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2021_summary.Rmd
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2021_summary.Rmd
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---
title: "FACE-IT WP1 summary"
author: "Robert Schlegel & Jean-Pierre Gattuso"
date: "`r Sys.Date()`"
output:
html_document:
# code_folding: hide
fig_crop: no
# description:
# bibliography: Presentations.bib
---
```{r global_options, include = FALSE}
knitr::opts_chunk$set(fig.width = 8, fig.align = 'center',
echo = FALSE, warning = FALSE, message = FALSE,
eval = TRUE, tidy = FALSE)
# Libraries
library(tidyverse)
library(kableExtra) # For formatting static tables
library(DT) # For interactive tables
# Table column names
DT_cols <- c("Type", "Driver", "Date", "Longitude", "Latitude", "Depth", "Files", "Link", "Reference", "Notes")
# Datatable options for all tables
options(DT.options = list(pageLength = 5,
deferRender = TRUE,
scrollY = 400,
scrollCollapse = TRUE,
lengthMenu = c(5, 10, 25, 50, 100)))
```
<center>
{ width=70% }
</center>
<br>
[Guiding structure not to be included in final presentation]
"WP reports: What has the WP as a whole done in the last year? How is the workflow going? How is interaction with other working? What were the issues? Next steps?"
# Structure
***
{ width=30% }
- WP Lead: Jean-Pierre Gattuso
<br>
{ width=30% }
- Data Scientist: Robert Schlegel
<br>
# Key drivers (D1.1: 6 months)
***
```{r key-drivers-table, eval=TRUE}
## Cryosphere
cryo_vars <- data.frame(Category = "Cryosphere", Drivers = "Coastal ice, fast ice, glacier, permafrost, sea ice, snow cover")
## Physical
phys_vars <- data.frame(Category = "Physical", Drivers = "Bathymetry, current, evaporation, heatflux, Kd, MLD, precipitation, river discharge, salinity, SLP, air/sea temperature, sedimentation rate, suspended matter, wind")
## Chemistry
chem_vars <- data.frame(Category = "Physical", Drivers = "Calcium carbonate (CaCO3), DIC, DOC, DON, O2, nutrients, pCO2, pH, total alkalinity")
## Biology
bio_vars <- data.frame(Category = "Biology", Drivers = "Calcification, nitrogen fixation, photosynthesis, primary production, respiration, species presence/abundance")
## Social
soc_vars <- data.frame(Category = "Social", Drivers = "Fish/game landings, local and national resource management, national statistics, tourist arrivals/vessels")
# Combine and print
knitr::kable(rbind(cryo_vars, phys_vars, chem_vars, bio_vars, soc_vars),
caption = "Table 1: The key drivers of changes on Arctic fjord and adjacent coastal systems as identified by the experts in FACE-IT for the relevant fields. The drivers have been separated into the following categories for convenience: Cryosphere, Physical, Chemistry, Biology, Social. Full list available via 'Key drivers' tab above.") %>%
kable_styling(bootstrap_options = c("striped", "hover", "responsive")) %>%
row_spec(1, background = "mintcream") %>% # Cryosphere
row_spec(2, color = "black", background = "skyblue") %>% # Physical
row_spec(3, background = "#F6EA7C") %>% # Chemistry
row_spec(4, background = "#A2ED84") %>% # Biology
row_spec(5, background = "#F48080") # Social
```
<br>
# Meta-database (D1.2: 12 months)
***
```{r isfjorden-meta-data}
# Mouth mooring North
is_mooring_N <- data.frame(type = "Mooring",
data_name = "Sea temperature; salinity; O2; current: velocity (U, V)",
date_range = "2015 to 2018",
lon_range = "13.37895", lat_range = "78.18048",
depth_range = "0 to 228",
file_name = '<a onclick="alert(\'mooring_N: IN1516.nc; IN1617.nc; N1718.nc\');">1 folder, 3 files</a>',
URL = '<a onclick="alert(\'https://data.npolar.no/dataset/111aca43-7f5c-4c15-9f31-dcd3214dbfcb; https://data.npolar.no/dataset/3078f619-9955-4a7f-9316-fab598fec382; https://data.npolar.no/dataset/e9106051-6c44-4849-9d62-04e4a82f1ca9\');">NPDC multiple</a>',
reference = '<a onclick="alert(\'
Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - North (I-N) during 31 Aug 2015 to 12 Aug 2016 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.111aca43; Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - North (I-N) during 15 Oct 2016 to 2 Oct 2017 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.3078f619; Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - North (I-N) during 5 Oct 2017 to 24 Aug 2018 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.e9106051\');">Skogseth et al. (2019)</a>',
note = NA)
# Mouth mooring South
is_mooring_S <- data.frame(type = "Mooring",
data_name = "Sea temperature; salinity; O2; current: velocity (U, V)",
date_range = "2005 to 2018",
lon_range = "13.522816", lat_range = "78.06083",
depth_range = "0 to 210",
file_name = '<a onclick="alert(\'mooring_S\');">1 folder, 13 files</a>',
URL = '<a onclick="alert(\'https://data.npolar.no/dataset/176eea39-7d99-49d7-a082-b18acf42850c; https://data.npolar.no/dataset/a1239ca3-79e6-4284-bba5-38028358994a; https://data.npolar.no/dataset/064a09b7-f590-4448-810e-3f287b182dd2; https://data.npolar.no/dataset/b0e473c4-b5b9-4ebc-96eb-411d47f1d850; https://data.npolar.no/dataset/2be7bdee-c899-45b8-901b-9ec5baa9397a; https://data.npolar.no/dataset/a247e9a9-4b62-4149-bbf4-83df3576a7c4; https://data.npolar.no/dataset/6813ce6d-bdc9-4375-a310-679e074bee6b; https://data.npolar.no/dataset/11b7e849-e53d-40d8-909b-13e29c7971a0; https://data.npolar.no/dataset/21838303-c9a0-4fc4-aac3-f537b37356df; https://data.npolar.no/dataset/cd7a2f7c-abed-4284-b7c5-a9ff43c89afc; https://data.npolar.no/dataset/54dcd0c9-b863-41b1-a72b-0827099ad2b0\');">NPDC</a>',
reference = '<a onclick="alert(\'Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - South (I-S) during September 2005 to September 2006 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.176eea39; Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - South (I-S) during September 2006 to September 2007 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.a1239ca3; Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the outer Isfjorden - South (I-S) during September 2007 to January 2008 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.064a09b7; Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - South (I-S) during 9 Sep 2010 to 3 Sep 2011 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.b0e473c4; Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - South (I-S) during 8 Sep 2011 to 3 Sep 2012 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.2be7bdee; Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - South (I-S) during 6 Sep 2012 to 28 Aug 2013 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.a247e9a9; Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - South (I-S) during 2 Sep 2013 to 26 Aug 2014 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.6813ce6d; Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - South (I-S) during 31 Aug 2014 to 24 Aug 2015 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.11b7e849; Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - South (I-S) during 31 Aug 2015 to 12 Aug 2016 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.21838303; Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - South (I-S) during 19 Aug 2016 to 2 Oct 2017 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.cd7a2f7c; Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from the Isfjorden Mouth - South (I-S) during 5 Oct 2017 to 25 Aug 2018 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.54dcd0c9\');">Skogseth et al. (2019)</a>',
note = NA)
# Mooring IFO
is_mooring_IFO <- data.frame(type = "Mooring",
data_name = "Sea temperature; salinity; O2; current: velocity (U, V)",
date_range = "2016 to 2017",
lon_range = "15.33116", lat_range = "78.247416",
depth_range = "0 to 60",
file_name = '<a onclick="alert(\'mooring_IFO: IFO1617.nc, IFO1617_ADCP.nc\');">1 folder, 2 files</a>',
URL = '<a onclick="alert(\'https://data.npolar.no/dataset/7718a106-5d13-42d9-bb79-1d2adf0f51c4\');">NPDC</a>',
reference = '<a onclick="alert(\'Skogseth, R., & Ellingsen, P. G. (2019). Mooring data from Isfjorden online mooring (IFO) during 30 Sep 2016 to 11 Mar 2017 [Data set]. Norwegian Polar Institute. https://doi.org/10.21334/npolar.2019.7718a106\');">Skogseth et al. (2019)</a>',
