Finch Studio

# Changelog and Release Notes

# v1.4.0 (January 27th, 2024)

  • New interactive plot type: Live monitoring of parameter/OFV convergence
  • Supports caclulation of CV% for more omega/sigma transformations.
    • exponential, additive, logit, proportional, heavy-tail, and box-cox.
  • Added plot setting option for residual diagnostic plot to select the independent x variable (i.e. use TSLD vs CWRES instead of TIME vs CWRES)
  • Added option to set symmetric x and y axis for residual diagnostic plots
  • Allows more granular selection of point size in default plot appearance settings.
  • Fixed display issue when model or project name was very long.

# v1.3.4 (August 27th, 2023)

  • Additional options for summary stats (percentiles, geo mean, etc).
  • When exporting table, it will indicate what filters were applied.
  • Fix bug when splitting summary stats table by categorical variable
  • Fix bug that caused binning issue when x variable contained missing value for mean plots
  • Fix parsing issue with some SAME omega blocks
  • Perform filtering before one row per ID in tables

# v1.3.3 (August 1st, 2023)

  • Fix bug in table stat summary when splitting by a variable (caused column headers to be undefined)
  • Fix bug in the order of legend groups.

# v1.3.2 (July 24th, 2023)

  • Add ability to export Finch plots to pdf files.
  • When duplicating model with final estimates from parent, option to set the number of significant digits for initial estimates
  • Plot legend improvements
    • Continuous covariate groups now show up as "start - end" instead of "> start"
    • Smaller so it doesn't take up plotting area
  • Bug fix: when switching between projects that have models with same name, output data now reads in correctly

# v1.3.1 (July 7th, 2023)

  • Add options for changing some plot aesthetics (i.e. point and line size, color and opacity)
    • Access through paint pallette icon on top right when in evaluate view.
  • New table type to create summary tables of your model output tables.
    • Similar to observed data summary types, except uses the model output tables
    • Allows you to create clearance summary stratified by race for example (or any other covariate group/parmeter of interest)
  • Option to choose which type of residuals to plot in residual vs TIME, PRED plots (i.e. CWRES, IWRES, NPDE, etc )
  • When modifying system $PATH variable in settings, it now uses that $PATH to look for the PsN location as well as in the built-in console.
    • If you don't have permissions to add the PsN path to your sytem path variable, you can now add the psn location to the system Path under Settings > Path Variables > Prepend to Path
  • Add option to establish SSH connection with password instead of only private key.
  • Better display of mean line
    • When adding mean line layer to the observed data plot, it now shows in the same color as the points, and the points are made transparent
  • Option to show dosing lines in population observed plots
    • Plot Settings > Plot Options > Show Dosing on Hover
  • Dosing lines in individual plots can now be shown as a vertical line or as small ticks

# v1.3.0 (May 31st, 2023)

  • Redesign model compare table and provide additional customization options
    • Ability to select reference model, collapse different sections of table, and option to hide fixed parameter estimates
  • Add option to export tables to word document (final parameter estimates table, model compare table, and stat summary tables)
  • Add setting to specify user name (Settings > Misc > Username).
    • Username appears in exported tables
  • Allow spaces in data for .csv files
  • For individual fit plots, add option to zoom based on DV, IPRED, and/or PRED
  • Fixed axes now work for individual fit and individual observed plots
  • Fix dataset explorer filtering issue for values of 0
  • When switching to log axis for residual plots, CWRES remains on linear scale.
  • Performance improvements for generation of interactive plots
  • Minor plot styling changes

# v1.2.2 (May 3rd, 2023)

  • Added functionality for keyboard insteractive SSH connection.

# v1.2.1 (April 26th, 2023)

  • Fixes for R path and scripts on linux

# v1.2.0 (March 10th, 2023)

  • Two new interactive diagnostic plots types
    • Plot of individual OFV values (requires mod1.phi file to be present)
    • Plot of parameter correlation matrix heat map (requires successful covariance step)
  • SLURM Job Monitor for monitoring and canceling SLURM jobs on remote cluster.
    • File > Open Job Monitor
  • Advanced Execute option for executing commands on remote cluster, with options to copy files to remote directory prior to execution
    • Right click model > Advanced Execute
  • Ability to indicate "missingness" value for dataset variables (e.g. -99)
    • Settings > Data >Missing Data Indicator
  • Ability to toggle on AIC/BIC statistic in model results table
  • Ability to create code folding blocks in control stream editor by starting line with ";--"
    • e.g. ";-- PK Parameters"
  • Speed improvements for loading large projects
  • Ability to export tables to csv files.
  • Switches to compact view (collapses side panels) when snapped to half screen
  • Help > About now displays current installed Finch version.
  • Fixed bug that resulted in model results table columns getting collapsed

# v1.1.0 (September 14th, 2022)

  • Added ability to configure location of persisted Finch settings
  • Added feature to allow user to discard unsaved changes (within model right click menu)
  • Remember editor state (scroll position, folded blocks, cursor position) when switching back and forth between models
  • Fixes bug with continuously expanding column in model results table.
  • Change default terminal to local.

