## ----include=FALSE------------------------------------------------------------ require(knitr) opts_chunk$set(concordance=TRUE,tidy=TRUE) ## ----config,echo=FALSE----------------------------------------- options(width = 65) options(continue=" ") options(warn=-1) ## ----pkg_install,eval=FALSE------------------------------------ # if(!requireNamespace("BiocManager", quietly = TRUE)){ # install.packages("BiocManager") # } # BiocManager::install("microbiomeDASim") ## ----tr_ex,fig.align='center',fig.height=4,fig.width=6,warning=FALSE,tidy=FALSE---- require(microbiomeDASim) triv_ex <- mvrnorm_sim(n_control=10, n_treat=10, control_mean=2, sigma=1, num_timepoints=2, t_interval=c(1, 2), rho=0.8, corr_str="ar1", func_form="linear", beta= c(1, 2), missing_pct=0, missing_per_subject=0, dis_plot=TRUE) head(triv_ex$df) triv_ex$Sigma[seq_len(2), seq_len(2)] ## ----hockey_stick, fig.align='center', fig.height=4, fig.width=6, tidy=FALSE---- true_mean <- mean_trend(timepoints=1:10, form="L_up", beta=0.5, IP=5, plot_trend=TRUE) hockey_sim <- mvrnorm_sim(n_control=10, n_treat=10, control_mean=2, sigma=1, num_timepoints=10, t_interval=c(0, 9), rho=0.8, corr_str="ar1", func_form="L_up", beta= 0.5, IP=5, missing_pct=0, missing_per_subject=0, dis_plot=TRUE, asynch_time=TRUE) ## ----bug_gen, tidy=FALSE--------------------------------------- bug_gen <- gen_norm_microbiome(features=6, diff_abun_features=3, n_control=30, n_treat=20, control_mean=2, sigma=2, num_timepoints=4, t_interval=c(0, 3), rho=0.9, corr_str="compound", func_form="M", beta=c(4, 3), IP=c(2, 3.3, 6), missing_pct=0.2, missing_per_subject=2, miss_val=0) head(bug_gen$bug_feat) bug_gen$Y[, 1:5] names(bug_gen) ## ----session_info---------------------------------------------- sessionInfo()