book.bib

@Book{xie2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {http://yihui.org/knitr/},
}
@article{Teixeira2020,
  author={Teixeira, Edmar. and Ausseil, Anne-Gaelle. and Burgue{\~{n}}o, Eric. and Brown, Hamish. and Cichota, Rogerio. and Davy, Marcus. and Ewert, Frank. and Guo, Jing. and Holmes, Allister. and Holzworth, Dean. and Hu, Wei. and de Ruiter, John. and Hume, Ellen. and Jesson, Linley. and Johnstone, Paul. and Powell, John. and Kersebaum, Kurt Christian. and Kong, Hymmi. and Liu, Jian
and Lilburne, Linda. and Meiyalaghan, Sathiyamoorthy. and Storey, Roy. and Richards, Kate. and Tait, Andrew. and van der Weerden, Tony},
  editor={Mirschel, Wilfried. and Terleev, Vitaly V. and Wenkel, Karl-Otto},
  title={A Spatial Analysis Framework to Assess Responses of Agricultural Landscapes to Climates and Soils at Regional Scale},
  bookTitle={Landscape Modelling and Decision Support},
  year={2020},
  publisher={Springer International Publishing},
  address={Cham},
  pages={495--508},
  isbn={978-3-030-37421-1},
  doi={10.1007/978-3-030-37421-1_25},
  url={https://doi.org/10.1007/978-3-030-37421-1_25}
}
@phdthesis{Sim2014,
author = {Sim, R. E.},
file = {:C\:/Users/cflfcl/Dropbox/1. master_background_reading/Thesis/Sim_phd1.pdf:pdf},
keywords = {Dryland,evaporation,extraction front velocity,g},
school = {Lincoln University, Canterbury, New Zealand},
title = {{Water extraction and use of seedling and established dryland lucerne crops}},
year = {2014}
}
@phdthesis{McCallum1998,
abstract = {The water and nitrogen (N) dynamics of a lucerne-based farming system (grazed lucerne-annual medic-ryegrass pastures grown in rotation with crops) was compared to continuous cropping (cereal, pulse and oilseed crops) in the Victorian Wimmera. The growth dynamics and CO2-exchange behaviour of lucerne in the pasture phase was also investigated. Soil profiles under lucerne-based pastures remained consistently drier during the year as compared to annual cropping. The amount of plant-available soil water (0.0 to 2.0 m) after 3 to 4 years of pasture was on average 48 mm less than after annual crops (wheat, field pea), most of which (81%) was extracted at depth (1.0 to 2.0 m). In the field, crop yields (canola, wheat) after lucerne were not reduced because water use by these crops was predominantly in the top 1.0 m of the soil profile. A wheat simulation study predicted that a small median yield loss of 0.4 t ha-1 (15%) could be expected for the first wheat crop grown after lucerne, although this yield penalty varied from 0 to 0.87 t ha-1 depending upon seasonal rainfall. The risk of a large yield penalty (>0.8 t ha-1) was low (5 years in 100). From simulation studies, the time taken to fully recharge the soil profile after lucerne to levels equivalent to that under continuous cropping was estimated to occur within 4 to 5 years. The contributions of N2 fixation by the legumes (lucerne, annual medic, field pea) to the N economy of the farming systems in this study depended upon the amount of dry matter production. N2 fixation by field pea (121-175 kg N ha-1 yr-1) was greater than pasture legumes (40-95 kg N ha-1 yr-1), although a large amount of N was removed in grain at harvest (115-151 kg N ha-1 yr-1). N2 fixation by lucerne (19-90 kg N ha-1 yr-1) was consistently greater than annual medic (2-56 kg N ha-1 because the effects of seasonal rainfall patterns on dry matter production were more pronounced for annual medic. Winter-cleaning of ryegrass in the pasture before cropping resulted in both a high legume content (85%) and generally increased N2 fixation (up to 55 kg N ha-1 yr-1 ). Despite some benefits in N fertility, large responses to N fertiliser were still observed in crops following pastures; in grain yield (increases of 0.33-0.55 t ha-1 for canola, 1.0 t ha-1 for wheat), protein (0.7-2.3% for canola, 1.3% for wheat) and oil yield in canola (124-205 kg ha-1). The growth pattern of lucerne was similar to that of annual species (annual medic, ryegrass) contained in the pasture, with the majority (70%) of growth occurring between July and November. The small amount of lucerne growth from summer to early autumn (December to March) was due to the small supply of water (rainfall and stored in soil) during this period. A more detailed study of two lucerne pastures during summer revealed that the plant was under considerable water stress; leaf:stem ratios increased (from 0.9-1.6 to 2.6-3.2), leaf folding and paraheliotropic movement decreased the amount of leaf area exposed to incoming radiation in the middle of the day (by 14-29%), and it was estimated that the some 75-83% of assimilated carbon was partitioned below-ground to roots and crowns.},
author = {McCallum, Matthew Harvie},
keywords = {Continuous cropping,Lucerne-based farming system,Victoria,Wimmera},
month = {aug},
title = {{The water and nitrogen dynamics of a lucerne-based farming system in the Victorian Wimmera}},
url = {http://hdl.handle.net/11343/114436 file:///bitstream/handle/11343/114436/b2380255-00001-00001.pdf?sequence=1&isAllowed=n},
year = {1998}
}
@techreport{Dalgliesh2016,
author = {Dalgliesh, Neal and Hochman, Zvi and Huth, Neil and Holzworth, Dean},
number = {September},
pages = {1--24},
