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MetaboDecon1D() that caused argument
file_path to be interpreted as a relative path, even if it
was an absolute path.read_spectrum() that caused argument
raw to not be passed on to
read_jcampdx().Finished the following tasks. For details about each task, see TODOS.md.
read_spectra()plot_spectrum()deconvolute_blood()-License,
+Timestamps)generate_lorentz_curves()MetaboDecon1D()
callscalc_prarp()API:
generate_lorentz_curves() that caused
the function to always use file format “bruker”, even when file format
“jcampdx” was specified.Datasets:
Bood_<nr> to blood_<nr>).example_datasets/jcampdx/urine/urine.dx to
example_datasets/jcampdx/urine/urine_1.dx and renamed
example_datasets/bruker/urine/urine/ to
example_datasets/bruker/urine/urine_1/. This was done
because list.files seems to return different orderings for
urine.dx and urine_2.dx in different operating
systems, whereas urine_1.dx and urine_2.dx are
sorted the same way everywhere. This makes it easier to write clear and
concise test cases, because we don’t need to check for file
ordering.Documentation:
Testing:
generate_lorentz_curves().tests/testthat/test-generate_lorentz_curves-[1-4].R.generate_lorentz_curves_v2() to
DESCRIPTION/Config/testthat/start-first.example_datasets (sample urine was renamed to
urine_1, as mentioned in above in section
Datasets)Internal:
%||%, msg() and
msgf to R/util.R.range_water_signal_ppm and
signal_free_region to returned list of function
deconvolute_spectrum.with now prints error messages to stderr even
if the message stream is redirected.deconvolution() from
R/MetaboDecon1D.R to R/main_v2.R as
.deconvolute_spectrum.deconvolution.download_example_datasets(). Argument
overwrite is passed correctly on to
cache_example_datasets().xds$url from
https://github.com/spang-lab/metabodecon/releases/download/v1.0.2/example_datasets.zip
to
https://github.com/spang-lab/metabodecon/releases/download/v1.1.0/example_datasets.zip.cache_example_datasets(). Extraction now only
is done if extract == TRUE AND the resulting folder does
not yet exist (saves approx. 2-3s on each call). To overwrite a possible
existing folder, argument overwrite can be set to
TRUE.test_helpers.R.lintrAPI:
download_example_datasets() by adding
caching and making it more stableget_data_dir() with
datadir() and its helper functions
datadir_persistent(), datadir_temp() and
tempdirget_data_dir() is now deprecated in favour of
datadir()Documentation:
Datasets:
misc/datasets to
misc/example_datasetsmisc/examples/usage_example.R to
misc/code_examples/sage_example.RInternal:
check_package.Rutil.R to
datadir.RgrDevices, stats and
utils as internal importsR/test_helpers.Rgenerate_lorentz_curves_v2() which will
replace generate_lorentz_curves() as soon as we have new
features AND 100% backwards compatibilitywith() that caused
get_datadir_mock() to be called after redirection took
place causing unexpected message outputdatadir() that caused the resulting path
to end with a slash on Unix-like systems and without a slash on Windows,
if file was not specifiedRUN_SLOW_TESTS is now set to TRUE for the CI
pipelineAPI:
get_data_dir() to accept "blood"
as new value for parameter dataset_namedownload_example_datasets() to download the
datasets from the github repo instead of the old spang-lab repoDocumentation:
README.md as it’s a bit
overkill for approx. 50 lines of textInternal:
MetaboDecon1Ddocs folder to .gitignore. Reason:
we changed all vignettes to pkgdown articles which will be displayed
only at our Github Pages website and can be regenerated from folder
vignettes upon deployment.TODOS.md and added it to
.Rbuildignore.gitignoreCONTRIBUTE.md (instead a section within
README.md is used)These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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