Package 'kronos' reference manual

Title:	Microbiome Oriented Circadian Rhythm Analysis Toolkit
Description:	The goal of 'kronos' is to provide an easy-to-use framework to analyse circadian or otherwise rhythmic data using the familiar R linear modelling syntax, while taking care of the trigonometry under the hood.
Authors:	Thomaz Bastiaanssen [aut, cre], Sarah-Jane Leigh [aut]
Maintainer:	Thomaz Bastiaanssen <[email protected]>
License:	GPL (>= 3)
Version:	1.0.0.9000
Built:	2025-02-15 04:24:19 UTC
Source:	https://github.com/thomazbastiaanssen/kronos

Snippet of example data to demonstrate the functionality of 'kronos' between and among three different groups

Description

Snippet of example data to demonstrate the functionality of 'kronos' between and among three different groups

Usage

bigdata
bigdata

Format

A long format data.frame object with three 113 columns, features, and 94 rows, samples.

Source

Dummy data modified from untargeted hippocampal metabolomics over the day to demonstrate rhythmicity between multiple groups in a large dataset.

Descriptional metadata for the 'bigdata' object, for the purpose of demonstration.

Description

Descriptional metadata for the 'bigdata' object, for the purpose of demonstration.

Usage

bigmeta
bigmeta

Format

A long format data.frame object with three 113 columns and 94 rows.

Source

Dummy metadata modified from untargeted hippocampal metabolomics over the day

Update 'kronos' formula in light of sine and cosine components

Description

Update 'kronos' formula.

Usage

build_kronos_formula(formula, time, verbose)
build_kronos_formula(formula, time, verbose)

Arguments

`formula`	A formula. Use the `time` function to designate which variable represents time.
`time`	A string. Should be the column name containing the time values.
`verbose`	A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large data sets.

Get Results from list of KronosOut Objects

Description

These functions provides a unified wrapper to retrieve results from a list of kronosOut objects.

Usage

delistKronos_groupwise(kronos_list, padjust = TRUE)
delistKronos_groupwise(kronos_list, padjust = TRUE)

Arguments

`kronos_list`	a list of preferrably named kronosOut objects.
`padjust`	a boolean. Toggles FDR using Benjamini Hochbergs procedure.

Value

A table with circadian output stats per group per feature.

Get Results from list of `KronosOut` Objects

Description

These functions provides a unified wrapper to retrieve results from a list of kronosOut objects.

Usage

delistKronos_pairwise(kronos_list, padjust = TRUE)
delistKronos_pairwise(kronos_list, padjust = TRUE)

Arguments

`kronos_list`	a list of preferrably named `kronosOut` objects.
`padjust`	a boolean. Toggles FDR using Benjamini Hochbergs procedure.

Value

ANOVA-like adjusted p-values for how each factor interacts with time.

Fit cosinor model

Description

Fit cosinor model for totality of data

Usage

fit_cosinor_model(
  formula,
  data,
  time = NULL,
  verbose = verbose,
  for_pw = FALSE
)
fit_cosinor_model(
  formula,
  data,
  time = NULL,
  verbose = verbose,
  for_pw = FALSE
)

Arguments

`formula`	A formula. Use the `time` function to designate which variable represents time.
`data`	Input data
`time`	A string. Should be the column name containing the time values.
`verbose`	A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large datasets.
`for_pw`	A boolean. Toggles whether to perform pairwise ANOVAs as a TukeyHSD-like post-hoc.

Fit cosinor model

Description

Fit cosinor model for one aspect of data. Called by main 'kronos' function.

Usage

fit_groupwise_model(data, group, time, period, verbose)
fit_groupwise_model(data, group, time, period, verbose)

Arguments

`data`	input data
`group`	A character string. Signifies which group will be assessed.
`time`	A string. Should be the column name containing the time values.
`period`	A numeric. The length of a period, in the same format as the `time` parameter.
`verbose`	A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large data sets.

Fit a cosinor model and extract relevant parameters on a feature table.

Description

This wrapper applies kronos(), the main workhorse function in the 'kronos' package. It manages the individual functionalities of 'kronos', including rhythmicity analysis and differential rhythmicity.

