[Stacomir-commits] r575 - in pkg/stacomir: . R R/po dev dev/config dev/cran-comments dev/po dev/po/fr dev/po/fr/LC_MESSAGES inst/examples man tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Nov 6 22:16:20 CET 2021
Author: briand
Date: 2021-11-06 22:16:18 +0100 (Sat, 06 Nov 2021)
New Revision: 575
Added:
pkg/stacomir/CODE_OF_CONDUCT.md
pkg/stacomir/R/ref_checkbox.R
pkg/stacomir/R/stacomiR-package.R
pkg/stacomir/dev/
pkg/stacomir/dev/01_start.R
pkg/stacomir/dev/02_dev.R
pkg/stacomir/dev/03_deploy.R
pkg/stacomir/dev/config/
pkg/stacomir/dev/config/generate_Roxygen2.R
pkg/stacomir/dev/config/generate_data.R
pkg/stacomir/dev/config/libraries.R
pkg/stacomir/dev/config/poedit.R
pkg/stacomir/dev/config/stacomi_checks.R
pkg/stacomir/dev/config/test_vignette.R
pkg/stacomir/dev/cran-comments/
pkg/stacomir/dev/cran-comments/cran-comments-v0.5.3.1.md
pkg/stacomir/dev/cran-comments/cran-comments-v0.5.4.0.md
pkg/stacomir/dev/po/
pkg/stacomir/dev/po/fr/
pkg/stacomir/dev/po/fr/LC_MESSAGES/
pkg/stacomir/dev/po/fr/LC_MESSAGES/R-stacomiR.mo
pkg/stacomir/dev/run_dev.R
Removed:
pkg/stacomir/man/calcmig.Rd
pkg/stacomir/man/charge-ref_checkbox-method.Rd
pkg/stacomir/man/chargecsv.Rd
pkg/stacomir/man/choice-ref_checkbox-method.Rd
pkg/stacomir/man/choice-ref_choice-method.Rd
pkg/stacomir/man/choice-ref_dc-method.Rd
pkg/stacomir/man/choice-ref_df-method.Rd
pkg/stacomir/man/choice-ref_env-method.Rd
pkg/stacomir/man/choice-ref_horodate-method.Rd
pkg/stacomir/man/choice-ref_list-method.Rd
pkg/stacomir/man/choice-ref_par-method.Rd
pkg/stacomir/man/choice-ref_parqual-method.Rd
pkg/stacomir/man/choice-ref_stage-method.Rd
pkg/stacomir/man/choice-ref_taxa-method.Rd
pkg/stacomir/man/choice-ref_textbox-method.Rd
pkg/stacomir/man/choice-ref_timestep-method.Rd
pkg/stacomir/man/choice-ref_timestep_daily-method.Rd
pkg/stacomir/man/choice-ref_year-method.Rd
pkg/stacomir/man/choice.Rd
pkg/stacomir/man/choicemult-ref_choice-method.Rd
pkg/stacomir/man/choicemult-ref_dc-method.Rd
pkg/stacomir/man/choicemult-ref_horodate-method.Rd
pkg/stacomir/man/choicemult-ref_par-method.Rd
pkg/stacomir/man/choicemult-ref_parqual-method.Rd
pkg/stacomir/man/choicemult-ref_stage-method.Rd
pkg/stacomir/man/choicemult-ref_taxa-method.Rd
pkg/stacomir/man/choicemult-ref_timestep-method.Rd
pkg/stacomir/man/choicemult.Rd
pkg/stacomir/man/funbarchart1DC.Rd
pkg/stacomir/man/funboxDC.Rd
pkg/stacomir/man/funchartDC.Rd
pkg/stacomir/man/funplotreport_sea_age.Rd
pkg/stacomir/man/funtablereport_ge_weight.Rd
pkg/stacomir/man/funtablereport_sample_char.Rd
pkg/stacomir/man/funtablereport_sea_age.Rd
pkg/stacomir/man/funtablereport_silver_eel.Rd
pkg/stacomir/man/getdbname.Rd
pkg/stacomir/man/hTablereport_mig.Rd
pkg/stacomir/man/hTablereport_mig_mult.Rd
pkg/stacomir/man/h_report_dc.Rd
pkg/stacomir/man/h_report_df.Rd
pkg/stacomir/man/h_report_dfdc.Rd
pkg/stacomir/man/h_report_env.Rd
pkg/stacomir/man/h_report_envgraph.Rd
pkg/stacomir/man/h_report_ge_weight.Rd
pkg/stacomir/man/h_report_mig.Rd
pkg/stacomir/man/h_report_mig_annual.Rd
pkg/stacomir/man/h_report_mig_char.Rd
pkg/stacomir/man/h_report_mig_env.Rd
pkg/stacomir/man/h_report_mig_interannual.Rd
pkg/stacomir/man/h_report_mig_mult.Rd
pkg/stacomir/man/h_report_mig_mult_graph.Rd
pkg/stacomir/man/h_report_mig_multcalc.Rd
pkg/stacomir/man/h_report_mig_multgraph2.Rd
pkg/stacomir/man/h_report_mig_multgraph3.Rd
pkg/stacomir/man/h_report_migcalc.Rd
pkg/stacomir/man/h_report_miggraph.Rd
pkg/stacomir/man/h_report_miggraph2.Rd
pkg/stacomir/man/h_report_migwrite.Rd
pkg/stacomir/man/h_report_ope.Rd
pkg/stacomir/man/h_report_pigment_stages.Rd
pkg/stacomir/man/h_report_sample_char.Rd
pkg/stacomir/man/h_report_sea_age.Rd
pkg/stacomir/man/h_report_silver.Rd
pkg/stacomir/man/h_report_size.Rd
pkg/stacomir/man/h_report_species.Rd
pkg/stacomir/man/hbarplotreport_annual.Rd
pkg/stacomir/man/hbilespcalc.Rd
pkg/stacomir/man/hbmCcalc.Rd
pkg/stacomir/man/hbmCplotcrossed.Rd
pkg/stacomir/man/hbmCplotqual.Rd
pkg/stacomir/man/hbmCplotquan.Rd
pkg/stacomir/man/hbmCstat.Rd
pkg/stacomir/man/hbmmCEcalc.Rd
pkg/stacomir/man/hbmmCEgraph.Rd
pkg/stacomir/man/hcalc.Rd
pkg/stacomir/man/hexp.Rd
pkg/stacomir/man/hgraph_report_mig_interannual.Rd
pkg/stacomir/man/hgraph_report_mig_interannual2.Rd
pkg/stacomir/man/hgraph_report_mig_interannual3.Rd
pkg/stacomir/man/hgraph_report_mig_interannual4.Rd
pkg/stacomir/man/hgraph_report_mig_interannual5.Rd
