add_attr_growth_fit_pars: Compute growth curves of an attribute

In vicstefanou/ViSCA: Cell-Movie Analysis and Visualization

Description

Computes the growth curve of a numeric attribute for each cell in a division tree, by fitting a linear or exponential model to the its attribute's time-series.

Usage

add_attr_growth_fit_pars(LT, DT, attr, model = c("lin", "exp"), frameR)

Arguments

LT	The lineage tree, an object of class "igraph".
DT	The corresponding division tree of the LT, an object of class "igraph".
attr	The name of the attribute in the LT, a character string. It can be any numeric attribute, as returned from get_attr_names, except for "colony", "generation", "frame" and "age".
model	A character string naming the growth model to be fitted: "lin" for fitting a linear model y = at + b using the linear least squares method provided by lm "exp" for fitting an exponential model y = y0 ekt using the non-linear least squares method provided by nls where y represents the attr and t the time in hours (starting from 0).
frameR	Frame rate of the movie in frames per minute, a non-zero positive numeric value.

Details

The estimated parameters as well as the RMSE of the fitted growth model are added as attributes to the DT:

• When model = "lin":

  • "<attr>_a", a non-zero positive numeric value in units of attr per hour

  • "<attr>_b", a positive numeric value in units of attr

  • "<attr>_linRMSE"

• When model = "exp":

  • "<attr>_k", a non-zero positive numeric value in units of attr per hour

  • "<attr>_0", a non-zero positive numeric value in units of attr

  • "<attr>_expRMSE"

NA values are stored for cells that failed to fit the selected model as well as for cells that are not included in the analysis, as returned from get_cells. Information messages for cells that failed to fit the model are printed on the screen.

Value

The updated DT with the new attributes added, an object of class "igraph".

vicstefanou/ViSCA documentation built on May 31, 2019, 10:50 p.m.