NEWS

phyloseq 1.13.6

BUG FIXES

droplevels suggestion for sample-data https://github.com/joey711/phyloseq/pull/476
DESeq2 migrated to suggests https://github.com/joey711/phyloseq/pull/533
'extend_metagenomeSeq' functionality https://github.com/joey711/phyloseq/pull/533
bugs related to previous version distance uptick, mostly in tests and vignette

phyloseq 1.13.5

USER-VISIBLE CHANGES

Help avoid cryptic errors due to name collision of 'distance' with external loaded packages by making 'distance' a formal S4 method in phyloseq.
Improve documentation of 'distance' function and the downstream procedures on which it depends
Migrate the list of supported methods to a documented, exported list object, called 'distanceMethodList'.
Improved distance unit tests with detailed checks that dispatch works and gives exactly expected distance matrices for all methods defined in distanceMethodList.
Improved JSD doc, performance, code, deprecated unnecessary 'parallel' argument in JSD

phyloseq 1.13.4

BUG FIXES

'psmelt' bug if user has also loaded the original "reshape" package, due to name collision on the function called 'melt'. 'psmelt' now explicitly calls 'reshape2::melt' to avoid confusion. https://github.com/joey711/phyloseq/pull/489
Fix following note... There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘JSD.pair’

phyloseq 1.11.3

BUG FIXES

plot_heatmap bug when PCoA/MDS used as ordination method for axis ordering. This solves issue 420 https://github.com/joey711/phyloseq/issues/420

phyloseq 1.11.2

USER-VISIBLE CHANGES

'plot_heatmap' replaces 'geom_tile' with 'geom_raster'. This should afford a substantial speed improvement during rendering of heatmaps, according to ggplot2 documentation. This also solves Issue 401 https://github.com/joey711/phyloseq/issues/401

phyloseq 1.11.1

BUG FIXES

plot_heatmap y-axis

phyloseq 1.9.15

BUG FIXES

'phyloseq_to_deseq2' was adding an unnecessary pseudocount of '1' to the count matrix. No longer.
Originally described at https://github.com/joey711/phyloseq/issues/387

phyloseq 1.9.14

BUG FIXES

'distance' erroneously transformed Rao distance results for method DPCoA. Now Fixed.
Originally described at https://github.com/joey711/phyloseq/issues/390

phyloseq 1.9.13

USER-VISIBLE CHANGES

'distance' function now supports "wunifrac" option, for 'UniFrac(..., weighted=TRUE)'
'distance' function regexpr-matching for range of variants for weighted-UniFrac, unweighted-UniFrac method option
'distance' function regexpr-matching for 'type' argument range of alternatives
Proposed in https://github.com/joey711/phyloseq/pull/384

phyloseq 1.9.12

BUG FIXES

'psmelt' function now properly handles single-OTU data
Related to https://github.com/joey711/phyloseq/issues/338
Builds on https://github.com/joey711/phyloseq/pull/373

phyloseq 1.9.11

USER-VISIBLE CHANGES

More robust 'plot_ordination' behavior with clearer warning/error messages.
Coordinates automatically checked/assigned to OTU or samples
Attempt to calculate OTU or sample weighted-average coordinates via 'vegan::wascores', if-needed
Species weighted-average via 'vegan::wascores' supported now in phyloseq::scores.pcoa
Related to https://github.com/joey711/phyloseq/pull/364

phyloseq 1.9.10

USER-VISIBLE CHANGES

Massive speed/memory improvement for UniFrac calculations (via 'UniFrac' or 'distance')
Added unit-tests for the correctness of UniFrac results (no bugs detected. results from pycogent)
Moved all unit tests to tests/testthat as recommended by CRAN maintainers and testthat doc

phyloseq 1.9.9

USER-VISIBLE CHANGES

'plot_net' faster, more-flexible network plot with improved defaults
https://github.com/joey711/phyloseq/pull/353

phyloseq 1.9.8

USER-VISIBLE CHANGES

'mt' includes other corrections, FDR by default.
Resolves [Issue 59](https://github.com/joey711/phyloseq/issues/59)

phyloseq 1.9.7

BUG FIXES

Now requires ggplot2 version 1.0.0
Fixes bug in which ggplot 1.0 breaks in a phyloseq vignette
Resolves [Issue 347](https://github.com/joey711/phyloseq/issues/347)

phyloseq 1.9.6

USER-VISIBLE CHANGES

New 'sortby' argument in 'plot_richness' function.
Sort discrete x by one or more alpha-diversity measures
Solves [Issue 342](https://github.com/joey711/phyloseq/issues/342)
Resolves/merges [Pull 343](https://github.com/joey711/phyloseq/pull/343)

phyloseq 1.9.5

USER-VISIBLE CHANGES

'microbio_me_qiime' function now handles string study number for first argument. This is in addition to numeric study number, already supported.