pkg/stacomir/man/hgraph_report_mig_interannual7.Rd
pkg/stacomir/man/houtDC.Rd
pkg/stacomir/man/houtDF.Rd
pkg/stacomir/man/houtreport_mig.Rd
pkg/stacomir/man/houtreport_mig_mult.Rd
pkg/stacomir/man/hplot.Rd
pkg/stacomir/man/hplotbilesp.Rd
pkg/stacomir/man/hplotreport_annual.Rd
pkg/stacomir/man/hreg.Rd
pkg/stacomir/man/hsummarybilesp.Rd
pkg/stacomir/man/hsummaryreport_migInterannuelle.Rd
pkg/stacomir/man/hxtablereport_annual.Rd
pkg/stacomir/man/interface_graphique.Rd
pkg/stacomir/man/interface_report_annual.Rd
pkg/stacomir/man/interface_report_dc.Rd
pkg/stacomir/man/interface_report_df.Rd
pkg/stacomir/man/interface_report_env.Rd
pkg/stacomir/man/interface_report_ge_weight.Rd
pkg/stacomir/man/interface_report_mig.Rd
pkg/stacomir/man/interface_report_mig_char.Rd
pkg/stacomir/man/interface_report_mig_env.Rd
pkg/stacomir/man/interface_report_mig_interannual.Rd
pkg/stacomir/man/interface_report_mig_mult.Rd
pkg/stacomir/man/interface_report_sample_char.Rd
pkg/stacomir/man/interface_report_sea_age.Rd
pkg/stacomir/man/interface_report_silver_eel.Rd
pkg/stacomir/man/interface_report_species.Rd
pkg/stacomir/man/progress_bar.Rd
pkg/stacomir/man/ref_checkbox-class.Rd
pkg/stacomir/man/stacomi_installed.Rd
Modified:
pkg/stacomir/.Rbuildignore
pkg/stacomir/.Rinstignore
pkg/stacomir/DESCRIPTION
pkg/stacomir/NAMESPACE
pkg/stacomir/NEWS.md
pkg/stacomir/R/create_generic.R
pkg/stacomir/R/data.R
pkg/stacomir/R/fun_table_per_dis.R
pkg/stacomir/R/fun_write_monthly.R
pkg/stacomir/R/fungraph.R
pkg/stacomir/R/fungraph_glasseel.R
pkg/stacomir/R/funstat.R
pkg/stacomir/R/funstat_daily.R
pkg/stacomir/R/funtable.R
pkg/stacomir/R/po/R-stacomiR_fr_FR.po
pkg/stacomir/R/ref_choice.R
pkg/stacomir/R/ref_coe.R
pkg/stacomir/R/ref_dc.R
pkg/stacomir/R/ref_df.R
pkg/stacomir/R/ref_env.R
pkg/stacomir/R/ref_horodate.R
pkg/stacomir/R/ref_list.R
pkg/stacomir/R/ref_par.R
pkg/stacomir/R/ref_parqual.R
pkg/stacomir/R/ref_parquan.R
pkg/stacomir/R/ref_period.R
pkg/stacomir/R/ref_stage.R
pkg/stacomir/R/ref_taxa.R
pkg/stacomir/R/ref_textbox.R
pkg/stacomir/R/ref_timestep.R
pkg/stacomir/R/ref_timestep_daily.R
pkg/stacomir/R/ref_year.R
pkg/stacomir/R/report_annual.R
pkg/stacomir/R/report_dc.R
pkg/stacomir/R/report_df.R
pkg/stacomir/R/report_env.R
pkg/stacomir/R/report_ge_weight.R
pkg/stacomir/R/report_mig.R
pkg/stacomir/R/report_mig_char.R
pkg/stacomir/R/report_mig_env.R
pkg/stacomir/R/report_mig_interannual.R
pkg/stacomir/R/report_mig_mult.R
pkg/stacomir/R/report_ope.R
pkg/stacomir/R/report_sample_char.R
pkg/stacomir/R/report_sea_age.R
pkg/stacomir/R/report_silver_eel.R
pkg/stacomir/R/report_species.R
pkg/stacomir/R/setAs.R
pkg/stacomir/R/stacomi.R
pkg/stacomir/R/utilities.R
pkg/stacomir/inst/examples/report_annual-example.R
pkg/stacomir/inst/examples/report_dc-example.R
pkg/stacomir/inst/examples/report_df-example.R
pkg/stacomir/inst/examples/report_env-example.R
pkg/stacomir/inst/examples/report_ge_weight-example.R
pkg/stacomir/inst/examples/report_mig-example.R
pkg/stacomir/inst/examples/report_mig_char-example.R
pkg/stacomir/inst/examples/report_mig_env-example.R
pkg/stacomir/inst/examples/report_mig_interannual-example.R
pkg/stacomir/inst/examples/report_mig_mult-example.R
pkg/stacomir/inst/examples/report_sample_char-example.R
pkg/stacomir/inst/examples/report_sea_age-example.R
pkg/stacomir/inst/examples/report_silver_eel-example.R
pkg/stacomir/inst/examples/report_species-example.R
pkg/stacomir/man/barplot-report_annual-method.Rd
pkg/stacomir/man/calcule-report_ge_weight-method.Rd
pkg/stacomir/man/calcule-report_mig-method.Rd
pkg/stacomir/man/calcule-report_mig_char-method.Rd
pkg/stacomir/man/calcule-report_mig_env-method.Rd
pkg/stacomir/man/calcule-report_mig_interannual-method.Rd
pkg/stacomir/man/calcule-report_mig_mult-method.Rd
pkg/stacomir/man/calcule-report_sample_char-method.Rd
pkg/stacomir/man/calcule-report_sea_age-method.Rd
pkg/stacomir/man/calcule-report_silver_eel-method.Rd
pkg/stacomir/man/calcule-report_species-method.Rd
pkg/stacomir/man/calcule.Rd
pkg/stacomir/man/charge-ref_choice-method.Rd
pkg/stacomir/man/charge-ref_coe-method.Rd
pkg/stacomir/man/charge-ref_dc-method.Rd
pkg/stacomir/man/charge-ref_df-method.Rd
pkg/stacomir/man/charge-ref_env-method.Rd
pkg/stacomir/man/charge-ref_list-method.Rd
pkg/stacomir/man/charge-ref_par-method.Rd
pkg/stacomir/man/charge-ref_parqual-method.Rd
