Distance 6.2 Release 1
Release Notes - 22 April 2014

Contents

Installation Notes
Upgrading from previous versions of Distance
Uninstalling Distance
Distance-sampling email list
Current restrictions
New features, resolved issues and known problems
Appendix 1: Files Added During Installation

Installation Notes

System Requirements for Distance 6.2

Operating System and Hardware Requirements
Any modern desktop PC will have no problem installing and running Distance 6.2.  It requires about 45MB of space on your hard drive, and either Windows XP, Vista, 7 or 8 operating systems. (Distance will likely also run under older versions of Windows operating systems; however this is no longer actively supported.  If you are using a legacy operating system, be aware that the practical minimum hardware requirements are a Pentium II Processor, 48MB RAM, 800x600 SVGA monitor with 256 colors.  Distance will also likely run under Windows 8 although this has not yet been tested.)

R Statistical Software
Two analysis engines in Distance 6 are implemented as libraries in the free statistical software R.  These are the Mark Recapture Distance Sampling (mrds) and Density Surface Modelling (dsm) libraries.  If you would like to run either of these engines, you must install R software on your computer first.  A copy of the setup package for the version of R tested for use with Distance is on the Support, Updates and Extras page of the Distance home page (http://www.ruwpa.st-and.ac.uk/distance/). You can also download R by browsing to the R web site, http://www.r-project.org/ and following the "download" or "CRAN" link.  You need the base precompiled binary distributions for Windows.  Note, however, that R is under very active development, and new versions are released quite frequently.  Unfortunately, new versions are sometimes not compatible with libraries compiled in old versions.  We will endeavour to test our libraries with each new version as it appears, and update it as required.  For more information about the version we are currently supporting, please browse to the Distance home page (http://www.ruwpa.st-and.ac.uk/distance/), Support, Updates and Extras page.

You can download and install R after you have installed Distance, and you can run Distance without having R installed - but you will get an error message if you try to run the MRDS or CDS engine without R.

For more information about the R-Distance link, see the Distance online help, Chapter 7.  There you will find a topic "R Statistical Software".

Windows Script 5.6
Distance requires that a working copy of Microsoft Windows Script 5.6 or later is installed on your computer.  The installation program contains a copy of the English language version of Windows Script 5.6, and you have the option to install this as part of the program setup.  If you are using a non-English version of Windows, you will probably want to download and install the version of Windows Script appropriate for your language -- you can get this from http://www.microsoft.com/scripting/.  If you have already installed the appropriate version of Windows Script on your computer, then you should say "No" when the Distance setup program asks you if you want to install its version.

If you have Windows Vista or later, you do not need to install Windows Script.

Adobe Acrobat Reader
The Distance User's Guide is also available in Adobe PDF format.  To read this file (which is installed in the Distance/Help directory), you need a copy of Adobe Acrobat reader, available from http://www.adobe.com.

Running Distance under other operating systems

To run Distance under non-Windows operating systems, a Windows emulator is required.  There is a section of the Distance web site, under "Support, Updates and Extras" that contains information about emulators that users have reported to work. 

Running Distance in extended character systems

If you use an extended character operating system (e.g., Chinese, Japanese or Korean language Windows) then you need to make the following change to the program preferences before you start using the program.  Once you have installed Distance:
1. Start Distance
2. From the menu, choose Tools | Preferences...
3. Click on the General tab.  Un-tick the box "Store results in compressed format in project databases"
4. Click OK.

You need to make this change because by default Distance compresses the results from analyses when it stores them in project databases, and at present it cannot decode these results on extended character operating systems.  For more information, see Known Problem 247 at http://distancesampling.org/Distance/old-versions/d60knownproblems.html.

Installing Distance under Windows

To launch the Distance setup program, run the file D6setup.exe.  You are then guided through the installation.  If you have an older operating system, you may be asked to re-boot again early in the installation process and then restart the install.  You may also be asked to reboot after install has finished.  If you are running Windows Vista or later, you need to have administrator privileges to install Distance.

Once Distance is installed, you can run Distance 6 from the Programs | Distance 6 folder off the Start menu on your windows Taskbar.

A list of the files added by Distance installation is given in Appendix 1.

