In Deleetdk/kirkegaard: kirkegaard

Init

#global options
options(
  digits = 2,
  contrasts = c("contr.treatment", "contr.treatment")
)

if (F) {
  devtools::install_github("merliseclyde/BAS")
}

#packages
library(kirkegaard)
load_packages(
  BAS,
  BMA,
  BMS,
  patchwork,
  readxl
)

#ggplot2
theme_set(theme_bw())

Data

#load SPI dataset
spi = readxl::read_xlsx("inst/extdata/SPI2019.xlsx", sheet = 2) %>% 
  df_legalize_names()

#impute it insofar as reasonable, drop the rest
spi_orig = spi
spi = spi %>%
  miss_impute()

#filter whatever is left with missing data
spi = spi %>% 
  miss_filter()

#standardize everything for comparison
spi = spi %>% 
  df_standardize(exclude_range_01 = F)

Examples

General modeling code

#make up some semi-plausible model
spi_model = str_glue("{names(spi)[34]} ~ {str_c(names(spi)[c(21:33, 37:40)], collapse = ' + ')}")

BAS

#fit a BAS model
spi_bas_fit = BAS::bas.lm(spi_model, data = spi)

spi_bas_fit

spi_bas_fit %>% summary()

(spi_bas_fit_coefs = spi_bas_fit %>% coef())

#test combined plot
spi_bas_fit_coefs %>% 
  GG_BMA()

BMA

#fit a BMA model
spi_bma_fit = BMA::bic.glm(as.formula(spi_model), data = spi, glm.family = "gaussian")

spi_bma_fit

spi_bma_fit %>% 
  GG_BMA()

BMS

#restyle the data since this package is annoying
spi_bms = spi[, formula.tools::get.vars(as.formula(spi_model))]

#fit a BMS model
spi_bms_fit = BMS::bms(spi_bms)

#coefs
spi_bms_fit_coefs = spi_bms_fit %>% coef()

spi_bms_fit %>% 
  GG_BMA()

Made up results

Input a data frame with the following columns: term, PIP, mean, sd

set.seed(1)
made_up = tibble(
  term = LETTERS[1:10],
  PIP = runif(10),
  mean = rnorm(10, sd = .5),
  sd = runif(10, .1, .5)
)

made_up %>% 
  GG_BMA()

Meta

write_sessioninfo()

#upload to OSF
#avoid uploading the data in case they freak out again
if (F) {
  library(osfr)

  #auth
  osf_auth(readr::read_lines("~/.config/osf_token"))

  #the project we will use
  osf_proj = osf_retrieve_node("https://osf.io/XXX/")

  #upload files
  #overwrite existing (versioning)
  osf_upload(osf_proj, conflicts = "overwrite", 
             path = c(
               "figs",
               "data",
               "notebook.html",
               "notebook.Rmd",
             ))
}