Dfunabc: Distance of observed taxa versus sample distribution via...

In snwikaij/NEMO: What the Package Does (One Line, Title Case)

Distance of observed taxa versus sample distribution via ABC-rejection

Description

Distance of observed taxa versus sample distribution via ABC-rejection

Usage

Dfunabc(
  gradient,
  taxa,
  dist = "lnorm",
  pr1dist = "lnorm",
  par1 = 1,
  pr2dist = "gamma",
  par2 = 1,
  nsim = 200000,
  qtol = 0.005,
  D_min = 0,
  xlab = "Gradient",
  size = 6,
  print.progress = T,
  timing = T,
  penalty = F
)

Arguments

gradient	A numeric vector representing the gradient along which the taxa has been observed (e.g. concentration of nutrients).
taxa	A character vector with the names of all taxa needs to be the same length at the gradient.
dist	Assumed distribution for the data generating model. This can either be a lognormal (lnrom; default) or gamma (gamma) distribution.
pr1dist	An argument that indicates what prior the location parameter takes "lnorm", "gamma" or "norm". for the gamma distribution this is not the scale but rate parameter, defaulting "lnorm" to scale 1.
par1	An numeric argument that indicates which indicates what the scale parameter should be.
pr2dist	An argument that indicates what prior the scale parameter takes for "lnorm", "gamma" or "norm". for the gamma distribution this is not the scale but rate parameter, defaulting "gamma" with rate 1.
par2	An numeric argument that indicates which indicates what the scale parameter should be.
nsim	Number of simulations used.
qtol	The value for the quantile tolerance. A lower value selects simulated parameters that fall closer to the observed parameters. Default is 0.01 and indicates that the closest 1 percent is accepted and the rest rejected.
xlab	An argument representing the name of the gradient.
size	Size of the points in plot "A". Default is 6 but might be to large.
print.progress	Prints the progress of the number of simulations completed (length of the priors). By default is TRUE
timing	Prints the time that was needed to complete the simulations. By default is TRUE.
penalty	The argument indicates whether the intervals of D and SP need to be adjusted based on the observed shift in loc linear adjustment of the distributional parameters.

Details

The function returns a list of 4 objects: a data frame with the Taxa with D an S, a data frame with S for all taxa, a plotted figure (ggplot2) and a data frame with the simulate, priors and distance of the accepted values of each taxa.

Examples

 ## Not run: 
 library(readr)
df <- read_csv(url("https://raw.githubusercontent.com/snwikaij/Data/main/Aquatic_Botany_Kaijser_et_al._2019.csv"))

#Place Cl (Median) in a vector
 gradient = df$Mediaan

#Place taxon names in a vector
taxa     = df$Soort

#Simulate model (may take up to 5-10 min)
results <- Dfunabc(df$Mediaan, df$Soort,
dist = "lnorm", pr1dist = "lnorm", par1 = 0.5,
nsim = 200000, qtol= 0.005, size=4)

#Display the results
results$Plot
## End(Not run)

snwikaij/NEMO documentation built on March 18, 2022, 12:03 a.m.