Package 'corncob'

Title: Count Regression for Correlated Observations with the Beta-Binomial
Description: Statistical modeling for correlated count data using the beta-binomial distribution, described in Martin et al. (2020) <doi:10.1214/19-AOAS1283>. It allows for both mean and overdispersion covariates.
Authors: Bryan D Martin [aut], Daniela Witten [aut], Sarah Teichman [ctb], Amy D Willis [aut, cre], Thomas W Yee [ctb] (VGAM library), Xiangjie Xue [ctb] (VGAM library)
Maintainer: Amy D Willis <[email protected]>
License: GPL (>= 2)
Version: 0.4.1
Built: 2024-11-03 05:23:18 UTC
Source: https://github.com/statdivlab/corncob

Help Index

Corncob package documentation.

Description

Corncob provides methods for estimating and plotting count data. Specifically, corncob is designed to account for the challenges of modeling sequencing data from microbial abundance studies.

Details

For details on the model implemented in this package, see Martin et al. (2020) <doi:10.1214/19-AOAS1283>.

The development version of the package will be maintained on https://github.com/statdivlab/corncob.

Value

No return value. Created for documentation.

Maximum Likelihood for the Beta-binomial Distribution

Description

Maximum Likelihood for the Beta-binomial Distribution

Usage

bbdml(
  formula,
  phi.formula,
  data,
  link = "logit",
  phi.link = "logit",
  method = "trust",
  control = list(maxit = 1000, reltol = 1e-14),
  numerical = FALSE,
  nstart = 1,
  inits = NULL,
  allow_noninteger = FALSE,
  robust = FALSE,
  ...
)

Arguments

formula

an object of class formula: a symbolic description of the model to be fitted to the abundance
phi.formula

an object of class formula without the response: a symbolic description of the model to be fitted to the dispersion
data

a data frame or phyloseq object containing the variables in the models
link

link function for abundance covariates, defaults to "logit"
phi.link

link function for dispersion covariates, defaults to "logit"
method

optimization method, defaults to "trust", or see optimr for other options
control

optimization control parameters (see optimr)
numerical

Boolean. Defaults to FALSE. Indicator of whether to use the numeric Hessian (not recommended).
nstart

Integer. Defaults to 1. Number of starts for optimization.
inits

Optional initializations as rows of a matrix. Defaults to NULL.
allow_noninteger

Boolean. Defaults to FALSE. Should noninteger W's and M's be allowed? This behavior was not permitted prior to v4.1, needs to be explicitly allowed.
robust

Should robust standard errors be returned? If not, model-based standard arras are used. Logical, defaults to FALSE.
...

Optional additional arguments for optimr or trust

Value

An object of class bbdml.

Examples

# data frame example
data(soil_phylum_small_otu1)
bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)

# phyloseq example (only run this if you have phyloseq installed)
## Not run: 
data(soil_phylum_small_sample)
data(soil_phylum_small_otu)
data_phylo <- phyloseq::phyloseq(phyloseq::sample_data(soil_phylum_small_sample),
phyloseq::otu_table(soil_phylum_small_otu, taxa_are_rows = TRUE))
bbdml(formula = Proteobacteria ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = data_phylo)

## End(Not run)

Check for nested models

Description

Check for nested models

Usage

checkNested(mod, mod_null)

Arguments

mod

an object of class bbdml
mod_null

an object of class bbdml

Value

TRUE if mod_null is nested within mod, otherwise it throws an error.

Examples

data(soil_phylum_small_otu1)
mod1 <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)

mod2 <- bbdml(formula = cbind(W, M - W) ~ 1,
phi.formula = ~ 1,
data = soil_phylum_small_otu1)

checkNested(mod1, mod2)

Rename taxa

Description

Renames taxa to have short human-readable names

Usage

clean_taxa_names(x, name = "OTU")

Arguments

x

Object of class phyloseq
name

Character, defaults to "OTU". Optional. String to use in every taxa name.

Details

The original taxa names are saved as the original_names attribute. See the example for an example of how to access the original names.

Value

Object of class phyloseq, with taxa renamed (defaults to OTU1, OTU2, ...), with the original taxa names saved as an attribute.

Identify differentially-abundant and differentially-variable taxa using contrasts

Description

Identify differentially-abundant and differentially-variable taxa using contrasts

Usage

contrastsTest(
  formula,
  phi.formula,
  contrasts_DA = NULL,
  contrasts_DV = NULL,
  data,
  link = "logit",
  phi.link = "logit",
  sample_data = NULL,
  taxa_are_rows = TRUE,
  filter_discriminant = TRUE,
  fdr_cutoff = 0.05,
  fdr = "fdr",
  inits = NULL,
  try_only = NULL,
  ...
)

Arguments

formula

an object of class formula without the response: a symbolic description of the model to be fitted to the abundance
phi.formula

an object of class formula without the response: a symbolic description of the model to be fitted to the dispersion
contrasts_DA

List. Optional. Constructs a contrast matrix. List elements should be characters specifying contrasts in the parameters within formula. Note that this is only available with "Wald" value for test. Must include at least one of contrasts_DA or contrasts_DV.
contrasts_DV

List. Optional. Constructs a contrast matrix. List elements should be characters specifying contrasts in the parameters within phi.formula. Note that this is only available with "Wald" value for test. Must include at least one of contrasts_DA or contrasts_DV.
data

a data frame containing the OTU table, or phyloseq object containing the variables in the models
link

link function for abundance covariates, defaults to "logit"
phi.link

link function for dispersion covariates, defaults to "logit"
sample_data

Data frame or matrix. Defaults to NULL. If data is a data frame or matrix, this must be included as covariates/sample data.
taxa_are_rows

Boolean. Optional. If data is a data frame or matrix, this indicates whether taxa are rows. Defaults to TRUE.
filter_discriminant

Boolean. Defaults to TRUE. If FALSE, discriminant taxa will not be filtered out.
fdr_cutoff

Integer. Defaults to 0.05. Desired type 1 error rate
fdr

Character. Defaults to "fdr". False discovery rate control method, see p.adjust for more options.
inits

Optional initializations for model fit using formula and phi.formula as rows of a matrix. Defaults to NULL.
try_only

Optional numeric. Will try only the try_only taxa, specified either via numeric input or character taxa names. Useful for speed when troubleshooting. Defaults to NULL, testing all taxa.
...

