Learn R Programming

⚠️There's a newer version (0.6.1) of this package.Take me there.

stacomiR (version 0.5.4.0)

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'.

Copy Link

Version

Install

install.packages('stacomiR')

Monthly Downloads

176

Version

0.5.4.0

License

GPL (>= 2)

Maintainer

Cedric Briand

Last Published

October 11th, 2018

Functions in stacomiR (0.5.4.0)

barplot,report_annual-method

barplot method for object report_annual-class

charge,ref_df-method

Loading method for DF referential objects

charge,ref_par-method

Loading method for Repar referential objects

charge_with_filter,ref_taxa-method

Loading method for ref_taxa referential objects searching only taxa existing for a DC

charge,ref_parqual-method

Loading method for Reparqual referential objects

charge,report_mig_mult-method

charge method for report_mig_mult

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,report_ope-method

charge method for report_ope

choice,ref_horodate-method

Graphical interface

choice,ref_list-method

Choice method for ref_list referential objects

calcule,report_mig_char-method

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

choice,ref_stage-method

Choice method for ref_stage referential objects

calcule,report_mig_env-method

Calculations for migration in the class report_mig_env-class

charge,ref_choice-method

Loading method for Rechoice referential objects

choice_c,ref_dc-method

Command line interface to select a counting device

choice,ref_taxa-method

Choice method for reftaxa referential objects with only one taxa selected

charge,ref_env-method

Loading method for ref_env referential object

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

choice_c,ref_df-method

Command line interface to choose a fishway

charge,ref_list-method

Loading method for refliste referential objects

charge,ref_coe-method

loads the coefficients for the period defined in class

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

charge,ref_parquan-method

Loading method for Reparquan referential objects

calcule,report_ge_weight-method

Calcule method for report_ge_weight

charge,report_dc-method

charge method for report_dc

charge,report_df-method

charge method for report_df

Generic method to load referentials

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_taxa-method

Loading method for ref_taxa referential objects

charge,ref_stage-method

Loading method for ref_stage referential objects

charge,ref_textbox-method

Loading method for ReTextBox referential objects

Generic method for calculations

charge_complement,ref_parqual-method

Loads an additional dataset this method is loaded to obtain the possible values of a qualitative parameter. Here data only contains one line

charge,report_sample_char-method

charge method for report_sample_char class

calcule,report_sample_char-method

Calculation for report_sample_char

choicemult,ref_horodate-method

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

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_par-method

Choice method for ref_par referential objects

choicemult,ref_par-method

Multiple Choice method for ref_par referential objects, internal use

calcule,report_silver_eel-method

Calculate individual silver eel parameters.

charge,ref_checkbox-method

Loading method for ref_checkbox referential objects

connect,report_mig_interannual-method

connect method for report_mig_interannual

connect,report_mig_env-method

connect method for report_mig_env class

Generic method for getting the final date

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

calcule,report_species-method

calcule method for report_species

charge,report_mig-method

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

charge,report_sea_age-method

Loads data and check that all choices in the graphical interface have been made.