pkg/stacomir/man/charge-ref_parquan-method.Rd
pkg/stacomir/man/charge-ref_stage-method.Rd
pkg/stacomir/man/charge-ref_taxa-method.Rd
pkg/stacomir/man/charge-ref_textbox-method.Rd
pkg/stacomir/man/charge-ref_year-method.Rd
pkg/stacomir/man/charge-report_annual-method.Rd
pkg/stacomir/man/charge-report_dc-method.Rd
pkg/stacomir/man/charge-report_df-method.Rd
pkg/stacomir/man/charge-report_env-method.Rd
pkg/stacomir/man/charge-report_ge_weight-method.Rd
pkg/stacomir/man/charge-report_mig-method.Rd
pkg/stacomir/man/charge-report_mig_char-method.Rd
pkg/stacomir/man/charge-report_mig_env-method.Rd
pkg/stacomir/man/charge-report_mig_interannual-method.Rd
pkg/stacomir/man/charge-report_mig_mult-method.Rd
pkg/stacomir/man/charge-report_ope-method.Rd
pkg/stacomir/man/charge-report_sample_char-method.Rd
pkg/stacomir/man/charge-report_sea_age-method.Rd
pkg/stacomir/man/charge-report_silver_eel-method.Rd
pkg/stacomir/man/charge-report_species-method.Rd
pkg/stacomir/man/charge.Rd
pkg/stacomir/man/charge_complement-ref_parqual-method.Rd
pkg/stacomir/man/charge_complement.Rd
pkg/stacomir/man/charge_with_filter-ref_par-method.Rd
pkg/stacomir/man/charge_with_filter-ref_parqual-method.Rd
pkg/stacomir/man/charge_with_filter-ref_parquan-method.Rd
pkg/stacomir/man/charge_with_filter-ref_stage-method.Rd
pkg/stacomir/man/charge_with_filter-ref_taxa-method.Rd
pkg/stacomir/man/charge_with_filter.Rd
pkg/stacomir/man/chargecomplement-methods.Rd
pkg/stacomir/man/choice_c-ref_choice-method.Rd
pkg/stacomir/man/choice_c-ref_dc-method.Rd
pkg/stacomir/man/choice_c-ref_df-method.Rd
pkg/stacomir/man/choice_c-ref_env-method.Rd
pkg/stacomir/man/choice_c-ref_horodate-method.Rd
pkg/stacomir/man/choice_c-ref_list-method.Rd
pkg/stacomir/man/choice_c-ref_par-method.Rd
pkg/stacomir/man/choice_c-ref_stage-method.Rd
pkg/stacomir/man/choice_c-ref_taxa-method.Rd
pkg/stacomir/man/choice_c-ref_textbox-method.Rd
pkg/stacomir/man/choice_c-ref_timestep_daily-method.Rd
pkg/stacomir/man/choice_c-ref_year-method.Rd
pkg/stacomir/man/choice_c-report_annual-method.Rd
pkg/stacomir/man/choice_c-report_dc-method.Rd
pkg/stacomir/man/choice_c-report_df-method.Rd
pkg/stacomir/man/choice_c-report_env-method.Rd
pkg/stacomir/man/choice_c-report_ge_weight-method.Rd
pkg/stacomir/man/choice_c-report_mig-method.Rd
pkg/stacomir/man/choice_c-report_mig_char-method.Rd
pkg/stacomir/man/choice_c-report_mig_env-method.Rd
pkg/stacomir/man/choice_c-report_mig_interannual-method.Rd
pkg/stacomir/man/choice_c-report_mig_mult-method.Rd
pkg/stacomir/man/choice_c-report_sample_char-method.Rd
pkg/stacomir/man/choice_c-report_sea_age-method.Rd
pkg/stacomir/man/choice_c-report_silver_eel-method.Rd
pkg/stacomir/man/choice_c-report_species-method.Rd
pkg/stacomir/man/choice_c.Rd
pkg/stacomir/man/coef_durif.Rd
pkg/stacomir/man/colortable.Rd
pkg/stacomir/man/connect-report_annual-method.Rd
pkg/stacomir/man/connect-report_dc-method.Rd
pkg/stacomir/man/connect-report_df-method.Rd
pkg/stacomir/man/connect-report_env-method.Rd
pkg/stacomir/man/connect-report_ge_weight-method.Rd
pkg/stacomir/man/connect-report_mig-method.Rd
pkg/stacomir/man/connect-report_mig_char-method.Rd
pkg/stacomir/man/connect-report_mig_env-method.Rd
pkg/stacomir/man/connect-report_mig_interannual-method.Rd
pkg/stacomir/man/connect-report_mig_mult-method.Rd
pkg/stacomir/man/connect-report_ope-method.Rd
pkg/stacomir/man/connect-report_sample_char-method.Rd
pkg/stacomir/man/connect-report_sea_age-method.Rd
pkg/stacomir/man/connect-report_silver_eel-method.Rd
pkg/stacomir/man/connect-report_species-method.Rd
pkg/stacomir/man/createmessage.Rd
pkg/stacomir/man/current_end_date-ref_timestep-method.Rd
pkg/stacomir/man/current_end_date.Rd
pkg/stacomir/man/currentstart_date-ref_timestep-method.Rd
pkg/stacomir/man/currentstart_date.Rd
pkg/stacomir/man/end_date-ref_timestep-method.Rd
pkg/stacomir/man/end_date.Rd
pkg/stacomir/man/envir_stacomi.Rd
pkg/stacomir/man/fun_aggreg_for_plot.Rd
pkg/stacomir/man/fun_char_spe.Rd
pkg/stacomir/man/fun_date_extraction.Rd
pkg/stacomir/man/fun_report_mig_interannual.Rd
pkg/stacomir/man/fun_report_mig_mult.Rd
pkg/stacomir/man/fun_report_mig_mult_overlaps.Rd
pkg/stacomir/man/fun_stage_durif.Rd
pkg/stacomir/man/fun_table_per_dis.Rd
pkg/stacomir/man/fun_weight_conversion.Rd
pkg/stacomir/man/fun_write_monthly.Rd
pkg/stacomir/man/funbarchart1DF.Rd
