From 2c8b959043f4d94e6dace751d1e857da0c97ad52 Mon Sep 17 00:00:00 2001 From: Kevin Kramer Date: Wed, 13 Dec 2023 15:11:35 +0100 Subject: [PATCH] paper: refs, acknowledgements --- R/weather.R | 15 +++++- inst/REFERENCES.bib | 27 +++++++++++ joss_paper/paper.bib | 111 +++++++++++++++++++++++++++++++++++++++++++ joss_paper/paper.md | 43 +++++++++++------ 4 files changed, 180 insertions(+), 16 deletions(-) diff --git a/R/weather.R b/R/weather.R index 31bceee..e3c290c 100644 --- a/R/weather.R +++ b/R/weather.R @@ -20,6 +20,13 @@ #' These parameters are stored in this object in the respective `PARAM_vec` #' fields. #' +#' # Snow model +#' +#' The precipitation and temperature inputs are used in order to estimate the +#' snow cover for each day by use of a snow model. +#' The employed model is as formulated by Kokkonen et al. 2006 and makes use +#' of parameters from Rango and Martinec, 1995. +#' #' @field weather_file Name of provided weather data file. #' @field years numeric Integer representation of the contained years. #' @field vec_size Length of the PARAM_vec vectors, which is equal to *number @@ -41,6 +48,10 @@ #' - snow #' - ndays (number of days in this year) #' +#' @references +#' \insertRef{rango1995RevisitingDegreeDayMethod}{growR} +#' \insertRef{kokkonen2006ConstructionDegreedaySnow}{growR} +#' #' @md #' @export WeatherData = R6Class( @@ -137,9 +148,9 @@ WeatherData = R6Class( T_melt = -1. # melt coefficient [mm C-1 d-1] (Rango and Martinec, 1995) C_melt = 3. - # freeze coefficient [mm C-1 d-1] (Kokkonen et al, ??) + # freeze coefficient [mm C-1 d-1] (Kokkonen et al, 2006) C_freeze = 0.05 - # liquid water retention coeff. (Kokkonen et al, ??) + # liquid water retention coeff. (Kokkonen et al, 2006) C_retention = 0.25 liquidP_vec = (1./(1. + exp(-1.5*(Ta_vec - 2.)))) * PP_vec diff --git a/inst/REFERENCES.bib b/inst/REFERENCES.bib index 5f79ee0..915c698 100644 --- a/inst/REFERENCES.bib +++ b/inst/REFERENCES.bib @@ -142,3 +142,30 @@ @article{kruijt2008EffectsRisingAtmospheric langid = {english}, keywords = {Climate scenario,CO-effect,CO2 growth,evapotranspiration,Evapotranspiration,skimmed,Soil moisture,Stomatal conductance,The Netherlands,Water management} } + +@inproceedings{kokkonen2006ConstructionDegreedaySnow, + title = {Construction of a Degree-Day Snow Model in the Light of the Ten Iterative Steps in Model Development}, + booktitle = {{{iEMSs}} Third Biennial Meeting: "{{Summit}} on {{Environmental Modelling}} and {{Software}}". {{International}} Environmental Modelling and Software Society, Burlington, {{USA}}, July 2006}, + author = {Kokkonen, Teemu and Koivusalo, Harri and Jakeman, Anthony and Norton, John}, + year = {2006}, + publisher = {{International Environmental Modelling and Software Society (iEMSs)}}, + address = {{Switzerland}}, + langid = {english}, + keywords = {growR,snow,snow processes} +} + +@article{rango1995RevisitingDegreeDayMethod, + title = {Revisiting the {{Degree-Day Method}} for {{Snowmelt Computations}}}, + author = {Rango, A. and Martinec, J.}, + year = {1995}, + journal = {JAWRA Journal of the American Water Resources Association}, + volume = {31}, + number = {4}, + pages = {657--669}, + issn = {1752-1688}, + doi = {10.1111/j.1752-1688.1995.tb03392.x}, + urldate = {2023-12-13}, + langid = {english}, + keywords = {degree-day method,growR,hydrograph analysis and modeling,snow,snow and ice hydrology,snowmelt} +} + diff --git a/joss_paper/paper.bib b/joss_paper/paper.bib index c4908b5..5ed5ff3 100644 --- a/joss_paper/paper.bib +++ b/joss_paper/paper.bib @@ -63,6 +63,18 @@ @inbook{IPCC2022Chapter05 type = {Book Section} } +@book{thornley1998GrasslandDynamicsEcosystem, + title = {Grassland {{Dynamics}}: {{An Ecosystem Simulation Model}}}, + shorttitle = {Grassland {{Dynamics}}}, + author = {Thornley, J. H. M.