Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE
, comment = "#>"
, warning = FALSE
, message = FALSE
, fig.width = 8
)
## ----update-packages, eval = FALSE--------------------------------------------
# install.packages("MPTmultiverse")
# update.packages(ask = FALSE)
## ----model-and-data, fig.height=5---------------------------------------------
# load packages
library("MPTmultiverse")
# If you're running the analysis from an .rmd file, you only need to ensure that
# the .rmd, .eqn, and .csv files are all in the same directory.
# ------------------------------------------------------------------------------
# MPT model definition & data
EQN_FILE <- system.file("extdata", "2HTSM_Submodel4.eqn", package = "MPTmultiverse")
DATA_FILE <- system.file("extdata", "Kuhlmann_dl7.csv", package = "MPTmultiverse")
# if .csv format uses semicolons ";" (German format):
data <- read.csv2(DATA_FILE, fileEncoding = "UTF-8-BOM") ## use correct encoding if necessary
# if .csv format uses commata "," (international format):
# data <- read.csv(DATA_FILE, fileEncoding = "UTF-8-BOM")
# We first take a look at the data using head()
head(data)
## We then plot the response frequencies using plotFreq from the TreeBUGS package
TreeBUGS::plotFreq(data, boxplot = FALSE, eqn = EQN_FILE)
## -----------------------------------------------------------------------------
COL_ID <- "Subject" # name of the variable encoding subject ID
COL_CONDITION <- "ExpCond" # name of the variable encoding group membership
# Experimental conditions should be labeled in a meaningful way. To accomplish
# this, you may want to use the `factor` function:
unique(data[, COL_CONDITION])
data[[COL_CONDITION]] <- factor(
data[[COL_CONDITION]]
, levels = c(1:2)
, labels = c("no_load", "load")
)
### check input data frame
head(data)
## ----options, results = 'hide'------------------------------------------------
# How to change a single option:
mpt_options(n.iter = 1e3)
# For testing purposes, you can use this shorthand to set fast, but unreliable options:
mpt_options("test")
# List all options that were set for the different analysis approaches:
mpt_options()
## ----analysis, results = 'hide', eval = FALSE---------------------------------
# set.seed(42)
# mpt_options("default")
#
# results <- fit_mpt(
# model = EQN_FILE
# , dataset = DATA_FILE
# , data = data
# , id = COL_ID
# , condition = COL_CONDITION
# , core = c("D", "d")
# )
## ----eval = FALSE-------------------------------------------------------------
# save(results, file = paste0(EQN_FILE, "-", DATA_FILE, ".RData"))
## ----eval = FALSE-------------------------------------------------------------
# save(results, file = "results_bayen_kuhlmann_2HTSM4.RData")
## ----eval=FALSE---------------------------------------------------------------
# save(results, file = "fits/results_bayen_kuhlmann_2HTSM4.RData")
## ----echo = FALSE, eval = FALSE-----------------------------------------------
# save(results, file = "../inst/extdata/results_bayen_kuhlmann.RData",
# version = 2, compress = "xz")
## ----echo = FALSE, eval = TRUE------------------------------------------------
load(file = system.file("extdata", "results_bayen_kuhlmann.RData", package = "MPTmultiverse"))
mpt_options("default")
## -----------------------------------------------------------------------------
check_results(results)
## -----------------------------------------------------------------------------
library("dplyr")
library("tidyr")
glimpse(results)
## -----------------------------------------------------------------------------
results %>%
select(pooling:method, test_between) %>%
unnest(cols = test_between) %>%
filter(parameter == "g") %>%
print(width = 150)
## -----------------------------------------------------------------------------
results %>%
select(pooling:method, test_within) %>%
unnest(cols = test_within) %>%
filter(condition == "no_load") %>%
filter(parameter1 == "d" & parameter2 == "D") %>%
print(width = 150)
## -----------------------------------------------------------------------------
plot(results, save = FALSE, "est")
## -----------------------------------------------------------------------------
plot(results, save = FALSE, "test_between")
## -----------------------------------------------------------------------------
plot(results, save = FALSE, "gof1")
## -----------------------------------------------------------------------------
plot(results, save = FALSE, "gof2")
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