| barplot method for object report_annual-class | barplot,report_annual-method barplot.report_annual |
| Generic method for calculations | calcule |
| Calcule method for report_ge_weight | calcule,report_ge_weight-method calcule.report_ge_weight |
| Computes data to a standard format for the summary and plot methods. | calcule,report_mig_char-method calcule.report_mig_char |
| Calculations for migration in the class report_mig_env-class | calcule,report_mig_env-method calcule.report_mig_env |
| calcule method for report_mig_interannual | calcule,report_mig_interannual-method calcule.report_mig_interannual |
| #' 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_mult-method 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). | calcule,report_mig-method calcule.report_mig |
| Calculation for report_sample_char | calcule,report_sample_char-method calcule.report_sample_char |
| Split data according to the limits set in the limit1hm, and limit2hm arguments of the report_sea_age-class. | calcule,report_sea_age-method calcule.report_sea_age |
| Calculate individual silver eel parameters. | calcule,report_silver_eel-method calcule.report_silver_eel |
| calcule method for report_species | calcule,report_species-method calcule.report_species |
| Generic method to load referentials | charge |
| Generic method to load additional data | charge_complement |
| Loads an additional dataset this method is loaded to obtain the possible values of a qualitative parameter. Here data only contains one line | charge_complement,ref_parqual-method |
| Loading method for 'ref_par referential' objects searching only those parameters existing for a DC, a Taxa, and a stage | charge_with_filter,ref_par-method charge_with_filter.ref_par |
| Loading method for Reparqual referential objects searching only those parameters existing for a DC, a Taxon, and a stage | charge_with_filter,ref_parqual-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,ref_parquan-method |
| Loading method for ref_stage referential objects searching only those stages existing for a DC and a Taxon | charge_with_filter,ref_stage-method |
| Loading method for ref_taxa referential objects searching only taxa existing for a DC | charge_with_filter,ref_taxa-method |
| Loading method for Refchoice referential objects | charge,ref_choice-method |
| loads the coefficients for the period defined in class | charge,ref_coe-method |
| Method to load the counting devices of the control station | charge,ref_dc-method |
| Loading method for DF referential objects | charge,ref_df-method |
| Loading method for ref_env referential object | charge,ref_env-method |
| Loading method for ref_list referential objects | charge,ref_list-method charge.ref_list |
| Loading method for ref_par referential objects | charge,ref_par-method charge.ref_par |
| Loading method for Reparqual referential objects | charge,ref_parqual-method |
| Loading method for Reparquan referential objects | charge,ref_parquan-method |
| Loading method for ref_stage referential objects | charge,ref_stage-method |
| Loading method for ref_taxa referential objects | charge,ref_taxa-method |
| Loading method for ref_textbox referential objects | charge,ref_textbox-method |
| Loading method for ref_year referential objects | charge,ref_year-method |
| charge method for report_mig_env class | charge,report_mig_env-method charge.report_mig_env |
| charge method for report_mig_mult | charge,report_mig_mult-method charge.report_mig_mult |
| Loads additional data on migration control operations, df (fishway) dc (counting device). | charge,report_mig-method charge.report_mig |
| Choice_c method for ref_choice referential objects | choice_c,ref_choice-method |
| Command line interface to select a counting device | choice_c,ref_dc-method |
| Command line interface to choose a fishway | choice_c,ref_df-method |
| Command line interface to select a monitoring station | choice_c,ref_env-method |
| Choice_c method for ref_horodate | choice_c,ref_horodate-method choice_c.ref_horodate |
| Choice_c method for ref_list referential objects | choice_c,ref_list-method choice_c.ref_list |
| Command line interface to select a parameter | choice_c,ref_par-method choice_c.ref_par |
| choice_c method for ref_stage | choice_c,ref_stage-method |
| choice_c method for ref_taxa | choice_c,ref_taxa-method |
| Choice_c method for ref_textbox referential objects | choice_c,ref_textbox-method |
| choice_c method for class ref_timestep_daily | choice_c,ref_timestep_daily-method |
