The method has a Matlab version and R version. The Matlab version codes are in this repository. The R version is on CRAN (click)
Here is the tutorial on both versions. (click)
This repository contains these files:
Simulation folder:
'uvax.mat': simulated ln lambda in Web Figure 1;
'examplefitted.csv': Example data for Web Figure 2.\
Real Data folder:
'alldataX.mat': ORIGINS data. (not included. Please email us if you need it.)
'originsdataMar2017.csv': Original ORIGINS data. (not included. Please email us if you need it.)
'finaluv.mat': ZIPFA results on ORIGINS data.
'final_u.csv'/'final_v.csv': ZIPFA results on ORIGINS data.
'lsvd_u.csv'/'lsvd_v.csv': log-PCA results on ORIGINS data.
'gomms_u.csv'/'gomms_v.csv': gomms results on ORIGINS data.
'psvdos_u.csv'/'psvdos_v.csv': psvdos results on ORIGINS data.
'pcoa_u.csv': PCoA results on ORIGINS data.
'nmds_u.csv': nMDS results on ORIGINS data.
'taxa.csv': Taxa name list.
'our_result.xlsx': Data for figure 5.\
'ZIPFA.m': Zero inflated Poisson factor analysis.
'cv_ZIPFA.m': Cross validation on ZIPFA.
'EMzeropoisson_mat.m': Zero inflated Poisson regression.
'Examples codes.m': Example runs for 'EMzeropoisson_mat','ZIPFA','cv_ZIPFA'.\
'Table and Figure in paper.m': All tables and figures in the paper. \
'gomms.R': GOMMS model.
'Simu.R': Some tables and figures in the paper. \
Accessory folder:
'cluster_fit.m'/'heatmap.m'/'pnew.m'/'hatchfill2_r8'/'FTM': Accessory codes. \