[Stacomir-commits] r614 - in pkg/stacomir: . R data dev dev/config doc inst/examples inst/po inst/po/fr/LC_MESSAGES man man/figures po tests/testthat vignettes www www/images
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jul 17 18:07:13 CEST 2022
Author: briand
Date: 2022-07-17 18:07:12 +0200 (Sun, 17 Jul 2022)
New Revision: 614
Added:
pkg/stacomir/R/funschema.R
pkg/stacomir/dev/config/
pkg/stacomir/dev/config/generate_data.R
pkg/stacomir/man/fun_schema.Rd
pkg/stacomir/man/plot-report_dc-missing-method.Rd
pkg/stacomir/man/plot-report_df-missing-method.Rd
pkg/stacomir/po/R-fr.po
pkg/stacomir/tests/testthat/test-00-functions.R
pkg/stacomir/vignettes/stacomir.html
pkg/stacomir/www/
pkg/stacomir/www/images/
pkg/stacomir/www/images/Logo.png
pkg/stacomir/www/images/Stations-de-comptage.jpg
pkg/stacomir/www/images/icon.png
pkg/stacomir/www/images/logo_AFB.png
pkg/stacomir/www/images/stacomi.png
pkg/stacomir/www/images/stacomi_logo.png
pkg/stacomir/www/images/video.png
pkg/stacomir/www/index.php
pkg/stacomir/www/rssclass.php
pkg/stacomir/www/styles.css
Removed:
pkg/stacomir/inst/po/stacomiR_fr_FR/
pkg/stacomir/man/chargecomplement-methods.Rd
pkg/stacomir/man/funbarchartDC.Rd
pkg/stacomir/man/funboxplotreport_sample_char.Rd
pkg/stacomir/man/fundensityreport_sample_char.Rd
pkg/stacomir/man/funpointreport_sample_char.Rd
pkg/stacomir/man/funtableDC.Rd
pkg/stacomir/man/graphe-methods.Rd
pkg/stacomir/man/plot-report_dc-ANY-method.Rd
pkg/stacomir/man/plot-report_df-ANY-method.Rd
pkg/stacomir/man/quitte.Rd
pkg/stacomir/man/stacomiR-package.Rd
pkg/stacomir/po/R-stacomiR_fr_FR.mo
pkg/stacomir/po/R-stacomiR_fr_FR.po
pkg/stacomir/tests/testthat/test-50-spell_checking.R
Modified:
pkg/stacomir/
pkg/stacomir/DESCRIPTION
pkg/stacomir/NAMESPACE
pkg/stacomir/NEWS.md
pkg/stacomir/R/create_generic.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/funtable.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/stacomiR-package.R
pkg/stacomir/R/utilities.R
pkg/stacomir/cran-comments.md
pkg/stacomir/data/r_ann.rda
pkg/stacomir/data/r_ann_adour.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/dev/03_deploy.R
pkg/stacomir/doc/stacomir.R
pkg/stacomir/doc/stacomir.Rmd
pkg/stacomir/doc/stacomir.html
pkg/stacomir/doc/stacomir.md
pkg/stacomir/inst/examples/report_annual-example.R
pkg/stacomir/inst/examples/report_dc-example.R
pkg/stacomir/inst/examples/report_ge_weight-example.R
pkg/stacomir/inst/examples/report_mig_char-example.R
pkg/stacomir/inst/examples/report_mig_interannual-example.R
pkg/stacomir/inst/examples/report_species-example.R
pkg/stacomir/inst/po/fr/LC_MESSAGES/R-stacomiR.mo
pkg/stacomir/man/barplot-report_annual-method.Rd
pkg/stacomir/man/calcule-report_ge_weight-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/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-report_env-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_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_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/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_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-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/colortable.Rd
pkg/stacomir/man/connect-report_annual-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_env-method.Rd
pkg/stacomir/man/connect-report_mig_interannual-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/envir_stacomi.Rd
pkg/stacomir/man/figures/
pkg/stacomir/man/figures/README-rmmstd-1.png
pkg/stacomir/man/figures/README-silver-1.png
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/funbarchartDF.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/funstat.Rd
pkg/stacomir/man/funtable.Rd
pkg/stacomir/man/get_org.Rd
pkg/stacomir/man/get_schema.Rd
pkg/stacomir/man/getvalue-ref_period-method.Rd
pkg/stacomir/man/graphdate.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_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_mig-method.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_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/setasqualitative-report_mig_char-method.Rd
