glmkrigepred {spm2}

Generate spatial predictions using the hybrid method of generalised linear models ('glm') and 'krige'

Description

This function is for generating spatial predictions using the hybrid method of 'glm' and 'krige', including all methods implemented in 'glmkrigecv'. (see reference #1 for further info).

Usage

glmkrigepred(
  formula.glm = NULL,
  longlat,
  trainxy,
  predx,
  y,
  longlatpredx,
  family = "gaussian",
  transformation = "none",
  delta = 1,
  formula.krige = res1 ~ 1,
  vgm.args = c("Sph"),
  anis = c(0, 1),
  alpha = 0,
  block = 0,
  beta,
  nmaxkrige = 12,
  ...
)

Arguments

formula.glm

a formula defining the response variable and predictive variables for 'glm'.

longlat

a dataframe contains longitude and latitude of point samples.

trainxy

a dataframe contains longitude (long), latitude (lat), predictive variables and the response variable of point samples.

predx

a dataframe or matrix contains columns of predictive variables for the grids to be predicted.

y

a vector of the response variable in the formula, that is, the left part of the formula.

longlatpredx

a dataframe contains longitude and latitude of point locations (i.e., the centers of grids) to be predicted.

family

a description of the error distribution and link function to be used in the model. See '?glm' for details.

transformation

transform the residuals of 'glm' to normalise the data; can be "sqrt" for square root, "arcsine" for arcsine, "log" or "none" for non transformation. By default, "none" is used.

delta

numeric; to avoid log(0) in the log transformation. The default is 1.

formula.krige

formula defining the response vector and (possible) regressor. an object (i.e., 'variogram.formula') for 'variogram' or a formula for 'krige'. see 'variogram' and 'krige' in 'gstat' for details.

vgm.args

arguments for 'vgm', e.g. variogram model of response variable and anisotropy parameters. see 'vgm' in 'gstat' for details. By default, "Sph" is used.

anis

anisotropy parameters: see notes 'vgm' in 'gstat' for details.

alpha

direction in plane (x,y). see variogram in 'gstat' for details.

block

block size. see 'krige' in 'gstat' for details.

beta

for simple kriging. see 'krige' in 'gstat' for details.

nmaxkrige

for a local predicting: the number of nearest observations that should be used for a prediction or simulation, where nearest is defined in terms of the space of the spatial locations. By default, 12 observations are used.

...

other arguments passed on to 'glm' and 'krige'.

Value

A dataframe of longitude, latitude, and predictions.

Author(s)

Jin Li

References

Li, J., Alvarez, B., Siwabessy, J., Tran, M., Huang, Z., Przeslawski, R., Radke, L., Howard, F. and Nichol, S. (2017). "Application of random forest, generalised linear model and their hybrid methods with geostatistical techniques to count data: Predicting sponge species richness." Environmental Modelling & Software 97: 112-129.

Pebesma, E.J., 2004. Multivariable geostatistics in S: the gstat package. Computers & Geosciences, 30: 683-691.

Examples

library(spm)

data(petrel)
data(petrel.grid)

gravel <- petrel[, c(1, 2, 6:9, 5)]
longlat <- petrel[, c(1, 2)]
model <- log(gravel + 1) ~  lat +  bathy + I(long^3) + I(lat^2) + I(lat^3)
y <- log(gravel[, 7] +1)

glmkrigepred1 <- glmkrigepred(formula.glm = model, longlat = longlat, trainxy =  gravel,
predx = petrel.grid, y = y, longlatpredx = petrel.grid[, c(1:2)],
transformation = "none", formula.krige = res1 ~ 1, vgm.args = "Sph", nmaxkrige = 12)
 # Since the default 'family' is used, actually a 'lm' model is used.

names(glmkrigepred1)

# Back transform 'glmkrigepred$predictions' to generate the final predictions
glmkrige.predictions <- exp(glmkrigepred1$predictions) - 1
range(glmkrige.predictions)