| choice_c method for ref_year referential from the command line | choice_c,ref_year-method |
| command line interface for report_annual-class | choice_c,report_annual-method choice_c.report_annual |
| command line interface for report_dc class | choice_c,report_dc-method choice_c.report_dc |
| command line interface for report_df class | choice_c,report_df-method choice_c.report_df |
| command line interface for report_env class | choice_c,report_env-method choice_c.report_env |
| command line interface for report_ge_weight-class | choice_c,report_ge_weight-method choice_c.report_ge_weight |
| command line interface for report_mig_char class | choice_c,report_mig_char-method choice_c.report_mig_char |
| command line interface for report_env class | choice_c,report_mig_env-method choice_c.report_mig_env |
| command line interface for report_mig_interannual class | choice_c,report_mig_interannual-method choice_c.report_mig_interannual |
| command line used to build report_mig_mult class | choice_c,report_mig_mult-method choice_c.report_mig_mult |
| command line interface for report_mig class | choice_c,report_mig-method choice_c.report_mig |
| command line interface for report_sample_char class | choice_c,report_sample_char-method choice_c.report_sample_char |
| command line interface for report_sea_age class | choice_c,report_sea_age-method choice_c.report_sea_age |
| command line interface for report_silver_eel class | choice_c,report_silver_eel-method choice_c.report_silver_eel |
| command line interface for report_species-class | choice_c,report_species-method choice_c.report_species |
| Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters | coef_durif |
| 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). | colortable |
| connect method for report_annual class this method performs the sum over the year attention this function does not count subsamples. | connect,report_annual-method connect.report_annual |
| connect method for report_dc | connect,report_dc-method connect.report_dc |
| connect method for report_df | connect,report_df-method connect.report_df |
| connect method for report_env class | connect,report_env-method connect.report_env |
| connect method for report_Poids_moyen | connect,report_ge_weight-method connect.report_ge_weight |
| connect method for report_mig_char | connect,report_mig_char-method connect.report_mig_char |
| connect method for report_mig_env class | connect,report_mig_env-method summary.report_mig_env |
| connect method for report_mig_interannual | connect,report_mig_interannual-method connect.report_mig_interannual |
| connect method for report_mig_mult | ' connect,report_mig_mult-method connect.report_mig_mult |
| connect method for report_mig | connect,report_mig-method connect.report_mig |
| connect method for report_ope | connect,report_ope-method connect.report_ope |
| connect method for report_sample_char | connect,report_sample_char-method connect.report_sample_char |
| connect method for report_sea_age | connect,report_sea_age-method connect.report_sea_age |
| connect method for report_silver_eel | connect,report_silver_eel-method connect.report_silver_eel |
| connect method for report_species | connect,report_species-method connect.report_species |
| Environment where most objects from the package are stored and then loaded by the charge method | envir_stacomi |
| Get table content for table t_bilanmigrationjournalier_bjo in report_mig_interannual | fn_connect_report_mig_interannual |
| Calculates a data.frame where all components within the list calcdata are aggregated and formatted for plot | fun_aggreg_for_plot |
| function used to remove special non utf8 character which cause the gtk interface to crash | fun_char_spe |
| This function extracts temporal characteristics from a dataframe | fun_date_extraction |
| statistics per time period | fun_report_mig_interannual |
| Calculate daily migration by simple repartition | fun_report_mig_mult |
| Function to calculate daily migration using overlaps functions | fun_report_mig_mult_overlaps |
| Creates a list of available schemas in the db | fun_schema |
| Function to calculate the stages from Durif | fun_stage_durif |
| functions called in DF and DC | fun_table_per_dis |
| returns a table where weights and number are calculated from number and weights respectively performs a query to collect the conversion coefficients | fun_weight_conversion |
| This writes monthly data in t_reportmensuel_mens table | fun_write_monthly |