note = NA)
# North mouth mooring GFI
is_mooring_GFI_N <- data.frame(type = "Mooring",
data_name = "Sea temperature; salinity; current: direction, speed; oxygen",
date_range = "2015 to 2016",
lon_range = "13.37895", lat_range = "78.18048",
depth_range = "40 to 210",
file_name = '<a onclick="alert(\'mooring_GFI_N: 1954_RCM_1318_QC.nc, 1955_RCM_645_QC.nc, 1956_RCM_646_QC.nc\');">1 folder, 3 files</a>',
URL = '<a target="_blank" rel="noopener noreferrer" href="ftp://ftp.nmdc.no/nmdc/UIB/Currents/moorings/SV_201508_Isfjorden/">NMDC</a>',
reference = '<a onclick="alert(\'Skogseth R., Olivier L.L.A., Nilsen F., Falck E., Fraser N., Tverberg V., Ledang A.B., Vader A., Jonassen M.O., Søreide J., Cottier F., Berge J., Ivanov B.V., and Falk-Petersen S. (2019). Variability and decadal trends in the Isfjorden (Svalbard) ocean climate and circulation - a thermometer for climate change in the Arctic Ocean, Submitted to Progress in Oceanography\');">Skogseth et al. (2019)</a>',
note = NA)
# South mouth mooring GFI
is_mooring_GFI_S <- data.frame(type = "Mooring",
data_name = "Sea temperature; salinity; turbidity; current: direction, speed; oxygen",
date_range = "2010 to 2013",
lon_range = "13.52211 to 13.59348", lat_range = "78.05833 to 78.06071",
depth_range = "50 to 182",
file_name = '<a onclick="alert(\'mooring_GFI: 0710_RCM_783_QC.nc, 0711_RCM_784_QC.nc, 1841_RCM_464_QC.nc\');">1 folder, 4 files</a>',
URL = '<a onclick="alert(\'href="ftp://ftp.nmdc.no/nmdc/UIB/Currents/moorings/SV_201209_A/; ftp://ftp.nmdc.no/nmdc/UIB/Currents/moorings/SV_201009_B/\');">NMDC</a>',
reference = '<a onclick="alert(\'No reference provided.\');">NMDC</a>',
note = NA)
# CO2 station at Tempelfjorden
is_CO2_tempelfjorden <- data.frame(type = "CTD",
data_name = "Sea temperature; salinity; TA; pH; EP TA",
date_range = "2015 to 2017",
lon_range = "16.945 to 17.353", lat_range = "78.391 to 78.441",
depth_range = "1.43 to 98",
file_name = '<a onclick="alert(\'Marine_CO2_system_data_from_Tempelfjorden_2015_to_2017.xlsx; Marine_CO2_system_data_from_Tempelfjorden_2015_to_2017.csv\');"2 files</a>',
URL = '<a target="_blank" rel="noopener noreferrer" href="https://sios-svalbard.org/metsis/search?fulltext=isfjorden&start_date=&end_date=&is_parent=All">SIOS</a>',
reference = '<a onclick="alert(\'No reference provided.\');">NA</a>',
note = NA)
# CO2 station at IsA
is_IsA_CO2 <- data.frame(type = "CTD",
data_name = "Sea temperature; salinity; TA; pH; EP TA",
date_range = "2015 to 2017",
lon_range = "15.5 to 15.533",
lat_range = "78.257 to 78.267",
depth_range = "1.44 to 90.52",
file_name = '<a onclick="alert(\'Marine_CO2_system_data_at_the_IsA_Station_2015_to_2017.xlsx; Marine_CO2_system_data_at_the_IsA_Station_2015_to_2017.csv\');"2 files</a>',
URL = '<a target="_blank" rel="noopener noreferrer" href="https://sios-svalbard.org/metsis/search?fulltext=isfjorden&start_date=&end_date=&is_parent=All">SIOS</a>',
reference = '<a onclick="alert(\'No reference provided.\');">NA</a>',
note = NA)
# Chlorophyl station at IsA
is_IsA_Chla <- data.frame(type = "Niskin bottle",
data_name = "ChlA",
date_range = "2011 to 2019",
lon_range = "15.53", lat_range = "78.26",
depth_range = "0 to 980",
file_name = '<a onclick="alert(\'chl_a: IsA_Svalbard_Chlorophyll_A_2011_2019_10um.nc; IsA_Svalbard_Chlorophyll_A_2011_2019_GFF.nc\');">1 folder, 2 files</a>',
URL = '<a target="_blank" rel="noopener noreferrer" href="https://sios-svalbard.org/metsis/search?fulltext=isfjorden&start_date=&end_date=&is_parent=All">SIOS</a>',
reference = '<a onclick="alert(\'No reference provided.\');">NA</a>',
note = NA)
# Light related data at the IsA station
is_IsA_light <- data.frame(type = "",
data_name = "PAR; suspended matter: organic, mineral",
date_range = "2012 to ?",
lon_range = "15.53", lat_range = "78.26",
depth_range = "0 to 15",
file_name = '<a onclick="alert(\' \');">0 files</a>',
URL = NA,
reference = '<a onclick="alert(\'No reference available yet.\');">Vader et al. (In prep.)</a>',
note = "Data are not yet publicly available.")
