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stacomiR (version 0.5.4.2)

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 Agency for Biodiversity (AFB) 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

173

Version

0.5.4.2

License

GPL (>= 2)

Maintainer

Cedric Briand

Last Published

March 6th, 2019

Functions in stacomiR (0.5.4.2)

calcule,report_mig_char-method

Computes data to a standard format for the summary and plot methods.

Generic method for calculations

charge,ref_par-method

Loading method for Repar referential objects

charge,ref_parqual-method

Loading method for Reparqual 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_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

charge,ref_checkbox-method

Loading method for ref_checkbox referential objects

chargecsv loads the informations stored in c:/program files/stacomi/calcmig.csv file

choice,ref_checkbox-method

Choice method for ref_checkbox referential objects

choice_c,ref_env-method

Command line interface to select a monitoring station

choice_c,ref_choice-method

Choice_c method for refchoix referential objects

Generic method for choice (using the gwidget graphical interface)

choice_c,ref_horodate-method

choice_c,ref_year-method

choice_c method for ref_year referential from the command line

choice_c,report_annual-method

command line interface for report_annual-class

choicemult,ref_horodate-method

Multiple Choice method for ref_horodate referential objects, to put together with notebook widgets

calcule,report_ge_weight-method

Calcule method for report_ge_weight

choicemult,ref_par-method

Multiple Choice method for ref_par referential objects, internal use

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).

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_dc-method

Method to load the counting devices of the control station

calcule,report_mig_interannual-method

calcule method for report_mig_interannual

barplot,report_annual-method

barplot method for object report_annual-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,ref_year-method

Loading method for ref_year referential objects

connect,report_mig-method

connect method for report_mig

charge,ref_df-method

Loading method for DF referential objects

connect,report_mig_char-method

connect method for report_mig_char

charge,report_annual-method

charge method for report_annual class

currentstart_date

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

calcule,report_silver_eel-method

Calculate individual silver eel parameters.

charge,report_mig-method

Loads additional data on migration control operations, df (fishway) dc (counting device).

calcule,report_species-method

calcule method for report_species

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,report_mig_char-method

charge method for report_mig_char

choice,ref_df-method

Graphical method to choose a fishway through the interface

fun_aggreg_for_plot

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

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.

charge,ref_choice-method

Loading method for Rechoice referential objects

charge,report_ge_weight-method

charge method for report_ge_weight class

charge,report_env-method

charge method for report_env class

charge,ref_coe-method

loads the coefficients for the period defined in class

function used for some lattice graph

charge,report_dc-method

charge method for report_dc

Internal use, rectangles to describe the DF work for report_df class, graphical interface handler

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,ref_env-method

Choice method for ref_env referential object

funplotreport_silver_eel

funplotreport_silver_eel

choice,ref_textbox-method

Choice method for ReTextBox referential objects

choice,ref_timestep-method

Method to select timesteps from the graphical interface

charge,report_mig_mult-method

charge method for report_mig_mult

charge,report_df-method

charge method for report_df

charge,ref_parquan-method

Loading method for Reparquan referential objects

charge_with_filter

Generic method to load referentials, with filters from the parent object in the database

chargecomplement-methods

Methods for Function chargecomplement

choice_c,ref_stage-method

choice_c method for ref_stage

choice_c,ref_taxa-method

choice_c method for ref_taxa

charge,report_ope-method

charge method for report_ope

choice_c,report_mig_env-method

command line interface for report_env class

choice_c,report_mig_interannual-method

command line interface for report_mig_interannual class

funpointreport_sample_char

Point graph from ggplot

Table output for report_df class

choice_c,report_species-method

command line interface for report_species-class

Generic method for manual choice using the command line

charge,ref_stage-method

Loading method for ref_stage referential objects

calcule,report_sample_char-method

Calculation for report_sample_char

charge,report_silver_eel-method

charge method for report_silver_eel class

charge,report_species-method

charge method for report_species

calcule,report_sea_age-method

Split data according to the limits set in the limit1hm, and limit2hm arguments of the report_sea_age-class.

choice,ref_horodate-method

Graphical interface

funtablereport_ge_weight

Internal handler for reg, class report_ge_weight-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,ref_env-method

