dev_history.R

#' Document functions and dependencies
#' attachment::att_to_description()
#' Check the package
#' devtools::check()

  #' 09/05/2022
#' Added tabs as modules (inputDF, your_data, data_structure, analysis, plots)
#' added observer code to populate boxes after uploading data and metadata
#' showing the list of uploaded files

  #' 10/05/2022
#' Add a function that checks if both data and metadata are present to then 
#' unlock the Data structure tab item
#' in utils_checks.R see check_uploads()
#' initialise data structure appearance hiding various sections

  #' 11/05/2022 
#' initialise data inside Raw_mouse_data object, creating myMice
#' function to convert 12/24h format separated from Raw_mouse_data::add()
#' function and added to utils_converters::convert_time()
#' !Problem! magrittr pipe operator doesn't work when used in modules

  #' 12/05/2022
#' separated R6 factory into different fct modules, one for each R6 object
#' help buttons connected 

  #' 13/05/2022
#' tried to make load data work. ATM not working because of setListMice fun


  #' 14/05/2022
#' connected Load data button with loadData function
#' created Clean_mouse_data object
#' created Annotate object
#' created Custom_tables object
#' rendered YourData and Analysis tabs
#' fixed help buttons 


  #' 16/05/2022
#' fixed wrong subsetting and assignment in setListMice, now data display
#' in yourData tab works

  #' 17/05/2022
#' started making dynamic rendering of DataStructure box 1 choices
#' activate observers to change UI in DataStructure

  #' 18/05/2022
#' activating functions in Custom_tables: Behavr_table,
#' Connect ui to functions in Custom_tables
#' 

  #' 19/05/2022
#' finish Behavr_table activation
#' activate HHActivity, dailyAct
#' mod_box_plot_fct_plotter module to generate boxes to show plots

  #' 20/05/2022 
#' connect buttons in Analysis tab to DP actogram, dailyActivity, HHActivity,
#'     and computePer

  #' 22/05/2022
#' connected computePer function

  #' 25/05/2022
#' activate Plot tab when any print button is clicked
#' insertUI() to insert a box with a plot every time a new plot is generated
#' couple the generated box with the plot that is generated: when the printing
#'     function is called there are other functions called:
#'     - generate the plot and store it in Annotate
#'     - render that plot inside the box, where the placeholder "plot_hold" is

  #' 26/05/2022
#' continue to 

  #' 31/05/2022
#' tried to fix the issue with insertUI for a long time. Problem with namespacing
#' inside the nested module, hard to solve because the placeholder struggles
#' to use ns(id) on the placeholder
#' moving to renderUI, with the caveat of generating only one box per type
#' of analysis

  #' 03/06/2022
#' move server actions belonging to modules inside module
#' access values inside modules using return()
#' App not lauching because of problem with output from Datastructure module
#' not able to return multiple values inside the same obj.

  #' 04/06/2022
#' cleaned code using modules properly until Analysis
#' now using output from modules to control action of following mod
#' use pretty buttons
#' render box_plot inside plots with random plot
#' print plots in boxes

  #' 05/06/2022
#' make downloadButton functional
#' managed to generalise plotting for actograms but for loop containing 
#'     renderUI doesn't work well when trying to plot multiple plots at the
#'     same time. It works if only one plot is selected and printed and then
#'     repeated

  #' 06/06/2022
#' change values of checkbox input to make them unique
#' expand table to include all plots
#' expand plotting to other plots -> need to debug the function

  #' 12/06/2022
#' Activate daily activity plotting

  #' 29/06/2022
#' Activate periodograms, still not displaying correctly

  #' 07/07/2022
#'  Fix plot generation
#'  Periodgrams are not generated upon request. Individual periodogram is 
#'      generated but when called inside mod_box_plot.R it appears as table 
#'      and cannot be loaded correctly by renderPlot()

  #' 08/07/2022
#'  Fixed display of periodograms
#'  Fix LD settings

  #' 11/07/2022
#'  make downloadButtons for tables available (data table, behavr Table, sum of 
#'      daily activity, period data)
#'  Create download function download_obj()
#'  donwload function not working for plots, still using old function

  #' 12/07/2022  
#'  Create custom Rhandsontable to write and download metadata

  #' 13/07/2022
#'  Fix double plotted actos
#'  fix DD plotting

  #' 14/07/2022  
#'  fixed data table not displaying data correctly
#'  changed buttons to prettyRadioButtons

  #'  16/07/2022
#'  review HHactivity function

  #'  21/07/2022
#'  add download buttons for data in mod_box_plot
#'  activate HHActivity fun plotting
#'  create Avg day of activity divided by id, sex, genotype
#'  problem with subscript in plotting genotype averaged

  #'  22/07/2022
#'  solve problem with plotting
#'  align avg day plot to start with lights on
#'  increased axis labels and titles size
#'  activate subsetting box

  #'  26/07/2022
#'  fixed subsetting not working for line plots

  #' 02/08/2022
#'  changed landing page

  #' 03/08/2022  
#'  create function to export 1st value of periodogram peak (done)
#'  create exportable wide format total activity table (done)
#'  export average day of activity table (done)
#'  SEM vs SD plotting option in line plots (done)
#'  change order of boxes in plots (done)
#'  manage error when not selecting animals in subsetting (started)

  #' 04/08/2022
#'  finish error handling in data subset (DONE?)
#'  change sidebar menu behaviour (done)

  #'  07/08/2022
#'  activate box in plots only if plots are inside (not working with
#'      shinyjs::hide() or shiny::hideTab())
#'  create plot of period distribution (done)
#'  activate download button only after plot generation (done)
#'  link skip row button (done)
#'  solve RMD check prob (done)

  #'  08/08/2022
#'  fix RMD checks failure (done)
#'  change print1 name (done)