Usage

fw_kronos(
  x,
  formula,
  metadata,
  time = NULL,
  period = 24,
  verbose = FALSE,
  pairwise = FALSE
)
fw_kronos(
  x,
  formula,
  metadata,
  time = NULL,
  period = 24,
  verbose = FALSE,
  pairwise = FALSE
)

Arguments

`x`	Input data. A table with rows being features and columns being samples
`formula`	A formula. Use the `time` function to designate which variable represents time. Leave the left-hand side of the formula empty as it will be sequentially replaced by every feature in the table.
`metadata`	A metadata table, with rows being samples and columns being metadata entries
`time`	A string. Should be the column name containing the time values.
`period`	A numeric. The length of a period, in the same format as the `time` parameter.
`verbose`	A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large datasets.
`pairwise`	A boolean. Toggles whether to perform pairwise ANOVAs as a TukeyHSD-like post-hoc.

Value

A list of kronosOut S4 objects containing coefficients and all operations.

Examples

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)
#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

Get sine and cosine components

Description

Based on 'cosinor' and 'limorhyde' packages

Usage

get_cos_sine(data, period, colnamePrefix = NULL)
get_cos_sine(data, period, colnamePrefix = NULL)

Arguments

`data`	input data
`period`	A numeric. The length of a period, in the same format as the `time` parameter.
`colnamePrefix`	A character string. Typically the name of the "Time" variable.

Figure out what variable represents time. Called by main 'kronos' function.

Description

Extracts time from the formula and from the time argument. Also handles inconsistencies.

Usage

get_vars(formula, time, data, verbose = verbose)
get_vars(formula, time, data, verbose = verbose)

Arguments

`formula`	A formula. Use the `time` function to designate which variable represents time.
`time`	A string. Should be the column name containing the time values.
`data`	input data
`verbose`	A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large data sets.

Get Results from `KronosOut` Object

Description

These functions provides a unified wrapper to retrieve results from a kronosOut object.

Usage

getKronos(kronosOut, target)
getKronos(kronosOut, target)

Arguments

`kronosOut`	a `kronosOut` output object.
`target`	the specific entry of the `kronosOut` object to be extracted.

Value

A data.frame of results.

Examples

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

Get Results from `KronosOut` Object

Description

These functions provides a unified wrapper to retrieve results from a kronosOut object.

Usage

getKronos_fit(kronosOut)
getKronos_fit(kronosOut)

Arguments

kronosOut

a kronosOut output object.

Value

The model fit used.

Examples

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)
#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

Get Results from `KronosOut` Object

Description

These functions provides a unified wrapper to retrieve results from a kronosOut object.

Usage

getKronos_groupwise(kronosOut)
getKronos_groupwise(kronosOut)

Arguments

kronosOut

a kronosOut output object.

Value

Rhythmicity parameters per group.

Examples

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

Get Results from `KronosOut` Object

Description

These functions provides a unified wrapper to retrieve results from a kronosOut object.

Usage

getKronos_input(kronosOut)
getKronos_input(kronosOut)

Arguments

kronosOut

a kronosOut output object.

Value

The data used as input for the model.

Examples

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

Get Results from `KronosOut` Object

Description

These functions provides a unified wrapper to retrieve results from a kronosOut object.

Usage

getKronos_pairwise(kronosOut)
getKronos_pairwise(kronosOut)

Arguments

kronosOut

a kronosOut output object.

Value

Pairwise comparisons between groups.

Examples


#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

Get Results from `KronosOut` Object

Description

These functions provides a unified wrapper to retrieve results from a kronosOut object.

Usage

getKronos_pairwise_p(kronosOut)
getKronos_pairwise_p(kronosOut)

Arguments

kronosOut

a kronosOut output object.

Value

ANOVA-like adjusted p-values for how each factor interacts with time.

Examples


#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

Get Results from `KronosOut` Object

Description

These functions provides a unified wrapper to retrieve results from a kronosOut object.

Usage

getKronos_params(kronosOut)
getKronos_params(kronosOut)

Arguments

kronosOut

a kronosOut output object.

Value

The names and values of additional circadian model parameters, mostly for plotting purposes.

Examples

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

Get Results from `KronosOut` Object

Description

These functions provides a unified wrapper to retrieve results from a kronosOut object.

Usage

getKronos_trace(kronosOut)
getKronos_trace(kronosOut)

Arguments

kronosOut

a kronosOut output object.

Value

The traces per group for plotting.

Examples

data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

A plotting method for acrophase circleplots using 'ggplot2'.

Description

Wrapper around 'ggplot2' to make circadian circleplots.

