isotop_ca

R Documentation

Correspondance Analysis on isotopes, chemical components, or elements.

Description

Correspondance Analysis on isotopes, chemical components, or elements data. Inspired by the 'zoo_ca()' function of the R package 'zoowork'

Usage

isotop_ca(
 
    df.iso = "https://raw.githubusercontent.com/zoometh/itineRis/main/inst/extdata/example_1.csv",
  iso.preselect = NA,
  num_column = "num",
  col.group = NA,
  color.def.ind = "blue",
  color.def.var = "black",
  pt_siz = 1.5,
  lbl.size = 2,
  print.caption = TRUE,
  export.plot = FALSE,
  dirOut = paste0(system.file(package = "itineRis"), "/results/"),
  ca.name = "ca.png",
  plot.width = 22.2,
  plot.height = 19.5,
  plot.dpi = 300,
  verbose = TRUE
)

Arguments

df.iso	a dataframe with isotop results
iso.preselect	a preselection of the variables that will be analysed, in a vector form, ex: 'c(1, 2, 3, 4, 5)'. If provided, will skip the user prompt. Default NA.
num_column	the column name of assemblage numbers
col.group	the column name of the sample group (a site, a culture, etc.). Default: NA. Will only affect the symbol color by overwriting the 'color.def.ind' variable.
pt_siz	the size of the symbols
print.caption	if TRUE will print information in the console (group colors, etc.)
export.plot	if TRUE (Default: FALSE), save the plot. If not, will plot it
dirOut	the output directory
ca.name	the name of the output plot if saved
plot.width, plot.height, plot.dpi	the dimensions and resolution of the plot if saved
verbose	if TRUE (default): verbose

Value

a gglot with the different CA by period

Examples

# Plot, with colors on groups, Itineris ANR data
isotop_ca(col.group = "Provenienza",
          pt_siz = 2,
          lbl.size = 3)

# Run on preselected isotops (1 to 5) only, Shadreck Chirikure data
isotop_ca(df.iso = "C:/Users/Thomas Huet/Desktop/Shadreck data/XRF_Majors.csv",
          iso.preselect = c(1, 2, 3, 4, 5))

# Export
isotop_ca(export.plot = T,
          dirOut = "C:/Users/Thomas Huet/Desktop/Shadreck data/")