phyloseq 1.9.4

BUG FIXES

'rarefy_even_depth()' function no longer enforces an orientation.
It used to always coerce to OTU-by-sample orientation.
Solves Issue 320 https://github.com/joey711/phyloseq/issues/320

phyloseq 1.9.3

USER-VISIBLE CHANGES

Massive Revision to plot_tree()
'plot_tree' now uses the 'psmelt' function
All covariates are available for aesthetic mapping.
'plot_tree' substantial speed improvement
Uses native ape-package C code for tree computation
Efficient 'data.table' consolidated graphic data passed to ggplot2
Additional arguments: 'treetheme' and 'justify'
'tree_layout' - new, user-accessible function
for building alternative trees from phyloseq data.
Foundation for solving Issue 313 and Issue 331
https://github.com/joey711/phyloseq/issues/313
https://github.com/joey711/phyloseq/issues/331

phyloseq 1.9.2

BUG FIXES

Large files cause import_usearch_uc() to have error. Error in paste0(readLines(ucfile), collapse = "\n") : result would exceed 2^31-1 bytes
Solves Issue 327: https://github.com/joey711/phyloseq/issues/327

phyloseq 1.9.1

BUG FIXES

Bug in 'psmelt' causing unnecessary error for phyloseq datasets with empty components.
Solves Issue 319: https://github.com/joey711/phyloseq/issues/319

phyloseq 1.7.24

USER-VISIBLE CHANGES

Added support for [Partial] Constrained Analysis of Principal Coordinates (CAP).
A supported/documented option in 'ordinate', supported by 'plot_ordination'.
This solves [Issue 312](https://github.com/joey711/phyloseq/issues/312).
The 'ordinate' function now takes an explicit 'formula' argument.
This facilitates reliable contrained ordination calls for:
CAP (this commit)
RDA (partial redundancy analysis)
CCA (constrained correspondence analysis)

phyloseq 1.7.23

USER-VISIBLE CHANGES

Refactor 'plot_ordination' to be more stable, error less and give informative warnings.
Expect no critical API changes. Some errors now informative warnings with useful auto-changes to parameters.
The ‘type=’biplot'' option no longer hard-specifies a discrete color scale. Available default pallette should work.
For ‘type=’biplot'', the non-variable (Taxa or Sample) label will always appear first in a discrete legend.

phyloseq 1.7.22

USER-VISIBLE CHANGES

Revised psmelt to automatically modify data column-name conflicts, with warning
Udpated 'psmelt' doc to formally notify users of these potential conflicts.
This solves Issue 307: https://github.com/joey711/phyloseq/issues/307

phyloseq 1.7.21

USER-VISIBLE CHANGES

Updated 'import_qiime' doc to emphasize it is intended for legacy QIIME files.
Much faster and mem-efficient import of legacy QIIME and usearch files.
Uses data.table syntax to better manage import of large files.
Entire HMPv35 now imports in about 1 minute, low risk of mem-swap.
Added dependency to data.table

phyloseq 1.7.20

USER-VISIBLE CHANGES

No user-visible changes. All future compatibility changes.

BUG FIXES

Unit test changes to work with upcoming R release and new testthat version.

phyloseq 1.7.19

USER-VISIBLE CHANGES

Documentation revisions. Faster examples, updated links.

phyloseq 1.7.18

USER-VISIBLE CHANGES

Fix minor bug that prohibited parallel execution of weighted UniFrac

phyloseq 1.7.17

USER-VISIBLE CHANGES

Added 'import_usearch_uc' Added first-time support for usearch “.uc” style output table. Addresses Issue 286, importing from UPARSE. https://github.com/joey711/phyloseq/issues/286 Further feedback on performance, use-cases, should be posted there.

phyloseq 1.7.16

USER-VISIBLE CHANGES

Fixed minor bug affecting legend-order in 'plot_network' Issue 288, https://github.com/joey711/phyloseq/issues/288

phyloseq 1.7.15

USER-VISIBLE CHANGES

'tip_glom' now uses standard R clustering tools, and takes their arguments documentation and tests updated to reflect the change much simpler, faster
'merge_taxa' now uses abundance to determine the achetype by default. Previously arbitrary.

phyloseq 1.7.14

USER-VISIBLE CHANGES

Minor change in mixture model vignette, revised graphic

phyloseq 1.7.13

USER-VISIBLE CHANGES

Deprecated originalUniFrac() internal function old (original) unifrac algorithm no longer supported. Addresses Issue 66: https://github.com/joey711/phyloseq/issues/66

phyloseq 1.7.12

USER-VISIBLE CHANGES

Formal deprecation of functions using .Deprecated Issue 269, https://github.com/joey711/phyloseq/issues/269
Fixed bug in interface with vegan::fisher.alpha(..., se=TRUE). vegan doc states that this returns a data.frame, but a data.frame is not returned in vegan version 1.7.10. phyloseq no checks output dimensions before processing in 'estimate_richness'
Replaced deprecated functions in tests and documentation.

