# Fish Migration Monitoring

## Documentation for package ‘stacomiR’ version 0.6.0.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

B C E F G M P R S V W X misc

## -- B --

barplot-method | barplot method for object report_annual-class
barplot.report_annual | barplot method for object report_annual-class

## -- C --

calcule | Generic method for calculations
calcule-method | Calcule method for report_ge_weight
calcule-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-method | Computes data to a standard format for the summary and plot methods.
calcule-method | Calculations for migration in the class report_mig_env-class
calcule-method | calcule method for report_mig_interannual
calcule-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-method | Calculation for report_sample_char
calcule-method | Split data according to the limits set in the limit1hm, and limit2hm arguments of the report_sea_age-class.
calcule-method | Calculate individual silver eel parameters.
calcule-method | calcule method for report_species
calcule.report_ge_weight | Calcule method for report_ge_weight
calcule.report_mig | 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_mig_char | Computes data to a standard format for the summary and plot methods.
calcule.report_mig_env | Calculations for migration in the class report_mig_env-class
calcule.report_mig_interannual | calcule method for report_mig_interannual
calcule.report_mig_mult | #' 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_sample_char | Calculation for report_sample_char
calcule.report_sea_age | Split data according to the limits set in the limit1hm, and limit2hm arguments of the report_sea_age-class.
calcule.report_silver_eel | Calculate individual silver eel parameters.
calcule.report_species | calcule method for report_species
charge | Generic method to load referentials
charge-method | Loading method for Refchoice referential objects
charge-method | loads the coefficients for the period defined in class
charge-method | Method to load the counting devices of the control station
charge-method | Loading method for DF referential objects
charge-method | Loading method for ref_env referential object
charge-method | Loading method for ref_list referential objects
charge-method | Loading method for ref_par referential objects
charge-method | Loading method for Reparqual referential objects
charge-method | Loading method for Reparquan referential objects
charge-method | Loading method for ref_stage referential objects
charge-method | Loading method for ref_taxa referential objects
charge-method | Loading method for ref_textbox referential objects
charge-method | Loading method for ref_year referential objects
charge-method | Loads additional data on migration control operations, df (fishway) dc (counting device).
charge-method | charge method for report_mig_env class
charge-method | charge method for report_mig_mult
charge.ref_list | Loading method for ref_list referential objects
charge.ref_par | Loading method for ref_par referential objects
charge.report_mig | Loads additional data on migration control operations, df (fishway) dc (counting device).
charge.report_mig_env | charge method for report_mig_env class
charge.report_mig_mult | charge method for report_mig_mult
charge_complement | Generic method to load additional data
charge_complement-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_with_filter-method | Loading method for 'ref_par referential' objects searching only those parameters existing for a DC, a Taxa, and a stage
charge_with_filter-method | Loading method for Reparqual referential objects searching only those parameters existing for a DC, a Taxon, and a stage
charge_with_filter-method | Loading method for Reparquan referential objects searching only those parameters existing for a DC (counting device), a Taxon, and a stage
charge_with_filter-method | Loading method for ref_stage referential objects searching only those stages existing for a DC and a Taxon
charge_with_filter-method | Loading method for ref_taxa referential objects searching only taxa existing for a DC
charge_with_filter.ref_par | Loading method for 'ref_par referential' objects searching only those parameters existing for a DC, a Taxa, and a stage
choice_c-method | Choice_c method for ref_choice referential objects
choice_c-method | Command line interface to select a counting device
choice_c-method | Command line interface to choose a fishway