Loading method for ref_env referential object

fun_date_extraction

This function extracts temporal characteristics from a dataframe

choice,ref_year-method

choice method for ref_year referential

charge,ref_list-method

Loading method for refliste referential objects

fun_report_mig_interannual

statistics per time period

charge_complement

Generic method to load additional data

h_report_mig_char

handler function used by the main interface

choice,ref_stage-method

Choice method for ref_stage referential objects

charge,ref_taxa-method

Loading method for ref_taxa referential objects

h_report_mig_env

handler function used by the main interface

h_report_mig_mult_graph

handler for plot method in report_mig_mult class

choice_c,report_mig-method

command line interface for report_mig class

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

h_report_mig_multcalc

handler for calculations

charge,report_mig_env-method

charge method for report_mig_env class

charge,ref_textbox-method

Loading method for ReTextBox referential objects

choice_c,report_mig_char-method

command line interface for report_mig_char class

Function to create a barchart (lattice) corresponding to the periods

h_report_silver

handler function used by the main interface

Handler for barchart for report_df class from the graphical interface

connect,report_dc-method

connect method for report_dc

charge,report_mig_interannual-method

loading method for report_mig_interannual class

handler function used by the main interface

this function uses gfile, edits a text with info and changing colors

choice,ref_taxa-method

Choice method for reftaxa referential objects with only one taxa selected

hgraph_report_mig_interannual

Plot of all interannual from top to bottom

choice_c,ref_list-method

Choice_c method for ref_list referential objects

choice_c,ref_par-method

Command line interface to select a parameter

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

hgraph_report_mig_interannual2

Plot of daily migrations

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

choice_c,report_sea_age-method

command line interface for report_sea_age 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_silver_eel-method

command line interface for report_silver_eel class

connect,report_df-method

connect method for report_df

funplotreport_sea_age

funplotreport_sea_age

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

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

choice_c,ref_dc-method

Command line interface to select a counting device

choice_c,ref_df-method

Command line interface to choose a fishway

choice,ref_choice-method

Choice method for Rechoice referential objects

choice,ref_dc-method

Graphical method to choose a fishway through the interface

connect,report_mig_mult-method

connect method for report_mig_mult

Generic method to get the years

Generic method for multiple choice (using the gwidget notebook for multiple choice)

choice,ref_par-method

Choice method for ref_par referential objects

hplotreport_annual

getdateDebut,ref_timestep-method

Returns the starting date as character

Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters

Internal handler for reg, class report_ge_weight-class.

function used for some lattice graphs with dates

connect,report_sample_char-method

connect method for report_sample_char

Methods for Function graphe

connect,report_ope-method

connect method for report_ope

connect,report_sea_age-method

connect method for report_sea_age

connect,report_silver_eel-method

connect method for report_silver_eel

h_report_miggraph2

handler for h_report_miggraph2

connect,report_species-method

connect method for report_species

choicemult,ref_choice-method

Multiple Choice method for ref_choice referential objects, to put together with notebook widgets

choicemult,ref_dc-method

choicemult, selection method for ref_dc allowing to select several DC

Internal function, tests the connection and if it works loads the stacomi interface

choice,ref_parqual-method

Choice method for ref_parqual referential objects, internal use

fun_stage_durif

Function to calculate the stages from Durif

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.

fun_table_per_dis

functions called in DF and DC

choice_c,ref_textbox-method

Choice_c method for ReTextBox referential objects

Generic method for getting the final date

h_report_migwrite

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

choice_c,ref_timestep_daily-method

choice_c method for class ref_timestep_daily

plot,report_mig_env,missing-method

Plot method for report_mig_env

Environment where most objects from the package are stored and then loaded by the charge method

plot,report_mig_interannual,missing-method

Plot method for report_mig_interannual

Generic method to get the string value of time step

choice_c,report_dc-method

command line interface for report_dc class

hbmCplotcrossed

handler for plot

choicemult,ref_parqual-method

Multiple Choice method for ref_parqual referential objects internal use

connect,report_env-method

connect method for report_env class

choicemult,ref_stage-method

Multiple Choice method for ref_stage referential objects

connect,report_ge_weight-method

connect method for report_Poids_moyen

Generic method to forward outputs

handler for plot

current_end_date,ref_timestep-method

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

choice_c,report_df-method

command line interface for report_df class

hxtablereport_annual

Counting Device (DC) operation from 2000 to 2015 at the Arzal dam (Vilaine, France)

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.

funboxplotreport_sample_char

Boxplots for ggplot2

choice_c,report_mig_mult-method

command line interface for report_mig_mult class

Overview of the fishway operation at Arzal in (Vilaine France).

choice_c,report_sample_char-method

command line interface for report_sample_char class

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

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.