title = {{Csiro Agriculture and Food a Protocol for the Development of Apsoil Parameter Values for Use in Apsim}},
year = {2016}
}
@book{Cortez2014,
abstract = {The goal of this book is to gather in a single document the most relevant concepts related to modern optimization methods, showing how such concepts and methods can be addressed using the open source, multi-platform R tool. Modern optimization methods, also known as metaheuristics, are particularly useful for solving complex problems for which no specialized optimization algorithm has been developed. These methods often yield high quality solutions with a more reasonable use of computational resources (e.g. memory and processing effort). Examples of popular modern methods discussed in this book are: simulated annealing; tabu search; genetic algorithms; differential evolution; and particle swarm optimization. This book is suitable for undergraduate and graduate students in Computer Science, Information Technology, and related areas, as well as data analysts interested in exploring modern optimization methods using R},
annote = {1. Introduction -- 2. R Basics -- 3. Blind Search -- 4. Local Search -- 5. Population-Based Search -- 6. Multi-Objective Optimization -- 7. Applications},
author = {Cortez, Paulo},
booktitle = {Use R!},
isbn = {9783319082622},
keywords = {COMPUTERS,Electronic books,Electronic data processing,General,MATHEMATICS,Probability & Statistics,Programming Languages,R (Computer program language),bisacsh,fast},
publisher = {Springer},
title = {{Modern optimization with R}},
url = {https://ezproxy.plantandfood.co.nz/login?url=https://ebookcentral.proquest.com/lib/plantandfood/detail.action?docID=1968177},
year = {2014}
}
@article{Pearson1972,
author = {Pearson, CJ. and Hunt, LA.},
isbn = {0780379446},
journal = {Canadian Journal of Plant Science},
number = {6},
pages = {1007--1015},
title = {{EFFECTS OF TEMPERATURE ON PRIMARY GROWTH AND REGROWTHS OF ALFALFA}},
volume = {52},
year = {1972}
}
@book{Hewitt2010,
author = {Hewitt, A. E.},
edition = {3rd},
isbn = {9780478347104},
pages = {136},
title = {{New Zealand Soil Classification. Landcare Research Science Series No. 1}},
year = {2010}
}
@article{McIntyre1995,
author = {McIntyre, B D and Riha, S J and Flower, D J},
issn = {0378-4290},
journal = {Field Crops Research},
number = {2-3},
pages = {67--76},
publisher = {Elsevier},
title = {{Water uptake by pearl millet in a semiarid environment}},
volume = {43},
year = {1995}
}
@article{Fick1988,
author = {Fick, G W and Holt, D A and Lugg, D G},
journal = {Alfalfa and alfalfa improvement},
pages = {163--194},
publisher = {Wiley Online Library},
title = {{Environmental physiology and crop growth}},
volume = {29},
year = {1988}
}
@misc{RCoreTeam2019,
author = {{R Core Team}},
booktitle = {R Foundation for Statistical Computing, Vienna, Austria.},
title = {{R: A language and environment for statistical computing}},
year = {2019}
}
@techreport{Mullan2018,
abstract = {Prepared for the Ministry for the Environment by Mullan B, Sood A, Stuart, S, National Institute of Water and Atmospheric Research (NIWA)},
author = {Mullan, B and Sood, A and Stuart, S and Carey-Smith, T},
booktitle = {Ministry for the Environment},
isbn = {9780908339440},
pages = {1--131},
title = {{Climate change projections for New Zealand: Atmospheric projections based on simulations undertaken for the IPCC 5th assessment 2nd addition}},
year = {2018}
}
@article{Monteith1986,
author = {Monteith, John Lennox and Greenwood, Duncan Joseph and Penman, Howard Latimer and Pereira, Sir Charles and Hamlin, M J and Mansell-Moullin, M},
doi = {10.1098/rsta.1986.0007},
journal = {Philosophical Transactions of the Royal Society of London. Series A, Mathematical and Physical Sciences},
month = {feb},
number = {1537},
pages = {245--259},
publisher = {Royal Society},
title = {{How do crops manipulate water supply and demand?}},
volume = {316},
year = {1986}
}
@article{Brown2009,
abstract = {A generic framework was developed and validated for predicting the water extraction and water stress responses of perennial lucerne (Medicago sativa) to improve existing crop models. Perennial forages have roots established throughout a soil profile so require a different approach to quantify water extraction patterns than annual crops. Two years of experimental data from two fields in New Zealand, each containing dryland and irrigated lucerne crops, were analysed to develop the theory of the water extraction framework. This showed that the temporal pattern of water extraction was consistent and each year commenced in the shallowest layer and progressed downward. Water extraction from each soil layer was quantified as the minimum of soil water supply and crop demand for that layer. For each soil layer, water demand was represented by transpiration demand (the product of potential evapotranspiration and crop cover) minus the sum of water extraction in overlying layers. This approach gave accurate descriptions of water extraction patterns over a range of rainfall and irrigation situations. Water supply from each soil layer (l) was quantified as the product of plant-available water and an extraction rate constant (kl l). The kll of lucerne could not be calculated using the traditional