General

What is the equation?

Q. What is the "formula" for a given model and how can I determine this using the coefficients in the model list?

A. These nonparametric models do not have coefficients in an equation in the usual sense.  The "tolerances" (smoothing parameters) are used instead of the regular coefficients.  So a prediction is made not with an equation but by obtaining an estimate from the calibration data set, using a given set of tolerances.

See also "Model Specification" in the companion PDF document.  If you are interested in using the models in a predictive mode (predicting responses for new sample units).  You might also find helpful the section in the help system under Prediction | New Sites.

Repeated measures data

Q. Is it appropriate to use HyperNiche to analyze data sets that contain numerous samples obtained at different times from the same limited number of sites?  Each sample will have different values of most predictor and all response variables.   Time/date is used as a predictor variable.

A. This fine for descriptive statistics, but be careful about formal hypothesis tests.   If the sample units are not considered independent, you may bias a hypothesis test -- exactly the same problem as with parametric statistics.

Statistical significance

Q. How can I evaluate the statistical significance for a given model? For example, how can I interpret xR2 values for models with large and small numbers of data?  How can I determine the relative significance of different predictors?

A. You can evaluate whether the model is stronger than expected by chance by using the randomization test.  After selecting a particular model, be sure that you have the same file of predictors open, then run Fit Model | Evaluate Selected Model.   Then select Monte Carlo test on the output options tab.  This is very slow with large data sets.

In late 2004 we added a sensitivity analysis.  Use this to evaluate the relative importance of different predictors in a particular model.  This is automatically given now with Fit Model | Evaluate Selected Model.

Editing spreadsheets

Q. Why doesn't HyperNiche allow cell-by-cell editing of spreadsheets?  I have to go back and forth between HyperNiche and a spreadsheet program when I am cleaning my data.

A. HyperNiche doesn't attempt to duplicate the spreadsheet functions.  However the HyperNiche allows simple editing of the main and second matrices.  More complicated editing and sorting is best done in your spreadsheet software.  It is so easy to go back and forth between applications using Windows that there should not be a great inconvenience.  You should note, however, that some spreadsheet programs, such as Excel, keep the file open, unless explicitly closed.  This means that while a file is open in Excel it is not available to HyperNiche.

Convert output to tables

Q. How can I convert tables in HyperNiche’s output files into tables in my word processor?

A. Your word processor probably has functions for converting tabular text files into tables.  For example, using Microsoft Word, you can highlight a table in a HyperNiche output file, then select Table | Convert Text To Table, to convert the output into a standard tabular format.  Be sure to set the delimiter to a space character and adjust the desired number of columns.

Mac version?

Q. Are versions of HyperNiche available for the Macintosh?

A. No. There is only a Windows versions of HyperNiche.

Mac emulation 3D crash

Q. I am using HyperNiche with Mac OS X running Windows XP via Parallels. Graphing 3D makes HyperNiche crash. Is there a solution?

A. Open XP Control Panels | Appearance and Themes | Display Properties | Settings | Advanced | Troubleshoot and set the Hardware acceleration slider to the second position from the left that says "Disable all but basic accelerations. Use this setting to correct more severe problems". Note this position also disables DirectDraw and Direct3D used by any other software.

HyperNiche CD will not install

Q. HyperNiche CD will not install on my system.  What is the solution?

A. Be sure to disable any antivirus program such as Norton before trying to install. If the CD still won't install, you may have the CD autorun feature disabled.  You can install manually from the Start Menu by selecting Run and entering x:Setup where x is the letter of your CD drive.  You also can click the Browse button and navigate to the Setup program.

OPENGL32.DLL not found

Q. I'm running Windows 95 operating system and when I start HyperNiche I get an error message saying, "A required .DLL file, OPENGL32.DLL, was not found.  What is the solution?

A. For Windows 95 you may need to download Opengl.exe (484K) to the Windows System folder or the HyperNiche folder and then execute the self-extracting program that includes OPENGL32.DLL.

Data Structure

Missing data

Q. What can I do about missing data (cells in my matrices for which I have no data)?

A. You must take steps to replace missing cells with numerical values, or you must delete the offending rows or columns.  If you ignore warnings about missing data, they are most likely to be interpreted as zeros, which may or may not be reasonable.   There are several approaches to substituting values for missing cells.  We recommend reading Tabachnik and Fidell (1989) for a good discussion of the pros and cons of various remedies for missing data.  HyperNiche expects you to deal with the missing value problem rather than having an automatic way of dealing with it.  The reason for this is that for most multivariate analyses there simply is no good universal way of handling missing values.

