p3_to_p2: Convert P3Veg to P2Veg

Description Usage Arguments Details Value References Examples

Description

Thin a species abundance matrix collected via all-inclusive P3Veg as though it were collected via semi-inclusive P2Veg.

Usage

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p3_to_p2(x, keylist, ...)

Arguments

x

array of 'P3Veg' species data, where rows = SUs and cols = species

keylist

list of species (col 1) and their growth habit group (col 2)

...

further arguments passed to other methods

Details

National FIA Phase 3 vegetation (P3Veg) sampling is 'all-inclusive' : it captures all species that occur within or overhanging a plot (based on nested quadrats and subplots in a plot). By contrast, FIA Phase 2 vegetation (P2Veg) sampling is 'semi-inclusive': it includes only the 4 most abundant species within each growth habit group (tree seedlings and saplings, shrubs/woody vines, forbs, graminoids, and overstory trees) that occupy at least 3 canopy cover on each 7.3-m radius subplot.

NB: this function only applies to FIA 'subplots', not plot-level.

Value

Array of 'P2Veg' species data.

References

FIA [Forest Inventory and Analysis Program]. 2012. Supplement to the Alaska Field Guide for Installation of FIA Plots in Experimental Forests and Associated Research Areas. 107 pgs. USDA Forest Service, Pacific Northwest Research Station, Anchorage, Alaska.

FIA [Forest Inventory and Analysis Program]. 2016. Field Instructions for the Annual Inventory of Coastal Alaska 2016. 420 pgs. USDA Forest Service, Pacific Northwest Research Station, Anchorage, Alaska.

Examples

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# fake data
set.seed(23)
Nspp <- Nsite <- 99
x <- matrix(floor(rbeta(Nspp*Nsite, .2, 10)*100), Nspp, Nsite)
dimnames(x)[[2]] <- paste0('Sp_', 1:Nspp)

# fake keylist
v <- c('seed/sap','shrub','forb','graminoid','tree')
s <- dimnames(x)[[2]]
keylist <- data.frame(species=s,
                      growthhabit=v[round(runif(length(s),1,5),0)])

# convert P3 to P2 Veg
res <- p3_to_p2(x, keylist)

# check, should be 20 (or fewer) per row
res[res>0] <- 1
any(rowSums(res) != 20) # expect FALSE
apply(  x > 0, 1, sum) # old P3 species count per site
apply(res > 0, 1, sum) # new P2 species count per site, expect <=20

phytomosaic/ecole documentation built on May 6, 2019, 3:45 p.m.