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stacomiR (version 0.6.0.7)

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 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

0.6.0.7

License

GPL (>= 2)

Maintainer

Cedric Briand

Last Published

July 18th, 2022

Functions in stacomiR (0.6.0.7)

calcule,report_sample_char-method

Calculation for report_sample_char

calcule,report_mig_interannual-method

calcule method for report_mig_interannual

calcule,report_silver_eel-method

Calculate individual silver eel parameters.

calcule,report_mig_char-method

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

barplot,report_annual-method

barplot method for object report_annual-class

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

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-method

Transforms migration per period to daily migrations, and performs the conversion from weights to number is data are stored as weights (glass eel).

calcule,report_ge_weight-method

Calcule method for report_ge_weight

calcule,report_species-method

calcule method for report_species

charge,ref_year-method

Loading method for ref_year referential objects

charge,report_annual-method

charge method for report_annual class

Generic method for calculations

charge,ref_list-method

Loading method for ref_list referential objects

charge,ref_env-method

Loading method for ref_env referential object

charge,ref_df-method

Loading method for DF referential objects

charge,report_mig-method

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

charge,ref_dc-method

Method to load the counting devices of the control station

charge,report_mig_interannual-method

loading method for report_mig_interannual class

charge,report_mig_mult-method

charge method for report_mig_mult

charge,report_env-method

charge method for report_env class

charge,ref_stage-method

Loading method for ref_stage referential objects

charge,ref_parquan-method

Loading method for Reparquan referential objects

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_with_filter,ref_par-method

Loading method for ref_par referential objects searching only those parameters existing for a DC, a Taxa, and a stage

charge,report_df-method

charge method for report_df

charge,ref_coe-method

loads the coefficients for the period defined in class

charge,ref_choice-method

Loading method for Refchoice referential objects

charge,report_species-method

charge method for report_species

charge,report_dc-method

charge method for report_dc

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,ref_list-method

Choice_c method for ref_list referential objects

choice_c,ref_horodate-method

Choice_c method for ref_horodate

choice_c,ref_taxa-method

choice_c method for ref_taxa

charge,report_ope-method

charge method for report_ope

choice_c,ref_textbox-method

Choice_c method for ref_textbox referential objects

charge,ref_textbox-method

Loading method for ref_textbox 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,ref_par-method

Loading method for ref_par referential objects

charge,ref_taxa-method

Loading method for ref_taxa referential objects

choice_c,report_mig_char-method

command line interface for report_mig_char class

charge_with_filter,ref_taxa-method

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

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

connect,report_dc-method

connect method for report_dc

choice_c,report_mig_env-method

command line interface for report_env class

choice_c,report_ge_weight-method

command line interface for report_ge_weight-class

charge_complement

Generic method to load additional data

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_dc-method

command line interface for report_dc class

Generic method for manual choice using the command line

choice_c,report_annual-method

command line interface for report_annual-class

fun_report_mig_interannual

statistics per time period

connect,report_mig_interannual-method

connect method for report_mig_interannual

connect,report_df-method

connect method for report_df

connect,report_mig_env-method

connect method for report_mig_env class

choice_c,ref_env-method

Command line interface to select a monitoring station

charge_with_filter

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

choice_c,ref_df-method

Command line interface to choose a fishway

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).

charge,report_mig_char-method

charge method for report_mig_char

charge_with_filter,ref_parquan-method

Loading method for Reparquan referential objects searching only those parameters existing for a DC (counting device), a Taxon, and a stage

Generic method to load referentials

choice_c,ref_par-method

Command line interface to select a parameter

choice_c,ref_stage-method

choice_c method for ref_stage

charge_with_filter,ref_stage-method

Loading method for ref_stage referential objects searching only those stages existing for a DC and a Taxon

connect,report_env-method

connect method for report_env class

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

connect,report_ge_weight-method

connect method for report_Poids_moyen

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.

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

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_report_mig_mult

Calculate daily migration by simple repartition

fun_write_monthly

This writes monthly data in t_reportmensuel_mens table

getvalue,ref_period-method

Returns the POSIXt value of a given name

Generic method to get the years

choice_c,report_mig-method

command line interface for report_mig class

choice_c,ref_choice-method

Choice_c method for ref_choice referential objects

charge,report_mig_env-method

charge method for report_mig_env class

end_date,ref_timestep-method

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

this function displays text and will be used to convey stacomiR message in shiny

Generic method for getting the final date

funplotreport_silver_eel

funplotreport_silver_eel

choice_c,report_df-method

command line interface for report_df class

function used to remove special non utf8 character which cause the gtk interface to crash

connect,report_mig_mult-method

connect method for report_mig_mult

choice_c,report_env-method

command line interface for report_env class

choice_c,ref_dc-method

Command line interface to select a counting device

connect,report_ope-method

connect method for report_ope

print,report_mig_mult-method

Method to print the command line of the object

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

Function to plot calendar like graph, internal use

choice_c,report_mig_interannual-method

command line interface for report_mig_interannual class

fun_date_extraction

This function extracts temporal characteristics from a dataframe

this function gets the schema from envir stacomi and throws warning

Internal use barchart for report_df class from the graphical interface

Internal use, function used in the graphical interface to create a barchart for report_df class

choice_c,report_silver_eel-method

command line interface for report_silver_eel class

choice_c,report_species-method

command line interface for report_species-class

get_year,ref_timestep-method

Gets the year or a vector of years corresponding to the timestep ("ref_timestep") object

connect,report_mig-method

handler for calculations report_mig

print,report_sample_char-method

Method to print the command line of the object

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.

