diff --git a/development/release_notes/release_notes_PsN_4_8_0.txt b/development/release_notes/release_notes_PsN_4_8_0.txt new file mode 100644 index 000000000..353dd087e --- /dev/null +++ b/development/release_notes/release_notes_PsN_4_8_0.txt @@ -0,0 +1,171 @@ +This PsN version has been tested on the following systems: + +Windows 10 64-bit with Strawberry Perl 5.22.3 , gfortran 4.9.2 and NONMEM 7.3.0 and 7.4.3 +Windows 7 64-bit with Strawberry Perl 5.24.1, gfortran 4.9.2 and NONMEM 7.3.0 and 7.4.3 +MacOS X 10.6.6 with ActiveState Perl 5.16.3, ifort 12.0.0 and NONMEM 7.2.0, 7.3.0 and 7.4.0 +Ubuntu Linux 17.04 with Perl 5.24.1, gfortran 6.3 and NONMEM 7.3.0 and 7.4.3 +CentOS 7 with Perl 5.16.3, gfortran 5.1.0 and NONMEM 7.3.0 and 7.4.3 + + +************************ +Installation +************************ + +Follow the installation instructions on +https://uupharmacometrics.github.io/PsN/install.html + +************************ +Documentation +************************ +All documentation is found in the doc subdirectory of the PsN +installation directory. During installation it is also possible +to have all documentation copied to a user-specified directory. + +All documentation can also be downloaded from +the PsN website https://uupharmacometrics.github.io/PsN/docs.html + +************************ +Dependencies +************************ + +- It is recommended to use Xpose version 4.5.3 or later for the -cwres functionality + and the default execute, vpc and bootstrap R plots. + +- Each userguide lists the R packages required to obtain the diagnostic R plots. + +************************ +Known issues +************************ + +- Windows users need to be careful to choose + a Perl version where the extra modules needed for PsN are available. + For new Perl installations the PsN team recommends Strawberry Perl + See the instructions on https://uupharmacometrics.github.io/PsN/install.html + +- Installation problem on some Windows systems where + perl 'system' command does not work. Make sure perl module File::Copy::Recursive + is installed *before* (re)running the installation script setup.pl + +********************************************* +Changes and bug fixes from PsN 4.7.0 to 4.8.0 +********************************************* + + + ___General___ + +- New required perl module YAML::XS +- PsN will now give an error if an OMEGA or SIGMA BLOCK contains multiple FIX + This would be inline with what NM-TRAN does. +- PsN runs now generate meta.yaml to systematically describe various metadata. + See the psn.pdf for documentation. +- Fix bug causing datasets not to be filtered properly if ignore statement was written as IGN(VISI>3), + i.e. with no equal sign. +- The psn_installation.pdf has been removed and all information it contained has been merged + into the installation section of the webpage. +- The PsN_and_NONMEM7.pdf has been removed and all information it contained has been moved to PsN.pdf and + other documentation. +- All userguides now have a table of content +- The vpctable script was removed from PsN +- The data_stats script was removed from PsN +- The -d2u common option was removed. PsN should support all encodings and dos2unix can be used separately if needed + + + ___common_options___ + +- New option -model_subdir to use an extra directory level between the calling directory and the run directory. +- The parafile option can now take non-trivial relative paths +- When the parafile option is not used it will no longer be shown as 'none' in version_and_option_info.txt or meta.yaml + + + ___NONMEM output parsing___ + +- Fix bug causing warnings when any parameter estimate was 'NaN' + + + ___nonpb___ + +- Fix broken -lst_file option + + + ___runrecord___ + +- No longer requires YAML::Tiny for csvy output. Will use the required YAML::XS + + + + ___frem___ + +- Postfrem now always creates its directory in the frem directory +- The option -model to postfrem was removed. +- The option -final_model was added to postfrem + + + ___proseval___ + +- Bugfix: proseval would crash if no filtering was needed due to no accept or ignore in $DATA + + + ___scm___ + +- Bugfix: Remove IGNORE or ACCEPT statements for linearized models that would else crash. +- Linearized scm will always evaluate the derivatives model and not estimate it. +- New option nointer to not use interaction for linearized scm +- Linearized scm supports finding parameter-eta relation in two steps i.e.: + ETA_CL = ETA(1), TVCL = THETA(1), CL = TVCL * EXP(ETA_CL) + will properly be detected. Search is also done in $ERROR +- Bugfix: Models with IGNORE=() and IGNORE=C where C is not @ caused scm to crash +- Changed boundaries for covariate effect theta on exponential effect to be adaptive given an effect size within 0.01 and 100 + This to reduce the risk of overflow. +- Fix formatting of OFV values in scm log to avoid two numbers be put directly next to each other +- Add support for categorical covariates with more levels than 2 for linearized scm + + + ___linearize___ + +- Ignore all MDV!