From e35b73e74f51ed7b8c002227f6c14f891024737f Mon Sep 17 00:00:00 2001 From: Zachary Kurtz Date: Wed, 25 Oct 2017 18:26:29 -0400 Subject: [PATCH] updated namespace and man via roxygen --- DESCRIPTION | 4 +- NAMESPACE | 1 - R/SparseICov.R | 74 ++++++++++++++++++----------------- man/adj2igraph.Rd | 1 - man/alr.Rd | 1 - man/as.data.frame.graph.Rd | 1 - man/as.matrix.graph.Rd | 1 - man/band.Rd | 1 - man/block.Rd | 1 - man/clr.Rd | 1 - man/cluster.Rd | 1 - man/cor2cov.Rd | 1 - man/cov2prec.Rd | 1 - man/erdos_renyi.Rd | 1 - man/fitdistr.Rd | 1 - man/getOptBeta.Rd | 1 - man/getOptMerge.Rd | 1 - man/get_comm_params.Rd | 1 - man/graph2prec.Rd | 1 - man/graph2prec2.Rd | 1 - man/hub.Rd | 1 - man/icov.select.Rd | 1 - man/make_graph.Rd | 1 - man/make_precision_mat.Rd | 1 - man/neff.Rd | 1 - man/norm_diric.Rd | 1 - man/norm_pseudo.Rd | 1 - man/norm_to_total.Rd | 1 - man/prec2cov.Rd | 1 - man/pval.sparccboot.Rd | 1 - man/qqdplot.Rd | 1 - man/qqdplot_comm.Rd | 1 - man/rmvnegbin.Rd | 1 - man/rmvnorm.Rd | 1 - man/rmvpois.Rd | 1 - man/rmvzinegbin.Rd | 1 - man/rmvzipois.Rd | 1 - man/rzipois.Rd | 1 - man/scale_free.Rd | 1 - man/shannon.Rd | 1 - man/sparcc.Rd | 1 - man/sparccboot.Rd | 1 - man/sparseiCov.Rd | 1 - man/spiec.easi.Rd | 1 - man/spiec.easi.default.Rd | 1 - man/spiec.easi.phyloseq.Rd | 1 - man/stars.roc.Rd | 3 +- man/symBeta.Rd | 1 - man/synth_comm_from_counts.Rd | 1 - 49 files changed, 41 insertions(+), 86 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5fe2b95..87f55fe 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: SpiecEasi Title: Sparse Inverse Covariance for Ecological Statistical Inference -Version: 0.1.2 +Version: 0.1.3 Authors.R: c(person("Zachary", "Kurtz", role = c("aut", "cre"), email="zachary.kurtz@med.nyu.edu"), person("Christian", "Mueller", role = c("aut")), person("Emily", "Miraldi", @@ -21,4 +21,4 @@ Suggests: testthat License: getOptions('devtools.desc.license') LazyData: true -RoxygenNote: 5.0.1 +RoxygenNote: 6.0.1 diff --git a/NAMESPACE b/NAMESPACE index 7baaa95..bc35ab9 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -48,7 +48,6 @@ export(synth_comm_from_counts) export(tril) export(triu) export(triu2diag) -import(phyloseq) importFrom(MASS,ginv) importFrom(VGAM,dzinegbin) importFrom(VGAM,dzipois) diff --git a/R/SparseICov.R b/R/SparseICov.R index 651c663..343ac11 100644 --- a/R/SparseICov.R +++ b/R/SparseICov.R @@ -8,9 +8,11 @@ spiec.easi <- function(obj, ...) { #' Spiec-Easi pipeline #' @method spiec.easi phyloseq -#' @import phyloseq #' @export spiec.easi.phyloseq <- function(obj, ...) { + if (!require('foo')) { + stop('\'Phyloseq\' package is not installed') + } OTU <- otu_table(obj)@.Data if (otu_table(obj)@taxa_are_rows) OTU <- t(OTU) spiec.easi.default(OTU, ...) @@ -25,15 +27,15 @@ spiec.easi.phyloseq <- function(obj, ...) { #' @param ... further arguments to sparseiCov #' @method spiec.easi default #' @export -spiec.easi.default <- function(data, method='glasso', sel.criterion='stars', verbose=TRUE, +spiec.easi.default <- function(data, method='glasso', sel.criterion='stars', verbose=TRUE, icov.select=TRUE, icov.select.params=list(), ...) { - + args <- list(...) if (verbose) message("Normalizing/clr transformation of data with pseudocount ...") data.clr <- t(clr(data+1, 1)) if (verbose) message(paste("Inverse Covariance Estimation with", method, "...", sep=" ")) est <- do.call('sparseiCov', c(list(data=data.clr, method=method), args)) - + if (icov.select) { if (verbose) message(paste("Model selection with", sel.criterion, "...", sep=" ")) est <- do.call('icov.select', c(list(est=est, criterion=sel.criterion), icov.select.params)) @@ -90,7 +92,7 @@ spiec.easi.default <- function(data, method='glasso', sel.criterion='stars', ver #' huge::huge.roc(est.f$path, Theta) #' sparseiCov <- function(data, method, npn=FALSE, verbose=FALSE, cov.output = TRUE, ...) { - + if (npn) data <- huge::huge.npn(data, verbose=verbose) args <- list(...) @@ -100,7 +102,7 @@ sparseiCov <- function(data, method, npn=FALSE, verbose=FALSE, cov.output = TRUE if (is.null(args$lambda.min.ratio)) args$lambda.min.ratio <- 1e-3 if (method %in% c("glasso")) { - do.call(huge::huge, c(args, list(x=data, method=method, verbose=verbose, + do.call(huge::huge, c(args, list(x=data, method=method, verbose=verbose, cov.output = cov.output))) } else if (method %in% c('mb')) { @@ -115,7 +117,7 @@ sparseiCov <- function(data, method, npn=FALSE, verbose=FALSE, cov.output = TRUE #' Model selection for picking the right \code{lambda} penalty. #' This is identical to huge::huge.stars except that the subsampling loop is replaced with an mclapply function to add parallelization capabilities. -#' +#' #' @param est an estimate/model as produced by the sparseiCov function #' @param criterion character string specifying criterion/method for model selection accepts 'stars' [default], 'ric', 'ebic' #' @param stars.thresh variability threshold for stars selection @@ -126,7 +128,7 @@ sparseiCov <- function(data, method, npn=FALSE, verbose=FALSE, cov.output = TRUE #' @param normfun normalize internally if data should be renormalized #' @importFrom parallel mclapply #' @export -icov.select <- function(est, criterion = 'stars', stars.thresh = 0.05, ebic.gamma = 0.5, +icov.select <- function(est, criterion = 'stars', stars.thresh = 0.05, ebic.gamma = 0.5, stars.subsample.ratio = NULL, rep.num = 20, ncores=1, normfun=function(x) x, verbose=FALSE) { gcinfo(FALSE) if (est$cov.input) { @@ -135,9 +137,9 @@ icov.select <- function(est, criterion = 'stars', stars.thresh = 0.05, ebic.gamm return(est) } if (!est$cov.input) { - if (est$method == "mb" && is.null(criterion)) + if (est$method == "mb" && is.null(criterion)) criterion = "stars" - if (est$method == "ct" && is.null(criterion)) + if (est$method == "ct" && is.null(criterion)) criterion = "ebic" n = nrow(est$data) d = ncol(est$data) @@ -155,8 +157,8 @@ icov.select <- function(est, criterion = 'stars', stars.thresh = 0.05, ebic.gamm nr = n r = 1:n } - out = .C("RIC", X = as.double(est$data), dd = as.integer(d), - nn = as.integer(n), r = as.integer(r), nr = as.integer(nr), + out = .C("RIC", X = as.double(est$data), dd = as.integer(d), + nn = as.integer(n), r = as.integer(r), nr = as.integer(nr), lambda_opt = as.double(0), PACKAGE = "huge") est$opt.lambda = out$lambda_opt/n rm(out) @@ -169,28 +171,28 @@ icov.select <- function(est, criterion = 'stars', stars.thresh = 0.05, ebic.gamm message("Computing the optimal graph....") # flush.console() } - if (est$opt.lambda > max(cor(est$data))) + if (est$opt.lambda > max(cor(est$data))) est$refit = Matrix(0, d, d) else { - if (est$method == "mb") - est$refit = huge::huge.mb(est$data, lambda = est$opt.lambda, + if (est$method == "mb") + est$refit = huge::huge.mb(est$data, lambda = est$opt.lambda, sym = est$sym, idx.mat = est$idx.mat, verbose = FALSE)$path[[1]] if (est$method == "glasso") { if (!is.null(est$cov)) { - tmp = huge::huge.glasso(est$data, lambda = est$opt.lambda, + tmp = huge::huge.glasso(est$data, lambda = est$opt.lambda, scr = est$scr, cov.output = TRUE, verbose = FALSE) est$opt.cov = tmp$cov[[1]] } - if (is.null(est$cov)) - tmp = huge::huge.glasso(est$data, lambda = est$opt.lambda, + if (is.null(est$cov)) + tmp = huge::huge.glasso(est$data, lambda = est$opt.lambda, verbose = FALSE) est$refit = tmp$path[[1]] est$opt.icov = tmp$icov[[1]] rm(tmp) gc() } - if (est$method == "ct") - est$refit = huge::huge.ct(est$data, lambda = est$opt.lambda, + if (est$method == "ct") + est$refit = huge::huge.ct(est$data, lambda = est$opt.lambda, verbose = FALSE)$path[[1]] } est$opt.sparsity = sum(est$refit)/d/(d - 1) @@ -208,7 +210,7 @@ icov.select <- function(est, criterion = 'stars', stars.thresh = 0.05, ebic.gamm est$opt.index = which.min(est$ebic.score) est$refit = est$path[[est$opt.index]] est$opt.icov = est$icov[[est$opt.index]] - if (est$cov.output) + if (est$cov.output) est$opt.cov = est$cov[[est$opt.index]] est$opt.lambda = est$lambda[est$opt.index] est$opt.sparsity = est$sparsity[est$opt.index] @@ -219,14 +221,14 @@ icov.select <- function(est, criterion = 'stars', stars.thresh = 0.05, ebic.gamm } if (criterion == "stars") { if (is.null(stars.subsample.ratio)) { - if (n > 144) + if (n > 144) stars.subsample.ratio = 10 * sqrt(n)/n - if (n <= 144) + if (n <= 144) stars.subsample.ratio = 0.8 } - + # for (i in 1:nlambda) merge[[i]] <- Matrix(0, d, d) - + if (verbose) { mes = "Conducting Subsampling....." message(mes, appendLF = FALSE) @@ -236,23 +238,23 @@ icov.select <- function(est, criterion = 'stars', stars.thresh = 0.05, ebic.gamm # for (i in 1:rep.num) { premerge <- parallel::mclapply(1:rep.num, function(i) { # if (verbose) { - # mes <- paste(c("Conducting Subsampling....in progress:", + # mes <- paste(c("Conducting Subsampling....in progress:", # floor(100 * i/rep.num), "%"), collapse = "") # cat(mes, "\r") # flush.console() # } # merge <- replicate(nlambda, Matrix(0, d,d)) - ind.sample = sample(c(1:n), floor(n * stars.subsample.ratio), + ind.sample = sample(c(1:n), floor(n * stars.subsample.ratio), replace = FALSE) - if (est$method == "mb") - tmp = huge::huge.mb(normfun(est$data[ind.sample, ]), lambda = est$lambda, - scr = est$scr, idx.mat = est$idx.mat, sym = est$sym, + if (est$method == "mb") + tmp = huge::huge.mb(normfun(est$data[ind.sample, ]), lambda = est$lambda, + scr = est$scr, idx.mat = est$idx.mat, sym = est$sym, verbose = FALSE)$path - if (est$method == "ct") - tmp = huge::huge.ct(normfun(est$data[ind.sample, ]), lambda = est$lambda, + if (est$method == "ct") + tmp = huge::huge.ct(normfun(est$data[ind.sample, ]), lambda = est$lambda, verbose = FALSE)$path - if (est$method == "glasso") - tmp = huge::huge.glasso(normfun(est$data[ind.sample, ]), lambda = est$lambda, + if (est$method == "glasso") + tmp = huge::huge.glasso(normfun(est$data[ind.sample, ]), lambda = est$lambda, scr = est$scr, verbose = FALSE)$path # for (j in 1:nlambda) merge[[j]] <- merge[[j]] + tmp[[j]] @@ -279,14 +281,14 @@ icov.select <- function(est, criterion = 'stars', stars.thresh = 0.05, ebic.gamm est$merge[[i]] <- merge[[i]]/rep.num est$variability[i] <- 4 * sum(est$merge[[i]] * (1 - est$merge[[i]]))/(d * (d - 1)) } - est$opt.index = max(which.max(est$variability >= + est$opt.index = max(which.max(est$variability >= stars.thresh)[1] - 1, 1) est$refit = est$path[[est$opt.index]] est$opt.lambda = est$lambda[est$opt.index] est$opt.sparsity = est$sparsity[est$opt.index] if (est$method == "glasso") { est$opt.icov = est$icov[[est$opt.index]] - if (!is.null(est$cov)) + if (!is.null(est$cov)) est$opt.cov = est$cov[[est$opt.index]] } } diff --git a/man/adj2igraph.Rd b/man/adj2igraph.Rd index d3c972c..daab797 100644 --- a/man/adj2igraph.Rd +++ b/man/adj2igraph.Rd @@ -21,4 +21,3 @@ adj2igraph(Adj, rmEmptyNodes = FALSE, diag = FALSE, edge.attr = list(), \description{ Convert an adjacency matrix (ie - from the \code{sparseiCov} function) to an igraph object } - diff --git a/man/alr.Rd b/man/alr.Rd index 2b9c8cc..341d1a2 100644 --- a/man/alr.Rd +++ b/man/alr.Rd @@ -9,4 +9,3 @@ alr(x, ...) \description{ Additive log-ratio functions } - diff --git a/man/as.data.frame.graph.Rd b/man/as.data.frame.graph.Rd index db4200a..ca7082f 100644 --- a/man/as.data.frame.graph.Rd +++ b/man/as.data.frame.graph.Rd @@ -9,4 +9,3 @@ \description{ s3 method for graph to other data types } - diff --git a/man/as.matrix.graph.Rd b/man/as.matrix.graph.Rd index d3a93b2..28efae7 100644 --- a/man/as.matrix.graph.Rd +++ b/man/as.matrix.graph.Rd @@ -9,4 +9,3 @@ \description{ s3 method for graph to other data types } - diff --git a/man/band.Rd b/man/band.Rd index 4767ed2..3923dd3 100644 --- a/man/band.Rd +++ b/man/band.Rd @@ -9,4 +9,3 @@ band(D, e) \description{ keywords internal } - diff --git a/man/block.Rd b/man/block.Rd index 5db6634..afeed37 100644 --- a/man/block.Rd +++ b/man/block.Rd @@ -9,4 +9,3 @@ block(D, e, numHubs) \description{ keywords internal } - diff --git a/man/clr.Rd b/man/clr.Rd index 318fef7..d545f51 100644 --- a/man/clr.Rd +++ b/man/clr.Rd @@ -9,4 +9,3 @@ clr(x, ...) \description{ Centered log-ratio functions } - diff --git a/man/cluster.Rd b/man/cluster.Rd index 0fbe1eb..c763f97 100644 --- a/man/cluster.Rd +++ b/man/cluster.Rd @@ -9,4 +9,3 @@ cluster(D, e, numHubs = floor((D/15) + (e/D)) - 1) \description{ keywords internal } - diff --git a/man/cor2cov.Rd b/man/cor2cov.Rd index 4b96103..dc48d21 100644 --- a/man/cor2cov.Rd +++ b/man/cor2cov.Rd @@ -19,4 +19,3 @@ Covariance matrix of sample dimension as cor Convert a symmetric correlation matrix to a covariance matrix given the standard deviation } - diff --git a/man/cov2prec.Rd b/man/cov2prec.Rd index cf73f60..76988d7 100644 --- a/man/cov2prec.Rd +++ b/man/cov2prec.Rd @@ -14,4 +14,3 @@ cov2prec(Cov, tol = 1e-04) \description{ Covariance matrix to its matrix inverse (Precision matrix) } - diff --git a/man/erdos_renyi.Rd b/man/erdos_renyi.Rd index 0b4bd91..9215582 100644 --- a/man/erdos_renyi.Rd +++ b/man/erdos_renyi.Rd @@ -9,4 +9,3 @@ erdos_renyi(D, e, p = e/(D * (D - 1)/2)) \description{ keywords internal } - diff --git a/man/fitdistr.Rd b/man/fitdistr.Rd index 25b6679..82e455d 100644 --- a/man/fitdistr.Rd +++ b/man/fitdistr.Rd @@ -20,4 +20,3 @@ fitdistr(x, densfun, start, control, ...) \description{ Fit parameters of a marginal distribution to some data vector } - diff --git a/man/getOptBeta.Rd b/man/getOptBeta.Rd index 3a951e8..7930753 100644 --- a/man/getOptBeta.Rd +++ b/man/getOptBeta.Rd @@ -15,4 +15,3 @@ Weighted, non-symmetric matrix of model coefficients. \description{ Get the optimal beta matrix when MB neighborhood selection is run with StARS } - diff --git a/man/getOptMerge.Rd b/man/getOptMerge.Rd index 5ca8cdb..765c354 100644 --- a/man/getOptMerge.Rd +++ b/man/getOptMerge.Rd @@ -15,4 +15,3 @@ Weighted, symmetric matrix of edge probability estimates. \description{ Get the optimal merge matrix StARS is run. } - diff --git a/man/get_comm_params.Rd b/man/get_comm_params.Rd index 687098b..a3c48d3 100644 --- a/man/get_comm_params.Rd +++ b/man/get_comm_params.Rd @@ -17,4 +17,3 @@ list of parameters \description{ Get the parameters for the OTUs (along mar) of each community } - diff --git a/man/graph2prec.Rd b/man/graph2prec.Rd index cedc754..175e54f 100644 --- a/man/graph2prec.Rd +++ b/man/graph2prec.Rd @@ -11,4 +11,3 @@ graph2prec(Graph, posThetaLims = c(2, 3), negThetaLims = -posThetaLims, Has internal rules for converting various graph topologies into the associated adjancency and, therefore, precision matrix } - diff --git a/man/graph2prec2.Rd b/man/graph2prec2.Rd index d38a45b..0ba2532 100644 --- a/man/graph2prec2.Rd +++ b/man/graph2prec2.Rd @@ -16,4 +16,3 @@ Has internal rules for converting various graph topologies into the associated adjancency and, therefore, precision matrix } \keyword{internal} - diff --git a/man/hub.Rd b/man/hub.Rd index 5efe2a9..62045be 100644 --- a/man/hub.Rd +++ b/man/hub.Rd @@ -9,4 +9,3 @@ hub(D, e, numHubs = ceiling(D/20)) \description{ keywords internal } - diff --git a/man/icov.select.Rd b/man/icov.select.Rd index 94aa68f..f7e4827 100644 --- a/man/icov.select.Rd +++ b/man/icov.select.Rd @@ -30,4 +30,3 @@ icov.select(est, criterion = "stars", stars.thresh = 0.05, Model selection for picking the right \code{lambda} penalty. This is identical to huge::huge.stars except that the subsampling loop is replaced with an mclapply function to add parallelization capabilities. } - diff --git a/man/make_graph.Rd b/man/make_graph.Rd index 6b91de6..2ccd8c9 100644 --- a/man/make_graph.Rd +++ b/man/make_graph.Rd @@ -20,4 +20,3 @@ make_graph(method, D, e, enforce = TRUE, ...) \description{ Procedure to generate graph topologies for Gaussian Graphical Models } - diff --git a/man/make_precision_mat.Rd b/man/make_precision_mat.Rd index fb371dd..fab9540 100644 --- a/man/make_precision_mat.Rd +++ b/man/make_precision_mat.Rd @@ -19,4 +19,3 @@ make_precision_mat(method, D, u, v, ...) DEPREICATED FUNCTION Wrapper function for generating a Precision matrix } \keyword{internal} - diff --git a/man/neff.Rd b/man/neff.Rd index 5734775..668d421 100644 --- a/man/neff.Rd +++ b/man/neff.Rd @@ -15,4 +15,3 @@ N_eff in base e \description{ N_effective: Compute the exponential of the shannon entropy. linearizes shannon