BC_model: Analysis: Logistic regression Brain-Cousens hormesis models

In AgronomiaR/seedreg: Regression Analysis for Seed Germination as a Function of Temperature

Description

The 'BC.4' and 'BC.5' logistical models provide Brain-Cousens' modified logistical models to describe u-shaped hormesis. This model was extracted from the 'drc' package and adapted for temperature analysis in seed germination

Usage

BC_model(
  trat,
  resp,
  npar = "BC.4",
  error = "SE",
  ylab = "Germination (%)",
  xlab = expression("Temperature ("^"o" * "C)"),
  theme = theme_classic(),
  legend.position = "top",
  cardinal = 0,
  r2 = "all",
  scale = "none"
)

Arguments

trat	Numerical or complex vector with treatments
resp	Numerical vector containing the response of the experiment.
npar	Number of model parameters (default is BC.4)
error	Error bar (It can be SE - default, SD or FALSE)
ylab	Variable response name (Accepts the expression() function)
xlab	treatments name (Accepts the expression() function)
theme	ggplot2 theme (default is theme_bw())
legend.position	legend position (default is c(0.3,0.8))
cardinal	defines the value of y considered extreme (default considers 0 germination)
r2	coefficient of determination of the mean or all values (default is all)
scale	Sets x scale (default is none, can be "log")

Details

The model function for the Brain-Cousens model (Brain and Cousens, 1989) is

f(x, b,c,d,e,f) = c + \frac{d-c+fx}{1+\exp(b(\log(x)-\log(e)))}

and it is a five-parameter model, obtained by extending the four-parameter log-logistic model (LL.4 to take into account inverse u-shaped hormesis effects. Fixing the lower limit at 0 yields the four-parameter model

f(x) = 0 + \frac{d-0+fx}{1+\exp(b(\log(x)-\log(e)))}

used by van Ewijk and Hoekstra (1993).

Value

The function returns the coefficients and respective p-values; statistical parameters such as AIC, BIC, pseudo-R2; cardinal and optimal temperatures and the graph using ggplot2 with the equation.

Note

if the maximum predicted value is equal to the maximum x, the curve does not have a maximum point within the studied range. If the minimum value is less than the lowest point studied, disregard the value.

Author(s)

Model imported from the drc package (Ritz et al., 2016)

Gabriel Danilo Shimizu

Leandro Simoes Azeredo Goncalves

References

Seber, G. A. F. and Wild, C. J (1989) Nonlinear Regression, New York: Wiley \& Sons (p. 330).

Ritz, C.; STREBIG, J.C. and RITZ, M.C. Package ‘drc’. Creative Commons: Mountain View, CA, USA, 2016.

Examples

library(seedreg)
data("aristolochia")
attach(aristolochia)
BC_model(trat,resp)

AgronomiaR/seedreg documentation built on May 19, 2021, 12:12 p.m.