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Created by Konrad Zych@zychMaintainer26 of 27 tasks completed26/27 tasks

Use getter's and setter's for accessing slots in your class

  • use phyloseq accessors and assignment functions

rebuild SIAMCAT object

This need to be done, otherwise we need accessors for each slot in each slot...

  • change data_split -> list
  • change label -> list

change phyloseq slot name to physeq

In order to avoid mother of all name conflicts.

  • siamcat@phyloseq => siamcat@physeq
  • phyloseq<- => physeq<-
  • phyloseq() => physeq()

create assigment functions

  • phyloseq<-
  • label<-
  • model_list<-
  • eval_data<-
  • norm_param<-
  • data_split<-
  • pred_matrix<-
  • orig_feat<-

correct accessors

  • generic slot accessor
  • phyloseq()
  • otu_table()
  • label()
  • model_list()
  • eval_data()
  • norm_param()
  • data_split()
  • pred_matrix()
  • orig_feat()
  • remove old ones when replaced

eliminate @

  • correct accessors
  • use assigments in the returns of the functions

/cc @zych @jawirbel

Edited by Konrad Zych
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