stacomiR v0.5.3.1
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Fish Migration Monitoring
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. Version 0.5.3.1 is available in French and
English. See <http://stacomir.r-forge.r-project.org/> for more information on
'STACOMI'.
Functions in stacomiR
| Name | Description | |
| 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. | |
| charge,report_dc-method | charge method for report_dc | |
| charge,report_df-method | charge method for report_df | |
| charge,report_env-method | charge method for report_env class | |
| calcule,report_mig_interannual-method | calcule method for report_mig_interannual | |
| barplot,report_annual-method | barplot method for object report_annual-class | |
| 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 | |
| charge,ref_checkbox-method | Loading method for ref_checkbox referential objects | |
| charge,ref_year-method | Loading method for ref_year referential objects | |
| calcule,report_mig_char-method | Computes data to a standard format for the summary and plot methods. | |
| charge,report_annual-method | charge method for report_annual class | |
| charge,report_mig-method | Loads additional data on migration control operations, df (fishway) dc (counting device). | |
| calcule,report_mig_env-method | Calculations for migration in the class report_mig_env-class | |
| calcule | Generic method for calculations | |
| charge,ref_env-method | Loading method for ref_env referential object | |
| charge,report_mig_char-method | charge method for report_mig_char | |
| charge,ref_list-method | Loading method for refliste referential objects | |
| charge_complement | Generic method to load additional data | |
| charge,ref_par-method | Loading method for Repar referential objects | |
| 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 | |
| charge,ref_parqual-method | Loading method for Reparqual referential objects | |
| chargecomplement-methods | Methods for Function chargecomplement | |
| choice_c,ref_stage-method | choice_c method for ref_stage | |
| charge,report_ge_weight-method | charge method for report_ge_weight class | |
| choice_c,ref_taxa-method | choice_c method for ref_taxa | |
| 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_with_filter,ref_taxa-method | Loading method for ref_taxa referential objects searching only taxa existing for a DC | |
| charge_with_filter | Generic method to load referentials, with filters from the parent object in the database | |
| charge,ref_dc-method | Method to load the counting devices of the control station | |
| choice,ref_choice-method | Choice method for Rechoice referential objects | |
| choice,ref_dc-method | Graphical method to choose a fishway through the interface | |
| charge,report_sample_char-method | charge method for report_sample_char class | |
| charge,report_sea_age-method | Loads data and check that all choices in the graphical interface have been made. | |
| choice | Generic method for choice (using the gwidget graphical interface) | |
| charge,report_silver_eel-method | charge method for report_silver_eel class | |
| choice_c,ref_choice-method | Choice_c method for refchoix referential objects | |
| choice_c,report_env-method | command line interface for report_env class | |
| choice_c,report_ge_weight-method | command line interface for report_ge_weight-class | |
| choice_c,report_species-method | command line interface for report_species-class | |
| choice_c | Generic method for manual choice using the command line | |
| choice_c,ref_dc-method | Command line interface to select a counting device | |
| choice_c,ref_df-method | Command line interface to choose a fishway | |
| choice_c,report_mig-method | command line interface for report_mig class | |
| choice_c,report_mig_char-method | command line interface for report_mig_char class | |
| choicemult,ref_horodate-method | Multiple Choice method for ref_horodate referential objects, to put together with notebook widgets | |
| choicemult,ref_par-method | Multiple Choice method for ref_par referential objects, internal use | |
| 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_annual-method | connect method for report_annual class this method performs the sum over the year attention this function does not count subsamples. | |
| calcule,report_sample_char-method | Calculation for report_sample_char | |
| calcule,report_sea_age-method | Split data according to the limits set in the limit1hm, and limit2hm arguments of the report_sea_age-class. | |
| calcule,report_silver_eel-method | Calculate individual silver eel parameters. | |
| connect,report_mig_env-method | connect method for report_mig_env class | |
| calcule,report_species-method | calcule method for report_species | |
