Package 'power.nb'

Description

Contour plot for showing predicted power

Usage

contour_plot_fun(
  combined_data,
  power_estimate,
  cont_breaks,
  multiple_samples = FALSE
)

Arguments

Value

ggplot2 object

Description

This function simulates count data for microbiome studies based on log mean, log fold change, and dispersion parameters. It supports generating data for multiple simulations and allows flexibility in specifying the number of control and treatment samples or samples per group.

Usage

countdata_sim_fun(
  logmean_param,
  logfoldchange_param,
  dispersion_param,
  nsamp_per_group = NULL,
  ncont = NULL,
  ntreat = NULL,
  notu,
  nsim = 1,
  disp_scale = 0.3,
  max_lfc = 15,
  maxlfc_iter = 1000,
  seed = NULL
)

Arguments

Value

A list containing:

• countdata_list: A list of count data matrices for each simulation.

• metadata_list: A list of metadata data frames for each simulation.

• logmean_list: A list of log mean vectors for each simulation.

• logfoldchange_list: A list of log fold change vectors for each simulation.

• treat_countdata_list: A list of treatment count data matrices for each simulation.

• control_countdata_list: A list of control count data matrices for each simulation.

Examples

# Load required packages
library(foreach)
library(doParallel)
# Define parameters
logmean_param <- list(mu = 0, sigma = 1)
logfoldchange_param <- list(par = rnorm(11), np = 2, sd_ord = 2)
dispersion_param <- list(asymptDisp = 0.1, extraPois = 0.05)

# Simulate count data
result <- countdata_sim_fun(
  logmean_param = logmean_param,
  logfoldchange_param = logfoldchange_param,
  dispersion_param = dispersion_param,
  nsamp_per_group = 10,
  notu = 50,
  nsim = 2,
  seed = 123
)

# Access simulation results
countdata <- result$countdata_list[[1]]
metadata <- result$metadata_list[[1]]

Description

Fold change and p-value estimations for simulations

Usage

deseq_fun_est(
  metadata_list,
  countdata_list,
  alpha_level = 0.1,
  group_colname,
  sample_colname,
  num_cores = 1,
  ref_name = NULL
)

Arguments

Value

A list logfoldchange log fold change estimates

logmean is the log mean count for taxa (arithmetic mean for taxa across all subjects)

dispersion: dispersion estimates for each taxa

deseq_estimate is a dataframe containing results from deseq baseMean,log2FoldChange, lfcSE, pvalue, padj

normalised_count is the normalised count data

Description

This function estimates log fold changes (LFC) for microbiome count data using the DESeq2 package. It is strongly recommended to keep the following defaults:

• minReplicatesForReplace=Inf

• cooksCutoff=TRUE

• independentFiltering=TRUE These options are particularly useful when estimating fold changes to fit the mixture of Gaussian distributions.

Usage

deseqfun(
  countdata,
  metadata,
  alpha_level = 0.1,
  ref_name = NULL,
  group_colname,
  sample_colname,
  minReplicatesForReplace = Inf,
  cooksCutoff = TRUE,
  independentFiltering = TRUE,
  shrinkage_method = "normal"
)

Arguments

Value

A list containing the following elements:

• logfoldchange: A vector of log fold change estimates for each taxa.

• dispersion: A vector of dispersion estimates for each taxa.

• deseq_estimate: A dataframe containing DESeq2 results, including baseMean, log2FoldChange, lfcSE, pvalue, and padj.

• normalised_count: A matrix of normalized count data.

• dds: DESeq object

Examples

# Example usage
set.seed(101)
nr = 10; nc = 35
countdata <- matrix(rpois(350, 3), ncol = nc, nrow = nr)
# Simulated OTU count data with 50 taxa and 10 samples
countdata  <- as.data.frame(countdata)
rownames(countdata)  <- paste("Sample", 1:nr, sep = "_")
colnames(countdata) <- paste("otu", 1:nc, sep = "_")
metadata <- data.frame(Samples = paste("Sample", 1:nr, sep = "_"),
             Groups = rep(c("Control", "Treatment"), each = 5))
sample_colname = "Samples"
group_colname  = "Groups"

result <- deseqfun(countdata, metadata, ref_name = "Control",
                    minReplicatesForReplace = Inf,
                    cooksCutoff = TRUE,
                    sample_colname = "Samples",
                    group_colname  = "Groups",
                    independentFiltering = TRUE,
                    shrinkage_method="normal")

# Examine the results
result$logfoldchange  # Log fold changes
result$logmean  # Log mean counts
result$dispersion  # Dispersion estimates
result$deseq_estimate  # DESeq2 results
result$normalised_count  # Normalized count data

Description

Dispersion are estimated from the DESeq2 package. The function fitted is of the form ⁠a + b/(mean count)⁠ where a represents the asymptotic dispersion level for high abundance taxa, and b captures additional dispersion variability.