choice_c-method | Command line interface to select a monitoring station
choice_c-method | Choice_c method for ref_horodate
choice_c-method | Choice_c method for ref_list referential objects
choice_c-method | Command line interface to select a parameter
choice_c-method | choice_c method for ref_stage
choice_c-method | choice_c method for ref_taxa
choice_c-method | Choice_c method for ref_textbox referential objects
choice_c-method | choice_c method for class ref_timestep_daily
choice_c-method | choice_c method for ref_year referential from the command line
choice_c-method | command line interface for report_annual-class
choice_c-method | command line interface for report_dc class
choice_c-method | command line interface for report_df class
choice_c-method | command line interface for report_env class
choice_c-method | command line interface for report_ge_weight-class
choice_c-method | command line interface for report_mig class
choice_c-method | command line interface for report_mig_char class
choice_c-method | command line interface for report_env class
choice_c-method | command line interface for report_mig_interannual class
choice_c-method | command line interface for report_mig_mult class
choice_c-method | command line interface for report_sample_char class
choice_c-method | command line interface for report_sea_age class
choice_c-method | command line interface for report_silver_eel class
choice_c-method | command line interface for report_species-class
choice_c.ref_horodate | Choice_c method for ref_horodate
choice_c.ref_list | Choice_c method for ref_list referential objects
choice_c.ref_par | Command line interface to select a parameter
choice_c.report_annual | command line interface for report_annual-class
choice_c.report_dc | command line interface for report_dc class
choice_c.report_df | command line interface for report_df class
choice_c.report_env | command line interface for report_env class
choice_c.report_ge_weight | command line interface for report_ge_weight-class
choice_c.report_mig | command line interface for report_mig class
choice_c.report_mig_char | command line interface for report_mig_char class
choice_c.report_mig_env | command line interface for report_env class
choice_c.report_mig_interannual | command line interface for report_mig_interannual class
choice_c.report_mig_mult | command line interface for report_mig_mult class
choice_c.report_sample_char | command line interface for report_sample_char class
choice_c.report_sea_age | command line interface for report_sea_age class
choice_c.report_silver_eel | command line interface for report_silver_eel class
choice_c.report_species | command line interface for report_species-class
coef_durif | Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters
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-method | connect method for report_annual class this method performs the sum over the year attention this function does not count subsamples.
connect-method | connect method for report_dc
connect-method | connect method for report_df
connect-method | connect method for report_env class
connect-method | connect method for report_Poids_moyen
connect-method | connect method for report_mig_char
connect-method | connect method for report_mig_env class
connect-method | connect method for report_mig_interannual
connect-method | connect method for report_mig_mult
connect-method | connect method for report_ope
connect-method | connect method for report_sample_char
connect-method | connect method for report_sea_age
connect-method | connect method for report_silver_eel
connect-method | connect method for report_species
connect.report_annual | connect method for report_annual class this method performs the sum over the year attention this function does not count subsamples.
connect.report_dc | connect method for report_dc
connect.report_df | connect method for report_df
connect.report_env | connect method for report_env class
connect.report_ge_weight | connect method for report_Poids_moyen
connect.report_mig_char | connect method for report_mig_char
connect.report_mig_interannual | connect method for report_mig_interannual
connect.report_mig_mult | connect method for report_mig_mult
connect.report_ope | connect method for report_ope
connect.report_sample_char | connect method for report_sample_char
connect.report_sea_age | connect method for report_sea_age
connect.report_silver_eel | connect method for report_silver_eel
connect.report_species | connect method for report_species