Installing Distance 6 alongside previous versions of Distance

Distance 6 is designed to exist happily alongside Distance 5, 4 and 3.5.  By default it is installed into a different directory (C:\Program Files\Distance 6), and so will not overwrite of the previous project files.  Distance 6 does, however, register itself to open .dst files when you double-click on them.

Distance 6 does cause one minor problem with Distance 4, because of new versions of shared components.  It is:
When editing set names in Distance 4, the new set name is not shown when you click enter.
 
Problems with Install

If you are having a problem, please (1) check your computer meets the minimum requirements (above); (2) check the list of know problems on the distance web site; (3) check the archives of the distance-sampling discussion list (see below); (4) look at the file c:\Program Files\Distance 6\Install.log to see if it gives you any clues as to the problem; (5) contact the program authors: http://distancesampling.org/contact.html.

Sample Projects
Information on the sample projects is given in Chapter 3 of the user guide.

Upgrading from previous versions of Distance

If you have Distance 6.0 (or 6.1) installed, you don't have to un-install it before installing the new version, which will overwrite the old files.  When you open Distance 6.0 or 6.1 project files in the new version, you will be offered the chance to upgrade them.  If you accept, by default the upgraded project is given a new name (although you can choose to overwrite the old project if you prefer).  Alternatively, you can open a Distance 6.0 or 6.1 project in the new version of Distance without upgrading it -- in this case you have access to all the items in it, but you cannot run any analyses or designs.

If you choose to update a project file, we strongly recommend you re-run your analyses if they are CDS or MCDS point transects, or they use the MRDS or DSM analysis engines.  There have been several improvements and bug fixes which you should avail yourself of.

If you have Distance 5.0 or earlier installed, you can install Distance 6 alongside it if you wish.  If you open an old project file in Distance 6 then it will be copied and then upgraded.

Please let us know if you have any problems transitioning to the new version of Distance.

Uninstalling Distance

To uninstall Distance, click on the Add/Remove Programs icon in the Windows Control Panel.  Choose Distance 6 from the list and click the Add/Remove button.   During the removal process, you will be asked whether you want to remove shared components.   Press "Yes to All".   The install program may not be able to remove all of the folders under C:\Program Files\Distance 6\ if you have changed any files in them (e.g., by creating new projects in \Sample projects).   In this case you will have to remove these folders manually after the installation has finished.

Distance makes no changes to the system registry, so there is nothing to delete there.

Distance-sampling email discussion list

The purpose of this list is to promote the sharing of ideas and information among researchers and practitioners interested in distance sampling techniques. It is a relatively low-volume list, and has been running since 1998.
Suitable topics for posting include: questions about survey design and analysis, new methodological developments ,use of software tools (program Distance and other software) ,news about upcoming meetings, workshops and conferences where distance methods will be discussed ,jobs in distance sampling-related fields .
To join this distance-sampling list see instructions at http://distancesampling.org/distancelist.html
Please check the archive of previous messages before posting!

Current restrictions for Distance 6.2 Release 1

Project setup and import
o	If length or distance fields are measured in one field but to be analyzed in another then only the measurement units are imported from the old D3.5 file.  Units of analysis must be set in the new data filter manually.  (This is because data filters are not imported when the project is imported, and analysis units are now in the data filters.) If the units are not one of those that Distance recognizes (from the default project settings database) then the units will not be imported.
MCDS Analysis Engine
o	Maximum number of covariates and factor levels is listed in the manual, under “Limitations”
o	When covariates are specified, only half-normal and hazard-rate key functions allowed
o	Cannot force the fitted function to be monotonic decreasing
o	When cluster size is a covariate, stratified analyses are not allowed
o	Cannot have non-factor covariate value -9999.
MRDS Analysis Engine
o	Line transect surveys only (not point transects - although these are available in the underlying R package)
o	Ignores units conversion specified in the Units tab of the Data Filter

Resolved Issues and Known Problems

Here's a brief list of new features and resolved issues in Distance 6.2, relative to 6.1:

CDS/MCDS Engine
An important bug that meant variance estimates for point transects were incorrect has been fixed - please re-run all point transect analyses from Distance 6.0 and 6.1
Other minor improvements in output labeling

MRDS Engine
R package mrds updated to 2.1.5 (compiled with R 3.1.0)
Multiple other changes and bug fixes -- see NEWS file of R package mrds
Monotonicity checks now performed in ds models
Left truncation for exact and interval data now possible in interface