phyloseq 1.7.11

USER-VISIBLE CHANGES

Adds warning in make_network() and error in plot_network if empty graph encountered Issue 275, check/warning for empty igraph objects https://github.com/joey711/phyloseq/issues/275
rarefy_even_depth() messages changed from cat() to messages(), and optional verbose argument added https://github.com/joey711/phyloseq/issues/263

phyloseq 1.7.10

USER-VISIBLE CHANGES

Fixes build-error originating from change in ade4 NAMESPACE in version 1.6.2
Change minimum ade4 version to 1.6.2
Uncommented examples now included in documentation for DPCoA function

phyloseq 1.7.9

USER-VISIBLE CHANGES

Fixed typo-derived bug in new vignette.
These changes allow user to build from source without error.

phyloseq 1.7.8

USER-VISIBLE CHANGES

Package dependencies reduced/clarified: https://github.com/joey711/phyloseq/issues/259 Should reduce chances for collisions with other packages, and related issues. Removed any dependencies on the picante package.
Replaced picante::node.age() with a faster implementation, node_ages() Appears to be 3 times faster. Speeds up UniFrac() and tip_glom() calculations.

phyloseq 1.7.7

USER-VISIBLE CHANGES

Tree fixes: https://github.com/joey711/phyloseq/issues/235 https://github.com/joey711/phyloseq/issues/255
If a tree has NA branch-length values, they are automatically set to 0. This occurs within both phyloseq(), and read_tree().
UniFrac calculations require a rooted tree. While a rooted tree is not required to be part of a phyloseq object, it is a helpful default behavior to select a random root when UniFrac is called and the tree is unrooted, flashing a notice to the user.
Precise import from ape-package, rather than full-import. Smaller chance for collisions. Precisely-defined dependencies listed in NAMESPACE
As a result of the previous, phyloseq defines a placeholder "phylo" class, extended from "list". This seems to match the class from a full import of ape, and is necessary since ape does not export the "phylo" class.

phyloseq 1.7.6

USER-VISIBLE CHANGES

Merged branches 1.7.4 and 1.7.5

phyloseq 1.7.5

NEW FEATURES

User-specified axis ordering to plot_heatmap()
User-specified axis edges to plot_heatmap()
This addresses: [Issue 237](https://github.com/joey711/phyloseq/issues/237) [Issue 230](https://github.com/joey711/phyloseq/issues/230)

USER-VISIBLE CHANGES

New arguments to plot_heatmap(): 'taxa.order', 'sample.order', 'first.sample', 'first.taxa'

phyloseq 1.7.4

NEW FEATURES

import_mothur now handles more formats
Added documentation to discourage .group/.list formats

phyloseq 1.7.3

NEW FEATURES

Added phyloseq_to_deseq2() wrapper function and examples for computing multiple OTU tests using Negative Binomial model and GLM (DESeq2).

USER-VISIBLE CHANGES

Also added new .Rmd vignette for using DESeq, with colorectal carcinoma data

phyloseq 1.7.2

USER-VISIBLE CHANGES

Reformat NEWS (this) file.

phyloseq 1.7.1

USER-VISIBLE CHANGES

Rmd/HTML-based vignettes. No more Rnw/Sweave/PDF
Updated installer

phyloseq 1.5.23

USER-VISIBLE CHANGES

Update dependency from igraph0 to igraph
Requested by CRAN
igraph0 is being deprecated, removed from CRAN
igraph is actively updated/maintained. igraph0 isn't / soon won't be.
The load bug that I could find from re-running the tutorial in the new dependency had to do with accessing the vertex names. The appropriate function is: 'get.vertex.attribute' which was not used previous, but is now imported and used in this version of phyloseq.
This also closes [Issue 247](https://github.com/joey711/phyloseq/issues/247)

phyloseq 1.5.22

USER-VISIBLE CHANGES

Fix minor bug in 'import_mothur'
Bug occurs only when sample names are pure integers. One line fix.
This addresses [Issue 242](https://github.com/joey711/phyloseq/issues/242)

phyloseq 1.5.21

USER-VISIBLE CHANGES

'plot_richness' / 'estimate_richness' updates
Additional alpha-diversity measures added to both functions.
New argument, 'measures', added to both functions, allows user to specify which measures to calculate/display.
Also added unit tests for both functions, absent in prior versions