pkg/stacomir/man/stacomi.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/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/po/R-stacomiR.pot
pkg/stacomir/tests/testthat/
pkg/stacomir/tests/testthat/.gitignore
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-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-14-report_ge_weight.R
pkg/stacomir/vignettes/
pkg/stacomir/vignettes/stacomir.Rmd
Log:
version 0.6.0.7
Index: pkg/stacomir
===================================================================
--- pkg/stacomir 2021-11-22 19:14:28 UTC (rev 613)
+++ pkg/stacomir 2022-07-17 16:07:12 UTC (rev 614)
Property changes on: pkg/stacomir
___________________________________________________________________
Modified: svn:ignore
## -9,3 +9,11 ##
test
.project
.settings
+.Rhistory
+.Rprofile
+.Rproj.user
+*.yml
+.git
+stacomir.Rproj
+Scripts
+.gitignore
Added: svn:global-ignores
## -0,0 +1 ##
+Meta
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2021-11-22 19:14:28 UTC (rev 613)
+++ pkg/stacomir/DESCRIPTION 2022-07-17 16:07:12 UTC (rev 614)
@@ -1,6 +1,6 @@
Package: stacomiR
-Version: 0.6.0
-Date: 2021-11-16
+Version: 0.6.0.7
+Date: 2022-07-16
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"),
@@ -24,6 +24,7 @@
'fun_write_monthly.R'
'fungraph.R'
'fungraph_glasseel.R'
+ 'funschema.R'
'funstat.R'
'funtable.R'
'ref_choice.R'
@@ -67,7 +68,7 @@
Depends:
R (>= 4.0.0),
methods,
- stacomirtools (>= 0.6.0)
+ stacomirtools (>= 0.6.0.1)
Imports:
magrittr,
intervals,
@@ -88,7 +89,8 @@
mgcv,
rlang,
pool,
- withr
+ withr,
+ scales
Suggests:
testthat,
viridis,
@@ -101,6 +103,6 @@
Lafage Denis [ctb],
Grall Sebastien [ctb]
Maintainer: Cedric Briand <cedric.briand00 at gmail.com>
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
NeedsCompilation: no
VignetteBuilder: knitr
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2021-11-22 19:14:28 UTC (rev 613)
+++ pkg/stacomir/NAMESPACE 2022-07-17 16:07:12 UTC (rev 614)
@@ -12,6 +12,7 @@
export(fun_report_mig_interannual)
export(fun_report_mig_mult)
export(fun_report_mig_mult_overlaps)
+export(fun_schema)
export(fun_stage_durif)
export(fun_write_monthly)
export(funstat)
@@ -55,6 +56,8 @@
import(xtable)
importFrom(Hmisc,capitalize)
importFrom(Hmisc,wtd.quantile)
+importFrom(dplyr,across)
+importFrom(dplyr,all_of)
importFrom(dplyr,desc)
importFrom(dplyr,do)
importFrom(dplyr,filter)
@@ -111,6 +114,7 @@
importFrom(pool,poolClose)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
+importFrom(scales,breaks_pretty)
importFrom(stats,AIC)
importFrom(stats,as.formula)
importFrom(stats,coef)
Modified: pkg/stacomir/NEWS.md
===================================================================
--- pkg/stacomir/NEWS.md 2021-11-22 19:14:28 UTC (rev 613)
+++ pkg/stacomir/NEWS.md 2022-07-17 16:07:12 UTC (rev 614)
@@ -1,3 +1,48 @@
+# stacomiR 0.6.0.7
+
+* created function to load schema
+* fixed problem with report_mig_char example (broken since new qualitative parameter for age was inserted in the database)
+* fixed problem with x scale ugly https://forgemia.inra.fr/stacomi/stacomir/-/issues/27 fixed
+
+
+# stacomiR 0.6.0.6
+
+* allows to load ggplots after plot for report_dc and report_df
+* fixes the problem of method for plot no longer working with signature(x = "report_dc", y = "ANY") and changed to
+"missing"
+* allows to pass arguments for colors in plot.report_dc
+* fixed problems with broken translation see https://forgemia.inra.fr/stacomi/stacomir/-/issues/20
+
+# stacomiR 0.6.0.5
+
+* fixes the way environmental stations are loaded.
+
+
+# stacomiR 0.6.0.4
+
+* fixed different output for parameters between charge and charge_with_filter from ref_parquan and ref_parqual.
+* the choice_c method also assigns subclasses in envir_stacomi.
+* updated the set_as_qualitative method to avoid bugs when running it several times.
+* rewrote tests
+
+
+# stacomiR 0.6.0.3
+
+* fixed problems for report interannual, allowing it for several DC including the graphs
+* fixed but in report_mig / report_mig_mug write database for numbers of type "PONCTUEL"
+* fixed problem in report_interannual, always writing the db when there is a difference between report_mig and report_annual e.g.
