[Stacomir-commits] r401 - in pkg: stacomir stacomir/R stacomir/data stacomir/inst/config stacomir/inst/examples stacomir/inst/tests/testthat stacomir/man stacomirtools stacomirtools/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jun 20 10:50:14 CEST 2017
Author: briand
Date: 2017-06-20 10:50:12 +0200 (Tue, 20 Jun 2017)
New Revision: 401
Added:
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/interface_report_annual.R
pkg/stacomir/R/interface_report_dc.R
pkg/stacomir/R/interface_report_df.R
pkg/stacomir/R/interface_report_env.R
pkg/stacomir/R/interface_report_ge_weight.R
pkg/stacomir/R/interface_report_mig.R
pkg/stacomir/R/interface_report_mig_char.R
pkg/stacomir/R/interface_report_mig_env.R
pkg/stacomir/R/interface_report_mig_interannual.R
pkg/stacomir/R/interface_report_mig_mult.R
pkg/stacomir/R/interface_report_sample_char.R
pkg/stacomir/R/interface_report_sea_age.R
pkg/stacomir/R/interface_report_silver_eel.R
pkg/stacomir/R/interface_report_species.R
pkg/stacomir/R/ref_checkbox.R
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/data/calcmig.rda
pkg/stacomir/data/coef_durif.rda
pkg/stacomir/data/r_ann.rda
pkg/stacomir/data/r_ann_adour.rda
pkg/stacomir/data/r_dc.rda
pkg/stacomir/data/r_df.rda
pkg/stacomir/data/r_env.rda
pkg/stacomir/data/r_gew.rda
pkg/stacomir/data/r_mig.rda
pkg/stacomir/data/r_mig_char.rda
pkg/stacomir/data/r_mig_dc.rda
pkg/stacomir/data/r_mig_df.rda
pkg/stacomir/data/r_mig_env.rda
pkg/stacomir/data/r_mig_interannual.rda
pkg/stacomir/data/r_mig_interannual_vichy.rda
pkg/stacomir/data/r_mig_mult.rda
pkg/stacomir/data/r_mig_mult_dc.rda
pkg/stacomir/data/r_mig_mult_df.rda
pkg/stacomir/data/r_mig_mult_ope.rda
pkg/stacomir/data/r_mig_ope.rda
pkg/stacomir/data/r_sample_char.rda
pkg/stacomir/data/r_seaa.rda
pkg/stacomir/data/r_silver.rda
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/inst/tests/testthat/test-00-stacomir.R
pkg/stacomir/inst/tests/testthat/test-00-zrefclasses.R
pkg/stacomir/inst/tests/testthat/test-01-report_mig_mult.R
pkg/stacomir/inst/tests/testthat/test-02-report_mig.R
pkg/stacomir/inst/tests/testthat/test-03-report_df.R
pkg/stacomir/inst/tests/testthat/test-04-report_dc.R
pkg/stacomir/inst/tests/testthat/test-05-report_sample_char.R
pkg/stacomir/inst/tests/testthat/test-06-report_mig_interannual.R
pkg/stacomir/inst/tests/testthat/test-07-report_sea_age.R
pkg/stacomir/inst/tests/testthat/test-08-report_silver.R
pkg/stacomir/inst/tests/testthat/test-09-report_annual.R
pkg/stacomir/inst/tests/testthat/test-10-report_env.R
pkg/stacomir/inst/tests/testthat/test-11-report_mig_env.R
pkg/stacomir/inst/tests/testthat/test-12-report_mig_char.R
pkg/stacomir/inst/tests/testthat/test-13-report_species.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/charge-ref_checkbox-method.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_complement-ref_parqual-method.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/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_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/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/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/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/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_write_monthly.Rd
pkg/stacomir/man/funboxplotreport_sample_char.Rd
pkg/stacomir/man/fundensityreport_sample_char.Rd
pkg/stacomir/man/fungraph_glasseel.Rd
pkg/stacomir/man/funplotreport_sea_age.Rd
pkg/stacomir/man/funplotreport_silver_eel.Rd
pkg/stacomir/man/funpointreport_sample_char.Rd
pkg/stacomir/man/funstat_daily.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/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/getnocurrent_step-ref_timestep-method.Rd
pkg/stacomir/man/getnocurrent_step.Rd
pkg/stacomir/man/getvalue-ref_period-method.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/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/houtreport_mig.Rd
pkg/stacomir/man/houtreport_mig_mult.Rd
pkg/stacomir/man/hplot.Rd
pkg/stacomir/man/hplotreport_annual.Rd
pkg/stacomir/man/hsummaryreport_migInterannuelle.Rd
pkg/stacomir/man/hxtablereport_annual.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/load_stacomi.Rd
pkg/stacomir/man/model-report_ge_weight-method.Rd
pkg/stacomir/man/plot-report_annual-missing-method.Rd
pkg/stacomir/man/plot-report_dc-ANY-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/progress_bar.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_checkbox-class.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/setref_horodate-ref_horodate-method.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/validite_ref_horodate.Rd
pkg/stacomir/man/validity_year.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/xtable-report_annual-method.Rd
pkg/stacomir/man/xtable-report_mig_char-method.Rd
pkg/stacomirtools/R/utilities.r
Removed:
pkg/stacomir/R/BilanAgedemer.r
pkg/stacomir/R/BilanAnnuels.r
pkg/stacomir/R/BilanArgentee.r
pkg/stacomir/R/BilanConditionEnv.r
pkg/stacomir/R/BilanEspeces.r
pkg/stacomir/R/BilanFonctionnementDC.r
pkg/stacomir/R/BilanFonctionnementDF.r
pkg/stacomir/R/BilanMigration.r
pkg/stacomir/R/BilanMigrationCar.r
pkg/stacomir/R/BilanMigrationInterAnnuelle.r
pkg/stacomir/R/BilanMigrationMult.r
pkg/stacomir/R/BilanMigrationMultConditionEnv.r
pkg/stacomir/R/BilanOperation.r
pkg/stacomir/R/Bilan_carlot.r
pkg/stacomir/R/Bilan_poids_moyen.r
pkg/stacomir/R/PasDeTempsJournalier.r
pkg/stacomir/R/PasdeTemps.r
pkg/stacomir/R/RefCheckBox.r
pkg/stacomir/R/RefChoix.r
pkg/stacomir/R/RefCoe.r
pkg/stacomir/R/RefDC.r
pkg/stacomir/R/RefDF.r
pkg/stacomir/R/RefHorodate.r
pkg/stacomir/R/RefListe.r
pkg/stacomir/R/RefStades.r
pkg/stacomir/R/RefStationMesure.r
pkg/stacomir/R/RefTaxon.r
pkg/stacomir/R/Ref_year.R
pkg/stacomir/R/Refpar.r
pkg/stacomir/R/Refparqual.r
pkg/stacomir/R/Refparquan.r
pkg/stacomir/R/Refperiode.r
pkg/stacomir/R/ReftextBox.r
pkg/stacomir/R/create_generic.r
pkg/stacomir/R/data.r
pkg/stacomir/R/fn_EcritBilanMensuel.r
pkg/stacomir/R/fn_table_per_dis.r
pkg/stacomir/R/funSousListeBilanMigrationPar.r
pkg/stacomir/R/fungraph.r
pkg/stacomir/R/fungraph_civelle.r
pkg/stacomir/R/funstat.r
pkg/stacomir/R/funstatJournalier.r
pkg/stacomir/R/funtable.r
pkg/stacomir/R/funtraitement_poids.r
pkg/stacomir/R/interface_BilanAgedemer.r
pkg/stacomir/R/interface_BilanAnnuels.r
pkg/stacomir/R/interface_BilanArgentee.r
pkg/stacomir/R/interface_BilanConditionEnv.r
pkg/stacomir/R/interface_BilanEspeces.r
pkg/stacomir/R/interface_BilanFonctionnementDC.r
