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).
charge,ref_textbox-method
Loading method for ReTextBox referential objects
loads the coefficients for the period defined in class
charge,report_mig_env-method
charge method for report_mig_env class
calcule,report_ge_weight-method
Calcule method for report_ge_weight
Loading method for ref_taxa referential objects
charge,report_mig_interannual-method
loading method for report_mig_interannual class
Loading method for Rechoice referential objects
Generic method to load referentials
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_interannual-method
calcule method for report_mig_interannual
barplot,report_annual-method
barplot method for object report_annual-class calcule,report_species-method
calcule method for report_species
calcule,report_silver_eel-method
Calculate individual silver eel parameters.
charge,ref_checkbox-method
Loading method for ref_checkbox referential objects
Generic method for calculations
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
Loading method for ref_year referential objects
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,ref_parquan-method
Loading method for Reparquan referential objects
charge_with_filter,ref_par-method
Loading method for Repar referential objects searching only those parameters existing for a DC, a Taxa, and a stage
Generic method to load additional data
Loading method for ref_stage referential objects
charge,report_sea_age-method
Loads data and check that all choices in the graphical interface have been made.
calcule,report_mig_char-method
Computes data to a standard format for the summary and plot methods.
charge,report_sample_char-method
charge method for report_sample_char class
calcule,report_sample_char-method
Calculation for report_sample_char
charge,report_annual-method
charge method for report_annual class
Choice method for Rechoice referential objects
charge method for report_env class
Loading method for refliste referential objects
Loading method for ref_env referential object
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 Loading method for DF referential objects
Method to load the counting devices of the control station
Loading method for Repar referential objects
choice_c,ref_textbox-method
Choice_c method for ReTextBox referential objects
choice,ref_horodate-method
Graphical interface
charge,ref_parqual-method
Loading method for Reparqual referential objects
Choice method for ref_stage referential objects
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_annual-method
command line interface for report_annual-class charge,report_mig_mult-method
charge method for report_mig_mult
Choice method for reftaxa referential objects with only one taxa selected
Graphical method to choose a fishway through the interface
charge method for report_dc
choice_c,ref_stage-method
choice_c method for ref_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 method for report_ope
charge method for report_df
choice method for ref_year referential
choice_c,report_mig_mult-method
command line interface for report_mig_mult class
Choice method for ref_list referential objects
choice,ref_timestep_daily-method
Method to select timesteps from the graphical interface
charge,report_ge_weight-method
charge method for report_ge_weight class
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).
Generic method for manual choice using the command line
connect,report_mig-method
connect method for report_mig
connect,report_mig_char-method
connect method for report_mig_char
choice_c,report_dc-method
command line interface for report_dc class
choice_c,report_species-method
command line interface for report_species-class choice_c method for ref_taxa
choice_c,report_df-method
command line interface for report_df class
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.
Loads additional data on migration control operations, df (fishway) dc (counting device).
charge_with_filter,ref_parquan-method
Loading method for Reparquan referential objects searching only those parameters existing for a DC, a Taxon, and a stage
Choice method for ref_env referential object
choice_c,ref_choice-method
Choice_c method for refchoix referential objects
choice_c,ref_horodate-method
Command line
Command line interface to select a monitoring station
Generic method for choice (using the gwidget graphical interface)
This function extracts temporal characteristics from a dataframe
fun_report_mig_interannual
statistics per time period
currentstart_date,ref_timestep-method
Gets the starting date of a time step for an object of class ref_timestep-class Graphical method to choose a fishway through the interface
choice_c,report_mig_env-method
command line interface for report_env class
Handler for barchart for report_df class from the graphical interface
Generic method for getting the ending date for current time step
charge,report_silver_eel-method
charge method for report_silver_eel class
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,report_mig_interannual-method
command line interface for report_mig_interannual class
Methods for Function chargecomplement
choice_c,report_sample_char-method
command line interface for report_sample_char class
choice,ref_parqual-method
Choice method for ref_parqual referential objects, internal use
choice_c,report_sea_age-method
command line interface for report_sea_age class
connect method for report_dc
charge,report_species-method
charge method for report_species
Command line interface to select a counting device
Choice method for ref_par referential objects
connect method for report_df
choice_c,report_mig-method
command line interface for report_mig class
charge,report_mig_char-method
charge method for report_mig_char
charge_with_filter,ref_taxa-method
Loading method for ref_taxa referential objects searching only taxa existing for a DC
Command line interface to choose a fishway
choice_c,report_silver_eel-method
command line interface for report_silver_eel class
Generic method to load referentials, with filters from the parent object in the database
choice_c,report_mig_char-method
command line interface for report_mig_char class
this function uses gfile, edits a text with info and changing colors
funplotreport_sea_age
Handler for barchart for report_df class from the graphical interface
connect,report_ope-method
connect method for report_ope
connect,report_mig_mult-method
connect method for report_mig_mult
choicemult,ref_taxa-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.
