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‎.Rbuildignore

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^_pkgdown\.yml$
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^\.github$
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^\.lintr$
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^\.Rplots\.pdf$
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^\.Rproj\.user$
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^\.vscode$
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^app\.R$
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^check/$
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^codecov\.yml$
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^cran-comments\.md$
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^CRAN-SUBMISSION$
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^Dockerfile$
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^docs$
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^FastRet\.Rproj$
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^misc$
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^pkgdown$
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^TODOS.md$
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^vignettes$
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^(?i)_pkgdown\.yml$
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^(?i)\.github$
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^(?i)\.lintr$
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^(?i)\.pytest_cache$
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^(?i)\.rplots\.pdf$
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^(?i)\.rproj\.user$
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^(?i)\.vscode$
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^(?i)app\.r$
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^(?i)check/$
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^(?i)codecov\.yml$
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^(?i)cran-comments\.md$
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^(?i)cran-submission$
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^(?i)dockerfile$
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^(?i)docs$
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^(?i)fastret\.rproj$
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^(?i)misc$
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^(?i)out\..*$
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^(?i)out$
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^(?i)pkgdown$
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^(?i)r*cmd*check.log$
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^(?i)r*cmd*check.md$
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^(?i)reports$
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^(?i)todos.md$
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^(?i)vignettes$

‎.gitignore

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.pytest_cache/
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.Rhistory
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.Rproj
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.Rproj.user
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.vscode/
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docs
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FastRet.Rproj
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inst/doc
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tests/testthat/Rplots.pdf
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*.bkp
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check/
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docs/
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FastRet.Rproj
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inst/doc/
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out/
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rcmdcheck.log
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tests/testthat/Rplots.pdf
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reproduce_results.html
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reproduce_results.md

‎DESCRIPTION

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Package: FastRet
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Title: Retention Time Prediction in Liquid Chromatography
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Version: 1.1.4
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Version: 1.1.5
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Authors@R: c(
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person(given = "Christian", family = "Amesoeder", role = c("aut", "cph"), email = "[email protected]", comment = c(ORCID = "0000-0002-1668-8351")),
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person(given = "Marian", family = "Schoen", role = c("aut", "cph"), email = "[email protected]"),
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ggplot2,
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glmnet,
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htmltools,
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openxlsx,
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promises,
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rcdk,
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readxl,
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shiny (>= 1.8.1),
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shinybusy,
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shinyhelper,
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shinyjs,
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xgboost,
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xlsx
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xgboost
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Suggests:
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cli,
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devtools,

