stacomiR-package {stacomiR} | R Documentation |
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. This version is available in French and English. See <http://stacomir.r-forge.r-project.org/> for more information on 'STACOMI'.
Package: | stacomiR |
Version: | 0.5.4.2 |
Date: | 2019-02-12 |
Title: | Fish Migration Monitoring |
Authors@R: | c(person("Cedric", "Briand", role = c("aut", "cre"), email = "cedric.briand00@gmail.com"), person("Marion", "Legrand", role = "aut", email="tableau-salt-loire@logrami.fr"), person("Timothee", "Besse", role = "aut", email="tableau-ang-loire@logrami.fr")) |
Description: | 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. This version is available in French and English. See <http://stacomir.r-forge.r-project.org/> for more information on 'STACOMI'. |
License: | GPL (>= 2) |
URL: | http://stacomir.r-forge.r-project.org/ |
BugReports: | https://github.com/MarionLegrandLogrami/stacomiR/issues |
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 |
Depends: | R (>= 3.5.0), methods, stacomirtools, RODBC |
Imports: | magrittr, intervals, RColorBrewer, stringr, gWidgets, gWidgetsRGtk2, RPostgreSQL, ggplot2, reshape2, sqldf, graphics, utils, stats, lattice, grDevices, Hmisc (>= 4.1-1), RGtk2, lubridate, dplyr, xtable, mgcv |
Suggests: | testthat, viridis, knitr, rmarkdown |
Author: | Cedric Briand [aut, cre], Marion Legrand [aut], Timothee Besse [aut] |
Maintainer: | Cedric Briand <cedric.briand00@gmail.com> |
RoxygenNote: | 6.1.0.9000 |
NeedsCompilation: | no |
VignetteBuilder: | knitr |
Repository: | R-Forge |
Repository/R-Forge/Project: | stacomir |
Repository/R-Forge/Revision: | 549 |
Repository/R-Forge/DateTimeStamp: | 2019-04-06 05:56:57 |
Date/Publication: | 2019-04-06 05:56:57 |
Index of help topics:
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 calcule Generic method for calculations calcule,report_ge_weight-method Calcule method for report_ge_weight 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). calcule,report_mig_char-method Computes data to a standard format for the summary and plot methods. calcule,report_mig_env-method Calculations for migration in the class report_mig_env-class calcule,report_mig_interannual-method calcule method for report_mig_interannual 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. 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. calcule,report_species-method calcule method for report_species charge Generic method to load referentials charge,ref_checkbox-method Loading method for ref_checkbox referential objects charge,ref_choice-method Loading method for Rechoice referential objects charge,ref_coe-method loads the coefficients for the period defined in class charge,ref_dc-method Method to load the counting devices of the control station charge,ref_df-method Loading method for DF referential objects charge,ref_env-method Loading method for ref_env referential object charge,ref_list-method Loading method for refliste referential objects charge,ref_par-method Loading method for Repar referential objects charge,ref_parqual-method Loading method for Reparqual referential objects charge,ref_parquan-method Loading method for Reparquan referential objects charge,ref_stage-method Loading method for ref_stage referential objects charge,ref_taxa-method Loading method for ref_taxa referential objects charge,ref_textbox-method Loading method for ReTextBox referential objects charge,ref_year-method Loading method for ref_year referential objects charge,report_ge_weight-method charge method for report_ge_weight class charge,report_mig-method Loads additional data on migration control operations, df (fishway) dc (counting device). charge,report_mig_env-method charge method for report_mig_env class charge,report_mig_mult-method charge method for report_mig_mult charge_complement Generic method to load additional data 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 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_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 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 chargecomplement-methods Methods for Function chargecomplement choice_c,ref_choice-method Choice_c method for refchoix referential objects 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,ref_env-method Command line interface to select a monitoring station choice_c,ref_horodate-method Command line 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 choice_c,ref_stage-method choice_c method for ref_stage choice_c,ref_taxa-method choice_c method for ref_taxa choice_c,ref_textbox-method Choice_c method for ReTextBox referential objects choice_c,ref_timestep_daily-method choice_c method for class ref_timestep_daily choice_c,ref_year-method choice_c method for ref_year referential from the command line choice_c,report_annual-method command line interface for report_annual-class choice_c,report_dc-method command