pkg/stacomir/R/interface_BilanFonctionnementDF.r
pkg/stacomir/R/interface_BilanMigration.r
pkg/stacomir/R/interface_BilanMigrationCar.r
pkg/stacomir/R/interface_BilanMigrationInterannuelle.r
pkg/stacomir/R/interface_BilanMigrationMult.r
pkg/stacomir/R/interface_BilanMigrationMultConditionEnv.r
pkg/stacomir/R/interface_Bilan_carlot.r
pkg/stacomir/R/interface_bilan_poids_moyen.r
pkg/stacomir/R/setAs.r
pkg/stacomir/R/stacomi.r
pkg/stacomir/R/utilitaires.r
pkg/stacomir/data/bMM_Arzal.rda
pkg/stacomir/data/bM_Arzal.rda
pkg/stacomir/data/b_carlot.rda
pkg/stacomir/data/bfDC.rda
pkg/stacomir/data/bfDF.rda
pkg/stacomir/data/bilA.rda
pkg/stacomir/data/bilAM.rda
pkg/stacomir/data/bilPM.rda
pkg/stacomir/data/bil_CE.rda
pkg/stacomir/data/bilanArg.rda
pkg/stacomir/data/bilanFonctionnementDC.rda
pkg/stacomir/data/bilanFonctionnementDC_bM.rda
pkg/stacomir/data/bilanFonctionnementDF.rda
pkg/stacomir/data/bilanFonctionnementDF_bM.rda
pkg/stacomir/data/bilanOperation.rda
pkg/stacomir/data/bilanOperation_bM.rda
pkg/stacomir/data/bilan_adm.rda
pkg/stacomir/data/bmC.rda
pkg/stacomir/data/bmi.rda
pkg/stacomir/data/bmi_vichy.rda
pkg/stacomir/data/bmmCE.rda
pkg/stacomir/data/coef_Durif.rda
pkg/stacomir/inst/examples/bilanAgedemer_example.R
pkg/stacomir/inst/examples/bilanAnnuels_example.R
pkg/stacomir/inst/examples/bilanArgentee_example.R
pkg/stacomir/inst/examples/bilanConditionEnv_example.R
pkg/stacomir/inst/examples/bilanEspeces_example.R
pkg/stacomir/inst/examples/bilanFonctionnementDC_example.R
pkg/stacomir/inst/examples/bilanFonctionnementDF_example.R
pkg/stacomir/inst/examples/bilanMigrationCar-example.R
pkg/stacomir/inst/examples/bilanMigrationInterannuelle_example.R
pkg/stacomir/inst/examples/bilanMigrationMultConditionEnv_example.R
pkg/stacomir/inst/examples/bilanMigrationMult_Arzal.R
pkg/stacomir/inst/examples/bilanMigration_Arzal.R
pkg/stacomir/inst/examples/bilan_poids_moyen_example.R
pkg/stacomir/inst/examples/bilancarlot_example.R
pkg/stacomir/inst/tests/testthat/test-00stacomir.R
pkg/stacomir/inst/tests/testthat/test-00zRefclasses.R
pkg/stacomir/inst/tests/testthat/test-01BilanMigrationMult.R
pkg/stacomir/inst/tests/testthat/test-02BilanMigration.R
pkg/stacomir/inst/tests/testthat/test-03BilanFonctionnementDF.R
pkg/stacomir/inst/tests/testthat/test-04BilanFonctionnementDC.R
pkg/stacomir/inst/tests/testthat/test-05Bilan_carlot.R
pkg/stacomir/inst/tests/testthat/test-06Bilan_MigrationInterAnnuelle.R
pkg/stacomir/inst/tests/testthat/test-07BilanAgedemer.R
pkg/stacomir/inst/tests/testthat/test-08BilanArgentee.R
pkg/stacomir/inst/tests/testthat/test-09BilanAnnuels.R
pkg/stacomir/inst/tests/testthat/test-10BilanConditionEnv.R
pkg/stacomir/inst/tests/testthat/test-11BilanMigrationMultConditionEnv.R
pkg/stacomir/inst/tests/testthat/test-12BilanMigrationCar.R
pkg/stacomir/inst/tests/testthat/test-13BilanAnnuels.R
pkg/stacomir/inst/tests/testthat/test-13BilanEspeces.R
pkg/stacomir/man/BilanAgedemer-class.Rd
pkg/stacomir/man/BilanAnnuels-class.Rd
pkg/stacomir/man/BilanArgentee-class.Rd
pkg/stacomir/man/BilanConditionEnv-class.Rd
pkg/stacomir/man/BilanEspeces-class.Rd
pkg/stacomir/man/BilanFonctionnementDC-class.Rd
pkg/stacomir/man/BilanFonctionnementDF-class.Rd
pkg/stacomir/man/BilanMigration-class.Rd
pkg/stacomir/man/BilanMigrationCar-class.Rd
pkg/stacomir/man/BilanMigrationInterAnnuelle-class.Rd
pkg/stacomir/man/BilanMigrationMult-class.Rd
pkg/stacomir/man/BilanMigrationMultConditionEnv-class.Rd
pkg/stacomir/man/BilanOperation-class.Rd
pkg/stacomir/man/Bilan_carlot-class.Rd
pkg/stacomir/man/Bilan_poids_moyen-class.Rd
pkg/stacomir/man/DateFin-PasDeTemps-method.Rd
pkg/stacomir/man/DateFin.Rd
pkg/stacomir/man/PasDeTemps-class.Rd
pkg/stacomir/man/PasDeTempsChar-class.Rd
pkg/stacomir/man/PasDeTempsJournalier-class.Rd
pkg/stacomir/man/RefAnnee-class.Rd
pkg/stacomir/man/RefCheckBox-class.Rd
pkg/stacomir/man/RefChoix-class.Rd
pkg/stacomir/man/RefCoe-class.Rd
pkg/stacomir/man/RefDC-class.Rd
pkg/stacomir/man/RefDF-class.Rd
pkg/stacomir/man/RefHorodate-class.Rd
pkg/stacomir/man/RefListe-class.Rd
pkg/stacomir/man/RefStades-class.Rd
pkg/stacomir/man/RefStationMesure-class.Rd
pkg/stacomir/man/RefTaxon-class.Rd
pkg/stacomir/man/RefTextBox-class.Rd
pkg/stacomir/man/Refpar-class.Rd
pkg/stacomir/man/Refparqual-class.Rd
pkg/stacomir/man/Refparquan-class.Rd
pkg/stacomir/man/Refperiode-class.Rd
pkg/stacomir/man/bMM_Arzal.Rd
pkg/stacomir/man/bM_Arzal.Rd
pkg/stacomir/man/b_carlot.Rd
pkg/stacomir/man/barplot-BilanAnnuels-method.Rd
pkg/stacomir/man/bfDC.Rd
pkg/stacomir/man/bfDF.Rd
pkg/stacomir/man/bilA.Rd
pkg/stacomir/man/bilAM.Rd
pkg/stacomir/man/bilPM.Rd
pkg/stacomir/man/bil_CE.Rd
pkg/stacomir/man/bilanArg.Rd
pkg/stacomir/man/bilanFonctionnementDC.Rd
pkg/stacomir/man/bilanFonctionnementDC_bM.Rd
pkg/stacomir/man/bilanFonctionnementDF.Rd
pkg/stacomir/man/bilanFonctionnementDF_bM.Rd
pkg/stacomir/man/bilanOperation.Rd
pkg/stacomir/man/bilanOperation_bM.Rd
pkg/stacomir/man/bilan_adm.Rd
pkg/stacomir/man/bmC.Rd
pkg/stacomir/man/bmi.Rd
pkg/stacomir/man/bmi_vichy.Rd
pkg/stacomir/man/bmmCE.Rd
pkg/stacomir/man/calcule-BilanAgedemer-method.Rd
pkg/stacomir/man/calcule-BilanArgentee-method.Rd
pkg/stacomir/man/calcule-BilanEspeces-method.Rd
pkg/stacomir/man/calcule-BilanMigration-method.Rd
pkg/stacomir/man/calcule-BilanMigrationCar-method.Rd
pkg/stacomir/man/calcule-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/calcule-BilanMigrationMult-method.Rd
pkg/stacomir/man/calcule-BilanMigrationMultConditionEnv-method.Rd
pkg/stacomir/man/calcule-Bilan_carlot-method.Rd
pkg/stacomir/man/calcule-Bilan_poids_moyen-method.Rd
pkg/stacomir/man/charge-BilanAgedemer-method.Rd
pkg/stacomir/man/charge-BilanAnnuels-method.Rd
pkg/stacomir/man/charge-BilanArgentee-method.Rd
pkg/stacomir/man/charge-BilanConditionEnv-method.Rd
pkg/stacomir/man/charge-BilanEspeces-method.Rd
pkg/stacomir/man/charge-BilanFonctionnementDC-method.Rd
pkg/stacomir/man/charge-BilanFonctionnementDF-method.Rd
pkg/stacomir/man/charge-BilanMigration-method.Rd
pkg/stacomir/man/charge-BilanMigrationCar-method.Rd
pkg/stacomir/man/charge-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/charge-BilanMigrationMult-method.Rd
pkg/stacomir/man/charge-BilanMigrationMultConditionEnv-method.Rd
pkg/stacomir/man/charge-BilanOperation-method.Rd
pkg/stacomir/man/charge-Bilan_carlot-method.Rd
pkg/stacomir/man/charge-Bilan_poids_moyen-method.Rd
pkg/stacomir/man/charge-RefAnnee-method.Rd
