I want to use a similarity or distance measure that is not offered by CAP
PISCES; we may be able to add the measure to the program
Error messages saying '' is not a valid floating point value or "Range Check Error"
This will occur if the raw data holds columns or rows that consist of all 0s. Remove blank columns and rows by using '0 issues' in the working data window. It may also occur if the raw data holds a blank cell. In some cases CAP will identify the problem cell which should be edited. Normally it is because the data has been prepared in a spreadsheet using blanks to represent zero values.
Invalid floating point operation
This often indicates that there are rows or columns with no data in them. Use the Zero Issues button on the working data tab to find and remove the offending row or column.
I have a huge data set. Can CAP handle it?
Older versions of CAP were limited to a 1000 species (rows) x 1000 samples (columns) data set. Version 3.0 allows effectively unlimited data set size: the power and available memory of your computer is the only limiting factor. Most reasonably fast computers should easily handle a 5000 x 5000 data set.
In TWINSPAN OUT: concerning the list of Indicators and their sign (i.e. Species 1 (+), Species 2 (-)), does the (+) represent species present in the class and (-) represent species NOT present in the class? If so, then are the only sample points (quadrats) representing the TWINSPAN classes those listed under the positive group?
In the TWINSPAN output Species1 (+) indicates that species1 is characteristic of the quadrates classified to the right of the centroid of the primary axis of the ordination. It does not mean that the Species1 is absent in all the quadrates to the left of the centroid. An output of, say, Species2 (-) would mean that Species2 is characteristic of quadrates to the left of the centroid. Remember that if TWINSPAN is not undertaken on presence/absence data it uses pseudospecies so the same species can be an indicator at different levels of abundance.
In the case of presence/absence data there will certainly be a strong tendency for a positive species only to be present in the group of quadrats to the right. However, this is not necessarily always the case.
My data set has a large number of columns (sites/samples), but Excel will only allow me to have up to 255
A common problem with large data sets. The simplest way is to arrage your data the other way round in Excel, so that rows represent samples/sites, and columns represent species. You can then have up to 255 species, and over 65,000 samples. When you open the data set in CAP, you can then use the Transpose function on the Working Data Set page to restore the data to the right way round before performing your analyses.
Alternatively, use our ListCombiner
utility to combine large data sets effortlessly!
Version 4 & earlier
The guides on the Help menu do not work
To ensure that the guides and tutorials work correctly, please make sure that both your default internet browser, and Internet Explorer, will allow popup windows (i.e., any popup-blocking utility is disabled). Also, playing the demonstrations requires that both Internet Explorer and your default browser have the Macromedia Flash player installed as a plugin. If the plugin is not installed, the program will seek to download and install it from the internet. If your PC is connected to the internet, this process will occur automatically. If your PC is not connected to the internet, or is blocked by a firewall, this may interfere with the playing of the guides.
I/O error 32 - access denied
This will occur if the data file you are trying to open is currently being used by another program - normally the spreadsheet which was used to organise the data. Close the file in other programs and try again.
Version 3 & earlier
Problems following instructions for zooming on graph
In some old printed copies of the CAP instruction manual on page five, it says that to zoom in on an area of a graph you move from the top right to bottom left. This should have read top left to bottom right. Please download the latest CAP manual
When a data file is opened, all the data are dumped into the first cell, rather than opening in the grid properly.
This is usually because there are one or more blank cells in the second row of data. If the
blanks are replaced by zeros, or another row with no blanks is put in the second position, the problem should disappear. Row 2 is the crucial one; blank cells are tolerated elsewhere.
I entered the data in a spreadsheet program, and saved it as a csv file. When I try to open it in CAP, the numbers are separated by ; not , so the analysis will not run.
This is because some non-British systems use ; instead of , to separate values in a csv file. Open Windows Explorer, and change the file extension from csv to txt (i.e. Filename.csv becomes Filename.txt). Open the txt file in Word or another word-processing program. Use the Find/Replace function to replace every ; with a , then save the file again. Change the txt file extension back to csv. It should now open and run perfectly in CAP.
How long will it take to run MDS on a large data set?
MDS computations on a 150 species by 150 sample array will be completed on a 266 Pentium in about 2 minutes. On faster modern machines, it will be just a few seconds, if not instantaneous.
The TWINSPAN dendrogram cluster id is not working
This was fixed in version 1.1.2.
I have removed sparse columns or rows from my data set, now some methods, including TWINSPAN, will not run properly
If you use the 'Remove Sparse Columns' and 'Remove Sparse Rows' functions, it is possible that rows and columns in the data set will now be left with no non-zero observations. When you remove sparse columns or rows, always follow up by using the 'Delete 0 columns' and 'Delete 0 rows' functions.
My files do not appear to be saved
This is often caused by the lack of the correct file extension. The program only shows files with the .csv extension. To see other files in the open file dialog type *.* into the file name box and press return. - WARNING this will show all the files in the directory - whether they are compatible with the program or not. If you have saved a file without an extension either add the extension outside the program or open the file and save with the correct extension using Save As.