+when operations are overlapping between years
+
+# stacomiR 0.6.0.2
+
+* fixes the way taxa and stage are loaded
+* replaced some french labels in slots
+
+# stacomiR 0.6.0.1
+
+* Minor fix for Solaris, non portable path '~' now issue a warning asking the user for a new path
+* Code coverage 79.2 %
+
# stacomiR 0.6.0
stacomir based on gwidget was dropped from CRAN in May 2020, it has been completely reprogrammed to remove all dependence to
Modified: pkg/stacomir/R/create_generic.R
===================================================================
--- pkg/stacomir/R/create_generic.R 2021-11-22 19:14:28 UTC (rev 613)
+++ pkg/stacomir/R/create_generic.R 2022-07-17 16:07:12 UTC (rev 614)
@@ -7,7 +7,7 @@
setGeneric("choice_c", def = function(object, ...) standardGeneric("choice_c"))
#' Generic method to load referentials
#' @param object Object
-#' @param ... Additional parms
+#' @param ... Additional parm
#' @author cedric.briand
#' @export
setGeneric("charge", def = function(object, ...) standardGeneric("charge"))
@@ -43,6 +43,10 @@
#' @param object Object
#' @param ... Additional parms
#' @author cedric.briand
+#' @seealso \link{calcule.report_ge_weight}, \link{calcule.report_mig_char}, \link{calcule.report_mig_env},
+#' \link{calcule.report_mig_interannual},\link{calcule.report_mig_mult},\link{calcule.report_mig_mult},
+#' \link{calcule.report_sample_char}, \link{calcule.report_sea_age}, \link{calcule.report_silver_eel},
+#' \link{calcule.report_species}
#' @export
setGeneric("supprime", def = function(object, ...) standardGeneric("supprime"))
#' Generic method write_database
@@ -89,5 +93,5 @@
#'
#' envir_stacomi \code{envir_stacomi <- new.env(parent = baseenv())} is the
#' environment where most object created by the interface are stored
-#' @author Cedric Briand \email{cedric.briand'at'eptb-vilaine.fr}
+#' @author Cedric Briand \email{cedric.briand at eptb-vilaine.fr}
"envir_stacomi"
Modified: pkg/stacomir/R/fun_table_per_dis.R
===================================================================
--- pkg/stacomir/R/fun_table_per_dis.R 2021-11-22 19:14:28 UTC (rev 613)
+++ pkg/stacomir/R/fun_table_per_dis.R 2022-07-17 16:07:12 UTC (rev 614)
@@ -10,11 +10,12 @@
#' the period
#' @param libelle The postgres column ref.tr_typearretdisp_tar(libelle )description of the period
#' type
+#' @param color A named vector of color matching libelle.
#' @param date Boolean, should the function return a POSIXt or date value
#' @return A list
#' @note returns either POSIXt or date if date=TRUE
-#' @author Cedric Briand \email{cedric.briand'at'eptb-vilaine.fr}
-fun_table_per_dis <- function(typeperiode, tempsdebut, tempsfin, libelle, date = TRUE) {
+#' @author Cedric Briand \email{cedric.briand at eptb-vilaine.fr}
+fun_table_per_dis <- function(typeperiode, tempsdebut, tempsfin, libelle, color, date = TRUE) {
listeg = list()
for (j in 1:5) {
if (!date) {
@@ -21,8 +22,10 @@
# pour utilisation ulterieure de la classe Posixct
if (sum(unique(typeperiode) == j) > 0) {
choice_periode <- typeperiode == j
- liste <- list(debut = tempsdebut[choice_periode], fin = tempsfin[choice_periode],
- nom = libelle[choice_periode][1])
+ liste <- list(debut = tempsdebut[choice_periode],
+ fin = tempsfin[choice_periode],
+ nom = libelle[choice_periode][1],
+ color = color[choice_periode][1])
listeg[[as.character(j)]] <- liste
}
# pour utilisation ulterieure de la classe date
@@ -29,8 +32,11 @@
} else {
if (sum(unique(typeperiode) == j) > 0) {
choice_periode <- typeperiode == j
- liste <- list(debut = as.Date(tempsdebut[choice_periode]), fin = as.Date(tempsfin[choice_periode]),
- nom = as.character(libelle[choice_periode][1]))
+ liste <- list(
+ debut = as.Date(tempsdebut[choice_periode]),
+ fin = as.Date(tempsfin[choice_periode]),
+ nom = as.character(libelle[choice_periode][1]),
+ color = color[choice_periode][1])
listeg[[as.character(j)]] <- liste
}
}
Modified: pkg/stacomir/R/fun_write_monthly.R
===================================================================
--- pkg/stacomir/R/fun_write_monthly.R 2021-11-22 19:14:28 UTC (rev 613)
+++ pkg/stacomir/R/fun_write_monthly.R 2022-07-17 16:07:12 UTC (rev 614)
@@ -1,6 +1,6 @@
#' This writes monthly data in t_reportmensuel_mens table
#'
-#' @note This function is launched by fun_Ecritreport_daily, the resum
+#' @note This function is launched by fun_write_daily, the resum
#' dataset is created by the \link{funstat} function
#'
#'
@@ -10,37 +10,42 @@
#' @return No return value, called for side effects
#' @export
fun_write_monthly<-function(report_mig,resum,silent){
- # voir essai_table_reportmensuel.sql pour le format du tableau
- # below not the most elegant way to do it but efficient
-
- t_reportmigrationmensuel_bme=stacomirtools::killfactor(
+ t_reportmigrationmensuel_bme <- stacomirtools::killfactor(
cbind(report_mig at dc@dc_selected,
- report_mig at taxa@data$tax_code,
- report_mig at stage@data$std_code,
- unique(strftime(as.POSIXlt(report_mig at time.sequence),"%Y")), # une valeur
- rep(rownames(resum),(ncol(resum)-2)), # nb of month except columns report and label
+ report_mig at taxa@taxa_selected,
+ report_mig at stage@stage_selected,
+ as.integer(unique(strftime(as.POSIXlt(report_mig at time.sequence),"%Y"))), # une valeur bme_annee
+ rep(rownames(resum),(ncol(resum)-2)), # nb of month except columns report and label # bme_labelquantite
stack(resum, select=c(2:(ncol(resum)-1))),# stack re-ordonne les tab de donnees !
- format(Sys.time(), "%Y-%m-%d %H:%M:%S"),
+ as.POSIXct(format(Sys.time(), "%Y-%m-%d %H:%M:%S")),
get_org()
)
)
+ colnames(t_reportmigrationmensuel_bme) <-
+ c("bme_dis_identifiant","bme_tax_code","bme_std_code","bme_annee","bme_labelquantite","bme_valeur",
+ "bme_mois","bme_horodateexport","bme_org_code")
+ t_reportmigrationmensuel_bme$bme_mois<- as.integer(t_reportmigrationmensuel_bme$bme_mois)
+ # ecriture dans la base...
+ con <- new("ConnectionDB")
+ con <- connect(con)
+ on.exit(pool::poolClose(con at connection))
+ pool::dbWriteTable(con at connection,
+ name = "temp_t_reportmigrationmensuel_bme",
+ value=t_reportmigrationmensuel_bme,
+ temporary=TRUE,
+ overwrite=TRUE)
- # la requete pour la suppression
+ sql=paste(
+ "INSERT INTO ",
+ get_schema(),
+ "t_bilanmigrationmensuel_bme (",
+ "bme_dis_identifiant,bme_tax_code,bme_std_code,bme_annee,bme_labelquantite,bme_valeur,
+ bme_mois,bme_horodateexport,bme_org_code)",
+ " SELECT * FROM temp_t_reportmigrationmensuel_bme")
+ nline <- pool::dbExecute(con at connection, statement = sql)
-
- # ecriture dans la base...
-
- for (i in 1:nrow(t_reportmigrationmensuel_bme)) {
- sql=paste("INSERT INTO ",get_schema(),"t_bilanmigrationmensuel_bme (",
- "bme_dis_identifiant,bme_tax_code,bme_std_code,bme_annee,bme_labelquantite,bme_valeur,bme_mois,bme_horodateexport,bme_org_code)",
- " VALUES ('",paste(t_reportmigrationmensuel_bme[i,],collapse="','"),"');",sep="")
- con <- new("ConnectionDB")
- con <- connect(con)
- on.exit(pool::poolClose(con at connection))
- invisible(utils::capture.output(pool::dbExecute(con at connection, statement = sql)))
- } # end for
- if (!silent) funout(gettext("Writing monthly summary in the database\n",domain="R-stacomiR"))
+ if (!silent) funout(gettextf("Writing monthly summary (n=%s) in the database\n", nline, domain="R-stacomiR"))
return(invisible(NULL))
} # end function
Modified: pkg/stacomir/R/fungraph.R
===================================================================
--- pkg/stacomir/R/fungraph.R 2021-11-22 19:14:28 UTC (rev 613)
+++ pkg/stacomir/R/fungraph.R 2022-07-17 16:07:12 UTC (rev 614)
@@ -19,7 +19,7 @@
#' @param ... additional parameters passed to matplot, main, ylab, ylim, lty, pch, bty, cex.main,
#' it is currenly not a good idea to change xlim (numbers are wrong, the month plot covers all month, and legend placement is wrong
#' @return No return value, called for side effects
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @author Cedric Briand \email{cedric.briand at eptb-vilaine.fr}
fungraph = function(report_mig,
tableau,
time.sequence,
@@ -44,11 +44,11 @@
mypalette = c(
"working" = tp[4],
"stopped" = tp[6],
- "listeperiode1" = tp[1],
- "listeperiode2" = tp[2],
- "listeperiode3" = tp[3],
- "listeperiode4" = tp[5],
- "listeperiode5" = tp[7],
+ "Fonc normal" = tp[1],
+ "Arr ponctuel" = tp[2],
+ "Arr maintenance" = tp[3],
+ "Dysfonc" = tp[5],
+ "Non connu" = tp[7],
"ponctuel" = "indianred",
"expert" = "chartreuse2",
"calcule" = "deepskyblue",
@@ -60,11 +60,11 @@
mypalette = c(
"working" = color[1],
"stopped" = color[2],
- "listeperiode1" = color[3],
- "listeperiode2" = color[4],
- "listeperiode3" = color[5],
- "listeperiode4" = color[6],
- "listeperiode5" = color[7],
+ "Fonc normal" = color[3],
+ "Arr ponctuel" = color[4],
+ "Arr maintenance" = color[5],
+ "Dysfonc" = color[6],
+ "Non connu" = color[7],
"mesure" = color[8],
"calcule" = color[9],
"expert" = color[10],
@@ -352,6 +352,7 @@
tempsdebut = report_df at data$per_date_debut,
tempsfin = report_df at data$per_date_fin,
libelle = report_df at data$libelle,
+ color= mypalette[report_df at data$libelle],
date = FALSE
)
nomperiode <- vector()
@@ -361,13 +362,13 @@
#recuperation du vecteur de noms (dans l'ordre) e partir de la liste
nomperiode[j] <- substr(listeperiode[[j]]$nom, 1, 17)
#ecriture pour chaque type de periode
- color_periode = stringr::str_c("listeperiode", j)
+ color_periode = listeperiode[[j]]$color
rect(
xleft = graphdate(listeperiode[[j]]$debut),
ybottom = 1.1,
xright = graphdate(listeperiode[[j]]$fin),
ytop = 2,
- col = mypalette[color_periode],
+ col = color_periode,
border = NA,
lwd = 1
)
@@ -379,7 +380,7 @@
y = 1.2,
legend = c(gettext("stop", domain = "R-stacomiR"), nomperiode),
pch = c(15, 15),
- col = c(mypalette["working"], mypalette["stopped"], mypalette[color_periodes]),
+ col = c(mypalette["working"], mypalette["stopped"], color_periodes),
bty = "n",
ncol = 7,
text.width = (fin - debut) / 10
@@ -474,6 +475,7 @@
tempsdebut = report_dc at data$per_date_debut,
tempsfin = report_dc at data$per_date_fin,
libelle = report_dc at data$libelle,
+ color= mypalette[report_df at data$libelle],
date = FALSE
)
nomperiode <- vector()
@@ -480,13 +482,13 @@
color_periodes <- vector()
for (j in 1:length(listeperiode)) {
nomperiode[j] <- substr(listeperiode[[j]]$nom, 1, 17)
- color_periode = stringr::str_c("listeperiode", j)
+ color_periode <- listeperiode[[j]]$color
rect(
xleft = graphdate(listeperiode[[j]]$debut),
ybottom = 1.1,
xright = graphdate(listeperiode[[j]]$fin),
ytop = 2,
- col = mypalette[color_periode],
+ col = color_periode,
border = NA,
lwd = 1
)
@@ -497,7 +499,7 @@
y = 1.2,
legend = gettext("working", "stopped", nomperiode, domain = "R-stacomiR"),
pch = c(15, 15),
- col = c(mypalette["working"], mypalette["stopped"], mypalette[color_periodes]),
+ col = c(mypalette["working"], mypalette["stopped"], color_periodes),
bty = "n",
ncol = length(listeperiode) + 2,
text.width = (fin - debut) / 10
Modified: pkg/stacomir/R/fungraph_glasseel.R
===================================================================
--- pkg/stacomir/R/fungraph_glasseel.R 2021-11-22 19:14:28 UTC (rev 613)
+++ pkg/stacomir/R/fungraph_glasseel.R 2022-07-17 16:07:12 UTC (rev 614)
@@ -20,615 +20,615 @@
#' @param ... additional parameters passed to plot, main, ylab, cex.main, font.main, type, xlim, ylim, lty, bty, pch
#' it is not possible to change xlim
#' @return No return value, called for side effects
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
+#' @author Cedric Briand \email{cedric.briand at eptb-vilaine.fr}
fungraph_glasseel = function(report_mig,
- table,
- time.sequence,
- taxa,
- stage,
- dc = null,
- silent,
- color = NULL,
- color_ope = NULL,
- ...) {
+ table,
+ time.sequence,
+ taxa,
+ stage,
+ dc = null,
+ silent,
+ color = NULL,
+ color_ope = NULL,
+ ...) {
oldpar <- par(no.readonly = TRUE)
on.exit(par(oldpar))
- # color=null
- # color calculation
- if (is.null(color)) {
- tp <- RColorBrewer::brewer.pal(12, "Paired")
- mypalette = c(
- "working" = tp[4],
- # green
- "stopped" = tp[6],
- # red
- "listeperiode1" = tp[1],
- "listeperiode2" = tp[2],
- "listeperiode3" = tp[3],
- "listeperiode4" = tp[5],
- "listeperiode5" = tp[7],
- "eff" = tp[8],
- #orange
- "weight" = tp[10],
- #purple
- "unused1" = tp[11],
- "unused1" = tp[12]
- )
- } else {
- if (length(color) != 11)
- stop("The length of color must be 11")
- mypalette = c(
- "working" = color[1],
- "stopped" = color[2],
- "listeperiode1" = color[3],
- "listeperiode2" = color[4],
- "listeperiode3" = color[5],
- "listeperiode4" = color[6],
- "listeperiode5" = color[7],
- "eff" = color[8],
- "weight" = color[9],
- "unused1" = color[10],
- "unused2" = color[11]
- )
- }
-
-
- if (is.null(color_ope)) {
- if (stacomirtools::is.odd(dc))
- brew = "Paired"
- else
- brew = "Accent"
- color_ope = RColorBrewer::brewer.pal(8, brew)
- }
-
- if (is.null(dc))
- dc = report_mig at dc@dc_selected[1]
- annee = paste(unique(strftime(as.POSIXlt(time.sequence), "%Y")), collapse =
- ",")
- mois = months(time.sequence)
- jour = strftime(as.POSIXlt(time.sequence), "%j")
- index = table$No.pas + 1
- eff = table$Effectif_total
- eff.p = table$Effectif_total.p
- debut = unclass(as.Date(time.sequence[min(index)]))[[1]]
- fin = unclass(as.Date(time.sequence[max(index)]))[[1]]
- eff[eff == 0] <- NA #for graph need
- eff.p[eff.p == 0] <- NA
- dis_commentaire = as.character(report_mig at dc@data$dis_commentaires[report_mig at dc@data$dc %in%
- dc])
- if (!silent)
- funout(gettextf("Glass eels graph %s\n", dis_commentaire))
- ###################################
- # Graph annuel couvrant sequence >0
- ####################################
-
- vec <- c(rep(1, 15), rep(2, 2), rep(3, 2), 4, rep(5, 6))
- mat <- matrix(vec, length(vec), 1)
- layout(mat)
- #par("bg"=grDevices::gray(0.8))
- graphics::par("mar" = c(3, 4, 3, 2) + 0.1)
- dots <- list(...)
- if (!"main" %in% names(dots))
- main = gettextf("Glass eels graph %s, %s, %s, %s",
- dis_commentaire,
- taxa,
- stage,
- annee,
- domain = "R-stacomiR")
- else
- main = dots[["main"]]
- if (!"ylab" %in% names(dots))
- ylab = gettext("Number of glass eels (x1000)", domain = "R-stacomiR")
- else
- ylab = dots[["ylab"]]
- if (!"cex.main" %in% names(dots))
- cex.main = 1
- else
- cex.main = dots[["cex.main"]]
- if (!"font.main" %in% names(dots))
- font.main = 1
- else
- font.main = dots[["font.main"]]
- if (!"type" %in% names(dots))
- type = "h"
- else
- type = dots[["type"]]
- if (!"xlim" %in% names(dots))
- xlim = c(debut, fin)
- else
- xlim = dots[["xlim"]]
- if (!"ylim" %in% names(dots))
- ylim = c(0, max(eff / 1000, na.rm = TRUE)) * 1.2
- else
- xlim = c(debut, fin)#dots[["xlim"]] # currently this argument is ignored
- if (!"cex" %in% names(dots))
- cex = 1
- else
- cex = dots[["cex"]]
- if (!"lty" %in% names(dots))
- lty = 1
- else
- lty = dots[["lty"]]
- if (!"pch" %in% names(dots))
- pch = 16
- else
- pch = dots[["pch"]]
- if (!"bty" %in% names(dots))
- bty = "l"
- else
- bty = dots[["bty"]]
- plot(
- x = as.Date(time.sequence, "Europe/Paris"),
- y = eff / 1000,
- col = mypalette["eff"],
- type = type,
- xlim = xlim,
- ylim = ylim,
- lty = lty,
- xaxt = "n",
- ylab = ylab,
- #xlab="date",
- cex.main = cex.main,
- font.main = font.main,
- main = main,
- cex = cex,
- pch = pch,
- bty = bty
- )
- #print(plot,position = c(0, .3, 1, .9), more = TRUE)
- r <- as.Date(round(range(time.sequence), "day"))
- axis.Date(1, at = seq(r[1], r[2], by = "weeks"), format = "%d-%b")
-
- points(
- as.Date(time.sequence, "Europe/Paris"),
- eff.p / 1000,
- type = type,
- lty = lty,
- col = mypalette["weight"]
- )
-
- legend(
- x = "topright",
- inset = 0.01,
- legend = gettext("weighted", "counted", domain = "R-stacomiR"),
- pch = c(16, 16),
- col = mypalette[c("weight", "eff")]
- )
- ######################################
- # text labels for numbers and weights
- ######################################
- text(
- x = debut + (fin - debut) / 8,
- y = max(eff / 1000, na.rm = TRUE) * 1.15,
- labels = paste(round(
- sum(table$poids_depuis_effectifs, na.rm = TRUE) / 1000, 2
- ), " kg"),
- col = mypalette["eff"],
- adj = 1,
- cex = cex
- )
- text(
- x = debut + 3 * (fin - debut) / 8 ,
- y = max(eff / 1000, na.rm = TRUE) * 1.15,
- labels = paste("N=", round(
- sum(table$Effectif_total.e, na.rm = TRUE)
- )),
- col = mypalette["eff"],
- adj = 1,
- cex = cex
- )
- text(
- x = debut + (fin - debut) / 8,
- y = max(eff / 1000, na.rm = TRUE) * 1.2,
- labels = paste(round(
- sum(table$Poids_total, na.rm = TRUE) / 1000, 2
- ), " kg"),
- col = mypalette["weight"],
- adj = 1,
- cex = cex
- )
- text(
- x = debut + 3 * (fin - debut) / 8,
- y = max(eff / 1000, na.rm = TRUE) * 1.2,
- labels = paste("N=", round(sum(eff.p, na.rm = TRUE))),
- col = mypalette["weight"],
- adj = 1,
- cex = cex
- )
- text(
- x = debut + 3 + (fin - debut) / 8,
- y = max(eff / 1000, na.rm = TRUE) * 1.1,
- labels = paste(round(
- sum(table$Poids_total, table$poids_depuis_effectifs, na.rm = TRUE) / 1000,
- 2
- ), " kg"),
- col = "black",
- adj = 1,
- cex = cex
- )
- text(
- x = debut + 3 * (fin - debut) / 8,
- y = max(eff / 1000, na.rm = TRUE) * 1.1,
- labels = paste("N=", round(sum(eff, na.rm = TRUE))),
- col = "black",
- adj = 1,
- cex = cex
- )
- segments(
- x0 = debut,
- y0 = max(eff / 1000, na.rm = TRUE) * 1.125,
- x1 = debut + 3 * (fin - debut) / 8,
- y1 = max(eff / 1000, na.rm = TRUE) * 1.125
- )
-
-
- report_ope <- get("report_ope", envir = envir_stacomi)
- t_operation_ope <-
- report_ope at data[report_ope at data$ope_dic_identifiant == dc, ]
- dif = difftime(t_operation_ope$ope_date_fin,
- t_operation_ope$ope_date_debut,
- units = "days")
-
- if (!silent) {
- funout(gettextf(
- "number of operations =%s\n",
- nrow(t_operation_ope),
- domain = "R-stacomiR"
- ))
- funout(gettextf("average trapping time = %sdays\n", round(mean(
- as.numeric(dif)
- ), 2), domain = "R-stacomiR"))