pkg/stacomir/man/charge-RefCheckBox-method.Rd
pkg/stacomir/man/charge-RefChoix-method.Rd
pkg/stacomir/man/charge-RefCoe-method.Rd
pkg/stacomir/man/charge-RefDC-method.Rd
pkg/stacomir/man/charge-RefDF-method.Rd
pkg/stacomir/man/charge-RefListe-method.Rd
pkg/stacomir/man/charge-RefStades-method.Rd
pkg/stacomir/man/charge-RefStationMesure-method.Rd
pkg/stacomir/man/charge-RefTaxon-method.Rd
pkg/stacomir/man/charge-RefTextBox-method.Rd
pkg/stacomir/man/charge-Refpar-method.Rd
pkg/stacomir/man/charge-Refparqual-method.Rd
pkg/stacomir/man/charge-Refparquan-method.Rd
pkg/stacomir/man/charge_avec_filtre-RefStades-method.Rd
pkg/stacomir/man/charge_avec_filtre-RefTaxon-method.Rd
pkg/stacomir/man/charge_avec_filtre-Refpar-method.Rd
pkg/stacomir/man/charge_avec_filtre-Refparqual-method.Rd
pkg/stacomir/man/charge_avec_filtre-Refparquan-method.Rd
pkg/stacomir/man/charge_avec_filtre.Rd
pkg/stacomir/man/charge_complement-Refparqual-method.Rd
pkg/stacomir/man/choice-PasDeTemps-method.Rd
pkg/stacomir/man/choice-PasDeTempsJournalier-method.Rd
pkg/stacomir/man/choice-RefAnnee-method.Rd
pkg/stacomir/man/choice-RefCheckBox-method.Rd
pkg/stacomir/man/choice-RefChoix-method.Rd
pkg/stacomir/man/choice-RefDC-method.Rd
pkg/stacomir/man/choice-RefDF-method.Rd
pkg/stacomir/man/choice-RefHorodate-method.Rd
pkg/stacomir/man/choice-RefListe-method.Rd
pkg/stacomir/man/choice-RefStades-method.Rd
pkg/stacomir/man/choice-RefStationMesure-method.Rd
pkg/stacomir/man/choice-RefTaxon-method.Rd
pkg/stacomir/man/choice-RefTextBox-method.Rd
pkg/stacomir/man/choice-Refpar-method.Rd
pkg/stacomir/man/choice-Refparqual-method.Rd
pkg/stacomir/man/choice_c-BilanAgedemer-method.Rd
pkg/stacomir/man/choice_c-BilanAnnuels-method.Rd
pkg/stacomir/man/choice_c-BilanArgentee-method.Rd
pkg/stacomir/man/choice_c-BilanConditionEnv-method.Rd
pkg/stacomir/man/choice_c-BilanEspeces-method.Rd
pkg/stacomir/man/choice_c-BilanFonctionnementDC-method.Rd
pkg/stacomir/man/choice_c-BilanFonctionnementDF-method.Rd
pkg/stacomir/man/choice_c-BilanMigration-method.Rd
pkg/stacomir/man/choice_c-BilanMigrationCar-method.Rd
pkg/stacomir/man/choice_c-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/choice_c-BilanMigrationMult-method.Rd
pkg/stacomir/man/choice_c-BilanMigrationMultConditionEnv-method.Rd
pkg/stacomir/man/choice_c-Bilan_carlot-method.Rd
pkg/stacomir/man/choice_c-Bilan_poids_moyen-method.Rd
pkg/stacomir/man/choice_c-PasDeTempsJournalier-method.Rd
pkg/stacomir/man/choice_c-RefAnnee-method.Rd
pkg/stacomir/man/choice_c-RefChoix-method.Rd
pkg/stacomir/man/choice_c-RefDC-method.Rd
pkg/stacomir/man/choice_c-RefDF-method.Rd
pkg/stacomir/man/choice_c-RefHorodate-method.Rd
pkg/stacomir/man/choice_c-RefListe-method.Rd
pkg/stacomir/man/choice_c-RefStades-method.Rd
pkg/stacomir/man/choice_c-RefStationMesure-method.Rd
pkg/stacomir/man/choice_c-RefTaxon-method.Rd
pkg/stacomir/man/choice_c-RefTextBox-method.Rd
pkg/stacomir/man/choice_c-Refpar-method.Rd
pkg/stacomir/man/choicemult-PasDeTemps-method.Rd
pkg/stacomir/man/choicemult-RefChoix-method.Rd
pkg/stacomir/man/choicemult-RefDC-method.Rd
pkg/stacomir/man/choicemult-RefHorodate-method.Rd
pkg/stacomir/man/choicemult-RefStades-method.Rd
pkg/stacomir/man/choicemult-RefTaxon-method.Rd
pkg/stacomir/man/choicemult-Refpar-method.Rd
pkg/stacomir/man/choicemult-Refparqual-method.Rd
pkg/stacomir/man/connect-BilanAgedemer-method.Rd
pkg/stacomir/man/connect-BilanAnnuels-method.Rd
pkg/stacomir/man/connect-BilanArgentee-method.Rd
pkg/stacomir/man/connect-BilanConditionEnv-method.Rd
pkg/stacomir/man/connect-BilanEspeces-method.Rd
pkg/stacomir/man/connect-BilanFonctionnementDC-method.Rd
pkg/stacomir/man/connect-BilanFonctionnementDF-method.Rd
pkg/stacomir/man/connect-BilanMigration-method.Rd
pkg/stacomir/man/connect-BilanMigrationCar-method.Rd
pkg/stacomir/man/connect-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/connect-BilanMigrationMult-method.Rd
pkg/stacomir/man/connect-BilanMigrationMultConditionEnv-method.Rd
pkg/stacomir/man/connect-BilanOperation-method.Rd
pkg/stacomir/man/connect-Bilan_carlot-method.Rd
pkg/stacomir/man/connect-Bilan_poids_moyen-method.Rd
pkg/stacomir/man/currentDateDebut-PasDeTemps-method.Rd
pkg/stacomir/man/currentDateDebut.Rd
pkg/stacomir/man/currentDateFin-PasDeTemps-method.Rd
pkg/stacomir/man/currentDateFin.Rd
pkg/stacomir/man/f_stade_Durif.Rd
pkg/stacomir/man/fn_EcritBilanMensuel.Rd
pkg/stacomir/man/fn_table_per_dis.Rd
pkg/stacomir/man/funSousListeBilanMigrationPar.Rd
pkg/stacomir/man/fun_bilanMigrationMult.Rd
pkg/stacomir/man/fun_bilanMigrationMult_Overlaps.Rd
pkg/stacomir/man/funboxplotBilan_carlot.Rd
pkg/stacomir/man/fundat.Rd
pkg/stacomir/man/fundensityBilan_carlot.Rd
pkg/stacomir/man/fungraph_civelle.Rd
pkg/stacomir/man/funplotBilanAgedemer.Rd
pkg/stacomir/man/funplotBilanArgentee.Rd
pkg/stacomir/man/funpointBilan_carlot.Rd
pkg/stacomir/man/funstatJournalier.Rd
pkg/stacomir/man/funtableBilanAgedemer.Rd
pkg/stacomir/man/funtableBilanArgentee.Rd
pkg/stacomir/man/funtableBilan_carlot.Rd
pkg/stacomir/man/funtraitement_poids.Rd
pkg/stacomir/man/funtraitementdate.Rd
pkg/stacomir/man/getAnnees-PasDeTemps-method.Rd
pkg/stacomir/man/getAnnees.Rd
pkg/stacomir/man/getLibellesPas-PasDeTemps-method.Rd
pkg/stacomir/man/getLibellesPas.Rd
pkg/stacomir/man/getdateDebut-PasDeTemps-method.Rd
pkg/stacomir/man/getnoPasCourant-PasDeTemps-method.Rd
pkg/stacomir/man/getnoPasCourant.Rd
pkg/stacomir/man/getvalue-Refperiode-method.Rd
pkg/stacomir/man/hBilanConditionEnv.Rd
pkg/stacomir/man/hBilanEspeces.Rd
pkg/stacomir/man/hBilanMigration.Rd
pkg/stacomir/man/hBilanMigrationInterAnnuelle.Rd
pkg/stacomir/man/hBilanMigrationMult.Rd
pkg/stacomir/man/hBilanMigrationMultConditionEnv.Rd
pkg/stacomir/man/hBilanMigrationPar.Rd
pkg/stacomir/man/hBilan_carlot.Rd
pkg/stacomir/man/hDC.Rd
pkg/stacomir/man/hDF.Rd
pkg/stacomir/man/hDFDC.Rd
pkg/stacomir/man/hOPE.Rd
pkg/stacomir/man/hSt.Rd
pkg/stacomir/man/hTableBilanMigration.Rd
pkg/stacomir/man/hTableBilanMigrationMult.Rd
pkg/stacomir/man/hTail.Rd
pkg/stacomir/man/hbarplotBilanAnnuels.Rd
pkg/stacomir/man/hbilA.Rd
pkg/stacomir/man/hbilanConditionEnvgraph.Rd
pkg/stacomir/man/hbilanMigrationMult_graph.Rd
pkg/stacomir/man/hbilanMigrationMultcalc.Rd
pkg/stacomir/man/hbilanMigrationMultgraph2.Rd
pkg/stacomir/man/hbilanMigrationMultgraph3.Rd
pkg/stacomir/man/hbilanMigrationcalc.Rd
pkg/stacomir/man/hbilanMigrationgraph.Rd
pkg/stacomir/man/hbilanMigrationgraph2.Rd
pkg/stacomir/man/hbilanMigrationwrite.Rd
pkg/stacomir/man/hbilanagedemer.Rd
