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paleopop

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paleopop is an extension to poems, a spatially-explicit, process-explicit, pattern-oriented framework for modeling population dynamics. This extension adds functionality for modeling large populations at generational time-steps over paleontological time-scales.

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("GlobalEcologyLab/paleopop")

About R6 classes

poems and paleopop are based on R6 class objects. R is primarily a functional programming language; if you want to simulate a population, you might use the lapply or replicate functions to repeat a generative function like rnorm. R6 creates an object-oriented programming language inside of R, so instead of using functions on other functions, in these packages we simulate populations using methods attached to objects. Think of R6 objects like machines, and methods like switches you can flip on the machines.

Example

One of the major additions in paleopop is the PaleoRegion R6 class, which allows for regions that change over time due to ice sheets, sea level, bathymetry, and so on. The plots below show the temporal mask functionality of the PaleoRegion object. The temporal mask indicates cells that are occupiable at each time step with a 1 and unoccupiable cells with a NA. In this example, I use the temporal_mask_raster method to show how “Ring Island” changes at time step 10 due to a drop in sea level.

library(poems)
library(paleopop)
coordinates <- data.frame(x = rep(seq(-178.02, -178.06, -0.01), 5),
                          y = rep(seq(19.02, 19.06, 0.01), each = 5),
                          z = rep(1, 25))
template_raster <- raster::rasterFromXYZ(coordinates, 
                                         crs = "+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0")
sealevel_raster <- template_raster
template_raster[][c(7:9, 12:14, 17:19)] <- NA # make Ring Island
sealevel_raster[][c(7:9, 12:14, 17:18)] <- NA
raster_stack <- raster::stack(x = append(replicate(9, template_raster), sealevel_raster))
region <- PaleoRegion$new(template_raster = raster_stack)
raster::plot(region$temporal_mask_raster()[[1]], main = "Ring Island (first timestep)",
             xlab = "Longitude (degrees)", ylab = "Latitude (degrees)",
             colNA = "blue")

raster::plot(region$temporal_mask_raster()[[10]], main = "Ring Island (last timestep)",
             xlab = "Longitude (degrees)", ylab = "Latitude (degrees)",
             colNA = "blue")

paleopop also includes the PaleoPopModel class, which sets up the population model structure. Here I show a very minimalist setup of a model template using this class.

model_template <- PaleoPopModel$new(
  region = region, # makes the simulation spatially explicit
  time_steps = 10, # number of time steps to simulate
  years_per_step = 12, # years per generational time-step
  standard_deviation = 0.1, # SD of growth rate
  growth_rate_max = 0.6, # maximum growth rate
  harvest = F, # are the populations harvested?
  populations = 17, # total occupiable cells over time
  initial_abundance = seq(9000, 0, -1000), # initial pop. sizes
  transition_rate = 1.0, # transition rate between generations
  carrying_capacity = rep(1000, 17), # static carrying capacity
  dispersal = (!diag(nrow = 17, ncol = 17))*0.05, # dispersal rates
  density_dependence = "logistic", # type of density dependence
  dispersal_target_k = 10, # minimum carrying capacity to attract dispersers
  occupancy_threshold = 1, # lower than this # of pops. means extinction
  abundance_threshold = 10, # threshold for Allee effect
  results_selection = c("abundance") # what outputs do you want in results?
)

The paleopop_simulator function accepts a PaleoPopModel object or a named list as input to simulate populations over paleo time scales, and the PaleoPopResults class stores the outputs from the paleo population simulator.

results <- paleopop_simulator(model_template)
results # examine
#> $abundance
#>       [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#>  [1,]    0    0    0    0    0    0    0    0    0     0
#>  [2,]   39   84  154  263  404  541  763  740  925  1144
#>  [3,]   20   48   88  166  249  388  488  620  633   728
#>  [4,]    0    0    0    0    0    0    0    0    0     0
#>  [5,]  220  297  461  641  879  983  908  936 1095   831
#>  [6,]  398  555  747  776 1076  896  939  912  984   936
#>  [7,]  726  820 1007 1053 1068 1063  857  865  982  1096
#>  [8,] 1189  778  856  856  939  871  826  927  996  1191
#>  [9,] 1174  979  806  928  931  997  938  923  980   866
#> [10,]    0    0    0    0    0    0    0    0    0     0
#> [11,]    0    0    0    0    0    0    0    0    0     0
#> [12,]    0    0    0    0    0    0    0    0    0     0
#> [13,]  157  288  474  658  806  843  930  951  959   905
#> [14,]  252  405  606  792  882  976 1011 1130 1113  1113
#> [15,]  113  209  344  468  633  808  842 1120 1189   990
#> [16,]  691  746  994  783  843  922  958  915 1101   922
#> [17,]  540  729  937  930  862  915  895  758  958  1039
raster::plot(region$raster_from_values(results$abundance[,10]),
             main = "Final abundance", xlab = "Longitude (degrees)", 
             ylab = "Latitude (degrees)", colNA = "blue")

A practical example of how to use paleopop, with more complex parameterization, can be found in the vignette.

Citation

You may cite paleopop in publications using our software paper in Global Ecology and Biogeography:

Pilowsky, J. A., Haythorne, S., Brown, S. C., Krapp, M., Armstrong, E., Brook, B. W., Rahbek, C., & Fordham, D. A. (2022). Range and extinction dynamics of the steppe bison in Siberia: A pattern‐oriented modelling approach. Global Ecology and Biogeography, 31(12), 2483-2497.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.