README.md

In jennguyen1/scriptR: Scripting in R

scriptR

This package contains a variety of functions for reproducible research in R. Provided are a variety of functions that simplify logging, asserting, scripting in R.

Load Libraries

• install_scriptR() installs scriptR from github
• lib() imports commonly used libraries

File Manipulation and Creation

• ensure_requisite_folders() ensures that a file path is available, otherwise creates it
• read.in() reads in DFs with a specified function and options
• write.out() writes out DFs to folder, depending on file extension

Logging

• dictConfig() intiates a logging session based off a list with configurations
• start_logging() initiates a logging session, using the logging package
• logging.*() logging functions at variety of levels
• print_cmd_args() prints out command line arguments to console and logfile if it exists
• process_args() intiates a script by (1) start log, (2) process command line args, (3) log command line args

Reporters report_function_name() wrapper function, logs the function's name report_args() wrapper function, logs arguments passed to function report_dim() wrapper function, logs the dimensions before and after report_na() wrapper function, logs number of NA per column of the data frame

Assertions assert_cols_in() asserts that columns are inside a DF assert_between_boundaries() wrapper function, asserts specified columns of DF are between specified boundaries assert_between_n_std() wrapper function, asserts specified columns of DF are between specified standard deviations from the mean assert_in() wrapper function, asserts specified columns of DF have values that are in specified lists assert_col_types() wrapper function, asserts specified columns of DF are specified types assert_dim() wrapper function, asserts resulting DF has certain dimensions assert_margins_after() wrapper function, asserts resulting DF margins compare to incoming DF assert_none_missing() wrapper function, asserts specified columns of DF are not NA * assert_unique() wrapper function, asserts specified columns of DF are unique

Miscellaneous * is_named_list() checks whether a list is a uniquely named list

Installation

devtools::install_github("jennguyen1/scriptR")

Prerequisites

These functions depend on the following packages: logging, argparse, optparse, tidyverse, data.table. Other data wrangling packages are optional (see lib function).

jennguyen1/scriptR documentation built on May 29, 2019, 1:05 a.m.