\name{NEWS} \title{RAM News} \encoding{UTF-8} \section{Changes in version 1.2.1.7}{ \subsection{GENERAL}{ \itemize{ \item This is a release that we fixed some bugs. } } % general \subsection{BUG FIXES}{ \itemize{ \item group.OTU: sort the OTUs by relative abundance. \item match.data: fixed some typos. } } % bug fixes } % version 1.2.1.7 \section{Changes in version 1.2.1.6}{ \subsection{GENERAL}{ \itemize{ \item This is a release that we fixed some bugs. } } % general \subsection{BUG FIXES}{ \itemize{ \item group.top.number: fixed a bug when selecting the taxa. \item network_data: fixed man page. } } % bug fixes } % version 1.2.1.6 \section{Changes in version 1.2.1.5}{ \subsection{GENERAL}{ \itemize{ \item This is a release that we fixed some bugs. } } % general \subsection{BUG FIXES}{ \itemize{ \item OTU.ord: fixed a bug when using cca. \item valid.taxonomy: fixed a bug in this function } } % bug fixes } % version 1.2.1.5 \section{Changes in version 1.2.1.4}{ \subsection{GENERAL}{ \itemize{ \item This is a release that we fixed some bugs. } } % general \subsection{BUG FIXES}{ \itemize{ \item .ggsave.helper: fixed this internal function due to the change of behaviour of ggsave.. } } % bug fixes } % version 1.2.1.4 \section{Changes in version 1.2.1.3}{ \subsection{GENERAL}{ \itemize{ \item This is a release that we fixed some bugs. } } % general \subsection{BUG FIXES}{ \itemize{ \item Fixed missing link or links in documentation object 'RAM-package.Rd': ‘[ggplot2:ggplot2-package]{ggplot2}’. \item Fixed a bug in \code{group.rich} } } % bug fixes } % version 1.2.1.3 \section{Changes in version 1.2.1.2}{ \subsection{GENERAL}{ \itemize{ \item This is a release that we fixed some bugs. } } % general \subsection{BUG FIXES}{ \itemize{ \item Fixed a bug in \code{shared.OTU} where an error occurs when no otus are shared by all samples. \item Fixed a bug in \code{shared.Taxa} where an error occurs when no taxa are shared by all samples. \item Resolved the conflit between the 'summary.cca' function of 'vegan' and the one of 'ade4'. in an internal function .analysis.helper \item Fixed seq_var to work with gridExtra version 2.0.0 } } % bug fixes } % version 1.2.1.2 \section{Changes in version 1.2.1.1}{ \subsection{GENERAL}{ \itemize{ \item This is a release that we fixed some bugs. } } % general \subsection{BUG FIXES}{ \itemize{ \item Fixed a bug in \code{filter.OTU} for filtering by number of sequences per sample. } } % bug fixes } % version 1.2.1.1 \section{Changes in version 1.2.1}{ \subsection{GENERAL}{ \itemize{ \item This is a release with new functions and features. In the same we also fix some issues of plot functions. } } % general \subsection{BUG FIXES}{ \itemize{ \item Fixed the labels on x axis of plots generated by \code{group.rich} & \code{group.spec} \item Fixed a bug in \code{filter.OTU} \item Fixed a bug in \code{tax.abund} substitues spaces in names of the output dataframes with "_". } } % bug fixes \subsection{NEW FUNCTIONS}{ \itemize{ \item Function \code{phylo_taxonomy} plot hierarchical taxonomic tree with relative abundance of all taxa at a give rank if category variables are provided. Nonsplitting nodes are collapsed as ape::plot.phylo does. \item Function \code{phylog_taxonomy} This function plot hierarchical taxonomic tree, the leaves are taxa at a give rank, nonsplitting nodes are not collapsed. \item Function \code{factor.abundance} reates a stacked bar plot showing the abundance of all classifications at the given taxonomic rank for each level of a metadata category variable. \item Function \code{seq_var} new function calculates and plots inter/intra specific variation for an alignment. \item Function \code{network_data} new function to generate a list of network nodes and edges based on an otu table and associated metadata \item Function \code{group.abundance.meta} an updated version of \code{\link{group.abundance}}, which groups samples by metadata category variables if provided. } } % NEW FUNCTIONS \subsection{NEW DATA}{ \itemize{ \item DATA \code{alignment} new data for \code{\link{seq_var}. } % NEW DATA } % version 1.2.1 \section{Changes in version 1.2.0}{ \subsection{GENERAL}{ \itemize{ \item This is a release with new functions and features. In the same we also fix some issues of plot functions. } } % general \subsection{BUG FIXES}{ \itemize{ \item Fixed a bug in Function \code{get.rank} that keeping otus without identified taxon name at a given rank; e.g. 'g__' or 'g__;' } } % bug fixes \subsection{NEW FUNCTIONS}{ \itemize{ \item Function \code{match.data} to match samples in ecology datasets and metadata set. Only samples that present in both will be kept and reordered to match all datasets. \item Function \code{OTU.revamp} returns a list to describe the percent of classifed otus and sequences at each given taxonomy ranks and visualize the output in a barplot. \item Function \code{transpose.LCA} transpose OTU tables with each OTU being annotated with its LCA. \item Function \code{theme_ggplot} provide two ggplot themes RAM.color and R.border for customized fancy plots. \item Function \code{combine.OTU} combine otus for the same sample. Suggested to be use for bacterial 16S datasets. \item Function \code{filter.META} Select METADATA Variables and remove the ones that only have one level, neither numeric