idopNetwork0.1.2 package

A Network Tool to Dissect Spatial Community Ecology

bifun_clu

main function for bifunctional clustering

bifun_clu_convert

convert result of bifunctional clustering result

bifun_clu_parallel

parallel version for functional clustering

bifun_clu_plot

bifunctional clustering plot

biget_par_int

acquire initial parameters for functional clustering

bipower_equation_plot

plot power equation fitting results for bi-variate model

biQ_function

Q-function to replace log-likelihood function

biqdODE_plot_all

plot all decompose plot for two data

biqdODE_plot_base

plot single decompose plot for two data

darken

make color more dark

data_cleaning

remove observation with too many 0 values

data_match

match power_equation fit result for bi-variate model

fun_clu

main function for functional clustering

fun_clu_BIC

plot BIC results for functional clustering

fun_clu_convert

convert result of functional clustering result

fun_clu_parallel

parallel version for functional clustering

fun_clu_plot

functional clustering plot

fun_clu_select

select result of functional clustering result

get_biSAD1

generate biSAD1 covariance matrix

get_interaction

Lasso-based variable selection

get_legendre_matrix

generate legendre matrix

get_legendre_par

use legendre polynomials to fit a given data

get_mu

curve fit with modified logistic function

get_mu2

generate mean vectors with ck and stress condition

get_par_int

acquire initial parameters for functional clustering

get_SAD1_covmatrix

generate standard SAD1 covariance matrix

legendre_fit

generate curve based on legendre polynomials

logsumexp

calculate log-sum-exp values

network_conversion

convert ODE results(ODE_solving2) to basic network plot table

network_maxeffect

convert ODE results(ODE_solving2) to basic network plot table

network_plot

generate network plot

normalization

min-max normalization

power_equation

use power equation parameters to generate y values

power_equation_all

use power equation to fit observed values

power_equation_base

use power equation to fit observed values

power_equation_fit

use power equation to fit given dataset

power_equation_plot

plot power equation fitting results

Q_function

Q-function to replace log-likelihood function

qdODE_all

wrapper for qdODE model

qdODE_fit

legendre polynomials fit to qdODE model

qdODE_ls

least-square fit for qdODE model

qdODE_parallel

wrapper for qdODE_all in parallel version

qdODE_plot_all

plot all decompose plot

qdODE_plot_base

plot single decompose plot

qdODEmod

quasi-dynamic lotka volterra model

qdODEplot_convert

convert qdODE results to plot data

Most existing approaches for network reconstruction can only infer an overall network and, also, fail to capture a complete set of network properties. To address these issues, a new model has been developed, which converts static data into their 'dynamic' form. 'idopNetwork' is an 'R' interface to this model, it can inferring informative, dynamic, omnidirectional and personalized networks. For more information on functional clustering part, see Kim et al. (2008) <doi:10.1534/genetics.108.093690>, Wang et al. (2011) <doi:10.1093/bib/bbr032>. For more information on our model, see Chen et al. (2019) <doi:10.1038/s41540-019-0116-1>, and Cao et al. (2022) <doi:10.1080/19490976.2022.2106103>.

  • Maintainer: Ang Dong
  • License: GPL (>= 3)
  • Last published: 2023-04-18