Usage

gg_kronos_acrogram(kronosOutList)
gg_kronos_acrogram(kronosOutList)

Arguments

kronosOutList

A list of KronosOut output objects from the main kronos function.

Value

a 'ggplot2' compatible object.

Examples

#Load prepared data stored in Kronos library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)
#Load prepared data stored in Kronos library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

A plotting method for circadian plots using 'ggplot2'.

Description

Wrapper around 'ggplot2' to make circadian circleplots.

Usage

gg_kronos_circle(kronosOut)
gg_kronos_circle(kronosOut)

Arguments

kronosOut

an output object from the main kronos function.

Value

a 'ggplot2' compatible object.

Examples

#Load prepared data stored in Kronos library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)
#Load prepared data stored in Kronos library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

A plotting method for circadian plots using 'ggplot2'.

Description

Wrapper around 'ggplot2' to make figures with a sinusoid trace.

Usage

gg_kronos_sinusoid(kronosOut, fill = "unique_group")
gg_kronos_sinusoid(kronosOut, fill = "unique_group")

Arguments

`kronosOut`	an output object from the main `kronos` function.
`fill`	The name of the variable that should be used to mark different groups. In the case of a single group, leave empty.

Value

a 'ggplot2' compatible object.

Examples

#Load prepared data stored in Kronos library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

#Load prepared data stored in Kronos library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

Snippet of example data to demonstrate the functionality of 'kronos' between and among three different groups

Description

Snippet of example data to demonstrate the functionality of 'kronos' between and among three different groups

Usage

groupdata
groupdata

Format

A long format data.frame object with three columns, and 94 rows, samples.

Source

Dummy data modified from PCR analysis of mouse ileum over the day to demonstrate rhythmicity between multiple groups.

Fit a cosinor model and extract relevant parameters

Description

This is the main workhorse function in the 'kronos' package. It manages the individual functionalities of 'kronos', including rhythmicity analysis and differential rhythmicity.

Usage

kronos(
  formula,
  data,
  time = NULL,
  period = 24,
  verbose = TRUE,
  pairwise = TRUE
)
kronos(
  formula,
  data,
  time = NULL,
  period = 24,
  verbose = TRUE,
  pairwise = TRUE
)

Arguments

`formula`	A formula. Use the `time` function to designate which variable represents time.
`data`	input data
`time`	A string. Should be the column name containing the time values.
`period`	A numeric. The length of a period, in the same format as the `time` variable
`verbose`	A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large data sets.
`pairwise`	A boolean. Toggles whether to perform pairwise ANOVAs as a TukeyHSD-like post-hoc.

Value

A kronosOut S4 object containing coefficients and all operations.

Examples

#Load prepared data stored in Kronos library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

#Load prepared data stored in Kronos library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)


#Plotting:
gg_kronos_acrogram(out_list)

Extract p-value from full fit

Description

Compute p-values from full fit.

Usage

kronos_anova(fit, time)
kronos_anova(fit, time)

Arguments

`fit`	A lm model fit.
`time`	A string. Should be the column name containing the time values.

Give tracing information for plotting purposes

Description

Generate data needed to plot cosinor trace line.

Usage

kronos_predict(fit, period, time, factors, verbose = verbose)
kronos_predict(fit, period, time, factors, verbose = verbose)

Arguments

`fit`	A model fit
`period`	A numeric. The length of a period, in the same format as the `time` parameter.
`time`	A string. Should be the column name containing the time values.
`factors`	A vector. The names of the independent variables.
`verbose`	A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large data sets.

Wrangle results from list of `KronosOut` Objects to publication ready table.

Description

These functions provides a unified wrapper to retrieve results from a list of kronosOut objects.

Usage

kronosListToTable(kronos_list, padjust = TRUE)
kronosListToTable(kronos_list, padjust = TRUE)

Arguments

`kronos_list`	a list of preferrably named `kronosOut` objects.
`padjust`	a boolean. Toggles FDR using Benjamini and Hochbergs procedure.

Value

A table with circadian output stats per group per feature.

