A problem was discovered with some of the p-values reported in the Standardized Mortality Ratio (SMR) analysis. In ‘Report Options’, if the ‘Report p-values instead of CI’ option under ‘Confidence Interval or p-value’ is selected, reported p-values are incorrect when both of the following conditions apply: (1) the observed number of deaths (D) is greater than 20 (i.e., when approximate p-values are calculated) and (2) the SMR<1 (i.e., when D is less than the expected number of deaths (E)). A notification of this problem was sent to registered users. We will post on this site when a corrected version is available for download. Please note that the reported confidence intervals and the significance flagging of SMRs are not affected by this issue and that the p-value formulas provided in the LTAS.NET User Documentation are correct.
A new version of LTAS.NET (ver. 3.1) was released. This version includes the following changes and enhancements:
- The NIOSH-119 and NIOSH-92 underlying cause of death (UCOD) and NIOSH-119 multiple cause of death (MCOD) rate files have been updated with actual data through 2009. There are some critical changes in the latest MCOD rate files. Please refer to the Rate File Information page for details of the changes.
- If you only want the new rate files without changing the LTAS.NET program, you can find the updates (in xml format) on our ftp site: http://ftp.cdc.gov/pub/LTAS-NET/. The instruction to import the new rate files can be found on page 99 of the LTAS manual.
For incidence analysis, the LTAS.NET may report incorrect person-years or outcome counts, if the input files include invalid outcomes or dates. We are currently working on a solution. In the meantime, the users are advised to carefully prepare their input files. For example, there should be no entry for subjects diagnosed with cancer before risk-begin date for first primary cancer analysis.
A new version of LTAS.NET (ver. 3.0.6) was released. This version includes the following changes and enhancements:
- Corrected intermittent problem that caused last imported person record to be missing from the study database.
- Corrected a problem with global risk begin date not being taken into consideration when rejecting persons whose risk end preceded the global risk begin.
A new version of LTAS.NET (ver. 3.0.5) was released. This version includes the following changes and enhancements:
- Updated NIOSH 119 multiple-cause of death (MCOD) rate files with data through 2007.
- Updated the SQL Server 2005 package included in the full install to Service Pack 4 to resolve installation issues on Windows XP.
- Corrected problem that caused LTAS to crash from selecting a global code revision when a non-ICD rate file is being used.
- Corrected problem that caused importing a rate file to fail due to blank lines appearing within the RateData element.
- Corrected a problem with Export Rates function that caused the column headings to be listed in the wrong order.
- Corrected a problem that prevented LTAS from locating standard rate files when installed under an account other than the user’s account.
- Updated user manual with higher quality images for statistical formulas and mathematical equations.
- A new version of the 92-cause map was included, with remapping of ICDA-8 Eighth Revision of the International Classification of Diseases Adapted for Use in the United States) cause 519.3 to minor 62 (chronic obstructive pulmonary disease).
- Corrected additional problem with exposure calculations in the Post-Stratify Personal Cumulative Dose (PCD) report that resulted in additional exposure to be reported for exposure that should have been completely lagged out.
- Corrected a problem with exposure calculations in the Post-Stratify PCD report that resulted in negative time since first/last employment/exposure TSFE/TSLE) values when exposure was lagged using days as units.
- Corrected a problem with exposure calculations in the Post-Stratify PCD report that can result in lower and sometimes negative values to be reported.
An error was discovered in using LTAS.NET to analyze data for a cancer incidence study. The Post-Stratify Personal Cumulative Dose (PCD) report may not be correct for the unlagged cumulative exposure for cases who continued to work after their diagnosis date. The unlagged cumulative exposure in the pre-stratify PCD report and all of the lagged exposures in the post-stratify PCD report are correct, even for cases who continued to work after diagnosis. This error, however, does not affect the stratified person-time on which the SMR and SRR statistics are based.
Because of a change in the data use agreement with the National Center for Health Statistics (NCHS), we can no longer provide the state mortality rate files.
A potential issue (“sparse data bias”) has been found in SRR analyses that are available in LTAS.NET – this relates primarily to time since first/last employment/exposure (TSFE/TSLE). The issue isn’t the LTAS algorithm, as different similar approaches (e.g., M-H) led to the same problem. Please be cautious in case you are looking at TSFE or TSLE using LTAS, and consider alternate methods of analyzing TSFE/TSLE in addition to LTAS SRRs.
The problems in our MCOD rate files have been fixed. A notification was sent to registered users of the updated rate files available for download at an ftp site. The current location is http://ftp.cdc.gov/pub/LTAS-NET/.
Problems were discovered in our MCOD rate files included in previous versions of LTAS.NET. A notification was sent to registered users to avoid using MCOD rate files before we corrected the error. The underlying cause of death (UCOD) rate files were not affected by the issue. To see more detailed descriptions of the problems, click MCOD Problems.
A major new version of LTAS.NET (ver. 3.0.1) was released. This version includes numerous changes summarized below. A full description of the changes is available in “ Major Changes in LTAS 3.0” on the Documentation page.