Optional additional arguments for bbdml

Details

This function uses contrast matrices to test for differential abundance and differential variability using a Wald-type chi-squared test. To use a formula implementation, see differentialTest.

Value

An object of class contrastsTest. List with elements p containing the p-values for each contrast, p_fdr containing the p-values after false discovery rate control, significant_taxa containing the taxa names of the statistically significant taxa, contrasts_DA containing the contrast matrix for parameters associated with the abundance, contrasts_DV containing the contrast matrix for parameters associated with the dispersion, discriminant_taxa_DA containing the taxa for which at least one covariate associated with the abundance was perfectly discriminant, discriminant_taxa_DV containing the taxa for which at least one covariate associated with the dispersion was perfectly discriminant, and data containing the data used to fit the models.

Examples

# data frame example
data(soil_phylum_contrasts_sample)
data(soil_phylum_contrasts_otu)
da_analysis <- contrastsTest(formula = ~ DayAmdmt,
                             phi.formula = ~ DayAmdmt,
                             contrasts_DA = list("DayAmdmt21 - DayAmdmt11",
                                                 "DayAmdmt22 - DayAmdmt21"),
                             data = soil_phylum_contrasts_otu,
                             sample_data = soil_phylum_contrasts_sample,
                             fdr_cutoff = 0.05,
                             try_only = 1:5)

# phyloseq example (only run if you have phyloseq installed)
## Not run: 
contrasts_phylo <- phyloseq::phyloseq(phyloseq::sample_data(soil_phylum_contrasts_sample),
phyloseq::otu_table(soil_phylum_contrasts_otu, taxa_are_rows = TRUE))
da_analysis <- contrastsTest(formula = ~ DayAmdmt,
                             phi.formula = ~ DayAmdmt,
                             contrasts_DA = list("DayAmdmt21 - DayAmdmt11",
                                                 "DayAmdmt22 - DayAmdmt21"),
                             data = contrasts_phylo,
                             fdr_cutoff = 0.05,
                             try_only = 1:5)

## End(Not run)

Function to subset and convert phyloseq data

Description

Function to subset and convert phyloseq data

Usage

convert_phylo(data, select)

Arguments

data

a phyloseq object
select

Name of OTU or taxa to select, must match taxa name in data

Value

A data.frame object, with elements W as the observed counts, M as the sequencing depth, and the sample data with their original names.

Hyperbolic cotangent transformation

Description

Hyperbolic cotangent transformation

Usage

coth(x)

Arguments

x

data

Value

Hyperbolic cotangent transformation of x

Examples

x <- .5
coth(x)

Betabinomial density

Description

Betabinomial density

Usage

dbetabin(theta, W, M, X, X_star, np, npstar, link, phi.link, logpar = TRUE)

Arguments

theta

Numeric vector. Parameters associated with X and X_star
W

Numeric vector of counts
M

Numeric vector of sequencing depth
X

Matrix of covariates associated with abundance (including intercept)
X_star

Matrix of covariates associated with dispersion (including intercept)
np

Number of covariates associated with abundance (including intercept)
npstar

Number of covariates associated with dispersion (including intercept)
link

ink function for abundance covariates
phi.link

ink function for dispersion covariates
logpar

Boolean. Defaults to TRUE. Indicator of whether to return log-likelihood.

Value

Negative beta-binomial (log-)likelihood

Negative betabinomial density

Description

Created as a convenient helper function for optimization. Not intended for users.

Usage

dbetabin_neg(theta, W, M, X, X_star, np, npstar, link, phi.link, logpar = TRUE)

Arguments

theta

Numeric vector. Parameters associated with X and X_star
W

Numeric vector of counts
M

Numeric vector of sequencing depth
X

Matrix of covariates associated with abundance (including intercept)
X_star

Matrix of covariates associated with dispersion (including intercept)
np

Number of covariates associated with abundance (including intercept)
npstar

Number of covariates associated with dispersion (including intercept)
link

ink function for abundance covariates
phi.link

ink function for dispersion covariates
logpar

Boolean. Defaults to TRUE. Indicator of whether to return log-likelihood.

Value

Negative beta-binomial (log-)likelihood

Densities of beta binomial distributions, permitting non integer x and size

Description

In some cases we may not have integer W and M's. In these cases, we can still use corncob to estimate parameters, but we need to think of them as no longer coming from the specific beta binomial parametric model, and instead from an estimating equations framework.

Usage

dbetabinom_cts(x, size, prob, rho = 0, log = FALSE)

Arguments

x

the value at which defined the density
size

number of trials
prob

the probability of success
rho

the correlation parameter
log

if TRUE, log-densities p are given

Author(s)

Thomas W Yee

Xiangjie Xue

Amy D Willis

Identify differentially-abundant and differentially-variable taxa

Description

Identify differentially-abundant and differentially-variable taxa

Usage

differentialTest(
  formula,
  phi.formula,
  formula_null,
  phi.formula_null,
  data,
  link = "logit",
  phi.link = "logit",
  test,
  boot = FALSE,
  B = 1000,
  sample_data = NULL,
  taxa_are_rows = TRUE,
  filter_discriminant = TRUE,
  fdr_cutoff = 0.05,
  fdr = "fdr",
  full_output = FALSE,
  inits = NULL,
  inits_null = NULL,
  try_only = NULL,
  verbose = FALSE,
  robust = FALSE,
  ...
)

Arguments

formula

an object of class formula without the response: a symbolic description of the model to be fitted to the abundance
phi.formula

an object of class formula without the response: a symbolic description of the model to be fitted to the dispersion
formula_null