| charge,ref_taxa-method | Loading method for ref_taxa referential objects | |
| connect,report_mig_interannual-method | connect method for report_mig_interannual | |
| connect,report_mig_mult-method | connect method for report_mig_mult | |
| current_end_date | Generic method for getting the ending date for current time step | |
| connect,report_ope-method | connect method for report_ope | |
| createmessage | Generic method to forward outputs | |
| charge,ref_df-method | Loading method for DF referential objects | |
| current_end_date,ref_timestep-method | Gets the ending date of a time step for an object of class ref_timestep-class | |
| charge,report_mig_env-method | charge method for report_mig_env class | |
| currentstart_date,ref_timestep-method | Gets the starting date of a time step for an object of class ref_timestep-class | |
| charge,report_mig_interannual-method | loading method for report_mig_interannual class | |
| 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 | |
| charge | Generic method to load referentials | |
| funboxDC | function used for some lattice graph | |
| 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 | |
| choice_c,ref_timestep_daily-method | choice_c method for class ref_timestep_daily | |
| choice_c,report_mig_env-method | command line interface for report_env class | |
| charge,report_species-method | charge method for report_species | |
| choice_c,report_mig_interannual-method | command line interface for report_mig_interannual class | |
| choice,ref_stage-method | Choice method for ref_stage referential objects | |
| charge,ref_textbox-method | Loading method for ReTextBox referential objects | |
| charge,report_mig_mult-method | charge method for report_mig_mult | |
| choice,ref_taxa-method | Choice method for reftaxa referential objects with only one taxa selected | |
| charge,report_ope-method | charge method for report_ope | |
| choice_c,ref_textbox-method | Choice_c method for ReTextBox referential objects | |
| chargecsv | chargecsv loads the informations stored in c:/program files/stacomi/calcmig.csv file | |
| choice,ref_df-method | Graphical method to choose a fishway through the interface | |
| funboxDF | Internal use, rectangles to describe the DF work for report_df class, graphical interface handler | |
| choice,ref_env-method | Choice method for ref_env referential object | |
| funstat | Function to calculate statistics per month | |
| choice,ref_par-method | Choice method for ref_par referential objects | |
| choice,ref_checkbox-method | Choice method for ref_checkbox referential objects | |
| funstat_daily | function to create daily statistics | |
| choice,ref_timestep_daily-method | Method to select timesteps from the graphical interface | |
| funtablereport_sample_char | table function | |
| choice,ref_year-method | choice method for ref_year referential | |
| funtablereport_sea_age | table function | |
| choice_c,ref_env-method | Command line interface to select a monitoring station | |
| choice_c,ref_horodate-method | Command line | |
| getnocurrent_step,ref_timestep-method | Gets the current time step of an object of class ref_timestep-class | |
| choice_c,ref_year-method | choice_c method for ref_year referential from the command line | |
| getnocurrent_step | Generic method to get current time step | |
| choice_c,report_annual-method | command line interface for report_annual-class | |
| choice_c,report_sea_age-method | command line interface for report_sea_age class | |
| h_report_mig | handler function used by the main interface | |
| end_date,ref_timestep-method | Gets the final horodate for an object of class ref_timestep-class | |
| 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. | |
| fun_date_extraction | This function extracts temporal characteristics from a dataframe | |
| fun_report_mig_interannual | statistics per time period | |
| choicemult,ref_timestep-method | Graphical interface for multiple choice method for PasdeTemps (used in report_mig_mult) | |
| choice_c,report_silver_eel-method | command line interface for report_silver_eel class | |
| connect,report_mig-method | connect method for report_mig | |
| choicemult | Generic method for multiple choice (using the gwidget notebook for multiple choice) | |
| coef_durif | Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters | |
| connect,report_mig_char-method | connect method for report_mig_char | |
| connect,report_silver_eel-method | connect method for report_silver_eel | |
| currentstart_date | Generic method for getting the beginning date for current time step | |
| connect,report_species-method | connect method for report_species | |
| 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 | |
| funplotreport_silver_eel | funplotreport_silver_eel | |
