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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'.

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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

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

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

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
charge

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
calcule

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

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
end_date

Generic method for getting the final date
envir_stacomi

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

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

Function to create a barchart (lattice) corresponding to the periods
choice,ref_checkbox-method

Choice method for ref_checkbox referential objects
funbarchartDF

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
funstat

Function to calculate statistics per month
funstat_daily

function to create daily statistics
choice_c,ref_year-method

choice_c method for ref_year referential from the command line
get_step_label

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
getdateDebut

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
getdbname

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

h_report_mig

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

handler
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
h_report_size

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

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
choice_c

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
houtDC

handler to print the command line
colortable

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
houtDF

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

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
funbarchart1DC

Handler for barchart for report_df class from the graphical interface
choice

Generic method for choice (using the gwidget graphical interface)
funbarchart1DF

Handler for barchart for report_df class from the graphical interface
connect,report_mig_char-method

connect method for report_mig_char
funchartDF

Handler function to plot calendar like graph, internal use
fungraph

Function for report_mig graphs including numbers DF DC operations
createmessage

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

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
funtable

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
funboxDC

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
funboxDF

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

table function
fundensityreport_sample_char

fundensityreport_sample_char uses ggplot2 to draw density plots
funout

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
funtableDF

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

funtableDC

FuntableDC create a table output for report_dc class
funtablereport_silver_eel

table function
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

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

Command line
getnocurrent_step

Generic method to get current time step
choicemult

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

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

table function
h_report_mig_interannual

handler function used by the main interface
graphe-methods

Methods for Function graphe
h_report_envgraph

h_report_envgraph Internal method
coef_durif

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

handler function used by the main interface
h_report_df

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
h_report_ope

handler function used by the main interface
h_report_miggraph2

handler for h_report_miggraph2
hbilespcalc

handler for calculation
hbmCplotqual

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
hbmCcalc

handler for report_mig_char
interface_report_mig_char

interface for report_migPar class
hcalc

currentstart_date,ref_timestep-method

fun_aggreg_for_plot

returns a table where all components within the list calcdata are aggregated and formatted for plot
fun_char_spe

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

Internal handler function
interface_report_mig_env

interface for report_migConditionEnv class
funboxplotreport_sample_char

Boxplots for ggplot2
funchartDC

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
hbmCplotquan

handler for plot
r_ann

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

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
hexp

houtreport_mig

handler to print the command line
houtreport_mig_mult

handler to print the command line
r_ann_adour

Annual migration of salmon in the Adour and tributaries
funpointreport_sample_char

Point graph from ggplot
r_mig_env

An object of class report_mig_env with data loaded
get_year

Generic method to get the years
hxtablereport_annual

xtable handler
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
hbmCstat

This handler calls the generic method stat
r_mig_dc

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
hplot

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
r_mig_mult_ope

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

handler for plot internal use
interface_report_env

Interface for class conditionEnv
hsummarybilesp

handler for summary report_species, internal use
r_mig_ope

ref_parqual-class

Class "ref_parqual"
getvalue,ref_period-method

Returns the POSIXt value of a given name
getvalue

Generic method getvalue
load_stacomi

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.
h_report_dfdc

handler function used by the main interface
plot,report_mig_char,missing-method

plot method for report_mig_char
r_mig_df

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

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
ref_year-class

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

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

plot handler
quitte

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

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
r_mig_mult

Anguilla migration at the Arzal station (report_mig_mult-class)
r_sample_char

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.
r_silver

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
r_seaa

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
ref_dc-class

Class "ref_dc"
validity_ref_horodate

Validity check for ref_horodate
print,report_silver_eel-method

Method to print the command line of the object
ref_df-class

Class "ref_df"
model

Generic for prediction
plot,report_annual,missing-method

Plot method for report_annual
validity_year

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
r_env

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.
ref_taxa-class

Class "ref_taxa"
print,report_mig-method

Method to print the command line of the object
ref_textbox-class

ref_textbox referencial class
split_per_day

Create a dataframe suitable for charts per 24h and day
ref_list-class

Class "ref_list"
r_dc

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

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

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

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

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

Class "ref_par"
report_annual-class

Class "report_annual"
r_mig_mult_df

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

Class "ref_period" referential class
r_gew

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"
ref_coe-class

Class "ref_coe"
stacomi

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"
ref_env-class

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
write_database

Generic method write_database
supprime

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

stacomiR
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

charge,ref_dc-method

Method to load the counting devices of the control station
calcmig

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