pkg/stacomir/man/hgraphBilanMigrationInterAnnuelle.Rd
pkg/stacomir/man/hgraphBilanMigrationInterAnnuelle2.Rd
pkg/stacomir/man/hgraphBilanMigrationInterAnnuelle3.Rd
pkg/stacomir/man/hgraphBilanMigrationInterAnnuelle4.Rd
pkg/stacomir/man/hgraphBilanMigrationInterAnnuelle5.Rd
pkg/stacomir/man/hgraphBilanMigrationInterAnnuelle7.Rd
pkg/stacomir/man/houtBilanMigration.Rd
pkg/stacomir/man/houtBilanMigrationMult.Rd
pkg/stacomir/man/hpds.Rd
pkg/stacomir/man/hplotBilanAnnuels.Rd
pkg/stacomir/man/hsilver.Rd
pkg/stacomir/man/hsummaryBilanMigrationInterannuelle.Rd
pkg/stacomir/man/husr.Rd
pkg/stacomir/man/hxtableBilanAnnuels.Rd
pkg/stacomir/man/interface_BilanAgedemer.Rd
pkg/stacomir/man/interface_BilanAnnuels.Rd
pkg/stacomir/man/interface_BilanArgentee.Rd
pkg/stacomir/man/interface_BilanEspeces.Rd
pkg/stacomir/man/interface_BilanFonctionnementDC.Rd
pkg/stacomir/man/interface_BilanFonctionnementDF.Rd
pkg/stacomir/man/interface_BilanMigration.Rd
pkg/stacomir/man/interface_BilanMigrationInterAnnuelle.Rd
pkg/stacomir/man/interface_BilanMigrationMult.Rd
pkg/stacomir/man/interface_BilanMigrationMultConditionEnv.Rd
pkg/stacomir/man/interface_BilanMigrationPar.Rd
pkg/stacomir/man/interface_BilanPoidsMoyen.Rd
pkg/stacomir/man/interface_Bilan_carlot.Rd
pkg/stacomir/man/interface_ConditionEnv.Rd
pkg/stacomir/man/model-Bilan_poids_moyen-method.Rd
pkg/stacomir/man/mygtkProgressBar.Rd
pkg/stacomir/man/out.Rd
pkg/stacomir/man/plot-BilanAgedemer-missing-method.Rd
pkg/stacomir/man/plot-BilanAnnuels-missing-method.Rd
pkg/stacomir/man/plot-BilanArgentee-missing-method.Rd
pkg/stacomir/man/plot-BilanConditionEnv-missing-method.Rd
pkg/stacomir/man/plot-BilanEspeces-missing-method.Rd
pkg/stacomir/man/plot-BilanFonctionnementDC-ANY-method.Rd
pkg/stacomir/man/plot-BilanFonctionnementDF-ANY-method.Rd
pkg/stacomir/man/plot-BilanMigration-ANY-method.Rd
pkg/stacomir/man/plot-BilanMigrationCar-missing-method.Rd
pkg/stacomir/man/plot-BilanMigrationInterAnnuelle-missing-method.Rd
pkg/stacomir/man/plot-BilanMigrationMult-missing-method.Rd
pkg/stacomir/man/plot-BilanMigrationMultConditionEnv-missing-method.Rd
pkg/stacomir/man/plot-Bilan_carlot-missing-method.Rd
pkg/stacomir/man/plot-Bilan_poids_moyen-missing-method.Rd
pkg/stacomir/man/print-BilanAgedemer-method.Rd
pkg/stacomir/man/print-BilanArgentee-method.Rd
pkg/stacomir/man/print-BilanFonctionnementDC-method.Rd
pkg/stacomir/man/print-BilanFonctionnementDF-method.Rd
pkg/stacomir/man/print-BilanMigration-method.Rd
pkg/stacomir/man/print-BilanMigrationMult-method.Rd
pkg/stacomir/man/print-Bilan_carlot-method.Rd
pkg/stacomir/man/setRefHorodate-RefHorodate-method.Rd
pkg/stacomir/man/setasqualitative-BilanMigrationCar-method.Rd
pkg/stacomir/man/setdateDebut-PasDeTemps-method.Rd
pkg/stacomir/man/setdateDebut.Rd
pkg/stacomir/man/suivant-PasDeTemps-method.Rd
pkg/stacomir/man/suivant.Rd
pkg/stacomir/man/summary-BilanAgedemer-method.Rd
pkg/stacomir/man/summary-BilanArgentee-method.Rd
pkg/stacomir/man/summary-BilanEspeces-method.Rd
pkg/stacomir/man/summary-BilanFonctionnementDC-method.Rd
pkg/stacomir/man/summary-BilanFonctionnementDF-method.Rd
pkg/stacomir/man/summary-BilanMigration-method.Rd
pkg/stacomir/man/summary-BilanMigrationCar-method.Rd
pkg/stacomir/man/summary-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/summary-BilanMigrationMult-method.Rd
pkg/stacomir/man/summary-Bilan_carlot-method.Rd
pkg/stacomir/man/supprime-BilanAgedemer-method.Rd
pkg/stacomir/man/supprime-BilanMigrationInterAnnuelle-method.Rd
pkg/stacomir/man/supprime-RefCoe-method.Rd
pkg/stacomir/man/validite_Annee.Rd
pkg/stacomir/man/validite_RefHorodate.Rd
pkg/stacomir/man/write_database-BilanAgedemer-method.Rd
pkg/stacomir/man/write_database-BilanMigration-method.Rd
pkg/stacomir/man/write_database-Bilan_poids_moyen-method.Rd
pkg/stacomir/man/xtable-BilanAnnuels-method.Rd
pkg/stacomir/man/xtable-BilanMigrationCar-method.Rd
pkg/stacomirtools/R/utilitaires.r
Modified:
pkg/stacomir/DESCRIPTION
pkg/stacomir/NAMESPACE
pkg/stacomir/inst/config/generate_Roxygen2.R
pkg/stacomir/inst/config/generate_data.R
pkg/stacomir/inst/config/stacomi_manual_launch.r
pkg/stacomir/inst/config/testthat.R
pkg/stacomir/man/calcmig.Rd
pkg/stacomir/man/calcule.Rd
pkg/stacomir/man/charge.Rd
pkg/stacomir/man/charge_complement.Rd
pkg/stacomir/man/chargecomplement-methods.Rd
pkg/stacomir/man/chargecsv.Rd
pkg/stacomir/man/choice.Rd
pkg/stacomir/man/choice_c.Rd
pkg/stacomir/man/choicemult.Rd
pkg/stacomir/man/coef_Durif.Rd
pkg/stacomir/man/colortable.Rd
pkg/stacomir/man/createmessage.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_weight_conversion.Rd
pkg/stacomir/man/funbarchart1DC.Rd
pkg/stacomir/man/funbarchart1DF.Rd
pkg/stacomir/man/funbarchartDC.Rd
pkg/stacomir/man/funbarchartDF.Rd
pkg/stacomir/man/funboxDC.Rd
pkg/stacomir/man/funboxDF.Rd
pkg/stacomir/man/funchartDC.Rd
pkg/stacomir/man/funchartDF.Rd
pkg/stacomir/man/fungraph.Rd
pkg/stacomir/man/funout.Rd
pkg/stacomir/man/funstat.Rd
pkg/stacomir/man/funtable.Rd
pkg/stacomir/man/funtableDC.Rd
pkg/stacomir/man/funtableDF.Rd
pkg/stacomir/man/getdateDebut.Rd
pkg/stacomir/man/getdbname.Rd
pkg/stacomir/man/getvalue.Rd
pkg/stacomir/man/graphdate.Rd
pkg/stacomir/man/graphe-methods.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/houtDC.Rd
pkg/stacomir/man/houtDF.Rd
pkg/stacomir/man/hplotbilesp.Rd
pkg/stacomir/man/hreg.Rd
pkg/stacomir/man/hsummarybilesp.Rd
pkg/stacomir/man/interface_graphique.Rd
pkg/stacomir/man/model.Rd
pkg/stacomir/man/quitte.Rd
pkg/stacomir/man/setasqualitative.Rd
pkg/stacomir/man/split_per_day.Rd
pkg/stacomir/man/stacomi.Rd
pkg/stacomir/man/stacomiR-package.Rd
pkg/stacomir/man/supprime.Rd
pkg/stacomir/man/vector_to_listsql.Rd
pkg/stacomir/man/write_database.Rd
pkg/stacomirtools/DESCRIPTION
Log:
adaption package to format/ language constraint
this is a major change
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2017-06-18 18:36:42 UTC (rev 400)
+++ pkg/stacomir/DESCRIPTION 2017-06-20 08:50:12 UTC (rev 401)
@@ -1,6 +1,6 @@
Package: stacomiR
-Version: 0.5.2
-Date: 2017-06-10
+Version: 0.5.3
+Date: 2017-06-19
Title: Fish Migration Monitoring (stacomiR)
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"),
@@ -8,71 +8,69 @@
Description: Graphical outputs and treatment for a database of fishway
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 fishway monitoring. Version 0.5.2 is available in French and
+ data obtained by fishway monitoring. Version 0.5.3 is available in French and
English.