curve-fitting procedure so kll was calculated by integrating the water extraction framework described above with a soil water balance and fitting kll to minimise residuals for water extraction predictions in each soil layer. This gave kll values that decreased from 0.035/day in the 00.2m layer of soil to 0.01/day in the deepest layer measured (1.82.3m). The water extraction framework was validated against another 3 years of dryland and irrigated lucerne data and gave accurate predictions of water extraction patterns throughout the soil profile. Water stress was quantified from actual transpiration relative to transpiration demand (T/T D). The most sensitive variable was leaf area expansion, which decreased from an optimum at T/TD≤1 to zero at T/T D≤0.2, followed by radiation-use efficiency, which decreased from an optimum at T/TD≤1 to zero at a T/TD of zero. The framework for quantifying water extraction and the techniques determined for identifying appropriate parameters to measure and characterise the framework are expected to be generally applicable to perennial forages in a wide range of environments. {\textcopyright} 2009 CSIRO.},
author = {Brown, Hamish E. and Moot, Derrick J. and Fletcher, Andrew L. and Jamieson, Peter D.},
doi = {10.1071/CP08415},
file = {:C\:/Users/cflfcl/Dropbox/1. master_background_reading/modelling/Brown2009.pdf:pdf},
issn = {18360947},
journal = {Crop and Pasture Science},
keywords = {Alfalfa (syn. lucerne),Leaf area index,Mechanistic simulation,Radiation-use efficiency,Soil water content,Transpiration,Water extraction depth.},
number = {8},
pages = {785--794},
title = {{A framework for quantifying water extraction and water stress responses of perennial lucerne}},
volume = {60},
year = {2009}
}
@techreport{Dalgliesh1997,
author = {Dalgliesh, Neal and Foale, Mike},
month = {jan},
title = {{Soil Matters—Monitoring Soil Water and Nutrients in Dryland Farming Systems}},
year = {1997}
}
@inproceedings{Jordan1980,
author = {Jordan, Wayne R and Miller, F},
title = {{Genetic variability in sorghum root systems: implication for drought tolerance.}},
year = {1980}
}
@article{EI2006,
abstract = {This research examined seasonal patterns of growth and development of lucerne crops grown with different levels of crown and taproot reserves in a cool temperate environment. The approach required derivation of explanatory mathematical relationships between crop physiological processes and the main environmental variables of temperature, photoperiod and incoming radiation. To create crops with contrasting levels of perennial reserves (i.e. carbon and nitrogen stored in crowns and taproots), four defoliation treatments were applied to an established 'Kaituna' lucerne crop at Lincoln University, Canterbury, New Zealand in the 2002/03 and 2003/04 growth seasons. Treatments consisted of a factorial combination of a (i) 28 day (short, S) or (ii) 42 days (long, L) regrowth cycle during (i) spring/mid-summer and/or (ii) mid-summer/autumn. The treatments had acronyms of LL, LS, SL or SS, in which each letter refers to the frequency of defoliation in the first and second period of the season, respectively. Regardless of defoliation treatment, perennial dry matter (DMper) differed seasonally. In LL crops, DMper increased from <3 t/ha in mid-summer to >5 t/ha in autumn. Frequent defoliations (SS) reduced both the DMper by 20-30% and the concentration and amount of soluble sugars, starch and nitrogen in taproots. As a result, the annual shoot yield ranged from 23 t/ha (LL) to 14 t/ha (SS) in 2003/04. Most of this difference was explained by changes in the weight of each individual shoot. Despite shoot yield differences, plant population declined at similar exponential rates in all crops from 140 plants/m² in August 2002 to 60 plants/m² in October 2004. Final shoot populations were conservative at $\sim$780 shoots/m² in all crops. Physiologically, yield differences were mostly explained (R²=0.84) by the accumulated intercepted photosynthetic active radiation ($\Sigma$PARi). The $\Sigma$PARi was limited in frequently defoliated crops because these crops had lower leaf area index (LAI) than LL crops but similar canopy architecture, with an extinction coefficient for diffuse light (kd) of 0.81. Differences in LAI were a direct effect of harvesting before full canopy cover (i.e. critical LAI of 3.6) in short regrowth cycles. In addition, leaf area expansion rates (LAER) in spring were reduced from 0.016 (LL) to 0.011 m²/m²/°Cd (SS) as taproot DM declined from 3.0 to 1.5 t/ha, respectively. The reduction in LAER was a result of smaller leaves after the 5th main stem-node and a reduction in{\ldots}},
author = {EI, Teixeira},
file = {:C\:/Users/cflfcl/Dropbox/1. master_background_reading/Thesis/teixeira_phd.pdf:pdf},
journal = {PhD Thesis Lincoln University},
title = {{Understanding growth and development of lucerne crops (Medicago sativa L.) with contrasting levels of perennial reserves. Canterbury New Zealand.}},
year = {2006}
}
@misc{Strand2019,
author = {Strand, Julia F and Brown, Violet A},
booktitle = {Frontiers in Psychology  },
isbn = {1664-1078},
pages = {564},
title = {{Publishing Open, Reproducible Research With Undergraduates   }},
volume = {10      },
year = {2019}