Usage

dispersion_fit(dispersion, logmean)

Arguments

Value

A list containing estimates for a and b and confidence intervals

Examples

logmean    =  rnorm(100)
dispersion =  abs(rnorm(100))
dispersion_fit(dispersion,logmean)

Description

This function calculates the dispersion value for microbiome data based on the provided parameters: mean abundance, asymptotic dispersion, and extra Poisson dispersion.

Usage

dispersion_fun(mean_abund, asymptDisp, extraPois)

Arguments

Details

The dispersion is calculated using the formula:

$dispersion = asymptDisp + \frac{extraPois}{meanAbund}$

Value

A numeric value representing the dispersion.

Examples

mean_abund <- 10
asymptDisp <- 0.1
extraPois <- 0.05
dispersion_fun(mean_abund, asymptDisp, extraPois)

Description

This function calculates the density of a normal mixture model for a given vector of parameters on the unconstrained scale (softmax(prob), mean, log(sd)).

Usage

dnormmix(x, par, logmean, ..., log = FALSE)

Arguments

Value

A numeric vector of density values (or log-density values if log = TRUE) for the mixture model.

Examples

# Example parameters
x <- seq(-3, 3, length.out = 100)
## par <- c(-0.5, 0.5, log(0.8), log(1.2))  # Example: softmax probabilities, mean, log(sd)
set.seed(101); par <- rnorm(11)
logmean <- rep(0.1, length(x))  ## constant log mean

# Calculate density
density <- dnormmix(x, par, logmean)

# Calculate log-density
log_density <- dnormmix(x, par, logmean, log = TRUE)

Description

takes pars as three vectors (prob, mean, sd), on constrained scale

Usage

dnormmix0(x, probs, muvals, sdvals, log = FALSE)

Arguments

Value

likelihood

Description

Filter to retain only taxa with at least abund_thresh counts in at least sample_thresh samples

Usage

filter_low_count(
  countdata,
  metadata,
  abund_thresh = 5,
  sample_thresh = 3,
  sample_colname,
  group_colname
)

Arguments

Value

filtered otu count data

Description

Title

Usage

gam_fit(
  deseq_est_list,
  true_lfoldchange_list,
  true_lmean_list,
  grid_len = 50,
  alpha_level = 0.1
)

Arguments

Value

A list fit_2d is the fitted scam object

power_estimate predicted power estimated using fit_2d

combined_data tibble containing pvlaues and used for GAM fit

Description

This function generates parameter names for a Gaussian mixture model based on the number of components (np) and the order of the polynomial function (sd_ord) used to model the standard deviation parameters.

Usage

gen_parnames(np, sd_ord)

Arguments

Value

A character vector of parameter names, including:

• Logit-transformed probabilities (logitprob_1, ..., logitprob_(np-1)).

• Mean parameters (mu_int_1, mu_slope_1, ..., for each component).

• Log-transformed standard deviations (logsd_.1_1, logsd_.L_1, ..., depending on sd_ord and np).

Examples

# Generate parameter names for a 3-component mixture with linear standard deviation function
gen_parnames(np = 3, sd_ord = 1)

# Generate parameter names for a 4-component mixture with quadratic standard deviation function
gen_parnames(np = 4, sd_ord = 2)

Description

generate normal mixture parameters (prob vector, mean vector, sd vector for a specified set of 'x' values (logmean)

Usage

genmixpars(x, pars, np = 2, sd_ord = 2)

Arguments

Value

A list

 probs: mixture proportions ()

 muvals: mean values

 sdvals: standard deviation values

Description

The standard deviation parameters are modeled either by linear or quadratic functions of log mean count and the mean parameter is modeled by linear functions of log mean count

Usage

logfoldchange_fit(
  logmean,
  logfoldchange,
  ncore = 2,
  max_sd_ord = 2,
  max_np = 5,
  minval = -5,
  maxval = 5,
  itermax = 100,
  NP = 800,
  seed = 100
)

Arguments

Value

A list.

   par is a vector of the estimates of the mixture proportion,
   the mean and standard deviation parameters,

   np is the number of gaussian components fitted

   sd_ord is the order for the function for the standard deviation

   aic is the aic of the best fit

Examples

logmean        =  rnorm(100)
logfoldchange  =  rnorm(100)
logfoldchange_fit(logmean,logfoldchange)

Description

This function generates simulated log fold change (LFC) values based on the provided log mean abundance and LFC parameters. The simulation ensures that the generated LFC values remain within a specified maximum range by iterating until convergence or until a maximum iteration limit is reached.

