The original MetaboDecon1D package (v0.2.2) provided four functions for deconvoluting spectra and visualizing results. With the introduction of metabodecon (v1.x), new functions for aligning deconvoluted spectra were added, along with improved replacements for the deconvolution functions. To maintain backwards compatibility, the old deconvolution functions are still available but marked as deprecated. These old functions will be removed entirely in Metabodecon v2.0.
A tabular overview of function introductions, deprecations, and scheduled removals is provided in Table 1: Version Matrix.
A similar graphical representation with additional information about accepted and returned types is provided in Figure 1: Metabodecon Workflow.
Table 1: Version Matrix
| Topic | Function | 0.2 | 1.0 | 1.2 | 1.3 | 2.0 |
|---|---|---|---|---|---|---|
| decon | MetaboDecon1D | s | s | s | d | - |
| decon | generate_lorentz_curves | - | s | s | s | d |
| decon | deconvolute | - | - | x | x | s |
| plot | calculate_lorentz_curves | s | s | s | d | - |
| plot | plot_lorentz_curves_save_as_png | s | s | s | d | - |
| plot | plot_triplets | s | s | s | d | - |
| plot | plot_spectrum | - | - | x | s | s |
| plot | plot_spectra | - | - | x | s | s |
| align | combine_peaks | - | s | s | d | - |
| align | gen_feat_mat | - | s | s | d | - |
| align | get_ppm_range | - | s | s | d | - |
| align | speaq_align | - | s | s | d | - |
| align | align | - | - | x | x | s |
| data | get_data_dir | - | s | s | d | - |
| data | datadir | - | - | s | s | s |
| data | datadir_persistent | - | - | s | s | s |
| data | datadir_temp | - | - | s | s | s |
| data | download_example_datasets | - | - | s | s | s |
- -: internal or not available in package
- ?: not yet decided
- d: deprecated
- s: stable
- x: experimental
Table 2: Feature Matrix
| Feature | BWC | F1 | F2 | F3 | Issue |
|---|---|---|---|---|---|
| Doesn’t write to disk by default | semi | x | x | x | CRAN-8 |
| Doesn’t change wd or global opts | semi | x | x | x | CRAN-9 |
| Uses faster peak selection | yes | x | x | CHECK-7 | |
| Batch Mode | yes | x | x | FEATURE-3 | |
| Parallelized | yes | x | x | FEATURE-4 | |
| Improved plotting speed | yes | x | x | REFACTOR-4 | |
| Uses micro functions | yes | x | x | REFACTOR-7 | |
| Doesn’t show License | semi | x | x | REFACTOR-2 | |
| Prints timestamps | semi | x | x | REFACTOR-2 | |
| Uses correctly scaled y values | no | x | CHECK-1 | ||
| Uses correct sfr calculation | no | x | CHECK-2 | ||
| Uses correct ws calculation | no | x | CHECK-3 | ||
| Uses dynamic signal removal | no | x | CHECK-5 | ||
| Uses improved return list | no | x | FEATURE-7 | ||
| Uses faster smoothing | no | x | REFACTOR-5 | ||
| Does all calculations in ppm | no | x | REFACTOR-6 |
- BWC == backwards compatible
- F1 == MetaboDecon1D
- F2 == generate_lorentz_curves
- F3 == deconvolute_ispecs
- The faster peak selection implementation also fixes an indexing bug, which in most cases shouldn’t have any effect, but in some rare cases might cause one peak to be missed.