maxlike: Model occurrence probability using presence-only data

In rbchan/maxlike: Model Species Distributions by Estimating the Probability of Occurrence Using Presence-Only Data

Description

This function estimates the probability of occurrence using presence-only data and spatially-referenced covariates. Species distribution maps can be created by plotting the expected values of occurrence probability. The model is described by Royle et al. (2012).

Usage

  maxlike(formula, rasters, points, x=NULL, z=NULL,
          link=c("logit", "cloglog"),
          starts, hessian = TRUE, fixed, removeDuplicates=FALSE,
          savedata=FALSE, na.action = "na.omit", ...)

Arguments

formula	A right-hand side formula describing the model. At least 1 continuous covariate must be present in the formula.
rasters	The spatially-referenced covariate data formatted as a 'raster stack' created by the stack function in the raster-package. It's a good idea to standardize these by subtracting the mean and dividing by the standard deviation. This will make it easier for optim to find the maximum-likelihood estimates.
points	A matrix or data.frame with the X and Y coordinates of the presence locations.
x	A matrix or data.frame with the explanatory data for presence locations. In case data is provided for x and z, arguments rasters and points will be ignored
z	A matrix or data.frame with the explanatory data for background locations. In case data is provided for x and z, arguments rasters and points will be ignored
link	The link function. Either "logit" (the default) or "cloglog".
starts	Starting values for the parameters. This should be a vector with as many elements as there are parameters. By default, all starting values are 0, which should be adequate if covariates are standardized.
hessian	Logical. Should the hessian be computed and the variance-covariance matrix returned?
fixed	Optional vector for fixing parameters. It must be of length equal to the number of parameters in the model. If an element of fixed is NA, then the parameter is estimated, otherwise if it is a real number, the parameter is fixed at this value.
removeDuplicates	Logical. Should duplicate points be removed? Defaults to FALSE, but note that the MAXENT default is TRUE.
savedata	Should the raster data be saved with the fitted model? Defaults to FALSE in order to reduce the size of the returned object. If you wish to make predictions, it is safer to set this to TRUE, otherwise the raster data are searched for in the working directory, and thus may not be the data used to fit the model.
na.action	See options for choices
...	Additional arguments passed to optim

Details

points and rasters should the same coordinate system. The program does not check this so it is up to the user.

Value

A list with 8 components

Est	data.frame containing the parameter estimates (Ests) and standard errors (SE).
vcov	variance-covariance matrix
AIC	AIC
call	the original call
pts.removed	The points removed due to missing values
pix.removed	The pixels removed due to missing values
optim	The object returned by optim
not.fixed	A logical vector indicating if a parameter was estimated or fixed.
link	The link function

Warnings

Maximizing the log-likelihood function is achieved using the optim function, which can fail to find the global optima if sensible starting values are not supplied. The default starting values are rep(0, npars), which will often be adequate if the covariates have been standardized. Standardizing covariates is thus recommended. Even when covariates are standardized, it is always a good idea to try various starting values to see if the log-likelihood can be increased. When fitting models with many parameters, good starting values can be found by fitting simpler models first.

Note

In general it is very hard to obtain a random sample of presence points, which is a requirement of both the Royle et al. (2012) method and of MAXENT. This is one of many reasons why presence-absence data are preferable to presence-only data. When presence-absence data are available, they can be modeled using functions such as glm. Creating species distribution maps from glm is easily accomplished using the predict method.

The MAXENT software assumes that species prevalence is known a priori. If the user does not specify a value for prevalence, prevalence is set to 0.5. MAXENT predictions of occurrence probability are highly sensitive to this setting. In contrast, maxlike directly estimates prevalence.

Another weakness of models for presence-only data is that they do not allow one to model detection probability, which is typically less than one in field conditions. If detection probability is affected by the same covariates that affect occurrence probability, then bias is inevitable. The R package unmarked (Fiske and Chandler 2011) offers numerous methods for jointly modeling both occurrence and detection probability when detection/non-detection data are available.

References

Royle, J.A., R.B. Chandler, C. Yackulic and J. D. Nichols. 2012. Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions. Methods in Ecology and Evolution. doi: 10.1111/j.2041-210X.2011.00182.x

Fiske, I. and R.B. Chandler. 2011. unmarked: An R Package for Fitting Hierarchical Models of Wildlife Occurrence and Abundance. Journal of Statistical Software 43(10).

