Rphree_SurrogateUtils.R

##  Functions for dealing with surrogate simulations

### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2018
### Time-stamp: "Last modified 2018-05-06 20:16:47 delucia"

##' Computes the average of absolute values of a vector
##' @title Average of absolute values
##' @param x numeric vector
##' @return mean(abs(x))
##' @author MDL
##' @export
mae <- function(x) mean(abs(x))

## ##' .. content for \description{} (no empty lines) ..
## ##'
## ##' .. content for \details{} ..
## ##' @title SoftMax transformation
## ##' @param obj numeric vector
## ##' @return 
## ##' @author 
## SoftMax <- function(obj) {
##     eo <- exp(obj-max(obj))
##     ss <- sum(eo)
##     scaled <- eo/ss
##     attr(res,"back") <- ss
##     return(res)
## }

## ## SoftMaxBackTransf <- function(vec, back) return(log(vec)+log(back))

## ##' @title Flatten out a Rphree list
## ##' @param list list of Rphree lists
## ##' @param strip logical, should we delete "ListInfo"? Defaults to
## ##'     true
## ##' @return a list whose elements are single Rphree simulations
## ##' @author MDL
## ##' @export
## FlattenList <- function(list) {
##    tot <- vector(mode="list", length=sum(sapply(stripped, length)))
##    k <- 1
##    for (i in seq_along(stripped)) {
##       for (j in seq_along(stripped[[i]])) {
##          tot[[k]] <- stripped[[i]][[j]]
##          k=k+1
##       }
##    }
##    return(tot)
## }


##' @title Find all species occurring in the ensemble
##' @param flatlist the flatted list of Rphree simulations
##' @return vector with unique occurrences of species names
##' @author MDL
##' @export
FindAllSpeciesNames <- function(flatlist)
    unique(sort(unlist(sapply(flatlist, function(sol) rownames(sol$species)))))


##' @title Find all pphases occurring in the ensemble
##' @param flatlist the flatted list of Rphree simulations
##' @return vector with unique occurrences of pphases names
##' @author MDL
##' @export
FindAllMinNames <- function(flatlist)
    unique(sort(unlist(sapply(flatlist, function(sol) rownames(sol$pphases)))))

##' @title Find all totals occurring in the ensemble
##' @param flatlist the flatted list of Rphree simulations
##' @return vector with unique occurrences of element names