knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
Spatial autocorrelation can severely bias transfer function performance estimates. If can also bias reconstruction significance tests, but I suspect the bias is not as severe.
This vignette show how to use the autosim
argument to randomTF()
to use an autocorrelated simulated environmental variables, instead of the default uniformly distributed independent environmental variables, to make the reference distribution.
#| label: load-packages #| message: false library(palaeoSig) library(rioja) library(sf) library(gstat) library(dplyr) library(tibble) library(tidyr) library(purrr) library(ggplot2) set.seed(42) # for reproducibility
We use the foraminifera dataset by Kucera et al. (2005). We use some of the samples to represent a core.
# load data data(Atlantic) meta <- c("Core", "Latitude", "Longitude", "summ50") Atlantic <- as.data.frame(Atlantic) # prevents rowname warnings # pseudocore as no fossil foram data in palaeoSig fosn <- Atlantic |> filter(between(summ50, 5, 10)) |> slice_sample(n = 20) # remaining samples as training set Atlantic <- Atlantic |> anti_join(fosn, by = "Core") |> slice_sample(n = 300) # random subset to speed analysis up Atlantic_meta <- Atlantic |> select(one_of(meta)) # to keep rdist.earth happy Atlantic <- Atlantic |> # species select(-one_of(meta)) fos <- fosn |> select(-one_of(meta))
We need to convert the meta data into an sf
object for further calculation.
Atlantic_meta <- st_as_sf( x = Atlantic_meta, coords = c("Longitude", "Latitude"), crs = 4326 )
Fitting the variogram is the hardest part. There are several types of variogram model available, e.g. exponential "Exp", spherical "Sph", gaussian "Gau" and Matérn "Mat". These have different shapes. It is important to find one that fits the data well.
# Estimate the variogram model for the environmental variable of interest ve <- variogram(summ50 ~ 1, data = Atlantic_meta) vem <- fit.variogram( object = ve, model = vgm(40, "Mat", 5000, .1, kappa = 1.8) ) plot(ve, vem) vem
Now we can use gstat::krige
to do Gaussian unconditional simulation and make simulated environmental fields with the same spatial structure as the observed variable.
This step is quite slow with large datasets.
#| label: kriging # Simulating environmental variables sim <- krige(sim ~ 1, locations = Atlantic_meta, dummy = TRUE, nsim = 100, beta = mean(Atlantic_meta$"summ50"), model = vem, newdata = Atlantic_meta ) # convert sf back to a regular data.frame sim <- sim |> st_drop_geometry()
Now we can run randomTF
using the simulated environmental variables.
#| label: randomTF-auto #| fig-cap: "Figure 2. Result of randomTF with an autocorrelated null model." rtf_auto <- randomTF( spp = Atlantic, env = Atlantic_meta$summ50, fos = fos, autosim = sim, fun = MAT, col = "MAT.wm" ) plot(rtf_auto)
#| label: randomTF-independent #| fig-cap: Figure 3. Result of randomTF with a spatially independent null model. rtf_ind <- randomTF( spp = Atlantic, env = Atlantic_meta$summ50, fos = fos, fun = MAT, col = "MAT.wm" ) plot(rtf_ind)
Kucera, M., Weinelt, M., Kiefer, T., Pflaumann, U., Hayes, A., Weinelt, M., Chen, M.-T., Mix, A.C., Barrows, T.T., Cortijo, E., Duprat, J., Juggins, S., Waelbroeck, C. 2005. Reconstruction of the glacial Atlantic and Pacific sea-surface temperatures from assemblages of planktonic foraminifera: multi-technique approach based on geographically constrained calibration datasets. Quaternary Science Reviews 24, 951-998 doi:10.1016/j.quascirev.2004.07.014.
Telford, R.J., Birks, H.J.B. 2009. Evaluation of transfer functions in spatially structured environments. Quaternary Science Reviews 28, 1309-1316 doi:10.1016/j.quascirev.2008.12.020.
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