Hello R Community,
Subject: Bayes Factor
A Bayesian ANOVA of the form:
competitionBayesOut <- anovaBF(biomass ~ clipping, data = competition)
Returns the following Error message:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ?compare? for
signature ?"BFlinearModel", "missing", "tbl_df"?
My guess the problem is in the ?class?, which is:
[1] ?tbl_df? ?tbl? ?data.frame?
The data was imported via the ?readr? package through R Studio, and
then saved as a RData file.
My code is below, and the data is attached as a text file.
Thanks for your assistance.
Best regards,
James
# Plots for Interpreting One-Way ANOVA
library(digest)
library(DT)
datatable(competition)
# Characterize the data.
class(competition)
str(competition)
competition$clipping <- as.factor(competition$clipping)
competition$biomass <- as.numeric(competition$biomass)
str(competition)
#
tapply(competition$biomass, competition$clipping, mean)
tapply(competition$biomass, competition$clipping, sd)
# Bayesian Procedure for ANOVA
# Calculate Bayes Factors
library(BayesFactor)
competitionBayesOut <- anovaBF(biomass ~ clipping, data = competition)
# Run mcmc iterations
mcmcOut2 <- posterior(competitionBayesOut, iterations = 10000)
# boxplot of the posteriors for the groups
boxplot(as.matrix(mcmcOut2[,2:6]))
# Show the HDIs
summary(mcmcOut2)
# Calculate the Bayes Factor
competitionBayesOut
# Pairwise "post hoc" tests
library(rjags)
library(BEST)
# competitionare 'r5' vs. 'control'
plot(BESTmcmc(competition[competition$clpping=="r5",2],
competition[competition$clipping=="control",2]))
#
plot(BESTmcmc(competition[competition$clpping=="r10",2],
competition[competition$clipping=="control",2]))
# competitionare 'n10' vs. 'control'
plot(BESTmcmc(competition[competition$clipping=="n10",2],
competition[competition$clipping=="control",2]))
# competitionare 'n50' vs. 'control'
plot(BESTmcmc(competition[competition$clipping=="n50",2],
competition[competition$clipping=="control",2]))
-------------- next part --------------
clipping biomass
n25 551
n25 457
n25 450
n25 731
n25 499
n25 632
n50 595
n50 580
n50 508
n50 583
n50 633
n50 517
r5 639
r5 615
r5 511
r5 573
r5 648
r5 677
control 417
control 449
control 517
control 438
control 415
control 555
r10 563
r10 631
r10 522
r10 613
r10 656
r10 679
