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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,110 +1,129 @@ | ||
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| # GcalignR 1.0.6 | ||
|
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| ------------------------------------------------------------------------ | ||
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| - Removing unused argument `gc_peak_df` from `align_peaks` | ||
|
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| # GCalignR 1.0.5 | ||
|
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| ------------------------------------------------------------------------ | ||
|
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| - Bugfix in `choose_optimal_reference` that always selected the first | ||
| sample as a reference. Thanks to Heberto del Rio who pointed this out | ||
| on <https://github.com/mottensmann/GCalignR/issues/27> | ||
|
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| # GCalignR 1.0.3.9 | ||
|
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| - Small bug fixed that caused problems when plotting x-axis labels in | ||
| `gc_heatmap`. An error occurred in case of two peaks that were | ||
| identical when rounded to decimal places. | ||
| - Added a test for detecting inconsistently ordered retention times | ||
| within samples. Retention times are expected in increasing order, | ||
| starting with the lowest number. If this assumption is violated, | ||
| retention times are reordered as indicated by a warning. | ||
| - **Speedboost** when setting `max_diff_peak2mean = 0`: In this special | ||
| case there is no need to use a time-consuming iterative approach but | ||
| peaks can be sorted simply based on absolute values. This is | ||
| implemented in two steps. (1) Across all samples, unique retention | ||
| times are extracted, sorted in increasing temporal order and written | ||
| to a template data frame. (2) For each sample, peaks are matched to | ||
| the corresponding row of the template data frame. | ||
| - Small bug fixed that caused problems when plotting x-axis labels in | ||
| `gc_heatmap`. | ||
| - Added a test for detecting inconsistently ordered retention times | ||
| within samples. Retention times are expected in increasing order, | ||
| starting with the lowest number. If this assumption is violated, | ||
| retention times are reordered and a warning is shown. | ||
|
|
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| # GCalignR 1.0.3 | ||
|
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||
| ----- | ||
|
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||
| - Added `fill = TRUE` as a parameter in `utils::read.table` when | ||
| reading data from text within internal functions. *Loading GC data | ||
| with utils::read.table failed in cases of missing values in a column | ||
| (i.e. empty). This is the correct behaviour as missing data should | ||
| always be coded explicitly by ‘NA’* | ||
| - Tibbles are now coerced to data frames | ||
| - Added a new boolean parameter `remove_empty` for the main function | ||
| `align_chromatograms`. If samples are empty (i.e.. no peak) this | ||
| parameter allows to remove those cases from the dataset to avoid | ||
| problems in post-hoc analyses. By default `FALSE`, i.e.. all but the | ||
| blank samples are kept. | ||
| - Added a new boolean parameter `permute` for the functions | ||
| `align_chromatograms` and `align_peaks`. This allows to change the | ||
| default behaviour of random permutation of samples during the | ||
| alignment and might be useful if exact replication is needed. | ||
| ------------------------------------------------------------------------ | ||
|
|
||
| - Added `fill = TRUE` as a parameter in `utils::read.table` when reading | ||
| data from text within internal functions. *Loading GC data with | ||
| utils::read.table failed in cases of missing values in a column | ||
| (i.e. empty). This is the correct behaviour as missing data should | ||
| always be coded explicitly by ‘NA’* | ||
| - Tibbles are now coerced to data frames | ||
| - Added a new boolean parameter `remove_empty` for the main function | ||
| `align_chromatograms`. If samples are empty (i.e.. no peak) this | ||
| parameter allows to remove those cases from the dataset to avoid | ||
| problems in post-hoc analyses. By default `FALSE`, i.e.. all but the | ||
| blank samples are kept. | ||
| - Added a new boolean parameter `permute` for the functions | ||
| `align_chromatograms` and `align_peaks`. This allows to change the | ||
| default behaviour of random permutation of samples during the | ||
| alignment and might be useful if exact replication is needed. | ||
|
|
||
| # GCalignR 1.0.2 | ||
|
|
||
| ----- | ||
| ------------------------------------------------------------------------ | ||
|
|
||
| - The accompanying manuscript is published | ||
| <https://doi.org/10.1371/journal.pone.0198311> and the citation has | ||
| been added | ||
| - The function *beta* `read_empower2` allows to import HPLC data that | ||
| has been generated using the EMPOWER 2 software | ||
| - The accompanying manuscript is published | ||
| <https://doi.org/10.1371/journal.pone.0198311> and the citation has | ||
| been added | ||
| - The function *beta* `read_empower2` allows to import HPLC data that | ||
| has been generated using the EMPOWER 2 software | ||
|
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||
| # GCalignR 1.0.1 | ||
|
|
||
| ----- | ||
| ------------------------------------------------------------------------ | ||
|
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||
| **Bugfixes** | ||
|
|
||
| - A bugfix was applied for handling multiple blanks correctly. | ||
| - Progressbars are removed in non-interactive R sessions | ||
| - A bugfix was applied for handling multiple blanks correctly. | ||
| - Progressbars are removed in non-interactive R sessions | ||
|
|
||
| ----- | ||
| ------------------------------------------------------------------------ | ||
|
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||
| # GCalignR 1.0.0 | ||
|
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| **New functions implemented** | ||
|
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||
| - `choose_optimal_reference` offers an automatism to pick suitable | ||
| references. | ||
| - `draw_chromatograms` allows to represent a peak list in form of | ||
| chromatogram. | ||
| - `remove_blanks`allows to get rid of peaks that represent | ||