Usage

logfoldchange_sim_fun(
  logmean_sim,
  logfoldchange_param,
  max_lfc = 15,
  max_iter = 10000,
  seed = 121
)

Arguments

Value

A numeric vector of simulated log fold change values (lfc).

Examples

set.seed(101)
# Define simulated log mean abundance
logmean_sim <- rnorm(100, mean = 0, sd = 1)

# Define parameters for log fold change simulation
logfoldchange_param <- list(
  par = rnorm(11),       # Example parameters
  np = 2,                # Number of components
  sd_ord = 2             # Order of polynomial for SD
)

# Simulate log fold change values
logfoldchange_sim_fun(
  logmean_sim = logmean_sim,
  logfoldchange_param = logfoldchange_param,
  max_lfc = 10,
  max_iter = 5000
)

Description

The optimal number of components to fit is chosen using parametric bootstrap method

Usage

logmean_fit(logmean, sig = 0.05, max.comp = 4, max.boot = 100, verb = FALSE)

Arguments

Value

A list containing the optimal number of Gaussian components fitted; and mean and variance parameter estimates from the fit

Examples

logmean  = rnorm(100)
logmean_fit(logmean,sig=0.05,max.comp=4,max.boot=100)

Description

This function generates log means for a specified number of OTUs (Operational Taxonomic Units) based on the provided parameters. If a single mean is specified, the log means are drawn from a normal distribution. If multiple means and corresponding weights are specified, the log means are drawn from a mixture of normal distributions.

Usage

logmean_sim_fun(logmean_param, notu)

Arguments

Value

A numeric vector of simulated log means for the specified number of OTUs.

Examples

# Example 1: Single normal distribution
params_single <- list(mu = 0, sigma = 1)
logmean_sim_fun(logmean_param = params_single, notu = 100)

# Example 2: Mixture of normal distributions
params_mixture <- list(
  mu = c(-1, 1),
  sigma = c(0.5, 0.5),
  lambda = c(0.4, 0.6)
)
logmean_sim_fun(logmean_param = params_mixture, notu = 100)

Description

Simulating from a mixture of Gaussian

Usage

myrnormmix(par, logmean, ...)

Arguments

Value

random values from a a mixture of Gaussian

Description

Objective function

Usage

nllfun(par, vals, logmean, np, sd_ord)

Arguments

Value

value for the objective function

Description

The number of gaussian components is determined using the using parametric bootstrap

Usage

optimal.comp(logmean, sig = 0.05, max.comp = 4, max.boot = 100)

Arguments

Value

The best number of components for fitting the distribution of log mean abundance

Examples

logmean  = rnorm(100)
optimal.comp(logmean,sig=0.05,max.comp=4,max.boot=100)

Description

General-purpose log-likelihood function, vectorized sum(pars*x^i)

Usage

polyfun(pars, x)

Arguments

Value

values representing output for the polynomial fuction (f(x))

Examples

polyfun(pars = c(1, 2, 3), x = 1:5)
polyfun(pars = c(1, 0, 3), x = 1)

Description

Fits a shape-constrained additive model (SCAM) to estimate statistical power as a function of mean abundance, absolute log fold change, and sample size. The function takes p-values obtained across simulation settings, converts them to rejection indicators based on a chosen significance level, and then models the probability of rejection using smooth terms.

Usage

power_fun_ss(
  pval_est_list,
  logmean_list,
  nsample_vec,
  logfoldchange_list,
  alpha_level = 0.1
)

Arguments

Details

The returned model can be used as a smooth approximation to the empirical power surface, which is useful for interpolation and sample size prediction.

The function first pools all p-values from pval_est_list and converts them into binary rejection indicators:

$I(p < \alpha)$

where alpha_level is the chosen significance threshold.

A data frame is then constructed with:

• logmean: log mean abundance,

• abs_lfc: absolute log fold change,

• pval_reject: binary rejection indicator,

• sample_size: sample size,

• logsample_size: base-2 logarithm of sample size.