}, + year = {1998}, + publisher = {{CAB International}}, + googlebooks = {aULwAAAAMAAJ}, + isbn = {978-0-85199-227-3}, + langid = {english}, + keywords = {Computers / Data Science / Data Modeling \& Design,Science / Environmental Science,Science / Life Sciences / Ecology} +} + @article{thornley1997TemperateGrasslandResponses, title = {Temperate {{Grassland Responses}} to {{Climate Change}}: An {{Analysis}} Using the {{Hurley Pasture Model}}}, shorttitle = {Temperate {{Grassland Responses}} to {{Climate Change}}}, @@ -245,3 +257,102 @@ @phdthesis{schaumberger2011RaeumlicheModelleZur annotation = {ISBN-13: 978-3-902559-67-8} } +@inproceedings{kokkonen2006ConstructionDegreedaySnow, + title = {Construction of a Degree-Day Snow Model in the Light of the Ten Iterative Steps in Model Development}, + booktitle = {{{iEMSs}} Third Biennial Meeting: "{{Summit}} on {{Environmental Modelling}} and {{Software}}". {{International}} Environmental Modelling and Software Society, Burlington, {{USA}}, July 2006}, + author = {Kokkonen, Teemu and Koivusalo, Harri and Jakeman, Anthony and Norton, John}, + year = {2006}, + publisher = {{International Environmental Modelling and Software Society (iEMSs)}}, + address = {{Switzerland}}, + langid = {english}, + keywords = {growR,snow,snow processes} +} + +@article{rango1995RevisitingDegreeDayMethod, + title = {Revisiting the {{Degree-Day Method}} for {{Snowmelt Computations}}}, + author = {Rango, A. and Martinec, J.}, + year = {1995}, + journal = {JAWRA Journal of the American Water Resources Association}, + volume = {31}, + number = {4}, + pages = {657--669}, + issn = {1752-1688}, + doi = {10.1111/j.1752-1688.1995.tb03392.x}, + urldate = {2023-12-13}, + langid = {english}, + keywords = {degree-day method,growR,hydrograph analysis and modeling,snow,snow and ice hydrology,snowmelt} +} + +@article{hoglind2020BASGRAModelGrassland, + title = {{{BASGRA}}\_{{N}}: {{A}} Model for Grassland Productivity, Quality and Greenhouse Gas Balance}, + shorttitle = {{{BASGRA}}\_{{N}}}, + author = {H{\"o}glind, Mats and Cameron, David and Persson, Tomas and Huang, Xiao and {van Oijen}, Marcel}, + year = {2020}, + month = feb, + journal = {Ecological Modelling}, + volume = {417}, + pages = {108925}, + issn = {0304-3800}, + doi = {10.1016/j.ecolmodel.2019.108925}, + urldate = {2023-04-20}, + langid = {english}, +} + +@misc{vanoijen2015BASGRA_2014, + title = {{{BASGRA}}\_2014}, + author = {Van Oijen, M. and H{\"o}glind, M. and Cameron, D.R. and Thorsen, S.M.}, + year = {2015}, + month = aug, + doi = {10.5281/zenodo.27867}, + urldate = {2023-12-13}, + abstract = {This is the first public release of BASGRA, the BASic GRAssland model, developed jointly by Marcel van Oijen, Mats H{\"o}glind, David Cameron and Stig Morten Thorsen. A full description of the model can be found in the User Guide included in this release.}, + howpublished = {Zenodo}, + keywords = {Grassland model} +} + +@article{moore1997GRAZPLANDecisionSupport, + title = {{{GRAZPLAN}}: {{Decision}} Support Systems for {{Australian}} Grazing Enterprises. {{III}}. {{Pasture}} Growth and Soil Moisture Submodels, and the {{GrassGro DSS}}}, + shorttitle = {{{GRAZPLAN}}}, + author = {Moore, A. D. and Donnelly, J. R. and Freer, M.}, + year = {1997}, + month = dec, + journal = {Agricultural Systems}, + volume = {55}, + number = {4}, + pages = {535--582}, + issn = {0308-521X}, + doi = {10.1016/S0308-521X(97)00023-1}, + urldate = {2023-12-13}, +} + +@article{lazzarotto2009DynamicsGrassClover, + title = {Dynamics of Grass{\textendash}Clover Mixtures{\textemdash}{{An}} Analysis of the Response to Management with the {{PROductive GRASsland Simulator}} ({{PROGRASS}})}, + author = {Lazzarotto, P. and Calanca, P. and Fuhrer, J.}, + year = {2009}, + month = mar, + journal = {Ecological Modelling}, + volume = {220}, + number = {5}, + pages = {703--724}, + issn = {0304-3800}, + doi = {10.1016/j.ecolmodel.2008.11.023}, + urldate = {2023-05-24}, + langid = {english}, + keywords = {Allocation,Feedback mechanisms,Fertilization,Grass/clover interactions,Grassland model,PROGRASS,Root development}, +} + +@article{graux2011DevelopmentPastureSimulation, + title = {Development of the {{Pasture Simulation Model}} for Assessing Livestock Production under Climate Change}, + author = {Graux, A. -I. and Gaurut, M. and Agabriel, J. and Baumont, R. and Delagarde, R. and Delaby, L. and Soussana, J. -F.