pkg/stacomir/man/funbarchartDC.Rd
pkg/stacomir/man/funbarchartDF.Rd
pkg/stacomir/man/funboxDF.Rd
pkg/stacomir/man/funboxplotreport_sample_char.Rd
pkg/stacomir/man/funchartDF.Rd
pkg/stacomir/man/fundensityreport_sample_char.Rd
pkg/stacomir/man/fungraph.Rd
pkg/stacomir/man/fungraph_glasseel.Rd
pkg/stacomir/man/funout.Rd
pkg/stacomir/man/funplotreport_silver_eel.Rd
pkg/stacomir/man/funpointreport_sample_char.Rd
pkg/stacomir/man/funstat.Rd
pkg/stacomir/man/funstat_daily.Rd
pkg/stacomir/man/funtable.Rd
pkg/stacomir/man/funtableDC.Rd
pkg/stacomir/man/funtableDF.Rd
pkg/stacomir/man/get_step_label-ref_timestep-method.Rd
pkg/stacomir/man/get_step_label.Rd
pkg/stacomir/man/get_year-ref_timestep-method.Rd
pkg/stacomir/man/get_year.Rd
pkg/stacomir/man/getdateDebut-ref_timestep-method.Rd
pkg/stacomir/man/getdateDebut.Rd
pkg/stacomir/man/getnocurrent_step-ref_timestep-method.Rd
pkg/stacomir/man/getnocurrent_step.Rd
pkg/stacomir/man/getvalue-ref_period-method.Rd
pkg/stacomir/man/getvalue.Rd
pkg/stacomir/man/graphdate.Rd
pkg/stacomir/man/graphe-methods.Rd
pkg/stacomir/man/load_stacomi.Rd
pkg/stacomir/man/model-report_ge_weight-method.Rd
pkg/stacomir/man/model.Rd
pkg/stacomir/man/plot-report_annual-missing-method.Rd
pkg/stacomir/man/plot-report_df-ANY-method.Rd
pkg/stacomir/man/plot-report_env-missing-method.Rd
pkg/stacomir/man/plot-report_ge_weight-missing-method.Rd
pkg/stacomir/man/plot-report_mig-ANY-method.Rd
pkg/stacomir/man/plot-report_mig_char-missing-method.Rd
pkg/stacomir/man/plot-report_mig_env-missing-method.Rd
pkg/stacomir/man/plot-report_mig_interannual-missing-method.Rd
pkg/stacomir/man/plot-report_mig_mult-missing-method.Rd
pkg/stacomir/man/plot-report_sample_char-missing-method.Rd
pkg/stacomir/man/plot-report_sea_age-missing-method.Rd
pkg/stacomir/man/plot-report_silver_eel-missing-method.Rd
pkg/stacomir/man/plot-report_species-missing-method.Rd
pkg/stacomir/man/print-report_dc-method.Rd
pkg/stacomir/man/print-report_df-method.Rd
pkg/stacomir/man/print-report_mig-method.Rd
pkg/stacomir/man/print-report_mig_mult-method.Rd
pkg/stacomir/man/print-report_sample_char-method.Rd
pkg/stacomir/man/print-report_sea_age-method.Rd
pkg/stacomir/man/print-report_silver_eel-method.Rd
pkg/stacomir/man/quitte.Rd
pkg/stacomir/man/r_ann.Rd
pkg/stacomir/man/r_ann_adour.Rd
pkg/stacomir/man/r_dc.Rd
pkg/stacomir/man/r_df.Rd
pkg/stacomir/man/r_env.Rd
pkg/stacomir/man/r_gew.Rd
pkg/stacomir/man/r_mig.Rd
pkg/stacomir/man/r_mig_char.Rd
pkg/stacomir/man/r_mig_dc.Rd
pkg/stacomir/man/r_mig_df.Rd
pkg/stacomir/man/r_mig_env.Rd
pkg/stacomir/man/r_mig_interannual.Rd
pkg/stacomir/man/r_mig_interannual_vichy.Rd
pkg/stacomir/man/r_mig_mult.Rd
pkg/stacomir/man/r_mig_mult_dc.Rd
pkg/stacomir/man/r_mig_mult_df.Rd
pkg/stacomir/man/r_mig_mult_ope.Rd
pkg/stacomir/man/r_mig_ope.Rd
pkg/stacomir/man/r_sample_char.Rd
pkg/stacomir/man/r_seaa.Rd
pkg/stacomir/man/r_silver.Rd
pkg/stacomir/man/ref_choice-class.Rd
pkg/stacomir/man/ref_coe-class.Rd
pkg/stacomir/man/ref_dc-class.Rd
pkg/stacomir/man/ref_df-class.Rd
pkg/stacomir/man/ref_env-class.Rd
pkg/stacomir/man/ref_horodate-class.Rd
pkg/stacomir/man/ref_list-class.Rd
pkg/stacomir/man/ref_par-class.Rd
pkg/stacomir/man/ref_parqual-class.Rd
pkg/stacomir/man/ref_parquan-class.Rd
pkg/stacomir/man/ref_period-class.Rd
pkg/stacomir/man/ref_stage-class.Rd
pkg/stacomir/man/ref_taxa-class.Rd
pkg/stacomir/man/ref_textbox-class.Rd
pkg/stacomir/man/ref_timestep-class.Rd
pkg/stacomir/man/ref_timestepChar-class.Rd
pkg/stacomir/man/ref_timestep_daily-class.Rd
pkg/stacomir/man/ref_year-class.Rd
pkg/stacomir/man/report_annual-class.Rd
pkg/stacomir/man/report_dc-class.Rd
pkg/stacomir/man/report_df-class.Rd
pkg/stacomir/man/report_env-class.Rd
pkg/stacomir/man/report_ge_weight-class.Rd
pkg/stacomir/man/report_mig-class.Rd
pkg/stacomir/man/report_mig_char-class.Rd
pkg/stacomir/man/report_mig_env-class.Rd
pkg/stacomir/man/report_mig_interannual-class.Rd
pkg/stacomir/man/report_mig_mult-class.Rd
pkg/stacomir/man/report_ope-class.Rd
pkg/stacomir/man/report_sample_char-class.Rd
pkg/stacomir/man/report_sea_age-class.Rd
pkg/stacomir/man/report_silver_eel-class.Rd
pkg/stacomir/man/report_species-class.Rd
pkg/stacomir/man/set_starting_date-ref_timestep-method.Rd
pkg/stacomir/man/set_starting_date.Rd
pkg/stacomir/man/setasqualitative-report_mig_char-method.Rd