print,report_dc-method

Method to print the command line of the object.

plot,report_mig_char,missing-method

plot method for report_mig_char

plot,report_species,missing-method

Plot method for report_species

plot,report_mig,ANY-method

Plots of various type for report_mig.

connect,report_mig_char-method

connect method for report_mig_char

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

fun_aggreg_for_plot

Calculates a data.frame where all components within the list calcdata are aggregated and formatted for plot

Generic method getvalue

function used for some lattice graphs with dates

plot,report_mig_mult,missing-method

Plots of various type for report_mig_mult

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

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

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

r_mig_interannual_vichy

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

report_sample_char-class

Class 'report_sample_char'

choice_c,report_sample_char-method

command line interface for report_sample_char class

connect,report_sample_char-method

connect method for report_sample_char

report_sea_age-class

Class "report_sea_age"

Anguilla migration at the Arzal station (report_mig_mult-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

An object of class report_sea_age with data loaded

plot,report_sample_char,missing-method

Plots of various type for reportcarlot

stacomi Main launcher for program stacomi

Create a dataframe suitable for charts per 24h and day

fun_report_mig_mult_overlaps

Function to calculate daily migration using overlaps functions

Generic method to delete entires from the database

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

write_database,report_mig-method

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

supprime,report_sea_age-method

supprime method for report_mig_interannual class

print,report_df-method

Method to print the command line of the object

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

Silver eel migration in the Somme

ref_choice-class

Class 'ref_choice'

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

ref_horodate-class

Class ref_horodate

print,report_mig-method

handler to print the command line

Function for report_mig graphs including numbers DF DC operations

fungraph_glasseel

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

Creates a list of available schemas in the db

report_dc-class

Class "report_dc" report du fonctionnement du dispositif de comptage

plot,report_df,missing-method

Different plots for report_df

plot,report_dc,missing-method

Different plots for report_dc

Class 'ref_list'

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

An object of class report_env with data loaded

Class 'ref_coe'

ref_parquan-class

Class 'ref_parquan'

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

connect,report_sea_age-method

connect method for report_sea_age

connect,report_silver_eel-method

connect method for report_silver_eel

connect,report_species-method

connect method for report_species

fun_table_per_dis

functions called in DF and DC

fun_stage_durif

Function to calculate the stages from Durif

ref_period-class

Class 'ref_period' referential class

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

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.

ref_stage-class

Class 'ref_stage'

report_df-class

Report on fishway operation

ref_timestepChar-class

Class "ref_timestepChar"

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_mig_mult-class

Migration reports for multiple DC / species / stages

ref_timestep_daily-class

Class 'ref_timestep_daily'

report_ope-class

Report on operations

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

Function to calculate statistics per month

plot,report_env,missing-method

Plot method for report_env

Table output for report_df class

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

plot,report_ge_weight,missing-method

Plot method for report_ge_weight'

this function gets the name of the stucture as it is set in the database

print,report_sea_age-method

Method to print the command line of the object

report_mig_env-class

Class "report_mig_env"

Class 'ref_taxa'

report_mig_interannual-class

Class "report_mig_interannual"

Generic for prediction

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

plot,report_mig_interannual,missing-method

Plot method for report_mig_interannual

plot,report_mig_env,missing-method

Plot method for report_mig_env

plot,report_annual,missing-method

Plot method for report_annual

Annual migration of salmon in the Adour and tributaries

An object of class report_mig_env with data loaded

validity_ref_horodate

Validity check for ref_horodate

Validity check for ref_year

r_mig_interannual

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)

summary,report_silver_eel-method

summary for report_silver_eel

summary,report_species-method

summary for report_species

setasqualitative

Generic method to transform quantitative par into a qualitative one

setasqualitative,report_mig_char-method

Turns a continuous parameter into discrete values

An object of class report_ope-class with data loaded

ref_parqual-class

Class 'ref_parqual'

print,report_silver_eel-method

Method to print the command line of the object

ref_textbox-class

ref_textbox referencial class

Class 'ref_par'

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

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

ref_timestep-class

Class "ref_timestep"

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

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

Generic method write_database

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.

Year reference class

report_mig-class

Migration report for one DC, one species and one stage

report_annual-class

Class "report_annual"

report_env-class

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

Class 'ref_env'

summary,report_dc-method

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

supprime,ref_coe-method

supprime method for 'ref_coe' class

summary,report_df-method

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

report_ge_weight-class

Trend of wet weight in glass eel

supprime,report_mig_interannual-method

supprime method for report_mig_interannual class, deletes values in table t_bilanmigrationjournalier_bjo

report_mig_char-class

Migration report along with quantitative and qualitative characteristics

report_silver_eel-class

Class "report_silver_eel"

summary,report_sample_char-method

summary for report_sample_char

summary,report_sea_age-method

summary for report_sea_age

report_species-class

Counts of number per taxa/stages

write_database,report_ge_weight-method

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

vector_to_listsql

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