| funpointreport_sample_char | Point graph from ggplot | |
| h_report_mig_annual | handler function used by the main interface | |
| h_report_mig_interannual | handler function used by the main interface | |
| h_report_mig_mult | handler function used by the main interface | |
| h_report_sample_char | handler function used by the main interface | |
| choice,ref_parqual-method | Choice method for ref_parqual referential objects, internal use | |
| choicemult,ref_choice-method | Multiple Choice method for ref_choice referential objects, to put together with notebook widgets | |
| connect,report_dc-method | connect method for report_dc | |
| connect,report_df-method | connect method for report_df | |
| connect,report_sample_char-method | connect method for report_sample_char | |
| connect,report_sea_age-method | connect method for report_sea_age | |
| choicemult,ref_dc-method | choicemult, selection method for ref_dc allowing to select several DC | |
| fun_stage_durif | Function to calculate the stages from Durif | |
| funboxplotreport_sample_char | Boxplots for ggplot2 | |
| funchartDC | Handler function to plot calendar like graph, internal use | |
| fun_table_per_dis | functions called in DF and DC | |
| 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 | |
| hTablereport_mig | handler for summary function, internal use calls functions funstat and funtable to build summary tables in html and csv files | |
| hTablereport_mig_mult | handler function table | |
| h_report_mig_mult_graph | handler for plot method in report_mig_mult class | |
| h_report_mig_multcalc | handler for calculations | |
| funbarchartDC | Function to create a barchart (lattice) corresponding to the periods | |
| funbarchartDF | Handler for barchart for report_df class from the graphical interface | |
| get_step_label | Generic method to get the string value of time step | |
| funout | this function uses gfile, edits a text with info and changing colors | |
| get_year,ref_timestep-method | Gets the year or a vector of years corresponding to the timestep ("ref_timestep") object | |
| funplotreport_sea_age | funplotreport_sea_age | |
| funtablereport_silver_eel | table function | |
| h_report_mig_char | handler function used by the main interface | |
| get_step_label,ref_timestep-method | Gets the string value of time step | |
| h_report_mig_env | handler function used by the main interface | |
| graphdate | function used for some lattice graphs with dates | |
| h_report_miggraph2 | handler for h_report_miggraph2 | |
| h_report_sea_age | handler function used by the main interface | |
| h_report_silver | handler function used by the main interface | |
| hbmCplotquan | handler for plot | |
| h_report_size | handler function used by the main interface | |
| hbmCstat | This handler calls the generic method stat | |
| hbmmCEcalc | Internal handler function | |
| hbmmCEgraph | internal method for graphical interface | |
| hsummarybilesp | handler for summary report_species, internal use | |
| houtDC | handler to print the command line | |
| funchartDF | Handler function to plot calendar like graph, internal use | |
| houtDF | handler to print the command line | |
| interface_report_df | interface for report_df class | |
| funtable | function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class | |
| interface_report_env | Interface for class conditionEnv | |
| funtableDC | FuntableDC create a table output for report_dc class | |
| funtablereport_ge_weight | Internal handler for reg, class report_ge_weight-class. | |
| getvalue,ref_period-method | Returns the POSIXt value of a given name | |
| funtableDF | Table output for report_df class | |
| getvalue | Generic method getvalue | |
| h_report_env | handler function used by the main interface | |
| h_report_dfdc | handler function used by the main interface | |
| h_report_migwrite | handler h_report_migwrite Allows the saving of daily and monthly counts in the database | |
| h_report_species | handler function used by the main interface | |
| h_report_ope | handler function used by the main interface | |
| hbarplotreport_annual | Barplot handler | |
| h_report_pigment_stages | handler function used by the main interface | |
| hsummaryreport_migInterannuelle | Summary handler internal method | |
| hcalc | Internal handler for reg, class report_ge_weight-class. | |
| model | Generic for prediction | |
| hexp | Internal handler for reg, class report_ge_weight-class. | |
| plot,report_annual,missing-method | Plot method for report_annual | |
| print,report_df-method | Method to print the command line of the object | |
| fundensityreport_sample_char | fundensityreport_sample_char uses ggplot2 to draw density plots | |
| graphe-methods | Methods for Function graphe | |