phyloseq 1.5.20

USER-VISIBLE CHANGES

Bugfixes, 'read_tree_greengenes', and a 'replace' optional parameter to rarefy_even_depth()
read_tree_greengenes() is a new function created specifically to address the problem created when the greengenes consortium chose to publish their official release trees with semicolon-delimited node labels, even though semicolons are also a special newick character. The semicolons only appear when a node has more than one taxonomic rank assigned to it, which is rare in the smaller (lower OTU similarity threshold) trees, but a big problem in all the most commonly used trees, e.g. 97% tree. The hard part was identifying the precise cause of the problem. Now that it is precisely known, the offending delimiters are temporarily replaced so that the standard parser 'read.tree' can create the phylo object, then they are reinstated. Unit tests have been added to check that this works properly on a GreenGenes release tree that otherwise breaks 'read.tree'. This also solves 224 https://github.com/joey711/phyloseq/issues/224
Fixed a bug in which the highest taxonomic rank fails in 'tax_glom' This was a bug resulting from the automatic coercion of single-column matrix subsetting to a vector. Simply changing the relevant line of code in 'tax_glom' such that [, , drop=FALSE], solve this issue, Issue 223 https://github.com/joey711/phyloseq/issues/223 Unit tests have been added that should catch this in the future.
rarefy_even_depth() new option to sample without replacement. Two implications to consider are that (1) sampling with replacement is faster and more memory efficient as currently implemented; (2) sampling with replacement means that there is a chance that the number of reads for a given OTU in a given sample could be larger than the original count value. This is in contrast to sampling without replacement where the original count value is the maximum possible. Prior to this phyloseq version, this 'replace' parameter did not exist and sampling with replacement was the only random subsampling implemented in the 'rarefy_even_depth' function. This prior behavior was selected for computational efficiency, but differs from the behavior of analogous functions in related packages (e.g. rarefying in QIIME).

phyloseq 1.5.19

USER-VISIBLE CHANGES

add gap statistic support for ordination results
gapstat_ord() - wrapper function for cluster::clusGap for ordination methods
plot_clusgap() - wrapper function for plotting gap statistic results from clusGap()
Full examples on the soilrep dataset for gap statistic.
Fix bug in eigenvalue proportions for axes other than the first two in ordination plots.

phyloseq 1.5.17

USER-VISIBLE CHANGES

replace URL with new phyloseq article http://dx.plos.org/10.1371/journal.pone.0061217

phyloseq 1.5.16

USER-VISIBLE CHANGES

rarefy_even_depth improvements User-side convenience upgrades to rarefy_even_depth() behavior.
More user feedback about process.
New argument for setting RNG seed, with a default value (reproducible by default).
Reports the RNG seed being used for random subsampling, encouraging users to record this for reproducibility.
Trims empty samples/OTUs automatically, and reports this to standard out.

phyloseq 1.5.13-15

USER-VISIBLE CHANGES

Shifted RJSONIO dependency to the new "biom" package in CRAN

phyloseq 1.5.11-12

USER-VISIBLE CHANGES

major feature: interface to microbio.me/qiime data repo
Now possible to directly download, unpack, import multi-component data into standard phyloseq form in R using a single command using the new microbio_me_qiime() command. Supports the following input styles:
full URL to the precise study on the server,
a local path to the same compressed raw data file on your system if you already downloaded
Just the study number on the microbio.me/qiime repo. For example: microbio_me_qiime(524) will download and import the "smokers" dataset.
See the following tutorial for more details: http://joey711.github.io/phyloseq/download-microbio.me.html

phyloseq 1.5.9

USER-VISIBLE CHANGES

Bugfix for psmelt()/plotting when entire columns in tax_table are empty

phyloseq 1.5.8

USER-VISIBLE CHANGES

This satisfies [issue 134](https://github.com/joey711/phyloseq/issues/134)

phyloseq 1.5.6

USER-VISIBLE CHANGES

plot_ordination() now includes percent variability on axis labels, if possible

phyloseq 1.5.5

USER-VISIBLE CHANGES

Update citation info for latest per-reviewed phyloseq article
http://dx.plos.org/10.1371/journal.pone.0061217

phyloseq 1.5.4

USER-VISIBLE CHANGES

This completes a feature request in [Issue 179](https://github.com/joey711/phyloseq/issues/179)

phyloseq 1.5.3

USER-VISIBLE CHANGES

bug fix in plot_heatmap labels derived from ggplot2 change
This solves a bug described in [Issue 192](https://github.com/joey711/phyloseq/issues/192)

phyloseq 1.5.2

USER-VISIBLE CHANGES

bug fix pass extra args to 'transform_sample_counts'

phyloseq 1.5.0

USER-VISIBLE CHANGES

Level up to R version 3.0.0

phyloseq 1.3.23

USER-VISIBLE CHANGES

bug fix for transform_sample_counts
Only appears to affect OTU tables in the "taxa are columns" orientation. It is the result of a surprising behavior of the apply() function, which in this circumstance transposes the table.
This solves a bug described in [Issue 186](https://github.com/joey711/phyloseq/issues/186)

phyloseq 1.3.22

USER-VISIBLE CHANGES

additional tests for prun_*() and phyloseq() functions
Before releasing v1.3.21 on GitHub:master some gaps in re-order checking were noticed. These are now caught by new unit tests and phyloseq/prune/etc have been further revised to ensure that properly-ordered OTUs are not disordered during a pruning step.

