braun: Emma Lucy Braun forest plots in eastern North America

In phytomosaic/ecole: ecole: School of Ecology Package

Description

Relative abundances of tree species for the forest plots described in E. Lucy Brauns (1950) book, Deciduous Forests of Eastern North America, as communicated by Ricklefs (2018).

Usage

braun

Format

A list of 2 data.frames:
- spe 347 observations of 122 woody plant species,
- env 347 observations of 33 environmental variables.

Details

Species matrix values are relative abundances of tree species in 347 plots (removing one of Ricklefs which had no species abundance information). Species names follow Ricklefs Table 3; those beginning with X_ indicate that no species name was provided.

Environmental matrix values include plot names, bibliographic information, location information and WorldClim climate values per Ricklefs (2018).

Source

Ricklefs (2018).

References

Braun, E. L. 1950. Deciduous Forests of Eastern North America. Hafner, New York.

Ricklefs, R. E. 2018. Emma Lucy Brauns forest plots in eastern North America. Ecology 99(2):504.

See Also

https://en.wikipedia.org/wiki/Emma_Lucy_Braun

Examples

# split into two data.frames
data(braun)
spe <- braun$spe
env <- braun$env

# describe the species abundance matrix
mx_diversity(spe) # high beta-diversity

# remove rare species and depauperate plots
rare <- (colSums((spe>0)*1) < 5)
poor <- (rowSums((spe>0)*1) < 3)
spe <- spe[!poor, !rare]
env <- env[!poor, ]
mx_diversity(spe)
mx_valid(spe)

# visualize the species abundance matrix
plot_heatmap(spe, logbase=10, labcex=0.5, yexp=1.3)

# gradient analysis (ordination)
m <- vegan::metaMDS(spe, 'bray') # tune for real usage!
s <- vegan::scores(m)
set_par(4, pch=16)
plot(s, col=colvec(env$bio3), main='Isothermality')
plot(s, col=colvec(env$bio1), main='Mean Ann Temp')
plot(env$lon, env$lat, col='#00000030', main='Plots')
plot(env$lon, env$lat, col=colvec(s[,1]), main='NMS1 scores')

phytomosaic/ecole documentation built on Jan. 2, 2022, 11:24 p.m.