Formula for mean under null, without response
phi.formula_null

Formula for overdispersion under null, without response
data

a data frame containing the OTU table, or phyloseq object containing the variables in the models
link

link function for abundance covariates, defaults to "logit"
phi.link

link function for dispersion covariates, defaults to "logit"
test

Character. Hypothesis testing procedure to use. One of "Wald", "LRT" (likelihood ratio test), or "Rao".
boot

Boolean. Defaults to FALSE. Indicator of whether or not to use parametric bootstrap algorithm. (See pbWald and pbLRT).
B

Optional integer. Number of bootstrap iterations. Ignored if boot is FALSE. Otherwise, defaults to 1000.
sample_data

Data frame or matrix. Defaults to NULL. If data is a data frame or matrix, this must be included as covariates/sample data.
taxa_are_rows

Boolean. Optional. If data is a data frame or matrix, this indicates whether taxa are rows. Defaults to TRUE.
filter_discriminant

Boolean. Defaults to TRUE. If FALSE, discriminant taxa will not be filtered out.
fdr_cutoff

Integer. Defaults to 0.05. Desired false discovery rate.
fdr

Character. Defaults to "fdr". False discovery rate control method, see p.adjust for more options.
full_output

Boolean. Opetional. Defaults to FALSE. Indicator of whether to include full bbdml model output for all taxa.
inits

Optional initializations for model fit using formula and phi.formula as rows of a matrix. Defaults to NULL.
inits_null

Optional initializations for model fit using formula_null and phi.formula_null as rows of a matrix. Defaults to NULL.
try_only

Optional numeric. Will try only the try_only taxa, specified either via numeric input or character taxa names. Useful for speed when troubleshooting. Defaults to NULL, testing all taxa.
verbose

Boolean. Defaults to FALSE; print status updates for long-running analyses
robust

Should robust standard errors be used? If not, model-based standard errors are used. Logical, defaults to FALSE.
...

Optional additional arguments for bbdml

Details

See package vignette for details and example usage. Make sure the number of columns in all of the initializations are correct! inits probably shouldn't match inits_null. To use a contrast matrix, see contrastsTest.

Value

An object of class differentialTest. List with elements p containing the p-values, p_fdr containing the p-values after false discovery rate control, significant_taxa containing the taxa names of the statistically significant taxa, significant_models containing a list of the model fits for the significant taxa, all_models containing a list of the model fits for all taxa, restrictions_DA containing a list of covariates that were tested for differential abundance, restrictions_DV containing a list of covariates that were tested for differential variability, discriminant_taxa_DA containing the taxa for which at least one covariate associated with the abundance was perfectly discriminant, discriminant_taxa_DV containing the taxa for which at least one covariate associated with the dispersion was perfectly discriminant, data containing the data used to fit the models. If full_output = TRUE, it will also include full_output, a list of all model output from bbdml.

Examples

# data frame example
data(soil_phylum_small_sample)
data(soil_phylum_small_otu)
da_analysis <- differentialTest(formula = ~ DayAmdmt,
                                phi.formula = ~ DayAmdmt,
                                formula_null = ~ 1,
                                phi.formula_null = ~ DayAmdmt,
                                test = "Wald", boot = FALSE,
                                data = soil_phylum_small_otu,
                                sample_data = soil_phylum_small_sample,
                                fdr_cutoff = 0.05,
                                try_only = 1:5)

# phyloseq example (only run if you have phyloseq installed)
## Not run: 
data_phylo <- phyloseq::phyloseq(phyloseq::sample_data(soil_phylum_small_sample),
phyloseq::otu_table(soil_phylum_small_otu, taxa_are_rows = TRUE))
da_analysis <- differentialTest(formula = ~ DayAmdmt,
                               phi.formula = ~ DayAmdmt,
                               formula_null = ~ 1,
                               phi.formula_null = ~ DayAmdmt,
                               test = "Wald", boot = FALSE,
                               data = data_phylo,
                               fdr_cutoff = 0.05,
                               try_only = 1:5)

## End(Not run)

Function to run a bootstrap iteration

Description

Internal function. Not intended for users.

Usage

doBoot(mod, mod_null, test, robust = FALSE)

Arguments

mod

an object of class bbdml
mod_null

an object of class bbdml
test

Character. Hypothesis testing procedure to use. One of "Wald" or "LRT" (likelihood ratio test).
robust

Should robust standard errors be used? If not, model-based standard arras are used. Logical, defaults to FALSE.

Value

test statistic from one bootstrap iteration

Fisher's z transformation

Description

Fisher's z transformation

Usage

fishZ(x)

Arguments

x

data

Value

Fisher's z transformation of x

Examples

x <- .5
fishZ(x)

Generate initialization for optimization

Description

Generate initialization for optimization

Usage

genInits(W, M, X, X_star, np, npstar, link, phi.link, nstart = 1, use = TRUE)

Arguments

W

Numeric vector of counts
M

Numeric vector of sequencing depth
X

Matrix of covariates associated with abundance (including intercept)
X_star

Matrix of covariates associated with dispersion (including intercept)
np

Number of covariates associated with abundance (including intercept)
npstar

Number of covariates associated with dispersion (including intercept)
link

ink function for abundance covariates
phi.link

ink function for dispersion covariates
nstart

Integer. Defaults to 1. Number of starts for optimization.
use

Boolean. Defaults to TRUE. Indicator of whether to use deterministic intialization.

Value

Matrix of initializations

Examples

set.seed(1)
seq_depth <- rpois(20, lambda = 10000)
my_counts <- rbinom(20, size = seq_depth, prob = 0.001) * 10
my_covariate <- cbind(rep(c(0,1), each = 10))
colnames(my_covariate) <- c("X1")

genInits(W = my_counts, M = seq_depth,
       X = cbind(1, my_covariate), X_star = cbind(1, my_covariate),
       np = 2, npstar = 2,
       link = "logit",
       phi.link = "logit", nstart = 2, use = TRUE)

Get index of restricted terms for Wald test

Description

Created as a convenient helper function. Not intended for users.

