kaz-yos

###  tableone export helpers
###   Turn tableone output matrix into tidyverse data_frame
tableone_mat_to_data_frame <- function(mat) {
    mat %>%
        as.data.frame() %>%
        tibble::rownames_to_column(var = "Variable") %>%
        tibble::as_data_frame()
}

kaz-yos

  ;; Swap dimension specification
  (defun my-reverse-org-table-dimension (size)
    (let* ((split (org-split-string size " *x *"))
           (pos1 (nth 1 split))
           (pos0 (car split)))
      (concat pos1 "x" pos0)))
  ;; Wrapper to fix the dimension
  (defun org-table-create-reverse-table-dimension (old-fun &optional size)
    "Query for a size and insert a table skeleton.
SIZE is a string Rows x Columns like for example \"2x3\".

kaz-yos

;;; Issue reported by Brian
;; An ipython code snippet does not execute upon C-c C-c in org-mode.
;; "Evaluation of this ipython code block is disabled." is encountered.

;;; ob-core.el
;; This is the function showing the error message.
(defun org-babel-check-evaluate (info)
  "Check if code block INFO should be evaluated.
Do not query the user, but do display an informative message if
evaluation is blocked.  Returns non-nil if evaluation is not blocked."

kaz-yos

#+BEGIN_SRC R :session *R* :results output :exports both
suppressPackageStartupMessages(library(tidyverse))
data1 <- read_tsv("./data.tsv")
print(data1,
      width = Inf)
library(jsonlite)
jsonlite::toJSON(data1, pretty = TRUE)
#+END_SRC

kaz-yos

###  Write multiple data_frames to a single xlsx file (use openxlsx)
write_lst_of_df_to_xlsx <- function(lst_df, file, font_size) {
    ## Create a workbook object with one sheet
    ## https://rdrr.io/cran/openxlsx/man/setColWidths.html
    wb <- createWorkbook()

    ## Work on each data_frame
    for (i in seq_along(lst_df)) {

        sheet_name <- ifelse(is.null(names(lst_df[i])),

kaz-yos

Taken from http://www.significantdigits.org/2017/10/switching-from-base-r-to-tidyverse/

| Base R command                    | Tidyverse Command                          | Comment                                                       |
|-----------------------------------+--------------------------------------------+---------------------------------------------------------------|
| read.csv()                        | read_csv()                                 | also see read_delim(), read_tsv() and readxl::read_xlsx()     |
| sort(), order()                   | arrange()                                  | see also order_by()                                           |
| mtcars$mpg = ...                  | mutate()                                   | see also transmute() which drops existing variables           |
| mtcars[,c(“mpg”, “am”)], subset() | select(), rename()                         | see also pull()                                               |
| mtcars[mtcars$am == 1,], subset() | filter()       

kaz-yos

###  Turn tableone output matrix into tidyverse data_frame
tableone_mat_to_data_frame <- function(mat) {
    bind_cols(data_frame(Variable = rownames(mat)),
              as_data_frame(mat))
}


###  Write a xlsx file
write_tableone_mat_to_xlsx <- function(tableone_mat, file) {
    ## Create a workbook object with one sheet

kaz-yos

class Jpeg < Formula
  desc "Image manipulation library"
  homepage "http://www.ijg.org"
  url "http://www.ijg.org/files/jpegsrc.v8d.tar.gz"
  sha256 "00029b1473f0f0ea72fbca3230e8cb25797fbb27e58ae2e46bb8bf5a806fe0b3"

  bottle do
    cellar :any
    rebuild 2
    sha256 "85d1f6055de99c1b764c697498bb86d003f5d24b324133f036f0393b97b3e869" => :sierra

kaz-yos

## Implement multivariate version of Rubin's formula
## eq 14 in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029775/
## Page 97 of https://www.amazon.com/Multiple-Imputation-Nonresponse-Surveys-Donald/dp/0471655740
AlternativeMIcombine.default <- function (results, variances, call = sys.call(), df.complete = Inf, ...) {
    m <- length(results)
    oldcall <- attr(results, "call")
    if (missing(variances)) {
        variances <- suppressWarnings(lapply(results, vcov))
        results <- lapply(results, coef)
    }

kaz-yos

(defun org-babel-get-all-src-block-info ()
  "Get information on all src blocks in an org file."
  (interactive)
  (let ((lst '()))
    (save-excursion
      ;; Go to the beginning of buffer
      (beginning-of-buffer)
      (while (condition-case err
                 ;; Try to move to the next src block.
                 (org-next-block nil nil org-babel-src-block-regexp)