Final changes which fix the comments from openjournals/joss-reviews#7094 (comment)

Author: michaeldenes

docs/paper/paper.md

@@ -25,6 +25,11 @@ link-bibliography: false
 
 The current version supports nano- and microplastic behaviour, with support for macroplastics planned in the near-future. It has been designed for use with hydrodynamic and biogeochemical data from the [Copernicus Marine Service](https://marine.copernicus.eu/), providing new plastic modelling capabilities as part of the [NECCTON (New Copernicus Capability for Trophic Ocean Networks)](https://neccton.eu/) project. `plasticparcels` is easily adapted to run on local machines and high-performance computing (HPC) architecture with various hydrodynamic, biogeochemical, and other model fields as input. A future goal is to embed `plasticparcels` within a cloud platform to allow for even more rapid prototyping, development, and simulations.
 
+The core features of `plasticparcels` are: 1) a user-friendly python notebook layer on top of `parcels` that provides a streamlined workflow for performing plastic dispersal simulations, 2) custom `parcels` kernels designed to simulate the fine-scale physical processes that influence the transport of nano- and microplastic particulates, and 3) global particle initialisation maps which represent the best estimate locations of plastic pollution emissions from coastal sources, river sources, open ocean fishing-related activity emission sources, and a current best estimate of buoyant plastic concentrations. We visualise these initialisation maps in Fig. \ref{fig:initialisation_maps}.
+
+![Particle initialisations maps based on a) coastal mismanaged plastic waste emissions [@Jambeck2015], b) riverine mismanaged plastic waste emissions [@Meijer2021], c) fishing activity related plastic emissions [@Kroodsma2018], and d) a current global surface concentration estimate [@Kaandorp2023].\label{fig:initialisation_maps}](initialisation_maps.png){width=100%}
+
+In addition, due to the flexibility of the package, users may use the functions and modular design of `plasticparcels` to enhance their existing `parcels` simulations and workflow. For example, users can use the initialisation maps, associated `ParticleSet` creation methods, and/or the custom physics kernels with their own `parcels` simulations. Post-processing and analysis of the generated trajectory datasets is purposefully left to the user, however some tutorials are provided in the [`plasticparcels` documentation](https://plastic.oceanparcels.org/en/latest/examples.html), along with the tutorials in the [`parcels` documentation](https://docs.oceanparcels.org/en/latest/documentation.html). Below we provide an example use case of `plasticparcels`.
 
 # Statement of need
 Marine plastic debris can be found almost everywhere in the ocean. A recent study estimates that there is approximately 3,200 kilotonnes of (initially) positively buoyant plastics in the global ocean in the year 2020 [@Kaandorp2023], where 59-62\% of these plastics are found at the ocean surface, 36-39\% within the deeper ocean, and 1.5-1.9\% along the coastline. They estimate that 500 kilotonnes of positively buoyant plastic enters the ocean each year, where 39-42\% originate from mismanaged waste along coastlines, 45-48\% originate from fishing-related activities (e.g. fishing lines, nets, traps, and crates), and 12-13\% from mismanaged waste entering the ocean via rivers.
@@ -35,20 +40,10 @@ Lagrangian ocean analysis, where virtual particles are tracked in hydrodynamic f
 
 The past decade has seen a growing number of community-developed software packages for performing Lagrangian simulations [@Paris2013; @Fredj2016; @Lange2017; @Doos2017; @Dagestad2018; @JalonRojas2019; @Delandmeter2019]. In many cases, these packages are specific to particular particle classes or hydrodynamic models, or are written and embedded in proprietary software languages, and can be inflexible or difficult to integrate into different applications. In the case of plastic dispersal simulations, the underlying physical processes are still being researched and their implementation is under development [@vanSebille2020]. Hence, an open-source, flexible, and modular approach to performing Lagrangian simulations is necessary for prototyping, developing, and testing new physical process parameterisation schemes. Easy-to-run simulations allow for a more reproducable results, and for simple-to-produce sensitivity analyses.
 