License: GPL (>= 2)
Collate:
- 'create_generic.r'
- 'Refpar.r'
- 'RefHorodate.r'
- 'RefStades.r'
- 'RefTaxon.r'
- 'RefDC.r'
- 'ReftextBox.r'
- 'BilanAgedemer.r'
- 'RefAnnee.r'
- 'BilanAnnuels.r'
- 'BilanArgentee.r'
- 'utilitaires.r'
- 'RefStationMesure.r'
- 'BilanConditionEnv.r'
- 'RefListe.r'
- 'BilanEspeces.r'
- 'BilanFonctionnementDC.r'
- 'RefDF.r'
- 'BilanFonctionnementDF.r'
- 'PasdeTemps.r'
- 'PasDeTempsJournalier.r'
- 'BilanMigration.r'
- 'Bilan_carlot.r'
- 'RefChoix.r'
- 'Refparqual.r'
- 'Refparquan.r'
- 'BilanMigrationCar.r'
- 'BilanMigrationInterAnnuelle.r'
- 'BilanMigrationMult.r'
- 'BilanMigrationMultConditionEnv.r'
- 'BilanOperation.r'
- 'RefCoe.r'
- 'Bilan_poids_moyen.r'
- 'RefCheckBox.r'
- 'Refperiode.r'
- 'data.r'
- 'fn_EcritBilanMensuel.r'
- 'fn_table_per_dis.r'
- 'funSousListeBilanMigrationPar.r'
- 'fungraph.r'
- 'fungraph_civelle.r'
- 'funstat.r'
- 'funstatJournalier.r'
- 'funtable.r'
- 'funtraitement_poids.r'
- 'interface_BilanAgedemer.r'
- 'interface_BilanAnnuels.r'
- 'interface_BilanArgentee.r'
- 'interface_BilanConditionEnv.r'
- 'interface_BilanEspeces.r'
- 'interface_BilanFonctionnementDC.r'
- 'interface_BilanFonctionnementDF.r'
- 'interface_BilanMigration.r'
- 'interface_BilanMigrationCar.r'
- 'interface_BilanMigrationInterannuelle.r'
- 'interface_BilanMigrationMult.r'
- 'interface_BilanMigrationMultConditionEnv.r'
- 'interface_Bilan_carlot.r'
- 'interface_bilan_poids_moyen.r'
- 'setAs.r'
- 'stacomi.r'
+ '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:
@@ -81,6 +79,7 @@
stacomirtools,
RODBC
Imports:
+ magrittr,
intervals,
RColorBrewer,
stringr,
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2017-06-18 18:36:42 UTC (rev 400)
+++ pkg/stacomir/NAMESPACE 2017-06-20 08:50:12 UTC (rev 401)
@@ -2,43 +2,42 @@
export(chargecsv)
export(colortable)
-export(f_stade_Durif)
-export(fn_EcritBilanMensuel)
export(fun_aggreg_for_plot)
-export(fun_bilanMigrationMult)
-export(fun_bilanMigrationMult_Overlaps)
export(fun_char_spe)
-export(fundat)
+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(funtraitement_poids)
-export(funtraitementdate)
-export(mygtkProgressBar)
+export(progress_bar)
export(split_per_day)
export(stacomi)
export(vector_to_listsql)
-exportClasses(BilanAgedemer)
-exportClasses(BilanAnnuels)
-exportClasses(BilanArgentee)
-exportClasses(BilanConditionEnv)
-exportClasses(BilanEspeces)
-exportClasses(BilanFonctionnementDC)
-exportClasses(BilanFonctionnementDF)
-exportClasses(BilanMigration)
-exportClasses(BilanMigrationCar)
-exportClasses(BilanMigrationInterAnnuelle)
-exportClasses(BilanMigrationMult)
-exportClasses(BilanMigrationMultConditionEnv)
-exportClasses(BilanOperation)
-exportClasses(Bilan_carlot)
-exportClasses(Bilan_poids_moyen)
-exportMethods(DateFin)
+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_avec_filtre)
+exportMethods(charge_with_filter)
exportMethods(choice_c)
exportMethods(connect)
+exportMethods(end_date)
exportMethods(getvalue)
exportMethods(model)
exportMethods(plot)
@@ -52,7 +51,6 @@
import(RGtk2)
import(RODBC)
import(RPostgreSQL)
-import(dplyr)
import(gWidgets)
import(gWidgetsRGtk2)
import(ggplot2)
@@ -63,6 +61,17 @@
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)
@@ -100,6 +109,7 @@
importFrom(lubridate,isoweek)
importFrom(lubridate,round_date)
importFrom(lubridate,years)
+importFrom(magrittr,"%>%")
importFrom(mgcv,gam)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
Deleted: pkg/stacomir/R/BilanAgedemer.r
===================================================================
--- pkg/stacomir/R/BilanAgedemer.r 2017-06-18 18:36:42 UTC (rev 400)
+++ pkg/stacomir/R/BilanAgedemer.r 2017-06-20 08:50:12 UTC (rev 401)
@@ -1,501 +0,0 @@
-# todo interface modifier, refaire les commentaires, tester avec testthat les methodes writedatabase et supprime
-
-
-#' Class "BilanAgedemer"
-#'
-#' the BilanAgedemer class is used to dispatch adult salmons to age class according to
-#' their size and to basin dependent limits set by the user. Once checked with graphs and summary
-#' statistics, the results are to be written to the database.