Error message about a cell outside data matrix

Q. When HyperNiche reads my data I get an error message about a cell that is outside of my data matrix.  Why?

A. There is something in your spreadsheet outside the matrix.  Even if the cell looks blank, there may be something there.  For example, if you go to a cell in a spreadsheet, hit the space bar, then move to another cell, the cell will look blank, but there are actually data written in that cell: first a code saying there is a label field, next the "blank" character.  When you put the cursor on the cell in question the spreadsheet will display one of the characters that signals a label field: usually ' " or ^.  This is displayed not in the cell itself, but in the separate display that shows the contents and any imbedded codes in the current cell.  You can get rid of these by erasing the cell in question or a whole block of cells.

Using numbers as row labels

Q. I wish to label my sample units with numbers, but HyperNiche insists on character data in the first column.  It seems that the only way to get number labels into HyperNiche is to either enter them in compact format and import, or reformat each cell by hand in Quattro or Lotus, or insert a character before the first number in Excel.

A. This is a problem with the Excel export. It's too smart for its own good, converting numbers defined as characters into numbers defined as numbers.  We could change it to allow numbers in that field, but at some risk of clarity -- some people will surely omit the row labels and the analyses will be based on one too few columns.

Bad entry in cell x. Expecting number

Q. I get the error: "Bad entry in cell x. Expecting number."  I looked at the spreadsheet and can find nothing wrong.  What is the problem?

A. HyperNiche is expecting a number but finding something else.  Sometimes the problem can be "invisible." Examples:
- the letter o instead of the number zero
- an imbedded space in a number (the spreadsheet automatically considers this character data)
- an equation instead of a number

If you can't see the problem, re-enter the data in the cell and explicitly format the cell to be a number.  This problem can also produce the error message: "Error reading main matrix. row x. Label encountered in spreadsheet when expecting number."

Another way to quickly remove all cell formatting that HyperNiche does not recognize is to save the file in Excel as a .CSV (comma delimited) file type rather than .wk1 and then import that file into HyperNiche.

Error reading main matrix. Data read error

Q. I've been having no success in importing a CSV file into HyperNiche. I get the message "Error reading main matrix. Data read error."  How can I correct the problem?

A. Check to be sure you have included the header rows.  Look at the text file "tempdat.tmp" in the HyperNiche folder. T his file contains info for the the last item at the time the import failed.  This file contains one data item per line.   You should be able to see the data for the row that failed or any other information out of place.

Number of rows

Q. I'm having some problems reading my data matrix (*.wk1) and I'm hoping you can help.   The matrix is 13228 rows X 12 columns.  When I try to open it, I get an error message saying that "13228 rows" doesn't match the actual number of rows (8188).   There are no missing data values and no apparent reason why it should stop at row 8188.  It always stops at that exact row, no matter what I try.

A. At least some versions of Excel export only the first 8192 rows (8188 not counting the 4 header rows) to the *.wk1 file.  This is true regardless of which of the three *.wk1 formats is selected in Excel.  You can get all 13228 rows (actually up to 32,000 rows) of your data into HyperNiche by saving the file from excel in CSV format.   Then, the first time you open it in HyperNiche, you will need to import it (File | Import | CSV).  Then save it as a *.wk1 file.  From then on you can use it as a normal data matrix in HyperNiche.  But if you reopen it and change it with Excel, you will need to go the CSV route again to get it to save the whole thing.

Excel won't save in .wk1 format

Q. Excel 2007 does not allow me to save a file in .wk1 format. Are you planning any changes to HyperNiche input/output formats related to that?

A. We have already fixed HyperNiche to allow direct access to *.xls and *.xlsx files. Those fixes have been posted, so you just need to download the latest modules. The way it now works is that now you can use either *.wk1, *.xls, or *.xlsx files. But *.wk1 is faster. Select File | Import | Excel to open an *.xls or *.xlsx file.

Registry policy blocks *.wk1 in Excel

Q. I get this error when I try to open a *.wk1 file with Excel: “You are attempting to open a file type that is blocked by your registry policy setting.” What's the problem and how can I get around it?

A. This is an issue that arises from Service Pack 3 for Office 2003. Microsoft is looking at reversing this change. Download a registry file from Microsoft to fix the issue. Run it on all computers that use these files.

Graphs

View two graphs at once

Q. How can I view two graphs at once?

A. Start two instances of PC-ORD, putting each in a window occupying half of your screen.  Then put up a graph in each one.  There is some potential for confusion if the two "sessions" are working from the same directory.  So it is safest to run each session from a different icon, the "Start In" property of each icon pointing to different directories.