Usage

getRestrictionTerms(
  mod,
  mod_null = NULL,
  restrictions = NULL,
  restrictions.phi = NULL
)

Arguments

mod

an object of class bbdml
mod_null

Optional. An object of class bbdml. Defaults to NULL
restrictions

Optional. Defaults to NULL. Numeric vector indicating the parameters associated with the abundance to test, or character vector with name of variable to test. Note that 1 is the intercept associated with the abundance.
restrictions.phi

Optional. Defaults to NULL. Numeric vector indicating the parameters associated with the dispersion to test, or character vector with name of variable to test. Note that 1 is the intercept associated with the dispersion.

Value

A list with mu representing the index of the restricted covariates associated with abundance and phi representing the index of the restricted covarates associated with the dispersion

Parameter Gradient Vector

Description

Used for internal optimization. Not intended for users.

Usage

gr_full(theta, W, M, X, X_star, np, npstar, link, phi.link, logpar = TRUE)

Arguments

theta

Numeric vector. Parameters associated with X and X_star
W

Numeric vector of counts
M

Numeric vector of sequencing depth
X

Matrix of covariates associated with abundance (including intercept)
X_star

Matrix of covariates associated with dispersion (including intercept)
np

Number of covariates associated with abundance (including intercept)
npstar

Number of covariates associated with dispersion (including intercept)
link

ink function for abundance covariates
phi.link

ink function for dispersion covariates
logpar

Boolean. Defaults to TRUE. Indicator of whether to return log-likelihood.

Value

Gradient of likelihood with respect to parameters

Get highest density interval of beta-binomial

Description

Get highest density interval of beta-binomial

Usage

HDIbetabinom(percent, M, mu, phi)

Arguments

percent

Numeric. Percent interval desired.
M

Numeric vector of sequencing depth
mu

Numeric vector of abundance parameter
phi

Numeric vector of dispersion parameter

Value

List where lower represents the lower bound and upper represents the upper bound

Examples

data(soil_phylum_small_otu1)
mod <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)
HDIbetabinom(.95, M = mod$M[1], mu = mod$mu.resp[1], phi = mod$phi.resp[1])

Compute Hessian matrix at the MLE

Description

Compute Hessian matrix at the MLE

Usage

hessian(mod, numerical = FALSE)

Arguments

mod

an object of class bbdml
numerical

Boolean. Defaults to FALSE. Indicator of whether to use the numeric Hessian (not recommended).

Value

Hessian matrix at the MLE. In this setting, it's hard to compute expectations to calculate the information matrix, so we return the consistent estimate using sample moments: A^(θ^)=∑i∂2∂θ∂θTl(θ,Wi)\hat{A}(\hat{\theta}) = \sum_i \frac{\partial^2}{\partial \theta \partial \theta^T} l(\theta, W_i) evaluated at θ=θ^\theta = \hat{\theta}.

Examples

data(soil_phylum_small_otu1)
mod <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)
hessian(mod)

IBD data, OTU count data frame.

Description

OTU data frame from a phyloseq object from an IBD microbiome study.

Usage

ibd_phylo_otu

Format

A data frame of OTU counts.

References

Papa, E., Docktor, M., Smillie, C., Weber, S., Preheim, S. P., Gevers, D., Giannoukos, G., Ciulla, D., Tabbaa, D., Ingram, J., Schauer, D. B., Ward, D. V., Korzenik, J. R., Xavier, R. J., Bousvaros, A., Alm, E. J. & Schauer, D. B. (2012). Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PloS One, 7(6), e39242. <doi.org/10.1371/journal.pone.0039242>.

Duvallet, C., Gibbons, S., Gurry, T., Irizarry, R., & Alm, E. (2017). MicrobiomeHD: the human gut microbiome in health and disease [Data set]. Zenodo. <doi.org/10.5281/zenodo.1146764>.

IBD data, sample data frame.

Description

Sample data from a phyloseq object from an IBD microbiome study.

Usage

ibd_phylo_sample

Format

A data frame of sample data.

References

Papa, E., Docktor, M., Smillie, C., Weber, S., Preheim, S. P., Gevers, D., Giannoukos, G., Ciulla, D., Tabbaa, D., Ingram, J., Schauer, D. B., Ward, D. V., Korzenik, J. R., Xavier, R. J., Bousvaros, A., Alm, E. J. & Schauer, D. B. (2012). Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PloS One, 7(6), e39242. <doi.org/10.1371/journal.pone.0039242>.

Duvallet, C., Gibbons, S., Gurry, T., Irizarry, R., & Alm, E. (2017). MicrobiomeHD: the human gut microbiome in health and disease [Data set]. Zenodo. <doi.org/10.5281/zenodo.1146764>.

IBD data, taxonomy data frame.

Description

Taxonomy data from a phyloseq object from an IBD microbiome study.

Usage

ibd_phylo_taxa

Format

A data frame of taxonomy data.

References

Papa, E., Docktor, M., Smillie, C., Weber, S., Preheim, S. P., Gevers, D., Giannoukos, G., Ciulla, D., Tabbaa, D., Ingram, J., Schauer, D. B., Ward, D. V., Korzenik, J. R., Xavier, R. J., Bousvaros, A., Alm, E. J. & Schauer, D. B. (2012). Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PloS One, 7(6), e39242. <doi.org/10.1371/journal.pone.0039242>.

Duvallet, C., Gibbons, S., Gurry, T., Irizarry, R., & Alm, E. (2017). MicrobiomeHD: the human gut microbiome in health and disease [Data set]. Zenodo. <doi.org/10.5281/zenodo.1146764>.

