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RiskMap

The goal of RiskMap is to provide a set of functions for visualisation, processing and likelihood-based analysis of geostatistical data.

Installation

You can install the development version of RiskMap from GitHub with:

# install.packages("devtools")
devtools::install_github("claudiofronterre/RiskMap")

Example

This is a basic example which shows you how to solve a common problem:

library(RiskMap)
## basic example code

What is special about using README.Rmd instead of just README.md? You can include R chunks like so:

summary(cars)
#>      speed           dist       
#>  Min.   : 4.0   Min.   :  2.00  
#>  1st Qu.:12.0   1st Qu.: 26.00  
#>  Median :15.0   Median : 36.00  
#>  Mean   :15.4   Mean   : 42.98  
#>  3rd Qu.:19.0   3rd Qu.: 56.00  
#>  Max.   :25.0   Max.   :120.00

You’ll still need to render README.Rmd regularly, to keep README.md up-to-date. devtools::build_readme() is handy for this. You could also use GitHub Actions to re-render README.Rmd every time you push. An example workflow can be found here: https://github.com/r-lib/actions/tree/v1/examples.

You can also embed plots, for example:

In that case, don’t forget to commit and push the resulting figure files, so they display on GitHub and CRAN.

Estimation function design

How should the user specify the model?

# OPTION 1
y ~ rainfall + gp(x, y) + re(id_school) + re(id_region)

# Arguments for gp function
gp(long = NULL, lat = NULL, kappa = (numeric_value, default = 0.5), nugget = c(T = default, F, fixed_numeric_value), ...)

# Arguments for re function
re(numeric or categorical variable, ...) only needs an index in the dataset

glgm <- function(formula,
                 distr_offset = NULL,
                 cov_offset = NULL,
                 data,
                 family,
                 convert_to_crs = NULL,
                 scale_to_km = TRUE,
                 control_MCMC = NULL,
                 S_samples = NULL,
                 save_samples = F,
                 messages = TRUE) 

My solution to incorporate “gp” into the formula

(tf <- terms(y ~ x + x:z + gp(kappa = 0.5, nugget = TRUE)+w, specials = "gp"))
attr(tf, "specials")    # index 's' variable(s)
gp <- rownames(attr(tf, "factors"))[[attr(tf, "specials")$gp]]
gp_list <- eval(parse(text = gsub("gp","list",gp)))
gp_list

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.
Health stats visible at Monitor.