quicR 2.1.0

New features

Included a new function calculate_metrics which will make calls to the “calculate” family of quicR functions, and return a dataframe of all the metrics passed to the function.
Added the plot_metrics function which accepts the output of the calculate_metrics function and returns a faceted plot of the calculated metrics.

Adjusted the delimiter in get_meta so that the second column doesn’t have a leading white space.
Fixed example scripts to work with the updated functions.
Now suppressing messages from get_wells. This wasn’t necessarily a bug, but was not ideal and the messages didn’t provide any relevant information about what the function was doing.
Fixed a typo in get_wells which caused the function to assigning a data frame as a variable instead of returning the data frame.
Fixed a bug where the plate view would not render properly if the plate was not completely full.

Provided the calculate_threshold function for calculating detection thresholds using a common method done in the literature.
Added a sep argument to get_sample_locations for delimiting sample IDs and dilution factors.
Converted the calculate_MS function to a vectorized function, and instead of using lm, the function looks at differences within the moving window. This provides a much faster calculation, but does reduce the accuracy slightly. May provide the option to do either methods in the future.
Added the default option “Sample IDs” for tab_name in the get_sample_locations function.

Made the quicR logo!
Provided better test files which have more ideal RT-QuIC data.
Now includes the manuscript in the man folder which will be submitted for publication.

Fixed organize_tables function to accept Excel files which do not have the metadata preamble. Will not affect output if file still has the preamble.
Sped up the get_meta function by having it read in sheet 1 from the Excel file which typically has much less data to read in.

Added a new function “transpose_real.R” which takes the output of “get_real.R” and transposes it. This format makes it such that each read is a column labelled with the time of the read.
Removed the transposition sub-function from “normalize_RFU.R” to be its own separate function.
Updated example scripts to incorporate the new transposition function.

Added janitor as a dependency.
Added a new test file which includes multiple real-time datasets. This is useful for the get_real function since the output returns a list of data frames if there are multiple real-time reads.
Converted many of the functions to be more in line with functional programming paradigm.
Included a documentation file that fixes the NOTE when using “.” in a dplyr pipeline.
Fixed bugs in the example scripts.