r_mig_interannual_vichy

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

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

choicemult,ref_timestep-method

Graphical interface for multiple choice method for PasdeTemps (used in report_mig_mult)

hTablereport_mig_mult

handler function table

handler function used by the main interface

handler function used by the main interface

hTablereport_mig

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

fun_write_monthly

This writes monthly data in t_reportmensuel_mens table

Handler function to plot calendar like graph, internal use

Handler function to plot calendar like graph, 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

handler function used by the main interface

Anguilla migration at the Arzal station (report_mig_mult-class)

function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class

Internal handler for reg, class report_ge_weight-class.

h_report_pigment_stages

handler function used by the main interface

FuntableDC create a table output for report_dc class

getvalue,ref_period-method

Returns the POSIXt value of a given name

Generic method getvalue

Internal handler for reg, class report_ge_weight-class.

handler function used by the main interface

interface_report_mig_mult

graphical interface for report_mig_mult class

Function to calculate statistics per month

fundensityreport_sample_char

fundensityreport_sample_char uses ggplot2 to draw density plots

current_end_date

Generic method for getting the ending date for current time step

h_report_mig_annual

handler function used by the main interface

hgraph_report_mig_interannual3

Step plot with different years displayed on the same graph. One year can be highlighted against the others

h_report_mig_interannual

handler function used by the main interface

plot,report_env,missing-method

Plot method for report_env

plot,report_ge_weight,missing-method

Plot method for report_ge_weight'

plot,report_sea_age,missing-method

Plots of various type for report_sea_age

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

currentstart_date,ref_timestep-method

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

h_report_mig_mult

handler function used by the main interface

h_report_species

handler function used by the main interface

hbarplotreport_annual

Barplot handler

interface_report_annual

interface for report_annual class

function to create daily statistics

interface_report_dc

interface for report_dc class

ref_parqual-class

Class "ref_parqual"

interface_report_silver_eel

An interface that calls the object to build the user interface

handler for plot

interface_report_species

Interface for report_species class

funtablereport_sample_char

Generic for prediction

funtablereport_sea_age

plot,report_silver_eel,missing-method

Plots of various type for report_silver_eel

Generic method the get starting date

fun_report_mig_mult

Calculate daily migration by simple repartition

This handler calls the generic method stat

plot,report_annual,missing-method

Plot method for report_annual

handler to print the command line

houtreport_mig_mult

handler to print the command line

handler for summary report_species, internal use

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

hsummaryreport_migInterannuelle

Summary handler internal method

ref_parquan-class

Class "ref_parquan"

interface_report_mig_char

interface for report_migPar class

report_df-class

Report on fishway operation

interface_report_mig_env

interface for report_migConditionEnv class

report_env-class

class report_env simple output of one or several environmental conditions...

An object of class report_sea_age with data loaded

Class "ref_list"

Fishway operation for the vertical slot fishway (Arzal dam, Vilaine, France).

Size of yellow and glass eel at the Arzal dam (Vilaine, France) in the fishway and main eel trapping ladder.

Class "ref_par"

fun_report_mig_mult_overlaps

Function to calculate daily migration using overlaps functions

print,report_mig_mult-method

Method to print the command line of the object

Retrieves the dbname from a connection using "baseODBC"

handler function used by the main interface

print,report_sample_char-method

Method to print the command line of the object

handler function used by the main interface

report_annual-class

Class "report_annual"

report_dc-class

Class "report_dc" report du fonctionnement du dispositif de comptage

Counting operations for three different counting device in Arzal (Vilaine, France)

An object of class report_ope-class with data loaded

Handler for barchart for report_df class from the graphical interface

Function for report_mig graphs including numbers DF DC operations

h_report_migcalc

handler for calculations report_mig

Handler for barchart for report_df class from the graphical interface

handler for calculation

handler for report_mig_char

h_report_miggraph

handler for h_report_miggraph

report_mig_char-class

Migration report along with quantitative and qualitative characteristics

fungraph_glasseel

Graph function for glass eel migration. Differs from fungraph as it does not draw the ggplot graph for month