phyloseq 1.3.21

USER-VISIBLE CHANGES

accessor efficiency
For instance, ntaxa() and taxa_names() are very slow on large dataset Some of the highly inefficient approaches are now replaced. The strategy is described further in [Issue 183](https://github.com/joey711/phyloseq/issues/183)

phyloseq 1.3.20

USER-VISIBLE CHANGES

reference sequence class update.
formally define the new version of phyloseq-class with refseq slot included
new/augmented accessors: taxa_names, ntaxa, refseq
phyloseq() constructor now supports XStringSet components
reconcile_species internal function removed/replaced
reconcile_species removed from constructor and package. internal, so no need to deprecate.
check the component slot list provided by the "splat" infrastructure
prune_taxa
Rebuild current example data.
print/show methods.
subset_taxa
add refseq (XStringSet) object argument to import functions. import_qiime, import_biom
merge_phyloseq: works with refseq data
Add merge_taxa method for XStringSet objects
Include reference sequences in example datasets
prune_* / reconcile_* / intersect_* . add intersect_samples() function, model after new version of intersect_species() rename intersect_species to intersect_taxa() rm/replace reconcile_* functions with prune_*(intersect_*(), ps). These changes make simpler / DRYer code. Easier to extend.
DRY (and hopefully speed) improvements to merge_taxa(). Additional speed improvements may be possible for tip_glom, tax_glom in later revisions

phyloseq 1.3.14

USER-VISIBLE CHANGES

Shortened/replaced examples in the longest-running doc examples. This substantially reduces the time it takes to run package checks.
Focused on worst offenders
Created a new online tutorial for 'subset_ord_plot'. Linked to it from 'plot_ordination'
'plot_taxa_bar' moved to deprecated function file where it belongs, and examples completely removed from doc.

phyloseq 1.3.13

USER-VISIBLE CHANGES

Fixed unofficial warning from missing (unregistered) classes of ordination objects. Stems from the internal get_eigenvalue being defined as S4 generic instead of S3. Solves the following logged issue: https://github.com/joey711/phyloseq/issues/166
Name of get_eigenvalue generic replaced with extract_eigenvalue, in addition to re-defining as S3 generic.
Fixed ggplot2 warning from over-specified "bins" in the plot_scree bar plot. Changed to stat="identity", solves problem
Fixed warning when eigenvalues get (slightly) negative. They are now set to 0.0 for the purposes of plotting in plot_scree.

phyloseq 1.3.12

USER-VISIBLE CHANGES

Fixed a parsing issue for some QIIME-produced .biom files that had leading space characters. Issue further described at https://github.com/joey711/phyloseq/issues/171 Fixed such that any number of leading/lagging space characters are removed from taxonomic classification entries
Fixed build issue on some windows machines derived from problem with figure files having colons in the filename.

phyloseq 1.3.11

USER-VISIBLE CHANGES

Added tree option for import_biom() importer so that users can avoid using merge_phyloseq() if their files are otherwise standard vanilla
Address Issue 169 and 167 https://github.com/joey711/phyloseq/issues/169 https://github.com/joey711/phyloseq/issues/167

phyloseq 1.3.10

USER-VISIBLE CHANGES

Added support for Shannon/Simpson alpha-diversity indices in plot_richness https://github.com/joey711/phyloseq/issues/164
All sample_data now embedded in plot_richness output graphic, in case want to use other covariates in additional layers not originally specified. For instance, if you wanted to include geom_text(label=addLayer1). See plot_richness online tutorial.

phyloseq 1.3.9

USER-VISIBLE CHANGES

Added ability to add node labels, bootstrap values to tree graphics generated by plot_tree.
The labeling itself is opened-up as a user-provided function to facilitate custom node-labeling needs (including symbols and other ggplot2 geoms)
Commonly-needed functions are provided as newly-documented exported functions in the package: nodeplotdefault - adds whatever is in the node label to the graphic nodeplotboot - Adds the labels as bootstrap values, coercing/rounding as needed nodeplotblank - Ensures that node labels are not added.
These new functions can be used to give valid arguments to the new 'nodelabf' argument in plot_tree().
Some other re-organization to plot_tree to show more code in the main plot_tree function.