line interface for report_dc class choice_c,report_df-method command line interface for report_df class 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_mig-method command line interface for report_mig class choice_c,report_mig_char-method command line interface for report_mig_char class choice_c,report_mig_env-method command line interface for report_env class choice_c,report_mig_interannual-method command line interface for report_mig_interannual class 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_c,report_sea_age-method command line interface for report_sea_age class choice_c,report_silver_eel-method command line interface for report_silver_eel class choice_c,report_species-method command line interface for report_species-class choicemult,ref_dc-method choicemult, selection method for ref_dc allowing to select several DC 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. 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,report_annual-method connect method for report_annual class this method performs the sum over the year attention this function does not count subsamples. connect,report_dc-method connect method for report_dc connect,report_df-method connect method for report_df connect,report_env-method connect method for report_env class connect,report_ge_weight-method connect method for report_Poids_moyen connect,report_mig-method connect method for report_mig connect,report_mig_char-method connect method for report_mig_char connect,report_mig_env-method connect method for report_mig_env class connect,report_mig_interannual-method connect method for report_mig_interannual connect,report_mig_mult-method connect method for report_mig_mult connect,report_ope-method connect method for report_ope connect,report_sample_char-method connect method for report_sample_char connect,report_sea_age-method connect method for report_sea_age connect,report_silver_eel-method connect method for report_silver_eel connect,report_species-method connect method for report_species createmessage Generic method to forward outputs current_end_date,ref_timestep-method Gets the ending date of a time step for an object of class ref_timestep-class envir_stacomi Environment where most objects from the package are stored and then loaded by the charge method 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 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_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 funbarchart1DC Handler for barchart for report_df class from the graphical interface 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 funstat_daily function to create daily statistics funtable function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class getdbname Retrieves the dbname from a connection using "baseODBC" getnocurrent_step Generic method to get current time step getvalue Generic method getvalue getvalue,ref_period-method Returns the POSIXt value of a given name graphdate function used for some lattice graphs with dates graphe-methods Methods for Function graphe model Generic for prediction 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_annual,missing-method Plot method for report_annual plot,report_dc,ANY-method Different plots for report_dc plot,report_df,ANY-method Different plots for report_df plot,report_env,missing-method Plot method for report_env plot,report_ge_weight,missing-method Plot method for report_ge_weight' plot,report_mig,ANY-method Plots of various type for report_mig. plot,report_mig_char,missing-method plot method for report_mig_char plot,report_mig_env,missing-method Plot method for report_mig_env plot,report_mig_interannual,missing-method Plot method for report_mig_interannual 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_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 plot,report_species,missing-method Plot method for report_species print,report_dc-method Method to print the command line of the object print,report_df-method Method to print the command line of the object print,report_mig-method Method to print the command line of the object print,report_mig_mult-method Method to print the command line of the object print,report_sample_char-method Method to print the command line of the object print,report_sea_age-method Method to print the command line of the object print,report_silver_eel-method Method to print the command line of the object 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_ann Annual migration of yellow and silver eel for three fishways / counting devices at the Arzal dam (data from 1995 to 2016) r_ann_adour Annual migration of salmon in the Adour and tributaries r_dc Counting Device (DC) operation from 2000 to 2015 at the Arzal dam (Vilaine, France) r_df Overview of the fishway operation at Arzal in (Vilaine France). r_env An object of class report_env with data loaded r_gew Wet weight of glass eel from the trapping ladder (Arzal, Vilaine France) r_mig Video counting of thin lipped mullet (Liza ramada) in 2015 in the Vilaine (France) r_mig_char Qualitative and quantitative parameters describing Salmon migration at Decize (Loire) r_mig_dc Counting device operation for the video recording (Arzal dam, Vilaine, France). r_mig_df Fishway operation for the vertical slot fishway (Arzal dam, Vilaine, France). r_mig_env An object of class report_mig_env with data loaded r_mig_interannual Daily glass eel and elver migration from 1984 to 2016 in the Sevre Niortaise r_mig_interannual_vichy Seasonality of salmon migration at the Vichy counting station (Loire) r_mig_mult Anguilla migration at the Arzal station (report_mig_mult-class) r_mig_mult_dc Counting device operation for three different counting device in Arzal (Vilaine, France) r_mig_mult_df Fishway operation at the Arzal Dam (Vilaine France) (3 Fishways in 2011) r_mig_mult_ope Counting operations for three different counting device in Arzal (Vilaine, France) r_mig_ope An object of class report_ope-class with data loaded r_sample_char Size of yellow and glass eel at the Arzal dam (Vilaine, France) in the fishway and main eel trapping ladder. r_seaa An object of class report_sea_age with data loaded r_silver Silver eel migration in the Somme ref_checkbox-class ref_checkbox referencial class ref_choice-class Class "ref_choice" ref_coe-class Class "ref_coe" ref_dc-class Class "ref_dc" ref_df-class Class "ref_df" ref_env-class Class "ref_env" ref_horodate-class Class ref_horodate ref_par-class Class "ref_par" ref_parqual-class Class "ref_parqual" ref_parquan-class Class "ref_parquan" ref_period-class Class "ref_period" referential class ref_stage-class Class "ref_stage" ref_taxa-class Class "ref_taxa" ref_textbox-class ref_textbox referencial class ref_timestep-class Class "ref_timestep" ref_timestepChar-class Class "ref_timestepChar" ref_timestep_daily-class Class "ref_timestep_daily" ref_year-class Year reference class report_annual-class Class "report_annual" report_dc-class Class "report_dc" report du fonctionnement du dispositif de comptage report_df-class Report on fishway operation report_env-class class report_env simple output of one or several environmental conditions... report_ge_weight-class Trend of wet weight in glass eel report_mig-class Migration report for one DC, one species and one stage report_mig_char-class Migration report along with quantitative and qualitative characteristics report_mig_env-class Class "report_mig_env" report_mig_interannual-class Class "report_mig_interannual" report_mig_mult-class Migration reports for multiple DC / species / stages report_ope-class Report on operations report_sample_char-class Class "report_sample_char" report_sea_age-class Class "report_sea_age" report_silver_eel-class Class "report_silver_eel" report_species-class Counts of number per taxa/stages setasqualitative Generic method to transform quantitative par into a qualitative one setasqualitative,report_mig_char-method Turns a quantitative parameter into qualitative split_per_day Create a dataframe suitable for charts per 24h and day stacomi Function that loads the loginwindow, tests connection, and then destroys the window stacomiR-package Fish Migration Monitoring stacomi_installed Test that the program is installed. summary,report_dc-method summary for report_dc, write csv and html output, and prints summary statistics 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 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. 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_sample_char-method summary for report_sample_char summary,report_sea_age-method summary for report_sea_age summary,report_silver_eel-method summary for report_silver_eel summary,report_species-method summary for report_species generate csv and html output in the user data directory supprime Generic method to delete entires from the database supprime,ref_coe-method supprime method for "ref_coe" class supprime,report_mig_interannual-method supprime method for report_mig_interannual class supprime,report_sea_age-method 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,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 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 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.
Further information is available in the following vignettes:
stacomir | Vignette Title (source) |
To use the stacomiR package, simply load the library using library(stacomiR)
. Once done, type stacomi()
in R terminal.
The use of stacomi(gr_interface=FALSE) allows to launch stacomi without graphical interface from the command line. The program is currently
translated to French, to switch to English or French type Sys.setenv(LANG = "en")
Sys.setenv(LANG = "fr")
Cedric Briand [aut, cre], Marion Legrand [aut], Timothee Besse [aut] Maintainer: Cedric Briand <cedric.briand00@gmail.com>
#stacomi()