PROBLEM SET #1
PBIO-415/515 (2004)
UNIVARIATE ANALYSIS
Background
Thompson
et al. (2002; Ecol. Appl. 12: 1344–1363) examined the effects of historical
land use on tropical forest in an effort to understand present forest
characteristics and to plan conservation strategies. They compared the effects
of past land use, topography, soil type, and other environmental variables on
tree species composition in a subtropical wet forest in the Luquillo Mountains, Puerto Rico. The study involved stems ³
10 cm diameter measured at 130 cm above the ground, within the 16-ha Luquillo
Forest Dynamics Plot (LFDP), and represents the forest at the time Hurricane
Hugo struck in 1989. Topography in the plot is rugged, and soils are variable.
Historical documents and local residents described past land uses such as
clear-felling and selective logging followed by farming, fruit and coffee
production, and timber stand improvement in the forest area that now includes
the LFDP. These uses ceased 40–60 yr before the study, but their impacts could
be differentiated by percent canopy cover seen in aerial photographs from 1936.
Using these photographs, they defined four historic cover classes within the
LFDP. These ranged from cover class 1, the least tree-covered area in 1936, to cover
class 4, with the least intensive historic land use (selective logging and
timber stand improvement). In 1989, cover class 1 had the lowest stem density
and proportion of large stems, whereas cover class 4 had the highest basal
area, species richness, and number of rare and endemic species. Ordination of
tree species composition (89 species, 13
167 stems) produced arrays that primarily corresponded
to the four cover classes (i.e., historic land uses). The ordination arrays
corresponded secondarily to soil characteristics and topography. Natural
disturbances (hurricanes, landslides, and local treefalls) affected tree
composition, but these effects did not correlate with the major patterns of
species distributions on the plot. Thus, it appears that forest development and
natural disturbance have not masked the effects of historical land use in this
tropical forest, and that past land use was the major influence on the patterns
of tree composition in the plot in 1989. The least disturbed stand harbors more
rare and endemic species, and such stands should be protected.
Analysis
Thompson et al. (2002) provide an online appendix of their tree data available through the Ecological Society of America Archives. Download the data set. Bring it in to Excel and clean it up for analysis. We are interested only in the LFDP density data (labeled “No. stems per ha”) and the size class data (labeled “Typical mature ht.”: Sm, M, L)—all other data are extraneous for this analysis and can be deleted.
First, sort the data into the 3 size classes. NB: some species are dual listed (e.g., Sm/M); for the purposes of this exercise, assign half of the density to each size class. Sort and summarize the data by size class, produce histograms, box plots, normal probability plots, etc. Evaluate the distribution of each data set for symmetry, kurtosis, modality, outliers, etc. (both quantitatively and qualitatively). Quantitatively describe the central tendency using the mean, median, and mode. Evaluate the spread of the data via estimates of the range, variance, standard deviation, percentile distributions, etc.
Provide a short expository explanation of your data, the summary stats and graphics, and discuss the possible implications of your findings.