glm.pred.JGR {CADStat}R Documentation

Dialog box to apply predictions from a regression model to assess test sites


The regression prediction tool provides a way to model natural variations in an environmental parameter (e.g., stream temperature) in reference (i.e., least-disturbed) sites. Then, one can use the reference site model to determine whether observations of that same parameter in test sites are within the range of variation defined by the reference sites.

The linear regression tool has more options available for diagnosing and assessing the fit of a regression model on the quality data. The regression prediction tool assumes that such diagnostics have been performed to define a regression model, and the goal is now to apply the model to new data.


User Interface

Select Analysis Tools -> Regression Prediction from the menus. A dialog box will open. Select the data set of interest from the pull-down menu, or browse for a tab-delimited text file. The Data Subsetting tab can be used to select a subset of the data file by choosing a variable from the pull down menu and then selecting the levels of that variable to include. You can hold down the <CTRL> key to add several levels.

Select Dependent variable and Independent variables as in the linear regression tool.

By default, an intercept is included in the model. The intercept can be excluded by selecting Remove Intercept under the Analysis Options, in which case at least one independent variable must have been selected.

Select a Reference Variable: a variable that contains (character) values which can be used to identify which rows correspond to reference data. Once the Reference Variable is selected, select the levels of that variable that correspond to reference data. You can hold down the <CTRL> key to select multiple levels that indicate reference.

Choose a Significance Level for identification of anomalous data points in the new data. Note that the significance level corresponds to a level for a single prediction, not a family-wise significance level; no correction is performed for multiple comparisons when multiple predictions are being made. Keep in mind that some new data is expected to be flagged as significant (on average, about the number of predictions times the significance level should appear significant, depending on correlation).

The ID Variable allows for a label variable to be specified, so that points that differ significantly from reference can be identified on the plot. If no ID Variable is selected, then the row number will be used instead.

The output of the regression prediction tool is a table for the test (non-reference) data, including the observed and predicted values, the standard error associated with the prediction, a p-value for the prediction, an indication of whether the sample differs significantly from reference, an indication of whether the independent variables for the new data are in range of the model fit, and finally an indication of whether or not the normal approximation used to calculate the p-value is appropriate (for poisson and binomial regression only). Note: for binomial data, the observed value is converted from a count to a proportion (dependent variable divided by sample size). A plot of observed versus predicted values is also produced, to help assess the model fit and identify anomalous data points.

[Package CADStat version 3.0.8 Index]