| h_report_envgraph | h_report_envgraph Internal method | |
| h_report_ge_weight | handler function used by the main interface | |
| interface_report_ge_weight | interface for report_ge_weight class | |
| interface_report_mig | Interface for report_mig class, internal use, this function is called by a handler in the main graphical interface | |
| h_report_migcalc | handler for calculations report_mig | |
| load_stacomi | Internal function, tests the connection and if it works loads the stacomi interface | |
| h_report_miggraph | handler for h_report_miggraph | |
| 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. | |
| 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 | |
| print,report_sea_age-method | Method to print the command line of the object | |
| houtreport_mig | handler to print the command line | |
| houtreport_mig_mult | handler to print the command line | |
| hplotreport_annual | plot handler | |
| hreg | Internal handler for reg, class report_ge_weight-class. | |
| hgraph_report_mig_interannual3 | Step plot with different years displayed on the same graph. One year can be highlighted against the others | |
| 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 | |
| interface_report_sample_char | An interface that calls the object to build the user interface | |
| print,report_mig-method | Method to print the command line of the object | |
| 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 | |
| interface_report_sea_age | An interface that calls the object to build the user interface | |
| print,report_silver_eel-method | Method to print the command line of the object | |
| plot,report_dc,ANY-method | Different plots for report_dc | |
| r_mig | Video counting of thin lipped mullet (Liza ramada) in 2015 in the Vilaine (France) | |
| plot,report_df,ANY-method | Different plots for report_df | |
| plot,report_mig_env,missing-method | Plot method for report_mig_env | |
| r_mig_char | Qualitative and quantitative parameters describing Salmon migration at Decize (Loire) | |
| plot,report_mig_interannual,missing-method | Plot method for report_mig_interannual | |
| hbmCplotcrossed | handler for plot | |
| r_mig_mult_dc | Counting device operation for three different counting device in Arzal (Vilaine, France) | |
| hbmCplotqual | handler for plot | |
| r_mig_mult_df | Fishway operation at the Arzal Dam (Vilaine France) (3 Fishways in 2011) | |
| 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 | |
| ref_dc-class | Class "ref_dc" | |
| 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 | |
| print,report_mig_mult-method | Method to print the command line of the object | |
| ref_df-class | Class "ref_df" | |
| print,report_sample_char-method | Method to print the command line of the object | |
| report_annual-class | Class "report_annual" | |
| 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 | |
| report_dc-class | Class "report_dc" report du fonctionnement du dispositif de comptage | |
| interface_report_annual | interface for report_annual class | |
| ref_parqual-class | Class "ref_parqual" | |
| interface_report_dc | interface for report_dc class | |
| interface_report_mig_interannual | interface for report_mig_interannual class | |
| ref_parquan-class | Class "ref_parquan" | |
| ref_choice-class | Class "ref_choice" | |
| report_mig_char-class | Migration report along with quantitative and qualitative characteristics | |
| ref_coe-class | Class "ref_coe" | |
| ref_timestep-class | Class "ref_timestep" | |
| report_mig_env-class | Class "report_mig_env" | |
| ref_timestepChar-class | Class "ref_timestepChar" | |
| split_per_day | Create a dataframe suitable for charts per 24h and day | |
| interface_report_silver_eel | An interface that calls the object to build the user interface | |
| interface_report_species | Interface for report_species class | |
| report_ope-class | Report on operations | |
| plot,report_species,missing-method | Plot method for report_species | |
| interface_report_mig_mult | graphical interface for report_mig_mult class | |
| report_sample_char-class | Class "report_sample_char" | |
| plot,report_env,missing-method | Plot method for report_env | |
| stacomiR-package | package Fish Migration Monitoring (stacomiR)- Stations de Controle des Migrations | |
| plot,report_ge_weight,missing-method | Plot method for report_ge_weight' | |
| r_ann | Annual migration of yellow and silver eel for three fishways / counting devices at the Arzal dam (data from 1995 to 2016) | |
| summary,report_dc-method | summary for report_dc, write csv and html output, and prints summary statistics | |
| stacomi | Function that loads the loginwindow, tests connection, and then destroys the window | |
| 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 | |