phyloseq 1.3.8

USER-VISIBLE CHANGES

Fix bug in plot_tree graphic if sample names start with a number
This fixes https://github.com/joey711/phyloseq/issues/149
Also added fill argument to default aesthetic map definition, useful if fillable shapes defined in subsequent layers

phyloseq 1.3.7

USER-VISIBLE CHANGES

Revisions to plot_tree to improve formatting, organization
"ladderize" contributed by Gregory Jordan
Color scale option removed from original pull request
already supported as core ggplot2 functionality through layering
Added links and roxygen2-header revisions for proper doc formatting
Fixed bug in which alternative size-variables still labeled as "abundance" in legend.

phyloseq 1.3.6

USER-VISIBLE CHANGES

Updated basics vignette

phyloseq 1.3.5

USER-VISIBLE CHANGES

Updated README.md to point to phyloseq home page (instead of redundant display of content).
Also added README.html

phyloseq 1.3.4

USER-VISIBLE CHANGES

Updated tests, examples for merge_samples()
Updated some dependency min versions
First 2013 commit

phyloseq 1.3.3

USER-VISIBLE CHANGES

updates to import_qiime()
modular building of taxonomy table in import_qiime() and import_biom()

phyloseq 1.3.2

USER-VISIBLE CHANGES

import_biom() fixes.
More robust data handling for taxonomy table
Flexibility: Can take custom parsing function for taxonomy vectors
tests added for new parsing functions parse_taxonomy_default parse_taxonomy_greengenes

phyloseq 1.3.1

USER-VISIBLE CHANGES

New function: plot_bar() that is simpler more reliable than plot_taxa_bar.
plot_taxa_bar now deprecated.
labeled deprecated in title doc
replaced examples in vignette with plot_bar examples

phyloseq 1.3.0

USER-VISIBLE CHANGES

Level up github devel version number to reflect devel order/status relative to latest BioC release

phyloseq 1.1.58

USER-VISIBLE CHANGES

Fixed a bug in import_qiime in which import fails if there are any empty taxonomy string fields in a file that otherwise has some taxonomic assignments. Now the taxonomy entries for that OTU (row in the taxonomy table) are left all NA_character_ by default.

phyloseq 1.1.57

USER-VISIBLE CHANGES

Added automatic removal of single and double quotes from phylogenetic tree tip names provided to the phyloseq-constructor. This should help avoid problems importing data that includes a tree, for the cases where the taxa/OTU names don't match because of these extra quotation marks. Added directly into the phyloseq() constructor, so that it doesn't matter how/where the tree was imported/add.
Removal of quotes is only initiated when OTU/taxa names fail to match AT ALL (intersection is length zero) between component taxa names.
This feature needs to be added to unit tests as well.

phyloseq 1.1.55

USER-VISIBLE CHANGES

Added "title" argument to plot_scree() and plot_ordination(…, type="scree"), for consistency.

phyloseq 1.1.54

USER-VISIBLE CHANGES

Changed "species" label in different plot_ordination() graphics to "taxa"
Fixed an issue with a default parameter in a related internal function (changed "samples" to "sites" for vegan compatibility).

phyloseq 1.1.53

USER-VISIBLE CHANGES

Fixed additional title issues in plot_network and plot_richness

phyloseq 1.1.52

USER-VISIBLE CHANGES

Added plot_scree() function for making eigenvalue "scree" plots in ggplot2
Added corresponding type="scree" option to plot_ordination, for convenience.

phyloseq 1.1.51

USER-VISIBLE CHANGES

Returned to "Imports:" dependency for ggplot2 following a ggplot2 bug fix

phyloseq 1.1.50

USER-VISIBLE CHANGES

Fixed several compatibility issues to support latest version of ggplot2 (0.9.2).
Also changes plot_richness_estimates() to plot_richness().

phyloseq 1.1.45

USER-VISIBLE CHANGES

Backward compatibility for import_qiime_sampleData, now superseded by import_qiime_sample_data
Added a functioning example based on the GlobalPatterns example sample-map file included in the package extdata.

phyloseq 1.1.44

USER-VISIBLE CHANGES

Fixed minor bug in tax_glom function. Thanks to Katie Shelef for the bug report. Bug only affected tax_glom behavior when the right-most rank was specified as the position for merging.

phyloseq 1.1.43

USER-VISIBLE CHANGES

fixed distance() issue from species/taxa replacement for type argument.

phyloseq 1.1.42

USER-VISIBLE CHANGES

fixed make_network/plot_network issue from species/taxa replacement for type argument.

phyloseq 1.1.41

USER-VISIBLE CHANGES

Fixed documentation for 'prune_taxa' and 'prune_samples'
Updated 'prune_samples' method to allow for logical vectors.
Fixed 'prune_taxa' so that it properly fails with a message if the taxa argument is a logical of wrong length. There was some potential (and no warning) for unpredictable vector-recycling with short vectors in the old implementation.

