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Merge pull request #51 from andrechalom/trueLL
True LL
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,28 +1,54 @@ | ||
| trueLL <- function(x, dens, coef, trunc, dec.places = 0, breaks, counts, log = TRUE, ...){ | ||
| dots <- list(...) | ||
| if(missing(breaks)){ | ||
| D <- 10^(-dec.places)/2 | ||
| x <- round(x, dec.places) | ||
| if(missing(trunc)){ | ||
| cdf <- get(paste("p", dens, sep=""), mode = "function") | ||
| probs <- do.call(cdf, c(list(q = x+D), as.list(coef), dots)) - do.call(cdf, c(list(q = x-D), as.list(coef), dots)) | ||
| } | ||
| else{ | ||
| probs <- do.call(ptrunc, c(list(dens, q = x+D, coef = as.list(coef), trunc=trunc), dots))- | ||
| do.call(ptrunc, c(list(dens, q = x-D, coef = as.list(coef), trunc=trunc), dots)) | ||
| } | ||
| } | ||
| else{ | ||
| h1 <- hist(x, breaks=breaks, plot=FALSE) | ||
| if(missing(trunc)){ | ||
| cdf <- get(paste("p", dens, sep=""), mode = "function") | ||
| probs <- diff(do.call(cdf, c(list(q = h1$breaks), as.list(coef), dots))) | ||
| } | ||
| else{ | ||
| probs <- diff(do.call(ptrunc, c(list(dens, q = h1$breaks, coef = as.list(coef), trunc=trunc), dots))) | ||
| } | ||
| if(missing(counts)) counts <- h1$counts | ||
| probs <- rep(probs, counts) | ||
| } | ||
| if(log) sum(log(probs)) else prod(probs) | ||
| } | ||
| # trueLL generic and methods | ||
| setGeneric("trueLL", | ||
| def=function(object, dist, coef, trunc, dec.places=0, breaks, ...) | ||
| standardGeneric("trueLL") | ||
| ) | ||
| setMethod("trueLL", signature(object="fitsad", dist="missing", coef="missing", trunc="missing", | ||
| dec.places="ANY", breaks="ANY"), | ||
| function(object, dec.places=0, breaks, ...){ | ||
| if(missing(breaks)) | ||
| return(trueLL(object=object@data$x, dist=object@sad, coef=as.list(bbmle::coef(object)), | ||
| trunc=object@trunc, dec.places=dec.places, ...)) | ||
| else | ||
| return(trueLL(object=object@data$x, dist=object@sad, coef=as.list(bbmle::coef(object)), | ||
| trunc=object@trunc, breaks=breaks, ...)) | ||
| }) | ||
| setMethod("trueLL", signature(object="fitrad", dist="missing", coef="missing", trunc="missing", | ||
| dec.places="ANY", breaks="ANY"), | ||
| function(object, dec.places=0, breaks, ...){ | ||
| if(missing(breaks)) | ||
| return(trueLL(object=object@rad.tab$abund, dist=object@rad, coef=as.list(bbmle::coef(object)), | ||
| trunc=object@trunc, dec.places=dec.places, breaks=breaks, ...)) | ||
| else | ||
| return(trueLL(object=object@rad.tab$abund, dist=object@rad, coef=as.list(bbmle::coef(object)), | ||
| trunc=object@trunc, breaks=breaks, ...)) | ||
| }) | ||
| # object is numeric | ||
| setMethod("trueLL", signature(object="numeric", dist="character", coef="list", trunc="ANY", | ||
| dec.places="ANY", breaks="ANY"), | ||
| function(object, dist, coef, trunc, dec.places=0, breaks, ...){ | ||
| dots <- list(...) | ||
| if(missing(breaks)){ | ||
| D <- 10^(-dec.places)/2 | ||
| breaks <- sort(unique(c(object - D, object + D))) | ||
| } | ||
| h1 <- hist(object, breaks=breaks, plot=FALSE) | ||
| if(missing(trunc)) trunc <- NaN | ||
| trueLL(object=h1, dist=dist, coef=coef, trunc=trunc) | ||
| }) | ||
| # workhorse method, all other methods redirect here | ||
| setMethod("trueLL", signature(object="histogram", dist="character", coef="list", trunc="ANY", | ||
| dec.places="missing", breaks="missing"), | ||
| function(object, dist, coef, trunc, ...){ | ||
| dots <- list(...) | ||
| if(missing(trunc)) trunc <- NaN | ||
| if(is.nan(trunc)){ | ||
| cdf <- get(paste("p", dist, sep=""), mode = "function") | ||
| probs <- diff(do.call(cdf, c(list(q = object$breaks), as.list(coef), dots))) | ||
| } | ||
| else{ | ||
| probs <- diff(do.call(ptrunc, c(list(dist, q = object$breaks, coef = as.list(coef), trunc=trunc), dots))) | ||
| } | ||
| probs <- rep(probs, object$counts) | ||
| return(sum(log(probs))) | ||
| }) |
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