}
@book{Jones1986,
address = {College Station},
author = {Jones, C Allan and Kiniry, J R (James Robert) and Dyke, P T},
edition = {1st ed..},
publisher = {College Station : Texas A&M University Press},
title = {{CERES-Maize : a simulation model of maize growth and development}},
year = {1986}
}
@article{Or2013,
abstract = {Globally, evaporation consumes about 25% of solar energy input and is a key hydrologic driver with 60% of terrestrial precipitation returning to the atmosphere via evapotranspiration. Quantifying evaporation is important for assessing changes in hydrologic reservoirs and surface energy balance and for many industrial and engineering applications. Evaporation dynamics from porous media reflect interactions between internal liquid and vapor transport, energy input for phase change, and mass transfer across air boundary layer. We reviewed recent advances on resolving interactions between soil intrinsic properties and evaporation dynamics with emphasis on the roles of capillarity and wettability affecting liquid phase continuity and capillary driving forces that sustain Stage I evaporation. We show that soil water characteristics contain information for predicting the drying front depth and mass loss at the end of Stage I and thus derive predictions for regional-scale evaporative water losses from soil textural maps. We discuss the formation of secondary drying front at the onset of Stage II evaporation and subsequent diffusion-controlled dynamics. An important aspect for remote sensing and modeling involves nonlinear interactions between wet evaporating surfaces and air boundary layer above (evaporation rate is not proportional to surface water content). Using pore scale models of evaporating surfaces and vapor transport across air boundary layer, we examined the necessary conditions for maintenance of nearly constant evaporation while the surface gradually dries and the drying front recedes into the soil. These new insights could be used to improve boundary conditions for models that are based on surface water content to quantify evaporation rates.},
author = {Or, Dani and Lehmann, Peter and Shahraeeni, Ebrahim and Shokri, Nima},
doi = {https://doi.org/10.2136/vzj2012.0163},
issn = {1539-1663},
journal = {Vadose Zone Journal},
month = {nov},
number = {4},
pages = {vzj2012.0163},
publisher = {John Wiley & Sons, Ltd},
title = {{Advances in Soil Evaporation Physics—A Review}},
volume = {12},
year = {2013}
}
@misc{Chacon2014,
author = {Chacon, Scott and Straub, Ben},
edition = {2nd},
isbn = {1484200772},
publisher = {Apress},
title = {{Pro Git}},
year = {2014}
}
@article{MichaelLandau2018,
abstract = {Licence Authors of JOSS papers retain copyright and release the work under a Creative Commons Attri-bution 4.0 International License (CC-BY). Summary The drake R package (Landau 2018) is a workflow manager and computational engine for data science projects. Its primary objective is to keep results up to date with the underlying code and data. When it runs a project, drake detects any pre-existing output and refreshes the pieces that are outdated or missing. Not every runthrough starts from scratch, and the final answers are reproducible. With a user-friendly R-focused interface , comprehensive documentation, and extensive implicit parallel computing support, drake surpasses the analogous functionality in similar tools such as Make (Stallman 1998), remake (FitzJohn 2017), memoise (Wickham et al. 2017), and knitr (Xie 2017). In reproducible research, drake's role is to provide tangible evidence that a project's results are re-creatable. Drake quickly detects when the code, data, and output are synchronized. In other words, drake helps determine if the starting materials would produce the expected output if the project were to start over and run from scratch. This approach decreases the time and effort it takes to evaluate research projects for reproducibility. Regarding high-performance computing, drake interfaces with a wide variety of technologies to deploy the steps of a data analysis project. Options range from local multicore computing to serious distributed computing on a cluster. In addition, the parallel computing is implicit. In other words, drake constructs the directed acyclic network of the workflow and determines which steps can run simultaneously and which need to wait for dependencies. This automation eases the cognitive and computational burdens on the user, enhancing the readability of code and thus reproducibility.},
author = {{Michael Landau}, William},
doi = {10.21105/joss.00550},
issn = {2475-9066},
journal = {The Journal of Open Source Software},
title = {{The drake R package: a pipeline toolkit for reproducibility and high-performance computing}},
year = {2018}
}
@incollection{Kirkham2014,