connect,report_env-method
connect method for report_env class
funtablereport_silver_eel
table function
connect,report_ge_weight-method
connect method for report_Poids_moyen
choicemult,ref_timestep-method
Graphical interface for multiple choice method for PasdeTemps (used in report_mig_mult)
returns a table where weights and number are calculated from number and weights respectively
performs a query to collect the conversion coefficients
This writes monthly data in t_reportmensuel_mens table
chargecsv loads the informations stored in c:/program
files/stacomi/calcmig.csv file
choicemult,ref_horodate-method
Multiple Choice method for ref_horodate referential objects, to put together with notebook widgets
Handler function to plot calendar like graph, internal use
Environment where most objects from the package are stored and then loaded
by the charge method
returns a table where all components within the list calcdata are aggregated
and formatted for plot
function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class
Generic method for multiple choice (using the gwidget notebook for multiple choice)
Generic method for getting the final date
Generic method for getting the beginning date for current time step
function used to remove special non utf8 character which cause the gtk
interface to crash
end_date,ref_timestep-method
Gets the final horodate for an object of class ref_timestep-class getvalue,ref_period-method
Returns the POSIXt value of a given name
choicemult,ref_par-method
Multiple Choice method for ref_par referential objects, internal use
choice,ref_checkbox-method
Choice method for ref_checkbox referential objects
Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters
Generic method getvalue
connect,report_sample_char-method
connect method for report_sample_char
funboxplotreport_sample_char
Boxplots for ggplot2
get_step_label,ref_timestep-method
Gets the string value of time step
connect,report_sea_age-method
connect method for report_sea_age
FuntableDC create a table output for report_dc class
Table output for report_df class
Internal handler for reg, class report_ge_weight-class Handler function to plot calendar like graph, internal use
h_report_envgraph Internal method
Retrieves the dbname from a connection using "baseODBC"
function to create daily statistics
Function to calculate statistics per month
funtablereport_sample_char
table function
Generic method the get starting date
Generic method to forward outputs
fundensityreport_sample_char
fundensityreport_sample_char uses ggplot2 to draw density plots
table function
current_end_date,ref_timestep-method
Gets the ending date of a time step for an object of class ref_timestep-class handler function used by the main interface
handler for plot method in report_mig_mult class
handler for calculations
handler to print the command line
interface for report_annual class
handler function used by the main interface
internal method for graphical interface
handler to print the command line
plot,report_annual,missing-method
Plot method for report_annual
Generic for prediction
Internal handler function
interface for report_dc class
An interface that calls the object to build the user interface
Calculate daily migration by simple repartition
Choice_c method for ref_list referential objects
choice,ref_textbox-method
Choice method for ReTextBox referential objects
handler function used by the main interface
handler function used by the main interface
fun_report_mig_mult_overlaps
Function to calculate daily migration using overlaps functions
plot,report_mig_mult,missing-method
Plots of various type for report_mig_mult
interface_report_sample_char
An interface that calls the object to build the user interface
choice,ref_timestep-method
Method to select timesteps from the graphical interface
Command line interface to select a parameter
Function to create a barchart (lattice) corresponding to the periods
hgraph_report_mig_interannual
Plot of all interannual from top to bottom
handler
plot,report_sample_char,missing-method
Plots of various type for reportcarlot
handler function used by the main interface
handler du calcul h_report_miggraph2
handler function used by the main interface
choice_c,report_env-method
command line interface for report_env class
handler function used by the main interface
Handler for barchart for report_df class from the graphical interface
choice_c,report_ge_weight-method
command line interface for report_ge_weight-class hgraph_report_mig_interannual2
Plot of daily migrations
Generic method to get current time step
getnocurrent_step,ref_timestep-method
Gets the current time step of an object of class ref_timestep-class Internal handler for reg, class report_ge_weight-class funplotreport_silver_eel
Class "ref_choice"
Generic method to get the years
Counting device operation for the video recording (Arzal dam, Vilaine, France).
handler function used by the main interface
funpointreport_sample_char
Point graph from ggplot
choicemult,ref_choice-method
Multiple Choice method for ref_choice referential objects, to put together with notebook widgets
Counting Device (DC) operation from 2000 to 2015 at the Arzal dam (Vilaine, France)
handler for plot internal use
interface for report_df class
Overview of the fishway operation at Arzal in (Vilaine France).
