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NicheMapR v2.0.0 - Now including an official release of the ectotherm model
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@mrke mrke released this 10 Oct 00:06
· 471 commits to master since this release
v2.0.0
b7ea5f4

This is a major update on the NicheMapR package, being an official release of the ectotherm model and associated Dynamic Energy Budget model scripts as well as introducing some major improvements to the microclimate model and including a beta version of the endotherm model. The release is timed with two publications on the package as indicated below. There is now also a website for the package:

https://mrke.github.io/

The Fortran code is now open source (except for aspects of the endotherm model, for the time being) and the whole package has been set up to compile the underlying Fortran code for the microclimate and ectotherm models on installation from github.

Microclimate model updates:

  1. The micro_ncep function is now included, which integrates with the recently released microclima package https://github.com/ilyamaclean/microclima, as well as the RNCEP package https://CRAN.R-project.org/package=RNCEP and elevatr package https://CRAN.R-project.org/package=elevatr to allow estimates of historical microclimates anywhere in the world, as described in this paper:

Kearney M. R., Gillingham P. K., Bramer I., Duffy J. P. & Maclean I. M. D. (2019) A method for computing hourly, historical, terrain-corrected microclimate anywhere on Earth. Methods in Ecology and Evolution.

  1. The micro_usa function is finalised, which connects to the gridMET ~4km USA climatology (see Kearney, M. R. (2019). microclimUS: hourly estimates of historical microclimates for the United States of America with example applications. Ecology, 0(ja), e02829. doi:10.1002/ecy.2829).

  2. The RnetCDF package is now used in place of ncdf4, which has the big bonus of allowing opendap connectivity on all platforms (ncdf4 wouldn't do this for Windows, although this has recently been rectified by pmjherman https://github.com/pmjherman/r-ncdf4-build-opendap-windows). This means you can set 'opendap =1' in micro_aust and micro_usa and you can web-query the weather grids of AWAP and gridMET, respectively.

  3. All the microclimate functions (micro_global, micro_ncep, micro_aust, micro_usa, micro_nz, micro_uk) are set to use the SoilGrids database as an option for extracting textural and bulk density data from which hydraulic properties are derived (set 'soilgrids = 1').

  4. An additional approach to computing the vertical air temperature profile has been added (in collaboration with Paul Mathewson), based on equations in Campbell, G. S., & Norman, J. M. (1998). Environmental Biophysics. New York: Springer. It can be invoked by making tne new parameter ZH greater than zero and explained further in the relevant help files and vignettes.

  5. The global climate data set (global.climate.zip) is now provided as part of the release and the get.global.climate downloads it from here.

Ectotherm model

  1. Although a beta version of the ectotherm model has been part of the package since its inception, it is now officially released with Fortran source included. The model is described in this software note:

Kearney M. R. & Porter W. P. (2019) NicheMapR - an R package for biophysical modelling: the ectotherm and Dynamic Energy Budget models. Ecography. doi 10.1111/ecog.04680

  1. Compared to the earlier versions, the release version has some revisions to the naming of parameters for improved consistency, especially in regard to the Dynamic Energy Budget (DEB) model terminology. There is also improved and updated documentation including a revision of the vignette 'ectotherm model tutorial' and a new 'DEB model tutorial'. The DEB model functionality is also described in the software note mentioned above.

  2. The DEB functionality has been improved by including the DOPRI5 integrator to do the integration through time (before a simple Euler method was used, and this option is still available), and the DEB models that can be run now include the standard model as before, but also the abj, abp and hex models (see http://www.debtheory.org/wiki/index.php?title=Typified_models). There are now also DEB R scripts for running the std, abj and abp DEB models independent of the ectotherm model. Code has been included to allow DEB model parameters to be passed directly from the DEB parameter database (now >2000 species), as explained in the 'DEB model tutorial' vignette.

Endotherm model

There is now a working beta version of the general endotherm model developed by Porter and colleagues over many years. This version is explained in two vignettes now included in the package and will be undergoing a number of updates over the next few months before being finalised. These updates will largely be cosmetic and the overall algorithm will remain unchanged. A software note will be produced explaining the model in detail.

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