README.md

In dynverse/dyneval: Evaluating trajectory inference methods

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Metrics to compare two trajectories

This R package implements several metrics for comparing two single-cell trajectories.

These include:

• Specific metrics, metrics which look at the similarity of a specific part of the trajectory, such as the topology or the cellular ordering

| Name | Long name | Category | | :------------------------- | :--------------------------------- | :---------------- | | cordist | Geodesic distance correlation | cell positions | | MSErf | Random Forest MSE | neighbourhood | | NMSErf | Random Forest Normalised MSE | neighbourhood | | R2rf | Random Forest R² | neighbourhood | | NMSElm | Linear regression Normalised MSE | neighbourhood | | MSElm | Linear regression MSE | neighbourhood | | R2lm | Linear regression R² | neighbourhood | | edgeflip | Edge flip | topology | | HIM | Hamming-Ipsen-Mikhailov similarity | topology | | Isomorphic | isomorphic | topology | | F1branches | Overlap between the branches | branch assignment | | F1milestones | Overlap between the milestones | branch assignment |

• Application metrics, which assess the accuracy of some downstream analyses of trajectories

| Name | Long name | | :----------------------- | :-------------------------------------- | | corfeatures | Feature importance correlation | | wcorfeatures | Feature importance weighted correlation | | ksfeature | Feature importance enrichment ks | | wilcoxfeature | Feature importance enrichment wilcox |

• Overall metrics, which combine several specific and/or application metrics to analyse the overall similarity of two trajectories

| Name | Long name | | :------------------------ | :-------------- | | meanharmonic | Harmonic mean | | meangeometric | Geometric mean | | meanarithmetic | Arithmetic mean |

Latest changes

Check out news(package = "dyneval") or NEWS.md for a full list of changes.

Recent changes in dyneval 0.9.9 (07-04-2019)

• MINOR CHANGE: Update categories of metrics

• MINOR CHANGE: Move metric functions from dyneval to dynutils.

• MINOR CHANGE: Bump version number for dynwrap 1.0.0

Recent changes in dyneval 0.2.2 (21-11-2018)

• DOCUMENTATION: Update and expand documentation.

• BUG FIX: Update dyneval for dynwrap 0.3.1 (#50).

• MINOR CHANGE: Clean up imports and suggests.

Dynverse dependencies

dynverse/dyneval documentation built on May 25, 2019, 4:25 p.m.