-Here, we have developed `plasticparcels` to unify plastic dispersion modelling into one easy-to-use code. While `plasticparcels` has been designed for researchers who routinely perform plastic particle dispersion simulations, it is equally useful to novice users who are new to Lagrangian ocean analysis techniques.
-
-# Description of the software
-`plasticparcels` has been designed as an extension of the `parcels` Lagrangian framework [@Lange2017; @Delandmeter2019]. The core functionality of `parcels` are its `FieldSet`, `ParticleSet`, and `Kernel` objects. In the context of `plasticparcels`, the `FieldSet` contains a collection of hydrodynamic, physical, and biogeochemical fields required for plastic particle advection. The `ParticleSet` contains a set of plastic particles with their time-evolving properties, such as their position, accumulated biofilm amount, and density. A `Kernel` defines the specific computational behaviour for simulating a physical process applied to a plastic particle. These objects are designed to be as flexible and customisable as possible so that users can perform Lagrangian simulations of a wide variety of particulates, such as tuna, plastic, plankton, icebergs, turtles [@Lange2017]. However, due to the flexible nature of the software, there is a steep learning curve for new users, who often find it difficult to setup their simulations in a rapid fashion due to the complexity of modern hydrodynamic model output. We have developed `plasticparcels` as user-friendly tool specifically designed for easy-to-generate plastic dispersal simulations. While `plasticparcels` is primarily designed for use in the cloud and in HPC environments (due to the typically terabyte-size of hydrodynamic datasets generated from ocean general circulation models), it can be easily installed and run on local machines. A schematic of `plasticparcels` is shown in Fig. \ref{fig:schematic}.
+Here, we have developed `plasticparcels` as an extension of the `parcels` Lagrangian framework [@Lange2017; @Delandmeter2019]in order to unify plastic dispersion modelling into one easy-to-use code. While `plasticparcels` has been designed for researchers who routinely perform plastic particle dispersion simulations, it is equally useful to novice users who are new to Lagrangian ocean analysis techniques. The core functionality of `parcels` are its `FieldSet`, `ParticleSet`, and `Kernel` objects. In the context of `plasticparcels`, the `FieldSet` contains a collection of hydrodynamic, physical, and biogeochemical fields required for plastic particle advection. The `ParticleSet` contains a set of plastic particles with their time-evolving properties, such as their position, accumulated biofilm amount, and density. A `Kernel` defines the specific computational behaviour for simulating a physical process applied to a plastic particle. These objects are designed to be as flexible and customisable as possible so that users can perform Lagrangian simulations of a wide variety of particulates, such as tuna, plastic, plankton, icebergs, turtles [@Lange2017]. However, due to the flexible nature of the software, there is a steep learning curve for new users, who often find it difficult to setup their simulations in a rapid fashion due to the complexity of modern hydrodynamic model output. We have developed `plasticparcels` as user-friendly tool specifically designed for easy-to-generate plastic dispersal simulations. While `plasticparcels` is primarily designed for use in the cloud and in HPC environments (due to the typically terabyte-size of hydrodynamic datasets generated from ocean general circulation models), it can be easily installed and run on local machines. A schematic of `plasticparcels` is shown in Fig. \ref{fig:schematic}.
 
 ![`plasticparcels` schematic.\label{fig:schematic}](schematic.png){width=100%}
 
-The core features of `plasticparcels` are: 1) a user-friendly python notebook layer on top of `parcels` that provides a streamlined workflow for performing plastic dispersal simulations, 2) custom `parcels` kernels designed to simulate the fine-scale physical processes that influence the transport of nano- and microplastic particulates, and 3) global particle initialisation maps which represent the best estimate locations of plastic pollution emissions from coastal sources, river sources, open ocean fishing-related activity emission sources, and a current best estimate of buoyant plastic concentrations. We visualise these initialisation maps in Fig. \ref{fig:initialisation_maps}.
-
-![Particle initialisations maps based on a) coastal mismanaged plastic waste emissions [@Jambeck2015], b) riverine mismanaged plastic waste emissions [@Meijer2021], c) fishing activity related plastic emissions [@Kroodsma2018], and d) a current global surface concentration estimate [@Kaandorp2023].\label{fig:initialisation_maps}](initialisation_maps.png){width=100%}
-
-In addition, due to the flexibility of the package, users may use the functions and modular design of `plasticparcels` to enhance their existing `parcels` simulations and workflow. For example, users can use the initialisation maps, associated `ParticleSet` creation methods, and/or the custom physics kernels with their own `parcels` simulations. Post-processing and analysis of the generated trajectory datasets is purposefully left to the user, however some tutorials are provided in the [`plasticparcels` documentation](https://plastic.oceanparcels.org/en/latest/examples.html), along with the tutorials in the [`parcels` documentation](https://docs.oceanparcels.org/en/latest/documentation.html). Below we provide an example use case of `plasticparcels`.
-
-
 # Usage Example
 Here, we briefly demonstrate how `plasticparcels` can be used for a microplastic dispersal simulation in the Mediterranean Sea. The tutorial can be found on the [`plasticparcels` documentation](https://plastic.oceanparcels.org/en/latest/examples/example_Italy_coast.html). Here, we use the coastal mismanaged plastic waste dataset [@Jambeck2015] to visualise the trajectories of buoyant (surface-bound) microplastic particles subject to the effects of Stokes drift and wind-induced drift, neglecting any vertical motion (along with any biofouling, or vertical mixing).