‎NEWS.md

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# FastRet 1.1.4
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# FastRet 1.1.5 <!-- Commit Date: 2025-06-26 -->
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* Added a cache cleanup handler that gets registered via `reg.finalizer()` upon package loading to ensure that the cache directory is removed if it doesn't contain any files that should persist between R sessions.
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* Added an article about installation details incl. a troubleshooting section
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* Improved function docs
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* Improved examples by removing `donttest` blocks
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* Improved examples & tests by using smaller example datasets to reduce runtime
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- Improved `read_retip_hilic_data()`:
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the dataset is now only downloaded from GitHub if the package is not installed.
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If it is installed, the dataset is loaded directly.
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# FastRet 1.1.3
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- Internal Changes:
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- Removed TODOS.md
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- Bumped version to 1.1.5
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- Moved all data related functions from `util.R` to `data.R`
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- Added a README to `misc/datasets`
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- Added functions `load_all()` and `document()` to `util.R`
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- Replaced `xlsx` and `readxl` packages with `openxlsx`
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* Fixed issues mentioned by CRAN reviewer after initial submission of FastRet (v1.1.2):
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- __Comment 1__: *Please do not modify the .GlobalEnv. This is not allowed by the CRAN policies. -> R/patch.R*
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- __Solution__: Moved `patch.R` from the `R` folder to `misc/scripts`, which is excluded from the package build using `.Rbuildignore`. The file is conditionally sourced by the private function `start_gui_in_devmode()` if available, allowing its use during development without including it in the package.
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- __Comment 2__: *Please add \value to .Rd files regarding exported methods and explain the functions' results in the documentation. Please write about the structure of the output (class) and also what the output means. (If a function does not return a value, document that too, e.g., \value{No return value, called for side effects} or similar) -> Missing Rd-tags: adjust_frm.Rd: \value, analyzeCDNames.Rd: \value, getCDs.Rd: \value, getCDsFor1Molecule.Rd: \value, read_rpadj_xlsx.Rd: \value*
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- __Solution__: Added `\value` tags to the mentioned `.Rd` files describing the functions' return values.
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- __Comment 3__: *If there are references describing the methods in your package, please add these in the description field of your DESCRIPTION file in the form authors (year) <doi:...> authors (year, ISBN:...) or if those are not available: <https:...> with no space after 'doi:', 'https:' and angle brackets for auto-linking. (If you want to add a title as well please put it in quotes: "Title")*
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- __Solution__: Added *Bonini et al. (2020) <doi:10.1021/acs.analchem.9b05765>* as reference to the description part of the DESCRIPTION file, listing it as *Related work*. This reference is used in the documentation for `read_retip_hilic_data()` and `ram_cache`. No additional references are used in the package documentation.
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* Added Fadi Fadil as a contributor. Fadi measured the example datasets shipped with FastRet.
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* Added ORCID IDs for contributors as described in [CRAN's checklist for submissions](https://cran.r-project.org/web/packages/submission_checklist.html).
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# FastRet 1.1.4 <!-- Commit Date: 2025-02-08 -->
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# FastRet 1.1.2
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- Added a cache cleanup handler that gets registered via
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`reg.finalizer()` upon package loading to ensure that the cache
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directory is removed if it doesn't contain any files that should
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persist between R sessions.
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* Wrapped examples of `read_rp_xlsx()` and `read_rpadj_xlsx()` into `donttest` to prevent note `Examples with CPU time > 2.5 times elapsed time: ...`. By now I'm pretty sure the culprit is the `xlsx` package, which uses a java process for reading the file. Maybe we should switch to openxlsx or readxl in the future.
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- Added an article about installation details incl. a
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troubleshooting section
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# FastRet 1.1.1
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- Improved function docs
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* Improved examples of `preprocess_data()` to prevent note `Examples with CPU time > 2.5 times elapsed time: preprocess_data (CPU=2.772, elapsed=0.788)`.
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- Improved examples by removing `donttest` blocks
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# FastRet 1.1.0
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- Improved examples & tests by using smaller example datasets to
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reduce runtime
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* Added RAM caching to `getCDs()`
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# FastRet 1.1.3 <!-- Commit Date: 2024-06-24 -->
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# FastRet 1.0.3
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- Moved `patch.R` from the `R` folder to `misc/scripts`, which is
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excluded from the package build using `.Rbuildignore`. The file
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is conditionally sourced by the private function
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`start_gui_in_devmode()` if available, allowing its use during
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development without including it in the package.
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* Initial CRAN Submission.
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- Added `\value` tags to the mentioned `.Rd` files describing the
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functions' return values.
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Rejected because the following examples caused at least one of the following notes on the CRAN testing machines: CPU time > 5s`, `CPU time > 2.5 times elapsed time`. In this context, `CPU time` is calculated as the sum of the easured `user` and `system` times.
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- Added *Bonini et al. (2020) <doi:10.1021/acs.analchem.9b05765>*
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as reference to the description part of the DESCRIPTION file,
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listing it as *Related work*. This reference is used in the
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documentation for `read_retip_hilic_data()` and `ram_cache`. No
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additional references are used in the package documentation.
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| function | user | system | elapsed | ratio |
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| -------------------- | --------- | ------ | ------- | --------- |
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| check_lm_suitability | **5.667** | 0.248 | 2.211 | **2.675** |
