In benjbuch/summerr: General Helpers for Lab Fun

knitr::opts_chunk$set(
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  fig.path = "man/figures/README-",
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summerr

The goal of summerr is to centralize the frequently used and some of the more exotic R functions and routines encountered during import, export, and processing of primary research data in the lab.

Many of these functions are re-used (imported) by more specialized packages of the summerr family.

Installation

Since this package is not part of CRAN, you must install and update the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("benjbuch/summerr")

Once installed, the suite can be updated using:

summerr::update_summerr()  # expands to other packages if loaded

Showcases

Some examples of general utility.

library(summerr)

Importing Data

Interactive access to files and folders through RStudio API (if available; else console-based chooser).

# select, e.g., an Excel file, ...
my_file <- select_single_file(suffix = "xlsx")

# ... or choose an entire directory to take forward
my_dir <- select_directory()

For example, a facility to import a 384-well plate layout created in Excel with metadata columns/rows:

my_file <- system.file("extdata", "platelayout_maldi.xlsx", package = "summerrmass")

my_layout <- import_layout_from_excel(file = my_file, meta_row = c(concentration = "1"))

my_layout

display_plate_layout(my_layout, fill = content, alpha = as.numeric(concentration)) + 
  ggplot2::labs(alpha = "Compound Concentration", fill = NULL)

Fitting Models

Calling broom::tidy, broom::glance and broom::augment on model fitted to each group of a grouped data frame and returning, fail-safe, these aspects:

library(magrittr)  # for the pipe operator

iris %>% 
  dplyr::group_by(Species) %>% 
  model_cleanly_groupwise(lm, formula = Sepal.Length ~ Sepal.Width)

You can use model_display to visualize the fit.

iris %>% 
  dplyr::group_by(Species) %>% 
  model_cleanly_groupwise(lm, formula = Sepal.Length ~ Sepal.Width) %>% 
  model_display(color = Species)

benjbuch/summerr documentation built on July 11, 2021, 9:40 a.m.