| Function for report_mig graphs including numbers DF DC operations | fungraph |
| Graph function for glass eel migration. Differs from fungraph as it does not draw the ggplot graph for month | fungraph_glasseel |
| Function to calculate statistics per month | funstat |
| function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class | funtable |
| Generic method getvalue | getvalue |
| function used for some lattice graphs with dates | graphdate |
| Generic for prediction | model |
| 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-method model.report_ge_weight |
| Plot method for report_annual | plot,report_annual,missing-method plot.report_annual |
| Different plots for report_dc | plot,report_dc,missing-method plot.report_dc |
| Different plots for report_df | plot,report_df,missing-method plot.report_df |
| Plot method for report_env | plot,report_env,missing-method plot.report_env |
| Plot method for report_ge_weight' | plot,report_ge_weight,missing-method plot.report_ge_weight |
| plot method for report_mig_char | plot,report_mig_char,missing-method plot.report_mig_char |
| Plot method for report_mig_env | plot,report_mig_env,missing-method plot.report_mig_env |
| Plot method for report_mig_interannual | plot,report_mig_interannual,missing-method plot.report_mig_interannual |
| Plots of various type for report_mig_mult | plot,report_mig_mult,missing-method plot.report_mig_mult |
| Plots of various type for report_mig. | plot,report_mig,ANY-method plot.report_mig |
| Plots of various type for reportcarlot | plot,report_sample_char,missing-method plot.report_sample_char |
| Plots of various type for report_sea_age | plot,report_sea_age,missing-method plot.report_sea_age |
| Plots of various type for report_silver_eel | plot,report_silver_eel,missing-method plot.report_silver_eel |
| Plot method for report_species | plot,report_species,missing-method plot.reportreport_species |
| Method to print the command line of the object. | print,report_dc-method print.report_dc |
| Method to print the command line of the object | print,report_df-method print.report_df |
| Method to print the command line of the object | print,report_mig_mult-method print.report_mig_mult |
| Method to print the command line of the object | print,report_mig-method print.report_mig |
| Method to print the command line of the object | print,report_sample_char-method print.report_sample_char |
| Method to print the command line of the object | print,report_sea_age-method print.report_sea_age |
| Method to print the command line of the object | print,report_silver_eel-method print.report_silver_eel |
| Annual migration of yellow and silver eel for three fishways / counting devices at the Arzal dam (data from 1995 to 2016) | r_ann |
| Annual migration of salmon in the Adour and tributaries | r_ann_adour |
| Counting Device (DC) operation from 2000 to 2015 at the Arzal dam (Vilaine, France) | r_dc |
| Overview of the fishway operation at Arzal in (Vilaine France). | r_df |
| An object of class report_env with data loaded | r_env |
| Wet weight of glass eel from the trapping ladder (Arzal, Vilaine France) | r_gew |
| Video counting of Marine lamprey (Petromyzon marinus) in 2012 in the Vilaine (France) | r_mig |
| Qualitative and quantitative parameters describing Salmon migration at Decize (Loire) | r_mig_char |
| Counting device operation for the video recording (Arzal dam, Vilaine, France). | r_mig_dc |
| Fishway operation for the vertical slot fishway (Arzal dam, Vilaine, France). | r_mig_df |
| An object of class report_mig_env with data loaded | r_mig_env |
| Daily glass eel and elver migration from 1984 to 2016 in the Sevre Niortaise | r_mig_interannual |
| Seasonality of salmon migration at the Vichy counting station (Loire) | r_mig_interannual_vichy |
| Anguilla migration at the Arzal station (report_mig_mult-class) | r_mig_mult |
| Counting device operation for three different counting device in Arzal (Vilaine, France) | r_mig_mult_dc |
| Fishway operation at the Arzal Dam (Vilaine France) (3 Fishways in 2011) | r_mig_mult_df |
| Counting operations for three different counting device in Arzal (Vilaine, France) | r_mig_mult_ope |
| An object of class report_ope-class with data loaded | r_mig_ope |
| Size of yellow and glass eel at the Arzal dam (Vilaine, France) in the fishway and main eel trapping ladder. | r_sample_char |
| An object of class report_sea_age with data loaded | r_seaa |
| Silver eel migration in the Somme | r_silver |
| Class 'ref_choice' | ref_choice-class |