| contamination after aligning a dataset | ||
| - `remove_singletons` allows to remove single peaks from the dataset | ||
| after aligning | ||
| - `merge_redundant_rows` allows to merge rows that were not recognised | ||
| as redundant during the alignment by increasing the threshold value | ||
| for the evaluation of similarity | ||
| - `choose_optimal_reference` offers an automatism to pick suitable | ||
| references. | ||
| - `draw_chromatograms` allows to represent a peak list in form of | ||
| chromatogram. | ||
| - `remove_blanks`allows to get rid of peaks that represent contamination | ||
| after aligning a dataset | ||
| - `remove_singletons` allows to remove single peaks from the dataset | ||
| after aligning | ||
| - `merge_redundant_rows` allows to merge rows that were not recognised | ||
| as redundant during the alignment by increasing the threshold value | ||
| for the evaluation of similarity | ||
|
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||
| **Algorithm** | ||
|
|
||
| - Using `pbapply`, we implemented progress bars to inform the user | ||
| about the progress and the estimated running time of intermediate | ||
| steps in the alignment of peak lists. | ||
| - By implementing more efficient code, we were able to speed up the | ||
| processing, especially picking references is faster by an order of | ||
| magnitude. | ||
| - Retention times are not rounded to two decimals anymore. | ||
| Calculations still capture a precision of two decimals for | ||
| computational reasons. | ||
| - Within the aligned results, retention times correspond to the input | ||
| values. Linear adjustments are only used internally and are | ||
| documented within the Logfile accessible in the output. | ||
| - Reference samples that are used for the coarse alignment of | ||
| retention times can be picked using a novel algorithm that | ||
| determines the average similarity across the dataset. | ||
| - Using `pbapply`, we implemented progress bars to inform the user about | ||
| the progress and the estimated running time of intermediate steps in | ||
| the alignment of peak lists. | ||
| - By implementing more efficient code, we were able to speed up the | ||
| processing, especially picking references is faster by an order of | ||
| magnitude. | ||
| - Retention times are not rounded to two decimals anymore. Calculations | ||
| still capture a precision of two decimals for computational reasons. | ||
| - Within the aligned results, retention times correspond to the input | ||
| values. Linear adjustments are only used internally and are documented | ||
| within the Logfile accessible in the output. | ||
| - Reference samples that are used for the coarse alignment of retention | ||
| times can be picked using a novel algorithm that determines the | ||
| average similarity across the dataset. | ||
|
|
||
| **warning messages** | ||
|
|
||
| - Warnings addressing formatting issues are now more explicit and | ||
| partly rephrased to avoid ambiguity. | ||
| - Warnings addressing formatting issues are now more explicit and partly | ||
| rephrased to avoid ambiguity. | ||
|
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||
| **Plots** | ||
|
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||
| - Added horizontal axis to barplots summarising peak numbers in | ||
| `plot.GCalign`. | ||
| - Changed to more prominent colours in binary heatmaps with | ||
| `gc_heatmap`. | ||
| - The function `draw_chromatograms` was added as another visualisation | ||
| tool. | ||
| - Added horizontal axis to barplots summarising peak numbers in | ||
| `plot.GCalign`. | ||
| - Changed to more prominent colours in binary heatmaps with | ||
| `gc_heatmap`. | ||
| - The function `draw_chromatograms` was added as another visualisation | ||
| tool. | ||
|
|
||
| **Vignettes** | ||
|
|
||
| - We included a second vignette that explains the algorithm and the | ||
| supported data in detail. | ||
| - We included a second vignette that explains the algorithm and the | ||
| supported data in detail. | ||
|
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| **Documentation** | ||
|
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||
| - Helpfiles were rewritten to enhance clarity. | ||
| - Helpfiles were rewritten to enhance clarity. | ||
|
|
||
| ----- | ||
| ------------------------------------------------------------------------ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,18 +1,34 @@ | ||
| ## Submission GCalignR version 1.0.5 | ||
| ## Submission GCalignR version 1.0.6 | ||
|
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| This is a minor release correcting an indexing error in the function choose_optimal_reference | ||
| This is a minor release, removing an unused function argument (gc_peak_df) from the function align_peaks. | ||
|
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| ## Test environments | ||
| * devtools::build_win() | ||
| * devtools::check_mac_release() | ||
| * devtools::check_win_devel() | ||
| * devtools::check_win_release() | ||
| * devtools::check_rhub() | ||
| * local Windows 10 Home | ||
| * Travis-CI | ||
| * local Windows 11 Home | ||
|
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| ## R CMD check results | ||
| There were no ERRORs or WARNINGs or Notes | ||
|
|
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| ## win_build check results | ||
| There were no ERRORs or WARNINGs or Notes | ||
| There were no ERRORs or WARNINGs | ||
|
|
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| ## travis-ci results | ||
| There were no ERRORs or WARNINGs or Notes | ||
| There are 2 NOTEs: | ||
|
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| Note 1: | ||
|
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| ``` | ||
| checking for non-standard things in the check directory ... NOTE | ||
| Found the following files/directories: | ||
| ''NULL'' | ||
| ``` | ||
| According to [R-hub issue #560](https://github.com/r-hub/rhub/issues/560), this seems to be an Rhub issue and so can likely be ignored. | ||
|
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| Note 2: | ||
|
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| ``` | ||
| * checking for detritus in the temp directory ... NOTE | ||
| Found the following files/directories: | ||
| 'lastMiKTeXException' | ||
| ``` | ||
| According to [R-hub issue #503](https://github.com/r-hub/rhub/issues/503), this could be due to a bug/crash in MiKTeX and can likely be ignored. |