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