-#' @include create_generic.r
-#' @include ReftextBox.r
-#' @include RefDC.r
-#' @include RefTaxon.r
-#' @include RefStades.r
-#' @include RefHorodate.r
-#' @include Refpar.r
-#' @note This class is displayed by interface_bilan_agedemer
-#' @slot data A data frame with data generated from the database
-#' @slot calcdata A list of dc with processed data. This lists consists of two elements
-#' \itemize{
-#' \item (1) data A dataset with age set to be used by the plot and summary methods
-#' \item (2) tj_caracteristitiquelot_car A dataset to import into the database
-#' }
-#' @slot dc Object of class \link{RefDC-class}: the control devices
-#' @slot taxons Object of class \link{RefTaxon-class}: the species
-#' @slot stades Object of class \link{RefStades-class} : the stages of the fish
-#' @slot par Object of class \link{Refpar-class}: the parameters used
-#' @slot horodatedebut An object of class \code{RefHorodate-class}
-#' @slot horodatefin An object of class \code{RefHorodate-class}
-#' @slot limit1hm The size limit, in mm between 1 sea winter fishes and 2 sea winter fishes
-#' @slot limit2hm The size limit, in mm between 2 sea winter fishes and 3 sea winter fishes
-#' @section Objects from the Class: Objects can be created by calls of the form
-#' \code{new("BilanAgedemer", ...)}
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @family Bilan Objects
-#' @keywords classes
-#' @example inst/examples/bilanAgedemer_example.R
-#' @aliases BilanAgedemer bilanagedemer bilanAgedeMer BilanAgeDeMer
-#' @export
-setClass(Class="BilanAgedemer",
- representation= representation(
- data="data.frame",
- calcdata="list",
- dc="RefDC",
- taxons="RefTaxon",
- stades="RefStades",
- par="Refpar",
- horodatedebut="RefHorodate",
- horodatefin="RefHorodate",
- limit1hm="RefTextBox",
- limit2hm="RefTextBox"
- ),
- prototype=prototype(data=data.frame(),
- calcdata=list(),
- dc=new("RefDC"),
- taxons=new("RefTaxon"),
- stades=new("RefStades"),
- par=new("Refpar"),
- horodatedebut=new("RefHorodate"),
- horodatefin=new("RefHorodate"),
- limit1hm=new("RefTextBox"),
- limit2hm=new("RefTextBox")
- ))
-setValidity("BilanAgedemer",function(object)
- {
- rep1=object at taxons@data$tax_code[1]=='2220'
- label1<-'BilanAgedemer should only be for salmon (tax_code=2220)'
- rep2=all(object at stades@data$std_code%in%c('5','11','BEC','BER','IND'))
- label2<-'Only stages 5,11,BEC,BER,IND should be used in BilanAgedemer'
- return(ifelse(rep1 & rep2 , TRUE ,c(label1,label2)[!c(rep1, rep2)]))
- }
-)
-#' connect method for BilanAgedemer
-#'
-#' @param object An object of class \link{BilanAgedemer-class}
-#' @param silent Default FALSE, if TRUE the program should no display messages
-#' @return An object of class \link{BilanAgedemer-class}
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
-setMethod("connect",signature=signature("BilanAgedemer"),definition=function(object,silent=FALSE) {
- requete<-new("RequeteODBCwheredate")
- requete at baseODBC=get("baseODBC",envir=envir_stacomi)
- requete at select= paste("SELECT * FROM ",get("sch",envir=envir_stacomi),"vue_lot_ope_car",sep="")
- requete at colonnedebut="ope_date_debut"
- requete at colonnefin="ope_date_fin"
- requete at datedebut<-object at horodatedebut@horodate
- requete at datefin<-object at horodatefin@horodate
- requete at order_by="ORDER BY ope_date_debut"
- requete at and=paste(" AND ope_dic_identifiant in ",vector_to_listsql(object at dc@dc_selectionne),
- " AND lot_tax_code in ", vector_to_listsql(object at taxons@data$tax_code),
- " AND lot_std_code in ", vector_to_listsql(object at stades@data$std_code),
- " AND car_par_code in ", vector_to_listsql(object at par@par_selectionne), sep="")
- requete<-stacomirtools::connect(requete)
- object at data<-requete at query
- if (!silent) funout(gettext("Data loaded",domain="R-stacomiR"))
- return(object)
- })
-
-
-#' Loads data and check that all choices in the graphical interface have been made.
-#'
-#' It is not necessary to run this method if the choice_c method has been run.
-#' This method verifies that boxes have been clicked in the user interface and gets the objects pasted in
-#' envir_stacomi
-#' @param object An object of class \link{BilanAgedemer-class}
-#' @param h a handler
-#' @return An object of class \link{BilanAgedemer-class} with slots filled with user choice
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @aliases charge.BilanAgedemer charge.bilanagedemer
-#' @export
-#' @keywords internal
-setMethod("charge",signature=signature("BilanAgedemer"),definition=function(object,h) {
- if (exists("refDC",envir_stacomi)) {
- object at dc<-get("refDC",envir_stacomi)
- } else {
- funout(gettext("You need to choose a counting device, clic on validate\n",domain="R-stacomiR"),arret=TRUE)
- }
- if (exists("refTaxon",envir_stacomi)) {
- object at taxons<-get("refTaxon",envir_stacomi)
- } else {
- funout(gettext("You need to choose a taxa, clic on validate\n",domain="R-stacomiR"),arret=TRUE)
- }
- if (exists("refStades",envir_stacomi)) {
- object at stades<-get("refStades",envir_stacomi)
- } else {
- funout(gettext("You need to choose a stage, clic on validate\n",domain="R-stacomiR"),arret=TRUE)
- }
- if (exists("refpar",envir_stacomi)) {
- object at par<-get("refpar",envir_stacomi)
- } else {
- funout(gettext("You need to choose a parameter, clic on validate\n",domain="R-stacomiR"),arret=TRUE)
- }
- # rem pas tres satisfaisant car ce nom est choisi dans l'interface
- if (exists("bilan_adm_date_debut",envir_stacomi)) {
- object at horodatedebut@horodate<-get("bilan_adm_date_debut",envir_stacomi)
- } else {
- funout(gettext("You need to choose the starting date\n",domain="R-stacomiR"),arret=TRUE)
- }
- # rem id
- if (exists("bilan_adm_date_fin",envir_stacomi)) {
- object at horodatefin@horodate<-get("bilan_adm_date_fin",envir_stacomi)
- } else {
- funout(gettext("You need to choose the ending date\n",domain="R-stacomiR"),arret=TRUE)
- }
- if (exists("limit1hm",envir_stacomi)) {
- object at limit1hm<-get("limit1hm",envir_stacomi)
- } else {
- funout(gettext("you need to choose a value for limit1hm",domain="R-stacomiR"),arret=TRUE)
- }
- if (exists("limit2hm",envir_stacomi)) {
- object at limit2hm<-get("limit2hm",envir_stacomi)
- } else {
- funout(gettext("you need to choose a value for limit2hm",domain="R-stacomiR"),arret=TRUE)
- }
- return(object)
- validObject(object)
- assign("bilan_adm",object,envir_stacomi)
- })
-
-
-#' command line interface for BilanAgedemer class
-#' @param object An object of class \link{BilanAgedemer-class}
-#' @param dc A numeric or integer, the code of the dc, coerced to integer,see \link{choice_c,RefDC-method}
-#' @param taxons '2220=Salmo salar',
-#' these should match the ref.tr_taxon_tax referential table in the stacomi database, see \link{choice_c,RefTaxon-method}
-#' @param stades '5','11','BEC','BER','IND'
-#' @param par Parameters chosen for the Bilan are mesured body size (1786), mesured fork length (1785),video size (C001) and number of year at sea (A124)
-#' @param horodatedebut The starting date as a character, formats like \code{\%Y-\%m-\%d} or \code{\%d-\%m-\%Y} can be used as input
-#' @param horodatefin The finishing date of the Bilan, for this class this will be used to calculate the number of daily steps.
-#' @param limit1hm Size limit of a salmon for an one sea winter fish
-#' @param limit2hm Size limit of a salmon for a two sea winter fish
-#' @param silent Default FALSE, if TRUE the program should no display messages
-#' @return An object of class \link{BilanAgedemer-class}
-#' The choice_c method fills in the data slot for classes \link{RefDC-class}, \link{RefTaxon-class}, \link{RefStades-class}, \link{Refpar-class} and two slots of \link{RefHorodate-class} and then
-#' uses the choice_c methods of these object to select the data.
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
-setMethod("choice_c",signature=signature("BilanAgedemer"),definition=function(object,
- dc,
- taxons=2220,
- stades=c('5','11','BEC','BER','IND'),
- par=c('1786','1785','C001','A124'),
- horodatedebut,
- horodatefin,
- limit1hm,
- limit2hm,
- silent=FALSE){
- # code for debug using example
- #horodatedebut="2012-01-01";horodatefin="2013-12-31";dc=c(107,108,101);
- #taxons=2220; stades=c('5','11','BEC','BER','IND');par=c('1786','1785','C001');silent=FALSE
- if (!(is.numeric(limit1hm)|is.integer(limit1hm))) funout(gettext("limit1hm should be numeric or integer",domain="R-stacomiR"),arret=TRUE)
- if (!(is.numeric(limit2hm)|is.integer(limit2hm))) funout(gettext("limit2hm should be numeric or integer",domain="R-stacomiR"),arret=TRUE)
-
- bilan_adm<-object
- bilan_adm at dc=charge(bilan_adm at dc)
- # loads and verifies the dc
- # this will set dc_selectionne slot
- bilan_adm at dc<-choice_c(object=bilan_adm at dc,dc)
- # only taxa present in the bilanMigration are used
- bilan_adm at taxons<-charge_avec_filtre(object=bilan_adm at taxons,bilan_adm at dc@dc_selectionne)
- bilan_adm at taxons<-choice_c(bilan_adm at taxons,taxons)
- bilan_adm at stades<-charge_avec_filtre(object=bilan_adm at stades,bilan_adm at dc@dc_selectionne,bilan_adm at taxons@data$tax_code)
- bilan_adm at stades<-choice_c(bilan_adm at stades,stades,silent=silent)
- bilan_adm at par<-charge_avec_filtre(object=bilan_adm at par,bilan_adm at dc@dc_selectionne,bilan_adm at taxons@data$tax_code,bilan_adm at stades@data$std_code)
- bilan_adm at par<-choice_c(bilan_adm at par,par,silent=silent)
- bilan_adm at horodatedebut<-choice_c(object=bilan_adm at horodatedebut,
- nomassign="bilan_adm_date_debut",
- funoutlabel=gettext("Beginning date has been chosen\n",domain="R-stacomiR"),
- horodate=horodatedebut,
- silent=silent)
- bilan_adm at horodatefin<-choice_c(bilan_adm at horodatefin,
- nomassign="bilan_adm_date_fin",
- funoutlabel=gettext("Ending date has been chosen\n",domain="R-stacomiR"),
- horodate=horodatefin,
- silent=silent)
- bilan_adm at limit1hm<-choice_c(bilan_adm at limit1hm,as.character(limit1hm),"limit1hm")
- bilan_adm at limit2hm<-choice_c(bilan_adm at limit2hm,as.character(limit2hm),"limit2hm")
- validObject(bilan_adm)
- return(bilan_adm)
- })
-
-#' Split data according to the limits
-#' set in the limit1hm, and limit2hm arguments of the \link{BilanAgedemer-class}.
-#'
-#' If no value are provided in the limit1hm slot, an error is returned, if
-#' no value is provided in the limit2hm slot a default upper value for salmon
-#' size is taken to ensure all salmon are either of age 1 or 2, but no age 3 are
-#' returned
-#' @param object An object of class \code{\link{BilanAgedemer-class}}
-#' @param silent Default FALSE, if TRUE the program should no display messages
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @return An object of class \link{BilanAgedemer-class} with calculated data in slot calcdata
-#' @export
-setMethod("calcule",signature=signature("BilanAgedemer"),definition=function(object,silent) {
- #bilan_adm<-b_carlot
- bilan_adm<-object
- if(nrow(bilan_adm at data)==0) {
- funout(gettext("you are in deep shit",domain="R-stacomiR"), arret=TRUE)
- }
- adm=bilan_adm at data # we get the data.frame
- # the age already present in the database don't interest us there
- adm=adm[adm$car_par_code!='A124',]
- if (is.na(as.numeric(bilan_adm at limit1hm@label))) stop("internal error")
- # if no value, a dummy value of 2m
- if (is.na(as.numeric(bilan_adm at limit2hm@label))) bilan_adm at limit2hm@label<-2000
- lescoupes<-c(0,as.numeric(bilan_adm at limit1hm@label),as.numeric(bilan_adm at limit2hm@label),2001)
- adm$age<-cut(x=adm$car_valeur_quantitatif,breaks=lescoupes,labels=FALSE)
- bilan_adm at calcdata[["data"]]<-adm
- assign("bilan_adm",bilan_adm,envir_stacomi)
- return(bilan_adm)
- })
-
-
-#' Plots of various type for BilanAgedemer
-#'
-#' @param x An object of class \link{BilanAgedemer-class}
-#' @param plot.type Default "1"
-#' \itemize{
-#' \item{plot.type="1"}{density plot by sea age}
-#' \item{plot.type="2"}{Density plot by sea age and dc}
-#' }
-#' @param silent Default FALSE, if TRUE the program should no display messages.
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @aliases plot.BilanAgedemer plot.bilan_adm
-#' @export
-setMethod("plot", signature(x = "BilanAgedemer", y = "missing"), definition=function(x, plot.type="1", silent=FALSE){
- #require(ggplot2);plot.type="1"
- #browser()
- bilan_adm<-x
- plot.type<-as.character(plot.type)# to pass also characters
- if (!plot.type%in%c("1","2")) stop('plot.type must be 1,2')
- if (nrow(bilan_adm at calcdata[["data"]])==0) {
- if (!silent) funout(gettext("You need to launch computation first, clic on calc\n",domain="R-stacomiR"),arret=TRUE)
- }
- dat<-bilan_adm at calcdata[["data"]]
- # cols are using viridis::inferno(6,alpha=0.9)
- les_coupes=as.numeric(c(bilan_adm at limit1hm@label,bilan_adm at limit2hm@label))
-
-
- #################################################
- # plot.type =1 density plot
- #################################################
-
- if (plot.type=="1"){
-
- p<-ggplot(dat)+geom_histogram(aes(x=car_valeur_quantitatif,fill=factor(age)),binwidth=10,alpha=0.8)+
- geom_vline(xintercept=les_coupes,lty=2,lwd=1)+
- annotate("text",x=les_coupes,y=0,label=les_coupes,vjust=1,hjust=-0.2)+
- theme_minimal()+
- scale_fill_manual("Age",values=c("1"="#379ec6","2"="#173957","3"="#b09953"))+
- xlab("Size in mm")+
- ylab("Effectif")
- print(p)
- assign("p",p,envir=envir_stacomi)
- funout(gettext("The graphical object is written is env_stacomi, type p<-get('p',envir=envir_stacomi)",domain="R-stacomiR"))
-
- }
- ######################################
- # Migration according to stage, month and year
- ######################################
- # todo see of anotation is possible
- if (plot.type=="2"){
- p<-ggplot(dat)+geom_histogram(aes(x=car_valeur_quantitatif,fill=factor(age)),binwidth=10,alpha=0.8)+
- geom_vline(xintercept=les_coupes,lty=2,lwd=1)+
- theme_minimal()+
- scale_fill_manual("Age",values=c("1"="#379ec6","2"="#173957","3"="#b09953"))+
- xlab("Size in mm")+
- ylab("Effectif")+
- facet_grid(ope_dic_identifiant~.)
- print(p)
- assign("p",p,envir=envir_stacomi)
- funout(gettext("The graphical object is written is env_stacomi, type p<-get('p',envir=envir_stacomi)",domain="R-stacomiR"))
- }
-
- })
-
-#' summary for BilanAgedemer
-#' @param object An object of class \link{BilanAgedemer-class}
-#' @param silent Default FALSE, if TRUE the program should no display messages.
-#' @param ... Additional parameters
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
-setMethod("summary",signature=signature(object="BilanAgedemer"),definition=function(object,silent=FALSE,...){
- bilan_adm<-object
- dat<-bilan_adm at calcdata[["data"]]
- if (nrow(dat)==0) {
- if (!silent) funout(gettext("You need to launch computation first, clic on calc\n",domain="R-stacomiR"),arret=TRUE)
- }
- ndc=unique(dat$ope_dic_identifiant)
- result<-list()
- for (i in 1:length(ndc)){
- datdc<- dat[dat$ope_dic_identifiant==ndc[i],]
- dc_code<-bilan_adm at dc@data$dc_code[bilan_adm at dc@data$dc==ndc[i]]
- ouvrage<-
- gsub("[\r\n]", "", bilan_adm at dc@data[bilan_adm at dc@data$dc==bilan_adm at dc@dc_selectionne[i],"ouv_libelle"])
- dc<-as.character(unique(datdc$ope_dic_identifiant))
- result[[dc]]<-list()
- result[[dc]][["ouvrage"]]<-ouvrage
- print(noquote(stringr::str_c("Age Statistics for dam : ",ouvrage," CD=",dc_code)))
- print(noquote("========================"))
- print(table(datdc$age))
- result[[dc]][["age"]]<-table(datdc$age)
-
- }
- if (length(ndc)>1){
- print(noquote(stringr::str_c("Age Statistics total")))
- print(noquote("========================"))
- print(table(dat$age))
-
- }
- return(result)
- })
-
-#' Command line method to write the caracteristic "sea age" (car_par_code='A124')
-#' into the tj_caracteristiquelot_car table in the user's scheme
-#'
-#' The sea age caracteristic is calculated from the mesured or calculated size of salmon and with a size/age rule
-#' defined by the user . the name of the database is retreived from the odbc link
-#' defined in calcmig.csv
-#' @param object an object of class \link{BilanAgedemer-class}
-#' @param silent : Default FALSE, if TRUE the program should no display messages.
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
-setMethod("write_database",signature=signature("BilanAgedemer"),definition=function(object,silent=TRUE){
- # dbname="bd_contmig_nat"
- bilan_adm<-object
- host=get("sqldf.options",envir=envir_stacomi)["sqldf.host"]
- port=get("sqldf.options",envir=envir_stacomi)["sqldf.port"]
- # getting the database name
- dbname<-getdbname()
- calcdata<-bilan_adm at calcdata[["data"]]
- data_in_base<-bilan_adm at data
- if (nrow(calcdata)==0) {
- if (!silent) funout(gettext("You need to launch computation first, clic on calc\n",domain="R-stacomiR"),arret=TRUE)
- }
- if (class(bilan_adm)!="BilanAgedemer") stop("the bilan_adm should be of class BilanAgedemer")
- if (class(silent)!="logical") stop("the silent argument should be a logical")
- data_in_base<-data_in_base[data_in_base$car_par_code=='A124',]
- if (nrow(data_in_base)>0){
- supprime(bilan_adm,silent=silent)
- }
- #--------------
- # creating the table to import
- #--------------
- code_parametre_age='A124'
- code_methode_obtention="CALCULE"
- comment=gettextf("Age calculated from the size of fish compared to reference value %s for the limit between 1 sea winter and 2 sea winter fish, and %s for the limit between 2 sea winter fish and 3 sea winter fish",bilan_adm at limit1hm@label,bilan_adm at limit2hm@label)
- bam=data.frame(
- bilan_adm at calcdata$data$lot_identifiant,
- code_parametre_age,
- code_methode_obtention,
- as.integer(NA),
- bilan_adm at calcdata$data$age,
- as.integer(NA),
- comment,
- substr(toupper(get("sch",envir=envir_stacomi)),1,nchar(toupper(get("sch",envir=envir_stacomi)))-1)
- )
- #--------------
- # writing the table in the database
- #--------------
- baseODBC<-get("baseODBC",envir=envir_stacomi)
- sql<-stringr::str_c("INSERT INTO ",get("sch",envir=envir_stacomi),
- "tj_caracteristiquelot_car SELECT * FROM bam;")
- invisible(utils::capture.output(
- sqldf::sqldf(x=sql,
- drv="PostgreSQL",
- user=baseODBC["uid"],
- dbname=dbname,
- password=baseODBC["pwd"],
- host=host,
- port=port)
- ))
-
-
- if (!silent){
- funout(gettextf("Writing %s age values in the database \n",nrow(bam)))
- }
- })
-
-#' Method to print the command line of the object
-#' @param x An object of class BilanAgedemer
-#' @param ... Additional parameters passed to print
-#' @return NULL
-#' @author cedric.briand
-#' @export
-setMethod("print",signature=signature("BilanAgedemer"),definition=function(x,...){
- sortie1<-"bilan_adm=new('BilanAgedemer')"
- sortie2<-stringr::str_c("bilan_adm=choice_c(bilan_adm,",
- "dc=c(",stringr::str_c(x at dc@dc_selectionne,collapse=","),"),",
- "taxons=c(",stringr::str_c(shQuote(x at taxons@data$tax_nom_latin),collapse=","),"),",
- "stades=c(",stringr::str_c(shQuote(x at stades@data$std_code),collapse=","),"),",
- "par=c(",stringr::str_c(shQuote(x at par@par_selectionne),collapse=","),"),",
- "horodatedebut=",shQuote(strftime(x at horodatedebut@horodate,format="%d/%m/%Y %H-%M-%S")),
- ",horodatefin=",shQuote(strftime(x at horodatefin@horodate,format="%d/%m/%Y %H-%M-%S")),")")
- # removing backslashes
- funout(sortie1)
- funout(stringr::str_c(sortie2,...))
- return(invisible(NULL))
- })
-
-
-#' funplotBilanAgedemer
-#'
-#' assigns an object g in envir_stacomi for eventual modification of the plot
-#' @param h A handler, with action 1,2,3 or 4
-#' @param ... Additional parameters
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @keywords internal
-funplotBilanAgedemer = function(h,...) {
- bilan_adm<-get(x="bilan_adm",envir=envir_stacomi)
- bilan_adm<-charge(bilan_adm)
- bilan_adm<-connect(bilan_adm)
- bilan_adm<-calcule(bilan_adm)
- #plot.type is determined by button in h$action
- the_plot<-plot(bilan_adm,plot.type=h$action)
- print(the_plot)
-}
-
-
-#' table function
-#'
-#' funtableBilanAgedemer shows a table of results in gdf
-#' @param h hanlder passed by the graphical interface
-#' @param ... Additional parameters
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @keywords internal
-funtableBilanAgedemer = function(h,...) {
- bilan_adm=charge(bilan_adm)
- bilan_adm<-connect(bilan_adm)
- bilan_adm<-calcule(bilan_adm)
- bilan_adm<-print(bilan_adm)
-}
-
-
-
-#' supprime method for BilanMigrationInterannuelle class
-#' @param object An object of class \link{BilanAgedemer-class}
-#' @param silent Default FALSE, if TRUE the program should no display messages
-#' @return nothing
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
-setMethod("supprime",signature=signature("BilanAgedemer"),
- definition=function(object,silent=FALSE)
- {
- bilan_adm<-object
- data_in_base<-bilan_adm at data
- data_in_base<-data_in_base[data_in_base$car_par_code=='A124',]
- if (nrow(data_in_base)==0) {
- if (!silent) funout(gettext("No data to remove"),arret=TRUE)
- }
- requete=new("RequeteODBCwhere")
- requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
- requete at select=stringr::str_c("DELETE from ",get("sch",envir=envir_stacomi),"tj_caracteristiquelot_car ")
- requete at where=paste("WHERE car_lot_identifiant IN ",
- vector_to_listsql(data_in_base$lot_identifiant),
- " AND car_par_code='A124';",
- sep="")
- invisible(utils::capture.output(requete<-stacomirtools::connect(requete)))
- return(invisible(NULL))
- }
-
-)
\ No newline at end of file
Deleted: pkg/stacomir/R/BilanAnnuels.r
===================================================================
--- pkg/stacomir/R/BilanAnnuels.r 2017-06-18 18:36:42 UTC (rev 400)
+++ pkg/stacomir/R/BilanAnnuels.r 2017-06-20 08:50:12 UTC (rev 401)
@@ -1,610 +0,0 @@
-#' Class "BilanAnnuels"
-#'
-#' This class displays annual migration counts, for several counting device, taxa or stages.
-#' @include RefDC.r
-#' @include RefTaxon.r
-#' @include RefStades.r
-#' @include Ref_year.r
-#' @slot dc Object of class \code{\link{RefDC-class}}, the counting device, multiple values allowed
-#' @slot data Object of class \code{"data.frame"} data for bilan lot
-#' @slot taxons An object of class \code{\link{RefTaxon-class}}, multiple values allowed
-#' @slot stades An object of class \code{\link{RefStades-class}}, multiple values allowed
-#' @slot anneedebut Object of class \code{\link{Ref_year-class}}. Ref_year allows to choose year of beginning
-#' @slot anneefin Object of class \code{\link{Ref_year-class}}
-#' Ref_year allows to choose last year of the Bilan
-#' @aliases calcule.BilanAnnuels calcule.bilanannuels
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @family Bilan Objects
-#' @keywords classes
-#' @example inst/examples/bilanAnnuels_example.R
-#' @export
-setClass(Class="BilanAnnuels",representation=
- representation(
- dc="RefDC",
- taxons="RefTaxon",
- stades="RefStades",
- data="data.frame",
- anneedebut="Ref_year",
- anneefin="Ref_year"
- ),
- prototype=prototype(dc=new("RefDC"),
- taxons=new("RefTaxon"),
- stades=new("RefStades"),
- data=data.frame(),
- anneedebut=new("Ref_year"),
- anneefin=new("Ref_year")
- )
-)
-
-#' charge method for BilanAnnuels class
-#'
-#' Method used by the graphical interface to load data and check that all choices have
-#' been made by the user
-#' @param object An object of class \link{BilanAnnuels-class}
-#' @param silent Stops messages from being displayed if silent=TRUE, default FALSE
-#' @keywords internal
-setMethod("charge",signature=signature("BilanAnnuels"),
- definition=function(object,silent=FALSE){
- bilA<-object
- if (exists("refDC",envir_stacomi)) {
- bilA at dc<-get("refDC",envir_stacomi)
- } else {
- funout(gettext("You need to choose a counting device, clic on validate\n",domain="R-stacomiR"),arret=TRUE)
- }
- if (exists("refTaxon",envir_stacomi)) {
- bilA at taxons<-get("refTaxon",envir_stacomi)
- } else {
- funout(gettext("You need to choose a taxa, clic on validate\n",domain="R-stacomiR"),arret=TRUE)
- }
- if (exists("refStades",envir_stacomi)){
- bilA at stades<-get("refStades",envir_stacomi)
- } else
- {
- funout(gettext("You need to choose a stage, clic on validate\n",domain="R-stacomiR"),arret=TRUE)
- }
- if (exists("anneedebut",envir_stacomi)) {
- bilA at anneedebut<-get("anneedebut",envir_stacomi)
- } else {
- funout(gettext("You need to choose the starting year\n",domain="R-stacomiR"),arret=TRUE)
- }
- if (exists("anneefin",envir_stacomi)) {
- bilA at anneefin<-get("anneefin",envir_stacomi)
- } else {
- funout(gettext("You need to choose the ending year\n",domain="R-stacomiR"),arret=TRUE)
- }
- assign("bilanAnnuels",bilA,envir_stacomi)
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 401
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