Getting started

To install Nuée, double-click "Nuee-Setup-<version>.exe" and follow the steps: for you alone (no administrator rights needed) or for every user of the computer. R is included. Nuée appears in Settings › Apps › Installed apps, where it can be uninstalled; projects and settings are kept.

If Windows shows "Windows protected your PC" (unknown publisher), click "More info", then "Run anyway".

For IT departments installing Nuée on many computers (silent installation, Intune, Configuration Manager, Group Policy, turning the update check off): the deployment guide, https://github.com/4rtefakt/nuee/blob/main/docs/deploiement.md

On Linux, Nuée uses the computer's R.

Debian, Ubuntu and their derivatives: sudo apt install ./Nuee-<version>-amd64.deb also installs R and the R packages needed. Nuée appears in the applications menu.
Other distributions: Nuee-<version>-x86_64.AppImage (make it executable, then run it) or Nuee-<version>-x64.tar.gz (unpack it, then run ./nuee). Install R first, then in R: install.packages(c("httpuv", "jsonlite", "openxlsx", "haven", "readxl", "foreign", "nlme", "mgcv", "MASS", "rpart", "cluster", "RSQLite", "ranger")).

.usp projects need python3. For another R than the PATH's: start Nuée with RSCRIPT=/path/to/Rscript. Settings are in ~/.config/Nuee.

Opening

File › Open (Ctrl+O):

a .usp project: the data, models and results stored in the file;
a project saved by the application (.nuee; .json for versions before 0.9.1);
a table, one row per observation:
```
Excel .xlsx, .xlsm, .xls        text .csv, .txt, .tsv (separator, decimal comma and
R .rds, .RData                    encoding detected, Excel's "Unicode text" included)
SPSS .sav, .zsav, .por          SAS .sas7bdat, .xpt
Stata .dta                      dBase .dbf, Weka .arff
jamovi .omv                     spectra: JCAMP-DX .jdx, .dx, .jcm and SPC .spc (see Spectra)
GeoPackage .gpkg (a layer of QGIS: see Maps and spatial data)
```
An export of KoboToolbox or ODK Central (.xlsx, .csv, or ODK's .zip) is recognised by its columns and opens through its import (see Field data from KoboToolbox or ODK).

The first column names the observations if it holds text, or if it is called "ID", "Obs", "Name"... (for an R file, the row names). Other text columns whose values all differ (one code per observation) become secondary identifiers: they serve as labels but don't enter the models. The remaining text columns, R factors and labelled SPSS or Stata variables are qualitative variables (in the order of their categories). For a workbook with several sheets, or an R file with several tables, the application asks which one to open.

A column of measurements with a few text cells (<0.5, <LOD, nd, n.d., #N/A...) stays a quantitative variable: those cells are read as missing, and the status bar says how many, in which variables (and which are below the detection limit). Excel dates and times stay dates (2024-05-03), as text, like those of a text file (as written: 14/05/2019) or of R: a column of dates is a qualitative variable when dates repeat (sectors counted the same day), a secondary identifier when they all differ, the observation names when it is the first column (move it further to make it a time); variable or identifier, it can be the time (see Dates as time). An Excel number without a date format (43599) stays a number. A text file with a line holding more values than the header is refused, with the line number, rather than shifting the columns. An R file must hold tables; any other object is refused. R files open only with R 4.4 or newer (included on Windows): with an older R, such as that of Ubuntu 22.04 or 24.04 or Debian 12, a .rds or .RData file could run code as soon as it is read (CVE-2024-27322), so Nuée refuses it; save the table as CSV or Excel instead.

File › Paste a table (Ctrl+V): cells copied from Excel, LibreOffice, Google Sheets or jamovi become a project (the first row gives the variable names). The project has no file yet: save it (Ctrl+S).

File › Import from KoboToolbox or ODK...: the phone surveys exported by KoboToolbox or ODK Central (see Field data from KoboToolbox or ODK).

File › Import spectra: files of spectra made into one project (see Spectra).

Dropping files on the window (drag and drop from Explorer) opens them the same way: JCAMP-DX or SPC spectra together make one project, as Import spectra; other files each open as with File › Open. Double-clicking a .nuee project in Windows Explorer opens it in Nuée (in the window already open, if there is one).

The last files opened are in File › Open recent.

To try it: Help › Example project opens 120 made-up apples (four varieties, organic or conventional growing, a dozen measurements and a tasting score) with four ready models: a PCA, a PLS of the score, a PLS-DA of the varieties and an OPLS-DA of the growing method. The original table, orchards.csv, is next to it (resources\exemple), to try opening a table.

Saving and getting your work back

File › Save project (Ctrl+S) writes the project (.nuee) with its data, its models and the current session: fitted models, open panels and their layout, plot settings (axes, colours, labels, titles), selections, VIP choices, dendrogram groups. When the project is opened again, the models are refitted and everything comes back in place.