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| predict.frm | 2.477 | 0.112 | 0.763 | **3.393** |
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| getCDs | 2.745 | 0.089 | 0.961 | **2.949** |
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- Added Fadi Fadil as a contributor. Fadi measured the example
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datasets shipped with FastRet.
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- Added ORCID IDs for contributors as described in [CRAN's
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checklist for submissions].
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[CRAN's checklist for submissions]:
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https://cran.r-project.org/web/packages/submission_checklist.html
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# FastRet 1.1.2 <!-- Commit Date: 2024-06-18 -->
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- Wrapped examples of `read_rp_xlsx()` and `read_rpadj_xlsx()`
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into `donttest` to prevent note "Examples with CPU time > 2.5
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times elapsed time: ...". By now I'm pretty sure the culprit is
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the `xlsx` package, which uses a java process for reading the
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file. Maybe we should switch to openxlsx or readxl in the
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future.
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# FastRet 1.1.1 <!-- Commit Date: 2024-06-18 -->
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- Improved examples of `preprocess_data()` to prevent note
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"Examples with CPU time > 2.5 times elapsed time:
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preprocess_data (CPU=2.772, elapsed=0.788)".
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# FastRet 1.1.0 <!-- Commit Date: 2024-06-17 -->
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- Added RAM caching to `getCDs()`
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# FastRet 1.0.3 <!-- Commit Date: 2024-06-13 -->
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- Added examples to `start_gui()`, `fastret_app()`, `getCDsFor1Molecule()`,
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`analyzeCDNames()`, `check_lm_suitabilitym()`, `plot_lm_suitability()`,
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`extendedTask()`, `selective_measuring()`, `train_frm()`, `adjust_frm()`,
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`get_predictors()`
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- Improved lots of existing examples
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- Added additionalo logging messages at various places
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- Submitted to CRAN, but rejected because the following examples
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caused at least one of the following notes on the CRAN testing
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machines: (1) "CPU time > 5s", (2) "CPU time > 2.5 times elapsed
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time". In this context, "CPU time" is calculated as the sum of
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the measured "user" and "system" times.
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| function | user | system | elapsed | ratio |
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| -------------------- | ------| ------ | ------- | ----- |
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| check_lm_suitability | 5.667 | 0.248 | 2.211 | 2.675 |
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| predict.frm | 2.477 | 0.112 | 0.763 | 3.393 |
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| getCDs | 2.745 | 0.089 | 0.961 | 2.949 |
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# FastRet 1.0.2 <!-- Commit Date: 2024-06-11 -->
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- Improved github actions
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# FastRet 1.0.1 <!-- Commit Date: 2024-06-07 -->
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- Improved github actions
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# FastRet 1.0.0 <!-- Commit Date: 2024-06-07 -->
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Completely refactored source code, e.g.:
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- Added a test suite covering all important functions
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- The UI now uses Extended Tasks for background processing,
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allowing GUI usage by multiple users at the same time
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- The clustering now uses Partitioning Around Medoids (PAM)
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instead of k-means, which is faster and much better suited for
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our use case
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- The training of the Lasso and/or XGBoost models is no longer
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done using `caret` but using `glmnet` and `xgboost` directly.
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The new implementation is much faster and allows for full
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control over the number of workers started.
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- Function `getCDs` now caches the results on Disk, making the
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retrieval of chemical descriptors much faster
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- The GUI now has a console element, showing the progress of the
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background tasks like clustering and model training
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- The GUI has a cleaner interface, because lots of the options are
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now hidden in the "Advanced" tab by default and are only
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displayed upon user request
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# FastRet 0.99.7 <!-- Commit Date: 2023-11-30 -->
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- Fixed R CMD check findings
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- Fixed Github Actions
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- Fixed Dockerfile
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# FastRet 0.99.6 <!-- Commit Date: 2023-11-30 -->
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- Added contact, privacy policy
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- Fixed Dockerfile
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# FastRet 0.99.4 <!-- Commit Date: 2023-11-29 -->
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- Improved Github Actions and Formatting of source code
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# FastRet 0.99.3 <!-- Commit Date: 2023-11-29 -->
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- Reduce required R version in DESCRIPTION from 4.2 to 4.1
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- Added Dockerfile
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- Fixed R CMD check warnings
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- Fixed R CMD check action
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# FastRet 0.99.2 <!-- Commit Date: 2023-11-27 -->
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- Added documentation website at:
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https://spang-lab.github.io/FastRet/
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# FastRet 0.99.1 <!-- Commit Date: 2023-11-27 -->
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- Initial version.
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Copy of commit cd243aa82a56df405df8060b84535633cf06b692 of
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[Christian Amesöders
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Repository](https://github.com/ChristianAmes/FastRet.git).
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(Christian wrote this initial version of FastRet as part of his
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master thesis at the Institute of functional Genomics,
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University of Regensburg).

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