phyloseq 1.1.40

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Huge Update and Renaming Event.
Made all functions use an *underscore* for English word delimiter, if they were using an abbreviation.
Replaced "species" in all function names with "taxa".
These changes are all backward compatible, for now, so your old code should work. Let me know if it doesn't and I will quickly make the adjustment. This will remain true through the next official release, but functional references to "species" will not be supported afterward, except in the occasions where you actually mean taxonomic species, like 'tax_glom(x, "species")'.

phyloseq 1.1.33

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Revise taxglom() such that it handles phyloseq and taxonomyTable classes, throws warning otherwise. It should not take a manually-produced character vector, as this is roughly equivalent to functionality supported in other method, especially prune_species()/merge_species().
Also added unit-tests and executable examples for taxglom(). Got rid of taxglom.internal, incorporated directly into taxglom(). taxglom() is no longer an S4-method, and doesn't need to be now that the character-vector argument option is omitted, with S4-class handling delegated to merge_species(). Updated "taxTab<-" to be S4 assignment, clearer handling of taxonomy Table assignments, especially useful for taxglom.

phyloseq 1.1.29

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Add unit tests and example files for import_biom (as well as import("biom",...) ).

phyloseq 1.1.28

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Added rarefy_even_depth() function for random subsampling of microbiome samples to the same number of reads. Default uses the minimum total reads among the samples in the dataset. This is based on the core "sample" function, which can have its random number generator fixed by set.seed for reproducibility.

phyloseq 1.1.27

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Fix bug in plot_ordination that caused an error rather than produce unannotated plots when sampleData absent in the input.

phyloseq 1.1.23-26

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Added unit tests and bugfixes

phyloseq 1.1.19-22

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Improving import_qiime() importer to handle large datasets, like the HMPv35 dataset, for example, while also providing useful status messages during non-trivial imports that might take 10 minutes or more to complete.

phyloseq 1.1.18

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Added replicate labels as a "Sample" factor in the soilrep dataset.

phyloseq 1.1.17

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Fix possible bug that results from the latest version (0.6+) of igraph not being backward compatible. A stable igraph0 package is available on CRAN as a stop-gap, and so all igraph dependencies were migrated to "igraph0" until the phyloseq-source can be updated to match the igraph latest.

phyloseq 1.1.15

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plot_heatmap: Added default (but adjustable) threshold to omit taxa/sample labels

phyloseq 1.1.14

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Update import_qiime() function to import latest non-BIOM qiime output files. Also added check for presence of taxonomy information (consensus lineage).

phyloseq 1.1.10

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Add plot_heatmap() function, for easy flexible heat maps built with ggplot2

phyloseq 1.1.8-9

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Fix bug for some variants of new BIOM format
Add import_RDP_otu() import function for new RDP pipeline export format

phyloseq 1.1.7

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Removed the old plot_tree_phyloseq() function, in favor of the new ggplot2-based plot_tree()
Uncommented / tested formal examples in documentation of plot-functions
Updated variable names and doc for the plot_taxa_bar() function

phyloseq 1.1.6

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Update vignette with plot_tree() example, replacing the old base-graphics function, plot_tree_phyloseq().
Fix bug in legend for trees with size mapped to abundance

phyloseq 1.1.5

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Add initial version of tree_plot(), built with ggplot2
Adds several internal functions borrowed from devel version of ggphylo

phyloseq 1.1.4

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Add errorIfNULL option to auxiliary accessors (e.g. sample.variables(), rank.names())

phyloseq 1.1.1-3

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R version updated to match Bioconductor, R-2.15.0+
ape-package version updated to 3.0+
ape-package now import dependency
ggplot2-package version updated to 0.9.0+
ggplot2-package now import dependency

phyloseq 0.99.48

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Updated README.md

phyloseq 0.99.47

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Add support for ordinate() to take dist-object instead of distance-method string.
Update the documentation for ordinate() to reflect change.
Updated README.md to describe new tools, distance() and ordinate()
Update JSD documentation.

phyloseq 0.99.46

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Added support and documentation for Jensen-Shannon Divergence to distance().
Some updates to distance() function and its documentation.

phyloseq 0.99.45

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Completely remove vegdist documentation from phyloseq by omitting all roxygen2 headers except for #' keywords internal
This finally fixes it, without build warnings/errors, once and for all.

phyloseq 0.99.44

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Make the phyloseq::vegdist() wrapper an internal function. Documentation updated as well. This is a solution to Issue 87 https://github.com/joey711/phyloseq/issues/87
Remove rda.phyloseq and cca.phyloseq from exported methods. Documentation had already been removed when these were first attempted to be converted to internal methods in CHANGES IN VERSION 0.99.42
Modify make_sample_network to use the new distance() function, and be able to pass on additional parameters to distance().
Re-order arguments to make_sample_network to better represent the stability of defaults.
Removed redundant parameters from make_sample_network(). Transformations to abundance tables should be performed upstream using phyloseq tools, not embedded in this function.
Modify vignettes to reflect these changes.
Rebuild vignette.
Update import() documentation to reflect support for BIOM format, import_biom() function.