- funout(gettextf("maximum term = %sdays\n", round(max(
- as.numeric(dif)
- ), 2), domain = "R-stacomiR"))
- funout(gettextf("minimum term = %sdays\n", round(min(
- as.numeric(dif)
- ), 2), domain = "R-stacomiR"))
- }
-
- df <- report_mig at dc@data$df[report_mig at dc@data$dc == dc]
- report_df <- get("report_df", envir = envir_stacomi)
- report_dc <- get("report_dc", envir = envir_stacomi)
- report_df at data <-
- report_df at data[report_df at data$per_dis_identifiant == df, ]
- report_dc at data <-
- report_dc at data[report_dc at data$per_dis_identifiant == dc, ]
-
-
- graphdate <- function(vectordate) {
- attributes(vectordate) <- NULL
- unclass(vectordate)
- }
-
-
- ###################################
- # creation d'un graphique vide (2)
- ###################################
-
- graphics::par("mar" = c(0, 4, 0, 2) + 0.1)
- plot(
- as.Date(time.sequence),
- seq(0, 3, length.out = length(eff)),
- xlim = xlim,
- type = "n",
- xlab = "",
- xaxt = "n",
- yaxt = "n",
- ylab = gettext("Fishway", domain = "R-stacomiR"),
- bty = "n",
- cex = cex + 0.2
- )
-
- ###################################
- # Time for dc operation
- ###################################
-
- if (dim(report_df at data)[1] == 0) {
- rect(
- xleft = debut,
- ybottom = 2.1,
- xright = fin,
- ytop = 3,
- col = "grey",
- border = NA,
- lwd = 1
- )
- rect(
- xleft = debut,
- ybottom = 1.1,
- xright = fin,
- ytop = 2,
- col = "grey40",
- border = NA,
- lwd = 1
- )
- legend(
- x = "bottom",
- legend = gettext("Unknown working", "Unknow operation type", domain =
- "R-stacomiR"),
- pch = c(16, 16),
- col = c("grey", "grey40"),
- horiz = TRUE,
- bty = "n"
- )
-
-
- } else {
- # si il sort quelque chose
- if (sum(report_df at data$per_etat_fonctionnement == 1) > 0) {
- rect(
- xleft = graphdate(as.Date(report_df at data$per_date_debut[report_df at data$per_etat_fonctionnement ==
- 1])),
- ybottom = 2.1,
- xright = graphdate(as.Date(report_df at data$per_date_fin[report_df at data$per_etat_fonctionnement ==
- 1])),
- ytop = 3,
- col = mypalette["working"],
- border = NA,
- lwd = 1
- )
- }
- if (sum(report_df at data$per_etat_fonctionnement == 0) > 0) {
- rect(
- xleft = graphdate(as.Date(report_df at data$per_date_debut[report_df at data$per_etat_fonctionnement ==
- 0])),
- ybottom = 2.1,
- xright = graphdate(as.Date(report_df at data$per_date_fin[report_df at data$per_etat_fonctionnement ==
- 0])),
- ytop = 3,
- col = mypalette["stopped"],
- border = NA,
- lwd = 1
- )
- }
- #creation d'une liste par categorie d'arret contenant vecteurs dates
- listeperiode <-
- fun_table_per_dis(
- typeperiode = report_df at data$per_tar_code,
- tempsdebut = report_df at data$per_date_debut,
- tempsfin = report_df at data$per_date_fin,
- libelle = report_df at data$libelle
- )
- nomperiode <- vector()
- color_periodes <-
- vector() # a vector of colors, one per period type in listeperiode
- for (j in 1:length(listeperiode)) {
- #recuperation du vecteur de noms (dans l'ordre) e partir de la liste
- nomperiode[j] <- substr(listeperiode[[j]]$nom, 1, 17)
- #ecriture pour chaque type de periode
- color_periode = stringr::str_c("listeperiode", j)
- rect(
- xleft = graphdate(listeperiode[[j]]$debut),
- ybottom = 1.1,
- xright = graphdate(listeperiode[[j]]$fin),
- ytop = 2,
- col = mypalette[color_periode],
- border = NA,
- lwd = 1
- )
- color_periodes <- c(color_periodes, color_periode)
- }
- # below the colors for operation are from 4 to 3+ntypeoperation
- legend (
- x = debut,
- y = 1.2,
- legend = gettext("working", "stopped", nomperiode, domain = "R-stacomiR"),
- pch = c(15, 15),
- col = c(mypalette["working"], mypalette["stopped"], mypalette[color_periodes]),
- bty = "n",
- ncol = length(listeperiode) + 2,
- text.width = (fin - debut) / 10
- )
- }
-
- ###################################
- # creation d'un graphique vide (3=DC)
- ###################################
-
-
- graphics::par("mar" = c(0, 4, 0, 2) + 0.1)
- plot(
- as.Date(time.sequence),
- seq(0, 3, length.out = length(eff)),
- xlim = xlim,
