# R/root_mass.R In Z10: Simple Ecological Statistics from the NEON Network

#### Documented in root.mass

```############################################################################################
#' @title Return Mean Root Masses by Depth

#' @author Robert Lee \email{[email protected]@colorado.edu}\cr

#' @description This function summarizes the root masses from all live
#'  roots in 10 cm depth increments
#'
#' @param site Parameter of class character.

#' @return Data frame of the average root mass measured in a given depth range
#'
#' @examples
#' \dontrun{
#' SCBI=Z10::root.mass(site = "SCBI")
#' }
#' @export

#' @seealso Currently none

# changelog and author contributions / copyrights
#   Robert Lee (2018-10-31)
#     original creation
#
##############################################################################################

root.mass=function(site){

dp.id="DP1.10066.001"

root.sites=dp.avail(dp.id)

if(!(site %in% root.sites\$site)){stop(paste0("Megapit root data is not available at ", site))}

all=lapply(root.sites\$months[root.sites\$site==site],
function(m)
get.data(site = site,
dp.id = dp.id,
month = m
)
)

flat=unlist(all, recursive = FALSE)

by.depth=flat[grepl(pattern = "perrootsample", x = names(flat))][[1]]

sample.spots=do.call(rbind, strsplit(by.depth\$depthIncrementID, split = "\\." ))

by.depth\$column=sample.spots[,2]

by.depth\$top.depth=sample.spots[,3]

temp=lapply(
unique(by.depth\$top.depth),
function(d) unlist(lapply(
unique(by.depth\$column),
function(c) sum(by.depth\$rootDryMass[by.depth\$top.depth==d&by.depth\$column==c]))
)
)

mean.mass=unlist(lapply(temp, mean))

root.df=data.frame(do.call(rbind, .common.fields(flat)), row.names = NULL)

top.depths=as.numeric(unique(by.depth\$top.depth))
top.depths=top.depths[order(top.depths)]
bottom.depths=c(top.depths[2:length(top.depths)], top.depths[length(top.depths)]+10)

out=data.frame(depths=paste0(top.depths, "-", bottom.depths), root.mass=round(mean.mass, digits = 2))
return(out)
}
```

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Z10 documentation built on May 2, 2019, 3:25 a.m.