$Date: 2018-05-13 12:06:44 +0200 (Sunday, 13 May 2018) $ RAM RELEASE VERSIONS at http://cran.r-project.org/ Version 1.2.1.7 (released May 13, 2018) * group.OTU: sort the OTUs by relative abundance. * match.data: fixed some typos. Version 1.2.1.6 (released April 06, 2016) * group.top.number: fixed a bug when selecting the taxa. * network_data: fixed man page. Version 1.2.1.5 (released March 24, 2016) * OTU.ord: fixed a bug when using cca. * valid.taxonomy: fixed a bug in this function. Version 1.2.1.4 (released January 21, 2016) * .ggsave.helper: fixed this internal function due to the change of behaviour of ggsave. Version 1.2.1.3 (released January 02, 2016) * group.rich: fixed a bug. Version 1.2.1.2 (released November 28, 2015) * shared.OTU: fixed a bug where an error has occured when no otus are shared by all samples. * shared.Taxa: fixed a bug where an error has occured when no taxa are shared by all samples. * .analysis.helper: internal function. Resolved the conflit between the 'summary.cca' function of 'vegan' and the one of 'ade4'. * seq_var: fixed to work with gridExtra version 2.0.0 Version 1.2.1.1 (released May 28, 2015) * filter.OTU: fixed a bug in row selection by number of seqs. Version 1.2.1 (released May 15, 2015) * group.rich: fixed the labels on x axis of plot * group.spec: fixed the labels on x axis of plot * filter.OTU: fixed a bug in row selection * tax.abund: substitues spaces in names of the output dataframes with "_" * phylo_taxonomy: new function to plot hierarchical taxonomic tree with relative abundance of all taxa at a given rank if category variables are provided. Nonsplitting nodes are collapsed as ape::plot.phylo does.. * phylog_taxonomy: new function to plot hierarchical taxonomic tree, the leaves are taxa at a given rank, nonsplitting nodes are not collapsed as ade4::plot.phylog does. * factor.abundance: new function to create a stacked bar plot showing the abundance of all classifications at the given taxonomic rank for each level of a metadata category variable. * seq_var: new function to calculate and plot inter/intra specific variation for an alignment. * network_data: new function to generate a list of network nodes and edges based on an otu table and associated metadata * group.abundance.meta: an updated version of \code{\link{group.abundance}}, which groups samples by metadata category variables if provided * alignment: new data for \code{\link{seq_var} Version 1.2.0 (released December 10, 2014) * fread.OTU: use data.table::fread for reading in large data set. * filter.OTU: Fixed a bug in selecting rownames. * fread.meta: use data.table::fread for reading in large data set. * write.data: write datasets to a csv file of a valid file path. * write.OTU: removed and replaced by write.data function * 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. * RAM.input.formatting: describe how the ecology data should be used as inputs for comparison functions. * 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. * 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. * get.rank: fixed a bug that keeping otus without identified taxon name at a given rank; e.g. g__ or g__; * transpose.LCA: transpose OTU tables with each OTU being annotated by its LCA. * theme_ggplot: provide two ggplot themes RAM.color and R.border for customized fancy plots. * read.OTU: now can import both "," or "\t" delimited files. * read.meta: now can import both "," or "\t" delimited files. * core.OTU: core.OTU in this version shows LCA of core OTUs. * OTU.recap: now can handle multiple otu tables at one run and do a barplot to visualize the output. * combine.OTU: combine otus for the same sample. Suggested to be use for bacterial 16S datasets. * filter.META: Select METADATA Variables and remove the ones that only have one level, neither numeric nor factor and / or with missing data. * .valid.data: check whether ecology data sets have same * assist.ado: perform ADONIS Analysis for ecology data sets. * filter.Taxa: filter taxonomic abundance matrices by total counts or maximum relative abundance. * data.clust: plot hierarchical clusters of samples based on ecology data set. * META.clust: Plot Hierarchical Cluster Of samples based on metadata * assist.NB: negative binomial test of seleted otuID or taxon name. * envis.NB: plot the negative binomial model for selected otuID or taxon name. * group.rich: Barplot of richness for a given metadata variable. * group.spec: Boxplot of richness for a given metadata variable. * OTU.ord: visualize cca/rda analysis on otus * Taxa.ord: visualize cca/rda analysis on taxa groups at a given rank. * group.Taxa.box: boxplot of taxa distribution among groups. * group.Taxa.bar: barplot of taxa distribution among groups. * group.abunda.taxa: barplot of selected taxa in each group. * group.venn: venn diagrams for taxa shared by different communities * shared.Taxa: summarize taxa shared by all samples * valid.taxonomy: check whether the format of the taxonomy lineages in the otu tables are supported by RAM * reformat.taxonomy: reformat the taxonomy lineages in the otu tables that supported by RAM * sample.map: plot the number of samples collected from each location. For plotting distant sampling sites. * sample.site: alternative view of RAM functons sample.map and sample.locations, suitable for plot closely located sampling sites. * group.diversity: plot diversity indices among different groups. * group.heatmap: add standardize and dis.method options * core.OTU.rank: changed the name of core.OTU in v1.1.0 to core.OTU.rank * group.abundance: can process more than 2 OTU tables now. * group.top.number: can process more than 2 OTU tables now. * group.top.percent: can process more than 2 OTU tables now. * group.indicators: can process more than 2 OTU tables now. * RAM.pal: generate customized color patterns. * The third public version. Version 1.1.0 (released October 20, 2014) * tax.abund: fixed drop.unclassified option. * group.abundance: plot with adjusted and aligned x axis labels. * tax.split: previously used a function concate.split from package splitstackshape, which is deprecated. Replaced with new function in RAM \code{split.col}. * group.indicators: RAM::tax.split. * tax.abund: fixed the bug that fails to remove unclassified taxon groups in defined blacklist when drop.unclassified is set as TRUE. * 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. * tax.fill: failed to recognize unclassified taxon groups in defined blacklist and replace them with the OTUs lowest comman ancestor. * OTU.diversity: calculates most used diversity indices for each samples based on OTU tables. * core.OTU: summarizes most prevelant otus. * core.Taxa: summarizes most prevelant taxon groups. * group.OTU: plot function for the distribution of selected otus. * filter.OTU: function to subset OTUs by either total count or relative abundance. * OTU.recap: summarizes classified OTUs at each taxonomic ranks. * .get.rank.name: internal function to generate the name of a given taxonomic rank. * 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. * correlation: plot function to display correlation coefficient (or covariance) among taxa at a give rank and / or numeric variables of metadata. * col.splitup: function to split a column of a data frame by predefined separator. * The second public version.