Inverse Fisher's z transformation

Description

Inverse Fisher's z transformation

Usage

invfishZ(x)

Arguments

x

data

Value

Inverse Fisher's z transformation of x

Examples

x <- .5
invfishZ(x)

Inverse logit transformation

Description

Inverse logit transformation

Usage

invlogit(x)

Arguments

x

data

Value

Inverse logit transformation of x

Examples

x <- .5
invlogit(x)

Logit transformation

Description

Logit transformation

Usage

logit(x)

Arguments

x

data

Value

logit of x

Examples

x <- .5
logit(x)

Likelihood ratio test

Description

Likelihood ratio test

Usage

lrtest(mod, mod_null)

Arguments

mod

an object of class bbdml
mod_null

an object of class bbdml, should be nested within mod

Value

P-value from likelihood ratio test.

Examples

data(soil_phylum_small_otu1)
mod1 <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)

mod2 <- bbdml(formula = cbind(W, M - W) ~ 1,
phi.formula = ~ 1,
data = soil_phylum_small_otu1)
lrtest(mod1, mod2)

Objective function

Description

Used for internal optimization. Not intended for users.

Usage

objfun(theta, W, M, X, X_star, np, npstar, link, phi.link)

Arguments

theta

Numeric vector. Parameters associated with X and X_star
W

Numeric vector of counts
M

Numeric vector of sequencing depth
X

Matrix of covariates associated with abundance (including intercept)
X_star

Matrix of covariates associated with dispersion (including intercept)
np

Number of covariates associated with abundance (including intercept)
npstar

Number of covariates associated with dispersion (including intercept)
link

ink function for abundance covariates
phi.link

ink function for dispersion covariates

Value

List of negative log-likelihood, gradient, and hessian

Transform OTUs to their taxonomic label

Description

Transform OTUs to their taxonomic label

Usage

otu_to_taxonomy(OTU, data, level = NULL)

Arguments

OTU

String vector. Names of OTU labels in data
data

phyloseq object with a taxonomy table
level

(Optional). Character vector. Desired taxonomic levels for output.

Value

String vector. Names of taxonomic labels matching labels of OTU.

Parametric bootstrap likelihood ratio test

Description

Parametric bootstrap likelihood ratio test

Usage

pbLRT(mod, mod_null, B = 1000)

Arguments

mod

an object of class bbdml
mod_null

an object of class bbdml, should be nested within mod
B

Integer. Defaults to 1000. Number of bootstrap iterations.

Value

P-value from parametric bootstrap likelihood ratio test.

Examples

data(soil_phylum_small_otu1)
mod1 <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)

mod2 <- bbdml(formula = cbind(W, M - W) ~ 1,
phi.formula = ~ 1,
data = soil_phylum_small_otu1)
pbLRT(mod1, mod2, B = 50)

Parametric bootstrap Rao test

Description

Parametric bootstrap Rao test

Usage

pbRao(mod, mod_null, B = 1000)

Arguments

mod

an object of class bbdml
mod_null

an object of class bbdml, should be nested within mod
B

Integer. Defaults to 1000. Number of bootstrap iterations.

Value

P-value from parametric bootstrap Rao test.

Examples

data(soil_phylum_small_otu1)
mod1 <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)

mod2 <- bbdml(formula = cbind(W, M - W) ~ 1,
phi.formula = ~ 1,
data = soil_phylum_small_otu1)
pbRao(mod1, mod2, B = 10)

Parametric bootstrap Wald test

Description

Parametric bootstrap Wald test

Usage

pbWald(mod, mod_null, B = 1000, robust = FALSE)

Arguments

mod

an object of class bbdml
mod_null

an object of class bbdml, should be nested within mod
B

Integer. Defaults to 1000. Number of bootstrap iterations.
robust

Should robust standard errors be used? If not, model-based standard arras are used. Logical, defaults to FALSE.

Value

P-value from parametric bootstrap Wald test.

Examples

data(soil_phylum_small_otu1)
mod1 <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)

mod2 <- bbdml(formula = cbind(W, M - W) ~ 1,
phi.formula = ~ 1,
data = soil_phylum_small_otu1)
pbWald(mod1, mod2, B = 50)

Plotting function

Description

Plotting function

Usage

## S3 method for class 'bbdml'
plot(
  x,
  total = FALSE,
  color = NULL,
  shape = NULL,
  facet = NULL,
  title = NULL,
  B = 1000,
  sample_names = TRUE,
  data_only = FALSE,
  ...
)

Arguments

x

Object of class bbdml.
total

(Optional). Default FALSE. Boolean indicator for whether to plot on total counts scale
color

(Optional). Default NULL. The sample variable to map to different colors. Can be a single character string of the variable name in sample_data or a custom supplied vector with length equal to the number of samples. Use a character vector to have ggplot2 default.
shape

(Optional). Default NULL. The sample variable to map to different shapes. Can be a single character string of the variable name in sample_data or a custom supplied vector with length equal to the number of samples.
facet

(Optional). Default NULL. The sample variable to map to different panels in a facet grid. Must be a single character string of a variable name in sample_data.
title

(Optional). Default NULL. Character string. The main title for the graphic.
B

(Optional). Default 1000. Integer. Number of bootstrap simulations for prediction intervals. Use B = 0 for no prediction intervals.
sample_names

(Optional). Default TRUE. Boolean. If FALSE, remove sample names from the plot.
data_only

(Optional). Default FALSE. Boolean. If TRUE, only returns data frame.
...

There are no optional parameters at this time.

Value

Object of class ggplot. Plot of bbdml model fit with 95

Examples

data(soil_phylum_small_otu1)
mod <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)
# Here we use B = 50 for quick demonstration purposes.
# In practice, we recommend a higher value for B for more accurate intervals
plot(mod, color = "DayAmdmt", B = 50)

differentialTest plot function

Description

differentialTest plot function

Usage

## S3 method for class 'differentialTest'
plot(x, level = NULL, data_only = FALSE, ...)

Arguments

x

Object of class differentialTest
level

(Optional). Character vector. Desired taxonomic levels for taxa labels.
data_only

(Optional). Default FALSE. Boolean. If TRUE, only returns data frame.
...

No optional arguments are accepted at this time.

