Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/articles/index.html b/articles/index.html index 000dbbc..3582b0c 100644 --- a/articles/index.html +++ b/articles/index.html @@ -50,7 +50,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/index.html b/reference/index.html index 210fd10..1f2db44 100644 --- a/reference/index.html +++ b/reference/index.html @@ -133,7 +133,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/make_receiver_push_summary.html b/reference/make_receiver_push_summary.html index 6cd527e..f03f914 100644 --- a/reference/make_receiver_push_summary.html +++ b/reference/make_receiver_push_summary.html @@ -170,7 +170,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/make_tag_push_summary.html b/reference/make_tag_push_summary.html index 865d077..d31e28c 100644 --- a/reference/make_tag_push_summary.html +++ b/reference/make_tag_push_summary.html @@ -124,7 +124,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/match_map-1.png b/reference/match_map-1.png index 33d9a54..4a21793 100644 Binary files a/reference/match_map-1.png and b/reference/match_map-1.png differ diff --git a/reference/match_map.html b/reference/match_map.html index 279b262..460ba4c 100644 --- a/reference/match_map.html +++ b/reference/match_map.html @@ -74,7 +74,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/match_table.html b/reference/match_table.html index d6e6022..bd86868 100644 --- a/reference/match_table.html +++ b/reference/match_table.html @@ -78,7 +78,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/matched_abacus.html b/reference/matched_abacus.html index 1b53d9e..15f34d4 100644 --- a/reference/matched_abacus.html +++ b/reference/matched_abacus.html @@ -77,7 +77,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/otn_query.html b/reference/otn_query.html index f43dc2c..2fd4057 100644 --- a/reference/otn_query.html +++ b/reference/otn_query.html @@ -67,9 +67,9 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/otndo-package.html b/reference/otndo-package.html index 1c17f7e..3b4f3f0 100644 --- a/reference/otndo-package.html +++ b/reference/otndo-package.html @@ -63,7 +63,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/prep_station_spatial.html b/reference/prep_station_spatial.html index a0d2a94..4c464da 100644 --- a/reference/prep_station_spatial.html +++ b/reference/prep_station_spatial.html @@ -76,7 +76,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/project_contacts.html b/reference/project_contacts.html index b72b912..2d86dbd 100644 --- a/reference/project_contacts.html +++ b/reference/project_contacts.html @@ -109,7 +109,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/remaining_transmitters.html b/reference/remaining_transmitters.html index d0f20dd..aa7bd46 100644 --- a/reference/remaining_transmitters.html +++ b/reference/remaining_transmitters.html @@ -113,7 +113,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/station_table.html b/reference/station_table.html index bca5499..39e720c 100644 --- a/reference/station_table.html +++ b/reference/station_table.html @@ -131,7 +131,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/temporal_distribution.html b/reference/temporal_distribution.html index 7ca3d38..d61e8ee 100644 --- a/reference/temporal_distribution.html +++ b/reference/temporal_distribution.html @@ -97,7 +97,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/reference/utilities-make.html b/reference/utilities-make.html index a021cdf..a391911 100644 --- a/reference/utilities-make.html +++ b/reference/utilities-make.html @@ -92,7 +92,7 @@Site built with pkgdown 2.1.0.
+Site built with pkgdown 2.1.1.
diff --git a/search.json b/search.json index e5e8ba4..855ff67 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https://otndo.obrien.page/articles/data-push-summaries.html","id":"getting-your-files","dir":"Articles","previous_headings":"","what":"Getting your files","title":"Data Push Summaries","text":"first thing ’ll want gather OTN matched detections detection extract files.","code":""},{"path":"https://otndo.obrien.page/articles/data-push-summaries.html","id":"otn-projects","dir":"Articles","previous_headings":"Getting your files","what":"OTN projects","title":"Data Push Summaries","text":"’ll use data Trudel 2018 (https://members.oceantrack.org/data/repository/pbsm) show might work. First, ’ll download files. Now, just note files saved. make easier pass smmary functions later. can matched detections","code":"# Create a folder in your temporary directory to hold the sample files td <- file.path(tempdir(), \"otndo_test_files\") dir.create(td) # Download deployment metadata download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/\", \"data-and-metadata/2018/pbsm-instrument-deployment-short-form-2018.xls\" ), destfile = file.path(td, \"pbsm-instrument-deployment-short-form-2018.xls\"), # Note \"mode = 'wb' is needed to download Excel files mode = \"wb\" ) # Download qualified detections download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/\", \"detection-extracts/pbsm_qualified_detections_2018.zip\" ), destfile = file.path(td, \"pbsm_qualified_detections_2018.zip\") ) # Download unqualified detections download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/\", \"detection-extracts/pbsm_unqualified_detections_2018.zip\" ), destfile = file.path(td, \"pbsm_unqualified_detections_2018.zip\") ) qualified_otn <- file.path(td, \"pbsm_qualified_detections_2018.zip\") unqualified_otn <- file.path(td, \"pbsm_unqualified_detections_2018.zip\") deployment_otn <- file.path(td, \"pbsm-instrument-deployment-short-form-2018.xls\") download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/\", \"detection-extracts/pbsm_matched_detections_2018.zip\" ), destfile = file.path(td, \"pbsm_matched_detections_2018.zip\") ) matched_otn <- file.path(td, \"pbsm_matched_detections_2018.zip\")"},{"path":"https://otndo.obrien.page/articles/data-push-summaries.html","id":"actmatos-projects","dir":"Articles","previous_headings":"Getting your files","what":"ACT/MATOS projects","title":"Data Push Summaries","text":"’re member ACT (project lives MATOS database), can access files via matos package. Two functions matos wrap otndo’s make_*_summary functions automatically download necessary files . See matos::matos_tag_summary matos::matos_receiver_summary details.","code":""},{"path":"https://otndo.obrien.page/articles/data-push-summaries.html","id":"fact-projects","dir":"Articles","previous_headings":"Getting your files","what":"FACT projects","title":"Data Push Summaries","text":"time writing, streamlined way get FACT data Research Workspace. moving next steps, make sure necessary files downloaded.","code":""},{"path":"https://otndo.obrien.page/articles/data-push-summaries.html","id":"running-the-functions","dir":"Articles","previous_headings":"","what":"Running the functions","title":"Data Push Summaries","text":"summary functions conduct bit data cleaning front end run everything Quarto RMarkdown template report. functions use Quarto default, RMarkdown selected : Quarto installed computer, rmd argument set TRUE. Functionality identical make_tag_push_summary:","code":"# Compiles with Quarto (default) make_receiver_push_summary( qualified = qualified_otn, unqualified = unqualified_otn, deployment = deployment_otn, rmd = F ) # Compiles with RMarkdown make_receiver_push_summary( qualified = qualified_otn, unqualified = unqualified_otn, deployment = deployment_otn, rmd = T ) make_tag_push_summary(matched = matched_otn)"},{"path":"https://otndo.obrien.page/articles/data-push-summaries.html","id":"new-matches-since-a-certain-date","dir":"Articles","previous_headings":"","what":"New matches “since” a certain date","title":"Data Push Summaries","text":"Usually want know changed since OTN nodes crossed talked (“data push”). usually get within-node detections, well. nominally scheduled February, July, October. Crossover dates stored within otndo; package updated new dates data push occurs. can also provide date “since” argument see summary data updated since date.","code":"make_tag_push_summary( matched = matched_otn, since = \"2018-05-01\" )"},{"path":"https://otndo.obrien.page/articles/data-push-summaries.html","id":"suggestions-to-improve-the-push-summaries","dir":"Articles","previous_headings":"","what":"Suggestions to improve the push summaries","title":"Data Push Summaries","text":"always open suggestions added change make useful . Please open issue GitHub email thoughts.","code":""},{"path":"https://otndo.obrien.page/articles/data-push-summaries.html","id":"errors-and-how-to-fix-them","dir":"Articles","previous_headings":"","what":"Errors and how to fix them","title":"Data Push Summaries","text":"error created old version mapview package (pre-June 2021) package’s switch using file geodatabase increase plotting performance. fix , two options: Update mapview (suggested), Run mapviewOptions(fgb = FALSE) attempting run make_receiver_push_summary make_tag_push_summary. Note make report build slowly.","code":"Could not determine mime type for `~\\Matcheddetections_layer.fgb' Error: pandoc document conversion failed with error 63"},{"path":"https://otndo.obrien.page/articles/data-push-summaries.