charge,ref_year-method

Loading method for ref_year referential objects

charge,report_mig_env-method

charge method for report_mig_env class

charge,report_mig_interannual-method

loading method for report_mig_interannual class

fun_report_mig_mult

Calculate daily migration by simple repartition

fun_report_mig_mult_overlaps

Function to calculate daily migration using overlaps functions

charge,report_silver_eel-method

charge method for report_silver_eel class

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

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

choice,ref_checkbox-method

Choice method for ref_checkbox referential objects

Handler for barchart for report_df class from the graphical interface

charge,report_mig_char-method

charge method for report_mig_char

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

choice,ref_parqual-method

Choice method for ref_parqual referential objects, internal use

charge,report_species-method

charge method for report_species

charge_with_filter

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

choice,ref_timestep_daily-method

Method to select timesteps from the graphical interface

chargecomplement-methods

Methods for Function chargecomplement

choice,ref_textbox-method

Choice method for ReTextBox referential objects

choice,ref_year-method

choice method for ref_year referential

choice_c,ref_stage-method

choice_c method for ref_stage

choice,ref_choice-method

Choice method for Rechoice referential objects

choice,ref_dc-method

Graphical method to choose a fishway through the interface

Function to calculate statistics per month

function to create daily statistics

choice_c,ref_year-method

choice_c method for ref_year referential from the command line

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

charge,report_annual-method

charge method for report_annual class

choice_c,ref_taxa-method

choice_c method for ref_taxa

Generic method the get starting date

choice_c,report_mig-method

command line interface for report_mig class

charge,report_env-method

charge method for report_env class

Retrieves the dbname from a connection using "baseODBC"

charge,report_ge_weight-method

charge method for report_ge_weight class

choice_c,report_annual-method

command line interface for report_annual-class

handler function used by the main interface

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_mig_char-method

command line interface for report_mig_char class

h_report_mig_annual

handler function used by the main interface

choice_c,report_df-method

command line interface for report_df class

choice_c,report_dc-method

command line interface for report_dc class

choice_c,report_sea_age-method

command line interface for report_sea_age class

choice_c,report_silver_eel-method

command line interface for report_silver_eel class

h_report_mig_multgraph2

handler du calcul h_report_miggraph2

h_report_mig_multgraph3

charge_complement

Generic method to load additional data

choice,ref_timestep-method

Method to select timesteps from the graphical interface

choice_c,ref_textbox-method

Choice_c method for ReTextBox referential objects

choice_c,report_sample_char-method

command line interface for report_sample_char class

h_report_silver

handler function used by the main interface

choice_c,report_mig_mult-method

command line interface for report_mig_mult class

handler function used by the main interface

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

hgraph_report_mig_interannual

Plot of all interannual from top to bottom

choicemult,ref_parqual-method

Multiple Choice method for ref_parqual referential objects internal use

connect,report_sample_char-method

connect method for report_sample_char

choicemult,ref_stage-method

Multiple Choice method for ref_stage referential objects

choice_c,ref_timestep_daily-method

choice_c method for class ref_timestep_daily

choice_c,report_species-method

command line interface for report_species-class

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

choicemult,ref_dc-method

choicemult, selection method for ref_dc allowing to select several DC

connect,report_mig_mult-method

connect method for report_mig_mult

choicemult,ref_timestep-method

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

choicemult,ref_choice-method

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

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_dc-method

connect method for report_dc

Generic method for manual choice using the command line

connect,report_sea_age-method

connect method for report_sea_age

hgraph_report_mig_interannual2

Plot of daily migrations

connect,report_df-method

connect method for report_df

handler to print 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).

connect,report_ope-method

connect method for report_ope

handler to print the command line

currentstart_date

Generic method for getting the beginning date for current time step

choice,ref_df-method

Graphical method to choose a fishway through the interface

fun_report_mig_interannual

statistics per time period

connect,report_env-method

connect method for report_env class

fun_date_extraction

This function extracts temporal characteristics from a dataframe

connect,report_ge_weight-method

connect method for report_Poids_moyen

end_date,ref_timestep-method

Gets the final horodate for an object of class ref_timestep-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.

choice,ref_env-method

Choice method for ref_env referential object

connect,report_mig-method

connect method for report_mig

interface_report_annual

interface for report_annual class

connect,report_silver_eel-method

connect method for report_silver_eel

connect,report_species-method

connect method for report_species

Handler for barchart for report_df class from the graphical interface

Generic method for choice (using the gwidget graphical interface)

