library(matos)
#> By continuing, you are agreeing to the ACT Network MATOS User Agreement and Data Policy, Version 1.2:
#>
#> <https://matos.asascience.com/static/MATOS.User.Agreement.V1.1.pdf>List available files
First, list_projects returns the project page, which is
useful to figure out what URLs are associated with each project. You do
not need MATOS permissions in order to view this page.
all_projects <- list_projects()
#> ℹ These ACT projects were unable to be matched with OTN: "MDR
#> Great White Shark Project", "Mid-Atlantic MBON", "NEFSC
#> STELLWAGEN MPA", "USGS Gulf of Maine sturgeon", "USGS
#> Merrimack River sturgeon", "USGS Piscataqua River sturgeon",
#> and "USGS Upper Connecticut River"
#> ℹ These OTN projects were unable to be matched with ACT:
#> "APG: Sturgeon Monitoring", "NEFSC Assessment of MPAs within
#> GoM", and "NEFSC_Ecosystem_Assessment"
head(all_projects)
#> name
#> 1 APG Atlantic and Shortnose Sturgeon
#> 2 ASI - Acoustic Array
#> 3 ASI - Porbeagle Shark Study
#> 4 ASI - Sand Tiger Shark Study
#> 5 ASI - Sandbar Shark Study
#> 6 ASI & O'Seas - White Shark Study, Montauk, NY
#> collectioncode number
#> 1 ATSHS 176
#> 2 ASIARRAY 100
#> 3 ASIPORBEAG 295
#> 4 ASISANDTIG 296
#> 5 ASISANDBAR 297
#> 6 ASIWHITE21 211
#> url status
#> 1 https://matos.asascience.com/project/detail/176 ongoing
#> 2 https://matos.asascience.com/project/detail/100 ongoing
#> 3 https://matos.asascience.com/project/detail/295 ongoing
#> 4 https://matos.asascience.com/project/detail/296 ongoing
#> 5 https://matos.asascience.com/project/detail/297 ongoing
#> 6 https://matos.asascience.com/project/detail/211 completed
#> longname
#> 1 Aberdeen Proving Ground - Atlantic and Shortnose Sturgeon Telemetry Project
#> 2 Using acoustic telemetry and video-based methods to characterize elasmobranch assemblage in Block Island, RI waters.
#> 3 This study involves the porbeagle shark in New England and adjacent waters.
#> 4 This study focuses on sand tiger sharks in Southern New England waters.
#> 5 This study focuses on sandbar sharks in Southern New England waters.
#> 6 Atlantic Shark Institute & O'Sea's Conservation Foundation- YOY/Juvenile White Shark Study
#> citation website
#> 1
#> 2 https://www.atlanticsharkinstitute.org/
#> 3 http://www.atlanticsharkinstitute.org
#> 4 http://www.atlanticsharkinstitute.org
#> 5 http://www.atlanticsharkinstitute.org
#> 6 http://www.atlanticsharkinstitute.org
#> collaborationtype
#> 1 Data
#> 2 Data
#> 3 Data
#> 4 Data
#> 5 Data
#> 6 Tracker
#> locality
#> 1 Aberdeen Proving Ground
#> 2 Block Island, Point Judith, Watch Hill and Fishers Island, NY
#> 3
#> 4
#> 5
#> 6 Block Island Sound
#> abstract
#> 1 Tracking Atlantic and shortnose sturgeon in the main stem of the upper Chesapeake Bay and in the Bush River. Tracking migration and spawning patterns is done to keep in compliance with the ESA. Mitigation is performed by the U.S. Army to prevent any adverse effects to the populations.
#> 2 Acoustic receivers had never been deployed in Rhode Island waters until 2019. In collaboration with the RI Department of Environmental Management, the Atlantic Shark Institute now has 19 receivers deployed, including the waters adjacent to Fisher’s Island, NY. When combined with the RI DEM, we are now have approximately 45 receivers actively monitoring these waters. The goal is use this acoustic telemetry data to document all the activity taking place in these waters for the very first time. We also plan to combine it with video obtained through Baited Remote Underwater Video Systems (BRUVS). We've deployed BRUVS for several years with the goal of characterizing and quantifying shark assemblages in Rhode Island state waters.
#> 3 This study involves the porbeagle shark in New England and adjacent waters.
#> 4 This study focuses on sand tiger sharks in Southern New England waters.
#> 5 This study focuses on sandbar sharks in Southern New England waters.
#> 6 The Atlantic Shark Institute partnered with Dr. Craig O'Connell from the O'Seas Conservation Foundation and Dr. Greg Skomal from MA Division of Marine Fisheries to use a variety of tagging technologies and methods to quantify the broad and fine-scale movements of white sharks, their feeding ecology and behavior, in the Montauk, NY area. This project was then expanded into a larger study area to get into greater specificity, more study elements, and with more tagged animals.I can also view the files that I’ve uploaded to my projects using
list_project_files, but that requires logging in first. The
family of list_ functions in this package will prompt you
to log in before moving on. Note that I’ll be entering my MATOS username
and password behind the scenes here.
project_files <- list_project_files(project = "umces boem offshore wind energy")
#> ! Please log in.
