From b68e88a7451018bdddc6880ba40fb7d0fb4a00fd Mon Sep 17 00:00:00 2001 From: David Beauchesne Date: Tue, 12 Nov 2024 13:58:09 -0500 Subject: [PATCH] update analysis for petroleum threat and update report --- _targets.R | 39 +- docs/1_research_compendium.html | 593 ++++++++++++++++++ docs/{1_shipping.html => 2_data.html} | 112 ++-- docs/{2_petroleum.html => 3_threats.html} | 218 ++----- docs/index.html | 36 +- docs/index_files/figure-html/fig-aoi-1.png | Bin 228631 -> 0 bytes docs/search.json | 118 +--- pubs/report/1_research_compendium.qmd | 5 + pubs/report/2_data.qmd | 53 ++ pubs/report/2_petroleum.qmd | 98 --- pubs/report/3_threats.qmd | 53 ++ pubs/report/_quarto.yml | 7 +- pubs/report/{3_VIIRS.qmd => del_VIIRS.qmd} | 0 .../{1_shipping.qmd => del_shipping.qmd} | 0 pubs/report/index.qmd | 6 +- .../petroleum_pollution_incidents.yaml | 51 +- .../ana_petroleum_pollution_incidents.R | 30 +- 17 files changed, 961 insertions(+), 458 deletions(-) create mode 100644 docs/1_research_compendium.html rename docs/{1_shipping.html => 2_data.html} (70%) rename docs/{2_petroleum.html => 3_threats.html} (56%) delete mode 100644 docs/index_files/figure-html/fig-aoi-1.png create mode 100644 pubs/report/1_research_compendium.qmd create mode 100644 pubs/report/2_data.qmd delete mode 100644 pubs/report/2_petroleum.qmd create mode 100644 pubs/report/3_threats.qmd rename pubs/report/{3_VIIRS.qmd => del_VIIRS.qmd} (100%) rename pubs/report/{1_shipping.qmd => del_shipping.qmd} (100%) diff --git a/_targets.R b/_targets.R index df18f20..ef97f72 100644 --- a/_targets.R +++ b/_targets.R @@ -1,11 +1,12 @@ +# Generated by pipedat: do not edit by hand # This file defines the pipeline for the ResearchCompendium project. library(targets) library(tarchetypes) library(pipedat) # To remove by the end of the project -tar_option_set(packages = c('curl', 'googleCloudStorageR', 'aws.s3', 'yaml', 'dplyr'), format = 'file') +tar_option_set(packages = c('curl', 'googleCloudStorageR', 'aws.s3', 'yaml', 'dplyr'), format = 'file') # To edit properly by the end of the project -tar_source('workspace/scripts/') +tar_source('workspace/scripts/') # To edit properly by the end of the project list( tar_target(bibtex_master, bibtex_master(), format = "file", cue = tar_cue(mode = "always")), list(list(tar_target(tg_835bc0d1_e57a_4e63_a327_908ee871bf2d_Scientific_article, @@ -448,35 +449,27 @@ list( }) "workspace/data/harvested/viirs_nighttime_light-1.0.0/raw" }, format = "file"))), - list(tar_target(tg_a726889e_848e_4d6c_8496_a7a772e70d85_istop_data_preparation, + list(tar_target(tg_a726889e_848e_4d6c_8496_a7a772e70d85_petroleum_pollution_incidents_istop, { ana_petroleum_pollution_incidents_istop(output_path = "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0", input_files = list(tg_835bc0d1_e57a_4e63_a327_908ee871bf2d_istop)) - "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0/istop_prep.gpkg" - }, format = "file"), tar_target(tg_a726889e_848e_4d6c_8496_a7a772e70d85_istop_diffusive_model, - { - ana_petroleum_pollution_incidents_istop_diffusive(output_path = "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0", - input_files = list(tg_a726889e_848e_4d6c_8496_a7a772e70d85_istop_data_preparation)) - "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0/petroleum_pollution_incidents_istop.tif" - }, format = "file"), tar_target(tg_a726889e_848e_4d6c_8496_a7a772e70d85_nasp_data_preparation, + "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0/petroleum_pollution_incidents_istop.gpkg" + }, format = "file"), tar_target(tg_a726889e_848e_4d6c_8496_a7a772e70d85_petroleum_pollution_incidents_nasp, { ana_petroleum_pollution_incidents_nasp(output_path = "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0", input_files = list(tg_e566fb8c_42d8_4013_8002_17af44a15a46_nasp)) - "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0/nasp_prep.gpkg" - }, format = "file"), tar_target(tg_a726889e_848e_4d6c_8496_a7a772e70d85_nasp_diffusive_model, - { - ana_petroleum_pollution_incidents_nasp_diffusive(output_path = "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0", - input_files = list(tg_a726889e_848e_4d6c_8496_a7a772e70d85_nasp_data_preparation)) - "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0/petroleum_pollution_incidents_nasp.tif" - }, format = "file"), tar_target(tg_a726889e_848e_4d6c_8496_a7a772e70d85_neec_data_preparation, + "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0/petroleum_pollution_incidents_nasp.gpkg" + }, format = "file"), tar_target(tg_a726889e_848e_4d6c_8496_a7a772e70d85_petroleum_pollution_incidents_neec, { ana_petroleum_pollution_incidents_neec(output_path = "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0", input_files = list(tg_56c710c3_1859_4eab_821f_e1e41dbbfd29_neec)) - "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0/neec_prep.gpkg" - }, format = "file"), tar_target(tg_a726889e_848e_4d6c_8496_a7a772e70d85_neec_diffusive_model, - { - ana_petroleum_pollution_incidents_neec_diffusive(output_path = "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0", - input_files = list(tg_a726889e_848e_4d6c_8496_a7a772e70d85_neec_data_preparation)) - "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0/petroleum_pollution_incidents_neec.tif" + "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0/petroleum_pollution_incidents_neec.gpkg" + }, format = "file"), tar_target(tg_a726889e_848e_4d6c_8496_a7a772e70d85_petroleum_pollution_incidents, + { + ana_petroleum_pollution_incidents(output_path = "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0", + input_files = list(tg_a726889e_848e_4d6c_8496_a7a772e70d85_petroleum_pollution_incidents_istop, + tg_a726889e_848e_4d6c_8496_a7a772e70d85_petroleum_pollution_incidents_nasp, + tg_a726889e_848e_4d6c_8496_a7a772e70d85_petroleum_pollution_incidents_neec)) + "workspace/data/analyzed/petroleum_pollution_incidents-1.0.0/petroleum_pollution_incidents.gpkg" }, format = "file")) ) diff --git a/docs/1_research_compendium.html b/docs/1_research_compendium.html new file mode 100644 index 0000000..3e7827c --- /dev/null +++ b/docs/1_research_compendium.html @@ -0,0 +1,593 @@ + + + + + + + + + +Mapping threats at sea to marine birds throughout their annual cycle to inform conservation and management in Atlantic Canada - 2  Research compendium + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ +
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2  Research compendium

+
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+ + + + + \ No newline at end of file diff --git a/docs/1_shipping.html b/docs/2_data.html similarity index 70% rename from docs/1_shipping.html rename to docs/2_data.html index cedb966..e2d89a7 100644 --- a/docs/1_shipping.html +++ b/docs/2_data.html @@ -7,7 +7,7 @@ -Mapping threats at sea to marine birds throughout their annual cycle to inform conservation and management in Atlantic Canada - 2  Shipping-based pollution +Mapping threats at sea to marine birds throughout their annual cycle to inform conservation and management in Atlantic Canada - 3  Data Sources Overview + @@ -50,7 +30,7 @@ - + @@ -88,35 +68,6 @@ } } - - - - @@ -129,7 +80,7 @@ - +