calcule,report_ge_weight-method
Calcule method for report_ge_weight
barplot,report_annual-method
barplot method for object report_annual-class 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
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).
loads the coefficients for the period defined in class
Loading method for Refchoice referential objects
charge,ref_parqual-method
Loading method for Reparqual referential objects
Loading method for ref_par referential objects
charge method for report_env class
Loads additional data on migration control operations, df (fishway) dc (counting device).
charge,report_mig_env-method
charge method for report_mig_env class
charge,report_mig_char-method
charge method for report_mig_char
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_sample_char-method
Calculation for report_sample_char
calcule,report_sea_age-method
Split data according to the limits
set in the limit1hm, and limit2hm arguments of the report_sea_age-class . charge method for report_dc
charge method for report_df
choice_c,ref_choice-method
Choice_c method for ref_choice referential objects
charge,report_sea_age-method
Loads data and check that all choices in the graphical interface have been made.
calcule,report_silver_eel-method
Calculate individual silver eel parameters.
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
Generic method for calculations
charge,ref_parquan-method
Loading method for Reparquan referential objects
calcule,report_species-method
calcule method for report_species
Loading method for ref_stage referential objects
choice_c,ref_horodate-method
Choice_c method for ref_horodate
Command line interface to select a counting device
Choice_c method for ref_list referential objects
charge,report_silver_eel-method
charge method for report_silver_eel class
Loading method for ref_env referential object
Loading method for ref_year referential objects
Method to load the counting devices of the control station
Loading method for DF referential objects
charge,report_annual-method
charge method for report_annual class
charge_with_filter,ref_taxa-method
Loading method for ref_taxa referential objects searching only taxa existing for a DC
charge method for report_ope
Loading method for ref_list referential objects
charge,ref_textbox-method
Loading method for ref_textbox referential objects
Loading method for ref_taxa referential objects
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_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
charge,report_mig_mult-method
charge method for report_mig_mult
Generic method to load additional data
Command line interface to select a parameter
choice_c,report_silver_eel-method
command line interface for report_silver_eel class
choice_c,report_ge_weight-method
command line interface for report_ge_weight-class 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,report_mig-method
command line interface for report_mig class
Generic method to load referentials, with filters from the parent object in the database
choice_c,ref_stage-method
choice_c method for ref_stage
choice_c method for ref_taxa
choice_c,ref_textbox-method
Choice_c method for ref_textbox referential objects
choice_c,report_mig_env-method
command line interface for report_env class
choice_c,report_mig_char-method
command line interface for report_mig_char class
choice_c,report_df-method
command line interface for report_df class
connect,report_sea_age-method
connect method for report_sea_age
connect,report_sample_char-method
connect method for report_sample_char
choice_c,report_species-method
command line interface for report_species-class Internal use, rectangles to describe the DF work for report_df class,
choice_c,report_env-method
command line interface for report_env class
Function to calculate statistics per month
Generic method for manual choice using the command line
funboxplotreport_sample_char
Boxplots for ggplot2
funpointreport_sample_char
Point graph from ggplot
end_date,ref_timestep-method
Gets the final horodate for an object of class ref_timestep-class Generic method to load referentials
charge,report_species-method
charge method for report_species
Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters
plot,report_annual,missing-method
Plot method for report_annual
Generic for prediction
plot,report_sea_age,missing-method
Plots of various type for report_sea_age
Generic method for getting the final date
plot,report_silver_eel,missing-method
Plots of various type for report_silver_eel
Function to create a barchart (lattice) corresponding to the periods
connect,report_mig_char-method
connect method for report_mig_char
connect,report_mig-method
handler for calculations report_mig
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,report_sea_age-method
command line interface for report_sea_age class
choice_c,report_sample_char-method
command line interface for report_sample_char class
connect,report_mig_env-method
connect method for report_mig_env class
connect,report_mig_interannual-method
connect method for report_mig_interannual
function used to clean the objects within the group and the graphs and
also elements remaining in the envir_stacomi environment
connect,report_silver_eel-method
connect method for report_silver_eel
choice_c,ref_timestep_daily-method
choice_c method for class ref_timestep_daily
charge_with_filter,ref_stage-method
Loading method for ref_stage referential objects searching only those stages existing for a DC and a Taxon
choice_c method for ref_year referential from the command line
Command line interface to choose a fishway
This writes monthly data in t_reportmensuel_mens table
Internal function, tests the connection and if it works loads the stacomi interface
connect,report_species-method
connect method for report_species
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.