pkg/stacomir/man/setasqualitative.Rd
pkg/stacomir/man/setref_horodate-ref_horodate-method.Rd
pkg/stacomir/man/split_per_day.Rd
pkg/stacomir/man/stacomi.Rd
pkg/stacomir/man/stacomiR-package.Rd
pkg/stacomir/man/summary-report_dc-method.Rd
pkg/stacomir/man/summary-report_df-method.Rd
pkg/stacomir/man/summary-report_mig-method.Rd
pkg/stacomir/man/summary-report_mig_char-method.Rd
pkg/stacomir/man/summary-report_mig_interannual-method.Rd
pkg/stacomir/man/summary-report_mig_mult-method.Rd
pkg/stacomir/man/summary-report_sample_char-method.Rd
pkg/stacomir/man/summary-report_sea_age-method.Rd
pkg/stacomir/man/summary-report_silver_eel-method.Rd
pkg/stacomir/man/summary-report_species-method.Rd
pkg/stacomir/man/supprime-ref_coe-method.Rd
pkg/stacomir/man/supprime-report_mig_interannual-method.Rd
pkg/stacomir/man/supprime-report_sea_age-method.Rd
pkg/stacomir/man/supprime.Rd
pkg/stacomir/man/validity_ref_horodate.Rd
pkg/stacomir/man/validity_year.Rd
pkg/stacomir/man/vector_to_listsql.Rd
pkg/stacomir/man/write_database-report_ge_weight-method.Rd
pkg/stacomir/man/write_database-report_mig-method.Rd
pkg/stacomir/man/write_database-report_sea_age-method.Rd
pkg/stacomir/man/write_database.Rd
pkg/stacomir/man/xtable-report_annual-method.Rd
pkg/stacomir/man/xtable-report_mig_char-method.Rd
pkg/stacomir/tests/testthat/test-00-stacomir.R
pkg/stacomir/tests/testthat/test-00-zrefclasses.R
pkg/stacomir/tests/testthat/test-01-report_mig_mult.R
pkg/stacomir/tests/testthat/test-02-report_mig.R
pkg/stacomir/tests/testthat/test-03-report_df.R
pkg/stacomir/tests/testthat/test-04-report_dc.R
pkg/stacomir/tests/testthat/test-05-report_sample_char.R
pkg/stacomir/tests/testthat/test-06-report_mig_interannual.R
pkg/stacomir/tests/testthat/test-07-report_sea_age.R
pkg/stacomir/tests/testthat/test-08-report_silver_eel.R
pkg/stacomir/tests/testthat/test-09-report_annual.R
pkg/stacomir/tests/testthat/test-10-report_env.R
pkg/stacomir/tests/testthat/test-11-report_mig_env.R
pkg/stacomir/tests/testthat/test-12-report_mig_char.R
pkg/stacomir/tests/testthat/test-13-report_species.R
pkg/stacomir/tests/testthat/test-50-spell_checking.R
pkg/stacomir/vignettes/stacomir.Rmd
Log:
Modified: pkg/stacomir/.Rbuildignore
===================================================================
--- pkg/stacomir/.Rbuildignore 2021-11-02 17:53:43 UTC (rev 574)
+++ pkg/stacomir/.Rbuildignore 2021-11-06 21:16:18 UTC (rev 575)
@@ -1,15 +1,17 @@
-^README\.Rmd$
-^README-.*\.png$
-^README\.md$
-^README\.html$
-^README\.log$
-^logo\.png$
-^NEWS.md$
-^NEWS.md.html$
-^README.md.html$
-^.NEWS.md.html$
-^.README.md.html$
-^cran-comments.md$
-^cran-comments$
-^paper\.bib$
-^paper\.md$
\ No newline at end of file
+^README\.Rmd$
+^README-.*\.png$
+^README\.md$
+^README\.html$
+^README\.log$
+^logo\.png$
+^NEWS.md$
+^NEWS.md.html$
+^README.md.html$
+^.NEWS.md.html$
+^.README.md.html$
+^cran-comments.md$
+^cran-comments$
+^paper\.bib$
+^paper\.md$
+^CODE_OF_CONDUCT\.md$
+^dev
\ No newline at end of file
Modified: pkg/stacomir/.Rinstignore
===================================================================
--- pkg/stacomir/.Rinstignore 2021-11-02 17:53:43 UTC (rev 574)
+++ pkg/stacomir/.Rinstignore 2021-11-06 21:16:18 UTC (rev 575)
@@ -1,8 +1,9 @@
-inst/config/generate_ROxygen2.R
-inst/config/libraries.R
-inst/config/poedit.R
-inst/config/stacomi_checks.R
-inst/stacomi_manual_launch.r
-inst/test_vignette.R
-inst/testthat.R
-inst/cran-comment
\ No newline at end of file
+dev/config/generate_ROxygen2.R
+dev/config/libraries.R
+dev/config/poedit.R
+dev/config/stacomi_checks.R
+dev/stacomi_manual_launch.r
+dev/test_vignette.R
+dev/testthat.R
+dev/cran-comment
+dev.*
\ No newline at end of file
Added: pkg/stacomir/CODE_OF_CONDUCT.md
===================================================================
--- pkg/stacomir/CODE_OF_CONDUCT.md (rev 0)
+++ pkg/stacomir/CODE_OF_CONDUCT.md 2021-11-06 21:16:18 UTC (rev 575)
@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards
+of acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies
+when an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at [INSERT CONTACT
+METHOD]. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0,
+available at https://www.contributor-covenant.org/version/2/0/
+code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at https://
+www.contributor-covenant.org/translations.