Fishway operation for the vertical slot fishway (Arzal dam, Vilaine, France).
Class "ref_list"
interface_report_silver_eel
An interface that calls the object to build the user interface
getdateDebut,ref_timestep-method
Returns the starting date as character
Class "ref_taxa"
Class "ref_coe"
choicemult, selection method for ref_dc allowing to select several DC
ref_textbox referencial class
handler for summary function, internal use
calls functions funstat and funtable to build summary tables in html and
csv files
Interface for class conditionEnv
handler function used by the main interface
Class "ref_par"
handler for h_report_miggraph
handler function used by the main interface
Internal handler for reg, class report_ge_weight-class Barplot handler
connect,report_mig_env-method
connect method for report_mig_env class
choicemult,ref_parqual-method
Multiple Choice method for ref_parqual referential objects internal use
Interface for report_species class
choicemult,ref_stage-method
Multiple Choice method for ref_stage referential objects
plot,report_dc,ANY-method
Different plots for report_dc
handler for calculations report_mig
Internal handler for reg, class report_ge_weight-class connect,report_mig_interannual-method
connect method for report_mig_interannual
plot,report_df,ANY-method
Different plots for report_df
handler function table
hgraph_report_mig_interannual3
Step plot with different years displayed on the same graph. One year
can be highlighted against the others
Generic method to transform quantitative par into a qualitative one
Method to print the command line of the object
Method to print the command line of the object
Migration reports for multiple DC / species / stages
print,report_sea_age-method
Method to print the command line of the object
hgraph_report_mig_interannual4
Plot comparing the migration to the migration
computed for all years available in the daily migration table.
This function plots comparisons for periods of 1 week, 2 weeks, month
report_mig_interannual-class
Class "report_mig_interannual"
print,report_silver_eel-method
Method to print the command line of the object
handler function used by the main interface
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
handler function used by the main interface
Seasonality of salmon migration at the Vichy counting station (Loire)
setref_horodate,ref_horodate-method
Method to set the Horodate
Interface for report_mig class, internal use, this function is called
by a handler in the main graphical 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.
connect,report_silver_eel-method
connect method for report_silver_eel
plot handler
interface_report_ge_weight
interface for report_ge_weight class
Internal handler for reg, class report_ge_weight-class plot,report_mig_env,missing-method
Plot method for report_mig_env
Internal function, tests the connection and if it works loads the stacomi interface
summary,report_mig_char-method
summary for report_mig_char
Validity check for ref_year
handler for h_report_miggraph2
connect,report_species-method
connect method for report_species
handler h_report_migwrite
Allows the saving of daily and monthly counts in the database
handler function used by the main interface
Validity check for ref_horodate
Function to calculate the stages from Durif
functions called in DF and DC
Counting operations for three different counting device in Arzal (Vilaine, France)
function used for some lattice graph
Anguilla migration at the Arzal station (report_mig_mult-class)
handler for plot
handler function used by the main interface
handler for plot
Class "ref_timestep"
Class ref_horodate
An object of class report_ope-class with data loaded Class "ref_env"
Internal use, rectangles to describe the DF work for report_df class,
graphical interface handler
plot,report_mig_interannual,missing-method
Plot method for report_mig_interannual
Report on operations
handler to print the command line
Progress bar using a gtkdialog, the progress bar is assigned in envir_stacomi
This progress bar has a button to close.
function used to clean the objects within the group and the graphs and
also elements remaining in the envir_stacomi environment
handler to print the command line
stacomiR
Test that the program is installed.
