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stacomiR (version 0.5.4.3)

Fish Migration Monitoring

Description

Graphical outputs and treatment for a database of fish pass monitoring. It is a part of the 'STACOMI' open source project developed in France by the French Office for Biodiversity (OFB) institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See for more information on 'STACOMI'.

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Version

Install

install.packages('stacomiR')

Monthly Downloads

192

Version

0.5.4.3

License

GPL (>= 2)

Maintainer

Cedric Briand

Last Published

March 18th, 2020

Functions in stacomiR (0.5.4.3)

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

charge,ref_coe-method

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

charge,ref_taxa-method

Loading method for ref_taxa referential objects

charge,report_mig_interannual-method

loading method for report_mig_interannual class

charge,ref_choice-method

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

charge,ref_year-method

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

charge_complement

Generic method to load additional data

charge,ref_stage-method

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,ref_choice-method

Choice method for Rechoice referential objects

charge,report_env-method

charge method for report_env class

charge,ref_list-method

Loading method for refliste referential objects

charge,ref_env-method

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

charge,ref_df-method

Loading method for DF referential objects

charge,ref_dc-method

Method to load the counting devices of the control station

charge,ref_par-method

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,ref_stage-method

Choice method for ref_stage referential objects

choice_c,ref_year-method

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,ref_taxa-method

Choice method for reftaxa referential objects with only one taxa selected

choice,ref_dc-method

Graphical method to choose a fishway through the interface

charge,report_dc-method

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,report_ope-method

charge method for report_ope

charge,report_df-method

charge method for report_df

choice,ref_year-method

choice method for ref_year referential

choice_c,report_mig_mult-method

command line interface for report_mig_mult class

choice,ref_list-method

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,ref_taxa-method

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.

charge,report_mig-method

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,ref_env-method

Choice method for ref_env referential object

choice_c,ref_choice-method

Choice_c method for refchoix referential objects

choice_c,ref_horodate-method

choice_c,ref_env-method

Command line interface to select a monitoring station

Generic method for choice (using the gwidget graphical interface)

fun_date_extraction

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

choice,ref_df-method

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

current_end_date

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

chargecomplement-methods

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,report_dc-method

connect method for report_dc

charge,report_species-method

charge method for report_species

choice_c,ref_dc-method

Command line interface to select a counting device

choice,ref_par-method

Choice method for ref_par referential objects

connect,report_df-method

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

choice_c,ref_df-method

Command line interface to choose a fishway

choice_c,report_silver_eel-method

command line interface for report_silver_eel class

charge_with_filter

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

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

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)

fun_weight_conversion

returns a table where weights and number are calculated from number and weights respectively performs a query to collect the conversion coefficients

fun_write_monthly

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

fun_aggreg_for_plot

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

currentstart_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

funtablereport_ge_weight

Internal handler for reg, class report_ge_weight-class.

Handler function to plot calendar like graph, internal use

h_report_envgraph

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

Generic method the get starting date

Generic method to forward outputs

fundensityreport_sample_char

fundensityreport_sample_char uses ggplot2 to draw density plots

funtablereport_sea_age

current_end_date,ref_timestep-method

Gets the ending date of a time step for an object of class ref_timestep-class

h_report_ge_weight

handler function used by the main interface

h_report_mig_mult_graph

handler for plot method in report_mig_mult class

h_report_mig_multcalc

handler for calculations

handler to print the command line

interface_report_annual

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_report_dc

interface for report_dc class

interface_report_sea_age

An interface that calls the object to build the user interface

fun_report_mig_mult

Calculate daily migration by simple repartition

choice_c,ref_list-method

Choice_c method for ref_list referential objects

choice,ref_textbox-method

Choice method for ReTextBox referential objects

h_report_silver

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

choice_c,ref_par-method

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

h_report_mig_multgraph3

plot,report_sample_char,missing-method

Plots of various type for reportcarlot

h_report_sea_age

handler function used by the main interface

h_report_mig_multgraph2

handler du calcul h_report_miggraph2

h_report_sample_char

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

getnocurrent_step

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

funplotreport_silver_eel

ref_choice-class

Class "ref_choice"

Generic method to get the years

Counting device operation for the video recording (Arzal dam, Vilaine, France).

h_report_mig_char

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_report_df

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,ref_dc-method

choicemult, selection method for ref_dc allowing to select several DC

ref_textbox-class

ref_textbox referencial class

hTablereport_mig

handler for summary function, internal use calls functions funstat and funtable to build summary tables in html and csv files

interface_report_env

Interface for class conditionEnv

h_report_mig_env

handler function used by the main interface

Class "ref_par"

h_report_miggraph

handler for h_report_miggraph

h_report_species

handler function used by the main interface

Internal handler for reg, class report_ge_weight-class.

hbarplotreport_annual

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_report_species

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

h_report_migcalc

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

hTablereport_mig_mult

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

setasqualitative

Generic method to transform quantitative par into a qualitative one

print,report_mig-method

Method to print the command line of the object

print,report_df-method

Method to print the command line of the object

report_mig_mult-class

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

h_report_mig_annual

handler function used by the main interface

r_mig_interannual_vichy

Seasonality of salmon migration at the Vichy counting station (Loire)

setref_horodate,ref_horodate-method

Method to set the Horodate

interface_report_mig

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

hplotreport_annual

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

h_report_miggraph2

handler for h_report_miggraph2

connect,report_species-method

connect method for report_species

h_report_migwrite

handler h_report_migwrite Allows the saving of daily and monthly counts in the database

handler function used by the main interface

validity_ref_horodate

Validity check for ref_horodate

fun_stage_durif

Function to calculate the stages from Durif

fun_table_per_dis

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

h_report_pigment_stages

handler function used by the main interface

hbmCplotcrossed

handler for plot

ref_timestep-class

Class "ref_timestep"

ref_horodate-class

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_ope-class

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

houtreport_mig_mult

handler to print the command line

stacomiR-package

stacomi_installed

Test that the program is installed.

report_sample_char-class

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

ref_timestepChar-class

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

fungraph_glasseel

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

print,report_dc-method

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

r_mig_interannual

Daily glass eel and elver migration from 1984 to 2016 in the Sevre Niortaise

vector_to_listsql

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-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

ref_period-class

Class "ref_period" referential class

ref_parqual-class

Class "ref_parqual"

ref_stage-class

Class "ref_stage"

report_sea_age-class

Class "report_sea_age"

Create a dataframe suitable for charts per 24h and day

handler function used by the main interface

ref_timestep_daily-class

Class "ref_timestep_daily"

h_report_mig_interannual

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

h_report_mig_mult

handler function used by the main interface

handler for calculation

report_silver_eel-class

Class "report_silver_eel"

ref_parquan-class

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

report_env-class

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_df-class

Report on fishway operation

handler for report_mig_char

Generic method write_database

summary,report_dc-method

summary for report_dc, write csv and html output, and prints summary statistics

setasqualitative,report_mig_char-method

Turns a quantitative parameter into qualitative

report_mig-class

Migration report for one DC, one species and one stage

report_ge_weight-class

Trend of wet weight in glass eel

summary,report_df-method

summary for report_df, write csv and html output, and prints summary statistics

set_starting_date

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'

hxtablereport_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

print,report_mig_mult-method

Method to print the command line of the object

interface_graphique

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

report_annual-class

Class "report_annual"

report_mig_char-class

Migration report along with quantitative and qualitative characteristics

report_mig_env-class

Class "report_mig_env"

report_species-class

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

report_dc-class

Class "report_dc" report du fonctionnement du dispositif de comptage

supprime,ref_coe-method

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_report_mig_env

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