Version 4.10 - 5/18/2007
note: due to the naming of the previous version, the update manager doesn't recognize this as a newer version. Please download the version by hand from the web site.
- New exceptions were added to the sites configuration that attempt to deal with some of the "transportation bypass" event that were discovered during analysis of run-of-river data from above Lower Granite during brood years 1996-2004.
- A problem with transportation sites settings was fixed.
- An issue with recaptures that span river kilometers was causing erroneous "fish removed before first capture history site" errors. This has been fixed. In addition, downloading from PTAGIS the river kilometer data as part or the reacpture and mortality file will solve any issues related to sites that have a range of river kilometers associated with them. The downloaded data should be accurate.
- The last field settings was being re-set whenever the Sites tab was viewed. This has been fixed.
- A print capability was added to the results manager.
- River kilometer comparisons of locations in different river systems would cause invalid ordering. For instance, a fish observed at PRA (Priest Rapids) would be counted as upriver of Lower Granite. This seems to be an issue mainly with straying adults.
- Full Flow Bypass observations of Adult fish were being ignored.
- Recaptures at the release site as adults were being ignored when the program was configured to ignore recaptures at the release site. This should only apply to recapture in the release year.
- Bypass was still trumping transported in some cases. This has been fixed.
- Sites with single hits were affecting the check for transported fish detected downstream. Now single hit sites are removed before this check. This affects only runs where "allow single hits" is not selected.
- A bypass detection was trumping a tansported detection when "removal trumps all" was selected. Now only sampled, held, or returned will trump a transported detection.
- Fixed bug that occured when using last detections and both Bonneville juvenile and Bonneville adult sites were defined capture history sites. The juvenile detections would be ignored.
PitPro has undergone rigorous testing to insure accuracy. Several issues were identified and fixed in the latest version, most of which effected the adult life cycle and the use of recapture data. A new check for fish observed "before" release date was added. Several interface enhancements were made including the ability to use interrogation from the PTAGIS interrogation summary data source (with only last detections and coil names instead of coils), and a new search capability for the site configuration, etc. The list that follows details the changes:
- Enhancements:
- It is now possible to use the PTAGIS interrogation summary data source for PitPro interrogation data (see PTAGIS/PitPro data formats). This data source provides only last detections which has some limitations. The reduced data file size and running time are the advantages.
- A new transportation configuration tab has been added. This only applies to ROSTER format output where transported fish are distinguished from censored fish (unlike in SURPH). This tab allows for the removal of a transportation site, causing all transported fish to be effectively censored at the site. It is also now possible to treat all fish sampled at a transport site as transported fish.
- A search feature has been added to the sites configuration window.
- The filtering of data based on data suffix for the run configuration menus is now optional. This allows the use of data with any suffix (e.g., .txt, .csv, etc.).
- PitPro now can use river kilometer data provided in the recapture and mortality data. This is the most accurate location data available. Previously PitPro used the recapture site to look up the defined river kilometer for the recapture site. Because some of these recapture sites represent a stretch of river and not a single location, this could be inaccurate. If the river kilometer is not provided in the data, PitPro will use the defined river km for the site. If this is a range, PitPro will use the upstream value for juvenile observations, and the downstream one for the adults. The river kilometer should be the fourth field in the recapture and mortality data (see PTAGIS/PitPro data formats).
- Changes:
- When a fish is observed on a return to river detector after a transport detector it is now flagged as return to river. Previously the transport detector would take precedence.
- The error of fish recaptured above the first capture history site has been combined with the check for fish censored above the first capture history site.
- A new error for fish observed "before" release date was added.
- Transported fish that are detected downstream as juveniles, except at TWX and the bird islands, are now censored at the transport site. Previously they were removed as errors.
- Fixes:
- A fish recaptured as an adult above the first capture history site was erroneously removed for being recaptured above the first (juvenile) capture history site.
- A recapture at a transport site that occurred after a fish was flagged for transportation would cause a transported and detected downstream error. Now it will cause the fish to be censored.
- Single hits were affecting some error checking routines (such as out-of-sequence) even when "allow single hits" was not selected. Now single hits are removed before an further error checking.
