| 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 used to build 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 used to build 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 |
| 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 |
connect method for report_mig |
| 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 |
| 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_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 Marine lamprey (Petromyzon marinus) in 2012 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 |
| 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 and they always include the current year 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 and they always include the current year 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 |
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