See Also

maxlike-package, raster, carw

Examples

# Carolina Wren data used in Royle et. al (2012)
data(carw)

# Covert data.frame to a list of rasters
rl <- lapply(carw.data$raster.data, function(x) {
   m <- matrix(x, nrow=carw.data$dim[1], ncol=carw.data$dim[2], byrow=TRUE)
   r <- raster(m)
   extent(r) <- carw.data$ext
   r
})

# Create a raster stack and add layer names
rs <- stack(rl[[1]], rl[[2]], rl[[3]], rl[[4]], rl[[5]], rl[[6]])
names(rs) <- names(carw.data$raster.data)

plot(rs)


# Fit a model
fm <- maxlike(~pcMix + I(pcMix^2) + pcDec + I(pcDec^2)+ pcCon +
    I(pcCon^2) + pcGr + I(pcGr^2) +
    Lat + I(Lat^2) + Lon + I(Lon^2), rs, carw.data$xy1,
    method="BFGS", removeDuplicates=TRUE, savedata=TRUE)

summary(fm)
confint(fm)
AIC(fm)
logLik(fm)


# Produce species distribution map (ie, expected probability of occurrence)
psi.hat <- predict(fm) # Will warn if savedata=FALSE
plot(psi.hat)
points(carw.data$xy1, pch=16, cex=0.1)



# MAXENT sets "default prevalence" to an arbitrary value, 0.5.
# We could do something similar by fixing the intercept at logit(0.5)=0.
# However, it seems more appropriate to estimate this parameter.

fm.fix <- update(fm, fixed=c(0, rep(NA,length(coef(fm))-1)))

# Predict data.frame
presenceData <- as.data.frame(extract(rs, carw.data$xy1))
presenceData <- presenceData[complete.cases(presenceData), ]
presence.predictions <- predict(fm, newdata=presenceData)
summary(presence.predictions)

# Calibrate with data.frames
PresenceUniqueCells <- unique(cellFromXY(rs, xy=carw.data$xy1))
PresenceUnique <- xyFromCell(rs, PresenceUniqueCells)
presenceData <- as.data.frame(extract(rs, PresenceUnique))
library(dismo)
background <- randomPoints(rs, n=ncell(rs), extf=1.00)
backgroundData <- as.data.frame(extract(rs, y=background))
backgroundData <- backgroundData[complete.cases(backgroundData), ]
fm2 <- maxlike(~pcMix + I(pcMix^2) + pcDec + I(pcDec^2)+ pcCon +
    I(pcCon^2) + pcGr + I(pcGr^2) +
    Lat + I(Lat^2) + Lon + I(Lon^2), 
    rasters=NULL, points=NULL,
    x=presenceData, z=backgroundData,
    method="BFGS", removeDuplicates=TRUE, savedata=TRUE)

summary(fm2)

fm2$rasters <- rs
psi.hat2 <- predict(fm2)




## Not run: 

# Simulation example

set.seed(131)
x1 <- sort(rnorm(100))
x1 <- raster(outer(x1, x1), xmn=0, xmx=100, ymn=0, ymx=100)

x2 <- raster(matrix(runif(1e4), 100, 100), 0, 100, 0, 100)

# Code factors as dummy variables.
# Note, using asFactor(x3) will not help
x3 <- raster(matrix(c(0,1), 100, 100), 0, 100, 0, 100)

logit.psi <- -1 + 1*x1 + 0*x2
psi <- exp(logit.psi)/(1+exp(logit.psi))
plot(psi)

r <- stack(x1, x2, x3)
names(r) <- c("x1", "x2", "x3")
plot(r)

pa <- matrix(NA, 100, 100)
pa[] <- rbinom(1e4, 1, as.matrix(psi))
str(pa)
table(pa)

pa <- raster(pa, 0, 100, 0, 100)
plot(pa)

xy <- xyFromCell(pa, sample(Which(pa==1, cells=TRUE), 1000))

plot(x1)
points(xy)

fm2 <- maxlike(~x1 + x2 + x3, r, xy)

summary(fm2)
confint(fm2)
AIC(fm2)
logLik(fm2)


## End(Not run)

rbchan/maxlike documentation built on Nov. 19, 2019, 11:56 p.m.