- Morality data was not be used in checking for censoring before the first capture history site.
- Recaptures/Mortalities at capture history sites were not being used for travel time calculations.
- Adult Bonneville observations were being recorded as juvenile Bonneville observations when Bonneville was not select as an adult site, but was selected as a juvenile site.
- Checking the box next to the Allow single coil detections had no effect. The program would ignore a single detection at a site regardless of the setting. This has been fixed. Check this box to allow a detection on a single coil at a site to be counted as valid. This is also the default setting now.
- A bug in the check for recaptures before the first release site led to removal of fish that were recaptured as adults above the first capture history site.
- A problem with the sites configuration file caused fish that were recapture for the first time at release sites BON, JDA, IHR, LMN, LGS, and LGR to have incorrect capture histories. This effected versions 4.1 through 4.7.
- Maintenance release: fixed bug that caused a program crash when encountering certain recapture sites.
- The mouse pointer icon would change to an hourglass and stay that way, even after a run was completed or canceled.
- The addition of code in Version 4.3 that checked interrogation data for proper sorting resulted in much slower computational speeds. This was replaced with a more efficient method. Note: interrogation data must have PIT-tags sorted in ascending alphabetical order
- This version improves progress reporting, and may improve performance in some cases.
- PitPro depends on interrogation data that is sorted by PIT-tag. This had been a point of confusion. PitPro now checks the interrogation data file for correct sorting, and displays an error message when it finds error.
- PitPro would crash when encountering a release site that was not internally defined while loading recapture or mortality data. Now a warning message is displayed anytime an unknown release site is encountered. Note: PTAGIS selects mortality and recapture sites from the list of release sites.
- When using the tag screening feature, any tag that followed a screened tag in the tag file was ignored. This could have led to decreased sample sizes, which may have increased errors, but should not have biased survival estimates. This was only an issue when tag screening settings were set to anything besides "All". This error effects versions 4.0 and 4.1.
- The PIT-Tag Tracker feature now tracks all data files when used on a grouped run
- The update manager will now download the latest PitPro version. The user must still proceed with the rest of the installation manually.
- PitPro 4.0.3 introduced a bug that caused PitPro to duplicate in the output the PIT-Tag that appeared last in the observation file. This has been fixed.
- PitPro 4.0.2 introduced a bug that caused PitPro to crash when the tag data file was empty. This has been fixed.
- Addition of length covariate in capture history file output was still buggy. It's fixed now!
- A single non-detected fish was being omitted from the capture history output file.
Version 4.0.1 - 7/25/2006
- Fixed issue with length covariates. The length was not being included in the SURPH file correctly.
- The program now insures that the capture history output file is compatible with the selected output format. Note: SURPH is not compatible with adult life cycle capture histories.
Version 4.0 - 5/31/2006
- Changed data input format to be more in line with the new PTAGIS data site offerings.
- Added the ability to include recapture data to augment interrogation data.
- Simplified and streamlined program configuration.
- Added new pages to the Results Manager: data summary, and Cormack-Jolly-Seber survival. The later was actually available in version 3.3a, but was undocumented.
- Added the update manager, allowing for easy notification program installations.
- Program now uses actual Julian dates in detection date output, instead of the hybrid used in prior versions.
- Fixed issue that caused a crash when running on a computer with a dual core processor.
- Updated documentation: PitPro 4 Manual.
Version 3.3a - 2/21/2006
- Fixed a bug that caused a crash when the release file had one or more blank lines. This may have effected other data files as well, also causing a crash.
Version 3.3 - 1/23/2006
- Harmonic travel times have been added to the results manager travel time output.
- An error has been fixed in travel time calculations that were being reported in the results manager travel time output. Travel times were being calculated based on values which had their fractional portions truncated. The travel times reported in the travel time output file were correct and were not effected by this change.
Version 3.2 - 1/5/2006
- Previously only observed fish were checked for correct species and rearing type; an undetected fish of incorrect species or rearing type would still be included in the SURPH or ROSTER data file. This has been changed so that any fish, detected or not, is screened for correct species and rearing type.