## -- E --

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

## -- F --

fungraph | 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
funstat | Function to calculate statistics per month
funtable | function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class
fun_aggreg_for_plot | Calculates a data.frame 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
fun_date_extraction | This function extracts temporal characteristics from a dataframe
fun_report_mig_interannual | statistics per time period
fun_report_mig_mult | Calculate daily migration by simple repartition
fun_report_mig_mult_overlaps | Function to calculate daily migration using overlaps functions
fun_schema | Creates a list of available schemas in the db
fun_stage_durif | Function to calculate the stages from Durif
fun_table_per_dis | functions called in DF and DC
fun_weight_conversion | returns a table where weights and number are calculated from number and weights respectively performs a query to collect the conversion coefficients
fun_write_monthly | This writes monthly data in t_reportmensuel_mens table

## -- G --

getvalue | Generic method getvalue
getvalue-method | Returns the POSIXt value of a given name
graphdate | function used for some lattice graphs with dates

## -- M --

model | Generic for prediction
model-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.
model.report_ge_weight | 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.

## -- P --

plot-method | Plot method for report_annual
plot-method | Different plots for report_dc
plot-method | Different plots for report_df
plot-method | Plot method for report_env
plot-method | Plot method for report_ge_weight'
plot-method | Plots of various type for report_mig.
plot-method | plot method for report_mig_char
plot-method | Plot method for report_mig_env
plot-method | Plot method for report_mig_interannual
plot-method | Plots of various type for report_mig_mult
plot-method | Plots of various type for reportcarlot
plot-method | Plots of various type for report_sea_age
plot-method | Plots of various type for report_silver_eel
plot-method | Plot method for report_species
plot.reportreport_species | Plot method for report_species
plot.report_annual | Plot method for report_annual
plot.report_dc | Different plots for report_dc
plot.report_df | Different plots for report_df
plot.report_env | Plot method for report_env
plot.report_ge_weight | Plot method for report_ge_weight'
plot.report_mig | Plots of various type for report_mig.
plot.report_mig_char | plot method for report_mig_char
plot.report_mig_env | Plot method for report_mig_env
plot.report_mig_interannual | Plot method for report_mig_interannual
plot.report_mig_mult | Plots of various type for report_mig_mult
plot.report_sample_char | Plots of various type for reportcarlot
plot.report_sea_age | Plots of various type for report_sea_age
plot.report_silver_eel | Plots of various type for report_silver_eel
print-method | Method to print the command line of the object.
print-method | Method to print the command line of the object
print-method | Method to print the command line of the object
print-method | Method to print the command line of the object
print-method | Method to print the command line of the object
print-method | Method to print the command line of the object
print.report_dc | Method to print the command line of the object.
print.report_df | Method to print the command line of the object
print.report_mig_mult | Method to print the command line of the object
print.report_sample_char | Method to print the command line of the object
print.report_sea_age | Method to print the command line of the object
print.report_silver_eel | Method to print the command line of the object

## -- R --

ref_choice-class | Class 'ref_choice'
ref_coe-class | Class 'ref_coe'
ref_dc-class | Class 'ref_dc'
ref_df-class | Class 'ref_df'
ref_env-class | Class 'ref_env'
ref_horodate-class | Class ref_horodate
ref_par-class | Class 'ref_par'
ref_parqual-class | Class 'ref_parqual'
ref_parquan-class | Class 'ref_parquan'
ref_period-class | Class 'ref_period' referential class
ref_stage-class | Class 'ref_stage'
ref_taxa-class | Class 'ref_taxa'
ref_textbox-class | ref_textbox referencial class
ref_timestep-class | Class "ref_timestep"
ref_timestepChar-class | Class "ref_timestepChar"
ref_timestep_daily-class | Class 'ref_timestep_daily'
ref_year-class | Year reference class
report_annual | Class "report_annual"
report_annual-class | Class "report_annual"
report_dc | Class "report_dc" report du fonctionnement du dispositif de comptage
report_dc-class | Class "report_dc" report du fonctionnement du dispositif de comptage
report_df | Report on fishway operation
report_df-class | Report on fishway operation
report_env | class report_env simple output of one or several environmental conditions...
report_env-class | class report_env simple output of one or several environmental conditions...
report_ge_weight | Trend of wet weight in glass eel
report_ge_weight-class | Trend of wet weight in glass eel
report_mig | Migration report for one DC, one species and one stage
report_mig-class | Migration report for one DC, one species and one stage
report_mig_char | Migration report along with quantitative and qualitative characteristics
report_mig_char-class | Migration report along with quantitative and qualitative characteristics
report_mig_env | Class "report_mig_env"
report_mig_env-class | Class "report_mig_env"
report_mig_interannual | Class "report_mig_interannual"
report_mig_interannual-class | Class "report_mig_interannual"
report_mig_mult | Migration reports for multiple DC / species / stages
report_mig_mult-class | Migration reports for multiple DC / species / stages
report_ope | Report on operations
report_ope-class | Report on operations
report_sample_char | Class 'report_sample_char'
report_sample_char-class | Class 'report_sample_char'
report_sea_age | Class "report_sea_age"
report_sea_age-class | Class "report_sea_age"
report_silver_eel | Class "report_silver_eel"
report_silver_eel-class | Class "report_silver_eel"
report_species | Counts of number per taxa/stages
report_species-class | Counts of number per taxa/stages
r_ann | Annual migration of yellow and silver eel for three fishways / counting devices at the Arzal dam (data from 1995 to 2016)
r_ann_adour | Annual migration of salmon in the Adour and tributaries
r_dc | Counting Device (DC) operation from 2000 to 2015 at the Arzal dam (Vilaine, France)
r_df | Overview of the fishway operation at Arzal in (Vilaine France).
r_env | An object of class report_env with data loaded
r_gew | Wet weight of glass eel from the trapping ladder (Arzal, 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_dc | Counting device operation for the video recording (Arzal dam, Vilaine, France).
r_mig_df | Fishway operation for the vertical slot fishway (Arzal dam, Vilaine, France).
r_mig_env | An object of class report_mig_env with data loaded
r_mig_interannual | Daily glass eel and elver migration from 1984 to 2016 in the Sevre Niortaise
r_mig_interannual_vichy | Seasonality of salmon migration at the Vichy counting station (Loire)
r_mig_mult | Anguilla migration at the Arzal station (report_mig_mult-class)
r_mig_mult_dc | Counting device operation for three different counting device in Arzal (Vilaine, France)
r_mig_mult_df | Fishway operation at the Arzal Dam (Vilaine France) (3 Fishways in 2011)
r_mig_mult_ope | Counting operations for three different counting device in Arzal (Vilaine, France)
r_mig_ope | An object of class report_ope-class with data loaded
r_sample_char | Size of yellow and glass eel at the Arzal dam (Vilaine, France) in the fishway and main eel trapping ladder.
r_seaa | An object of class report_sea_age with data loaded
r_silver | Silver eel migration in the Somme

