NAME -------------------------- NeOGen AUTHORS -------------------------- Dean C. Blower, Cynthia Riginos, & Jennifer Ovenden. CHANGE LOG -------------------------- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Version 1.3.0.6.a1 (June 2019) Released 2019-06-06 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Summary: Version number not changed. Version date changed to (Jun 2019). First update since post-published version (Aug 2018). Changes: -Enhanced INSTALLER (setup.exe) program to check for existing NeOGen installation. -Fixed GUI (NOGP.exe) Sampling Strategy (SS) sampling plan creation. Index error with empty list of "other sampling plans". -Fixed GUI (NOGP.exe) Sampling Strategy widgets not initialising properly. -Fixed GUI (NOGP.exe) Batch scenario changing Max age on existing scenario. -Fixed GUI (NOGP.exe) Switching to a project with a Batch Scenario with allele frequency file failed silently if the allele frequency file did not exist. -Fixed GUI (NOGP.EXE) Sampling Strategy Sampling Plan screen would not allow 4 decimal points to be entered. -Fixed BACKEND (NeOGen.exe) Demographic plot getting decimal conversion error for AgeNe_Ne and AgeNe_Nb values ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Version 1.3.0.6.a1 (Aug 2018) Released 2018-08-20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Summary: Published version. Changes: -Fixed Sampling Strategy (SS) sampling plan. Corrected sampling based on user proportions specified for small numbers of cohorts. -Fixed status: "User changed parameters." from propagating to all SS files in error. -Parameterise the running of alternative "accuracy line" sampling plans and additional reference sampling plans. -Fixed mean and std deviation decimal spinboxes rounding to 1 decimal place. Allow 3 decimals places (settings.ini change). -Change default Ne2.exe zombie count to 100 (settings.ini change). -Fixed SS error when more than one Batch Scenario (BS) run exists (i.e. due to a BS run has failure). Now the SS always uses the most recent BS run folder. -When loci are imported from a file ensure the locus number parameter in the BS and the SS match the imported locus number. -Parameterise the running of alternative "accuracy line" sampling plans and additional reference sampling plans. -Allow import of empirical loci from GENEPOP file. The allele frequencies determined from this data (excluding missing data) are used for the loci the allele frequencies create simupop POP. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Version 1.3.0.6.a1 (April 2017) Released 2018-03-16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Summary: Alpha version for peer review. Changes: -Changed version specific backend data folder (i.e. v3_0_5) to generic folder (i.e. usr) -Changed from arithmetic mean LDNe calculation to harmonic mean LDNe calculation following R. Waples advice. -Sampling Strategy plot outputted as vector graphics (.svg) in addition to raster graphics (.png) -Fix incorrect calculation of alleles per locus BINOMIAL distribution -Fix GUI input error when choosing biallelic loci -Change alleles frequency distribution name from UNIFORM to NON_RANDOM -Linkage-disequilibrium genetic Ne analyses use the LDNe method of NeEstimator 2.01 (see help file for references) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Version 1.3.0.5.b2 Released 2016-08-29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Summary: Beta version with improved installation performance & bug fixes. Changes: -Setup EXE: Quiet check and install of 2008 C++ Redistributable required for SimuPop -Fixed directory issues when spaces in installation path ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Version 1.3.0.5.b1 Released 2016-08-12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Summary: Beta version with guided installation. Changes: -Created Setup EXE for guided installation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Version 1.3.0.5b Released 2016-05-18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Summary: Original beta version End of document.