Package 'cosinor'

Shiny application to demonstrate cosinor fit

Description

Given a dataset, specify the outcome, time variable, and optional covariates. The app will then perform a cosinor analysis and plot the results.

Usage

cosinor_analyzer(data = NULL)

Arguments

data	Data frame to analyze

Examples

## Not run: 
library(shiny)
cosinor_analyzer(vitamind)

## End(Not run)

---

Fit cosinor model

Description

Given an outcome and time variable, fit the cosinor model with optional covariate effects.

Usage

cosinor.lm(formula, period = 12, data, na.action = na.omit)

Arguments

formula	Formula specifying the model. Indicate the time variable with time() and covariate effects on the amplitude and acrophase with amp.acro(). See details for more information.
period	Length of time for a complete period of the sine curve.
data	Data frame where variable can be found
na.action	What to do with missing data

Details

This defines special functions that are used in the formula to indicate the time variable and which covariates effect the amplitude. To indicate the time variable wrap the name of it in the function time(). To indicate a variable which affects the acrophase/amplitude, wrap the name in amp.acro(). This will then do all the transformations for you. See examples for usage.

References

Tong, YL. Parameter Estimation in Studying Circadian Rhythms, Biometrics (1976). 32(1):85–94.

Examples

cosinor.lm(Y ~ time(time) + X + amp.acro(X), data = vitamind)

---

Fit cosinor model

Description

Given an outcome and time variable, fit the cosinor model with optional covariate effects.

Usage

cosinor.lm.default(formula, ...)

Arguments

formula	Forumla specifying the model. Indicate the time variable with time() and covariate effects on the amplitude and acrophase with amp.acro(). See details.
...	other arguments

Details

This defines special functions that are used in the formula to indicate the time variable and which covariates effect the amplitude. To indicate the time variable wrap the name of it in the function time(). To indicate a variable which affects the acrophase/amplitude, wrap the name in amp.acro(). This will then do all the transformations for you. See examples for usage.

Examples

cosinor.lm(Y ~ time(time) + X + amp.acro(X), data = vitamind)

---

Extract variable names from terms object, handling specials

Description

Extract variable names from terms object, handling specials

Usage

get_varnames(Terms)

Arguments

Terms

a terms object

---

Plot a cosinor model

Description

Given a cosinor.lm model fit, generate a plot of the data with the fitted values. Optionally allows for plotting by covariate levels 0 and 1.

Usage

ggplot_cosinor.lm(object, x_str = NULL)

Arguments

object	An object of class cosinor.lm
x_str	Character vector naming the covariate(s) to be plotted. May be NULL to plot overall curve

Examples

fit <- cosinor.lm(Y ~ time(time) + X + amp.acro(X), data = vitamind)
ggplot_cosinor.lm(fit, "X")

---

Predict from a cosinor model

Description

Given a time variable and optional covariates, generate predicted values from a cosinor fit. Default prediction is the mean value, optionally can predict at a given month

Usage

## S3 method for class 'cosinor.lm'
predict(object, newdata, ...)

Arguments

object	An object of class cosinor.lm
newdata	Optional new data
...	other arguments

Examples

fit <- cosinor.lm(Y ~ time(time) + X + amp.acro(X), data = vitamind)
predict(fit)

---

Print cosinor model

Description

Given an outcome and time variable, fit the cosinor model with optional covariate effects.

Usage

## S3 method for class 'cosinor.lm'
print(x, ...)

Arguments

x	cosinor.lm object
...	passed to summary

---

Print the summary of a cosinor model

Description

Print the summary of a cosinor model

Usage

## S3 method for class 'summary.cosinor.lm'
print(x, ...)

Arguments

x	An object of class summary.cosinor.lm
...	Currently unused

Examples

fit <- cosinor.lm(Y ~ time(time) + X + amp.acro(X), data = vitamind)
summary(fit)

---

Print test of model

Description

Print test of model

Usage

## S3 method for class 'test'
print(x)

Arguments

x	test object

---

Print results of test of cosinor model

Description

Print results of test of cosinor model

Usage

## S3 method for class 'test_cosinor'
print(x, ...)

Arguments

x	test_cosinor object
...	Arguments passed to print

---

Simulate data from a cosinor model

Description

This function simulates data from a cosinor model with a single covariate, where the time scale is month, and optionally allows for single covariate effects on the mean, amplitude, and acrophase.

Usage

simulate_cosinor(n, beta.mean = 2, beta.amp = 0, beta.acro = 0)

Arguments

n	Sample size
beta.mean	Effect on the mean (intercept)
beta.amp	Effect on the amplitude
beta.acro	Effect on the acrophase

---

Summarize a cosinor model

Description

Given a time variable and optional covariates, generate inference a cosinor fit. Gives estimates, confidence intervals, and tests for the raw parameters, and for the mean, amplitude, and acrophase parameters. If the model includes covariates, the function returns the estimates of the mean, amplitude, and acrophase for the group with covariates equal to 1 and equal to 0. This may not be the desired result for continuous covariates.

Usage

## S3 method for class 'cosinor.lm'
summary(object, ...)

Arguments

object	An object of class cosinor.lm
...	Currently unused

Examples

fit <- cosinor.lm(Y ~ time(time) + X + amp.acro(X), data = vitamind)
summary(fit)

---

Test for differences in a cosinor model

Description

Given a time variable and optional covariates, generate inference a cosinor fit. For the covariate named (or vector of covariates), this function performs a Wald test comparing the group with covariates equal to 1 to the group with covariates equal to 0. This may not be the desired result for continuous covariates.

Usage

test_cosinor(object, x_str, param = "amp")

Arguments

object	An object of class cosinor.lm
x_str	Character naming the covariate whose amplitude/acrophase will be tested
param	Character string naming the parameter to test, either "amp" for amplitude or "acr" for acrophase

Examples

fit <- cosinor.lm(Y ~ time(time) + X + amp.acro(X), data = vitamind)
test_cosinor(fit, "X", "amp")

---

Replace covariate names with descriptive text

Description

Replace covariate names with descriptive text

Usage

update_covnames(names)

Arguments

names

Coefficient names to update

---

Vitamin D

Description

Simulated data set to illustrate the cosinor model. Y is an outcome variable that varies of time time according to a cosine curve. The binary covariate X is associated with the mean and amplitude of the cosine curve.

Usage

vitamind

Format

A data frame with 3 variables: X, Y, time.

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