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2021-11-02 17:53:43 UTC (rev 574)
+++ pkg/stacomir/DESCRIPTION 2021-11-06 21:16:18 UTC (rev 575)
@@ -1,118 +1,100 @@
-Package: stacomiR
-Version: 0.5.4.5
-Date: 2020-08-05
-Title: Fish Migration Monitoring
-Authors at R: c(person("Cedric", "Briand", role = c("aut", "cre"), email = "cedric.briand00 at gmail.com"),
- person("Marion", "Legrand", role = "aut", email="tableau-salt-loire at logrami.fr"),
- person("Timothee", "Besse", role = "aut", email="tableau-ang-loire at 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 Office for Biodiversity (OFB) 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,
- rlang
-Suggests:
- testthat,
- viridis,
- knitr,
- rmarkdown
-Author: Cedric Briand [aut, cre],
- Marion Legrand [aut],
- Timothee Besse [aut]
-Maintainer: Cedric Briand <cedric.briand00 at gmail.com>
-RoxygenNote: 6.1.0.9000
-NeedsCompilation: no
-VignetteBuilder: knitr
+Package: stacomiR
+Version: 0.6.9000
+Date: 2020-08-05
+Title: Fish Migration Monitoring
+Authors at R: c(person("Cedric", "Briand", role = c("aut", "cre"), email = "cedric.briand00 at gmail.com"),
+ person("Marion", "Legrand", role = "aut", email="tableau-salt-loire at 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 Office for Biodiversity (OFB) 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'
+ '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'
+ 'stacomiR-package.R'
+LazyLoad: yes
+LazyData: true
+Depends:
+ R (>= 4.0.0),
+ methods,
+ stacomirtools
+Imports:
+ magrittr,
+ intervals,
+ RColorBrewer,
+ stringr,
+ RPostgreSQL,
+ ggplot2,
+ reshape2,
+ sqldf,
+ graphics,
+ utils,
+ stats,
+ lattice,
+ grDevices,
+ Hmisc (>= 4.1-1),
+ lubridate,
+ dplyr,
+ xtable,
+ mgcv,
+ rlang,
+ pool
+Suggests:
+ testthat,
+ viridis,
+ knitr,
+ rmarkdown
+Author: Cedric Briand [aut, cre],
+ Marion Legrand [aut],
+ Timothee Besse [aut]
+Maintainer: Cedric Briand <cedric.briand00 at gmail.com>
+RoxygenNote: 7.1.2
+NeedsCompilation: no
+VignetteBuilder: knitr
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2021-11-02 17:53:43 UTC (rev 574)
+++ pkg/stacomir/NAMESPACE 2021-11-06 21:16:18 UTC (rev 575)
@@ -1,135 +1,136 @@
-# Generated by roxygen2: do not edit by hand
-
-export(chargecsv)
-export(colortable)
-export(envir_stacomi)
-export(fun_aggreg_for_plot)
-export(fun_char_spe)
-export(fun_date_extraction)
-export(fun_report_mig_interannual)
-export(fun_report_mig_mult)
-export(fun_report_mig_mult_overlaps)
-export(fun_stage_durif)
-export(fun_write_monthly)
-export(funout)
-export(funstat)
-export(progress_bar)
-export(split_per_day)
-export(stacomi)
-export(vector_to_listsql)
-exportClasses(report_annual)
-exportClasses(report_dc)
-exportClasses(report_df)
-exportClasses(report_env)
-exportClasses(report_ge_weight)
-exportClasses(report_mig)
-exportClasses(report_mig_char)
-exportClasses(report_mig_env)
-exportClasses(report_mig_interannual)
-exportClasses(report_mig_mult)
-exportClasses(report_ope)
-exportClasses(report_sample_char)
-exportClasses(report_sea_age)
-exportClasses(report_silver_eel)
-exportClasses(report_species)
-exportMethods(barplot)
-exportMethods(calcule)
-exportMethods(charge)
-exportMethods(charge_with_filter)
-exportMethods(choice_c)
-exportMethods(connect)
-exportMethods(end_date)
-exportMethods(getvalue)
-exportMethods(model)
-exportMethods(plot)
-exportMethods(print)
-exportMethods(setasqualitative)
-exportMethods(summary)
-exportMethods(supprime)
-exportMethods(write_database)
-exportMethods(xtable)
-import(RColorBrewer)
-import(RGtk2)
-import(RODBC)
-import(rlang)
-import(RPostgreSQL)
-import(gWidgets)
-import(gWidgetsRGtk2)
-import(ggplot2)
-import(methods)
-import(sqldf)
-import(stacomirtools)
-import(stringr)
-import(xtable)
-importFrom(Hmisc,capitalize)
-importFrom(Hmisc,wtd.quantile)
-importFrom(dplyr,desc)
-importFrom(dplyr,do)
-importFrom(dplyr,filter)
-importFrom(dplyr,first)
-importFrom(dplyr,group_by)
-importFrom(dplyr,min_rank)
-importFrom(dplyr,mutate)
-importFrom(dplyr,rename)
-importFrom(dplyr,select)
-importFrom(dplyr,summarize)
-importFrom(dplyr,ungroup)
-importFrom(grDevices,adjustcolor)
-importFrom(grDevices,dev.new)
-importFrom(grDevices,gray)
-importFrom(grDevices,gray.colors)
-importFrom(grDevices,rainbow)
-importFrom(graphics,abline)
-importFrom(graphics,arrows)
-importFrom(graphics,axis)
-importFrom(graphics,axis.Date)
-importFrom(graphics,hist)
-importFrom(graphics,layout)
-importFrom(graphics,legend)
-importFrom(graphics,matplot)
-importFrom(graphics,mtext)
-importFrom(graphics,par)
-importFrom(graphics,points)
-importFrom(graphics,polygon)
-importFrom(graphics,rect)
-importFrom(graphics,segments)
-importFrom(graphics,text)
-importFrom(grid,gpar)
-importFrom(grid,grid.layout)
-importFrom(grid,grid.newpage)
-importFrom(grid,pushViewport)
-importFrom(grid,viewport)
-importFrom(intervals,"closed<-")
-importFrom(intervals,Intervals)
-importFrom(intervals,interval_overlap)
-importFrom(lattice,barchart)
-importFrom(lattice,simpleKey)
-importFrom(lattice,trellis.par.get)
-importFrom(lattice,trellis.par.set)
-importFrom(lubridate,"%m+%")
-importFrom(lubridate,floor_date)
-importFrom(lubridate,isoweek)
-importFrom(lubridate,round_date)
-importFrom(lubridate,years)
-importFrom(magrittr,"%>%")
-importFrom(mgcv,gam)
-importFrom(reshape2,dcast)
-importFrom(reshape2,melt)
-importFrom(stats,AIC)
-importFrom(stats,as.formula)