Before installing LTAS.NET 3.0, please keep in mind the following information:
- The major change in LTAS.NET 3.0 was to make it compatible with Windows Vista and Windows 7. It also supports Windows XP. If you are using an earlier Windows operating system (e.g., 2000, NT, 98), you must continue to use LTAS. NET version 2.0.16.
- We also changed the way the rate files are loaded in (we combined the cause map with the rate file). If you have special rate files that you’ve created in the previous version, you will need to create a new version that is compatible with LTAS.NET 3.0, using the instructions in the LTAS manual that is installed with the program.
- The first time you install LTAS.NET 3.0, you must install the full version, not the upgrade version, even if you previously had a version of LTAS.NET on your computer. This is because we have improved the SQL Server database engine. Note that in future minor releases, you will be able to install an “upgrade” version.
- When you install the full version, if you are working on a limited-access account, please contact your LAN administrator (for CDC account users, contact ITSO) to perform the install. Be sure to ask them to perform the install under your account (with administrative privileges temporarily granted) and verify that your account has ownership of the LTAS program folder upon completion.
- LTAS.NET 3.0 supports Windows XP, Vista, and 7 operating systems. If you install LTAS.NET 3.0 on an XP system that already has a previous version of LTAS.NET, you will notice that LTAS.NET 3.0 is installed side-by-side with your previous version of LTAS. You may use either version on a PC running XP; however, we recommend transitioning to LTAS.NET version 3.0 as soon as possible. Please note that rate files for the previous versions of LTAS will no longer be updated.
- In LTAS.NET 3.0, you can also open projects from the previous version of LTAS and save them in the new version.
LTAS.NET 3.0 Enhancements: (For a complete list of changes and enhancements, please see “ Version History”.)
- Support for Windows Vista and Windows 7
- New rate file structure
- The cause map and the rate file have been merged into a single file.
- Updated US underlying and multiple-cause rates and proportions through 2007.
- Changes affecting software functionality
- Support for reporting p-values in SRR and SMR reports.
- Changed the ordering of fields in the Import Wizard drop-down menu.
- Changed the ordering of fields in the Import Options report so that they are ordered by column position (instead of alphabetically).
- Changes affecting software usability
- Updated Report Viewer to use SQL Server Reports, resulting in better export capabilities.
- Updated Database Engine to use SQL Server 2005, doubling the storage capacity from 2GB to 4GB.
- User documentation is now section 508 compliant.
- Changes to improve reports and data export capabilities
- Inclusion of Supermajor (“All Causes” and “All Cancers”) and Major cause-of-death categories in cohort export file.
- Added a new capability in Stratify, allowing user to report or export the Post-Stratify Personal Cumulative Dose for each subject, which will give lagged cumulative exposures.
- Changed analysis reports so that exposure lag information is included with the page variables.
There were also numerous bug fixes since version 2.0.16:
- Changed the way exposure lag time is calculated so that zero lagged cumulative exposure beyond the lag time period is appropriately mapped to the lowest exposure category.
- Corrected a problem with person-time prior to achieving minimum exposure not being discarded.
- Updated Stratify Reject report, export and progress dialog to account for person-time that is discarded.
- Increased timeout values on all database queries to prevent timeouts on large studies.
- Corrected a problem that caused stratify to fail if too many stratifier variables were selected. While a limit still exists, it is larger (see documentation for details).
- Resolved Stratify issue that caused the wizard to fail when selecting a global categorical and no exposure agent.
- Added validation to the Import Wizard to prevent duplicate names from being used for exposure agents, temporal categoricals, fixed stratifiers or global categoricals.
- Resolved issue with exporting observed deaths and diagnosis for MCOD studies that caused the export file to be empty.
- Enhanced the import data validation to reject history records with invalid exposure agent values.
Special neurodegenerative disease mortality rate files have been updated for LTAS.NET 3.0 and are now available on the download page. These files represent US UCOD rate data between 1960 and 2007. Previous updates through 2002 for LTAS.NET 2.0 are no longer supported and have since been removed. There are four neurodegenerative mappings [Dementia & Alzheimer's excluding Arteriosclerosis dementia, Arteriosclerosis dementia, Amyotrophic Lateral Sclerosis (ALS), and Parkinson's Disease] and one "other cause" mapping. The four neurodegenerative mappings are grouped under a super major similar to the Cancer mappings in the 92 and 119 rate files.
A new version of LTAS.NET (ver. 2.0.16) was released. This version includes the following changes:
- A table that shows the relationship between rate file and outcome file options has been added to the 'Outcome Import File' section of the documentation.
- Corrected upgrade installation to properly restore custom rate files and cause maps. Custom rate files that were imported before an upgrade to a new version of LTAS.NET did not work properly under the following conditions:
- The custom rate file referenced a custom cause map
- Two or more custom cause maps were imported prior to the upgrade.
- The custom cause maps were imported in an order other than alphabetical order.
After upgrading, users should re-import any custom rate files they are using. Even though the problem is now fixed and won't occur as a result of upgrading to this release, re-importing will eliminate the effects of previous upgrades.