Handler for barchart for report_df class from the graphical interface

connect,report_mig_char-method

connect method for report_mig_char

Handler function to plot calendar like graph, internal use

Function for report_mig graphs including numbers DF DC operations

Generic method to forward outputs

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

interface_report_dc

interface for report_dc class

fun_write_monthly

This writes monthly data in t_reportmensuel_mens table

current_end_date,ref_timestep-method

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

fun_stage_durif

Function to calculate the stages from Durif

fungraph_glasseel

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

fun_table_per_dis

functions called in DF and DC

choice_c,ref_choice-method

Choice_c method for refchoix referential objects

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

interface_report_mig_interannual

interface for report_mig_interannual class

function used for some lattice graph

hTablereport_mig

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

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

funtablereport_sample_char

fundensityreport_sample_char

fundensityreport_sample_char uses ggplot2 to draw density plots

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

funplotreport_sea_age

funplotreport_sea_age

interface_report_mig_mult

graphical interface for report_mig_mult class

Table output for report_df class

hTablereport_mig_mult

handler function table

choice_c,ref_env-method

Command line interface to select a monitoring station

funtablereport_ge_weight

Internal handler for reg, class report_ge_weight-class.

FuntableDC create a table output for report_dc class

funtablereport_silver_eel

h_report_mig_mult_graph

handler for plot method in report_mig_mult class

h_report_mig_char

handler function used by the main interface

getnocurrent_step,ref_timestep-method

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

get_step_label,ref_timestep-method

Gets the string value of time step

h_report_mig_multcalc

handler for calculations

choice_c,ref_horodate-method

getnocurrent_step

Generic method to get current time step

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

function used for some lattice graphs with dates

h_report_sea_age

handler function used by the main interface

hbmCplotcrossed

handler for plot

h_report_mig_env

handler function used by the main interface

h_report_sample_char

handler function used by the main interface

funtablereport_sea_age

h_report_mig_interannual

handler function used by the main interface

Methods for Function graphe

h_report_envgraph

h_report_envgraph Internal method

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

handler function used by the main interface

handler function used by the main interface

plot,report_env,missing-method

Plot method for report_env

h_report_mig_mult

handler function used by the main interface

h_report_ge_weight

handler function used by the main interface

handler function used by the main interface

h_report_miggraph2

handler for h_report_miggraph2

handler for calculation

handler for plot

current_end_date

Generic method for getting the ending date for current time step

h_report_pigment_stages

handler function used by the main interface

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

hgraph_report_mig_interannual3

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

plot,report_ge_weight,missing-method

Plot method for report_ge_weight'

h_report_migwrite

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

handler for report_mig_char

interface_report_mig_char

interface for report_migPar class

Internal handler for reg, class report_ge_weight-class.

currentstart_date,ref_timestep-method

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

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

Internal handler function

interface_report_mig_env

interface for report_migConditionEnv class

funboxplotreport_sample_char

Boxplots for ggplot2

Handler function to plot calendar like graph, internal use

plot,report_mig_interannual,missing-method

Plot method for report_mig_interannual

funplotreport_silver_eel

funplotreport_silver_eel

plot,report_species,missing-method

Plot method for report_species

print,report_dc-method

Method to print the command line of the object

handler for plot

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

internal method for graphical interface

print,report_mig_mult-method

Method to print the command line of the object

plot,report_mig_env,missing-method

Plot method for report_mig_env

Internal handler for reg, class report_ge_weight-class.

handler to print the command line

houtreport_mig_mult

handler to print the command line

Annual migration of salmon in the Adour and tributaries

funpointreport_sample_char

Point graph from ggplot

An object of class report_mig_env with data loaded

Generic method to get the years

hxtablereport_annual

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

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.

interface_report_silver_eel

An interface that calls the object to build the user interface

print,report_sample_char-method

Method to print the command line of the object

This handler calls the generic method stat

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

interface_report_species

Interface for report_species class

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

Internal handler for reg, class report_ge_weight-class.

r_mig_interannual

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

interface_report_df

interface for report_df class

getdateDebut,ref_timestep-method

Returns the starting date as character

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

handler for plot internal use

interface_report_env

Interface for class conditionEnv

handler for summary report_species, internal use

An object of class report_ope-class with data loaded

ref_parqual-class

Class "ref_parqual"

getvalue,ref_period-method

Returns the POSIXt value of a given name

Generic method getvalue

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

plot,report_mig,ANY-method

Plots of various type for report_mig.

