stacomiR: Fish Migration Monitoring

# stacomiR 0.6.0.7* created function to load schema* fixed problem with report_mig_char example (broken since new qualitative parameter for age was inserted in the database)* fixed problem with x scale ugly https://forgemia.inra.fr/stacomi/stacomir/-/issues/27 fixed # stacomiR 0.6.0.6* allows to load ggplots after plot for report_dc and report_df* fixes the problem of method for plot no longer working with signature(x = "report_dc", y = "ANY") and changed to"missing"* allows to pass arguments for colors in plot.report_dc* fixed problems with broken translation see https://forgemia.inra.fr/stacomi/stacomir/-/issues/20# stacomiR 0.6.0.5* fixes the way environmental stations are loaded.# stacomiR 0.6.0.4* fixed different output for parameters between charge and charge_with_filter from ref_parquan and ref_parqual.* the choice_c method also assigns subclasses in envir_stacomi.* updated the set_as_qualitative method to avoid bugs when running it several times.* rewrote tests# stacomiR 0.6.0.3* fixed problems for report interannual, allowing it for several DC including the graphs* fixed but in report_mig / report_mig_mug write database for numbers of type "PONCTUEL"* fixed problem in report_interannual, always writing the db when there is a difference between report_mig and report_annual e.g.when operations are overlapping between years# stacomiR 0.6.0.2* fixes the way taxa and stage are loaded* replaced some french labels in slots# stacomiR 0.6.0.1* Minor fix for Solaris, non portable path '~' now issue a warning asking the user for a new path* Code coverage 79.2 %# stacomiR 0.6.0stacomir based on gwidget was dropped from CRAN in May 2020, it has been completely reprogrammed to remove all dependence togwidget and the graphical interface will be a new shiny package (under developpement). Stacomirtools has been rewritten and submitted to CRAN to connect via pool and DBI.* added import to package `rlang` * Change to adapt to new dplyr format `dplyr:n()` instead of `n()` see dplyr breaking change in version 1.0.0* adapted to stacomirtools new connection and connection options (using pool and DBI instead of RODC)* removed all dependency to gwidgetRGTK2 so in practise there is no longer a graphical interface, the shiny package is due soon.* added code of conduct* rewrote unit tests increased coverage from 50 to 78 %# stacomiR 0.5.4.4 (not released on CRAN)* added import to package `rlang` * Change to adapt to new dplyr format `dplyr:n()` instead of `n()` see dplyr breaking change in version 1.0.0# stacomiR 0.5.4.3* fixed problem when report with just one line in one year where total number is zero* fixed bug in monthly report when there is just a single month* fixed new bug in report_interannual where no value returned from the database created a character which was crashing the program* fixed bug in bilan interannual when quantiles were calculated on a single line, now reports exactly the value of that line for all quantiles and avoid crashes.* fixed problem in plot,report_sample_char,missing-method, a ... additional was documented but not present (sent from CRAN)* The vignette crashes as the program finds difference between rounded numbers, while I don't understand why, round(sum(datasub$value, na.rm = TRUE), 2) and round(sum(datasub2$value, na.rm = TRUE), 2) are not equal: and provide a difference that is not rounded (e.g. 0.000996741) I have changed the test.# stacomiR 0.5.4.2* fixed new issues with rounding error when building vignette# stacomiR 0.5.4.1* fixed issue with prototype generating check warning on CRAN# stacomiR 0.5.4.0* removed reference to test database, and use of dplyr for internal calculations. Trying to launch as test database with postgres failed on distant computers for tests.... (@marion #484-502)* Updated testhat tests (@marion @cedric #502-506)* developped vignette for package (@marion #480-484)# stacomiR 0.5.3.2* changed stacomiR-package.md according to Kurt Hornik (CRAN) demand to use macro in share (@cedric #481)* bug in interface report_dc corrected (@cedric #489)* Problem with ceilPOSIXt now named only ceil in package Hmisc. (@cedric #489)# stacomiR 0.5.3.1* added and edited readme.Rmd file (@cedric and @marion #447-#452)* compilation of messages, fixes bug for for some year in report\_mig\_mult (@cedric #444)* Editing translation messages (@cedric #446)* fix bug for setasqualitative method in report\_sea__age (@cedric #443)* updated documentation (@cedric #440)* Modification in glass eel graph (@cedric #441)* changes to the summary-report\_mig\_interannual-method (@cedric # 439)* change to the presentation page in R-forge (@timothée #425 #436-#438)# stacomiR 0.5.3* Language with poedit (@cedric and @timothee).* suppress all assignments to .globalEnv.* adapt documentation and package to pass with zero warning and zero note.# stacomiR 0.5.2 (R-Forge)* Development of the command line interface (@cedric)* Adaptation to the database change to adapt French SANDRE directives (@cedric)* added 4 new report (silver eel, sea age, report\_mig\_mult, report_annual) and adapted all old script to use in both command line and graphical interface. (@ cedric and @marion)# stacomiR 0.5.1 (R-Forge)* tests with testthat (@cedric)# stacomiR 0.5.0 (R-Forge)* Roxygen documentation (@cedric)# stacomiR 0.4 (R-Forge)* classes adapted to the new database format# stacomiR 0.3 (R-Forge)* Adapting to one schema per user in the postgres database * initial development of all classes following version 0.3 of the database

Inglés. 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 Office for Biodiversity institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See https://forgemia.inra.fr/stacomi/stacomir