stgam: Spatially and Temporally Varying Coefficient Models Using Generalized Additive Models (GAMs)
This package provides a framework for specifying spatially, temporally and spatially-and-temporally varying coefficient models using Generalized Additive Models (GAMs) with smooths. It builds on GAM functionality from the mgcv package. The smooths are parameterised with location, time and predictor variables. The framework supports the investigation of the presence and nature of any space-time dependencies in the data by evaluating multiple model forms (specifications) using a Generalized Cross-Validation (GCV) score. The workflow sequence is to i) Prepare the data (data.frame, tibble or sf object) by lengthening it to have a single location and time variables for each observation. ii) Evaluate all possible spatial and/or temporal models in which each predictor is specified in different ways. iii) Evaluate the models via their GCV score and to pick the best model (the one with the lowest GCV). iv) Create the final model. v) Calculate the varying coefficient estimates to quantify how the relationships between the target and predictor variables vary over space, time or space-time. vi) Create maps, time series plots etc. For more details see: Comber et al (2023) [https://doi.org/10.4230/LIPIcs.GIScience.2023.22], Comber et al (2024) [https://doi.org/10.1080/13658816.2023.2270285] and Comber et al (2004) [https://doi.org/10.3390/ijgi13120459].
You can install the CRAN version of stgam :
install.packages("stgam")
Or the development version:
# just the package
remotes::install_github("lexcomber/stgam")
# with the vignettes - takes a bit longer
remotes::install_github("lexcomber/stgam", build_vignettes = TRUE, force = T)
This code below loads the package and undertakes the proposed workflow for a spatially varying coefficient model using GAMs with spatial smooths:
# a spatially varying coefficient model example
library(stgam)
library(dplyr)
library(ggplot2)
# define input data
data("hp_data")
input_data <-
hp_data |>
# create Intercept as an addressable term
mutate(Intercept = 1)
# evaluate different model forms
svc_mods <-
evaluate_models(
input_data = input_data,
target_var = "priceper",
vars = c("pef", "beds"),
coords_x = "X",
coords_y = "Y",
STVC = FALSE,
time_var = NULL,
ncores = 2
)
# rank the models
mod_comp <- gam_model_rank(svc_mods)
# have a look
mod_comp |> select(-f)
# select best model
f = as.formula(mod_comp$f[1])
# put into a `mgcv` GAM model
gam.m = gam(f, data = input_data)
# calculate the Varying Coefficients
terms = c("Intercept", "pef")
vcs = calculate_vcs(input_data, gam.m, terms)
vcs |> select(priceper, yot, X, Y, starts_with(c("b_", "se_")), yhat)
# map them
data(lb)
tit <-expression(paste(""*beta[`pef`]*""))
ggplot() +
geom_sf(data = lb, col = "lightgrey") +
geom_point(data = vcs, aes(x = X, y = Y, col = b_pef)) +
scale_colour_continuous_c4a_div("brewer.rd_yl_bu", name = tit) +
theme_bw() +
coord_sf() +
xlab("") + ylab("")
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