structure.plotV2: structure plot version 2

In RenaudJau/ComSII: Community Structure Integrity Index Calculations

Description

same as structure.plot but with some more arguments (especially error bars)

Usage

structure.plotV2(INDICE, FACTOR, MULTI = T, MTITLE = "", ABMAX = 5,
  col1 = "grey60", col2 = "white", col3 = "red", col4 = "orange",
  noms = "T", cex_noms = 1, erreur = "sem", w_err = 1, sp_star = 1,
  adj_meth = "BH", stars = "T", BASE = T, ...)

Arguments

INDICE	An object issued from ComStructIndices function
FACTOR	A factor list, a barplot of species mean abundances will be performed for each factor level. If no factor is specified, MULTI=F should be specified.
MULTI	If no factor is specified, MULTI=F should be specified
MTITLE	Main title of the plot
ABMAX	Numerical value of the maximum abundance
col1	Colour information for the Reference mean abundances barplot
col2	Colour information for the Reference mean abundances in assessed community barplot, i.e. "missing abundances"
col3	Colour information for the abundances of target species in the assessed community
col4	Colour information for the "higher abundances" in the assessed community
noms	If other than "T", species names are not given
cex_noms	expansion factor for species names
erreur	(facultative) error calculation "sem" (default) is standard error of the mean "IC" will calculate confidence interval at 5 percent "var" or "sd" or any other R function can be use (but beware, you can't use the na.rm=T argument..).
w_err	error bar width
sp_star	width between stars and error bars
adj_meth	p adjust method: "bond","BH","hoch", etc. or "none" (then p correspond to a wilcoxon test between reference and modality)
stars	"T" (default), draw or note the stars, anything but "T" does not draw the stars
BASE	T (default), draw or not the reference community for each modality
...	any arguments from a barplot function can be used

Details

Be careful, the p adjustment is done only within a modality, perhaps that would be better to adjust it through all the modalitties (to be modified later). The warnings come from ties, but it seems it does not change the outcome of tests...

See Also

ComStructIndices et structure.plot

RenaudJau/ComSII documentation built on May 16, 2019, 7:22 a.m.