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"Data Push Summaries","text":"Trudel, Marc. “Pilot Study Investigate Migration Atlantic Salmon Post-Smolts Interactions Aquaculture Passamaquoddy Bay, New Brunswick, Canada.” Ocean Tracking Network, 2018. https://members.oceantrack.org/project?ccode=PBSM.","code":""},{"path":"https://otndo.obrien.page/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Michael O'Brien. Author, maintainer.","code":""},{"path":"https://otndo.obrien.page/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"O'Brien M (2024). otndo: Understand OTN data. R package version 0.2.3, https://otndo.obrien.page/, https://mhpob.github.io/otndo/.","code":"@Manual{, title = {otndo: Understand your OTN data}, author = {Michael O'Brien}, year = {2024}, note = {R package version 0.2.3, https://otndo.obrien.page/}, url = {https://mhpob.github.io/otndo/}, }"},{"path":"https://otndo.obrien.page/index.html","id":"otndo","dir":"","previous_headings":"","what":"Understand your OTN data","title":"Understand your OTN data","text":"entiendo /ˌenˈtjendo/ [ˌẽn̪ˈt̪jẽn̪.̪o] Spanish, 1st person indicative; “understand” otndo /ˌoʊˈtjendo/ [ˌoʊ̪ˈt̪jẽn̪.d̪o] English, bad pun; “understand (OTN data)” purpose otndo provide high-level summary acoustic telemetry transmitter matches Ocean Tracking Network, putting “network” back “tracking network” noting related projects investigators.","code":""},{"path":"https://otndo.obrien.page/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Understand your OTN data","text":"can install ---date version R-universe GitHub. R-universe: GitHub:","code":"install.packages( \"otndo\", repos = c( \"https://mhpob.r-universe.dev\", \"https://cloud.r-project.org\" ) ) # install.packages(\"remotes\") remotes::install_github(\"mhpob/otndo\")"},{"path":"https://otndo.obrien.page/index.html","id":"tag-push-summary-example","dir":"","previous_headings":"","what":"Tag push summary example","title":"Understand your OTN data","text":"basic example might use otndo summarize transmitter data: get report working directory goodies! summary number matched individuals detections researcher project: overall extent projects tags matched: fish heard project: ever-ubiquitous “abacus plot”, showing tag heard, colored project: interactive map showing detections receiver: general estimate number transmitters active given date:","code":"# Download some example data td <- file.path(tempdir(), \"otndo_test_files\") dir.create(td) download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/detection-extracts/\", \"pbsm_matched_detections_2018.zip/@@download/file\" ), destfile = file.path(td, \"pbsm_matched_detections_2018.zip\"), mode = \"wb\" ) unzip(file.path(td, \"pbsm_matched_detections_2018.zip\"), exdir = td ) # Make a tag push summary library(otndo) make_tag_push_summary( matched = file.path(td, \"pbsm_matched_detections_2018.csv\") )"},{"path":"https://otndo.obrien.page/index.html","id":"receiver-push-summary-example","dir":"","previous_headings":"","what":"Receiver push summary example","title":"Understand your OTN data","text":"basic example might use otndo summarize receiver data: summary number matched individuals detections researcher project: overall extent projects associated tags receivers heard: receivers heard project’s fish: Gantt chart receivers’ deployments: number detections individuals per receiver: interactive map showing detections receiver: summary unmatched detections, including likely false… …may real! summary unmatched detections occurred, receiver:","code":"# Download some example data ## Deployment metadata download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/data-and-metadata/\", \"archived-records/2018/pbsm-instrument-deployment-short-form-2018.xls/@@download/file\" ), destfile = file.path(td, \"pbsm-instrument-deployment-short-form-2018.xls\"), mode = \"wb\" ) ## Qualified detections download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/detection-extracts/\", \"pbsm_qualified_detections_2018.zip/@@download/file\" ), destfile = file.path(td, \"pbsm_qualified_detections_2018.zip\") ) unzip(file.path(td, \"pbsm_qualified_detections_2018.zip\"), exdir = td ) ## Unqualified detections download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/detection-extracts/\", \"pbsm_unqualified_detections_2018.zip/@@download/file\" ), destfile = file.path(td, \"pbsm_unqualified_detections_2018.zip\") ) unzip(file.path(td, \"pbsm_unqualified_detections_2018.zip\"), exdir = td ) # Make a receiver push summary make_receiver_push_summary( qualified = file.path(td, \"pbsm_qualified_detections_2018.csv\"), unqualified = file.path(td, \"pbsm_unqualified_detections_2018.csv\"), deployment = file.path(td, \"pbsm-instrument-deployment-short-form-2018.xls\") )"},{"path":"https://otndo.obrien.page/index.html","id":"getting-in-contact","dir":"","previous_headings":"","what":"Getting in contact","title":"Understand your OTN data","text":"something doesn’t work way just need little help, feel free open issue GitHub email (Mike O’Brien: obrien@umces.edu) directly.","code":""},{"path":"https://otndo.obrien.page/reference/deployment_gantt.