Changelog

Source: NEWS.md

ceas 1.2.1

• read_data() throws an error if the “Group” column of the input data is only one word that cannot be separated with the delimiter provided by the user.

ceas 1.2.0

• Linear mixed-effects models can now be used to get mean and confidence intervals for datasets with replicates. ATP production, OCR and ECAR are modelled as the response with experimental group as a fixed effect and replicate as a random effect. Mixed-effects modelling is supported by get_energetics_summary(), get_rate_summary(), bioscope_plot(), atp_plot(), and rate_plot().

ceas 1.1.2

• get_energetics() now warns about possible mismatches between the replicates in the MITO and GLYCO groups instead of stopping as datasets with different replicate counts can cause a mismatch that may not be erroneous.

ceas 1.1.1

• rate_plot() now has a linewidth parameter to set the width of its geom_lines

ceas 1.1.0

• Separating replicates is now supported for getting get_energetics_summary(), bioscope_plot(), atp_plot() and rate_plot() with sep_reps = TRUE. This will calculate summary statistics for each replicate within a group instead of combining them. atp_plot() now uses a linerange plot instead of a crossbar plot and color to distinguish between replicates instead of experimental groups. There is no color if there are no replicates or if they are combined.

  Note: the current default is to combine replicates (sep_reps = FALSE) to maintain backwards compatibility, but future releases will separate them by default. If sep_reps is not explicitly set to FALSE, the functions will warn the user about this future change in defaults.

ceas 1.0.3

• Preserve the replicate column when returning energetics from get_energetics()

ceas 1.0.2

• read_data() returns the replicate column as a factor instead of numeric

ceas 1.0.1

• Replace geom_line’s deprecated size option with linewidth in rate_plot

ceas 1.0.0

CRAN release: 2024-05-07

• First CRAN release.

ceas 0.3.3

• Don’t divide by 0 when normalizing if already 0; PER is now normalized with OCR and ECAR.

ceas 0.3.2

• Warn if data are not normalized by checking that the “Background” group’s OCR, ECAR, and PER values are 0.

ceas 0.3.1

• Add assay type as argument to plot ECAR/OCR meaningfully as all assay types were previously being summarized instead of just one.

ceas 0.3.0

• Add normalize(), a cell count/protein mass normalization function. read_data now can take a csv file with cell counts or protein mass (\(\mu\)g) for each of the experimental groups to normalize the data. An example csv is provided below for a dataset with 4 experimental groups:

  exp_group	measure
  Group_1	30000
  Group_2	30000
  Group_3	5000
  Group_4	5000

ceas 0.2.0

• Add delimiter between group and assay labels as argument in read_data() to support delimiters other than .

ceas 0.1.1

• Fix the calculation of coupled mitochondrial respiration (#4). This correction was published in https://doi.org/10.1074/jbc.AAC118.004855.

ceas 0.1.0

First release before initial submission for publication.