MHB2014 {AHMbook}R Documentation

Data from the Swiss Breeding Bird Survey MHB 2014


The Swiss breeding bird survey ("Monitoring Häufige Brutvögel" 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.




MHB2014 is a list with 5 elements:


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.


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.


a sites x replicates x species array of counts


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


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


Section 11.3 of the AHM1 book has code to read in data from a CSV file, "MHB_2014.csv". This is a huge file, because the site data are repeated for all 158 species and the species data are repeated for all 267 sites. The MHB2014 list has all the same data, but in a more compact format. See Examples for ways to generate the objects used in the book from the list.


Swiss Ornithological Institute


Kéry, M. & Royle, J.A. (2016) Applied Hierarchical Modeling in Ecology AHM1 - 11.3.



# 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

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

[Package AHMbook version 0.2.9 Index]