Value

Object of class ggplot. Plot of coefficients from models for significant taxa from differentialTest

Examples

# phyloseq example
data(soil_phylum_small_sample)
data(soil_phylum_small_otu)
da_analysis <- differentialTest(formula = ~ DayAmdmt,
                                phi.formula = ~ DayAmdmt,
                                formula_null = ~ 1,
                                phi.formula_null = ~ DayAmdmt,
                                test = "Wald", boot = FALSE,
                                data = soil_phylum_small_otu,
                                sample_data = soil_phylum_small_sample,
                                fdr_cutoff = 0.05,
                                try_only = 1:5)
plot(da_analysis, level = "Phylum")

Print function

Description

Print function

Usage

## S3 method for class 'bbdml'
print(
  x,
  digits = max(3L, getOption("digits") - 3L),
  signif.stars = getOption("show.signif.stars"),
  ...
)

Arguments

x

Object of class bbdml
digits

the number of significant digits to use when printing.
signif.stars

logical. If TRUE, ‘significance stars’ are printed for each coefficient.
...

No optional arguments are accepted at this time.

Value

NULL. Displays printed model summary.

Examples

data(soil_phylum_small_otu1)
mod <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)
print(mod)

differentialTest print function

Description

differentialTest print function

Usage

## S3 method for class 'differentialTest'
print(x, ...)

Arguments

x

Object of class bbdml
...

No optional arguments are accepted at this time.

Value

NULL. Displays printed differentialTest summary.

Examples

# phyloseq example
data(soil_phylum_small_sample)
data(soil_phylum_small_otu)
da_analysis <- differentialTest(formula = ~ DayAmdmt,
                                phi.formula = ~ DayAmdmt,
                                formula_null = ~ 1,
                                phi.formula_null = ~ DayAmdmt,
                                test = "Wald", boot = FALSE,
                                data = soil_phylum_small_otu,
                                sample_data = soil_phylum_small_sample,
                                fdr_cutoff = 0.05,
                                try_only = 1:5)
print(da_analysis)

Print summary function

Description

Print summary function

Usage

## S3 method for class 'summary.bbdml'
print(
  x,
  digits = max(3L, getOption("digits") - 3L),
  signif.stars = getOption("show.signif.stars"),
  ...
)

Arguments

x

Object of class bbdml
digits

the number of significant digits to use when printing.
signif.stars

logical. If TRUE, ‘significance stars’ are printed for each coefficient.
...

No optional arguments are accepted at this time.

Value

NULL. Displays printed model summary.

Examples

data(soil_phylum_small_otu1)
mod <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)
print(summary(mod))

Get quantiles of beta binom

Description

Get quantiles of beta binom

Usage

qbetabinom(p, M, mu, phi)

Arguments

p

Numeric. Probability for quantile
M

Numeric vector of sequencing depth
mu

Numeric vector of abundance parameter
phi

Numeric vector of dispersion parameter

Value

quantile

Examples

data(soil_phylum_small_otu1)
mod <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)
qbetabinom(.5, M = mod$M[1], mu = mod$mu.resp[1], phi = mod$phi.resp[1])

Rao-type chi-squared test (model-based or robust)

Description

Rao-type chi-squared test (model-based or robust)

Usage

raotest(mod, mod_null)

Arguments

mod

an object of class bbdml
mod_null

an object of class bbdml, should be nested within mod

Value

P-value from likelihood ratio test.

Examples

data(soil_phylum_small_otu1)
mod1 <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)

mod2 <- bbdml(formula = cbind(W, M - W) ~ 1,
phi.formula = ~ 1,
data = soil_phylum_small_otu1)
raotest(mod1, mod2)

Compute sandwich estimate of variance-covariance matrix

Description

Compute sandwich estimate of variance-covariance matrix

Usage

sand_vcov(mod, numerical = FALSE)

Arguments

mod

an object of class bbdml
numerical

Boolean. Defaults to FALSE. Indicator of whether to use the numeric Hessian and score (not recommended).

Value

Sandwich variance-covariance matrix. A^−1B^A^−1\hat{A}^{-1} \hat{B} \hat{A}^{-1}.

Examples

data(soil_phylum_small_otu1)
mod <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)
sand_vcov(mod)

Compute sandwich standard errors. Legacy function. Use sand_vcov instead.

Description

Compute sandwich standard errors. Legacy function. Use sand_vcov instead.

Usage

sandSE(mod, numerical = FALSE)

Arguments

mod

an object of class bbdml
numerical

Boolean. Defaults to FALSE. Indicator of whether to use the numeric Hessian and score (not recommended).

Value

Sandwich variance-covariance matrix

Examples

data(soil_phylum_small_otu1)
mod <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)
sandSE(mod)

Compute score at the MLE

Description

Compute score at the MLE

Usage

score(mod, numerical = FALSE, get_score_covariance = FALSE)

Arguments

mod

an object of class bbdml
numerical

Boolean. Defaults to FALSE. Indicator of whether to use the numeric Hessian and score (not recommended).
get_score_covariance

Boolean. Defaults to FALSE. Should we return a robust estimate of variance of score: B^(θ^)=∑iG(θ^;Wi)G(θ^;Wi)T\hat{B}(\hat{\theta}) = \sum_i G(\hat{\theta}; W_i) G(\hat{\theta}; W_i)^T. This parameter is not intended for users.

Value

Score at the MLE. For G(θ,w)G(\theta, w) score function, returns ∑iG(θ^,Wi)\sum_i G(\hat{\theta}, W_i) if get_score_covariance = FALSE.

Examples

data(soil_phylum_small_otu1)
mod <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)
score(mod)

Simulate from beta-binomial model

Description

Simulate from beta-binomial model

Usage

## S3 method for class 'bbdml'
simulate(object, nsim, seed = NULL, ...)

Arguments

object

an object of class bbdml
nsim

Integer. Number of simulations
seed

Optional integer to set a random seed
...

There are no additional parameters at this time.

Value

nsim simulations from object

Soil data, otu table as data frame.

Description

A data frame made from a soil 'phyloseq' object with only otu count data.