  #'  09/08/2022
#'  update help buttons
#'  if time subsetting recompute LD values subtracting timeRange[1] to ddStart (done)
#'  clean data structure from unnecessary parts
#'  activate options to download different table (changed to first peak table)
#'  error when subsetting with no animal selected (done)

  #' 13/09/2022
#'  started planning the addition of new factors in metadata + some general comments

  #' 15/09/2022
#'  added optional factors in myMice and myCleanMice objects
#'  added optional factors in add and compile functions

  #' 16/09/2022
#'  add data reduction for datasets that are longer than x


  #'  09/08/2022
#'  update help buttons
#'  if time subsetting recompute LD values subtracting timeRange[1] to ddStart (done)
#'  clean data structure from unnecessary parts
#'  activate options to download different table (changed to first peak table)
#'  error when subsetting with no animal selected (done)

  #'  14/10/2022  
#'  write help messages (half done)
#'  implement timepoint setting (done)
#'  implement real time setting (done)
#'  remove time windows subsetting (done)
#'  help button in LD cycle settings (done)
#'  help button in Load files (done)
#'  implement display full metadata
#'  implement display full metadata
  
  #'  14/11/2022
#'  added code to create tables to be exported as actogram data

  #'  15/11/2022
#'  activated exporting of other tables from actograms
#'  activated exporting of wide table for sum of daily activity
#'  activated exporting of wide table for average day of activity

  #'  22/11/2022
#'  created functions to export means and errors for average day tables

  #'  30/11/2022  
#'  handle error when the wrong type of file is uploaded in metadata
#'  to change from line 64 in fct_R6_Raw_mouse_data

  #'  13/10/2023
#'  uploaded R verion to 4.3.1

  #' To be implemented
#' finish adding custom table divided by sex or genotype for average day and total activity (to be activated)
#' 
#' #'  in the future add more tables: with different statsrelative to timeseries 
#'  data. SD of data, and all the parameters that is possible to obtain using 
#'  the rethomics package and others
#'  
#'  Think about shading problem in single line actograms (shade is too light +
#'      there are different level of opacity based on the number of lines in 
#'      the plot. How to account for that)
#'      
#'  Create wide table output for sum of daily activity table (done)
#'  
#'  Box not having unique names in each section of the plotting tab
#'  
#'  Select a specific subset of data to be analysed for periodogram
#'  
#'  only extract period with peak = 1 for data outputted from periodograms (done)
#'  
#'  remove period boxplots that are not generated (first two)
#'  
#'  make wide table output for average day of activity (done)
#'  

#' PRIORITIES
#' - add optional factor
#' - Think of a new name that is not taken on CRAN (RACETrack)
#' - check workflow for data upload
#' - activate functions to display/hide elements in Datastructure tab
#' - remake analysis tab with more user friendly flipbox
#' - update help buttons
#' - RMarkdown document
#' - Filtering for analysis of activity only at specific times of day 
#'     (only for sum of daily activity)

#' CODING
#'     option selection. See mod_analysis for details.
#' - when generating periodograms, add option for analysisng only DD period     
#' - activate option when plotting individual plots to select for ids
#' - create analysis presets (e.g. 1 periodogram, 1 daily activity, 1 periodogram, etc..)
#' - In plots, hide tabs that do not contain any plot
#' 
#' UI
#' - Make periodogram selection more visual, introducing actogram preview
#'     to decide where to place boundaries for analysys, or preview of available 
#'     plots.as a big box with previews in the right and command selection on 
#'     the left.Could be triggering from flipbox if possible to switch between 
#'     objects.
#' - Update landing page
#' - redesign plotting to be more user friendly, use of boxes to display
#'     plots. Box are generated from module call 
#'     (mod_box_plot_ui() + mod_box_plot_server()), which generates a new box each
#'     time is called.
#' 
#' WRITING
#' 
#' - write documentation for R6 objects
#' - rewrite documentation for all @param, @field and @return 
#' - go through foo and fix when passing env to follow a std way
#'
#' FIXINGS 
#' 
#' - problem with significance threshold in LS periodogram when timeserience are long
#' - fix updating of LD information
#' - add error if not selecting any id when subsetting time
#' - select an option that when plotting individual double plotted actograms caps
#'     the maximum number to four
#' - when time subsetting recompute the LD cycle settings accordingly
#' - make download buttons in analysis appear after tables have been generated
#' - All boxes display the same title
#' - all plots being exported with the same title
#' 
#' To do: 
#' 
#'     : create a function to filter data based on ZT (i.e. extract only data 
#'     about the dark phase)
#'     
#'     : Below the data subsetting box, create action buttons to start new 
#'     analyses, like actogram, Daily activity, etc. Use 
#'     shinydashboardPlus set of new ui objects to make it sexy. Each time a 
#'     new Analysis is generated, either flip the card and ask for parameters
#'     settings or open a box where the user can select all the parameters and
#'     see the output.
#'     
#'     : make plot tab as nested moduled with each new horizontal tab is appended 
#'     next to the previous and contain all the analyses submitted to that plot type.   
#'     
#' Questions:
#' 
#'  - Is it possible to write automations that bring the app to a specified point?
#'      Useful for testing (bring the app to a certain state), but the experienced 
#'      user could use it to chain processes and speed up analyses across platforms. 
#'      Feature, generator of code for automations in the app sort of Macro recorder.
#'      
#' Solved questions:
#' 
#' - #' - is it possible to have an observer from inside a module?
#'     Yes, if the object to observe is correctly namespaced in the UI and the
#'     server is related to that UI.
#' - is it possible to generate multiple boxes by reusing the same module?
#'     and how to put the placeholder in the ui file? -> use insertUI() coupled
#'     with a placeholder div(id = "")
#'