| summary,report_species-method | summary for report_species generate csv and html output in the user data directory | |
| supprime,ref_coe-method | supprime method for "ref_coe" class | |
| summary,report_sample_char-method | summary for report_sample_char | |
| supprime | Generic method to delete entires from the database | |
| supprime,report_mig_interannual-method | supprime method for report_mig_interannual class | |
| r_ann_adour | Annual migration of salmon in the Adour and tributaries | |
| 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) | |
| ref_env-class | Class "ref_env" | |
| progress_bar | Progress bar using a gtkdialog, the progress bar is assigned in envir_stacomi This progress bar has a button to close. | |
| quitte | function used to clean the objects within the group and the graphs and also elements remaining in the envir_stacomi environment | |
| r_env | An object of class report_env with data loaded | |
| report_mig_interannual-class | Class "report_mig_interannual" | |
| print,report_dc-method | Method to print the command line of the object | |
| report_mig_mult-class | Migration reports for multiple DC / species / stages | |
| ref_horodate-class | Class ref_horodate | |
| report_df-class | Report on fishway operation | |
| report_mig-class | Migration report for one DC, one species and one stage | |
| set_starting_date | Generic method to set the starting date | |
| report_env-class | class report_env simple output of one or several environmental conditions... | |
| setasqualitative,report_mig_char-method | Turns a quantitative parameter into qualitative | |
| report_ge_weight-class | Trend of wet weight in glass eel | |
| supprime,report_sea_age-method | supprime method for report_mig_interannual class | |
| r_gew | Wet weight of glass eel from the trapping ladder (Arzal, Vilaine France) | |
| r_silver | Silver eel migration in the Somme | |
| ref_checkbox-class | ref_checkbox referencial class | |
| summary,report_df-method | summary for report_df, write csv and html output, and prints summary statistics | |
| 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 | |
| validity_year | Validity check for ref_year | |
| vector_to_listsql | Transforms a vector into a string called within an sql command e.g. c('A','B','C') => in ('A','B','C') | |
| validity_ref_horodate | Validity check for ref_horodate | |
| 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. | |
| 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_list-class | Class "ref_list" | |
| ref_par-class | Class "ref_par" | |
| ref_taxa-class | Class "ref_taxa" | |
| ref_textbox-class | ref_textbox referencial class | |
| setasqualitative | Generic method to transform quantitative par into a qualitative one | |
| setref_horodate,ref_horodate-method | Method to set the Horodate | |
| summary,report_sea_age-method | summary for report_sea_age | |
| summary,report_silver_eel-method | summary for report_silver_eel | |
| 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 | |
| write_database | Generic method write_database | |
| calcule,report_ge_weight-method | Calcule method for report_ge_weight | |
| 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_textbox-method | Choice method for ReTextBox referential objects | |
| 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_choice-method | Loading method for Rechoice referential objects | |
| charge,ref_coe-method | loads the coefficients for the period defined in class | |
| choice,ref_timestep-method | Method to select timesteps from the graphical interface | |
| charge,ref_parquan-method | Loading method for Reparquan referential objects | |
| charge,ref_stage-method | Loading method for ref_stage referential objects | |
| choice_c,report_mig_mult-method | command line interface for report_mig_mult class | |
| choice_c,report_sample_char-method | command line interface for report_sample_char class | |
| choice,ref_horodate-method | Graphical interface | |
| choice,ref_list-method | Choice method for ref_list referential objects | |
| h_report_df | handler function used by the main interface | |
| hbilespcalc | handler for calculation | |
| hbmCcalc | handler for report_mig_char | |
| hplot | Internal handler for reg, class report_ge_weight-class. | |
| hplotbilesp | handler for plot internal use | |
| h_report_dc | handler function used by the main interface | |
| interface_report_mig_char | interface for report_migPar class | |
| interface_report_mig_env | interface for report_migConditionEnv class | |
| 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 | |
| h_report_mig_multgraph2 | handler du calcul h_report_miggraph2 | |
| choice_c,report_dc-method | command line interface for report_dc class | |
| choice_c,report_df-method | command line interface for report_df class | |