-importFrom(stats,coef)
-importFrom(stats,coefficients)
-importFrom(stats,complete.cases)
-importFrom(stats,ftable)
-importFrom(stats,na.fail)
-importFrom(stats,nls)
-importFrom(stats,pbeta)
-importFrom(stats,predict)
-importFrom(stats,sd)
-importFrom(stats,xtabs)
-importFrom(utils,data)
-importFrom(utils,globalVariables)
-importFrom(utils,read.csv)
-importFrom(utils,select.list)
-importFrom(utils,stack)
-importFrom(utils,write.table)
+# Generated by roxygen2: do not edit by hand
+
+export(calcule)
+export(charge)
+export(charge_complement)
+export(charge_with_filter)
+export(choice_c)
+export(colortable)
+export(createmessage)
+export(envir_stacomi)
+export(fun_aggreg_for_plot)
+export(fun_date_extraction)
+export(fun_report_mig_interannual)
+export(fun_report_mig_mult)
+export(fun_report_mig_mult_overlaps)
+export(fun_stage_durif)
+export(fun_write_monthly)
+export(funstat)
+export(getvalue)
+export(model)
+export(setasqualitative)
+export(split_per_day)
+export(stacomi)
+export(supprime)
+export(vector_to_listsql)
+export(write_database)
+exportClasses(report_annual)
+exportClasses(report_dc)
+exportClasses(report_df)
+exportClasses(report_env)
+exportClasses(report_ge_weight)
+exportClasses(report_mig)
+exportClasses(report_mig_char)
+exportClasses(report_mig_env)
+exportClasses(report_mig_interannual)
+exportClasses(report_mig_mult)
+exportClasses(report_ope)
+exportClasses(report_sample_char)
+exportClasses(report_sea_age)
+exportClasses(report_silver_eel)
+exportClasses(report_species)
+exportMethods(barplot)
+exportMethods(choice_c)
+exportMethods(plot)
+exportMethods(print)
+exportMethods(summary)
+exportMethods(supprime)
+exportMethods(write_database)
+exportMethods(xtable)
+import(RColorBrewer)
+import(RPostgreSQL)
+import(ggplot2)
+import(methods)
+import(stacomirtools)
+import(stringr)
+import(xtable)
+importFrom(Hmisc,capitalize)
+importFrom(Hmisc,wtd.quantile)
+importFrom(dplyr,desc)
+importFrom(dplyr,do)
+importFrom(dplyr,filter)
+importFrom(dplyr,first)
+importFrom(dplyr,group_by)
+importFrom(dplyr,min_rank)
+importFrom(dplyr,mutate)
+importFrom(dplyr,rename)
+importFrom(dplyr,select)
+importFrom(dplyr,summarize)
+importFrom(dplyr,ungroup)
+importFrom(grDevices,adjustcolor)
+importFrom(grDevices,dev.new)
+importFrom(grDevices,gray)
+importFrom(grDevices,gray.colors)
+importFrom(grDevices,rainbow)
+importFrom(graphics,abline)
+importFrom(graphics,arrows)
+importFrom(graphics,axis)
+importFrom(graphics,axis.Date)
+importFrom(graphics,hist)
+importFrom(graphics,layout)
+importFrom(graphics,legend)
+importFrom(graphics,matplot)
+importFrom(graphics,mtext)
+importFrom(graphics,par)
+importFrom(graphics,points)
+importFrom(graphics,polygon)
+importFrom(graphics,rect)
+importFrom(graphics,segments)
+importFrom(graphics,text)
+importFrom(grid,gpar)
+importFrom(grid,grid.layout)
+importFrom(grid,grid.newpage)
+importFrom(grid,pushViewport)
+importFrom(grid,viewport)
+importFrom(intervals,"closed<-")
+importFrom(intervals,Intervals)
+importFrom(intervals,interval_overlap)
+importFrom(lattice,barchart)
+importFrom(lattice,simpleKey)
+importFrom(lattice,trellis.par.get)
+importFrom(lattice,trellis.par.set)
+importFrom(lubridate,"%m+%")
+importFrom(lubridate,floor_date)
+importFrom(lubridate,isoweek)
+importFrom(lubridate,round_date)
+importFrom(lubridate,years)
+importFrom(magrittr,"%>%")
+importFrom(mgcv,gam)
+importFrom(pool,dbExecute)
+importFrom(pool,dbGetQuery)
+importFrom(pool,dbWriteTable)
+importFrom(pool,poolClose)
+importFrom(reshape2,dcast)
+importFrom(reshape2,melt)
+importFrom(stats,AIC)
+importFrom(stats,as.formula)
+importFrom(stats,coef)
+importFrom(stats,coefficients)
+importFrom(stats,complete.cases)
+importFrom(stats,ftable)
+importFrom(stats,na.fail)
+importFrom(stats,nls)
+importFrom(stats,pbeta)
+importFrom(stats,predict)
+importFrom(stats,sd)
+importFrom(stats,update)
+importFrom(stats,xtabs)
+importFrom(utils,data)
+importFrom(utils,globalVariables)
+importFrom(utils,menu)
+importFrom(utils,read.csv)
+importFrom(utils,select.list)
+importFrom(utils,setTxtProgressBar)
+importFrom(utils,stack)
+importFrom(utils,txtProgressBar)
+importFrom(utils,write.table)
Modified: pkg/stacomir/NEWS.md
===================================================================
--- pkg/stacomir/NEWS.md 2021-11-02 17:53:43 UTC (rev 574)
+++ pkg/stacomir/NEWS.md 2021-11-06 21:16:18 UTC (rev 575)
@@ -1,98 +1,99 @@
-# stacomiR 0.5.4.XXX
-
-## Minor improvement and bug fix
-* 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
-
-* Langage 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
+# stacomiR 0.5.4.XXX
+
+## Minor improvement and bug fix
+
+* 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
+
+* Langage 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
\ No newline at end of file
Modified: pkg/stacomir/R/create_generic.R
===================================================================
--- pkg/stacomir/R/create_generic.R 2021-11-02 17:53:43 UTC (rev 574)
+++ pkg/stacomir/R/create_generic.R 2021-11-06 21:16:18 UTC (rev 575)
@@ -1,83 +1,151 @@
-
-#' Generic method for choice (using the gwidget graphical interface)
+#' Generic method for manual choice using the command line
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
#' @keywords internal
-#deprecated0.6
-#setGeneric("choice",def=function(object,...) standardGeneric("choice"))
-##' Generic method for multiple choice (using the gwidget notebook for multiple choice)