# Biology related data at the IsA station
is_IsA_bio <- data.frame(type = "Niskin bottle",
data_name = "Nutrients: nitrate, nitrite, phosphate, silicate; DNA; phytoplankton: species, abundance; ChlA concentration; protists; bacteria",
date_range = "2011 to ?",
lon_range = "15.53", lat_range = "78.26",
depth_range = "0, 15, and 75",
file_name = '<a onclick="alert(\' \');">0 files</a>',
URL = NA,
reference = '<a onclick="alert(\'No reference available yet.\');">Vader et al. (In prep.)</a>',
note = "Data are not yet publicly available.")
# Biology related data at the BAB station
is_BAB_bio <- data.frame(type = "Niskin bottle",
data_name = "Nutrients: nitrate, nitrite, phosphate, silicate; DNA; phytoplankton: species, abundance; ChlA concentration; protists",
date_range = "2020 to ?",
lon_range = "16.68", lat_range = "78.66",
depth_range = "0, 15, and 150",
file_name = '<a onclick="alert(\' \');">0 files</a>',
URL = NA,
reference = '<a onclick="alert(\'No reference available yet.\');">Vader et al. (In prep.)</a>',
note = "Data are not yet publicly available.")
# Zooplankton data
is_zoo <- data.frame(type = "Multinet",
data_name = "Zooplankton: species, abundance, biomass",
date_range = "2001 to ?",
lon_range = "14.00 to 16.68",
lat_range = "78.13 to 78.66",
depth_range = "?",
file_name = '<a onclick="alert(\' \');">0 files</a>',
URL = NA,
reference = '<a onclick="alert(\'No reference available yet.\');">Søreide et al. (In prep.)</a>',
note = "Data are not yet publicly available.")
# Isfjord radio meteorological station
is_met_radio <- data.frame(type = "Met station",
data_name = "Air: temperature (2m), air pressure (sea level; 2m); wind: speed, direction (10m); relative humidity",
date_range = "1934 to 2019",
lon_range = "13.6192",
lat_range = "78.0625",
depth_range = NA,
file_name = '<a onclick="alert(\'SN99790.nc\');">1 file</a>',
URL = '<a target="_blank" rel="noopener noreferrer" href="https://thredds.met.no/thredds/catalog/met.no/observations/stations/catalog.html?dataset=met.no/observations/stations/SN99790.nc">NMI</a>',
reference = '<a onclick="alert(\'No reference provided.\');">NA</a>',
note = NA)
# Longyearbyen airport meteorological station
is_met_airport <- data.frame(type = "Met station",
data_name = "Air: temperature (2m), air pressure (sea level; 2m); wind: speed, direction (10m); relative humidity",
date_range = "1975 to 2019",
lon_range = "15.5015",
lat_range = "78.2453",
depth_range = NA,
file_name = '<a onclick="alert(\'SN99840.nc\');">1 file</a>',
URL = '<a target="_blank" rel="noopener noreferrer" href="https://thredds.met.no/thredds/catalog/met.no/observations/stations/catalog.html?dataset=met.no/observations/stations/SN99840.nc">NMI</a>',
reference = '<a onclick="alert(\'No reference provided.\');">NA</a>',
note = NA)
# Pyramiden meteorological station
is_met_pyramiden <- data.frame(type = "Met station",
data_name = "Air: temperature (2m), air pressure (sea level; 2m); wind: speed, direction (10m); relative humidity",
date_range = "2012 to 2019",
lon_range = "16.3603",
lat_range = "78.6557",
depth_range = NA,
file_name = '<a onclick="alert(\'SN99880.nc\');">1 file</a>',
URL = '<a target="_blank" rel="noopener noreferrer" href="https://thredds.met.no/thredds/catalog/met.no/observations/stations/catalog.html?dataset=met.no/observations/stations/SN99880.nc">NMI</a>',
reference = '<a onclick="alert(\'No reference provided.\');">NA</a>',
note = NA)
# Social data for Isfjorden
is_social <- data.frame(type = "",
data_name = "Game landings; local management; national statistics; tourist vessels: mileage; tourist arrivals",
date_range = NA, lon_range = NA, lat_range = NA, depth_range = NA,
file_name = '<a onclick="alert(\'\');">0 files</a>',
URL = NA, reference = NA,
note = "Data are still being pursued.")