abstract = {This chapter defines potential evapotranspiration (PET). The concept was put forth separately in 1948 by Thornthwaite in America and Penman in England. The factors that affect PET are discussed. They include fetch, crop height, crop cover, plant resistance to water flow, soil-water availability, and advection. Advection is defined including the clothesline effect and the oasis effect. It is pointed out that evaporation from the soil surface is a two-stage process. The first stage is a constant-rate stage in which evaporation from the soil surface is limited by the energy on the surface of the soil. The second stage is the falling-rate stage in which water movement to the soil surface is controlled by the hydraulic properties of the soil. An easy method is given to determine PET. It requires knowledge only of solar radiation and the average daily temperature or noon temperature. An appendix gives the biography of Penman.},
address = {Boston},
author = {Kirkham, M.B.},
doi = {https://doi.org/10.1016/B978-0-12-420022-7.00028-8},
editor = {Kirkham, M B B T - Principles of Soil and Plant Water Relations (Second Edition)},
isbn = {978-0-12-420022-7},
pages = {501--514},
publisher = {Academic Press},
title = {{Chapter 28 - Potential Evapotranspiration}},
year = {2014}
}
@article{Moot2012,
abstract = {With limited funds, and the relatively low importance of dryland pastures in New Zealand, research has been targeted at the species most likely to induce transformational change on-farm. Lucerne research into biophysical influences on plant growth and development has added flexibility to spring grazing management. Coupled with additional agronomic research and extension, farmers now have the confidence to use lucerne as a direct feed source for sheep, beef and deer. Research on Caucasian clover seedling development identified the long duration to secondary leaf production as the physiological basis for slow clover establishment in mixed swards. Despite agronomic strategies to overcome this, its use is now limited by commercial constraints. A 10-year ‘MaxClover' grazing experiment at Lincoln University demonstrated the superiority of subterranean clover with cocksfoot over perennial ryegrass and white clover for pasture persistence, quality and animal performance. Pastures with high legume content had higher water-use efficiency and produced greater animal and pasture production. Balansa and gland clovers both show a strong influence of photoperiod on time of flowering, which suggests they may be suitable for oversowing into areas of winter wet and summer dry hill and high country. Further research into their ecological niche and ability to regenerate each autumn is required. For all legumes, the role of inoculation requires further research with recent results suggesting indigenous, rather than commercially introduced, bacterial populations are dominant in root nodules. Uptake of dryland pasture species for on-farm use has only been successful when research, extension and agribusiness interests have been aligned.},
author = {Moot, D. J.},
journal = {Crop and Pasture Science},
number = {9},
pages = {726--733},
title = {{An overview of dryland legume research in New Zealand}},
volume = {63},
year = {2012}
}
@misc{Liu2020,
author = {Liu, Jian},
title = {{Working example of ApsimX Edit feature}},
year = {2020}
}
@article{Passioura1983,
abstract = {The influence of roots on the yield of water-limited crops is analysed with the help of the identity: yield = water used X water-use efficiency X harvest index Despite being severely water-stressed, many droughted crops leave substantial amounts of apparently available water in the subsoil at maturity. The factors influencing this amount are outlined, particularly those concerning the morphology of the root system. Prospects for improving yield by extracting the residual water are discussed. Because roots are difficult to harvest, water-use efficiency is usually defined as above-ground-biomass/water-used. It follows that the more assimilate a plant transfers to its roots the lower will be its water-use efficiency. There is presumably an optimal root/shoot ratio (in terms of water relations) at which above-ground biomass is maximal for a given water supply. This ratio appears to exceed the optimum in many cases. For a given biomass, the yield of a grain crop depends in part on the pattern of water use during the season, because harvest index is often related to the proportion of the total water supply that is used after anthesis. For crops relying on a limited supply of stored water, a high axial resistance to flow in the roots may ensure that water in the subsoil is not used so quickly that too little remains at anthesis for the plants to set and fill an adequate number of grains. A breeding program aimed at changing this resistance in wheat roots is described. Finally, the principles are discussed on which physiological research can be useful in improving drought resistance. The need to dissect water-limited yield into largely independent components is emphasised, for such a dissection greatly improves the focus of the research.},
author = {Passioura, J B},
doi = {https://doi.org/10.1016/0378-3774(83)90089-6},
issn = {0378-3774},
journal = {Agricultural Water Management},
number = {1},
pages = {265--280},
title = {{Roots and drought resistance}},
volume = {7},
year = {1983}
}
@incollection{Molloy1988,
author = {Molloy, L},
booktitle = {Soils in the New Zealand Landscape: The Living Mantle},
chapter = {Chapter-12},
pages = {179--191},
title = {{Stony plains, silty downs}},
year = {1988}
}
@article{Ritchie1972,
