fromParallelTP: Function to extract raw data from parallel calculations of...

In clquezada/tRophicPosition: Bayesian Trophic Position Estimation with Stable Isotopes

Function to extract raw data from parallel calculations of trophic position

Description

This function parses a data frame where it was stored the data from parallel calculations using multiModelTP and a list of isotopeData class objects.

Usage

fromParallelTP(df = NULL, get = NULL)

Arguments

df	data frame, variable where it was saved the output from parallel calculations of TP
get	string, could be either "TP", "alpha" or "summary." In case of TP this function will extract the trophic position data, in case of alpha, this function will extract the alpha parameter data, and in case of summary, it will return a data frame ready to plot with the function credibilityIntervals.

Value

when selecting "TP" or "alpha", this function returns a posteriorTP or a posteriorAlpha object with the data. When selecting "summary", this function returns a data frame ready to be used with credibilityIntervals().

Examples

## Not run: 
data("Bilagay")
BilagayList <- extractIsotopeData(Bilagay,
communityColumn = "Location",speciesColumn = "FG",
b1 = "Pelagic_BL", b2 = "Benthic_BL",
baselineColumn = "FG",
deltaC = TDF(author = "McCutchan", element = "C", type = "muscle"),
deltaN = TDF(author = "McCutchan", element = "N", type = "muscle"))
Bilagay_TPmodels <- parallel::parLapply(cluster,
BilagayList, multiModelTP, adapt = 20000,
n.iter = 20000, burnin = 20000, n.chains = 5,
model = "twoBaselinesFull")
ggplot_df <- fromParallelTP(Bilagay_TPmodels, get = "summary")
credibilityIntervals(ggplot_df, x = "community",
xlab = "Location along N-S gradient")

## End(Not run)

clquezada/tRophicPosition documentation built on Jan. 4, 2023, 12:31 p.m.