Package: MicrobTiSDA 0.1.0

Shijia Li

MicrobTiSDA: Microbiome Time-Series Data Analysis

Provides tools specifically designed for analyzing longitudinal microbiome data. This tool integrates seven functional modules, providing a systematic framework for microbiome time-series analysis. For more details on inferences involving interspecies interactions see Fisher (2014) <doi:10.1371/journal.pone.0102451>. Details on this package are also described in an unpublished manuscript.

Authors:Shijia Li [aut, cre]

MicrobTiSDA_0.1.0.tar.gz
MicrobTiSDA_0.1.0.zip(r-4.7-any)MicrobTiSDA_0.1.0.zip(r-4.6-any)MicrobTiSDA_0.1.0.zip(r-4.5-any)
MicrobTiSDA_0.1.0.tgz(r-4.6-any)MicrobTiSDA_0.1.0.tgz(r-4.5-any)
MicrobTiSDA_0.1.0.tar.gz(r-4.7-any)MicrobTiSDA_0.1.0.tar.gz(r-4.6-any)
MicrobTiSDA_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MicrobTiSDA/json (API)

# Install 'MicrobTiSDA' in R:

install.packages('MicrobTiSDA', repos = c('https://lishijiagg.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lishijiagg/microbtisda/issues

Datasets:

fujita.data - Example dataset 2 - The in vitro aquatic microbiota dataset.
fujita.meta - Example dataset 2 - sample metadata.
fujita.taxa - Example dataset 2 - taxonomic information.
OSLO.infant.data - Example dataset 1 - The OSLO term infant gut microbiota dataset.
OSLO.infant.meta - Example dataset 1 - sample metadata.
OSLO.infant.taxa - Example dataset 1 - taxonomic information.
preterm.data - Example dataset 3 - The preterm infant gut microbiota dataset.
preterm.meta - Example dataset 3 - sample metadata.
preterm.taxa - Example dataset 3 - taxonomic information.

On CRAN:

4.48 score 6 stars 267 downloads 19 exports 114 dependencies

Last updated from:425b709f37. Checks:7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	WARNING	291
source / vignettes	OK	575
linux-release	WARNING	331
macos-release	WARNING	240
macos-oldrel	WARNING	409
windows-devel	WARNING	215
windows-release	WARNING	242
windows-oldrel	WARNING	240
wasm-release	OK	224

Exports:Classify.vis Data.cluster Data.cluster.cut Data.filter Data.interpolate Data.opp.cor.vis Data.rf.classifier Data.trans Data.visual Data.visual.MESR Design Interact.dyvis mclr.transform Pred.data Pred.data.MESR Reg.MESR Reg.SPLR Rf.biomarkers Spec.interact

Dependencies:base64enc bslib cachem caret class cli clock cluster codetools cpp11 data.table diagram digest dplyr e1071 evaluate farver fastmap fontawesome foreach fs future future.apply generics ggdendro ggforce ggplot2 ggraph ggrepel globals glue gower graphlayouts gridExtra gtable hardhat highr htmltools htmlwidgets igraph ipred isoband iterators jquerylib jsonlite KernSmooth knitr labeling lattice lava lifecycle listenv lubridate magrittr MASS Matrix memoise mgcv mime ModelMetrics nlme nnet numDeriv parallelly permute pillar pkgconfig plyr polyclip pracma pROC prodlim progressr proxy purrr R6 randomForest rappdirs RColorBrewer Rcpp RcppArmadillo recipes reshape2 rlang rmarkdown rpart S7 sass scales shape sparsevctrs SQUAREM stringi stringr survival systemfonts tibble tidygraph tidyr tidyselect timechange timeDate tinytex tweenr tzdb utf8 vctrs vegan viridis viridisLite visNetwork withr xfun yaml

MicrobTiSDA

Getting started | Case study 1: Infant gut microbiome dataset | Case study 2: Gut microbiome dataset of preterm infant with sepsis.

