cardinale: Nutrient experiment on patches of algae in Californian...

In lavaan.survey: Complex Survey Structural Equation Modeling (SEM)

Description

An experiment on patches of algae in Californian streams by Cardinale, Bennett, Nelson, and Gross (2009). The authors chose 20 streams in the Mono Lake and Owens River basins in the Sierra Nevada. In each stream, they placed 5 or 10 PVC elbows containing different levels of nutrients and a small patch of agar on which algae could grow. They then returned to the streams about 42 days later and measured 1) species diversity in the stream, 2) species diversity in each patch, 3) biomass of the algae, and 4) rate of oxygen production on each patch.

Usage

data(cardinale)

Format

A data frame with 127 observations of 7 variables.

PatchDiversity

Number of species on agar.

Biomass

Standing algal biomass.

O2Production

Gross primary oxygen production.

logNutrient

Experimentally manipulated nutrient supply rate (log_10 transformed).

logNutrient2

log(nutrient, base=10)^2.

StreamDiversity

Number of species in stream.

Stream

The stream in which the experiment was performed.

Author(s)

Daniel Oberski - http://daob.nl/ - [e-mail]

Source

The results of the fit may be compared with Figure 5 in Cardinale et al. (2009, p. 1237).

Model and data from this example were obtained from Jarrett Byrnes' GitHub: https://github.com/jebyrnes/Ecological-SEMs-in-lavaan

Note that I changed the variable names to be easier to understand, e.g. logNutrient was logN, PatchDiversity was SA, etc.

References

Cardinale BJ, Bennett DM, Nelson CE, Gross K (2009). "Does Productivity Drive Diversity or Vice Versa? A Test of the Multivariate Productivity-Diversity Hypothesis in Streams." Ecology, 90(5), 1227-1241.

Oberski, D.L. (2014). lavaan.survey: An R Package for Complex Survey Analysis of Structural Equation Models. Journal of Statistical Software, 57(1), 1-27. http://www.jstatsoft.org/v57/i01/.

See Also

lavaan.survey

Examples

  data(cardinale)
  summary(cardinale)
  
  model.card <- '
     PatchDiversity ~ logNutrient + logNutrient2 + StreamDiversity
     Biomass ~ PatchDiversity + logNutrient
     O2Production ~ logNutrient + Biomass
     logNutrient ~~ logNutrient2'
  
  fit.card <- sem(model.card, data = cardinale, fixed.x = FALSE, estimator = "MLM")
  
  des.card <- svydesign(ids = ~Stream, probs = ~1, data = cardinale)
  fit.card.survey <- lavaan.survey(fit.card, des.card, estimator = "MLM")
  
  pval.pFsum(fit.card.survey, survey.design = des.card)

lavaan.survey documentation built on May 2, 2019, 3:41 p.m.