barplot-method | barplot method for object report_annual-class |
barplot.report_annual | barplot method for object report_annual-class |
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 |
envir_stacomi | Environment where most objects from the package are stored and then loaded by the charge method |
fn_connect_report_mig_interannual | Get table content for table t_bilanmigrationjournalier_bjo in report_mig_interannual |
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 |
getvalue | Generic method getvalue |
graphdate | function used for some lattice graphs with dates |
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. |
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-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 | 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 |
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 |
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 | 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 |
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. |
' | connect method for report_mig_mult |