Insert graphs into MS Word

Q. What is the best way to insert HyperNiche graphics into word documents?

A. Consider the following tips:

• Edit the graph completely in HyperNiche -- do not attempt to re-edit the picture in Word.
• Use "save black & white" option (Graph | Options | Preferences) to avoid gray scales for figures destined for black-and-white reports and manuscripts.
• Drag labels into clear spaces for legibility. (Not possible in 3-D graphics.)
• Edit title, axes, and legend in HyperNiche for clarity and informativeness
• When a figure is going to be reduced greatly in its final form, select larger font sizes and larger symbols in HyperNiche.
• Use options for Legend Symbol/Color to select easily distinguished symbols.
• Results may differ in sizing and other ways if you insert pictures from saved files vs. cut/paste using the clipboard. You may need to experiment with this.
• Resize the pictures in Word only by dragging the corners, not the sides, so that the proportions of the graphic are not altered.
• To include additional text, symbols, or graphics, do it _on_top_of_ the imported pictures, not within them.  This avoids editing the picture with Word, which will usually force unwanted changes on the graphic.

Vertical axis becomes horizontal in MS Word

Q. When I insert a graphic into Word, the text in the vertical axis label becomes horizontal.  How do I fix this?

A.
1. Right click the graphic and select Edit Picture from the popup menu
2. Select the text box that you want vertical
3. From the menu select Format | Text Direction

Categories with text labels

Q. Is a way in which categories can be given short text labels on ordination graphs, so that points are labeled with a letter indicating their category?

A. You can plot the row names from the second matrix, instead of getting those names from the graph file.  You can use this facility to assign ANY labels you wish, to be included in the ordination.  One application would be to give text names to groups, as you suggest.  First create a second matrix with row names that reflect group categories and open this matrix as the second matrix in HyperNiche.  Assuming you already have done the analysis and have a graph file, open the graph window.  Select preferences in the menu and then select Labels From Second Matrix.

Edit and save graphics

Q. How can I edit and save graphic images?

A. Create a Graph. Then select File | Save Graphic As. The graph is saved as a Windows metafile (*.wmf).  This file can then be inserted into many word processors and other programs where you can easily resize and edit it.

Convert Graphics to PDF

Q. Sometimes figures do not convert well to PDF.  The left axis label consistently ends up horizontal. How can I fix this?

A. Two suggestions:

1. Use the enhanced windows metafile format (*.emf) if you are not doing so already.
2. Try Adobe Acrobat Distiller. Graphics are, in general, more reliably converted to a PDF by Distiller than by regular Adobe Acrobat.

3D Graph Label Quality

Q. The labels on my 3D graphs are not crisp and have ragged edges. Is there a solution?

A. This is a problem with Windows smoothing of fonts. Select Start | Control Panel | Display | Appearance | Effects and uncheck 'smooth edges of screen fonts'. Click OK and Apply.

NMPR Models

NMPR equation

Q. Is there is a way to get an equation or a series of equations out for an NPMR model?   I find it difficult to evaluate the differences in behavior among models with the same numbers of variables but different tolerances or xR2.  So it feels very much like a black box.

A. The flexibility and power of NPMR actually comes from forfeiting a single equation.   But you can study the model behavior in a several ways:

1. Do 2D plots (Graph | Response Points) of various combinations of variables (including the residuals, estimated values, observed values, and various predictors).
2. Do 3D plots (Graphs | Response Curves | 3D) with the response variable against 2 predictors, then rotating the graph to observe the form of the relationship.
3. Use Graph | Response Points to force values of certain predictors while varying another predictor.

GIS Data

ArcView segmentation violations

Q. When exporting a GIS grid I'm having trouble with segmentation violations when I import the new grid to ArcView.

A. Be sure that you are following the naming conventions for ArcView files.  Do not include a space anywhere in the whole path name.  Certain other non-alphabetic and non-numeric characters are disallowed too.  It is safest to follow the 8+3 naming convention for file names with older software.  To do this, use 8 characters maximum in the first part of the file name, followed by a dot, followed by an extension of 3 characters at most (usually "asc" in this application).

ArcView FLOAT or INT error

Q. When exporting GIS grids to ArcView, it could only read the file if it contained binned data.  If I had it output as real numbers, I would get a FlOAT or INT error from arcview.

A. In the ArcView import dialogs you are asked what kind of data you have.  For example, after selecting File | Import Data Source | ASCII Raster, you select the *.asc file, then specify the output grid, then it asks if it should read "cell values as integers."  You should answer NO if you have real numbers, YES if you have binned estimates.

No GIS estimates

Q. I am trying to export GIS grids from Hyperniche.  Sometimes I get the error "No GIS estimates were calculated successfully".  I have checked the GIS grid file and it looks right and I have experimented with a variety of minimum neighborhood sizes.

A. The most likely cause of this is that the whole grid is being assigned the missing value.  This could happen in a number of ways, for example:

1. The values of one or more predictors are out of range of the calibration data set (for all parts of the grid).
2. One or more input grid is in different units than the corresponding variable in the calibration data.
3. The format of one or more input files is incorrect.
4. We have encountered one case of that, when a program (non-ESRI) wrote the text file in a slightly different format.  You can check this by comparing the first few lines of one of your input grids to the format given in the online help.