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a Gantt-like chart of receiver deployments and recoveries — deployment_gantt","title":"Create a Gantt-like chart of receiver deployments and recoveries — deployment_gantt","text":"Create Gantt-like chart receiver deployments recoveries","code":""},{"path":"https://otndo.obrien.page/reference/deployment_gantt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a Gantt-like chart of receiver deployments and recoveries — deployment_gantt","text":"","code":"deployment_gantt(deployment)"},{"path":"https://otndo.obrien.page/reference/deployment_gantt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a Gantt-like chart of receiver deployments and recoveries — deployment_gantt","text":"deployment Cleaned deployment metadata sheet(s). Assumes cleaned internal otndo:::clean_otn_deployment function, read , converted data.table.","code":""},{"path":"https://otndo.obrien.page/reference/deployment_gantt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a Gantt-like chart of receiver deployments and recoveries — deployment_gantt","text":"","code":"if (FALSE) { # \\dontrun{ # Download a deployment metadata file td <- file.path(tempdir(), \"matos_test_files\") dir.create(td) download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/\", \"data-and-metadata/2018/pbsm-instrument-deployment-short-form-2018.xls/\", \"@download/file\" ), destfile = file.path(td, \"pbsm-instrument-deployment-short-form-2018.xls\"), mode = \"wb\" ) # Use internal function to clean deployment_filepath <- otndo:::write_to_tempdir( type = \"deployment\", files = file.path(td, \"pbsm-instrument-deployment-short-form-2018.xls\"), temp_dir = td ) # Make the Gantt chart deployment_gantt( data.table::fread(deployment_filepath) ) } # }"},{"path":"https://otndo.obrien.page/reference/make_receiver_push_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Create summary reports of receiver project data from the OTN data push — make_receiver_push_summary","title":"Create summary reports of receiver project data from the OTN data push — make_receiver_push_summary","text":"Create summary reports receiver project data OTN data push","code":""},{"path":"https://otndo.obrien.page/reference/make_receiver_push_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create summary reports of receiver project data from the OTN data push — make_receiver_push_summary","text":"","code":"make_receiver_push_summary( qualified = NULL, unqualified = NULL, update_push_log = FALSE, deployment = NULL, out_dir = getwd(), since = NULL, rmd = FALSE )"},{"path":"https://otndo.obrien.page/reference/make_receiver_push_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create summary reports of receiver project data from the OTN data push — make_receiver_push_summary","text":"qualified, unqualified Default NULL: character vector file paths qualified/unqualified detections. can CSVs zipped folders. update_push_log wish use updated push log? Default FALSE, switch TRUE updated package since push occurred. deployment File path user-supplied master OTN receiver deployment metadata. out_dir Defaults working directory. directory like save report? since Date YYYY-MM-DD format. Summarizes new since provided date. rmd Logical. Compile via RMarkdown rather Quarto?","code":""},{"path":"https://otndo.obrien.page/reference/make_receiver_push_summary.html","id":"push-log","dir":"Reference","previous_headings":"","what":"Push log","title":"Create summary reports of receiver project data from the OTN data push — make_receiver_push_summary","text":"keep track ACT data pushes occur, log kept package's GitHub page. automatically downloaded every time download update package, can avoid re-downloading package changing update_push_log TRUE. can get similar behavior providing date since argument.","code":""},{"path":"https://otndo.obrien.page/reference/make_receiver_push_summary.html","id":"output","dir":"Reference","previous_headings":"","what":"Output","title":"Create summary reports of receiver project data from the OTN data push — make_receiver_push_summary","text":"function creates HTML report can viewed web browser.","code":""},{"path":"https://otndo.obrien.page/reference/make_receiver_push_summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create summary reports of receiver project data from the OTN data push — make_receiver_push_summary","text":"","code":"if (FALSE) { # \\dontrun{ td <- file.path(tempdir(), \"matos_test_files\") dir.create(td) download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/\", \"data-and-metadata/archived-records/2018/\", \"pbsm-instrument-deployment-short-form-2018.xls/\", \"@download/file\" ), destfile = file.path(td, \"pbsm-instrument-deployment-short-form-2018.xls\"), mode = \"wb\" ) download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/\", \"detection-extracts/pbsm_qualified_detections_2018.zip/\", \"@download/file\" ), destfile = file.path(td, \"pbsm_qualified_detections_2018.zip\"), mode = \"wb\" ) unzip( file.path(td, \"pbsm_qualified_detections_2018.zip\"), exdir = td ) download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/\", \"detection-extracts/pbsm_unqualified_detections_2018.zip/\", \"@download/file\" ), destfile = file.path(td, \"pbsm_unqualified_detections_2018.zip\"), mode = \"wb\" ) unzip( file.path(td, \"pbsm_unqualified_detections_2018.zip\"), exdir = td ) qualified_files <- file.path(td, \"pbsm_qualified_detections_2018.csv\") unqualified_files <- file.path(td, \"pbsm_unqualified_detections_2018.csv\") deployment_files <- file.path(td, \"pbsm-instrument-deployment-short-form-2018.xls\") make_receiver_push_summary( qualified = qualified_files, unqualified = unqualified_files, deployment = deployment_files, since = \"2018-11-01\" ) } # }"},{"path":"https://otndo.obrien.page/reference/make_tag_push_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Create summary reports of receiver project data from the OTN data push — make_tag_push_summary","title":"Create summary reports of receiver project data from the OTN data push — make_tag_push_summary","text":"Create summary reports receiver project data OTN data push","code":""},{"path":"https://otndo.obrien.page/reference/make_tag_push_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create summary reports of receiver project data from the OTN data push — make_tag_push_summary","text":"","code":"make_tag_push_summary( matched = NULL, update_push_log = FALSE, since = NULL, sensor_decoding = NULL, out_dir = getwd(), rmd = FALSE )"},{"path":"https://otndo.obrien.page/reference/make_tag_push_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create summary reports of receiver project data from the OTN data push — make_tag_push_summary","text":"matched argument also accepts character vector file paths matched detections. can CSVs zipped folders. update_push_log wish use updated push log? Default FALSE, switch TRUE updated package since push occurred. since date YYYY-MM-DD format. Provides summary detections matched/edited since date. sensor_decoding yet implemented. place provide information decode summarize sensor data, out_dir Defaults working directory. directory like save report? rmd Logical. Compile via RMarkdown rather Quarto?","code":""},{"path":"https://otndo.obrien.page/reference/make_tag_push_summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create summary reports of receiver project data from the OTN data push — make_tag_push_summary","text":"","code":"if (FALSE) { # \\dontrun{ # The code below downloads some matched detections from OTN, then calls the function. td <- file.path(tempdir(), \"matos_test_files\") dir.create(td) download.file( paste0( \"https://members.oceantrack.org/data/repository/\", \"pbsm/detection-extracts/pbsm_matched_detections_2018.zip/\", \"@download/file\" ), destfile = file.path(td, \"pbsm_matched_detections_2018.zip\"), mode = \"wb\" ) unzip(file.path(td, \"pbsm_matched_detections_2018.zip\"), exdir = td ) # Provide the detection file(s) to the \\code{matched} argument, with an # optional date to the \\code{since} argument to summarize what was new since # that date. make_tag_push_summary( matched = file.path( td, \"pbsm_matched_detections_2018.csv\" ), since = \"2018-11-01\" ) } # }"},{"path":"https://otndo.obrien.page/reference/match_map.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the geographic extent of OTN projects — match_map","title":"Plot the geographic extent of OTN projects — match_map","text":"Plot geographic extent OTN projects","code":""},{"path":"https://otndo.obrien.page/reference/match_map.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the geographic extent of OTN projects — match_map","text":"","code":"match_map(otn_tables)"},{"path":"https://otndo.obrien.page/reference/match_map.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the geographic extent of OTN projects — match_map","text":"otn_tables list containing OTN's otn_resources_metadata_points GeoServer layer. Usually created using otn_query.","code":""},{"path":"https://otndo.obrien.page/reference/match_map.