Usage

soil_phylo_otu

Format

A phyloseq-class experiment-level object with an OTU table.

otu_table

OTU table with 7,770 taxa and 119 samples

References

Whitman, T., Pepe-Ranney, C., Enders, A., Koechli, C., Campbell, A., Buckley, D. H., Lehmann, J. (2016). Dynamics of microbial community composi-tion and soil organic carbon mineralization in soil following addition of pyrogenic andfresh organic matter. The ISME journal, 10(12):2918. <doi: 10.1038/ismej.2016.68>.

Soil data, sample data.

Description

A data frame made from a soil 'phyloseq' object with only sample data.

Usage

soil_phylo_sample

Format

A phyloseq-class experiment-level object with sample data.

sam_data

sample data with the following covariates:

  • Plants, values 0 and 1. Index for different plants

  • Day, values 0 (initial sampling point), 1 (12 days after treatment additions), and 2 (82 days after treatment additions). Index for different days of measurement

  • Amdmt, values 0 (no additions), 1 (biochar additions), and 2 (fresh biomass additions). Index for different soil additives.

  • DayAmdmt, values 00, 01, 02, 10, 11, 12, 20, 21, and 22. A single index for the combination of Day and Amdmt with Day as the first digit and Amdmt as the second digit.

  • ID, values A, B, C, D, and F. Index for different soil plots.

References

Whitman, T., Pepe-Ranney, C., Enders, A., Koechli, C., Campbell, A., Buckley, D. H., Lehmann, J. (2016). Dynamics of microbial community composi-tion and soil organic carbon mineralization in soil following addition of pyrogenic andfresh organic matter. The ISME journal, 10(12):2918. <doi: 10.1038/ismej.2016.68>.

Soil data, taxa table as data frame.

Description

A data frame made from a soil 'phyloseq' object with only taxonomy data.

Usage

soil_phylo_taxa

Format

A phyloseq-class experiment-level object with an OTU table.

tax_table

taxonomy table

References

Whitman, T., Pepe-Ranney, C., Enders, A., Koechli, C., Campbell, A., Buckley, D. H., Lehmann, J. (2016). Dynamics of microbial community composi-tion and soil organic carbon mineralization in soil following addition of pyrogenic andfresh organic matter. The ISME journal, 10(12):2918. <doi: 10.1038/ismej.2016.68>.

Small soil phylum data for contrasts examples, otu table as data frame

Description

A small subset of soil_phylo_otu used for examples of testing contrasts. A data frame made from the 'phyloseq' object with only otu counts.

Usage

soil_phylum_contrasts_otu

Format

A phyloseq-class experiment-level object with an OTU table.

otu_table

OTU table with 39 taxa and 56 samples

References

Whitman, T., Pepe-Ranney, C., Enders, A., Koechli, C., Campbell, A., Buckley, D. H., Lehmann, J. (2016). Dynamics of microbial community composi-tion and soil organic carbon mineralization in soil following addition of pyrogenic andfresh organic matter. The ISME journal, 10(12):2918. <doi: 10.1038/ismej.2016.68>.

Small soil phylum data for contrasts examples, sample data as data frame

Description

A small subset of soil_phylo_sample used for examples of testing contrasts. A data frame made from the 'phyloseq' object with only sample data.

Usage

soil_phylum_contrasts_sample

Format

A phyloseq-class experiment-level object with sample data.

sam_data

sample data with the following covariates:

  • Plants, values 0 and 1. Index for different plants

  • Day, values 0 (initial sampling point), 1 (12 days after treatment additions), and 2 (82 days after treatment additions). Index for different days of measurement

  • Amdmt, values 0 (no additions), 1 (biochar additions), and 2 (fresh biomass additions). Index for different soil additives.

  • DayAmdmt, values 00, 01, 02, 10, 11, 12, 20, 21, and 22. A single index for the combination of Day and Amdmt with Day as the first digit and Amdmt as the second digit.

  • ID, values A, B, C, D, and F. Index for different soil plots.

References

Whitman, T., Pepe-Ranney, C., Enders, A., Koechli, C., Campbell, A., Buckley, D. H., Lehmann, J. (2016). Dynamics of microbial community composi-tion and soil organic carbon mineralization in soil following addition of pyrogenic andfresh organic matter. The ISME journal, 10(12):2918. <doi: 10.1038/ismej.2016.68>.

Small soil phylum data for examples, otu table as data frame

Description

A small subset of soil_phylo_otu used for examples. A data frame made from the 'phyloseq' object with only otu counts.

Usage

soil_phylum_small_otu

Format

A phyloseq-class experiment-level object with an OTU table.

otu_table

OTU table with 39 taxa and 32 samples

References

Whitman, T., Pepe-Ranney, C., Enders, A., Koechli, C., Campbell, A., Buckley, D. H., Lehmann, J. (2016). Dynamics of microbial community composi-tion and soil organic carbon mineralization in soil following addition of pyrogenic andfresh organic matter. The ISME journal, 10(12):2918. <doi: 10.1038/ismej.2016.68>.

Small soil phylum data for examples, sample data as data frame combined with counts for OTU 1 and sequencing depth.

Description

A small subset of soil_phylo_sample used for examples. A data frame made from the 'phyloseq' object with only sample data and counts for OTU 1.

Usage

soil_phylum_small_otu1

Format

A phyloseq-class experiment-level object with sample data and OTU 1 counts.

sam_data

sample data with the following covariates:

  • Plants, values 0 and 1. Index for different plants

  • Day, values 0 (initial sampling point), 1 (12 days after treatment additions), and 2 (82 days after treatment additions). Index for different days of measurement

  • Amdmt, values 0 (no additions), 1 (biochar additions), and 2 (fresh biomass additions). Index for different soil additives.

  • DayAmdmt, values 00, 01, 02, 10, 11, 12, 20, 21, and 22. A single index for the combination of Day and Amdmt with Day as the first digit and Amdmt as the second digit.

  • ID, values A, B, C, D, and F. Index for different soil plots.

