Download the repository and, as necessary, update installed R packages from the dependency list below. Run the font setup.R admin tool line by line.
tidyverse >= 2.0.0
data.table >= 1.14.6
ggplot2 >= 3.4.0
glue >= 1.6.2
openxlsx >= 4.2.5.1
psycho >= 0.6.1
R.matlab >= 3.7.0
zip >= 2.2.2The versions of many of these packages matter, particularly openxlsx and the tidyverse packages. Be sure to update to at least the listed versions of the dependencies above.
Throughout each day, persons responsible for running the experimental boxes (probably undergraduates) will run app.R, filling out the form for an individual rat's run and using the file picker (the Browse... button) to select the corresponding .mat file, then press Analyze. The user will be asked to examine two graphs (and possibly more, if there are any concerns raised by the initial two) to verify that the rat's weight and trial count trends are acceptable, that the data looks accurate and consistent with this rat's prior performance, etc. Once there is high confidence that the data is good and belongs to the named rat, the user will choose 'Save Run' at which point the results will be added to the archives on disk.
At the end of the day, the person responsible for making the assingments to be used the next day will run supervisor-summarize.R. It will create and open a summary .xlsx (Excel) file that displays the data and statistics for each rat that are used in choosing assignments. The supervisor will use the drop-down menus and the filename entry field to specify the configuration files that each rat should next be run on. The supervisor can also leave a note on any rat that will remain until it is cleared, intended for e.g. planning ahead.
Adding a new experiment requires, at minimum, updating experiment_details.csv to add the new experiment and denote its corresponding phases. If the experiment uses existing phase types, no further work is required.
If new phase types are added, main.R and supervisor-summarize.R must be updated to correctly process them. Non-exhaustively, in main, Identify_Analysis_Type() and Build_Filename() will need new definitions, and it is possible that Calculate_Summary_Statistics() will also. In supervisor-summarize, Build_Counts() and the task-specific and phase-specific portions of Build_Table() will need updating. In addition, the phase's tasks and details will have to be listed in experiment_details.csv.
The new rat should be added to the rat_archive.csv file, either by opening it with a spreadsheet program or through R.
The rat_archive.csv file should be updated with the corresponding information. Never delete rows (rats) from the archive, simply update their end_date column.
Initial whiteboard - https://miro.com/app/board/uXjVO2HtI6U=/
The basic architecture is Model-View-Controller.
The *_archive.Rdata files contain the model, i.e. the storage of data. These include the rat_archive (CSV not Rdata), the run_archive, and the per-experiment trial archives (e.g. Fmr1-LE_archive).
The primary view is provided by supervisor-summarize.R. This script outputs a well-formatted .xlsx (Excel) file that allows the experimental supervisor to view summary data and statistics for the last several days for each rat, along with any warnings found when processing each day's files.
The primary controller is main.R, used through its frontend interface app.R. This file imports .mat files, which are the output from each run of the matlab control program. The data is converted into usable formats and the file is extensively checked for errors, especially mismatches between the expected or assigned parameters of that experimental run to the actual parameters used by the computer during the run. Data from the run's .mat file and input from app.R (such as the animal's current weight) is saved into the appropriate archives.
The supervisor-assign.R file, combined with the summary .xlsx file, also acts as a controller. This script transfers the future assignments (created by the supervisor using the summary sheet) to the model. This data is then checked against during main.R's execution.
settings.R - contains settings used by the main and supervisor scripts, such as the TH Cutoff, the desired minimum number of completed trials, or the amount of weight change required to trigger a warning message.experiment_details.csv - This file lists the active experiments, the phases that correspond to each experiment, and the tasks and details that correspond to each phase. Combined, this nomenclature specifies most of the parameters used to create the configuration files that are loaded into the matlab control program that specify the behavior of the experimental boxes. Future work is intended to use these parameters to generate the matlab configuration files directly; in 0.1-ALPHA these values are used for post-run validation instead.graphing unrolled.R - contains graph generation used by the shiny app.Several small scripts are available for those comfortable with R. Note that these have not been made user friendly or robust. Use at your own risk.
Load enviornment.R - This should be used following a cleaning of the global environment. It can be out of sync from mainCommon lookups.R - This contain short scripts that filter run_archive or rat_archive for information that I have looked up several times. These have not been made into functions.supervisor-summarize-custom.R - If you want to export something other than the default, use this script. Note it is identical to the common tool except for the addition of file_name = "supervisor.xlsx" that allows you to NOT overwrite the default output.check and backup.R - checks the trial counts between the run_archive and all the trial archives. Attempts to remedy any issues using code independent but similar to the remove entry.R and import_deleted_entries.R. KNOWN FAILURE CASE: if an entry is listed more than once, i.e. its been deleted more than once it will cause it to not know which one to use and so will not attempt to reload. Reduce to one entry.Modify an entry.R - This contains a quick way to set a run invalid, change the weight or assignment. It should be kept in the safe state i.e. comment out from = to the new value.remove entry.R - Use to clean poor entries. They are under active development to make them safe for others to use. Remove entry has been made into a function that backs-up deleted data and requires confirmation to use. Should typically be used in conjunction with import_deleted_entries, which will attempt to reload them based on the deleted_entries.csv.import_deleted_entries.R - Attempts to find any previously deleted entries (that have been recorded in the deleted_entries.csv) that have not already been re-entered and then auto-loads them. KNOWN FAILURE CASE: if an entry is listed more than once, i.e. its been deleted more than once it will cause it to not know which one to use and so will not attempt to reload. Reduce to one entry.Exporter.R - used to export the run_archive as a csv. This is a work in progress.Graphing (Weight).R - Similar but supervisor version of the weight graph shown during data entry. Has some extra data and is in a different color scheme.Graphing.R- Can be used to graph rxn or dprime similar to the one shown during undergrad data entry. Has additional settings like setting a specific cut off date. Shows fitted line with every point. For reaction graph points are colored by step size.fixer.R - a useful starting point for making repeated changes to run_archive. Note this script is NOT complete and requires modification for each explicit use. This is paritially intentional because it should NOT be used lightly.import_old_excel.R - This is a utility to read a directory tree and import information from the old experimental excel sheets that PiedPiper is designed to replace.