- type = "n",
- xlab = "",
- xaxt = "n",
- yaxt = "n",
- ylab = gettext("CD", domain = "R-stacomiR"),
- bty = "n",
- cex = cex + 0.2
- )
- ###################################
- # time for DC (counting device) operation
- ###################################
-
-
- if (dim(report_dc at data)[1] == 0) {
- rect(
- xleft = debut,
- ybottom = 2.1,
- xright = fin,
- ytop = 3,
- col = "grey",
- border = NA,
- lwd = 1
- )
-
- rect(
- xleft = debut,
- ybottom = 1.1,
- xright = fin,
- ytop = 2,
- col = "grey40",
- border = NA,
- lwd = 1
- )
- legend(
- x = "bottom",
- legend = gettext("Unknown working", "Unknow operation type", domain =
- "R-stacomiR"),
- pch = c(16, 16),
- col = c("grey", "grey40"),
- horiz = TRUE,
- #ncol=5,
- bty = "n"
- )
-
-
- } else {
- if (sum(report_dc at data$per_etat_fonctionnement == 1) > 0) {
- rect(
- xleft = graphdate(as.Date(report_dc at data$per_date_debut[report_dc at data$per_etat_fonctionnement ==
- 1])),
- ybottom = 2.1,
- xright = graphdate(as.Date(report_dc at data$per_date_fin[report_dc at data$per_etat_fonctionnement ==
- 1])),
- ytop = 3,
- col = mypalette["working"],
- border = NA,
- lwd = 1
- )
- }
- if (sum(report_dc at data$per_etat_fonctionnement == 0) > 0)
- {
- rect(
- xleft = graphdate(as.Date(report_dc at data$per_date_debut[report_dc at data$per_etat_fonctionnement ==
- 0])),
- ybottom = 2.1,
- xright = graphdate(as.Date(report_dc at data$per_date_fin[report_dc at data$per_etat_fonctionnement ==
- 0])),
- ytop = 3,
- col = mypalette["stopped"],
- border = NA,
- lwd = 1
- )
- }
- listeperiode <-
- fun_table_per_dis(
- typeperiode = report_dc at data$per_tar_code,
- tempsdebut = report_dc at data$per_date_debut,
- tempsfin = report_dc at data$per_date_fin,
- libelle = report_dc at data$libelle
- )
- nomperiode <- vector()
- color_periodes <- vector()
- for (j in 1:length(listeperiode)) {
- nomperiode[j] <- substr(listeperiode[[j]]$nom, 1, 17)
- color_periode = stringr::str_c("listeperiode", j)
- rect(
- xleft = graphdate(listeperiode[[j]]$debut),
- ybottom = 1.1,
- xright = graphdate(listeperiode[[j]]$fin),
- ytop = 2,
- col = mypalette[color_periode],
- border = NA,
- lwd = 1
- )
- color_periodes <- c(color_periodes, color_periode)
- }
-
- legend (
- x = debut,
- y = 1.2,
- legend = gettext("working", "stopped", nomperiode, domain = "R-stacomiR"),
- pch = c(15, 15),
- col = c(mypalette["working"], mypalette["stopped"], mypalette[color_periodes]),
- bty = "n",
- ncol = length(listeperiode) + 2,
- text.width = (fin - debut) / 10
- )
- }
-
- ###################################
- # creation d'un graphique vide (4=OP)
- ###################################
-
-
- graphics::par("mar" = c(0, 4, 0, 2) + 0.1)
- plot(
- as.Date(time.sequence),
- seq(0, 1, length.out = length(eff)),
- xlim = xlim,
- type = "n",
- xlab = "",
- xaxt = "n",
- yaxt = "n",
- ylab = gettext("Op", domain = "R-stacomiR"),
- bty = "n",
- cex = cex + 0.2
- )
- ###################################
- # operations
- ###################################
- rect(
- xleft = graphdate(as.Date(t_operation_ope$ope_date_debut)),
- ybottom = 0,
- xright = graphdate(as.Date(t_operation_ope$ope_date_fin)),
- ytop = 1,
- col = color_ope,
- border = NA,
- lwd = 1
- )
-
-
- ###################################
- # Graph mensuel
- ####################################
- graphics::par("mar" = c(4, 4, 1, 2) + 0.1)
- petitmois = substr(as.character(mois), 1, 3)
- effmois = tapply(eff, mois, sum, na.rm = TRUE)[c(5, 4, 9, 2, 8, 7, 6, 1, 12, 11, 10, 3)]
- effmois.p = tapply(eff.p, mois, sum, na.rm = TRUE)[c(5, 4, 9, 2, 8, 7, 6, 1, 12, 11, 10, 3)]
- effmois <- data.frame("eff" = effmois)
- effmois.p <- data.frame("eff" = effmois.p)
- tablemens <-
- rbind(
- cbind(
- "eff" = effmois - effmois.p,
- "type" = 2,
- "mois" = 1:12
- ),
- cbind(effmois.p, "type" = "1", "mois" = 1:12)
- )
-
-
- superpose.polygon <- lattice::trellis.par.get("superpose.polygon")
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 614
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