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