| Class 'ref_coe' | ref_coe-class |
| Class 'ref_dc' | ref_dc-class |
| Class 'ref_df' | ref_df-class |
| Class 'ref_env' | ref_env-class |
| Class ref_horodate | ref_horodate-class |
| Class 'ref_par' | ref_par-class |
| Class 'ref_parqual' | ref_parqual-class |
| Class 'ref_parquan' | ref_parquan-class |
| Class 'ref_stage' | ref_stage-class |
| Class 'ref_taxa' | ref_taxa-class |
| ref_textbox referencial class | ref_textbox-class |
| Class 'ref_timestep_daily' | ref_timestep_daily-class |
| Class "ref_timestep" | ref_timestep-class |
| Class "ref_timestepChar" | ref_timestepChar-class |
| Year reference class | ref_year-class |
| Class "report_annual" | report_annual report_annual-class |
| Class "report_dc" report du fonctionnement du dispositif de comptage | report_dc report_dc-class |
| Report on fishway operation | report_df report_df-class |
| class report_env simple output of one or several environmental conditions... | report_env report_env-class |
| Trend of wet weight in glass eel | report_ge_weight report_ge_weight-class |
| Migration report along with quantitative and qualitative characteristics | report_mig_char report_mig_char-class |
| Class "report_mig_env" | report_mig_env report_mig_env-class |
| Class "report_mig_interannual" | report_mig_interannual report_mig_interannual-class |
| Migration reports for multiple DC / species / stages | report_mig_mult report_mig_mult-class |
| Migration report for one DC, one species and one stage | report_mig report_mig-class |
| Report on operations | report_ope report_ope-class |
| Class 'report_sample_char' | report_sample_char report_sample_char-class |
| Class "report_sea_age" | report_sea_age report_sea_age-class |
| Class "report_silver_eel" | report_silver_eel report_silver_eel-class |
| Counts of number per taxa/stages | report_species report_species-class |
| Generic method to transform quantitative par into a qualitative one | setasqualitative |
| Turns a continuous parameter into discrete values | setasqualitative,report_mig_char-method |
| Create a dataframe suitable for charts per 24h and day | split_per_day |
| stacomi Main launcher for program stacomi | stacomi |
| summary for report_dc, write csv and html output, and prints summary statistics | summary,report_dc-method summary.report_dc |
| summary for report_df, write csv and html output, and prints summary statistics | summary,report_df-method summary.report_df |
| summary for report_mig_char | summary,report_mig_char-method summary.report_mig_char |
| 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 and they always include the current year from the historical dataset. | summary,report_mig_interannual-method summary.report_mig_interannual |
| 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_mult-method summary.report_mig_mult |
| 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-method summary.report_mig |
| summary for report_sample_char | summary,report_sample_char-method summary.report_sample_char |
| summary for report_sea_age | summary,report_sea_age-method summary.report_sea_age |
| summary for report_silver_eel | summary,report_silver_eel-method summary.report_silver_eel |
| summary for report_species | summary,report_species-method summary.report_species |
| Generic method to delete entires from the database | supprime |
| supprime method for 'ref_coe' class | supprime,ref_coe-method |
| supprime method for report_mig_interannual class, deletes values in table t_bilanmigrationjournalier_bjo | supprime,report_mig_interannual-method supprime.report_mig_interannual |
| supprime method for report_mig_interannual class | supprime,report_sea_age-method supprime.report_sea_age |
| Transforms a vector into a string called within an sql command e.g. c('A','B','C') => in ('A','B','C') | vector_to_listsql |
| Generic method write_database | write_database |
| Method to write data to the stacomi database for report_ge_weight-class | write_database,report_ge_weight-method write_database.report_ge_weight |
| Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table | write_database,report_mig-method write_database.report_mig |
| 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_sea_age-method write_database.report_sea_age |
| 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_annual-method xtable.report_annual |
| xtable function for report_mig_char-class create an xtable objet to be later used by the print.xtable method. | xtable,report_mig_char-method xtable.report_mig_char |
