User guide

Nuée’s full guide, in pages. It is the guide installed with the application (Help › User guide › Full guide), written for version 1.0.0. To start with, the tutorials follow three studies from start to finish.

• Getting started — Installing, opening a table, saving and getting your work back, the explorer, the menus, the windows.
  • Getting started
  • Opening
  • Saving and getting your work back
  • If the R engine stops
  • The explorer
  • Menus and toolbar
  • Windows
• The data — Field data from KoboToolbox or ODK, editing the data, making variables, cleaning, joining another table, summarizing by group, dates.
  • Field data from KoboToolbox or ODK
  • Editing the data, making variables
  • Cleaning the data: find and replace, categories, units
  • Adding columns from another table
  • Summarizing by group
  • Variable statistics
  • Dates as time
• Choosing and building a model — Which analysis?, New model, the observations, cross-validation, the test set, predicting.
  • Which analysis?
  • New model
  • Observations chosen by a condition
  • Cross-validation
  • Test set
  • Predicting
  • Hierarchical models
• Plots and figures — Colours and labels, formatting, contributions, figures for publication.
  • Plots: colours and labels
  • Other plots
  • Formatting plots
  • Contributions
  • Figures for publication
• PCA, PLS, OPLS and spectra — OPLS, VIP, validating a PLS, class models, spectra and their preprocessing.
  • OPLS and OPLS-DA
  • VIP
  • Validation
  • Class models and the Coomans plot
  • Spectra
• Linear, generalized and mixed models — Regressions, mixed models, GLMs and GAMs, model conditions, adjusted means, AIC selection, one model per response.
  • Linear, generalized and mixed models
  • One model per response
• Statistical tests — Between classes, between two variables, paired tests, correlation matrix, before/after (BACI).
  • Statistical tests
• Community ecology — RDA, CA, CCA, indicator species, rarefaction, PCoA, NMDS, PERMANOVA, Mantel test.
  • Redundancy analysis and correspondence analysis
  • Canonical correspondence analysis
  • Indicator species
  • Rarefaction and species accumulation
  • PCoA, NMDS, PERMANOVA and Mantel test
• Monitoring: series, TRIM, distance sampling — Series and trends, indices and trends of counts (TRIM), density and abundance by distance sampling.
  • Series
  • TRIM: indices and trends of counts
  • Distance sampling: density and abundance
• Maps and spatial data — Coordinates and the map, GeoPackage and QGIS, raster values, spatial autocorrelation.
  • Maps and spatial data
• Trees, forests, discriminant analysis, k-means — Decision trees, linear discriminant analysis, k-means, random forests, boosted trees.
  • Decision trees, linear discriminant analysis and k-means
  • Random forests and boosted trees
• Results, documents and R — Methods text, report, documents with citations, exports to other software, Export to R, R console.
  • Methods text
  • Model report
  • Documents
  • Exporting to other software
  • Export to R
  • R console
  • The code
• .usp projects — The file history, what matches the stored values and what differs.
  • File history
  • What matches the stored values
  • What differs

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