class
Class "report_mig_interannual"
Class "report_sea_age"
Migration report along with quantitative and
qualitative characteristics
summary,report_species-method
summary for report_species
supprime,report_mig_interannual-method
supprime method for report_mig_interannual class, deletes values in table t_bilanmigrationjournalier_bjo
stacomi Main launcher for program stacomi
summary for report_dc, write csv and html output, and prints summary statistics
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.
plot,report_mig_char,missing-method
plot method for report_mig_char
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 and they always include the current year from the
historical dataset.
summary,report_sea_age-method
summary for report_sea_age
Class "report_mig_env"
Migration reports for multiple DC / species / stages
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.
supprime,report_sea_age-method
supprime method for report_mig_interannual class
Generic method to delete entires from the database
Method to print the command line of the object.
plot,report_species,missing-method
Plot method for report_species
Validity check for ref_year
Validity check for ref_horodate
supprime method for 'ref_coe' class
Transforms a vector into a string called within an sql command e.g.
c('A','B','C') => in ('A','B','C')
summary,report_silver_eel-method
summary for report_silver_eel
Overview of the fishway operation at Arzal in (Vilaine France).
An object of class report_sea_age with data loaded
Size of yellow and glass eel at the Arzal dam (Vilaine, France) in the fishway and main eel trapping ladder.
Counting Device (DC) operation from 2000 to 2015 at the Arzal dam (Vilaine, France)
ref_textbox referencial class
Generic method to transform quantitative par into a qualitative one
Create a dataframe suitable for charts per 24h and day
Class 'ref_taxa'
Report on operations
Class 'report_sample_char'
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
write_database,report_ge_weight-method
Method 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
summary,report_sample_char-method
summary for report_sample_char
Generic method write_database
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
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
barplot,report_annual-method
barplot method for object report_annual-class
calcule,report_silver_eel-method
Calculate individual silver eel parameters.
calcule,report_mig_char-method
Computes data to a standard format for the summary and plot methods.
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_sea_age-method
Split data according to the limits
set in the limit1hm, and limit2hm arguments of the report_sea_age-class.
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_ge_weight-method
Calcule method for report_ge_weight
calcule,report_sample_char-method
Calculation for report_sample_char