Downscaling Species Occupancy

Uses species occupancy at coarse grain sizes to predict species occupancy at fine grain sizes. Ten models are provided to fit and extrapolate the occupancy-area relationship, as well as methods for preparing atlas data for modelling. See Marsh et. al. (2018) .


NEWS for downscale package

Changes for 3.0-1

31/08/2018 Extra information and reference added to description

Changes for 3.0-0

30/08/2018 CITATION file added for JSS article and that and MEE article added to references

Changes for 2.0-3

24/08/2017 CITATION file added for JSS in press article

Changes for 2.0-2

08/08/2017 SpatialPointsDataFrame input added to upgrain helpfile downscale helpfile updated

Changes for 2.0-1

01/08/2017 Bug when using SpatialPointsDataFrame corrected

Changes for 2.0-0

28/07/2017 'lat' and 'lon' replaced with 'x' and 'y' in data frame input SpatialPointsDataFrame allowed as input

Changes for 1.2-4

24/11/2016 Bug fixed with error checking in predict.downscale and ensemble.downscale

Changes for 1.2-3

29/09/2016 No need to input cell width in hui.downscale with raster or upgrain object

Changes for 1.2-2

18/08/2016 Default upgraining method changed to "All_Sampled" Names of parameters harmonised with JSS paper

Changes for 1.2-1

10/03/2016 Tutorials checked and adjusted

Changes for 1.2-0

09/03/2016 'spocc' replaced by 'rgbif' in tutorial

Changes for 1.1-0

25/02/2016 Bug for calculating extent in upgrain function fixed upgrain now can return all upgrained rasters ExtendRaster function deleted (now obsolete)

Changes for 1.0

09/10/2015 upgrain and upgrain.threshold: 'All Presences' changed to 'All_Occurrences' upgrain and upgrain.threshold: bugs fixed when selecting number of scales upgrain: plotting now optional DataInput: bug in scale of endemism corrected Vignettes updated

Changes for 1.0

18/05/2015 plot and predict changed to s3 methods help files and examples updated Tutorial vignette added

Changes for 1.0

08/05/2015 Raster package now depends Argument names harmonised across functions Option to specify starting parameters More plotting arguments Calculates AOO as well as occupancy Upgraining vignette added

Changes for 0.7

24/04/2015 Function upgrain.threshold added to explore trade-offs in threshold selection upgrain now allows thresholds of the four default thresholds

Changes for 0.6

14/04/2015 Plotting added to upgrain function Hui model added

Changes for 0.5

13/03/2015 Starting parameters modified Corrected plotting when 0's predicted

Changes for 0.5

24/02/2015 ensemble.predict: means calculated as mean of log occupancies ensemble.predict: warning messages for inconsistent results

23/02/2015 package.rd file updated ensemble - different tolerances allowed for modelling and predicting

Changes for 0.4

05/02/2015 plot=TRUE added to ensemble plotting optimisation of logistic model now includes lower bounds optimisation of GNB model now includes upper and lower bounds

Changes for 0.3

04/02/2015 ensemble.downscale function added

Changes for 0.2

03/02/2015 plotting function added and plotting option added to 'predict.downscale' output of function downscale defined as class 'downscale' output of function predict.downscale defined as class 'predict.downscale' outputs updated to include observed data for use in the plot function help files for downscale and predict.downscale updated

Reference manual

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4.2-0 by Charles Marsh, 3 days ago

Browse source code at

Authors: Charles Marsh [aut, cre]

Documentation:   PDF Manual  

GPL-2 license

Imports cubature, graphics, grDevices, methods, minpack.lm, Rmpfr, sp, stats

Depends on raster

Suggests rgeos, rgdal, rgbif, knitr, rmarkdown, bookdown

See at CRAN