phyloseq 0.99.43

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Revise component assignment operators, e.g. "sampleData(physeq)<-" to coerce/access from more diverse objects based on context. Documentation for these operators updated. This is a more general solution to Issue 68 https://github.com/joey711/phyloseq/issues/68

phyloseq 0.99.42

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purge rda.phyloseq and cca.phyloseq from documentation, vignettes. Internal functions.
analysis vignette revisions

phyloseq 0.99.41

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Added ordinate() function, general ordination wrapper.

phyloseq 0.99.40

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Fixed case issues with source filenames. Required multiple commits, break in versioning for source files that had improper letter case (e.g. ".r")

phyloseq 0.99.37

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Vignette updates.

phyloseq 0.99.36

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Added general distance calculation wrapper, distance()
Consolidated it with unifrac.R code in a new "distance-methods.R" source file.

phyloseq 0.99.35

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Added tool to retain user-defined subset of points from an ordination, subset_ord_plot
Updates to vignette
Remove a poorly-documented, unpublished example dataset, ex1 -> and all references to it in documentation

phyloseq 0.99.34

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Updates to vignette

phyloseq 0.99.33

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Allow color specification for "biplot" type in plot_ordination()
bug fix for certain combinations of biplot options.

phyloseq 0.99.32

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Remove plot_ordination_biplot() from phyloseq -> replaced by: plot_ordination()
pipes "|->" also removed from vignette.
Remove calcplot(). -> Will be replaced by pipeline_() methods
plot_ordination() shown in vignette for "species" plot type.
Fix - Allow flexible axis labels for plot_ordination()

phyloseq 0.99.31

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Aesthetic fixes in plot_ordination()
Remove plot_ordination_samples() -> redundant, covered by plot_ordination().

phyloseq 0.99.30

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Added plot_ordination -> general ordination plotting function

phyloseq 0.99.29

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Added first-draft of analysis vignette to package
Total package-space and build/check times tested

phyloseq 0.99.28

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Fixed bug when specifying alternative axes in plot_ordination_samples()

phyloseq 0.99.27

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Added DPCoA() function for Double Principle Coordinate Analysis, relies heavily on ade4.
Added ade4 dependency. Some masking, but no errors apparent.
Added dpcoa extension for scores()
minor bugfix in plot_ordination_biplot().

phyloseq 0.99.26

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Add plot_ordination_samples() for convenient ordination plotting
Renamed plot_ordination_phyloseq to more precise, plot_ordination_biplot()
Added extension to vegan::scores for ape:pcoa results, scores.pcoa()

phyloseq 0.99.25

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Fix build warning from duplicate import in namespace
Update README.md

phyloseq 0.99.24

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Advanced network/graph plotting/visualization wrappers: make_sample_network(), plot_sample_network()
Advanced alpha diversity wrappers: plot_richness_estimates(), estimate_richness()
Added taxafilter() function for even more convenient filtering of species/taxa
Added reshape dependency for explicit use of melt() function.

phyloseq 0.99.23

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Added a rooted tree to "GlobalPatterns" dataset
Allow multi-class tests with mt()

phyloseq 0.99.20

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Added "GlobalPatterns" dataset, and some other minor improvements
added "GlobalPatterns" dataset, with doc and some analysis examples. More examples will be added to the vignette.
add getVariable accessor function, for streamlining access to values/vectors/factors/etc of the variates contained in the sampleData component
revise documentation about parallelization of import_biom()
revise documentation for enterotype dataset

phyloseq 0.99.19

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fixed a bug in general import() function in which it properly processed import command, but then failed to return result.

phyloseq 0.99.18

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Added import_biom() function to import BIOM format OTU-clustered data / metadata
Added (direct) dependency for plyr, as well as RJSONIO

phyloseq 0.4.2-7

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Improvements to import_mothur() via import_mothur_otulist().
merge_samples() function added, in preparation for hypergeometric (fisher.test) test wrapper.
Fixed bug in merge_phyloseq() for certain combinations of objects.
Various other fixes and improvements.

phyloseq 0.4.1

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First official submission to Bioconductor
Includes many build-fixes, bug-fixes
Final tweaks to conform to Bioconductor guidelines

phyloseq 0.3

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Added Importers for mothur, RDP-pipeline, and PyroTagger
Lots of new plotting and analysis support
Parallelized UniFrac calculations using foreach package
Some improvements to the class inheritance structure to simplify method extension and future development.
Function-level documentation
Vignette-level documentation
Package dependencies achieved via import for all packages with a namespace. Depends (full load) otherwise.

phyloseq 0.2.4

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Added ordination and plotting pipeline, calcplot() and plot.ordination.phyloseq()
All trees converted to phylo4 by default. Support for phyla achieved by coercion to phylo4.