Merge branch 'master' into 'devel'

Master

See merge request !1

README.org

-#+TITLE: RMassBank Compound Mix Workflow
+#+TITLE: The Shinyscreen Package
 
 
 * Usage
@@ -21,44 +21,3 @@
       to be placed into the current working directory.
       
       
-   
-** Record generation
-   The entire sequentual procedure,
-   #+BEGIN_SRC: R
-   pos<-rmbmix::sw.do(list.files(patt=".*pos.mzML"),fn_cmpd_list="ChemistryDashboard-Batch-Search_2019-05-15_07_27_26.csv",mode="pH")
-   pos_pmb<-rmbmix::mb.prep(pos)
-   pos_mb<-rmbmix::mb.do(pos_pmb)
-   
-   neg<-rmbmix::sw.do(list.files(patt=".*neg.mzML"),fn_cmpd_list="ChemistryDashboard-Batch-Search_2019-05-15_07_27_26.csv",mode="mH")
-   neg_pmb<-rmbmix::mb.prep(neg)
-   neg_mb<-rmbmix::mb.do(neg_pmb)
-  
-   #+END_SRC
-   
-   The entire parallel procedure,
-   #+BEGIN_SRC: R
-   pos<-rmbmix::sw.do(list.files(patt=".*pos.mzML"),fn_cmpd_list="ChemistryDashboard-Batch-Search_2019-05-15_07_27_26.csv",mode="pH",proc=4)
-   pos_pmb<-rmbmix::mb.prep(pos)
-   pos_mb<-rmbmix::mb.do(pos_pmb,proc=4)
-   
-   neg<-rmbmix::sw.do(list.files(patt=".*neg.mzML"),fn_cmpd_list="ChemistryDashboard-Batch-Search_2019-05-15_07_27_26.csv",mode="mH",proc=4)
-   neg_pmb<-rmbmix::mb.prep(neg)
-   neg_mb<-rmbmix::mb.do(neg_pmb,proc=4)
-   
-   #+END_SRC
-   
-   The ~fn_cmpd_list~ argument is the compound list, from Chemistry
-   Dashboard, or in a RMassBank format. The first argument to ~sw.do~ is
-   the list of /mzML/ files containing spectral data to be processed
-   using the spectral workflow. Each mzML file should have an associated
-   /YAML/ file with RMassBank settings describing it. The settings file
-   does not need to be complete, it can only contain the settings which
-   are different from the settings template.
-   
-   Once the spectral workflow is complete, first run the MassBank
-   preparation procedure using ~mb.prep~ function. Then, finalise the
-   MassBank record workflow by using the ~mb.do~ function.
-   
-   The resulting record files and info lists are under
-   "<data-dir>/info/XX" paths, where /data-dir/ is the mzML filename
-   without the mzML suffix.