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 |
biqdODE_plot_all |
plot all decompose plot for two data |
biqdODE_plot_base |
plot single decompose plot for two data |
biQ_function |
Q-function to replace log-likelihood function |
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 |
gut_microbe |
gut microbe OTU data (species level) |
legendre_fit |
generate curve based on legendre polynomials |
logsumexp |
calculate log-sum-exp values |
mustard_microbe |
mustard microbe OTU data |
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 |
qdODEmod |
quasi-dynamic lotka volterra model |
qdODEplot_convert |
convert qdODE results to plot data |
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 |
Q_function |
Q-function to replace log-likelihood function |