Internal use barchart for report_df class from the graphical interface
fun_report_mig_interannual
statistics per time period
Command line interface to select a monitoring station
choice_c,report_mig_mult-method
command line interface for report_mig_mult class
choice_c,report_annual-method
command line interface for report_annual-class Calculate daily migration by simple repartition
choice_c,report_mig_interannual-method
command line interface for report_mig_interannual class
Internal use, function used in the graphical interface to create a barchart for report_df class
fun_report_mig_mult_overlaps
Function to calculate daily migration using overlaps functions
Function to plot calendar like graph, internal use
plot,report_mig_mult,missing-method
Plots of various type for report_mig_mult
choice_c,report_dc-method
command line interface for report_dc class
connect method for report_dc
Class 'ref_dc'
Class 'ref_df'
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,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_mig_mult-method
connect method for report_mig_mult
Seasonality of salmon migration at the Vichy counting station (Loire)
Annual migration of yellow and silver eel for three fishways / counting devices at the
Arzal dam (data from 1995 to 2016)
Daily glass eel and elver migration from 1984 to 2016 in the Sevre Niortaise
Class 'ref_taxa'
connect,report_ope-method
connect method for report_ope
connect method for report_df
fundensityreport_sample_char
fundensityreport_sample_char uses ggplot2 to draw density plots
Function to calculate the stages from Durif
Calculates a data.frame where all components within the list calcdata are aggregated
and formatted for plot
Environment where most objects from the package are stored and then loaded
by the charge method
functions called in DF and DC
print,report_sea_age-method
Method to print the command line of the object
print,report_silver_eel-method
Method to print the command line of the object
Counting operations for three different counting device in Arzal (Vilaine, France)
plot,report_sample_char,missing-method
Plots of various type for reportcarlot
connect,report_env-method
connect method for report_env class
ref_textbox referencial class
An object of class report_sea_age with data loaded
Class 'ref_list'
Fishway operation at the Arzal Dam (Vilaine France) (3 Fishways in 2011)
Silver eel migration in the Somme
this function displays text and will be used to convey stacomiR message in shiny
connect,report_ge_weight-method
connect method for report_Poids_moyen
Class "report_mig_env"
Migration report along with quantitative and
qualitative characteristics
returns a table where weights and number are calculated from number and weights respectively
performs a query to collect the conversion coefficients
Create a dataframe suitable for charts per 24h and day
Generic method to transform quantitative par into a qualitative one
Function for report_mig graphs including numbers DF DC operations
this function gets the schema from envir stacomi and throws warning
Graph function for glass eel migration. Differs from fungraph as it does not
draw the ggplot graph for month
Class 'ref_par'
function used to remove special non utf8 character which cause the gtk
interface to crash
function used for some lattice graphs with dates
Generic method getvalue
plot,report_dc,ANY-method
Different plots for report_dc
Generic method to get the years
getvalue,ref_period-method
Returns the POSIXt value of a given name
funplotreport_silver_eel
Counts of number per taxa/stages
plot,report_mig,ANY-method
Plots of various type for report_mig.
setasqualitative,report_mig_char-method
handler for report_mig_char
get_year,ref_timestep-method
Gets the year or a vector of years corresponding to the timestep ("ref_timestep") object
plot,report_df,ANY-method
Different plots for report_df
print,report_mig_mult-method
Method to print the command line of the object
print,report_sample_char-method
Method to print the command line of the object
This function extracts temporal characteristics from a dataframe
Annual migration of salmon in the Adour and tributaries
function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class
Counting Device (DC) operation from 2000 to 2015 at the Arzal dam (Vilaine, France)
Method to print the command line of the object.
plot,report_ge_weight,missing-method
Plot method for report_ge_weight'
plot,report_species,missing-method
Plot method for report_species
plot,report_mig_char,missing-method
handler for plot
Overview of the fishway operation at Arzal in (Vilaine France).
An object of class report_env with data loaded
plot,report_env,missing-method
h_report_envgraph Internal method
Fishway operation for the vertical slot fishway (Arzal dam, Vilaine, France).
Anguilla migration at the Arzal station (report_mig_mult-class)
funtableDC create a table output for report_dc class
Table output for report_df class
An object of class report_mig_env with data loaded
Method to print the command line of the object
plot,report_mig_interannual,missing-method
Plot method for report_mig_interannual
plot,report_mig_env,missing-method
Plot method for report_mig_env
this function gets the name of the stucture as it is set in the database
summary,report_sea_age-method
summary for report_sea_age
Qualitative and quantitative parameters describing Salmon migration at Decize (Loire)
Class ref_horodate
Counting device operation for the video recording (Arzal dam, Vilaine, France).
Class 'ref_env'
An object of class report_ope-class with data loaded summary,report_silver_eel-method
summary for report_silver_eel
Class "ref_timestep"
Size of yellow and glass eel at the Arzal dam (Vilaine, France) in the fishway and main eel trapping ladder.
handler to print the command line
Class "ref_timestepChar"
Trend of wet weight in glass eel
Report on fishway operation
Generic method to delete entires from the database
Class 'ref_parqual'
Class 'ref_parquan'
Counting device operation for three different counting device in Arzal (Vilaine, France)
class report_env simple output of one or several environmental
conditions...
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
Validity check for ref_horodate
Wet weight of glass eel from the trapping ladder (Arzal, Vilaine France)
Migration report for one DC, one species and one stage
Class 'ref_stage'
Class 'ref_coe'
Video counting of thin lipped mullet (Liza ramada) in 2015 in the Vilaine (France)
Class 'ref_choice'
Class "report_annual"
Class 'ref_period' referential class
Generic method write_database
write_database,report_mig-method
Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table
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.
write_database,report_ge_weight-method
Method to write data to the stacomi database for report_ge_weight-class summary,report_mig_char-method
summary for report_mig_char
Class "report_sea_age"
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
Class "report_dc" report du fonctionnement du dispositif de
comptage
Class "report_silver_eel"
stacomi Main launcher for program stacomi
Class 'ref_timestep_daily'
Report on operations
Class 'report_sample_char'
summary for report_dc, write csv and html output, and prints summary statistics
Transforms a vector into a string called within an sql command e.g.
c('A','B','C') => in ('A','B','C')
Validity check for ref_year
summary,report_sample_char-method
summary for report_sample_char
supprime,report_mig_interannual-method
supprime method for report_mig_interannual class, deletes values in table t_bilanmigrationjournalier_bjo
Year reference class
summary for report_df, write csv and html output, and prints summary statistics
report_mig_interannual-class
Class "report_mig_interannual"
Migration reports for multiple DC / species / stages
supprime,report_sea_age-method
supprime method for report_mig_interannual class
summary,report_species-method
summary for report_species
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
supprime method for 'ref_coe' class
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. 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.