Class "report_sample_char"
Function for report_mig graphs including numbers DF DC operations
hsummaryreport_migInterannuelle
Summary handler internal method
handler for summary report_species, internal use
Class "ref_timestepChar"
Video counting of thin lipped mullet (Liza ramada) in 2015 in the Vilaine (France)
Qualitative and quantitative parameters describing Salmon migration at Decize (Loire)
Generic method to get the string value of time step
Graph function for glass eel migration. Differs from fungraph as it does not
draw the ggplot graph for month
interface_report_mig_interannual
interface for report_mig_interannual class
get_year,ref_timestep-method
Gets the year or a vector of years corresponding to the timestep ("ref_timestep") object
plot,report_mig,ANY-method
Plots of various type for report_mig.
plot,report_mig_char,missing-method
plot method for report_mig_char
Method to print the command line of the object
plot,report_species,missing-method
Plot method for report_species
Annual migration of yellow and silver eel for three fishways / counting devices at the
Arzal dam (data from 1995 to 2016)
An object of class report_mig_env with data loaded
summary,report_sample_char-method
summary for report_sample_char
summary,report_sea_age-method
summary for report_sea_age
Daily glass eel and elver migration from 1984 to 2016 in the Sevre Niortaise
Transforms a vector into a string called within an sql command e.g.
c('A','B','C') => in ('A','B','C')
function used for some lattice graphs with dates
Silver eel migration in the Somme
Annual migration of salmon in the Adour and tributaries
write_database,report_ge_weight-method
Function to write data to the stacomi database for report_ge_weight-class interface_report_mig_mult
graphical interface for report_mig_mult class
ref_checkbox referencial class
Size of yellow and glass eel at the Arzal dam (Vilaine, France) in the fishway and main eel trapping ladder.
An object of class report_sea_age with data loaded
Class "ref_period" referential class
Class "ref_parqual"
Class "ref_stage"
Class "report_sea_age"
Create a dataframe suitable for charts per 24h and day
handler function used by the main interface
Class "ref_timestep_daily"
handler function used by the main interface
Function that loads the loginwindow, tests connection, and then destroys the
window
summary,report_silver_eel-method
summary for report_silver_eel
handler function used by the main interface
handler for calculation
Class "report_silver_eel"
Class "ref_parquan"
Methods for Function graphe
summary,report_species-method
summary for report_species
generate csv and html output in the user data directory
handler function used by the main interface
handler for plot
class report_env simple output of one or several environmental
conditions...
supprime,report_sea_age-method
supprime method for report_mig_interannual class
Generic method to delete entires from the database
This handler calls the generic method stat
Year reference class
Report on fishway operation
handler for report_mig_char
Generic method write_database
summary for report_dc, write csv and html output, and prints summary statistics
setasqualitative,report_mig_char-method
Turns a quantitative parameter into qualitative
Migration report for one DC, one species and one stage
Trend of wet weight in glass eel
summary for report_df, write csv and html output, and prints summary statistics
Generic method to set the starting date
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. write_database,report_mig-method
Command line method to write the daily and monthly counts to the
t_bilanmigrationjournalier_bjo table
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
hgraph_report_mig_interannual5
Function displaying comparison similar to hgraph_report_mig_interannual4 but using pointrange and geom_bar
This function plots comparisons for periods of 1 week, 2 weeks, month hgraph_report_mig_interannual7
This function creates a cumulated area plot to highlight seasonal trends in migration. Data are calculated by
2 weeks period then centered and reduced
plot,report_env,missing-method
Plot method for report_env
plot,report_ge_weight,missing-method
Plot method for report_ge_weight'
xtable handler
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
print,report_mig_mult-method
Method to print the command line of the object
Program launch, this function launches the GwidgetRgtk graphical
interface to stacomi. To be able to run, some widgets (win, grouptotal, group...)
are assigned in the user environment .GlobalEnv.
print,report_sample_char-method
Method to print the command line of the object
interface_report_mig_char
interface for report_migPar class
Class "ref_df"
Class "report_annual"
Migration report along with quantitative and
qualitative characteristics
Class "ref_dc"
Class "report_mig_env"
Counts of number per taxa/stages
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.
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
supprime method for "ref_coe" class
supprime,report_mig_interannual-method
supprime method for report_mig_interannual class
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. Counting device operation for three different counting device in Arzal (Vilaine, France)
Wet weight of glass eel from the trapping ladder (Arzal, Vilaine France)
Fishway operation at the Arzal Dam (Vilaine France) (3 Fishways in 2011)
interface for report_migConditionEnv class
set_starting_date,ref_timestep-method
Sets starting date from a character
An object of class report_env with data loaded