The project is written to a file next to the old one, which then takes its place: a network cut or a full disk during the save leaves the old file intact. If another program keeps the file open (a sync client, an antivirus), Nuée tries again for five seconds, then leaves it as it was and says so: save again, or Save as.... If the file was changed elsewhere since you opened or saved it (a colleague, on a shared folder; another window), Nuée says so and offers Save as..., Overwrite or Cancel, also for a project recovered after a crash. The file also records which versions of Nuée and R wrote it; a project saved by a newer Nuée is pointed out when it opens.

Opening a file that is already open (a recent file, a double-click in Explorer) shows the open project instead of opening a second copy.

Closing the application with unsaved changes offers "Save and close". Every two minutes it also keeps a recovery copy of unsaved projects: if it stops without being closed (crash, power cut), it offers to recover them at the next start. Closing that question without an answer keeps the copies for next time; only "Ignore" deletes them.

Edit › Undo (Ctrl+Z) takes back the last change to a project's data (edited value, new variable, class, scores as variables, deleted definition...), up to 20 steps back.

Notes: each model's summary has a notes area, saved with the project and included in the report; a pencil marks it in the explorer.

Removing a model (Model › Delete model) asks for confirmation. Its definition stays in the project; for a model made in the application, a checkbox removes it as well (undoable).

If the R engine stops

The application says so and offers to restart it; you can also do it yourself (Help › Restart the R engine) if a computation doesn't finish. Projects reopen with their models and views, from their recovery copy if they had changes, otherwise from the file they save to; changes made since the last recovery copy (two minutes at most) are lost. Closing Nuée when the engine no longer answers keeps the recovery copies, offered at the next start. After a minute of computing, the status bar says so.

Help › What's new: the changes in each version (shown once after an update). The installed copy (Nuee-Setup, or the Linux packages) looks for a new version at start-up (a single request to GitHub, nothing else is sent) and mentions it in the status bar; on Linux, a click opens the version's page. On Windows, one click offers to update: the installer is downloaded and checked (its SHA-256 checksum must be the one GitHub gives), then Nuée closes (offering to save the projects you changed), installs it and starts again. For an installation for all users, Windows asks for permission. Help › Check for updates does the same at any time, even with the start-up check off; Help › Look for a new version at start-up turns the check off.

The explorer (on the left)

Projects, data, models imported from a .usp file, fitted models and their views.

Double-click: open. Right-click: every action (fit, edit, add or remove a component, export, delete...). Double-clicking an imported model refits it in R; the Summary marks each value: "=" the same as the value stored in the file, "≈" close (less than 0.01), "≠" different. Q2 usually differs: an imported model is validated like the others (see "Cross-validation"); "Full model's centres and weights" gives back the file's.

Menus and toolbar

File, Edit, Model, Plots, Predict, Window, View, Help. Shortcuts:

Ctrl+O open              Ctrl+S save                Ctrl+E export the results
Ctrl+V paste a table
Ctrl+N new model         Ctrl+M edit the model      Ctrl+= / Ctrl+- components
Esc    clear the selection       Ctrl+Del exclude the selection and refit
Ctrl+Shift+N new window          Ctrl+Shift+D detach the panel    Ctrl+W close the panel
Ctrl+B explorer          F1 guide

View: dark theme, French / English, text size.

Windows

In the centre, one tab per model ("M1 · PLS"), and a tab for each view of the project (Data, Variable statistics, History). A model's tab is its page: its summary on the left, its scores and loadings on the right; its other views (VIP, DModX...) join it as tabs. Choosing a model in the explorer shows its page; closing a page's last view closes the page.

In a page as in the centre, views move by their tab (drag and drop), split and stack; dragging a model's tab next to another one compares two models. Right-click on a tab, or the icon at the top right of a group: detach into its own window (on a second screen, for example), maximise, close.

Window › New window opens a second full window. A selection of observations (box or lasso in a plot, click on a point or a list row) shows in every view and every window of the same model.

Plots: mouse wheel to zoom; right-click to copy or save the image (PNG, SVG), see the selection's contributions or make it a class.

Ctrl+C in a view that shows a table (summary, lists, statistics...) copies the table as tab-separated text, to paste into Excel (a list: all its rows, at full precision); with text selected, Ctrl+C copies the text as usual.

View › Find a command (Ctrl+K): type part of the name of a command or of its menu ("vip", "export r"), then Enter.

Help › Diagnostic information: the versions of Nuée, the system, R and its packages, to paste into a report of a problem (github.com/4rtefakt/nuee/issues; no paths, no data).

This page is part of the guide installed with Nuée (USER-GUIDE.txt, also in Help › User guide).