PhytoIn

PhytoIn

PhytoIn

Tools for vegetation analysis and forest inventory in R.

PhytoIn provides functions and example datasets for phytosociological analysis, forest inventory, biomass and carbon estimation, and visualization of vegetation data.

Installation

From CRAN (when available)

install.packages("PhytoIn")

Development version (GitHub)

# install.packages("remotes")
remotes::install_github("PhytoIn/PhytoIn")

Overview

Main features:

Structural parameters and diversity
phytoparam(), summary.param(), plot.param()
Biomass and carbon
AGB() — wrapper around BIOMASS for above-ground biomass (AGB), C, and CO₂e
Volume stratification
stratvol() — wood volume by DBH classes
Species accumulation and rarefaction
collector.curve(), rarefaction()
Basal area visualization
BAplot() — basal areas on quadrat maps (supports rectangular plots and individual coords)

Example datasets included: quadrat.df, point.df, quadrat2_plot.df, quadrat2_tree.df, quadrat3_rect.df.

Quick start

Example chunks are not executed when building this README. Run them interactively.

Phytosociological parameters

library(PhytoIn)

res <- phytoparam(
  x = quadrat.df, measure.label = "CBH", taxon = "Species",
  family = "Family", su = "Plot", su.size = 25
)

summary(res)      # S3 summary
plot(res)         # S3 plot
head(res$param)   # Taxon-level table
res$global        # Global metrics

Rarefaction curve

rarefaction(formula = Species ~ Plot - Morta, data = quadrat.df, plot = TRUE)

Collector’s curve

collector.curve(formula = Species ~ Plot - Morta, data = quadrat.df,
                times = 1000, plot = TRUE, theme = "theme_classic")

Biomass and carbon (AGB)

out <- AGB(
  x = quadrat.df, measure.label = "CBH", h = "h", taxon = "Species",
  dead = "Morta", circumference = TRUE, su = "Plot", area = 0.0625,
  rm.dead = TRUE, check.spelling = FALSE, correct.taxon = TRUE, long = TRUE
)

head(out$tree)
out$taxon
out$total
out$WD.level

Note: AGB() uses BIOMASS internally. Internet access is not required;
taxon standardization via TNRS is used only if httr2 is available.

Basal areas on quadrat maps

BAplot(
  formula = CBH ~ x + y, data = quadrat2_plot.df, taxon = "Species",
  circumference = TRUE, quadrat.size = 5, dead = "Morta",
  rm.dead = FALSE, alpha = 0.4, cex.radius = 2,
  legend = TRUE, long = FALSE, ind.coord = FALSE
)

Citation

If you use PhytoIn in scientific work, please cite this package and the underlying methods (e.g., Hurlbert 1971; Heck et al. 1975; Chave et al. 2014).

citation("PhytoIn")

Contributing

Issues and pull requests are welcome:

Issue tracker: https://github.com/PhytoIn/PhytoIn/issues

Please follow a minimal reproducible example (reprex) when reporting bugs.

License

Development notes

This README is generated from README.Rmd. To build:

rmarkdown::render("README.Rmd")

Add to .Rbuildignore:

^README\.Rmd$
^\.github$