harnik: Effects of biological factors on extinction risk in fossil...

In gustavobio/semeco: Examples of Structural Equation Modelling Usage in Ecology

Description

Raw data and model syntaxes for the paper by Harnik (2011) on the direct and indirect effects of biological factors on extinction risk in fossil bivalves.

Format

A data frame with 108 observations on 8 variables and three character vectors containing model syntaxes.

Note

The models are in page 2 (figure 1). All models converge. The coefficients in model A come from three independent linear regressions. The dataset is included as it was made available in the supporting information. Data transformations should be done following the manuscript in order to get the same results. Model C involves groups (superfamilies).

Data transformation:

1. Abundance and range extent were transformed with the square root of the arcsine method. 2. Abundance and body size were log-transformed. 3. Abundance, range extent and body size were scaled and centered (we are replicating what was reported in the manuscript, but maximum likelihood estimation expects unstandardized data).

Source

Article:

http://www.pnas.org/cgi/doi/10.1073/pnas.1100572108

Supplementary information:

http://www.pnas.org/content/suppl/2011/07/25/1100572108.DCSupplemental

References

Harnik P. 2011. Direct and indirect effects of biological factors on extinction risk in fossil bivalves. PNAS early view. doi:10.1073/pnas.1100572108.

Examples

## Not run: 
data(harnik)
harnik.t <- harnik

harnik.t$abundance <- asin(sqrt(harnik.t$abundance))
harnik.t$range.extent <- asin(sqrt(harnik.t$range.extent))

harnik.t$abundance <- log(harnik.t$abundance)
harnik.t$body.size <- log(harnik.t$body.size)

harnik.t$abundance <- scale(harnik.t$abundance, center = TRUE, scale = TRUE)
harnik.t$range.extent <- scale(harnik.t$range.extent, center = TRUE, scale =
                                 TRUE)
harnik.t$body.size <- scale(harnik.t$body.size, center = TRUE, scale = TRUE)

harnik.model.A.1.fit <- sem(harnik.model.A[[1]], data = harnik.t)
harnik.model.A.2.fit <- sem(harnik.model.A[[2]], data = harnik.t)
harnik.model.A.3.fit <- sem(harnik.model.A[[3]], data = harnik.t)
harnik.model.B.fit <- sem(harnik.model.B, data = harnik.t)
harnik.model.C.fit <- sem(harnik.model.C, data = harnik.t, group =
                            "superfamily",
                          group.equal = "regressions",
                          group.partial = "duration ~ body.size")

summary(harnik.model.A.fit)
summary(harnik.model.B.fit)
summary(harnik.model.C.fit)

## End(Not run)

gustavobio/semeco documentation built on May 17, 2019, 9:29 a.m.