- Corrected Personal Cumulative Dose report to show correct person time in diagnosis-based studies for persons having multiple history records. For diagnosis-based studies, the Personal Cumulative Dose report was incorrectly including time after the date of diagnosis. This problem was specific to the Person Cumulative Dose report and did not affect any other reports including analysis reports.
- Updated NIOSH-119 rates and cause map
The NIOSH-119 UCOD and Proportion rate files have been updated with rate data for years 2003-2005. The LTAS.NET state rates have also been updated with the additional years of data. Additionally, the NIOSH-119 cause map file has changed slightly to correct the mapping for COPD in ICD Revision 8 along with a couple other minor re-mappings affecting Minors 64, 73 and 119.
- Added support for diagnosis-based (i.e., incidence) studies
- Changed import validation logic to properly handle diagnosis-based studies.
See the Outcome File Requirements section in the LTAS.NET User's Guide for details.
- For studies using diagnosis based rates, modify Stratify to include diagnosis for non-deceased persons.
- Added ability to export observed diagnosis for studies that use diagnosis-based rates.
- Corrected end of risk accumulation logic for diagnosis-based studies
Time at risk should not accumulate past the date of diagnosis for diagnosis-based studies. In addition to correcting the logic, the import wizard was changed to clarify the end of risk options for diagnosis-based studies.
- Fixed problem causing incorrect results in SRR reports when all causes are selected
Selecting all causes for an SRR report caused incorrect results. In many cases, the same results were mistakenly reported for each cause.
- Added support for revisions in non-ICD cause maps
Studies that are based on non-ICD codes can specify either a global revision or specify the revision in the outcome file.
- Corrected inconsistent calculation error when running Major/Minor Summary report.
This removed an error message received when running a Major/Minor Summary report or any variant of an SMR List report that included Cause as the row variable.
In addition, the LTAS.NET FAQ and USER Manual documents have been updated.
Finally, the MCOD rates are now available for download. A separate mapping file is needed because these rates are still using the 1960-2002 data. They will be updated in the future to include the 2003-2005 data.
A new version of LTAS.NET (ver. 2.0.8) was released. This version corrects the following problems that had been identified in interim versions:
- Fixed problem in person-year and event allocation for exposures occurring before follow-up time begins when a lag is also used.
- Fixed problem with SMR analysis reporting incorrect expected and observed values in some situations.
- Fixed rounding problem when stratifying Duration categories using Years for units.
- Fixed errant warnings in Import Exception reports when a global risk begin date is used.
- Modified 119 Mapping files to fix minor errors.
In addition, the LTAS.NET FAQ document has been updated and the PC-LTAS state rates have been updated to the comparable LTAS.NET versions. Note that if you wish to use PC-LTAS state rates, you will have to pre-map the causes of death in your demographic file to the minor number (this is not necessary in LTAS.NET).
Special neurodegenerative disease mortality rate files have been prepared for LTAS.NET and are now available on the download page. These files represent US UCOD rate data between 1960 and 2002. There are four neurodegenerative mappings [Dementia & Alzheimer's excluding Arteriosclerosis dementia, Arteriosclerosis dementia, Amyotrophic Lateral Sclerosis (ALS), and Parkinson's Disease] and one "other cause" mapping. The four neurodegenerative mappings are grouped under a super major similar to the Cancer mappings in the 92 and 119 rate files. When you import these rates into LTAS.NET remember to import the Cause Map Definition file first and then the Rate Data file; otherwise the Rate Data import will fail.
A new version of LTAS.NET (ver. 2.0.1) was released. This version corrects two bugs: One bug occurred in Stratify for studies that have person-time and deaths extending beyond the last date for which rates are available (12/31/2004). If users included data beyond this date, the bug caused Stratify to crash the first time it encountered such a date. This bug was fixed by applying the rates from the previous five-year category to any person-time and events that occur after the end date of the rate files, based on the user-specified end of study date (up to five years beyond the last rate end date). The second bug affected only studies that imported time-since-last-exposure (TSLE) but not time-since-first-exposure for the exposure variable, and it caused TSLE to be inappropriately classified.
The new Windows-based version of LTAS, called LTAS.NET, is available for download. The software is more interactive and provides greater flexibility for data input, export, and analysis. The U.S. underlying cause ratio and proportions are provided with LTAS.NET.
Objectives in creating LTAS.NET
- Create a stable, user-friendly and reliable NIOSH life table analysis system for the Windows environment, as the DOS environment has become unreliable
- Add features requested by users to increase utility of the program
- Correct minor discrepancies noted in date handling and some statistical calculations within PC-LTAS
Major new features of LTAS.NET
- User can stratify on and analyze
- Two or more time-varying exposures simultaneously
- User-defined fixed and time-dependent covariates
- A global date for all persons in the cohort
- Active employment status (with a user-defined lag for inactive status) to evaluate the healthy worker survivor effect
- LTAS.NET has more flexible import, analysis and reporting options
- User can export stratified event and person-time data for Poisson regression analysis
The PC-LTAS version is no longer available.