- A new feature has been added: sites sorting. A sort button has been added to the juvenile and adult sites lists. This will sort the selected sites based on total distance from the ocean (based on river km).
Version 3.1 - 11/3/2005
- Fixed problem that affected some adult detections and travel times. When a fish was detected as a juvenile and then subsequently as an adult at the same site with no intervening detections the adult detections would be ignore. In addition, the last juvenile detection time would be incorrectly set to the last adult detection time.
- Added finer grained control of jacks. This only effects adult capture histories. Previously jacks were a separate age class (J). No jacks are handled on of three ways: as a separate age class but now they are the first age class (A), combined with ocean age 1 fish into the first age class (A in this case also), or removed.
- A checkbox in the Adult configuration tab has been added to put the program in a mode that assumes that all detections are juvenile detections. This simplifies the program in circumstances where the data is known not to have adult detections. In capthist, this is the default mode. Using the -A flag for adult mode will switch on the adult style capture histories as well as the complexities of determining life stage.
Version 3.0.4 - 10/19/2005
- The group runs feature was not working in PitPro and has been fixed. When group runs was selected, only the first defined run would execute.
Version 3.0.3 - 8/8/2005
- The number tagged as specified in the surph file did not have the fish removed due to errors subtracted out.
- Capthist: when no prefix is specified the prefix was being set to "composite" instead of the actual prefix
- Capthist: when using the -l flag to add length covariates, the zero length fish were not being removed.
Version 3.0.2 - 8/3/2005
- Tag ids found in observation file but not in tag file were not being removed by default.
- Transported fish detected downstream as juveniles were being removed completely in both juvenile and adult mode. These are now censored in juvenile mode (default) but removed in adult mode (-A).
- Capthist: the -J flag with a date in yyyymmdd format will cause any observations after the given date to be marked as adult observations. This was already available in PitPro.
Version 3.0.1 - 8/2/2005
- Caphist: -T and -p flag were not working
- When grouping runs, surph file was truncated
- Revision added to version string
Version 3.0 - 7/27/2005
- Adapted adult life stage processing to account for fallback
- New input parameters and logic for adult/juvenile life stage differentiation
- New diagnostics output file with observation sequences and transformations
- Ability to read CSV data files directly as downloaded from PTAGIS
- Ability to view sites configuration and program logic and to manipulate the configuration as needed.
- Full names used instead of abbreviations in menus
Version 2.2 - 2/16/2004
- Added flag to set release date for the entire data set (ignoring anything found in the release file). This is done using -dyyyymmdd
- Added flag to control date output format in dd files. By default, the date is given as day of year plus day fraction. By giving the -j flag the date will be given as julian date instead.
Version 2.1 - 1/12/2004
- In the travel time section of the Result Manager output the reported means have been changed from arithmetic means (and standard errors ) to harmonic means (and standard errors). In later versions this will be provided as an option.
- The order of precedence given to detectors in the route evaluations was changed. Previously any detection on a return to river detector was given precedence over any transport detector so that a fish detected on both was flagged as return to river. This has been reversed. Now if a fish is detected on both a return to river detector and a transport detector, the fish is flagged as transported.
- Established consistent policy regarding population names in surph data file output. Population names are included in both traditional and surph 2 format files but names are truncated to 15 characters. This is to protect against possible crash when loading files into surph.
Version 2.0d - 12/8/2004:
- GRX detector came online for the 1995 season, not in 1996 as indicated in the PTAGIS configuration history documentation. This has be fixed in PitPro/capthist
- Prosser dam site configuration has been changed to allow non-sample fish detected on the separator only to be categorized as return to river fish.
Version 2.0c - 10/18/2004:
- When combining several groups into one run the output for the travel time, detection date, coil, and error files were each combined into one file. The program has been changed so that a separate file is generated for each group.
Version 2.0b - 8/16/2004:
- Population names for multiple group runs were not being printed out in the surph data file. The population names are now being printed but limited to 15 characters to be compatible with SURPH population name length limitations.