# PANGAEA data product
is_PG <- data.frame(type = "PANGAEA",
data_name = "Many",
date_range = "1871-07-19 to 2020-10-02",
lon_range = "13.6204 to 17.1090",
lat_range = "78.0300 to 78.7022",
depth_range = "-754 to 415.8",
file_name = '<a onclick="alert(\'pg_is_ALL.csv/.RData\');">2 files</a>',
URL = '<a onclick="alert(\'pg_is_ALL.csv/.RData\');">See URL column</a>',
reference = '<a onclick="alert(\'pg_is_ALL.csv/.RData\');">See citation column</a>',
note = "This is a combination of 215 PANGAEA data files.")
# Fully combined product
full_product_is <- data.frame(type = "Full",
data_name = "Many",
date_range = "1871-07-19 to 2020-10-02",
lon_range = "13.37895 to 17.35300",
lat_range = "78.0300 to 78.7022",
depth_range = "-754 to 415.8",
file_name = '<a onclick="alert(\'full_product_is.csv/.RData\');">1 file, 2 formats</a>',
URL = '<a onclick="alert(\'full_product_is.csv/.RData\');">See URL column</a>',
reference = '<a onclick="alert(\'full_product_is.csv/.RData\');">See citation column</a>',
note = "This is the full combined data product.")
# Bind them together
metadata_isfjorden <- rbind(is_mooring_N, is_mooring_S, is_mooring_IFO, is_mooring_GFI_N, is_mooring_GFI_S,
is_CO2_tempelfjorden, is_IsA_CO2, is_IsA_Chla, is_IsA_light, is_IsA_bio, is_BAB_bio, is_zoo,
is_met_radio, is_met_airport, is_met_pyramiden, is_social, is_PG, full_product_is)
```
```{r isfjorden-meta-data-table}
DT::datatable(metadata_isfjorden, rownames = FALSE, escape = FALSE, colnames = DT_cols,
caption = "All data files in this table are found within '~/pCloudDrive/FACE-IT_data/isfjorden/'.")
```
<br>
# Other deliverables
***
- Data management plan (D8.1: 6 months)
- Created FACE-IT [GitHub repository](https://github.com/FACE-IT-project)
- All WP1 progress available on [public website](https://face-it-project.github.io/WP1/index.html)
<br>
# Cross-package interactions
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- Ny-Ålesund, Kongsfjorden, Svalbard (July - August, 2021)
- Participated in fieldwork for WP3
- Worked adjacent to WP2
- Data collections efforts
## Effective coordination of data collection
- Who is responsible for what?
- Who has other people working with data collection?
- WP1 is of service to everybody, but we can't provide this service without replies to our inquiries
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# Data issues
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- What to do with complex data types
- e.g. Seabird database and geospatial glacier fronts
## Inglefieldbukta
- Is the current Inglefieldbukta bounding box to small?
- What is the scientific justification of choosing a much larger semi-open fjord?
- Current area (figure)
- Potential expanded area (figure)
## Social data
- [List the social science data that have been identified]
- What other sources may there be for FACE-IT sites?
- Including Greenland
- What sort of non-social data do social scientists want?
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# What's next?
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- Review article (D1.3: 24 months)
- Intended as broad overview of drivers of change in FACE-IT study sites
- Will require expertise from many FACE-IT researchers
- WP1 will reach out to site coordinators as fist step in collaborative process
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# Summary
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- Who has use for the collected data?
- How would they like to access them?
- What format(s) is most useful?
- Who has there own data collection efforts?
- What shall be done about Inglefieldbukta site?
- How shall we begin to merge the data needs of scoial science?