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot the geographic extent of OTN projects — match_map","text":"","code":"match_map( otn_query(\"MDWEA\") )"},{"path":"https://otndo.obrien.page/reference/match_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a reactable table of matched detections — match_table","title":"Create a reactable table of matched detections — match_table","text":"Create reactable table matched detections","code":""},{"path":"https://otndo.obrien.page/reference/match_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a reactable table of matched detections — match_table","text":"","code":"match_table(extract, type = c(\"tag\", \"receiver\"))"},{"path":"https://otndo.obrien.page/reference/match_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a reactable table of matched detections — match_table","text":"extract matched (transmitter) qualified (receiver) OTN detections type Tag receiver data? Takes values \"tag\" \"receiver\"; defaults \"tag\".","code":""},{"path":"https://otndo.obrien.page/reference/match_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a reactable table of matched detections — match_table","text":"","code":"if (FALSE) { # \\dontrun{ # Receiver download.file( paste0( \"https://members.oceantrack.org/data/repository/pbsm/\", \"detection-extracts/pbsm_qualified_detections_2018.zip/\", \"@download/file\" ), destfile = file.path(td, \"pbsm_qualified_detections_2018.zip\"), mode = \"wb\" ) unzip( file.path(td, \"pbsm_qualified_detections_2018.zip\"), exdir = td ) qualified_dets <- data.table::fread( file.path(td, \"pbsm_qualified_detections_2018.csv\") ) match_table( extract = qualified_dets, type = \"receiver\" ) # Transmitters download.file( paste0( \"https://members.oceantrack.org/data/repository/\", \"pbsm/detection-extracts/pbsm_matched_detections_2018.zip/\", \"@download/file\" ), destfile = file.path(td, \"pbsm_matched_detections_2018.zip\"), mode = \"wb\" ) unzip(file.path(td, \"pbsm_matched_detections_2018.zip\"), exdir = td ) matched_dets <- data.table::fread( file.path(td, \"pbsm_matched_detections_2018.csv\") ) match_table( extract = matched_dets, type = \"tag\" ) } # }"},{"path":"https://otndo.obrien.page/reference/matched_abacus.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an abacus plot of matched detections — matched_abacus","title":"Create an abacus plot of matched detections — matched_abacus","text":"Create abacus plot matched detections","code":""},{"path":"https://otndo.obrien.page/reference/matched_abacus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an abacus plot of matched detections — matched_abacus","text":"","code":"matched_abacus(temp_dist, release)"},{"path":"https://otndo.obrien.page/reference/matched_abacus.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an abacus plot of matched detections — matched_abacus","text":"temp_dist Data output temporal_distribution() release Data frame release times/locations; subset matched detections data","code":""},{"path":"https://otndo.obrien.page/reference/matched_abacus.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an abacus plot of matched detections — matched_abacus","text":"","code":"if (FALSE) { # \\dontrun{ # Get a detection file download.file( paste0( \"https://members.oceantrack.org/data/repository/\", \"pbsm/detection-extracts/pbsm_matched_detections_2018.zip/\", \"@download/file\" ), destfile = file.path(td, \"pbsm_matched_detections_2018.zip\"), mode = \"wb\" ) unzip(file.path(td, \"pbsm_matched_detections_2018.zip\"), exdir = td ) matched_dets <- data.table::fread( file.path(td, \"pbsm_matched_detections_2018.csv\") ) # Run temporal_distribution temporal <- temporal_distribution(matched_dets, \"tag\") # Run matched_abacus matched_abacus(temporal$data, matched_dets[receiver == \"release\"]) } # }"},{"path":"https://otndo.obrien.page/reference/otn_query.html","id":null,"dir":"Reference","previous_headings":"","what":"Query the OTN Geoserver — otn_query","title":"Query the OTN Geoserver — otn_query","text":"Query OTN Geoserver","code":""},{"path":"https://otndo.obrien.page/reference/otn_query.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Query the OTN Geoserver — otn_query","text":"","code":"otn_query(projects)"},{"path":"https://otndo.obrien.page/reference/otn_query.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Query the OTN Geoserver — otn_query","text":"projects Character vector OTN project codes like project metadata. Prepended networks can provided, necessary.","code":""},{"path":"https://otndo.obrien.page/reference/otn_query.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Query the OTN Geoserver — otn_query","text":"list \"otn_resources_metadata_points\" \"project_metadata\" given projects","code":""},{"path":"https://otndo.obrien.page/reference/otn_query.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Query the OTN Geoserver — otn_query","text":"","code":"otn_query(c(\"EST\", \"FACT.SCDNRDFP\", \"ACT.MDBSB\", \"MDBSB\")) #> $otn_resources_metadata_points #> FID collectioncode #>