#> ✔ Login successful!
head(project_files)
#> project file_type
#> 1 87 Deployed Receivers – Deployment Metadata
#> 2 87 Tag Detections - .vfl file
#> 3 87 Tag Detections - .vfl file
#> 4 87 Tag Detections - .vfl file
#> 5 87 Tag Detections - .vfl file
#> 6 87 Tag Detections - .vfl file
#> upload_date file_name
#> 1 2020-03-30 BOEM_metadata_deployment.xls
#> 2 2020-05-28 VR2AR_546455_20170328_1.vrl
#> 3 2020-05-28 VR2AR_546456_20170328_1.vrl
#> 4 2020-05-28 VR2AR_546457_20170329_1.vrl
#> 5 2020-05-28 VR2AR_546458_20170329_1.vrl
#> 6 2020-05-28 VR2AR_546459_20170328_1.vrl
#> url
#> 1 https://matos.asascience.com/projectfile/download/375
#> 2 https://matos.asascience.com/projectfile/download/1810
#> 3 https://matos.asascience.com/projectfile/download/1811
#> 4 https://matos.asascience.com/projectfile/download/1812
#> 5 https://matos.asascience.com/projectfile/download/1813
#> 6 https://matos.asascience.com/projectfile/download/1814User credentials
A side note on your MATOS username and password: matos
defaults to asking you for your login credentials every time you start a
new session. To skirt around this you can use
set_matos_credentials(), which installs your username and
password in your .Renviron file.
You will be automatically logged in every time you use your current
computer after doing this, but beware: someone else could theoretically
access your username and password if they gain access to your
computer.
Back to the regularly-scheduled programming
I can also list any of my OTN node Data Extraction Files.
ACT_MATOS_files <- list_extract_files(
project = "umces boem offshore wind energy",
detection_type = "all"
)
head(ACT_MATOS_files)
#> project file_type detection_type detection_year
#> 1 87 Data Extraction File matched 2017
#> 2 87 Data Extraction File matched 2018
#> 3 87 Data Extraction File matched 2019
#> 4 87 Data Extraction File matched 2020
#> 5 87 Data Extraction File matched 2021
#> 6 87 Data Extraction File matched 2022
#> upload_date file_name
#> 1 2023-07-06 mdwea_matched_detections_2017.zip
#> 2 2024-11-08 mdwea_matched_detections_2018.zip
#> 3 2024-11-08 mdwea_matched_detections_2019.zip
#> 4 2024-11-08 mdwea_matched_detections_2020.zip
#> 5 2024-11-08 mdwea_matched_detections_2021.zip
#> 6 2024-11-08 mdwea_matched_detections_2022.zip
#> url
#> 1 https://matos.asascience.com/projectfile/downloadExtraction/87_1
#> 2 https://matos.asascience.com/projectfile/downloadExtraction/87_2
#> 3 https://matos.asascience.com/projectfile/downloadExtraction/87_3
#> 4 https://matos.asascience.com/projectfile/downloadExtraction/87_4
#> 5 https://matos.asascience.com/projectfile/downloadExtraction/87_5
#> 6 https://matos.asascience.com/projectfile/downloadExtraction/87_6Download project or data extraction files
There are a few ways to download the different types of files held by MATOS. I can download directly if I know the URL of the file:
project_files$url[1]
#> [1] "https://matos.asascience.com/projectfile/download/375"
get_project_file(url = project_files$url[1])
#>
#> ── Downloading files ─────────────────────────────────────────
#> ✔ File(s) saved to:
#> C:\Users\darpa2\Analysis\matos\vignettes\BOEM_metadata_deployment.xls
#> [1] "C:\\Users\\darpa2\\Analysis\\matos\\vignettes\\BOEM_metadata_deployment.xls"I can download by using an index from the
ACT_MATOS_files table above, here the file on the second
row.
get_extract_file(file = 2, project = "umces boem offshore wind energy")
#>
#> ── Downloading files ─────────────────────────────────────────
#> ✔ File(s) saved to:
#> C:\Users\darpa2\Analysis\matos\vignettes\mdwea_matched_detections_2018.zip
#>
#> ── Unzipping files ───────────────────────────────────────────
#> ✔ File(s) unzipped to:
#> C:/Users/darpa2/Analysis/matos/vignettes/mdwea_matched_detections_2018.csv
#> C:/Users/darpa2/Analysis/matos/vignettes/data_description.txt
#> [1] "C:/Users/darpa2/Analysis/matos/vignettes/mdwea_matched_detections_2018.csv"
#> [2] "C:/Users/darpa2/Analysis/matos/vignettes/data_description.txt"Search and download tag detections
Using the tag_search function, I can interface with
MATOS’ tag search
page. Be very careful with this function – it can take a
very, VERY long time to return your files.
This function downloads the requested CSV into your working directory,
and, if import = T is used, reads it into your R
session.
Upload files to MATOS
There are times when you want to upload new data to MATOS. The currently accepted data types and formats are:
- newly-deployed transmitters (CSV/XLS[X])
- detection logs (CSV/VRL/VDAT)
- receiver and glider deployment metadata (CSV/XLS[X])
- receiver events like temperature, tilt, etc. (CSV)
- glider GPS tracks (CSV)
A few data types use designated Ocean Tracking Network templates:
- tag metadata
- receiver deployment metadata
- glider deployment metadata
If you don’t have one of these templates downloaded, you can download it through the package. For example:
get_otn_template("glider")
#> [1] "C:/Users/darpa2/Analysis/matos/vignettes/glider-deployment-metadata-v2.xlsx"Then, get to uploading!
upload_file(
project = "umces boem offshore wind energy",
file = c("this_is_a_dummy_file.csv", "so_is_this.csv"),
data_type = "new_tags"
)