Rendered fromMicrobTiSDA.Rmdusingknitr::rmarkdown

Last update: 2025-08-30
Started: 2025-08-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Visualize Microbial Feature Classification Results Using NMDS	Classify.vis
Cluster OTU Time-Series Data Based on Regression Model prediction and Generate Dendrogram Plots	Data.cluster
Cut and Annotate Dendrogram Based on a Specified Cut-Off Height	Data.cluster.cut
Filtering for Microbial Features of Low Abundance and Low Prevalence.	Data.filter
Interpolate Time-Series Data Based on Sample Time	Data.interpolate
Visualize Opposing Temporal profiles among Microbial features.	Data.opp.cor.vis
Random Forest classification for OTU/ASV Data	Data.rf.classifier
Transform Microbial Composition Data.	Data.trans
Visualize Temporal OTU Profiles from Clustered Predicted Data	Data.visual
Visualize Group-Level OTU Temporal Profiles from Clustered Predicted Data	Data.visual.MESR
Create Design Matrix for Regression Analysis	Design
Example dataset 2 - The in vitro aquatic microbiota dataset.	fujita.data
Example dataset 2 - sample metadata.	fujita.meta
Example dataset 2 - taxonomic information.	fujita.taxa
Dynamic Visualization of Microbial Interaction Networks	Interact.dyvis
Modified Centered Log-Ratio (MCLR) Transformation	mclr.transform
Example dataset 1 - The OSLO term infant gut microbiota dataset.	OSLO.infant.data
Example dataset 1 - sample metadata.	OSLO.infant.meta
Example dataset 1 - taxonomic information.	OSLO.infant.taxa
Plot Method for DataOppCorVis Objects	plot.DataOppCorVis
Plot Method for DataRFClassifier Objects	plot.DataRFClassifier
Plot Method for microbTiSDA Dynamic Visualization Objects	plot.microbTiSDA_dynamic_vis
Plot Method for MicrobTiSDA Cluster Objects	plot.MicrobTiSDA.cluster
Plot Method for MicrobTiSDA Cluster Cut Objects	plot.MicrobTiSDA.clusterCut
Plot Method for MicrobTiSDA MSER Visualization Objects	plot.MicrobTiSDA.MSERvisual
Plot Method for MicrobTiSDA Visual Objects	plot.MicrobTiSDA.visual
Plot Method for RfBiomarker Objects	plot.RfBiomarker
Predict Time-Series Data from Fitted Spline Models	Pred.data
Predict Time-Series Data from Fitted Mixed-Effect Spline regression Models	Pred.data.MESR
Example dataset 3 - The preterm infant gut microbiota dataset.	preterm.data
Example dataset 3 - sample metadata.	preterm.meta
Example dataset 3 - taxonomic information.	preterm.taxa
Information of Microbial features with opposite temporal shapes to users selected feature	print.DataOppCorVis
Information of the constructed Random Forest classification model	print.DataRFClassifier
Print information of the Design matrix	print.Design
Print Method for FilteredData Object	print.FilteredData
Print MicrobTiSDA objects	print.microbTiSDA
Print information of species interaction dynamic visualizations	print.microbTiSDA_dynamic_vis
Print information of fitted natural spline regression models	print.MicrobTiSDA_spline_regression
Print the information of fitted temporal profile clusters	print.MicrobTiSDA.cluster
Print the plot information of user selected feature clustering figures	print.MicrobTiSDA.clusterCut
Print MicrobTiSDA.interpolate object	print.MicrobTiSDA.interpolate
Information of visualizations of feature temporal patterns fitted with mixed-effect spline regression models	print.MicrobTiSDA.MSERvisual
Print the information of those clustered microbial features' temporal patterns	print.MicrobTiSDA.visual
Print the information of fitted regression model predicted data	print.PredictedData
Print method for PredictedDataMESR objects	print.PredictedDataMESR
Information of the fitted mixed-effect spline regression models	print.RegMESR
Print Method for TransformedData Object	print.TransformedData
Fit Mixed-Effects Spline Regression Models with GAM for Microbial Features on Group-Level	Reg.MESR
Fit Spline Regression Models with Knot Selection	Reg.SPLR
Select Biomarkers Based on Random Forest Cross-Validation Results	Rf.biomarkers
Species Interaction Inferrences	Spec.interact
Summary Method for Design Objects	summary.Design
Summary Method for FilteredData Object	summary.FilteredData
Summary method for MicrobTiSDA objects Provides a structure summary of a 'microbTiSDA' object, including its parameters and results. It prints object class, parameters settings, number of result groups/items, and previews of tabular of list-based result elements.	summary.microbTiSDA
Summary Method for MicrobTiSDA Dynamic Interaction Visualization Objects	summary.microbTiSDA_dynamic_vis
Summary Method for MicrobTiSDA Spline Regression Objects	summary.MicrobTiSDA_spline_regression
Summary Method for MicrobTiSDA Cluster Objects	summary.MicrobTiSDA.cluster
Summary Method for MicrobTiSDA ClusterCut OBjects	summary.MicrobTiSDA.clusterCut
Summary method for MicrobTiSDA.interpolate objects	summary.MicrobTiSDA.interpolate
Summary Method for MicrobTiSDA Visual Objects	summary.MicrobTiSDA.visual
Summary Method for PredictedData Objects	summary.PredictedData
Summary method for PredictedDataMESR objects	summary.PredictedDataMESR
Summary method for RegMESR objects	summary.RegMESR
Summary method for RfBiomarker objects	summary.RfBiomarker
Summary Method for TransformedData Objects	summary.TransformedData