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Created with Raphaël 2.2.028May316Apr9Mar854328Feb2725222119181716151312111087326Jan2420181716151312111098123Dec9Nov31Oct1222Sep16131298762131Aug3025231916141211109754327Jul2515141312111096542129Jun2824232218152Mar128Feb272524238Oct6530Sep29222119181513922Jun2116159810May2AprUpdate documentation.v1.3.21 masterv1.3.21 masterUpdate documentation.Article draft: Initial commitjossjossClean up before adding the paper draftUpdate version.Adapt tests to changes so far.Close many stale FIXMEs.Fix comment.Update test-integration.Remove comment.Adapted `mf_narrow_summ' and `pack_ms2_w_summ' to new data model.shiny-state: -> -> = .The output `print_spec_tab' now adapted to new data model.Clean up some comments in `make_spec_ms2_plot'.test-integration: Saves obtained test state for further diagnosis.Fix wrong assigment of MS2 from precids non-existant for a given file in `relate_ms2_to_precid'.Adapt make_*plot calls in shiny-ui-base.Drop `extr_ms1' argument of `make_eic_ms1_plot'.Adapt `make_spec_ms2_plot' to work with new data-model.Cleaned up get_data_4_eic_ms2Cleaned up make_eic_ms1_plot and related functions.Function `gen_val_unc' now represents errors with uncertanties.Prevent generating tables with multiple identical cols by `get_data_from_key'.Test for `narrow_summ' and start testing `make_eic_ms1_plot'.Starting from a trimmed down state in test-plotting to enable prescreening.System to synthetise bogus MS spectra completed.Update keys in empty_cgram_ms1 and empty_cgram_ms2.Functions empty_cgram_ms1 and empty_cgram_ms2 construct empty chromatograms.<- -> =Adapted get_data_from_key and its calees.data-model: Fix precid/isocoarse merge for isobars.get_data_4_eic_ms1: Add 'db' argument.Function make_eic_ms1_plot got a new argument `db'.tests/testthat/test-plotting: Commented out bits under refactoring.extr$ms? -> db$extr$cgm$ms?an -> scanRefactored `gen_summ' to work off new data model.Move gen_summ from mix to data-model.analyse_extracted_data: Adapted to db inputs. Also fixed sec/mins conversions in a couple of places.extraction: find_ms1_max: Now correctly works with NAs in intensity.