aba_write: Write an aba object to file.

In aba: Automated Biomarker Analysis

Description

This is a generic function for writing an aba object to file. Objects can be written to file as a "table" (formatted), as "raw" (long-form results), or as an "object" (actual aba object).

Usage

aba_write(
  object,
  filename,
  format = c("table", "raw", "object"),
  separate = FALSE
)

Arguments

object	an aba object. The object to save to file.
filename	string. The filename to save to. Supported extensions include "csv", "xls", and "xlsx".
format	string. How to save the object to file. Options include "table" (formatted results like you see when you print the object to the console), "raw" (long-form results like what you see when you call object$results), or "object" (the actual aba object which can be later be loaded into memory and used again).
separate	logical. Whether to save the results in separate files (for csv) or separate sheets (for excel) based on group - outcome - stat combinations. This argument is ignored if format == "object".

Value

N/A

Examples

# create temp files to save to
tmp_filename_csv <- tempfile(fileext = '.csv')
tmp_filename_rda <- tempfile(fileext = '.Rda')

# grab built-in data
data <- adnimerge %>% dplyr::filter(VISCODE == 'bl')

# fit model
model <- data %>% aba_model() %>%
  set_groups(everyone()) %>%
  set_outcomes(ConvertedToAlzheimers, CSF_ABETA_STATUS_bl) %>%
  set_predictors(
    PLASMA_ABETA_bl, PLASMA_PTAU181_bl, PLASMA_NFL_bl,
    c(PLASMA_ABETA_bl, PLASMA_PTAU181_bl, PLASMA_NFL_bl)
  ) %>%
  set_stats('glm') %>%
  fit()

# summarise model
model_summary <- model %>% summary()

# save model summary to file as table
model_summary %>% aba_write(tmp_filename_csv)

# save model summary to file as raw long-form results
model_summary %>% aba_write(tmp_filename_csv, format = 'raw')

# save model summary as an object which can be loaded back into memory
model_summary %>% aba_write(tmp_filename_rda, format = 'object')

# load summary back to file to show it works
model_summary2 <- aba_read(tmp_filename_rda)
print(model_summary2)

# delete temp files
removed <- file.remove(tmp_filename_csv)
removed <- file.remove(tmp_filename_rda)

aba documentation built on Dec. 17, 2021, 1:06 a.m.