

HyperNiche for Windows 98, 00, ME, NT,
XP, Vista, 7, 8, and 10
Multivariate Analysis of Ecological Data
Version 2
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Use Overview
1. Prepare Your Data
 Put your data in a spreadsheet (e.g. Excel) with the sites as rows and variables as
columns. Assign a name to each row and column.
 Partition your variables into two worksheets, one with species response variables
(presence, abundance, or other measure of performance), and the other with predictors
(habitat variables). Copy the row names into both worksheets.
 Insert header rows declaring the contents of your response matrix, and whether each
variable is quantitative (Q) or categorical (C).
 Save each of these two worksheets as a separate spreadsheet in *.wk1 format.

2. Open HyperNiche and Your Data Files
Start HyperNiche, then open your response matrix, the file containing your response
variables:
Open your predictor matrix in the same way. 
3. Fit Models to Your Data
 Use Fit Model  Free Search with your method of choice. For
general purposes we recommend nonparametric multiplicative regression based on a local
mean and Gaussian weighting function (LMNPMR).
 HyperNiche examines a large number of models (2008 in this case), then lists the results
for those models in the Model List window in the upper right corner of your screen.
 Filter and save the best models for each response variable for each number of
predictors. Use Edit  Delete All But Best For N Predictors.
This results in 12 models retained. For each of the four response variables, the best 1,
2, and 3predictor models are saved. The model list is then saved by choosing File
 Save As  Unsaved Model List, then supplying the file name, in this case
CraneExample.spx.
 Choose the number of predictors by evaluating the diminishing returns of adding
predictors. Consider the fourth response variable, abundance of species Isomyo.
Adding a third predictor "Live", resulted in little improvement in fit
(measured by xR^{2}, the crossvalidated R^{2}). So we chose to
pursue the model with two predictors, LogDia and Height.

4. Explore Your Models Graphically
You can explore your models with:
 2D and 3D response surfaces
 Estimated vs. observed values
 Residual plots
 Partial models
For example, generate a 3D response surface as follows. Select the model you wish
to graph by clicking on the model in the model list window. In this case we chose
model number 1540, relating Isomyo to the two predictors LogDia and Height.
We get the following graphic:
It is a bit difficult to see the full response shape, so let's rotate the graph for a
different view:
The response surface is broken in the areas where there was insufficient data, as set
by the minimum average neighborhood size. This parameter was set during the model
fitting phase. To achieve a smoother, continuous curve we can increase that
parameter from 3 to 10.
The following graphic shows the best 2D model with this stronger smoothing:


