R/calculations.R
changed.
Other files ignored by Codecov
man/ncbi_taxon_sample.Rd
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DESCRIPTION
has changed.
tests/testthat/testparsers_and_writers.R
has changed.
249  249  do_calc_on_num_cols(obj, data, cols = cols, groups = groups, 

250  250  other_cols = other_cols, out_names = out_names, 

251  251  func = function(count_table, cols = cols, groups = groups) { 

252    tibble::as.tibble(lapply(split(cols, groups), function(col_index) { 

252  +  tibble::as_tibble(lapply(split(cols, groups), function(col_index) { 

253  253  apply(count_table[, col_index], MARGIN = 1, FUN = func) 

254  254  })) 

255  255  } 
418  418  } 

419  419  count_table[to_zero] < 0 

420  420  } 

421    names(count_table) < groups # needed because do_calc_on_num_cols assumes column named by groups even though this function does not use groups currently 

421  +  names(count_table) < as.character(groups) # needed because do_calc_on_num_cols assumes column named by groups even though this function does not use groups currently 

422  422  return(count_table) 

423  423  } 

424  424 
489  489  sample_size < min(colSums(count_table)) # Calculate minimum count if no sample size is given 

490  490  my_print("Rarefying to ", sample_size, " since that is the lowest sample total.") 

491  491  } 

492    output < tibble::as.tibble(t(vegan::rrarefy(t(count_table), sample = sample_size))) 

493    names(output) < groups # needed because do_calc_on_num_cols assumes column named by groups even though this function does not use groups currently 

492  +  output < tibble::as_tibble(t(vegan::rrarefy(t(count_table), sample = sample_size))) 

493  +  names(output) < as.character(groups) # needed because do_calc_on_num_cols assumes column named by groups even though this function does not use groups currently 

494  494  return(output) 

495  495  } 

496  496  ) 
781  781  } 

782  782  }, numeric(1)) 

783  783  }) 

784    output < tibble::as.tibble(output, stringsAsFactors = FALSE) 

784  +  output < tibble::as_tibble(output, stringsAsFactors = FALSE) 

785  785  
786  786  return(output) 

787  787  } 
Files  Coverage 

R  57.75% 
src/repel_boxes.cpp  59.07% 
Project Totals (24 files)  57.86% 