Germination of Eryngium sparganophyllum

Germination data from an experiments investigating the effect of different concentration of gibberellic acid on germination of Eryngium sparganophyllum seeds. Two datasets are provided: one resembling how data are entered in the first place ("Eryngium.sparganophyllum0") and one formatted and ready-to-use for the statistical analysis ("Eryngium.sparganophyllum")

Usage

Eryngium.sparganophyllum

Format

A data frame with 583 observations on the following variables.

Treat

a factor with 15 levels denoting the concentration of gibberellic acid (in ppm)

Type

a factor with two levels denoting the type of treatment (gibberellic acid or temperature)

Day

a numeric vector recording time (in days) since the beginning of the experiment

Germ

a numeric vector of counts of germinated seeds

Start

a numeric vector of starting time points of monitoring intervals

End

a numeric vector of ending time points of monitoring intervals

Germinated

a numeric vector of counts of germinated seeds in a given interval

Rep

a numeric vector corresponding to the replicated sub-experiments; it is only a unique enumeration for the dataset "Eryngium.sparganophyllum"

References

Wolkis, D., Blackwell, S., Kaninaualiʻi Villanueva, S. (2020). Conservation seed physiology of the ciénega endemic, Eryngium sparganophyllum (Apiaceae). Conservation Physiology, 8, coaa017. https://doi.org/10.1093/conphys/coaa017

Examples

library(drc)

## Displaying the data
head(Eryngium.sparganophyllum)
#>   Day Treat Type         Rep Start End Germinated
#> 1   2 GA3.0  GA3 GA3.GA3-0.1     0   2          0
#> 2   2 GA3.0  GA3 GA3.GA3-0.1     2   4          0
#> 3   4 GA3.0  GA3 GA3.GA3-0.1     4   7          0
#> 4   7 GA3.0  GA3 GA3.GA3-0.1     7   9          1
#> 5   9 GA3.0  GA3 GA3.GA3-0.1     9  11          1
#> 6  11 GA3.0  GA3 GA3.GA3-0.1    11  14          0

## Fitting an event-time model for germination
Eryngium.m1 <- drm(Germinated ~ Start + End, data = Eryngium.sparganophyllum,
fct = LL.3(), type = "event")
#> Warning: longer object length is not a multiple of shorter object length
#> Warning: longer object length is not a multiple of shorter object length
#> Warning: data length [1166] is not a sub-multiple or multiple of the number of rows [14]
#> Warning: longer object length is not a multiple of shorter object length
#> Warning: longer object length is not a multiple of shorter object length
summary(Eryngium.m1)
#> 
#> Model fitted: Log-logistic (ED50 as parameter) with lower limit at 0 (3 parms)
#> 
#> Parameter estimates:
#> 
#>                Estimate Std. Error t-value   p-value    
#> b:(Intercept) -2.715614   0.126975 -21.387 < 2.2e-16 ***
#> d:(Intercept)  0.663221   0.018812  35.254 < 2.2e-16 ***
#> e:(Intercept)  6.698683   0.215910  31.025 < 2.2e-16 ***
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

## Plotting the fitted germination curve
plot(Eryngium.m1, xlab = "Time (days)", ylab = "Proportion germinated", log = "")