Internal handler function

plot,report_mig_mult,missing-method

Plots of various type for report_mig_mult

internal method for graphical interface

funtablereport_silver_eel

report_mig_env-class

Class "report_mig_env"

handler to print the command line

handler to print the command line

summary,report_dc-method

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

get_step_label,ref_timestep-method

Gets the string value of time step

supprime,report_sea_age-method

supprime method for report_mig_interannual class

report_sea_age-class

Class "report_sea_age"

report_silver_eel-class

Class "report_silver_eel"

plot,report_sample_char,missing-method

Plots of various type for reportcarlot

getnocurrent_step,ref_timestep-method

Gets the current time step of an object of class ref_timestep-class

getnocurrent_step

Generic method to get current time step

vector_to_listsql

Transforms a vector into a string called within an sql command e.g. c('A','B','C') => in ('A','B','C')

interface_report_ge_weight

interface for report_ge_weight class

h_report_envgraph

h_report_envgraph Internal method

Create a dataframe suitable for charts per 24h and day

h_report_ge_weight

handler function used by the main interface

h_report_mig_multgraph2

handler du calcul h_report_miggraph2

Class "ref_taxa"

h_report_mig_multgraph3

ref_textbox-class

ref_textbox referencial class

Annual migration of yellow and silver eel for three fishways / counting devices at the Arzal dam (data from 1995 to 2016)

report_species-class

Counts of number per taxa/stages

set_starting_date,ref_timestep-method

Sets starting date from a character

Annual migration of salmon in the Adour and tributaries

Function that loads the loginwindow, tests connection, and then destroys the window

interface_report_mig

Interface for report_mig class, internal use, this function is called by a handler in the main graphical interface

An object of class report_env with data loaded

plot,report_mig,ANY-method

Plots of various type for report_mig.

h_report_sample_char

handler function used by the main interface

h_report_sea_age

handler function used by the main interface

Internal handler for reg, class report_ge_weight-class.

handler for plot internal use

interface_report_df

interface for report_df class

summary,report_silver_eel-method

summary for report_silver_eel

interface_report_env

Interface for class conditionEnv

Wet weight of glass eel from the trapping ladder (Arzal, Vilaine France)

Silver eel migration in the Somme

ref_checkbox-class

ref_checkbox referencial class

plot,report_mig_char,missing-method

plot method for report_mig_char

summary,report_df-method

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

interface_report_sample_char

An interface that calls the object to build the user interface

write_database,report_ge_weight-method

Function to write data to the stacomi database for report_ge_weight-class

Generic method write_database

plot,report_species,missing-method

Plot method for report_species

summary,report_species-method

summary for report_species generate csv and html output in the user data directory

report_mig_interannual-class

Class "report_mig_interannual"

print,report_sea_age-method

Method to print the command line of the object

print,report_dc-method

Method to print the command line of the object

interface_report_sea_age

An interface that calls the object to build the user interface

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.

Generic method to delete entires from the database

plot,report_dc,ANY-method

Different plots for report_dc

print,report_silver_eel-method

Method to print the command line of the object

ref_timestep-class

Class "ref_timestep"

report_mig_mult-class

Migration reports for multiple DC / species / stages

r_mig_interannual

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

An object of class report_mig_env with data loaded

plot,report_df,ANY-method

Different plots for report_df

ref_timestepChar-class

Class "ref_timestepChar"

Counting device operation for three different counting device in Arzal (Vilaine, France)

Fishway operation at the Arzal Dam (Vilaine France) (3 Fishways in 2011)

print,report_df-method

Method to print the command line of the object

print,report_mig-method

Method to print the command line of the object

report_ge_weight-class

Trend of wet weight in glass eel

report_mig-class

Migration report for one DC, one species and one stage

setasqualitative

Generic method to transform quantitative par into a qualitative one

Class "ref_env"

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

stacomiR-package

Video counting of thin lipped mullet (Liza ramada) in 2015 in the Vilaine (France)

summary,report_sample_char-method

summary for report_sample_char

stacomi_installed

Test that the program is installed.

ref_horodate-class

Class ref_horodate

ref_choice-class

Class "ref_choice"

Qualitative and quantitative parameters describing Salmon migration at Decize (Loire)

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

setref_horodate,ref_horodate-method

Method to set the Horodate

Class "ref_coe"

summary,report_sea_age-method

summary for report_sea_age

ref_period-class

Class "ref_period" referential class

write_database,report_mig-method

Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table

ref_stage-class

Class "ref_stage"

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.

report_ope-class

Report on operations

ref_timestep_daily-class

Class "ref_timestep_daily"

report_sample_char-class

Class "report_sample_char"

Year reference class

set_starting_date

Generic method to set the starting date

setasqualitative,report_mig_char-method

Turns a quantitative parameter into qualitative

summary,report_mig-method

summary for report_mig calls functions funstat and funtable to create migration overviews and generate csv and html output in the user data directory

summary,report_mig_char-method

summary for report_mig_char

validity_ref_horodate

Validity check for ref_horodate

Validity check for ref_year

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

calcule,report_mig_env-method

Calculations for migration in the class report_mig_env-class