incorporating further suggested edits

Author: j-atkins

docs/paper/paper.bib

@@ -202,3 +202,17 @@ @article{Gordon2014
 abstract = {Abstract A northward flowing current, emanating from the North Equatorial Current (NEC) bifurcation at the Philippine margin, enters Lamon Bay along Luzon's eastern coast. There the NEC tropical water masses merge with subtropical water of the western North Pacific to form the Kuroshio. A northward flowing western boundary current is first observed near 16.5°N, marking the initiation of the Kuroshio. The current feeding into the nascent Kuroshio of Lamon Bay is bracketed by an anticyclonic dipole to its northeast and a cyclonic dipole to its southwest. Ship-based observational programs in the spring seasons of 2011 and 2012 detect a shift of the Lamon Bay thermohaline stratification with marked enrichment of NEC tropical thermocline water in 2012 relative to a dominant western North Pacific subtropical stratification of 2011. Temperature-salinity time series from moorings spanning the two ship-based observations identify the timing of the transition as December 2011. The NEC bifurcation was further south in May 2012 than in May 2011. We suggest that the more southern bifurcation in May 2012 induced increased NEC thermocline water injection into Lamon Bay and nascent Kuroshio, increasing the linkage of the western North Pacific subtropical and tropical thermoclines. This connection was reduced in May 2011 as the NEC bifurcation shifted into a more northerly position and western North Pacific subtropical thermocline dominated Lamon Bay stratification.},
 year = {2014}
 }
+
+@article {Johnson2007,
+      author = "Gregory C.  Johnson and John M.  Toole and Nordeen G.  Larson",
+      title = "Sensor Corrections for Sea-Bird SBE-41CP and SBE-41 CTDs",
+      journal = "Journal of Atmospheric and Oceanic Technology",
+      year = "2007",
+      publisher = "American Meteorological Society",
+      address = "Boston MA, USA",
+      volume = "24",
+      number = "6",
+      doi = "10.1175/JTECH2016.1",
+      pages=      "1117 - 1130",
+      url = "https://journals.ametsoc.org/view/journals/atot/24/6/jtech2016_1.xml"
+}

docs/paper/paper.md

@@ -38,7 +38,7 @@ bibliography: paper.bib
 
 # Summary
 
-`VirtualShip` is a Python-based package for simulating measurements as if they were coming from real-life oceanographic instruments, facilitating student training, expedition planning, and design of instrument/sampling strategies. The software exploits the customisability of the open-source `Parcels` Lagrangian simulation framework [@Lange2017; @Delandmeter2019] and builds a virtual ocean by streaming data from the [Copernicus Marine Data Store](https://marine.copernicus.eu/) on-the-fly, enabling virtual expeditions anywhere on the globe.
+`VirtualShip` is a Python-based package for simulating measurements as if they were coming from real-life oceanographic instruments, facilitating student training, expedition planning, and design of instrument/sampling strategies. The software exploits the customisability of the open-source `Parcels` Lagrangian simulation framework [@Lange2017; @Delandmeter2019] and builds a virtual ocean by streaming data from the [Copernicus Marine Data Store](https://marine.copernicus.eu/) on-the-fly, enabling expeditions anywhere on the globe.
 
 # Statement of need
 
@@ -50,7 +50,7 @@ Marine science relies on fieldwork for data collection, yet sea-going opportunit
 
 <!-- TODO: CTD needs an e.g. reference for the specific cable mounted style! -->
 
-`VirtualShip` simulates the deployment of virtual instruments commonly used in oceanographic fieldwork, with emphasis on realism in how users plan and execute expeditions. For example, users must consider ship speed and instrument deployment/recovery times to ensure their expedition is feasible within given time constraints. Possible instrument selections include surface `Drifter` [@Lumpkin2017], `CTD` (Conductivity-Temperature-Depth), `Argo float` [@Jayne2017], `XBT` (Expendable Bathythermograph; @Goni2019), underway `ADCP` (Acoustic Doppler Current Profiler; @Kostaschuk2005), and underway `Underwater_temperature/salinity` [@Gordon2014] probes. More detail on each instrument is available in the [documentation](https://virtualship.readthedocs.io/en/latest/user-guide/assignments/Research_proposal_intro.html#Measurement-Options).
+`VirtualShip` simulates the deployment of virtual instruments commonly used in oceanographic fieldwork, with emphasis on realism in how users plan and execute expeditions. For example, users must consider ship speed and instrument deployment/recovery times to ensure their expedition is feasible within given time constraints. Possible instrument selections include surface `Drifter` [@Lumpkin2017], `CTD` (Conductivity-Temperature-Depth; @Johnson2007), `Argo float` [@Jayne2017], `XBT` (Expendable Bathythermograph; @Goni2019), underway `ADCP` (Acoustic Doppler Current Profiler; @Kostaschuk2005), and underway `Underwater_temperature/salinity` [@Gordon2014] probes. More detail on each instrument is available in the [documentation](https://virtualship.readthedocs.io/en/latest/user-guide/assignments/Research_proposal_intro.html#Measurement-Options).
 
 The software can simulate complex multidisciplinary expeditions. One example is a virtual expedition across the Agulhas Current and the South Eastern Atlantic that deploys a suite of instruments to sample physical and biogeochemical properties (\autoref{fig:fig1}). Key circulation features appear early in the expedition track, with enhanced ADCP velocities marking the strong Agulhas Current (\autoref{fig:fig1}b) and drifters that turn back toward the Indian Ocean indicating the Agulhas Retroflection (\autoref{fig:fig1}c). The CTD profiles capture the vertical structure of temperature and oxygen along the route, including the warmer surface waters of the Agulhas region (\autoref{fig:fig1}d, early waypoints) and the Oxygen Minimum Zone in the South Eastern Atlantic (\autoref{fig:fig1}e, final waypoints).
 
@@ -63,7 +63,7 @@ The software is designed to be highly accessible to the user. It is wrapped into
 
 1. `virtualship init`: Initialises the expedition directory structure and an `expedition.yaml` configuration file, which controls the expedition route, instrument choices and deployment timings. A common workflow is for users to import pre-determined waypoint coordinates using the `--from-mfp` flag in combination with a coordinates `.csv` or `.xlsx` file (e.g. exported from the NIOZ MFP tool).
 2. `virtualship plan`: Launches a user-friendly Terminal-based expedition planning User Interface (UI), built using [`Textual`](https://textual.textualize.io/). This allows users to intuitively set their waypoint timings and instrument selections, and also modify their waypoint locations.
-3. `virtualship run`: Executes the virtual expedition according to the planned configuration. This includes streaming data via the Copernicus Marine Data Store, simulating the instrument beahviours and sampling, and saving the output in [`Zarr`](https://zarr.dev/) format.
+3. `virtualship run`: Executes the virtual expedition according to the planned configuration. This includes streaming data via the [Copernicus Marine Data Store](https://marine.copernicus.eu/), simulating the instrument beahviours and sampling, and saving the output in [`Zarr`](https://zarr.dev/) format.
 
 A full example workflow is outlined in the [Quickstart Guide](https://virtualship.readthedocs.io/en/latest/user-guide/quickstart.html) documentation.