abstract = {A model is presented for calculating the daily evaporation rate from a crop surface. It applies to a row crop canopy situation in which the soil water supply to the plant roots is not limited and the crop has not come into an advanced stage of maturation or senescence. The crop evaporation rate is calculated by adding the soil surface and plant surface components (each of these requiring daily numbers for the leaf area index), the potential evaporation, the rainfall, and the net radiation above the canopy. The evaporation from the soil surface Es is calculated in two stages: (1) the constant rate stage in which Es is limited only by the supply of energy to the surface and (2) the falling rate stage in which water movement to the evaporating sites near the surface is controlled by the hydraulic properties of the soil. The evaporation from the plant surfaces Ep is predicted by using an empirical relation based on local data, which shows how Ep is related to Eo through the leaf area index. The model was used to obtain the total evaporation rate E = Es + Ep of a developing grain sorghum (Sorghum bicolor L.) canopy in central Texas. The results agreed well with values for E measured directly with a weighing lysimeter.},
author = {Ritchie, Joe T},
doi = {https://doi.org/10.1029/WR008i005p01204},
issn = {0043-1397},
journal = {Water Resources Research},
month = {oct},
number = {5},
pages = {1204--1213},
publisher = {John Wiley & Sons, Ltd},
title = {{Model for predicting evaporation from a row crop with incomplete cover}},
volume = {8},
year = {1972}
}
@book{McLaren1996,
abstract = {"Designed for use by students studying soil science as part of degree and diploma courses"--Back cover.},
address = {Auckland [N.Z.]},
author = {McLaren, R G (Ronald G.)},
edition = {New ed..},
editor = {Cameron, K C (Keith C.)},
publisher = {Auckland N.Z. : Oxford University Press},
title = {{Soil science : sustainable production and environmental protection}},
year = {1996}
}
@article{Dardanelli1997,
abstract = {This study was carried out: (i) to estimate from soil water depletion curves the apparent rooting depth (RD) for several crops; (ii) to calculate the soil water extraction parameters; and (iii) to compare inter- and intraspecific differences in the water extraction parameters. Experiments were conducted at the Manfredi Experimental Station (INTA), Argentina (31°49'S, 63°48' W), and at the Institute of Phytopathology and Vegetal Physiology (IFFIVE), Cordoba, Argentina (31°24' S, 64°11' W). The soil was a silty loam Entic Haplustoll (USDA Soil Taxonomy) with A, AC and C horizons. The crops studied were: maize (Zea mays L.), sunflower (Helianthus annuus L.), peanut (Arachis hypogaea L.), soybean (Glycine max L. Merr.), and alfalfa (Medicago sativa L.). Differences in apparent rooting depths among species and cultivars, ranging from 130 to 290 cm, were found. The comparison of the extraction front velocity (EFV) revealed differences among species but not among cultivars of the same species. EFV ranged from 44 mm day -1 for sunflower to 23 mm day -1 for peanut. In all the crops, the downward progress of the extraction front stopped at the beginning of the grain filling. Comparisons among the pooled rates of water extraction (kl) for depths from 10 to 110 cm, revealed significant differences among crops and cultivars within crops. The kl values ranged from 0.110 day -1 for Contiflor 3 sunflower to 0.029 day -1 for alfalfa. No significant correlation between kl values and root length density over 40 to 120 cm depths was found for soybean, indicating that the specific water uptake rate varies considerably in the soil profile.},
author = {Dardanelli, J. L. and Bachmeier, O. A. and Sereno, R. and Gil, R.},
doi = {10.1016/S0378-4290(97)00017-8},
issn = {03784290},
journal = {Field Crops Research},
keywords = {Alfalfa,Maize,Peanut,Soybean,Sunflower,Water extraction},
month = {aug},
number = {1},
pages = {29--38},
title = {{Rooting depth and soil water extraction patterns of different crops in a silty loam haplustoll}},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0378429097000178},
volume = {54},
year = {1997}
}
@article{Lehmann2008,
author = {Lehmann, Peter and Assouline, Shmuel and Or, Dani},
doi = {10.1103/PhysRevE.77.056309},
issn = {1539-3755},
journal = {Physical Review E},
month = {may},
number = {5},
pages = {056309},
publisher = {American Physical Society},
title = {{Characteristic lengths affecting evaporative drying of porous media}},
url = {https://link.aps.org/doi/10.1103/PhysRevE.77.056309},
volume = {77},
year = {2008}
}
@misc{Zambrano-Bigiarini2020,
author = {Zambrano-Bigiarini, M.},
doi = {10.5281/ZENODO.3707013},
month = {mar},
title = {{hzambran/hydroGOF: v0.4-0}},
year = {2020}
}
@inproceedings{Moot2003,
