README

The goal of seinfitR is to fit the Seinhorst equation to experimental data describing the relationship between preplant nematode densities and plant growth using nonlinear least squares fitting.

Installation

# install.packages("pak")
pak::pak("dslabcena/seinfitR")

Alternatively, if you’d like to install the stable version of seinfitR from CRAN, run:

install.packages("seinfitR")

Basic Use

The syntax of seinfitR is straightforward, with the main function being seinfitR(…).

Example

Modeling plant response to nematode densities using the “glasshouse” dataset:

library(seinfitR)

data(glasshouse, package = "seinfitR")


# Fit the model
model <- seinfitR(p_i = "p_i", y = "y", data = glasshouse,
                  start = list(m = 6, t = 6),
                  control = seinfitR_control(maxiter = 20), z_fixed = TRUE)
#> The Z_fixed parameter is set to TRUE: using the default value for z^t from Seinhorst (1986).
#> Model fitting completed successfully.

# View model summary
summary(model)
#> Seinhorst Model - Parameter Estimates
#> -----------------------------------------------------
#>         Estimate  Std. Error   t value     Pr(>|t|)
#> m      0.5951683 0.008177824  72.77832 4.096851e-16
#> t      1.6829177 0.116059892  14.50042 1.627030e-08
#> y_max 10.3675895 0.053752628 192.87596 9.127161e-21
#> -----------------------------------------------------
#> R2 - R squared (Coefficient of Determination):  0.9949782 
#> Adjusted_R2 - Adjusted R squared:               0.9940652 
#> -----------------------------------------------------

The seinfitR package provides some methods for model evaluation and visualization:

# Print model dependent/predictor variables, number of observations, and parameter estimates
print(model)
#> Seinhorst Model Fit Summary
#> -----------------------------------------------------
#> Dependent Variable:              y 
#> Predictor Variable:              p_i 
#> Number of Observations:          14 
#> 
#> Coefficients:
#>       Estimate Std. Error t value  Pr(>|t|)
#> m       0.5952   0.008178   72.78 4.097e-16
#> t       1.6829   0.116060   14.50 1.627e-08
#> y_max  10.3676   0.053753  192.88 9.127e-21
#> -----------------------------------------------------

# Extract variance-covariance matrix
vcov(model)
#>                   m            t         y_max
#> m      6.687681e-05 -0.000364986 -0.0001181826
#> t     -3.649860e-04  0.013469898 -0.0024948229
#> y_max -1.181826e-04 -0.002494823  0.0028893450

#Extract model coefficients
coef(model)
#>          m          t      y_max 
#>  0.5951683  1.6829177 10.3675895

# Calculate R-squared
r_squared(model)
#> $R2
#> [1] 0.9949782
#> 
#> $Adjusted_R2
#> [1] 0.9940652

# Calculate Plot
plot(model)

methods(class = "seinfitR")
#> [1] coef      plot      predict   print     r_squared summary   vcov     
#> see '?methods' for accessing help and source code

seinfitR: Modeling the Relationship Between Nematode Densities and Plant Growth

Installation

Basic Use

Example