A data cleaning package, by Katherine Schaumberg
For a detailed example of how this package works, see package vignette
The goal of scorekeeper is to support the development of accessible, approachable, and reproducible scoring algorithms for multi-item measures. This package was designed with psychological assessment measures in mind, but can be broadly applicable to other multi-item assessments. The package requires a raw data file and a scoresheet (an RData or .csv metadata file) as input. Scorekeeper uses dplyr functionality to manipulate and clean data in a systematic way, as specified in the scoresheet. The scoresheet can then serve as a resource that will make your data cleaning process both reproducible and easily shared (e.g. if a colleague would like to score a measure in the same way that you did for their project on a different sample, you can send or post your RData or .csv/.xlsx scoresheet and it should easily replicate your scoring algorithm – no need to send or post additional code). While scoresheets are structured to be more easily developed and interpreted as compared to raw code, I also recommend a companion text file outlining each step in your data cleaning to maximize ease of interpretation when sharing with others (or your future self!). Currently, scoresheets must be formatted in accordance with guidelines outlined in each of the ‘operation’ functions and with steps that proceed in an appropriate order.
I recommend building a scoresheet step-by-step. Add one ‘step’ at a time in your data manipulaton and complete error checking by running functions in the scorekeeper package as you build the scoresheet.
Scoresheet Structure
Columns in a scoresheet include:
raw_vars : a raw variable or list of raw variables (either a vector or a single, comma separated character string) needed for an operation
new_var: the desired name of a new variable created during the operation
label: the new variable label, if needed
operation: the operation to preform (select, filter_at, recode, sum, if_else, case_when, rename, mean)
step: identifies the order of operations to be preformed, starting with ‘1’. I recommend entering any raw metadata as ‘0’ to increase transparency of your scoring method when sharing a scoresheet
val_labs: value labels for a new variable. Follow the convention label = value. label/value pairs can be listed as a single, comma separated character string or as a vector of character strings.
new_vals: values to be recoded in a recode operation. Follow the convention old = new. old/new pairs can be listed as a single, comma separated character string or as a vector of character strings.
if_condition: a logical condition to be evaluated for an if_else operation
if_true_return: value that is returned if the ‘if_condition’ == TRUE in if_else operations
else_return: value that is returned if the ‘if_condition’ != TRUE in if_else operations
code: code for performing a ‘filter_at’ or ‘case_when’ operation. Not needed for other operations.
The required columns in a scoresheet currently have limited flexibility – see documentation for the individual functions for details on these limitations. I anticipate adding additional functionality in the future.
Operations
Current operations supported are:
select : selects variables that you identify in scoresheet$raw_vars.
filter_at: filters rows of a dataset. Use filter_at dplyr conventions using scoresheet$code
recode: recodes a variable into a new variable, using values defined in scoresheet$new_vals. Renames the new variable to the name defined in scoresheet$new_var. creates value labels defined in scoresheet$val_labs. labels new variable according to scoresheet$label
sum: sums variables identified in scoresheet$raw_vars, new raw sum variable (NA values counted as 0) is named the value in scoresheet$new_var. In addition to the raw sum, four additional new variables are appended - complete case sums, the number of and proportion of NA values in the sum, and a weighted sum based on the number of variables included in the sum.
if_else : creates a new variable, scoresheet$new_var, defined in scoresheet$if_condition, scoresheet$if_true return, soresheet$else_return
case_when : creates a new variable, scoresheet$new_var, using case_when code defined in scoresheet$code
rename: renames a single variable entered in scoresheet$raw_vars to scoresheet$new_var
mean: creates a mean of variables identified in scoresheet$raw_vars, named in accordance with scoresheet$new_var. In addition to the mean, three additional new variables are appended - the mean of complete cases only, and the number of an proportion of NA values in the mean.
Installation
Install scorekeeper from its GitHub repository. If you do not have the remotes package installed, first install the remotes package.
install.packages("remotes")then install R/scorekeeper using the install_github function in remotes.