| h_report_mig_multgraph3 | handler | |
| getdateDebut,ref_timestep-method | Returns the starting date as character | |
| get_year | Generic method to get the years | |
| hgraph_report_mig_interannual | Plot of all interannual from top to bottom | |
| hgraph_report_mig_interannual2 | Plot of daily migrations | |
| hxtablereport_annual | xtable handler | |
| ref_period-class | Class "ref_period" referential class | |
| ref_stage-class | Class "ref_stage" | |
| report_sea_age-class | Class "report_sea_age" | |
| choicemult,ref_parqual-method | Multiple Choice method for ref_parqual referential objects internal use | |
| choicemult,ref_stage-method | Multiple Choice method for ref_stage referential objects | |
| connect,report_env-method | connect method for report_env class | |
| report_silver_eel-class | Class "report_silver_eel" | |
| ref_timestep_daily-class | Class "ref_timestep_daily" | |
| ref_year-class | Year reference class | |
| funbarchart1DC | Handler for barchart for report_df class from the graphical interface | |
| connect,report_ge_weight-method | connect method for report_Poids_moyen | |
| end_date | Generic method for getting the final date | |
| funbarchart1DF | Handler for barchart for report_df class from the graphical interface | |
| envir_stacomi | Environment where most objects from the package are stored and then loaded by the charge method | |
| fun_report_mig_mult | Calculate daily migration by simple repartition | |
| fun_report_mig_mult_overlaps | Function to calculate daily migration using overlaps functions | |
| 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. | |
| 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). | |
| getdateDebut | Generic method the get starting date | |
| getdbname | Retrieves the dbname from a connection using "baseODBC" | |
| plot,report_mig_char,missing-method | plot method for report_mig_char | |
| plot,report_mig_mult,missing-method | Plots of various type for report_mig_mult | |
| plot,report_sample_char,missing-method | Plots of various type for reportcarlot | |
| plot,report_mig,ANY-method | Plots of various type for report_mig. | |
| report_species-class | Counts of number per taxa/stages | |
| set_starting_date,ref_timestep-method | Sets starting date from a character | |
| write_database,report_ge_weight-method | Function to write data to the stacomi database for report_ge_weight-class | |
| write_database,report_mig-method | Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table | |
| 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_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 | |
| 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. | |
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| Date | 2018-01-04 |
| License | GPL (>= 2) |
| URL | http://stacomir.r-forge.r-project.org/ |
| Collate | 'create_generic.R' 'data.R' 'fun_table_per_dis.R' 'fun_write_monthly.R' 'fungraph.R' 'fungraph_glasseel.R' 'funstat.R' 'funstat_daily.R' 'funtable.R' 'interface_report_annual.R' 'interface_report_dc.R' 'interface_report_df.R' 'interface_report_env.R' 'interface_report_ge_weight.R' 'interface_report_mig.R' 'interface_report_mig_char.R' 'interface_report_mig_env.R' 'interface_report_mig_interannual.R' 'interface_report_mig_mult.R' 'interface_report_sample_char.R' 'interface_report_sea_age.R' 'interface_report_silver_eel.R' 'interface_report_species.R' 'ref_checkbox.R' 'ref_choice.R' 'ref_coe.R' 'ref_dc.R' 'ref_df.R' 'ref_env.R' 'ref_horodate.R' 'ref_list.R' 'ref_par.R' 'ref_parqual.R' 'ref_parquan.R' 'ref_period.R' 'ref_stage.R' 'ref_taxa.R' 'ref_textbox.R' 'ref_timestep.R' 'ref_timestep_daily.R' 'ref_year.R' 'report_annual.R' 'report_dc.R' 'report_df.R' 'utilities.R' 'report_env.R' 'report_ge_weight.R' 'report_ope.R' 'report_mig.R' 'report_sample_char.R' 'report_mig_char.R' 'report_mig_mult.R' 'report_mig_env.R' 'report_mig_interannual.R' 'report_sea_age.R' 'report_silver_eel.R' 'report_species.R' 'setAs.R' 'stacomi.R' |
| LazyLoad | yes |
| LazyData | true |
| RoxygenNote | 5.0.1 |
| NeedsCompilation | no |
| Repository | CRAN |
| Repository/R-Forge/Project | stacomir |
| Repository/R-Forge/Revision | 470 |
| Repository/R-Forge/DateTimeStamp | 2018-01-04 13:31:37 |
| Date/Publication | 2018-01-04 20:35:21 UTC |
| Packaged | 2018-01-04 13:45:18 UTC; rforge |
| imports | dplyr , ggplot2 , graphics , grDevices , gWidgets , gWidgetsRGtk2 , Hmisc , intervals , lattice , lubridate , magrittr , mgcv , RColorBrewer , reshape2 , RGtk2 , RPostgreSQL , sqldf , stats , stringr , utils , xtable |
| depends | methods , R (>= 3.0.0) , RODBC , stacomirtools |
| suggests | testthat , viridis |
| Contributors | Marion Legrand, Timothee Besse |
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