## -- S --

setasqualitative | Generic method to transform quantitative par into a qualitative one
setasqualitative-method | Turns a continuous parameter into discrete values
split_per_day | Create a dataframe suitable for charts per 24h and day
stacomi | stacomi Main launcher for program stacomi
summary-method | summary for report_dc, write csv and html output, and prints summary statistics
summary-method | summary for report_df, write csv and html output, and prints summary statistics
summary-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-method | summary for report_mig_char
summary-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-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-method | summary for report_sample_char
summary-method | summary for report_sea_age
summary-method | summary for report_silver_eel
summary-method | summary for report_species
summary.report_dc | summary for report_dc, write csv and html output, and prints summary statistics
summary.report_df | summary for report_df, write csv and html output, and prints summary statistics
summary.report_mig | 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 | summary for report_mig_char
summary.report_mig_env | connect method for report_mig_env class
summary.report_mig_interannual | 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 | 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_sample_char | summary for report_sample_char
summary.report_sea_age | summary for report_sea_age
summary.report_silver_eel | summary for report_silver_eel
summary.report_species | summary for report_species
supprime | Generic method to delete entires from the database
supprime-method | supprime method for 'ref_coe' class
supprime-method | supprime method for report_mig_interannual class, deletes values in table t_bilanmigrationjournalier_bjo
supprime-method | supprime method for report_mig_interannual class
supprime.report_mig_interannual | supprime method for report_mig_interannual class, deletes values in table t_bilanmigrationjournalier_bjo
supprime.report_sea_age | supprime method for report_mig_interannual class

## -- V --

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

## -- W --

write_database | Generic method write_database
write_database-method | Method to write data to the stacomi database for report_ge_weight-class
write_database-method | Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table
write_database-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_ge_weight | Method to write data to the stacomi database for report_ge_weight-class
write_database.report_mig | Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table
write_database.report_sea_age | Command line method to write the characteristic "sea age" (car_par_code='A124') into the tj_caracteristiquelot_car table in the user's scheme

## -- X --

xtable-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.
xtable-method | xtable function for report_mig_char-class create an xtable objet to be later used by the print.xtable method.
xtable.report_annual | 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.
xtable.report_mig_char | xtable function for report_mig_char-class create an xtable objet to be later used by the print.xtable method.

## -- misc --

' | connect method for report_mig_mult