entropy, for a better diveristy metric (effective number of species) } - diff --git a/man/norm_diric.Rd b/man/norm_diric.Rd index 8cfb7f9..165a89e 100644 --- a/man/norm_diric.Rd +++ b/man/norm_diric.Rd @@ -9,4 +9,3 @@ norm_diric(x, rep = 1) \description{ importFrom VGAM rdiric } - diff --git a/man/norm_pseudo.Rd b/man/norm_pseudo.Rd index 3ee18dc..206499a 100644 --- a/man/norm_pseudo.Rd +++ b/man/norm_pseudo.Rd @@ -9,4 +9,3 @@ norm_pseudo(x) \description{ add pseudocount before normalizing a vector } - diff --git a/man/norm_to_total.Rd b/man/norm_to_total.Rd index a760ce5..be18809 100644 --- a/man/norm_to_total.Rd +++ b/man/norm_to_total.Rd @@ -9,4 +9,3 @@ norm_to_total(x) \description{ Total sum normalization of a (presumably positive) data vector } - diff --git a/man/prec2cov.Rd b/man/prec2cov.Rd index 0756414..6cb836b 100644 --- a/man/prec2cov.Rd +++ b/man/prec2cov.Rd @@ -14,4 +14,3 @@ prec2cov(Precision, tol = 1e-04) \description{ Precision matrix (inverse covariance) to a covariance matrix } - diff --git a/man/pval.sparccboot.Rd b/man/pval.sparccboot.Rd index e52696a..f531dfc 100644 --- a/man/pval.sparccboot.Rd +++ b/man/pval.sparccboot.Rd @@ -14,4 +14,3 @@ pval.sparccboot(x, sided = "both") \description{ Compute empirical p-values from \code{sparccboot} output } - diff --git a/man/qqdplot.Rd b/man/qqdplot.Rd index c259759..6d73058 100644 --- a/man/qqdplot.Rd +++ b/man/qqdplot.Rd @@ -10,4 +10,3 @@ qqdplot(y, distr, param, plot = TRUE, ...) deprecated?? } \keyword{internal} - diff --git a/man/qqdplot_comm.Rd b/man/qqdplot_comm.Rd index 582284f..f5da516 100644 --- a/man/qqdplot_comm.Rd +++ b/man/qqdplot_comm.Rd @@ -9,4 +9,3 @@ qqdplot_comm(comm, distr, param, plot = TRUE, ...) \description{ qq-plot for theoretical vs observed communities } - diff --git a/man/rmvnegbin.Rd b/man/rmvnegbin.Rd index 9189830..509285f 100644 --- a/man/rmvnegbin.Rd +++ b/man/rmvnegbin.Rd @@ -29,4 +29,3 @@ rmvnegbin(n, mu, Sigma, ks, ...) Generate multivariate, Zero-inflated negative binomial data, with counts approximately correlated according to Sigma } - diff --git a/man/rmvnorm.Rd b/man/rmvnorm.Rd index cea47f0..99bc556 100644 --- a/man/rmvnorm.Rd +++ b/man/rmvnorm.Rd @@ -26,4 +26,3 @@ rmvnorm(n = 100, mu = rep(0, 10), Sigma = diag(10), tol = 1e-06, Draw samples from multivariate, correlated normal distribution with counts correlated according to Sigma } - diff --git a/man/rmvpois.Rd b/man/rmvpois.Rd index 72b5a3a..50be9a1 100644 --- a/man/rmvpois.Rd +++ b/man/rmvpois.Rd @@ -25,4 +25,3 @@ rmvpois(n, mu, Sigma, ...) Generate multivariate poisson data, with counts approximately correlated according to Sigma } - diff --git a/man/rmvzinegbin.Rd b/man/rmvzinegbin.Rd index 6cd8c9a..7a04796 100644 --- a/man/rmvzinegbin.Rd +++ b/man/rmvzinegbin.Rd @@ -27,4 +27,3 @@ rmvzinegbin(n, mu, Sigma, munbs, ks, ps, ...) Generate multivariate, negative binomial data, with counts approximately correlated according to Sigma } - diff --git a/man/rmvzipois.Rd b/man/rmvzipois.Rd index 67447a3..998c8b9 100644 --- a/man/rmvzipois.Rd +++ b/man/rmvzipois.Rd @@ -25,4 +25,3 @@ rmvzipois(n, mu, Sigma, lambdas, ps, ...) Generate multivariate, Zero-inflated poisson data, with counts approximately correlated according to Sigma } - diff --git a/man/rzipois.Rd b/man/rzipois.Rd index 370f198..0268751 100644 --- a/man/rzipois.Rd +++ b/man/rzipois.Rd @@ -19,4 +19,3 @@ Poisson counts of length \eqn{n} \description{ Draw samples from a zero-inflated poisson distribution } - diff --git a/man/scale_free.Rd b/man/scale_free.Rd index f5371b8..2426c17 100644 --- a/man/scale_free.Rd +++ b/man/scale_free.Rd @@ -9,4 +9,3 @@ scale_free(D, e, pfun) \description{ keywords internal } - diff --git a/man/shannon.Rd b/man/shannon.Rd index 2195a50..e29be5b 100644 --- a/man/shannon.Rd +++ b/man/shannon.Rd @@ -16,4 +16,3 @@ shannon entropy in base e Shannon entropy is: sum [ x_i log(x_i) ] } - diff --git a/man/sparcc.Rd b/man/sparcc.Rd index fd74962..0972e0b 100644 --- a/man/sparcc.Rd +++ b/man/sparcc.Rd @@ -16,4 +16,3 @@ sparcc(data, iter = 20, inner_iter = 10, th = 0.1) \description{ reimplementation of SparCC in R } - diff --git a/man/sparccboot.Rd b/man/sparccboot.Rd index 57636ed..c26f807 100644 --- a/man/sparccboot.Rd +++ b/man/sparccboot.Rd @@ -22,4 +22,3 @@ sparccboot object. Pass to \code{pval.sparccboot} to get empirical p-values \description{ Bootstrapped Sparcc to get empirical and null distributions for correlations } - diff --git a/man/sparseiCov.Rd b/man/sparseiCov.Rd index 6210c17..c93e3ed 100644 --- a/man/sparseiCov.Rd +++ b/man/sparseiCov.Rd @@ -57,4 +57,3 @@ huge::huge.roc(est.log$path, Theta) huge::huge.roc(est.f$path, Theta) } - diff --git a/man/spiec.easi.Rd b/man/spiec.easi.Rd index c4006c3..45684c7 100644 --- a/man/spiec.easi.Rd +++ b/man/spiec.easi.Rd @@ -13,4 +13,3 @@ Spiec-Easi pipeline Run the whole analysis, from data transformation, iCov estimation and model selection. Inputs are a non-normalized OTU table and pipeline options. } - diff --git a/man/spiec.easi.default.Rd b/man/spiec.easi.default.Rd index 7f7c481..139c23a 100644 --- a/man/spiec.easi.default.Rd +++ b/man/spiec.easi.default.Rd @@ -22,4 +22,3 @@ \description{ Spiec-Easi pipeline } - diff --git a/man/spiec.easi.phyloseq.Rd b/man/spiec.easi.phyloseq.Rd index 4557233..9d4aa76 100644 --- a/man/spiec.easi.phyloseq.Rd +++ b/man/spiec.easi.phyloseq.Rd @@ -9,4 +9,3 @@ \description{ Spiec-Easi pipeline } - diff --git a/man/stars.roc.Rd b/man/stars.roc.Rd index a838065..d145b36 100644 --- a/man/stars.roc.Rd +++ b/man/stars.roc.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/roc.R \name{stars.roc} -\alias{stars.pr} \alias{stars.roc} +\alias{stars.pr} \title{stars.roc, stars.pr} \usage{ stars.roc(optmerge, theta, verbose = TRUE, plot = TRUE, ll = 15) @@ -24,4 +24,3 @@ along the stars 'confidence path'. Each edge is a number in [0,1], which is on the fraction of inferred graphs over subsamples in which that edge appeared in stars. } - diff --git a/man/symBeta.Rd b/man/symBeta.Rd index 9b03af6..60b9a41 100644 --- a/man/symBeta.Rd +++ b/man/symBeta.Rd @@ -26,4 +26,3 @@ Mode can be: \item lower: Take the values from the lower triangle } } - diff --git a/man/synth_comm_from_counts.Rd b/man/synth_comm_from_counts.Rd index 2aa754a..aea8a2f 100644 --- a/man/synth_comm_from_counts.Rd +++ b/man/synth_comm_from_counts.Rd @@ -29,4 +29,3 @@ community from count data (ex HMP) fit parameters to OTU margins and simulate a new community with those properties } -