QurvE (version 1.1.1)

lm_parms: Helper functions for handling linear fits.

Description

lm_window performs a linear regression with the Theil-Sen estimator on a subset of data.

Usage

lm_parms(m)
lm_window(x, y, i0, h = 5)

Value

linear model object of class lm (lm_window) resp. vector with parameters of the fit (lm_parms).

Arguments

m

linear model (lm) object

x

vector of independent variable (e.g. time).

y

vector of dependent variable (concentration of organisms).

i0

index of first value used for a window.

h

with of the window (number of data).

References

Hall, B. G., H. Acar and M. Barlow 2013. Growth Rates Made Easy. Mol. Biol. Evol. 31: 232-238 tools:::Rd_expr_doi("10.1093/molbev/mst197")

Examples

# Create random growth dataset
rnd.dataset <- rdm.data(d = 35, mu = 0.8, A = 5, label = "Test1")

# Extract time and growth data for single sample
time <- rnd.dataset$time[1,]
data <- as.numeric(rnd.dataset$data[1,-(1:3)]) # Remove identifier columns
data.log <- log(data/data[1])

# Perform linear fit on 8th window of size 8
linreg <- lm_window(time, data.log, 8, h=8)

summary(linreg)

lm_parms(linreg)