The function attempts to fit the following SCAM model:

$\mathrm{logit}\{P(\text{reject})\} = s(\text{logmean}, \text{abs\_lfc}, \text{bs = "tedmi"}) + s(\text{abs\_lfc}, \text{logsample\_size}, \text{bs = "tedmi"}) + s(\text{logmean}, \text{logsample\_size}, \text{bs = "tedmi"})$

using a binomial family.

If the full model fails due to numerical instability, a simpler fallback model is fitted instead:

$\mathrm{logit}\{P(\text{reject})\} = s(\text{logmean}, \text{abs\_lfc}, \text{bs = "tedmi"}) + s(\text{logsample\_size}, \text{bs = "mpi"})$

A warning is issued when the fallback model is used.

Value

A list with two components:

• combined_data: A tibble containing the combined simulation inputs and rejection indicators used for model fitting.

• gam_mod: The fitted scam model object.

See Also

scam::scam()

Examples

#' @examples

# Example structure only
set.seed(101)
n = 70
pval_est_list = list(rnorm(n),rnorm(n))
logmean_list = list(rnorm(n),rnorm(n))
logfoldchange_list = list(rnorm(n),rnorm(n))
nsample_vec <- c(20, 40)
out <- power_fun_ss(
pval_est_list = pval_est_list,
logmean_list = logmean_list,
nsample_vec = nsample_vec,
logfoldchange_list = logfoldchange_list,
alpha_level = 0.1
)
out$combined_data
out$gam_mod

Description

This function extracts a specific component (data) from a list of datasets. The component to extract is specified by the extract_name parameter, and the function returns a list containing the extracted data from each dataset.

Usage

read_data(dataset_list, extract_name)

Arguments

Value

A list containing the extracted data. Each element corresponds to the extracted component from the datasets in dataset_list. The names of the list elements are taken from the names of dataset_list.

Examples

# Example dataset list
dataset1 <- list(countdata = matrix(1:9, nrow = 3), metadata = data.frame(id = 1:3))
dataset2 <- list(countdata = matrix(10:18, nrow = 3), metadata = data.frame(id = 4:6))
dataset_list <- list(dataset1 = dataset1, dataset2 = dataset2)

# Extract 'countdata' from each dataset in the list
result <- read_data(dataset_list, "countdata")
print(result)

Description

general-purpose normal-mixture deviate generator: takes matrices of probabilities, means, sds

Usage

rnormmix0(n, probs, muvals, sdvals)

Arguments

Value

simulations

Description

This function estimates the sample size required to achieve a specified target power using predictions from a fitted GAM/SCAM power model. The function evaluates predicted power across a grid of candidate sample sizes and identifies the smallest sample size for which the predicted power reaches or exceeds the target value. Linear interpolation is then used on the log2(sample size) scale to obtain a more precise estimate.

Usage

sample_size_ss_interp(
  target_power,
  logmean,
  abs_lfc,
  model,
  xmin = log2(5),
  xmax = log2(500),
  ngrid = 1000
)

Arguments

Details

The function first constructs a grid of candidate sample sizes on the log2 scale between xmin and xmax. Predicted power values are then obtained from the fitted model for each grid point. The smallest sample size at which the predicted power reaches the target value is identified, and linear interpolation is used to refine the estimate.

Value

A numeric value representing the estimated sample size required to achieve the target power. Returns NA if the target power is not reached within the specified search range.

Description

This function estimates the sample size required to achieve a specified target statistical power using a fitted GAM/SCAM power model. The function first attempts to solve for the sample size using a root-finding algorithm. If the root-finding procedure fails, a grid-based interpolation method is used as a fallback to obtain an approximate solution.

Usage

ss_solver(
  target_power,
  logmean,
  abs_lfc,
  model,
  xmin = log2(5),
  xmax = log2(500)
)

Arguments

Details

The function first attempts to compute the required sample size using a root-finding approach implemented in uniroot_ss(). If this method fails (for example, due to numerical issues or if the root cannot be bracketed within the specified interval), the function falls back to a grid-based interpolation approach implemented in sample_size_ss_interp().

A warning is issued if the target power is specified as 0 or 1, since these values correspond to unrealistic design targets in most practical applications.

Value

A numeric value representing the estimated sample size required to achieve the target power.

Description

Sample Size estimation function using uniroot

Usage

uniroot_ss(
  target_power,
  logmean,
  abs_lfc,
  model,
  xmin = log2(10),
  xmax = log2(5000),
  maxiter = 10000,
  max_report = 2000
)

Arguments

Value

A numeric value corresponding to the estimated sample size required to achieve the target power.