AHMbook (version 0.2.10)

Finnmark: Data from surveys of birds in Finnmark in NE Norway

Description

A total of 37 plots were placed spanning the existing variation in extent and fragmentation of willow thickets. Each plot was visited 3-5 times in early July each year from 2005 to 2008. Birds observed within 100m during a 15 min period were recorded.

Usage

data("Finnmark")

Format

Finnmark is a list with 4 elements:

species

a data frame with a row for each species and the following columns:

• species : the English name.

• latin : the Latin name.

• assemblage : the guild to which each species belongs.

sites

a data frame with a row for each plot and the following columns:

• region : a factor, 3 levels, Ilford, Komag, and Vestre Jakobselv.

• catchment : a factor, 11 levels.

• plot : a factor, the alphanumeric ID of each plot.

• plotnr : the ID number of each plot.

• area : the percentage of a 400 x 400m quadrat centered on the sampling point covered by tall willow thickets.

• edge : the length (m) of the edge of the willow thickets in the quadrat.

• height : the mean height of willows at 4 measuring points.

• density : a measure of thicket density at 4 measuring points.

counts

a sites x replicates x years x species array of counts

timeOfDay

a sites x replicates x years array with the time of day that the survey was carried out.

References

Henden, J.-A., Yoccoz, N.G., Ims, R.A., Langeland, K. (2013) How Spatial Variation in Areal Extent and Configuration of Labile Vegetation States Affect the Riparian Bird Community in Arctic Tundra. PLoS ONE 8(5): e63312.

Kéry, M. & Royle, J.A. (2021) Applied Hierarchical Modeling in Ecology AHM2 - 5.

Examples

data(Finnmark)
str(Finnmark)

# Create the objects needed for the analysis:
# Extract the numeric covariates and standardise
str(Finnmark$sites)
scov <- scale(Finnmark$sites[, 5:8])
str(scov)

# Convert the 'counts' array to detection/nondetection data:
y <- Finnmark$counts > 0
storage.mode(y) <- "integer"
str(y)

# Get the guild information for each species
guild <- Finnmark$species$assemblage

# Standardise the timeOfDay and replace NAs with 0
tod <- with(Finnmark, (timeOfDay - mean(timeOfDay, na.rm=TRUE))/ sd(timeOfDay, na.rm=TRUE))
tod[is.na(tod)] <- 0
str(tod)