# v1.0.2 (September 12th, 2022)

  • Fix bug which prevented data settings from being saved
  • Hide select X and Y options in plot types where they were not used
  • Fix bug which prevented data at Time == 0 from being plotted in population plot

# v1.0.1 (August 30th, 2022)

  • Fix bug which prevented projectCommands.json from being created (leading to Run Model button not working)

# v1.0.0 (August 23rd, 2022) 🎉

  • Add functionality for customizing paths to data and models folders

  • Update license validation interface

    • Beta licenses will no longer work starting in this version

  • Update EULA text during install

  • Remove unused features

  • Add more post-processing scripts

  • Fix bug that prevented covariates from refreshing automatically sometimes

  • Scroll bar for model results table on smaller screens

# v0.2.2 (August 7th, 2022)

  • Fix UI bug which caused plot and table menus to go off screen

  • On Mac, allow saving control stream with Command + S

  • Fix Help Menu on Mac (now goes to correct Finch links)

  • Better handling of missing covariate data within interactive plots/tables

  • Use sample standard deviation and variance in stat summary calculations (consistent with R)

  • Fix bug which caused directory listeners to not work when there was a bracket in project name

  • Read in output data when there is a detected change in ANY of the output tables (sdtab1, patab1, cotab1, catab1).

# v0.2.1 (July 22nd, 2022)

  • MacOS specific fixes
    • Environment $PATH now set correctly
    • R defult path now set
    • Model library updated

# v0.2.0 (July 19th, 2022)

  • Breaking change - license file and application settings now stored in directory named Finch Studio in users home directory

    • This makes it easier to configure the app for a group of individuals
    • Also, you are now able to open multiple Finch Studio windows which did not work in the past.
    • Will only require current users to reenter license key and persisted settings (i.e. any custom global run commands)
    • This will not effect any project related files or functionality.

  • Interactive Statistical Summary Tables

  • Functionality for transforming plotted variables

    • E.g. if the dataset has a DV column, and a DOSE column, you can now plot DV/DOSE
    • Also works for transforming units - if TIME is in hours, you can now plot TIME/24 to transform units to days.

  • Option to overlay mean and SD in observed data plot

  • Links under the Help drop down menu now go to the correct Finch sites

  • Only show MDV === 0 rows in residual diagnostic plots.

  • Added MDV and EVID variables to output plot right panel to give ability for filtering out of MDV and/or EVID values.

# v0.1.0 (June 6th, 2022)

  • Model library updates

    • Better UX for browsing and filtering models

    • Added more model diagrams and control streams

  • Final estimates panel now shows how far final estimate moved from initial.

  • Option to lock a model, which prevents further edits to the model.

  • In Run Settings tab, there is now an option to run the command in a separate console window (Windows and Mac only)

  • In scripts Tab, functionality for copying a global script to local scripts folder for project specific editing of script.

  • Better performance for Files tab

  • Add autocomplete for user defined variables in control stream

  • Persist sort order of results table

  • When duplicating a model, the new model is now set as the active model.

  • ETA(1:LAST) added to $TABLE for patab1 when creating a new model (requests all ETA parameters).

  • Better display of summary stats in data viewer. (values are rounded and percents are shown for counts)

  • Bug fixes

    • $THETA parser bug fixed when FIXED was outside of parentheses.
    • "output" folder changed to "outputs". For some reason nmfe will not run properly if a file or folder called output exists.
    • Added horizontal scroll bar for overflowing content (i.e. dtat viewer)

# v0.0.8 (April 25th, 2022)

  • SSH/SFTP integration - ability to view files and execute commands on a remote server

  • Functionality to download/save plot

  • Add data table viewer to view nonmem dataset

    • 'View' button on left panel next to data

  • Updates to model library modal

    • Ability to set the values for the diagonal/off diagonals in the omega matrix
    • Options for estimation method

  • Select multiple models on left panel with shift + click (similar to native file explorer behavior)

  • Add alert for confirmation before deleting a model or run command

  • Added toggle to include dosing lines in individual observed data plots and individual fit plots

  • Performance enhancements for plots (notable improvements for larger datasets)

