P8Q1.csv

1. These data are the results of a chemical analysis of wines grown in the same region in Italy but derived from three different cultivars. The analysis determined the quantities of 13 constituents found in each of the three types of wines.
   1. What chemicals have we included in the data?
   2. Examine the correlation of the chemicals (excluding the cultivar) using scatterplotMatrix() from library(car). What chemicals are highly correlated with each other?
   3. Is normalisation necessary if we want to compute a PCA for this data set? Why?
   4. Run the PCA with prcomp(), remember to set the scale = and center = as appropriate. Store this as wine.pca.
   5. By using summary() on the PCA object, examine the proportion of variance explained by each of the PCs.
   6. How many principal components should we retain? Use screeplot() to produce a scree plot and determine the cut-off point.
   7. We will observe the loadings for the first PC using wine.pca$rotation[,1]. What do these values mean?
   8. What do you observe from the biplot()?
   • Answer

P8Q2.csv

1. We are interested in the habitat preference of the clouded leopard in Peninsular Malaysia, specifically what are the factors that might influence the frequency of detection of clouded leopard on camera traps (Fig 1). Data were consolidated from 8 different non-governmental organisations (Fig 2), providing a total of approximately 900 camera trap detection data. At each camera trap location, Geographic Information System (GIS) maps were used to quantify the environmental variables. Map with the camera-trap surveyed areas (sites) used to model mainland clouded leopard habitat use in the Peninsula Malaysia. The dataset thus consists of the values of the environmental variables and the frequency of detection at each camera trap. Your task is to analyse this data and deduce meaningful biological implications, taking into account the possible correlations that might exist between the environmental variables.
   1. Is there any relationship between environmental covariates and the frequency of detection?
   2. What is the relationship between the different environmental covariates?
   • Suggested answer

Figure 1

Figure 2