get.nbcurve.tpc: Fit Norberg curve to growth rate vs. temperature data

In ctkremer/growthTools: Tools for analyzing time series of microbial abundances to estimate growth rates

Description

Note: this function fits a re-parameterized version of the original Norberg curve (Norberg et al. 2001, Thomas et al. 2012), altered to depend directly on a parameter that provides the true optimum temperature (ie, the temperature at which growth rate is maximal). See nbcurve() for more.

Usage

get.nbcurve.tpc(
  temperature,
  mu,
  method = "grid.mle2",
  plotQ = FALSE,
  conf.bandQ = TRUE,
  fpath = NA,
  id = NA,
  suppress.grid.mle2.warnings = TRUE,
  ...
)

Arguments

temperature	Temperature
mu	Exponential growth rate
method	Specify which fitting algorithm to use, 'mle2' or 'grid.mle2'
plotQ	Should regression be visualized?
conf.bandQ	Should we calculate a confidence band around the regression? logical.
fpath	If visual requested, and valid file path provided here, plot will be saved as a .pdf file. Default is NA.
id	Character string providing any information ID'ing the specifc curve being fit; used to label plots, if any are requested. Default is NA.
suppress.grid.mle2.warnings	logical; should warnings arising from grid.mle2 invocation be suppressed (TRUE), or displayed (FALSE)? Default is TRUE.
...	Additional arguments passed to grid.mle2 (e.g., control=list(maxit=2000))

Examples

data("example_TPC_data")
sp1 <- example_TPC_data %>% filter(isolate.id=='CH30_4_RI_03' & dilution==1)
nbcurve.traits<-get.nbcurve.tpc(sp1$temperature,sp1$mu,method='grid.mle2',
plotQ=TRUE,conf.bandQ = TRUE,fpath=NA)
nbcurve.traits

ctkremer/growthTools documentation built on July 27, 2021, 4:19 p.m.