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Data

The example data sets.

scurve
S-curve dataset with noise dimensions
scurve_model_obj
Object for S-curve dataset
scurve_plts
List of plots
scurve_umap
UMAP embedding for `scurve` with n_neighbors = 15 and min_dist = 0.1
scurve_umap_predict
Predicted UMAP embedding for `scurve` data
scurve_umap2
UMAP embedding for `scurve` with n_neighbors = 10 and min_dist = 0.4
scurve_umap3
UMAP embedding for `scurve` with n_neighbors = 62 and min_dist = 0.1
scurve_umap4
UMAP embedding for `scurve` with n_neighbors = 30 and min_dist = 0.5
scurve_umap_rmse
Summary with different number of bins for `scurve_umap`
scurve_umap_rmse2
Summary with different number of bins for `scurve_umap2`
scurve_umap_rmse3
Summary with different number of bins for `scurve_umap3`
scurve_umap_rmse4
Summary with different number of bins for `scurve_umap4`

Data preprocessing

These are for data preprocessing.

gen_scaled_data()
Scaling the NLDR data

Hexagonal binning

These are for hexagonal binning.

calc_bins_y()
Calculate the effective number of bins along x-axis and y-axis
gen_centroids()
Generate centroid coordinate
gen_hex_coord()
Generate hexagonal polygon coordinates
assign_data()
Assign data to hexagons
compute_std_counts()
Compute standardise counts in hexagons
hex_binning()
Hexagonal binning

2-D model construction

These are to construct the 2-D model.

extract_hexbin_centroids()
Extract hexagonal bin centroids coordinates and the corresponding standardise counts.
extract_hexbin_mean()
Extract hexagonal bin mean coordinates and the corresponding standardize counts.
tri_bin_centroids()
Triangulate bin centroids
gen_edges()
Generate edge information
update_trimesh_index()
Update from and to values in trimesh data

Parameters

These are to compute default parameter values.

compute_mean_density_hex()
Compute mean density of hexagonal bins
find_low_dens_hex()
Find low-density Hexagons

Lift to high dimensions

The function is to lift the constructed 2-D model into high-dimensions.

avg_highd_data()
Create a tibble with averaged high-dimensional data

Fit the model

The function is to fit the model.

fit_highd_model()
Construct the 2-D model and lift into high-dimensions

Model summaries

These are to obtain model summaries.

glance()
Generate evaluation metrics
predict_emb()
Predict 2-D embeddings
augment()
Augment Data with Predictions and Error Metrics
gen_diffbin1_errors()
Generate erros and MSE for different bin widths
plot_rmse_layouts()
Arrange RMSE plot and 2-D layouts

2-D visualisation

These are to visualise the model in 2-D.

GeomHexgrid
GeomHexgrid: A Custom ggplot2 Geom for Hexagonal Grid
stat_hexgrid()
stat_hexgrid Custom Stat for hexagonal grid plot
geom_hexgrid()
Create a hexgrid plot
GeomTrimesh
GeomTrimesh: A Custom ggplot2 Geom for Triangular Meshes
stat_trimesh()
stat_trimesh Custom Stat for trimesh plot
geom_trimesh()
Create a trimesh plot

High-dimensional visualisation

These are to visualise the model in high-dimensional space.

comb_data_model()
Create a tibble with averaged high-dimensional data and high-dimensional data
show_langevitour()
Visualise the model overlaid on high-dimensional data

Projection

These are to generate 2-D projections from tour.

gen_axes()
Generate Axes for Projection
get_projection()
Compute Projection for High-Dimensional Data
plot_proj()
Plot Projected Data with Axes and Circles

These are to diagnoise with interactivity.

comb_all_data_model()
Create a tibble with averaged high-dimensional data and high-dimensional data, non-linear dimension reduction data
show_link_plots()
Visualise the model overlaid on high-dimensional data along with 2-D wireframe model.
comb_all_data_model_error()
Create a tibble with averaged high-dimensional data and high-dimensional data, non-linear dimension reduction data, model error data
show_error_link_plots()
Visualise the model overlaid on high-dimensional data along with 2-D wireframe model and error.

Additional

These are additional functionalities.

find_pts()
Find points in hexagonal bins
find_non_empty_bins()
Find the number of bins required to achieve required number of non-empty bins.
gen_design()
Generate a design to layout 2-D representations
quad()
Solve Quadratic Equation for Positive Real Roots
calc_2d_dist()
Calculate 2-D Euclidean distances between vertices