Commit f6770d2d authored by Jakob Wirbel's avatar Jakob Wirbel
Browse files

bugfix for external predictions, version bump to trigger new build.

parent 6d7db8fd
......@@ -2,7 +2,7 @@ Package: SIAMCAT
Type: Package
Title: Statistical Inference of Associations between Microbial
Communities And host phenoTypes
Version: 1.99.3
Version: 1.99.4
Authors@R: c(person("Konrad", "Zych", role = c("aut"),
email = "konrad.zych@embl.de",
comment = c(ORCID = "0000-0001-7426-0516")),
......@@ -60,7 +60,7 @@ Imports:
lgr
License: GPL-3
LazyData: true
RoxygenNote: 7.1.1
RoxygenNote: 7.1.2
biocViews: ImmunoOncology, Metagenomics, Classification, Microbiome,
Sequencing, Preprocessing, Clustering, FeatureExtraction,
GeneticVariability, MultipleComparison,Regression
......
......@@ -247,7 +247,8 @@ make.external.predictions <- function(siamcat.trained, siamcat.external,
" on complete external dataset", " (", i, " of ",
num.models, ")..."))
if (label$type == 'BINARY'){
data$label <- as.factor(sample(c(0,1), size=nrow(data),
data$label <- as.factor(sample(unique(label$label),
size=nrow(data),
replace=TRUE))
test.task <- TaskClassif$new(id='classif', backend=data,
target='label')
......
......@@ -4,23 +4,11 @@
\name{SIAMCAT-package}
\alias{SIAMCAT}
\alias{SIAMCAT-package}
\title{SIAMCAT: Statistical Inference of Associations between Microbial
Communities And host phenoTypes}
\title{SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes}
\description{
\if{html}{\figure{logo.png}{options: align='right' alt='logo' width='120'}}
Pipeline for Statistical Inference of Associations between
Microbial Communities And host phenoTypes (SIAMCAT). A primary goal
of analyzing microbiome data is to determine changes in community
composition that are associated with environmental factors. In particular,
linking human microbiome composition to host phenotypes such as diseases
has become an area of intense research. For this, robust statistical
modeling and biomarker extraction toolkits are crucially needed. SIAMCAT
provides a full pipeline supporting data preprocessing, statistical
association testing, statistical modeling (LASSO logistic regression)
including tools for evaluation and interpretation of these models (such as
cross validation, parameter selection, ROC analysis and diagnostic
model plots).
Pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes (SIAMCAT). A primary goal of analyzing microbiome data is to determine changes in community composition that are associated with environmental factors. In particular, linking human microbiome composition to host phenotypes such as diseases has become an area of intense research. For this, robust statistical modeling and biomarker extraction toolkits are crucially needed. SIAMCAT provides a full pipeline supporting data preprocessing, statistical association testing, statistical modeling (LASSO logistic regression) including tools for evaluation and interpretation of these models (such as cross validation, parameter selection, ROC analysis and diagnostic model plots).
}
\details{
SIAMCAT is a pipeline for Statistical Inference of Associations between
......
......@@ -4,7 +4,7 @@
\alias{filter.label}
\title{Filter the label of a SIMACAT object}
\usage{
\method{filter}{label}(siamcat, ids, verbose = 1)
filter.label(siamcat, ids, verbose = 1)
}
\arguments{
\item{siamcat}{an object of class \link{siamcat-class}}
......
......@@ -5,9 +5,9 @@
\alias{model.interpretation.plot}
\title{Model Interpretation Plot}
\usage{
model.interpretation.plot(siamcat, fn.plot = NULL,
model.interpretation.plot(siamcat, fn.plot = NULL,
color.scheme = "BrBG", consens.thres = 0.5, heatmap.type = "zscore",
limits = c(-3, 3), log.n0 = 1e-06, max.show = 50, prompt=TRUE,
limits = c(-3, 3), log.n0 = 1e-06, max.show = 50, prompt=TRUE,
verbose = 1)
}
\arguments{
......
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