DSM Engine
R package dsm updated to 2.2.3 (compiled with R 3.1.0)
Some added features: autocorrelation plots, gam.check fitting diagnostics
Regarding diagnostic output, shows diagnostic plots from rqgam.check (which uses randomized quantile residuals (Dunn and Smyth 1996)) rather than gam.check.  Also displays the text output from gam.check, which it did not before.
For other changes to the R package, see NEWS file of R package dsm
Some minor changes to properties pages:
- Some options dropped - ability to control the weights; ability to specify a table of detectablity values; ability to set an overdispersion value
- Multiple changes to the density surface tab of dsm engine
- No need to specify a tilda when writing out the DS model in Density Surface | DS Model | Formula.
- Changed the header in the results details of the component smooth plots from "Diagnostic-plot" to "Component smooth".  Better describes what they are.  (Plot files are also renamed from diag... to smooth...)

An up-to-date list of resolved issues, known problems and work-arounds is kept on GitHub: https://github.com/DistanceDevelopment/distance-bugs/issues

Appendix 1: Files added during Distance 6 Installation

Note - if older versions of these files are already present, they will be overwritten.   If newer versions are already present, they will not be changed.  (An exception to this is RichEd32.dll, which caused some incompatibility problems in test installations.  This file will only be installed if one is not present on the target system.)  If you selected the backup option during Setup, backups of all overwritten files will be stored in the BACKUP subdirectory, off the Distance 5 program directory.  A log of all files installed is kept in the program directory in the file install.log.

Common Files \ Data Dynamics folder
Actbar2.ocx

Common files \ ESRI
Mo20.ocx
AF20.dll
Shape20.dll
pe81.dll
sg81.dll
mtch.dll
JetTable20.dll

Microsoft \ Shared Tools \ DAO
Dao2535.tlb
Dao250.dll
Jettable20.dll
Msjet35.dll
Msjint35.dll
Msjter35.dll
Msrd2x35.dll
dbajet32.dll

Windows System 32 folder
Asycfilt.dll
Comcat.dll
Comctl32.ocx
Comdlg32.ocx
Expsrv.dll
Mfc42.dll
Msvbvm60.dll
Msvcirt.dll
Msvcp60.dll
Msvcrt.dll
Msvcrt40.dll
mtch.dll
Oleaut32.dll
Oledlg.dll
OlePro32.dll
Riched32.dll
Scrrun.dll
Stdole2.tlb
vb5db.dll
vbar332.dll
vbscript.dll
VsFlex7d.ocx
ccrpdbs6.dll
tab32x30.ocx
mschrt20.ocx
richtx32.ocx
dwAXExtn.dll
Dwsdes32.dll
D6Zip.dll
PolarZip.ocx
PolarZipSpan.dll
RichEd32.dll
Splitter.ocx

Program Files (x86) \ Distance 6
Ec.exe
DistanceProject.ico
Distance.exe
D6DbEng.dll
CDlg.dll
CTmr.dll
CSDesc.ocx
LLine.ocx
LogStr.dll
LogWin.ocx
SList.ocx
PrjParams.dll
D6Map.ocx
D6Legend.ocx
DistIni.mdb
ID6NEng.dll
D6NEH.exe
D6NSvr.dll
D6NEIUtil.dll
D6CDSNEI.dll
D6MRDSNEI.dll
D6DSMNEI.dll
MCDS.exe
D6DesNEI.dll
D6DesEng.dll
D6SvyNEI.dll
D6DFPrp.ocx
D6MDPrp.ocx
D6CDSPrp.ocx
D6MRDSPrp.ocx
D6DSMPrp.ocx
D6DesPrp.ocx
D6SvyPrp.ocx
D6DesDet.ocx
D6SPWiz.dll
DeIDWiz.dll
DistanceLogo.jpg
ReadMe.rtf
support.r
dsm.support.r
mrds.support.r

Program Files (x86) / Distance / Help
distance.chm
distance.pdf
Sponsors.rtf
Authors.rtf
DataEntryIntroduction.rtf
DataEntryGlobal.rtf
DataEntryStratum.rtf
DataEntryObservation.rtf
DataEntryFinished.rtf
TipOfTheDay.txt

Program Files (x86) / Distance / Sample Projects
[a number of sample project files]

Program Files (x86) / Distance / RPackages
Copies of all the packages required by the Distance engines that use R.