README.md

In boyanangelov/sdmbench: Benchmark Species Distribution Models

sdmbench

Species Distribution Modeling (SDM) is a field of increasing importance in ecology1. Several popular applications of SDMs are understanding climate change effects on species2, natural reserve planning3 and invasive species monitoring4. The sdmbench package solves several issues related to the development and evaluation of those models by providing a consistent benchmarking workflow:

• consistent species occurence data acquisition and preprocessing
• consistent environmental data acquisition and preprocessing (both current data and future projections)
• consistent spatial data partitioning
• integration of a wide variety of machine learning models
• graphical user interface for non/semi-technical users

The end result of a sdmbench SDM analysis is to determine the model - data processing combination that results in the highest predictive power for the species of interest. Such an analysis is useful to researchers who want to avoid issues of model selection and evaluation, and want to rapidly test prototypes of species distribution models.

Installation

# add build_vignettes = TRUE if you want the package vignette
devtools::install_github("boyanangelov/sdmbench")

There are several additional packages you need to install if you want to access the complete sdmbench functionality. First Tensorflow. You can use the keras package to install that (it is installed by the previous command). Note that this step requires a working Python installation on your system. Most modern operating systems have Python pre-installed, but if you are not sure you can check the official website.

# consult the keras documentation if you want GPU support
keras::install_keras(tensorflow = "default")

Additionally you will need MaxEnt. Installation instructions are available here. Note that this requires Java which you can get get from here.

Examples

Here are several examples of what you can do with sdmbench. Downloading and prepare benchmarking data:

library(sdmbench)
#> sdmbench: Tools for benchmarking Species Distribution Models 
#> ============================================================
#> For more information visit http://github.com/ 
#> To start the GUI: run_sdmbench()

benchmarking_data <- get_benchmarking_data("Loxodonta africana", limit = 1200, climate_resolution = 10)
#> [1] "Getting benchmarking data...."
#> [1] "Cleaning benchmarking data...."
#> Assuming 'decimalLatitude' is latitude
#> Assuming 'decimalLongitude' is longitude
#> Assuming 'latitude' is latitude
#> Assuming 'longitude' is longitude
#> Assuming 'latitude' is latitude
#> Assuming 'longitude' is longitude
#> [1] "Done!"
head(benchmarking_data$df_data)
#>   bio1 bio2 bio3 bio4 bio5 bio6 bio7 bio8 bio9 bio10 bio11 bio12 bio13
#> 1  181  132   59 3078  283   60  223  187  141   220   141   425    48
#> 2  180  142   58 3336  292   51  241  210  136   222   136   410    50
#> 3  208  115   86  259  275  142  133  208  207   211   206   956   168
#> 4  180  142   58 3336  292   51  241  210  136   222   136   410    50
#> 5  215  129   56 3244  311   84  227  251  168   251   168   673   120
#> 6  236  167   87  691  335  145  190  233  228   244   228   505   133
#>   bio14 bio15 bio16 bio17 bio18 bio19 label
#> 1    25    19   122    87   114    87     1
#> 2    21    24   122    73   121    73     1
#> 3     5    58   382    42   178   112     1
#> 4    21    24   122    73   121    73     1
#> 5    10    70   334    34   334    34     1
#> 6     4    96   236    14   189    14     1

Preparing data for benchmarking (i.e. add a spatial partitioning method):

data("wrld_simpl", package = "maptools")
benchmarking_data$df_data <- partition_data(dataset_raster = benchmarking_data$raster_data,
                                            dataset = benchmarking_data$df_data,
                                            env = benchmarking_data$raster_data$climate_variables,
                                            method = "block")

learners <- list(mlr::makeLearner("classif.randomForest", predict.type = "prob"),
                 mlr::makeLearner("classif.logreg", predict.type = "prob"),
                 mlr::makeLearner("classif.rpart", predict.type = "prob"),
                 mlr::makeLearner("classif.ksvm", predict.type = "prob"))
benchmarking_data$df_data <- na.omit(benchmarking_data$df_data)

Benchmarking machine learning models on parsed species occurence data:

bmr <- benchmark_sdm(benchmarking_data$df_data, 
                     learners = learners, 
                     dataset_type = "block", 
                     sample = FALSE)
best_results <- get_best_model_results(bmr)
best_results
#> # A tibble: 4 x 3
#> # Groups:   learner.id [4]
#>   learner.id            iter   auc
#>   <fct>                <int> <dbl>
#> 1 classif.randomForest     1 0.992
#> 2 classif.logreg           2 0.915
#> 3 classif.rpart            3 0.900
#> 4 classif.ksvm             4 0.963

Plot best model results:

bmr_models <- mlr::getBMRModels(bmr)
plot_sdm_map(raster_data = benchmarking_data$raster_data,
            bmr_models = bmr_models,
            model_id = best_results$learner.id[1],
            model_iteration = best_results$iter[1],
             map_type = "static") +
            raster::plot(wrld_simpl, 
                         add = TRUE, 
                         border = "darkgrey")

#> integer(0)

Using custom data

If you are interested in bringing your own data, rather than using GBIF, you can toggle the checkmark in the sidebar and upload it. The required format is as follows:

| bio1 | bio2 | bio3 | bio4 | bio […] | bio 19 | label | |------|------|------|------|-----------|--------|-------| | | | | | | | | | | | | | | | |

where label is 0/1. At the monent custom data is supported only for General Models, and has no mapping capability.

A good starting point to discover the full package functionality is to start the GUI with run_sdmbench(). Here are some screenshots:

Vignette

A thorough introduction to the package is available as a vignette in the package, and online.

# open vignette
vignette("sdmbench")

Tests

The package tests are in the tests directory, and can be run by using devtools::test or Ctrl/Cmd + Shift + T within RStudio.

Contributors

Contributions are welcome and guidelines are stated in CONTRIBUTING.md.

License

MIT (LICENSE.md)

References

1. Elith, J. & Leathwick, J. R. Species Distribution Models: Ecological Explanation and Prediction Across Space and Time. Annu. Rev. Ecol. Evol. Syst. 40, 677–697 (2009).

2. Austin, M. P. & Van Niel, K. P. Improving species distribution models for climate change studies: Variable selection and scale. J. Biogeogr. 38, 1–8 (2011).

3. Guisan, A. et al. Predicting species distributions for conservation decisions. Ecol. Lett. 16, 1424–1435 (2013).

4. Descombes, P. et al. Monitoring and distribution modelling of invasive species along riverine habitats at very high resolution. Biol. Invasions 18, 3665–3679 (2016).

boyanangelov/sdmbench documentation built on Dec. 14, 2020, 1:08 a.m.