handler function used by the main interface

plot,report_mig_char,missing-method

plot method for report_mig_char

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

handler function used by the main interface

ref_parquan-class

Class "ref_parquan"

report_ope-class

Report on operations

ref_timestep_daily-class

Class "ref_timestep_daily"

hsummaryreport_migInterannuelle

Summary handler internal method

Year reference class

report_sample_char-class

Class "report_sample_char"

report_mig_char-class

Migration report along with quantitative and qualitative characteristics

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

setasqualitative

Generic method to transform quantitative par into a qualitative one

h_report_migcalc

handler for calculations report_mig

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.

report_mig_env-class

Class "report_mig_env"

interface_report_ge_weight

interface for report_ge_weight class

h_report_miggraph

handler for h_report_miggraph

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

Progress bar using a gtkdialog, the progress bar is assigned in envir_stacomi This progress bar has a button to close.

interface_report_mig

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

setref_horodate,ref_horodate-method

Method to set the Horodate

plot,report_dc,ANY-method

Different plots for report_dc

plot,report_df,ANY-method

Different plots for report_df

h_report_species

handler function used by the main interface

plot,report_mig_mult,missing-method

Plots of various type for report_mig_mult

hbarplotreport_annual

Barplot handler

hplotreport_annual

function used to clean the objects within the group and the graphs and also elements remaining in the envir_stacomi environment

Internal handler for reg, class report_ge_weight-class.

r_mig_interannual_vichy

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

plot,report_sample_char,missing-method

Plots of various type for reportcarlot

Anguilla migration at the Arzal station (report_mig_mult-class)

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

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.

Silver eel migration in the Somme

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

An object of class report_sea_age with data loaded

ref_checkbox-class

ref_checkbox referencial class

supprime,ref_coe-method

supprime method for "ref_coe" class

interface_report_sea_age

An interface that calls the object to build the user interface

interface_report_sample_char

An interface that calls the object to build the user interface

print,report_sea_age-method

Method to print the command line of the object

validity_ref_horodate

Validity check for ref_horodate

print,report_silver_eel-method

Method to print the command line of the object

Generic for prediction

plot,report_annual,missing-method

Plot method for report_annual

Validity check for ref_year

supprime,report_mig_interannual-method

supprime method for report_mig_interannual class

print,report_df-method

Method to print the command line of the object

An object of class report_env with data loaded

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.

Class "ref_taxa"

print,report_mig-method

Method to print the command line of the object

ref_textbox-class

ref_textbox referencial class

Create a dataframe suitable for charts per 24h and day

Class "ref_list"

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

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

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

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

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

Class "ref_par"

report_annual-class

Class "report_annual"

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

ref_period-class

Class "ref_period" referential class

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

ref_stage-class

Class "ref_stage"

report_df-class

Report on fishway operation

report_env-class

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

ref_choice-class

Class "ref_choice"

Class "ref_coe"

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

report_species-class

Counts of number per taxa/stages

report_mig_mult-class

Migration reports for multiple DC / species / stages

report_mig_interannual-class

Class "report_mig_interannual"

Class "ref_env"

ref_horodate-class

Class ref_horodate

set_starting_date,ref_timestep-method

Sets starting date from a character

summary,report_silver_eel-method

summary for report_silver_eel

ref_timestep-class

Class "ref_timestep"

summary,report_sample_char-method

summary for report_sample_char

summary,report_sea_age-method

summary for report_sea_age

summary,report_species-method

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

ref_timestepChar-class

Class "ref_timestepChar"

supprime,report_sea_age-method

supprime method for report_mig_interannual class

Generic method write_database

Generic method to delete entires from the database

report_silver_eel-class

Class "report_silver_eel"

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

report_sea_age-class

Class "report_sea_age"

report_dc-class

Class "report_dc" report du fonctionnement du dispositif de comptage

report_ge_weight-class

Trend of wet weight in glass eel

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.

report_mig-class

Migration report for one DC, one species and one stage

stacomiR-package

stacomi_installed

Test that the program is installed.

summary,report_dc-method

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

summary,report_df-method

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

vector_to_listsql

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

write_database,report_ge_weight-method

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

charge,ref_dc-method

Method to load the counting devices of the control station

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