Function renaming

[vincentvanhees]

I keep finding it difficult to navigate the code in this repo as function names are often not clear.

For example, the terminology short and long map is confusing, they structure data per day or per recording. So, I think it is more intuitive to refer to day or recording level structuring.

Current function dependencies and what each function does:

• generate_sequence_maps (script in root of repo that shows how to run use the functionality)
  • sequence_mapping_main_last (high level function that ties all functions together)
  • readdata (reads data from files)
  • aggAccFile_self (aggregates count values, but could be interpretted as a resampling step)
    • tsFromEpoch_self (calculates the timestamp from epoch number or epoch number from timestamp)
  • bouts_length_filter (generates the short and long sequence maps)
    • labelNonWear (detects nonwear and labels it as -999)
    • tolerated_bouts (detect bout segments)
    • tolerance (Xinhui's bout detection algorithm)
    • generate_sequence_map (adds labels to detected segments) --> symbols
    • shorting.map (organises the sequence map as a new line per day)
  • long.map (reformats short sequence maps to long format)

Proposed revision of function names:

Old name	Proposed new name
generate_sequence_maps	main_script
sequence_mapping_main_last	run_pipeline
readdata	read_file
aggAccFile_self	resample
tsFromEpoch_self	reformat_time_indicator
bouts_length_filter	generate_sequence
labelNonWear	detect_nonwear
tolerated_bouts	detect_bouts
tolerance	xinhui_bout_algorithm
generate_sequence_map	add_symbols
shorting.map	structure_per_day
long.map	structure_per_recording

[vincentvanhees]

Further I think argument "tolerance_function" should be replaced bout_algorithm.

Detecting bouts and using a certain tolerance is effectively part of the same algorithm. We currently have bout_algorithm V1 (Xinhui) and V2 (mine).

[vincentvanhees]

@Anne-Linde let's discuss this next week, before we start implementing any of this.

[Anne-Linde]

renamed function generate_sequence_map to add_symbols instead of add_class_labels. I find class labels confusing: I take that as intensity classes

[Anne-Linde]

Renamed list items

In function	Old name	Proposed new name
run_pipeline	short_sequence	sequence_day_level
run_pipeline	long_sequence	sequence_recording_level
generate_sequence	short_mapping	day_level_mapping
generate_sequence	long_mapping	recording_level_mapping
generate_sequence	short_mapping_length	day_level_mapping_length
generate_sequence	long_mapping_length	recording_level_mapping_length

Renamed function arguments

In function	Old name	Proposed new name
structure_per_recording	short_mapping	day_level_mapping
structure_per_recording	short_mapping	day_level_map
structure_per_day	short_mapping	day_level_mapping

Renamed variable names

In function	Old name	Proposed new name
run_pipeline & generate_sequence	short_mapping	day_level_mapping
run_pipeline & generate_sequence	long_mapping	recording_level_mapping
run_pipeline & generate_sequence	short_mapping_length	day_level_mapping_length
run_pipeline & generate_sequence	long_mapping_length	recording_level_mapping_length
generate_sequence	map_per_day	map_loop_day
main.script.R	sm_short	sm_day_level
main.script.R	sm_long	sm_recording_level