Version 2.0a - 6/14/2004: (note: original distribution was missing a few necessary dlls, the current distribution fixes that - 7/8/2004)
- Fixed bug in Version 2.0 that caused most fish not bypassed via the full flow bypass at McNary dam to be flagged as transported. This affects observations from 2003 and 2004.
- Added configuration display capability. You can view the site configuration in PitPro by selecting Data->Show site configuration or by giving the -C flag to capthist.
Version 2.0 - 5/6/2004:
- Updated site configuration for 2004
- Fixed problem with site releases. These are fish releases at the release site.
- Smoothed out GUI updating issues.
- Laid ground work for automatically updating site configurations. The site configuration, based on the PTAGIS Site Configuration History, is now available for viewing from the File menu. In the future the program will be able to check for updates automatically.
Version 1.1c - 1/14/2004:
- Changed the way the program handles Lower Granite in relation to the GRX detector. GRX was installed, according to Dave Marvin, on April 1, 1995. Prior to this date diversion coils are classified as return to river in the program. After this date, with the installation of an actual return to river coil on the GRX system, diversion coils are classified as diversion which, without a subsequent return to river detection, result in an unknown (2) flag. Previously the installation date for GRX was set at Feb. 27, 1996 as specified in the PTAGIS Historic Interrogation Site Configuration report. From 1994 until Feb. 27, 1996 the program would never give a return to river designation at Granite! In addition, after Feb. 27, 1996 the diversion detectors would wrongly result in a return to river designation.
Version 1.1b - 6/3/2003:
- Changed type in Bonneville adult site monitor names. BO1, BO2, and BO3 where spelled with zeros instead of ohs.
- Added a check for input and output directory existence.
- Added convenience features to configuration load and save process.
Version 1.1a - 6/3/2003:
- Updated site configuration to most recent PTAGIS site configuration history report (06-Mar-2003).
- Added error handling code to CaptHist.
Version 1.1 - 5/21/2003:
- CSV Converter feature added
- Fish flagged as censored would have a non-zero last field when running in adult mode. This should only be true of transported fish. This has been fixed.
Version 1.0f - 5/6/2003:
- Fish flagged as censored subsequently have non-zero capture histories. This should only be true for transported fish. This has been fixed.
Version 1.0e - 4/15/2003:
- When grouping runs, only the release file from the first run definition was used. This has been fixed
- The way the year of an adult return is calculated has been upgraded. Now the return year flag is based on the difference between the release year and the detection year.
Version 1.0d - 4/10/2003:
- Fixed bug when running in multiple, non-combined mode. Previously, the output from each run would overwrite the output from the first run
- Fixed glitch in the way .ppc files are displayed when loading a saved configuration
Version 1.0c - 3/5/2003:
- Fixed bug in the update behavior of the mortality and release date file interface.
- Fixed the surph file comment that gives fields names. The last field
was being displayed incorrectly. - Lower Granite - 2001 from late 5/15 to early 5/18 the raceway fish
were being diverted back to river. - Documentation has been added under the "doc" directory (folder) in both html and Word format. To view the html documentation open the document titled "index.html".
Version 1.0b - 2/19/2003:
- E1, E2, and E3 GOJ coils are actually sample detectors. This has been fixed.
- Added comments to surph output files that gives the name of the fields
Version 1.0a - 2/14/2003:
- Fixed problem with juvenile/adult mode flags appearing in normal mode
- Fixed problem where flags would appear in capture history after fish had been censored.
- Added E1, E2, and E3 GOJ coils as river exit detector
Version 1.0 - 2/11/2003:
First release of PitPro.
CaptHist is now the batch version for PitPro, the GUI version of Capthist.
In
other words, they share code and it is kept in the pitpro directory. The
changes visible to the user from the previous version of CaptHist to the
current one are:
- Batch version only: The chrc file format is more forgiving, allowing tabs, and spaces, between arguments.
- More sites have been added. All PIT tag sites, in fact.
- There is an option to allow for either Surph1 or Surph2 output
format. In the batch version, the relevant flag is -T for traditional, meaning the old format. Surph2 format is now the default. - The new juvenile/adult format is available, using the -A flag.
- Internally, the site configuration in site.c has been re-organized for ease of updating
For earlier capthist versions, go here.