AHMbook (version 0.2.5)

MHB2014: Data from the Swiss Breeding Bird Survey MHB 2014

Description

The Swiss breeding bird survey ("Monitoring H<U+00E4>ufige Brutv<U+00F6>gel" MHB) has monitored the populations of approximately 150 common species since 1999. The MHB sample consists of 267 1-km squares that are laid out as a grid across Switzerland. Fieldwork is conducted by about 200 skilled birdwatchers annually, most of them volunteers. Avian populations are monitored using a simplified territory mapping protocol (also called spot-mapping West of the Atlantic), where each square is surveyed up to three times during the breeding season (only twice above the tree line around 2000 m elevation). Surveys are conducted along a transect that does not change over the years and is 4-6 kms in length on average.

The list MHB2014 has the full survey data for the year 2014.

Usage

data("MHB2014")

Format

MHB2014 is a list with 5 elements:

species

a data frame with rows for 158 species, including 15 species not recorded in the year 2014, and the following columns:

• specid : a numeric species ID based on phylogeny.

• latabb : a 6-letter abbreviation of the Latin name.

• engname : the English name.

• latname : the Latin name.

• body.length : body length in cm.

• body.mass : body mass in g.

• wing.span : wing span in cm.

sites

a data frame with rows for 267 1x1 km quadrat, including 1 quadrat not surveyed in 2014, and the following columns:

• siteID : an alphanumeric site identifier.

• coordx : the x coordinate of the center of the quadrat; the coordinate reference system is intentionally not specified.

• coordy : the y coordinate of the center of the quadrat.

• elev : the mean elevation of the quadrat in m.

• rlength : the length of the route walked in the quadrat in km.

• nsurvey : the number of replicate surveys planned in the quadrat; above the tree-line 2, otherwise 3.

• forest : percentage forest cover.

• obs14 : identifying number of the observer.

counts

a sites x replicates x species array of counts

date

a sites x replicates matrix with Julian dates of the surveys, 1 April = 1

dur

a sites x replicates matrix with the duration of each survey, mins

References

K<U+00E9>ry, M. & Royle, J.A. (2016) Applied Hierarchical Modeling in Ecology AHM1 - 11.3.

Examples

# NOT RUN {
data(MHB2014)
str(MHB2014)

# Create the objects at foot of p.644:
( nsite <- nrow(MHB2014$sites) )    # number of sites in Swiss MHB
nrep <- 3                           # maximum number of replicate surveys per season
( nspec <- nrow(MHB2014$species) )  # 158 species occur in the 2014 data
# Check the dimensions of the 'count' array:
dim(MHB2014$count) == c(nsite, nrep, nspec)

# Create the detection/nondetection matrix 'y':
y <- MHB2014$count > 0        # this is logical, convert to integer
storage.mode(y) <- "integer"  # don't use 'as.integer', that strips out dimensions and names
str(y)

# Pull out and check the data for common chaffinch, p.645:
head(tmp <- y[, , "Common Chaffinch"])
tail(tmp)

# }