=0 in linear model if MDV obtainable +- Support models with extension .ctl +- Do not propagate name of -dir to subtools (i.e. underlying scm directory will always be called scm_dir1) +- Only evaluate (MAXEVALS=0) the derivatives model. If lst file is available update initial values first. +- New option nointer to not use interaction +- Do not use COM in derivatives.mod to avoid name clash +- Avoid NONMEM crash by adding dummy thetas for omegas that have not ETA(X) in code. + + ___nca___ + +- Set number of samples to default 300. + + + ___runrecord___ + +- Fix bug causing est_time and cov_time to not be added to table for NONMEM 7.4 + + + ___precond___ + +- Give error if model does not have any THETAS (i.e. linearized model) + + + ___cdd___ + +- Fix critical bug (#50) casusing dofv to be calculated in a wrong way if any individual was ignored. +- Do not propagate -dir to subtools (i.e. subdir of modelfit of cdd runs will always be 'modelfit_dir1') + + + ___nmoutput2so___ + +- Bugfixes for simulation results that caused nmoutput2so to crash +- Change columnType for TIME in SimulatedProfiles from time to idv + + + ___transform___ + +- Added remove_0fix_omegas, tdist, full_block, add_tv, add_iov, iiv_on_ruv, power_on_ruv, remove_nonobs and omit_ids transformations + + + ___resmod___ + +- Don't run dtbs and power for models giving negative IPRED + + ___qa___ + +- New tool diff --git a/development/release_notes/release_notes_PsN_next_version.txt b/development/release_notes/release_notes_PsN_next_version.txt index 1c58379e7..3b91806a1 100644 --- a/development/release_notes/release_notes_PsN_next_version.txt +++ b/development/release_notes/release_notes_PsN_next_version.txt @@ -51,7 +51,7 @@ Known issues is installed *before* (re)running the installation script setup.pl ********************************************* -Changes and bug fixes from PsN 4.7.0 to x.x.x +Changes and bug fixes from PsN 4.8.0 to x.x.x ********************************************* @@ -59,33 +59,14 @@ Changes and bug fixes from PsN 4.7.0 to x.x.x ___General___ -- New required perl module YAML::XS -- PsN will now give an error if an OMEGA or SIGMA BLOCK contains multiple FIX - This would be inline with what NM-TRAN does. -- PsN runs now generate meta.yaml to systematically describe various metadata. - See the psn.pdf for documentation. -- Fix bug causing datasets not to be filtered properly if ignore statement was written as IGN(VISI>3), - i.e. with no equal sign. -- The psn_installation.pdf has been removed and all information it contained has been merged - into the installation section of the webpage. -- The PsN_and_NONMEM7.pdf has been removed and all information it contained has been moved to PsN.pdf and - other documentation. -- All userguides now have a table of content -- The vpctable script was removed from PsN -- The data_stats script was removed from PsN -- The -d2u common option was removed. PsN should support all encodings and dos2unix can be used separately if needed ___common_options___ -- New option -model_subdir to use an extra directory level between the calling directory and the run directory. -- The parafile option can now take non-trivial relative paths -- When the parafile option is not used it will no longer be shown as 'none' in version_and_option_info.txt or meta.yaml ___NONMEM output parsing___ -- Fix bug causing warnings when any parameter estimate was 'NaN' ___Cluster/Grid___ @@ -98,13 +79,10 @@ Changes and bug fixes from PsN 4.7.0 to x.x.x ___nonpb___ -- Fix broken -lst_file option ___runrecord___ -- No longer requires YAML::Tiny for csvy output. Will use the required YAML::XS - ___sumo___ @@ -119,46 +97,21 @@ Changes and bug fixes from PsN 4.7.0 to x.x.x ___frem___ -- Postfrem now always creates its directory in the frem directory -- The option -model to postfrem was removed. -- The option -final_model was added to postfrem ___proseval___ -- Bugfix: proseval would crash if no filtering was needed due to no accept or ignore in $DATA ___scm___ -- Bugfix: Remove IGNORE or ACCEPT statements for linearized models that would else crash. -- Linearized scm will always evaluate the derivatives model and not estimate it. -- New option nointer to not use interaction for linearized scm -- Linearized scm supports finding parameter-eta relation in two steps i.e.: - ETA_CL = ETA(1), TVCL = THETA(1), CL = TVCL * EXP(ETA_CL) - will properly be detected. Search is also done in $ERROR -- Bugfix: Models with IGNORE=() and IGNORE=C where C is not @ caused scm to crash -- Changed boundaries for covariate effect theta on exponential effect to be adaptive given an effect size within 0.01 and 100 - This to reduce the risk of overflow. -- Fix formatting of OFV values in scm log to avoid two numbers be put directly next to each other -- Add support for categorical covariates with more levels than 2 for linearized scm ___linearize___ -- Ignore all MDV!=0 in linear model if MDV obtainable -- Support models with extension .ctl -- Do not propagate name of -dir to subtools (i.e. underlying scm directory will always be called scm_dir1) -- Only evaluate (MAXEVALS=0) the derivatives model. If lst file is available update initial values first. -- New option nointer to not use interaction -- Do not use COM in derivatives.mod to avoid name clash -- Avoid NONMEM crash by adding dummy thetas for omegas that have not ETA(X) in code. ___nca___ -- Set number of samples to default 300. - - ___xv_scm___ @@ -173,7 +126,6 @@ Changes and bug fixes from PsN 4.7.0 to x.x.x ___runrecord___ -- Fix bug causing est_time and cov_time to not be added to table for NONMEM 7.4 ___update_inits___ @@ -186,27 +138,18 @@ Changes and bug fixes from PsN 4.7.0 to x.x.x ___precond___ -- Give error if model does not have any THETAS (i.e. linearized model) - ___cdd___ -- Fix critical bug (#50) casusing dofv to be calculated in a wrong way if any individual was ignored. -- Do not propagate -dir to subtools (i.e. subdir of modelfit of cdd runs will always be 'modelfit_dir1') ___rplots___ ___nmoutput2so___ -- Bugfixes for simulation results that caused nmoutput2so to crash -- Change columnType for TIME in SimulatedProfiles from time to idv - ___transform___ -- Added remove_0fix_omegas, tdist, full_block, add_tv, add_iov, iiv_on_ruv, power_on_ruv, remove_nonobs and omit_ids transformations ___resmod___ -- Don't run dtbs and power for models giving negative IPRED