Examples

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)

#Plotting:
gg_kronos_acrogram(out_list)

#Load prepared data stored in 'kronos' library
data("kronos_demo")
output <- kronos(formula = Variable_1 ~ time(Timepoint), 
data = onevariable, period = 24, verbose = TRUE, pairwise = FALSE)

#Extracting data from the output object:
getKronos_fit(output)
getKronos_trace(output)
getKronos_groupwise(output)

#Plotting:
gg_kronos_circle(output)
gg_kronos_sinusoid(output)

#For high-dimensional data, use fw_kronos:
out_list = fw_kronos(x = bigdata[1:50,], formula = ~ Group + time(Timepoint), 
metadata = bigmeta, period = 24, verbose = FALSE, pairwise = TRUE) 

#Extracting data from the output object: 
kronosListToTable(out_list)

#Plotting:
gg_kronos_acrogram(out_list)

An S4 class to contain all output parameters and plotting information from the 'kronos' main pipeline

Description

kronosOut is the main output container of the main 'kronos' functions.

Slots

input: A data.frame with the data that was fed to the main workhorse function as 'x'
fit: An lm fit for the entire model for the purpose of assessing differential rhytmicity.
to_plot: A data.frame with the traces required to plot individual sinusoid curves
ind_fit: A data.frame with the parameters from individual rhythmic model fits.
pairwise_t: A data.frame with the p.values for pairwise comparisons, if applicable.

Snippet of example data to demonstrate the functionality of 'kronos' in the most simple scenario.

Description

Snippet of example data to demonstrate the functionality of 'kronos' in the most simple scenario.

Usage

onevariable
onevariable

Format

A long format data.frame object with three columns, and 31 rows, samples.

Source

Dummy data modified from metagenomic analysis of mouse caecal contents over the day to demonstrate rhythmicity within one group.

Fit pairwise cosinor models as some sort of TukeyHSD.

Description

Fit cosinor model for subset of data. Called by main 'kronos' function.

Usage

pairwise_cosinor_model(data, formula, time, verbose)
pairwise_cosinor_model(data, formula, time, verbose)

Arguments

`data`	input data
`formula`	A formula. Use the `time` function to designate which variable represents time.
`time`	A string. Should be the column name containing the time values.
`verbose`	A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large data sets.

Show method for `kronosOut` object.

Description

method to print kronosOut object by calling show. Since kronosOut objects are typically unwieldy, also gives some tips on how to handle it.

Usage

## S4 method for signature 'kronosOut'
show(object)
## S4 method for signature 'kronosOut'
show(object)

Arguments

object

An kronosOut object.

Value

Does not return anything, for efficiency reasons. The obvious side effect is output to the terminal.

Snippet of example data to demonstrate the functionality of 'kronos' in the two-factor design scenario.

Description

Snippet of example data to demonstrate the functionality of 'kronos' in the two-factor design scenario.

Usage

twowaydata
twowaydata

Format

A wide format data.frame object with nine columns, and 150 rows, samples.

Source

Dummy data modified from metagenomic analysis of mouse caecal contents over the day to demonstrate rhythmicity within one group.

Package 'kronos'

Help Index

Snippet of example data to demonstrate the functionality of 'kronos' between and among three different groups

Description

Usage

Format

Source

Descriptional metadata for the 'bigdata' object, for the purpose of demonstration.

Description

Usage

Format

Source

Update 'kronos' formula in light of sine and cosine components

Description

Usage

Arguments

Get Results from list of KronosOut Objects

Description

Usage

Arguments

Value

Get Results from list of KronosOut Objects

Description

Usage

Arguments

Value

Fit cosinor model

Description

Usage

Arguments

Fit cosinor model

Description

Usage

Arguments

Fit a cosinor model and extract relevant parameters on a feature table.

Description

Usage

Arguments

Value

Examples

Get sine and cosine components

Description

Usage

Arguments

Figure out what variable represents time. Called by main 'kronos' function.

Description

Usage

Arguments

Get Results from KronosOut Object

Description

Usage

Arguments

Value

Examples

Get Results from KronosOut Object

Description

Usage

Arguments

Value

Examples

Get Results from KronosOut Object

Description

Usage

Arguments

Value

Examples

Get Results from KronosOut Object

Description

Usage

Arguments

Value

Examples

Get Results from KronosOut Object

Description

Usage

Arguments

Value

Examples

Get Results from KronosOut Object

Description

Get Results from list of `KronosOut` Objects

Get Results from `KronosOut` Object

Get Results from `KronosOut` Object

Get Results from `KronosOut` Object

Get Results from `KronosOut` Object

Get Results from `KronosOut` Object

Get Results from `KronosOut` Object

Get Results from `KronosOut` Object

Get Results from `KronosOut` Object

Wrangle results from list of `KronosOut` Objects to publication ready table.