abstract = {Successful lucerne stand management requires balancing animal and plant requirements to produce crops of high quality and yield at times of high animal demand. Understanding the impact of environmental signals on crop growth and development can aid management decisions throughout the season. In spring, crops remobilise reserves from the roots to shoots and expand nodes accumulated through the winter, producing rapid stem extension and canopy closure as temperatures increase. The timing of spring defoliation should be based on crop yield and animal requirements rather than any specific developmental stage. Through spring and summer, crops should be rotationally grazed, with highest lamb live-weights achieved from 6-8 weeks grazing solely on lucerne. Summer crop production is dependent on rainfall and the plant available water content. During summer, grazing at the appearance of open flowers or basal buds is recommended as a compromise between maximum yield and quality. In autumn, the priority of assimilates allocation in the crop changes from above to below ground growth. To enhance the recharge of root reserves, an extended period of flowering is recommended in February or March. The time of flowering is dependent on the accumulation of thermal time and increases as photoperiod shortens. In periods of prolonged drought, lucerne herbage should be hard grazed and then spelled until the end of late autumn regrowth. A final hard grazing in June or early July, to remove overwintering aphids, should be followed by spraying 7-14 days later. Crops continue to develop nodes through the winter, and stands should be spelled until spring to ensure nodes are not removed by grazing, as this delays regrowth and reduces dry matter production.},
author = {Moot, D. J. and Brown, H. E. and Teixeira, E. I. and Pollock, K. M.},
booktitle = {Legumes for Dryland Pastures},
isbn = {0-864761570},
pages = {201--208},
title = {{Crop growth and development affect seasonal priorities for lucerne management}},
volume = {11},
year = {2003}
}
@article{Moot2019,
abstract = {In 2008, Bog Roy was run as a typical high-country station with merino ewes and lambs set stocked for long periods of the year, with 60 ha of lucerne grown for hay. Over the next 7 years, the lucerne and ryecorn areas increased by 30 ha per year. Total lamb meat weaned increased from 91 to 130 t in the first three years direct feeding of lucerne commenced, which improved ewe and two-tooth performance at lambing (% and survival). In the second phase, ewe numbers and pre-weaning lamb growth rates increased. Lambs were weaned earlier and ewes returned to higher pasture covers on hills, which improved their condition score and weights at mating and lambing. In 2016, a change from flood to pivot irrigation resulted in a further production increase to 160 t weaned lamb. By 2018, the mixed age ewes had 141% lambing (to tailing), and pre-weaning lamb growth rates of over 270 g/hd/d which allowed weaning after 80 days. The lamb weaned per ewe mated has increased from 25 to 37 kg over the decade despite increased feed demand from 900 more ewes. These animal performance indicators quantify the transformational change achieved through a focus on grazing and increasing the area of lucerne. This was followed by lucerne and red clover based pastures being established under pivots. The ability to record and quantify changes in stock performance has given the farmer confidence to trust and embrace the transformational change.},
author = {Moot, Derrick J. and Anderson, Pete V.A. and Anderson, Lisa J. and Anderson, David K.},
doi = {10.33584/jnzg.2019.81.390},
issn = {2463-2880},
journal = {Journal of New Zealand Grasslands},
month = {oct},
pages = {75--80},
title = {{Animal performance changes over 11 years after implementing a lucerne grazing system on Bog Roy Station}},
volume = {81},
year = {2019}
}
@misc{Bonhomme2000,
abstract = {Degree.day units, for which there are also several synonymous terms, are often used in agronomy essentially to estimate or predict the lengths of the different phases of development. The physiological and mathematical bases upon which they are founded are, however, sometimes forgotten, resulting in questionable interpretations. Such is particularly the case for anything relating to variations in the temperature thresholds which enter into the calculation of these degree.day sums. Without seeking to draw up a synthesis of the extremely numerous works published in the field, this review article sets out to present the basic principles of the degree.day unit notion as well as the limits of its use. On this last point, we will particularly emphasise the influence of the non-linearity of the temperature response of the method used in determining the threshold temperature as well as the pertinence of the temperature taken into account in studying the phenomenon. Several practical conclusions are drawn from this review article. (C) 2000 Elsevier Science B.V.},
author = {Bonhomme, Raymond},
booktitle = {European Journal of Agronomy},
doi = {10.1016/S1161-0301(00)00058-7},
issn = {11610301},
month = {jul},
number = {1},
pages = {1--10},
publisher = {Elsevier},
title = {{Bases and limits to using 'degree.day' units}},
volume = {13},
year = {2000}
}
@techreport{APSIMInitiative2020,
author = {APSIMInitiative},
pages = {28},
title = {{SoilWater}},
year = {2020}
}
@misc{APSIMInitiative,
author = {APSIMInitiative},
title = {{Edit .apsimx files from command line}}
}
@misc{Tanner1983,