  • Bug fixes/minor improvements

    • Don't allow spaces at beginning or end of model name since Windows doesn't like this (spaces are automatically trimmed from beginning and end of model name if user accidentally adds them)
    • Fixed scrolling issue in model comparison modal
    • Fixed issue with RSEs displaying as negative value
    • Fixed bug that prevented models from being read in when one model has a broken/incomplete xml file
    • Better performance when duplicating a model
    • When comparing model control streams, parent model is shown as first on the list
    • Honor reference model in drop down when duplicating instead of defaulting to parent model

# v0.0.7 (March 13th, 2022)

  • Added two new plot types

    • Parameter distribution/correlations
    • Covariate distribution/correlations

  • Model library now live with more model templates added

  • Batch find and replace across models (magnifying glass icon on left menu)

  • Project export feature

    • Ability to export final/key models and data to flat file directory or new Finch project

  • Ability to switch between models when in the evaluate tab to easily compare results between models

  • Covariates for output plots are now identified from cotab and catab.

  • Fixed axes now available to more plot types

  • Tooltip is now available to more plots types

  • Added more snippets to code completion

  • Fixed bug when duplicating model with multiple omega block that put final estimates in wrong place in child control stream.

  • Performance improvements when working with large datasets

# v0.0.6 (January 1st, 2022)

  • Functionality for defining custom commands

  • Added queue for running process

    • Ability to set maximum number of running processes

  • Ability to toggle hide fixed omega parameters in final estimates table

  • Omega and sigma parameter names are now shown in final estimates table and model comparisn table

  • CV% is now shown in model comparison table with ability to use simple or full method for the calculation

  • When in comparison editor mode, both model names are now shown on the top bar

  • Fixed issue that prevented other models from being read in when there was an problem with one xml file

  • Various bug fixes and UI enhancements

# v0.0.4 (September 7th, 2021)

  • End user liscense agreement added (displayed during installation)

  • Options for displaying BLQ values in ind fit plots

  • Functionaility to toggle display of points, lines, and trend lines in plots

  • Initial estimates panel now displays names for ETAs and SIGMAs

  • When multiple OMEGA and/or SIGMA blocks are present, you can now view all of them with arrows in inital estimates panel

  • Toggle between covariances and correlations when block matrices present

  • Plot enhancements

    • Ability to select X and Y axis variables

      • e.g. can use TSFD instead of TIME as independent variable

    • Ability to select compartment

      • Need CMT column in dataset

    • Additional flexibility in stratifying/coloring/filtering plots with the ability to now stratify by variables that are not constant within an inidividual ('cat-var')

      • In data mapping, select cat-var for any variable you wish to color/stratify/filter

      • Use cases include variables such as OMIT, treatment period, dosing day, or time-varying categorical covariate.

  • User's R version now defaults to their latest installed version

# v0.0.3 (August 23rd, 2021)

  • Collapsible view for model results

    • Ability to collapse children of a parent model based on reference models

  • Copy to clipboard button for final model parameters

    • Model parameters, units, and RSE are copied to the clipboard. Paste directly into excel to get in MS office table format (then you can paste into MS powerpoint or word)

  • Plot enhancements:

    • Legends are included when coloring plots

    • Better order for stratified plots

      • For example, DOSE: 25 mg would come before DOSE: 125 mg

    • Covariate panels on right side of plots are now collapsible

    • Ability to turn on/off all groups of a covariate with a toggle

    • Improved look of plot settings panel

# v0.0.2 (August 10th, 2021)

  • UI improvements to more easily see what model tabs are open

    • More space between editors and clearer model title

  • Advanced Delete modal to delete specific files/directories across all models

    • Accessed through right-click on model in left panel

  • Dataset no longer needs to be named NM_data.csv (but still must be .csv) and user can switch between datasets

  • Multi-select (Ctrl + Click) and associated batch actions (delete, color, send to compare, open)

  • Ctrl + Shift + Click opens models side by side

  • Etas with signficant p-value for etabar are shown in yellow in final parameters estimates table

    • Hovering over OM(n,n) in final estimates will show Eta-bar and p-value

  • When duplicating model, default name iterates numbering/lettering from parent model (e.g. one-cmt-v1 -> one-cmt-v2)

  • Added option to fix parameter estimates when duplicating

  • NONMEM estimation errors/warning messages after run are displayed under final estimates

  • Control streams when comparing if diff editor are switched (original on left, comparator on right)

  • .ext file is outputted to main model folder

  • Minor bug fixes

    • Data mapping is reset when switching projects

# v0.0.1 (July 29th, 2021)

  • Initial internal release

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