gen_norm_microbiome_obs {microbiomeDASim} | R Documentation |
Generate Longitduinal Differential Abundance from Multivariate Normal with Observed Data
gen_norm_microbiome_obs( features = 10, diff_abun_features = 5, id, time, group, ref, control_mean, sigma, rho, corr_str = c("ar1", "compound", "ind"), func_form = c("linear", "quadratic", "cubic", "M", "W", "L_up", "L_down"), beta, IP = NULL, dis_plot = FALSE, plot_trend = FALSE, zero_trunc = TRUE )
features |
numeric value specifying the number of features/microbes to simulate. Default is 10. |
diff_abun_features |
numeric value specifying the number of differentially abundant features. Default is 5. |
id |
vector of length |
time |
vector of length |
group |
factor vector with two levels indicating the group assignment for each respective id |
ref |
character value identifying which group value to treat as control and which value to treat as treatment |
control_mean |
numeric value specifying the mean value for control subjects. all control subjects are assummed to have the same population mean value. |
sigma |
numeric value specifying the global population standard deviation for both control and treated individuals. |
rho |
value for the correlation parameter. must be between [0, 1].
see |
corr_str |
correlation structure selected. see
|
func_form |
character value specifying the functional form for the
longitduinal mean trend. see |
beta |
vector value specifying the parameters for the differential
abundance function. see |
IP |
vector specifying any inflection points. depends on the type of
functional form specified. see |
dis_plot |
logical argument on whether to plot the simulated data or not. by default plotting is turned off. |
plot_trend |
specifies whether to plot the true mean trend. see
|
zero_trunc |
logical indicator designating whether simulated outcomes should be zero truncated. default is set to TRUE |
This function returns a list with the following objects
Y
The full simulated feature sample matrix where each row represent a
feature and each column a sample. Note that the differential and
non-differential bugs are marked by row.names
set.seed(011520) id_list <- lapply(seq_len(60), function(i){ obs <- sample(5:10, size=1) id_rep <- rep(i, obs) }) time_interval <- c(0, 10) time_list <- lapply(id_list, function(x){ time_len <- length(x) times <- runif(time_len, min=time_interval[1], max=time_interval[2]) times <- times[order(times)] }) group_list <- lapply(id_list, function(x){ group_len <- length(x) tx_ind <- sample(seq_len(2), 1) tx_group <- ifelse(tx_ind==1, "Control", "Treatment") groups <- rep(tx_group, group_len) }) id <- unlist(id_list) group <- factor(unlist(group_list), levels = c("Control", "Treatment")) time <- unlist(time_list) # control times ct <- unlist(lapply(unique(id[group=="Control"]), function(x){ length(id[id==x]) })) tt <- unlist(lapply(unique(id[group=="Treatment"]), function(x){ length(id[id==x]) })) mean(ct) mean(tt) gen_norm_microbiome_obs(features=4, diff_abun_features=2, id=id, time=time, group=group, ref="Control", control_mean=2, sigma=1, rho=0.7, corr_str="compound", func_form="L_up", beta=1, IP=5, zero_trunc=TRUE)