abstract = {Summary For centuries man has been concerned to some degree with the efficient use of water in the production of his crops. This chapter provides a general historical and current perspective to the detailed and specific discussions that are essential to understanding efficient water use. It re-evaluates the fundamental concept of water-use efficiency. The central question examined is the nature of the ratio of biomass productivity to evapotranspiration, and its inherent variability. Even field crops on good soils that only occasionally suffer severe yield decreases are irrigated to provide production stability, which is important with high land values and other high operational costs. Costs of the water are minimized by improving irrigation techniques, reducing soil evaporation, increasing water recovery by the crop, etc. The chapter also presents an overview of the key concepts discussed in this book.},
author = {Tanner, C B and Sinclair, T R},
booktitle = {Limitations to Efficient Water Use in Crop Production},
doi = {https://doi.org/10.2134/1983.limitationstoefficientwateruse.c1},
isbn = {9780891182412},
month = {jan},
pages = {1--27},
series = {ASA, CSSA, and SSSA Books},
title = {{Efficient Water Use in Crop Production: Research or Re-Search?}},
year = {1983}
}
@misc{APSIMInitiativea,
author = {APSIMInitiative},
title = {{Construct a factorial simulation in the User Interface}}
}
@incollection{Schabenberger2001,
author = {Schabenberger, O and Pierce, Fran},
booktitle = {Contemporary Statistical Models for the Plant and Soil Sciences},
chapter = {5},
month = {jan},
pages = {183--293},
publisher = {CRC Press},
title = {{Nonlinear models}},
year = {2001}
}
@article{Iqbal2016,
abstract = {Examination of recent trends in reproducibility and transparency practices in biomedical research reveals an ongoing lack of access to full datasets and detailed protocols for both clinical and non-clinical studies.},
author = {Iqbal, Shareen A and Wallach, Joshua D and Khoury, Muin J and Schully, Sheri D and Ioannidis, John P A},
journal = {PLOS Biology},
month = {jan},
number = {1},
pages = {e1002333},
publisher = {Public Library of Science},
title = {{Reproducible Research Practices and Transparency across the Biomedical Literature}},
volume = {14},
year = {2016}
}
@article{Teixeira2007,
abstract = {The frequency of defoliation is the major management tool that modulates shoot yield and the accumulation of C and N root reserves in lucerne crops. A fully irrigated, 2-year-old lucerne (Medicago sativa L.) crop was grown at Lincoln University (43°38′S and 172°28′E) and subjected to four defoliation treatments. These involved the combination of two grazing frequencies (28 or 42 days) applied before and/or after mid-summer. Annual shoot dry matter (DM) yield ranged from 12 to 23 t/ha. These differences were largely explained by the amount of intercepted photosynthetically active radiation (PARi) using a conservative conversion efficiency of 1.6 g DM/MJ PARi. Part of the reduced PARi in the frequently defoliated treatments was caused by the shorter regrowth period that impeded crop canopy closure to the critical leaf area index (LAIcrit) of 3.6. Canopy architecture was unaffected by treatments and a single extinction coefficient for diffuse PARi (kd) of 0.81 was found for 'Grasslands Kaituna' lucerne. The pool of endogenous nitrogen (N) in taproots was reduced by frequent defoliations. This explained differences in leaf area expansion rate (LAER), which decreased from 0.016 m2/(m2 °C day) at 60 kg N/ha to 0.011 m2/(m2 °C day) at 20 kg N/ha. The pool of soluble sugars was also positively associated with LAER but the concentrations of carbohydrates and N reserves and the pool of taproot starch were poorly related to LAER. The slower LAER in the frequently defoliated treatments was mostly caused by the smaller area of primary and axillary leaves, particularly above the 6th node position on the main-stem. Developmental processes were less affected by defoliation frequency. For example, the phyllochron was similar in all treatments at 34 °C day (base temperature of 5 °C) per primary leaf during spring/summer but increased in autumn and ranged between 44 and 60 °C day. Branching and senescence started after the appearance of the 4th main-stem node, and both were unaffected by defoliation frequency. These results suggest that the expansion of individual leaves, both primary and axillary, was the most plastic component of canopy formation, particularly after the appearance of the 6th primary leaf. Future mechanistic modelling of lucerne crops may incorporate the management or environmental responses of LAER that control PARi and impact on shoot DM yields. {\textcopyright} 2007 Elsevier B.V. All rights reserved.},
author = {Teixeira, Edmar I. and Moot, Derrick J. and Brown, Hamish E. and Pollock, Keith M.},
doi = {10.1016/j.eja.2007.03.001},
file = {:C\:/Users/cflfcl/Dropbox/1. master_background_reading/physiology/ed2007.pdf:pdf},
issn = {11610301},
journal = {European Journal of Agronomy},
keywords = {"alfalfa,Alfalfa,Branching,Grazing management,Leaf area index,Phyllochron,Root reserves,Senescence,branching,grazing management,leaf area},
month = {jul},
number = {1},
pages = {154--164},
title = {{How does defoliation management impact on yield, canopy forming processes and light interception of lucerne (Medicago sativa L.) crops?}},
url = {https://linkinghub.elsevier.com/retrieve/pii/S1161030107000408},
volume = {27},
year = {2007}
}