-##' @param object Object
-##' @param ... Additional parms
-##' @author cedric.briand
-##' @keywords internal
-#deprecated0.6
-#setGeneric("choicemult",def=function(object,...) standardGeneric("choicemult"))
-##' Generic method for manual choice using the command line
-##' @param object Object
-##' @param ... Additional parms
-##' @author cedric.briand
-##' @keywords internal
-setGeneric("choice_c",def=function(object,...) standardGeneric("choice_c"))
+#' @export
+setGeneric("choice_c", def = function(object, ...) standardGeneric("choice_c"))
#' Generic method to load referentials
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
-setGeneric("charge",def=function(object,...) standardGeneric("charge"))
+#' @export
+setGeneric("charge", def = function(object, ...) standardGeneric("charge"))
#' Generic method to load referentials, with filters from the parent object in the database
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
#' @keywords internal
-setGeneric("charge_with_filter",def=function(object,...) standardGeneric("charge_with_filter"))
-#setGeneric("connect",def=function(object,...) standardGeneric("connect")) # package stacomirtools
-#setGeneric("plot",def=function(x,y,...) standardGeneric("plot"))
+#' @export
+setGeneric("charge_with_filter", def = function(object, ...) standardGeneric("charge_with_filter"))
+# setGeneric('connect',def=function(object,...) standardGeneric('connect')) #
+# package stacomirtools setGeneric('plot',def=function(x,y,...)
+# standardGeneric('plot'))
#' Generic for prediction
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
-setGeneric("model",def=function(object,...) standardGeneric("model"))
+#' @export
+setGeneric("model", def = function(object, ...) standardGeneric("model"))
#' Generic method to load additional data
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
-setGeneric("charge_complement",def=function(object,...) standardGeneric("charge_complement"))
+#' @export
+setGeneric("charge_complement", def = function(object, ...) standardGeneric("charge_complement"))
#' Generic method for calculations
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
-setGeneric("calcule",def=function(object,...) standardGeneric("calcule"))
+#' @export
+setGeneric("calcule", def = function(object, ...) standardGeneric("calcule"))
#' Generic method to delete entires from the database
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
-setGeneric("supprime",def=function(object,...) standardGeneric("supprime"))
+#' @export
+setGeneric("supprime", def = function(object, ...) standardGeneric("supprime"))
#' Generic method write_database
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
-setGeneric("write_database",def=function(object,...) standardGeneric("write_database"))
+#' @export
+setGeneric("write_database", def = function(object, ...) standardGeneric("write_database"))
#' Generic method getvalue
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
-setGeneric("getvalue",def=function(object,...) standardGeneric("getvalue"))
+#' @export
+setGeneric("getvalue", def = function(object, ...) standardGeneric("getvalue"))
#' Generic method to forward outputs
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
-setGeneric("createmessage",def=function(object,...) standardGeneric("createmessage"))
+#' @export
+setGeneric("createmessage", def = function(object, ...) standardGeneric("createmessage"))
#' Generic method to transform quantitative par into a qualitative one
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
-setGeneric("setasqualitative",def=function(object,...) standardGeneric("setasqualitative"))
+#' @export
+setGeneric("setasqualitative", def = function(object, ...) standardGeneric("setasqualitative"))
+#' Generic method for getting the final date
+#' @param object An object
+#' @param ... Additional parameters passed to the method
+#' @keywords internal
+setGeneric(
+ "end_date",
+ def = function(object, ...)
+ standardGeneric("end_date")
+)
+#' Generic method for getting the beginning date for current time step
+#' @param object An object
+#' @param ... Additional parameters passed to the method
+#' @keywords internal
+setGeneric(
+ "currentstart_date",
+ def = function(object, ...)
+ standardGeneric("currentstart_date")
+)
+#' Generic method for getting the ending date for current time step
+#' @param object An object
+#' @param ... Additional parameters passed to the method
+#' @keywords internal
+setGeneric(
+ "current_end_date",
+ def = function(object, ...)
+ standardGeneric("current_end_date")
+)
+
+
+#' Generic method the get starting date
+#' @param object An object
+#' @param ... Additional parameters passed to the method
+#' @keywords internal
+setGeneric(
+ "getdateDebut",
+ def = function(object, ...)
+ standardGeneric("getdateDebut")
+)
+
+#' Generic method to set the starting date
+#' @param object An object
+#' @param ... Additional parameters passed to the method
+#' @keywords internal
+setGeneric(
+ "set_starting_date",
+ def = function(object, ...)
+ standardGeneric("set_starting_date")
+)
+
+
+#' Generic method to get the string value of time step
+#' @param object An object
+#' @param ... Additional parameters passed to the method
+#' @keywords internal
+setGeneric(
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 575
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