nor factor and / or with missing data. \item Function \code{.valid.data} check whether ecology data sets have same \item Function \code{assist.ado} perform ADONIS Analysis for ecology data sets. \item Function \code{filter.Taxa} filter taxonomic abundance matrices by total counts or maximum relative abundance. \item Function \code{data.clust} plot hierarchical clusters of samples based on ecology data set. \item Function \code{META.clust} Plot Hierarchical Cluster Of samples based on metadata \item Function \code{assist.NB} negative binomial test of seleted otuID or taxon name. \item Function \code{envis.NB} plot the negative binomial model for selected otuID or taxon name. \item Function \code{group.rich} Barplot of richness for a given metadata variable. \item Function \code{group.spec} Boxplot of richness for a given metadata variable. \item Function \code{OTU.ord} visualize cca/rda analysis on otus \item Function \code{Taxa.ord} visualize cca/rda analysis on taxa groups at a given rank. \item Function \code{group.Taxa.box} boxplot of taxa distribution among groups. \item Function \code{group.Taxa.bar} barplot of taxa distribution among groups. \item Function \code{group.abunda.taxa} barplot of selected taxa in each group. \item Function \code{group.venn} venn diagrams for taxa shared by different communities \item Function \code{shared.Taxa} summarize taxa shared by all samples \item Function \code{valid.taxonomy} check whether the format of the taxonomy lineages in the otu tables are supported by RAM \item Function \code{reformat.taxonomy} reformat the taxonomy lineages in the otu tables that supported by RAM \item Function \code{sample.map} plot the number of samples collected from each location. For plotting distant sampling sites. \item Function \code{sample.site} alternative view of RAM functons sample.map and sample.locations, suitable for plot closely located sampling sites. \item Function \code{group.diversity} plot diversity indices among different groups. \item Function \code{RAM.pal} generate customized color pattern. } } % new functions \subsection{NEW FEATURES}{ \itemize{ \item Function \code{read.OTU} now can import both "," or "\t" delimited files. \item Function \code{read.meta} now can import both "," or "\t" delimited files. \item Function \code{OTU.recap} returns a list to describe the percent of classifed otus and sequences at each given taxonomy ranks and visualize the output in a barplot. \item Added standardize and dist.method options to Function \code{group.heatmap}. \item Function \code{group.abundance} can process more than 2 OTU tables now. \item Function \code{group.top.number} can process more than 2 OTU tables now. \item Function \code{group.top.percent} can process more than 2 OTU tables now. \item Function \code{group.indicators} can process more than 2 OTU tables now. } } % new features % \subsection{INSTALLATION AND BUILDING}{ % \itemize{ % \item Function % \item Function % } % } % installation and building \subsection{DEPRECATED}{ \itemize{ \item Function \code{write.OTU} removed and replaced by \code{write.data} function } } % deprecated } % version 1.2.0 \section{Changes in version 1.1.0}{ \subsection{GENERAL}{ \itemize{ \item This is a release with new functions and features. In the same we also fix some issues of plot functions. } } % general \subsection{BUG FIXES}{ \itemize{ \item Function \code{tax.split} previously used a function \code{splitstackshape::concat.split}, which is deprecated. Replaced with new function in RAM \code{split.col}. \item Function \code{group.indicators} fix the bug caused by previous version of tax.split, which call function \code{splitstackshape::concat.split}, which is not required any more. \item Function \code{tax.abund} failed to remove unclassified taxon groups in defined blacklist when drop.unclassified is set as TRUE. \item Function \code{group.abundance} needs \code{tax.abund} when plot relative abundance of top taxon groups at each ranks. Now it correctly remove unclassified taxon groups when drop.unclassified option is set TRUE. \item \code{tax.fill} failed to recognize unclassified taxon groups in defined blacklist and replace them with the OTUs lowest comman ancestor. \item \code{...} } } % bug fixes \subsection{NEW FUNCTIONS}{ \itemize{ \item Function \code{OTU.diversity} calculates most used diversity indices for each samples based on OTU tables. \item Function \code{core.OTU} summarizes most prevelant otus. \item Function \code{core.Taxa} summarizes most prevelant taxon groups. \item \code{group.OTU} plot function for the distribution of selected otus. \item \code{filter.OTU} function to subset OTUs by either total count or relative abundance. \item \code{OTU.recap} summarizes classified OTUs at each taxonomic ranks. \item \code{.get.rank.name} internal function to generate the name of a given taxonomic rank. \item \code{LCA.OTU} function to obtain LCA for each otu. Unclassified taxa are removed and the lowest rank that an otu can be assigned to is returned. \item \code{correlation} plot function to display correlation coefficient (or covariance) among taxa at a give rank and / or numeric variables of metadata. \item \code{col.splitup} function to split a column of a data frame by predefined separator. } } % new functions } % version 1.1.0