  • W, counts for OTU1 in each sample. This OTU corresponds with the phylum Proteobacteria.

  • M, the sequencing depth for each sample.

References

Whitman, T., Pepe-Ranney, C., Enders, A., Koechli, C., Campbell, A., Buckley, D. H., Lehmann, J. (2016). Dynamics of microbial community composi-tion and soil organic carbon mineralization in soil following addition of pyrogenic andfresh organic matter. The ISME journal, 10(12):2918. <doi: 10.1038/ismej.2016.68>.

Small soil phylum data for examples, sample data as data frame

Description

A small subset of soil_phylo_sample used for examples. A data frame made from the 'phyloseq' object with only sample data.

Usage

soil_phylum_small_sample

Format

A phyloseq-class experiment-level object with sample data.

sam_data

sample data with the following covariates:

  • Plants, values 0 and 1. Index for different plants

  • Day, values 0 (initial sampling point), 1 (12 days after treatment additions), and 2 (82 days after treatment additions). Index for different days of measurement

  • Amdmt, values 0 (no additions), 1 (biochar additions), and 2 (fresh biomass additions). Index for different soil additives.

  • DayAmdmt, values 00, 01, 02, 10, 11, 12, 20, 21, and 22. A single index for the combination of Day and Amdmt with Day as the first digit and Amdmt as the second digit.

  • ID, values A, B, C, D, and F. Index for different soil plots.

References

Whitman, T., Pepe-Ranney, C., Enders, A., Koechli, C., Campbell, A., Buckley, D. H., Lehmann, J. (2016). Dynamics of microbial community composi-tion and soil organic carbon mineralization in soil following addition of pyrogenic andfresh organic matter. The ISME journal, 10(12):2918. <doi: 10.1038/ismej.2016.68>.

Summary function

Description

Summary function

Usage

## S3 method for class 'bbdml'
summary(object, ...)

Arguments

object

Object of class bbdml
...

No optional arguments are accepted at this time.

Value

Object of class summary.bbdml. Displays printed model summary.

Examples

data(soil_phylum_small_otu1)
mod <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)
summary(mod)

Wald-type chi-squared test

Description

Wald-type chi-squared test

Usage

waldchisq(
  mod,
  mod_null = NULL,
  restrictions = NULL,
  restrictions.phi = NULL,
  contrasts_DA = NULL,
  contrasts_DV = NULL,
  robust = FALSE
)

Arguments

mod

an object of class bbdml
mod_null

Optional. An object of class bbdml, should be nested within mod. If not included, need to include restrictions or restrictions.phi.
restrictions

Optional. Defaults to NULL. Numeric vector indicating the parameters associated with the abundance to test, or character vector with name of variable to test. Note that 1 is the intercept associated with the abundance.
restrictions.phi

Optional. Defaults to NULL. Numeric vector indicating the parameters associated with the dispersion to test, or character vector with name of variable to test. Note that 1 is the intercept associated with the dispersion.
contrasts_DA

List. Optional. Constructs a contrast matrix. List elements should be characters specifying contrasts in the parameters within formula. Note that this is only available with "Wald" value for test.
contrasts_DV

List. Optional. Constructs a contrast matrix. List elements should be characters specifying contrasts in the parameters within phi.formula. Note that this is only available with "Wald" value for test.
robust

Should robust standard errors be used? If not, model-based standard arras are used. Logical, defaults to FALSE.

Value

Matrix with wald test statistics and p-values. Only performs univariate tests.

P-value from Wald test.

Examples

data(soil_phylum_small_otu1)
mod1 <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)

mod2 <- bbdml(formula = cbind(W, M - W) ~ 1,
phi.formula = ~ 1,
data = soil_phylum_small_otu1)

# Example using mod_null
waldchisq(mod = mod1, mod_null = mod2)
waldchisq(mod = mod1, mod_null = mod2, robust = TRUE)

# Example using restrictions and restrictions.phi
waldchisq(mod = mod1, restrictions = 2, restrictions.phi = 2)
waldchisq(mod = mod1, restrictions = "DayAmdmt", restrictions.phi = "DayAmdmt")
waldchisq(mod = mod1, restrictions = 2, restrictions.phi = "DayAmdmt")
waldchisq(mod = mod1, restrictions = 2, restrictions.phi = 2, robust = TRUE)

Wald-type chi-squared test statistic (model-based or robust)

Description

This is a helper function and not intended for users

Usage

waldchisq_test(
  mod,
  restrictions = NULL,
  restrictions.phi = NULL,
  contrasts_DA = NULL,
  contrasts_DV = NULL,
  robust = FALSE
)

Arguments

mod

an object of class bbdml
restrictions

Optional. Defaults to NULL. Numeric vector indicating the parameters associated with the abundance to test, or character vector with name of variable to test. Note that 1 is the intercept associated with the abundance.
restrictions.phi

Optional. Defaults to NULL. Numeric vector indicating the parameters associated with the dispersion to test, or character vector with name of variable to test. Note that 1 is the intercept associated with the dispersion.
contrasts_DA

List. Optional. Constructs a contrast matrix. List elements should be characters specifying contrasts in the parameters within formula. Note that this is only available with "Wald" value for test.
contrasts_DV

List. Optional. Constructs a contrast matrix. List elements should be characters specifying contrasts in the parameters within phi.formula. Note that this is only available with "Wald" value for test.
robust

Should robust standard errors be used? If not, model-based standard arras are used. Logical, defaults to FALSE.

Value

Test statistic for Wald test.

Wald-type t test (model-based or robust)

Description

Wald-type t test (model-based or robust)

Usage

waldt(mod)

Arguments

mod

an object of class bbdml

Value

Matrix with wald test statistics and p-values. Only performs univariate tests.

Examples

data(soil_phylum_small_otu1)
mod <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)
waldt(mod)

Function to throw error if the 'phyloseq' package is called but it is not installed

Description

Function to throw error if the 'phyloseq' package is called but it is not installed

Usage

warn_phyloseq()