}, + year = {2011}, + month = nov, + journal = {Agriculture, Ecosystems \& Environment}, + volume = {144}, + number = {1}, + pages = {69--91}, + issn = {0167-8809}, + doi = {10.1016/j.agee.2011.07.001}, + urldate = {2023-12-13}, + keywords = {Biogeochemical cycles,CH emission,Grassland,Grazing,Ruminants}, +} + diff --git a/joss_paper/paper.md b/joss_paper/paper.md index 6e2fff0..444bec3 100644 --- a/joss_paper/paper.md +++ b/joss_paper/paper.md @@ -38,24 +38,28 @@ anthropogenic climate change [@IPCC2022Chapter05]. There is thus ample motivation to study the properties and dynamics of grasslands. -Experimental approaches, while of fundamental importance, suffer from high -costs in time resources required, as a study site typically has to be maintained -over several years in order to make a scientific observation. -For this reason, the method of investigating grassland dynamics by means of -mathematical models and simulatory approaches has found widespread -application, with dozens of models being formulated, employed and further -developed. -Each of these models has been developed with different applications in mind +Mathematical models offer an efficient pathway to investigating grassland +dynamics. +Additionally, such models can be employed in agricultural and political +decision support systems, see e.g. [GrazPlan](https://grazplan.csiro.au/) +[@moore1997GRAZPLANDecisionSupport]. +Simulatory approaches have therefore found widespread application, with +dozens of models being formulated, employed and further developed. +Each of these models has been created with different applications in mind and thus comes with its own focal points and a set of advantages and disadvantages. To give just a few examples: -- The Hurley Pasture Model [@thornley1997TemperateGrasslandResponses] is a - rather complete and detailed mechanistic model for managed pastures. -- [RothC](https://www.rothamsted.ac.uk/rothamsted-carbon-model-rothc) was - developed for the long-term - Rothamsted Parkgrass Experiment [@jenkinson1994TrendsHerbageYields] and - thus uses comparatively long time scales with a focus on the carbon balance. +- The [Hurley Pasture Model](https://sites.massey.ac.nz/hurleypasturemodel/hurley-pasture-model/)[@thornley1998GrasslandDynamicsEcosystem] + is a rather complete and detailed mechanistic model for managed pastures. +- [BASGRA](https://github.com/davcam/BASGRA/) [@hoglind2020BASGRAModelGrassland] + and its descendant [BASGRA_N](https://github.com/MarcelVanOijen/BASGRA_N) + [@vanoijen2015BASGRA_2014] are multi-year grassland models which + prominently include tiller dynamics. +- PROGRASS [@lazzarotto2009DynamicsGrassClover] was developed to capture the + interactions in grass/clover mixtures. +- The focus of PaSim [@graux2011DevelopmentPastureSimulation] is the + investigation of livestock production under climate change conditions. - ModVege @[jouven2006ModelPredictingDynamics] is another mechanistic model that is designed to capture the dominant processes with a minimum of required input parameters. @@ -115,6 +119,10 @@ work with the model in its original formulation or with any combination of the provided extensions. These additions include: +- Simulation of snow cover by use of a model by + @kokkonen2006ConstructionDegreedaySnow and + @rango1995RevisitingDegreeDayMethod, important when modelling grassland in + mountainous regions. - A cut decision algorithm, which allows the model to simulate management decisions in the absence of such input data. The decision process is based on work by @petersen2021DynamicSimulationManagement and @@ -140,5 +148,12 @@ The distribution as an `R` package on [CRAN](https://cran.r-project.org/) ensures an easy installation procedure and a relatively high standard of code quality and documentation through CRAN's submission policies. +# Acknowledgements + +The work of K.~K. has been supported by +[Agroscope](https://www.agroscope.admin.ch/), the [National Center for +Climate Sevices (NCCS)[https://www.nccs.admin.ch/nccs/de/home.html] and the +[Federal Office for Agriculture](https://www.blw.admin.ch/blw/en/home.html). + # References