| NEWS | R Documentation |
removed ambiguities in dispatch of MOPMX methods
constant data do not cause aggregation to crash any more with some spline fitting methods
param_names() is now generic
using str() is now discouraged by the code, too
a warning is now issued in the case of constant measurements
MOPMX plotting functions
do_aggr() can detect number of computational cores
new arguments for gen_iii(), read_opm() and batch_opm()
new arguments and signatures for some database I/O methods
opmx() has more abilities and treats 'NA' values more gracefully
updated stored substrate information
new example data file from distinct plate reader
nice HTML online documentation
additions to the vignettes and the manual and many textual improvements of the main tutorial
fixed bug in merge() potentially causing duplicate time points
better behaviour of splines with long run times
included missing 'potato' data set
dependency on R >= 3.1.0 and 'mboost', removed 'mboostDevel'
do_aggr() default is now 'method = "splines" boot = 0L'
heat_map() uses 'ward.D2' by default
support of LIMS CSV style input format
fixes of minor bugs in extract() and flatten()
bug fixes in 'MOPMX' bracket method and 'MOPMX' object creation
more consistent behaviour of read_opm()
metadata assignment with numeric keys and data frames as values works now correctly
automatically generated conversion methods previously yielding invalid objects now explicitly raise an error
fixed missing export of virtual classes
list method of contains() and all map_names() and map_values() methods moved to 'pkgutils'
removed deprecated functions filename(), position() and setup_time()
removed deprecated arguments 'what' of phylo_data(), 'examples' of opm_files()
wells() does not partially match plate names any more
the 'normalize' argument of csv_data() now triggers additional replacements
more restricted use of the 'paren.sep' argument of wells() and other functions
new data set 'boccuto_et_al'
new register_plate() and opmx() methods for managing user-defined data
new methods opm_dbput(), opm_dbget(), opm_dbnext(), opm_dbfind(), opm_dbclass() and opm_dbcheck(); new classes OPM_DB, OPMA_DB and OPMD_DB
new MOPMX methods: for extract(), heat_map(), thin_out(), edit(), flatten(), as.data.frame(), find_positions(), substrate_info(), wells(), infix operators, bracket operator, duplicated(), anyDuplicated(), sort(), '+'(), contains(), split(), to_metadata(), phylo_data(), opm_mcp(), listing(), subset()
SEED compounds IDs have been added to the substrate information
new arguments: 'group.col' for radial_plot(), 'rm.num' and 'simplify' for wells(), 'abbrev' and 'log1' for heat_map(), 'exact' and 'strict' for duplicated(), 'no.html' and 'embed.css' for html_args(), 'rcr' for xy_plot()
the OPMS method of ‘['() allows a large variety of ’i' arguments
new virtual class 'WMDS' into which 'OPMS' methods have been factored out, similarly, more OPM methods are now WMD methods
much expanded vignette on substrate information, particularly regarding feature selection
added vignette on analysing growth-curve (and user-defined PM) data
many new demos
the dependency on the R version is now correctly stated as '>= 3.0.0' (as noted by the CRAN team)
use of the 'direct' argument of extract_columns() is slightly different (easier to use)
colour assignment by radial_plot() is slightly different (improved)
new parallelplot() plotting approach for OPMX objects
new new OPM method for extract_columns()
more arguments for as.data.frame() and substrate_info()
replaced fast_estimate() by the matrix method of do_aggr(); removed deprecated functions well_to_substrate() and batch_opm_to_yaml()
removed deprecated arguments of to_metadata() and do_aggr()
position(), setup_time() and filename() are deprecated; use csv_data() instead
output of read_opm() and opms() in 'grp' mode has changed to MOPMX objects (which inherit from lists, which were returned in previous versions)
the order of arguments of some of the methods of to_metadata(), discrete(), phylo_data(), radial_plot() and level_plot() have slightly changed; the OPMD listing() method gets a mandatory 'as.groups' argument
substrate naming is slightly different in some cases
additions to the stored discretisation settings, thus older YAML files will be automatically converted (with a warning)
the vignettes are now available only as PDF files
new generic function annotated() with a variety of methods and options
opm_mcp() now handles non-syntactical names in metadata, computes specific 'Pairs...' contrast-types and more easily specifies the 'base' for the 'Dunnett' contrast type
new MOPMX class for holding plates with distinct plate types, with methods for, e.g., do_aggr() and do_disc()
faster input of CSV and YAML files
new spline-fitting facilities (see set_spline_options())
new methods for length(), merge(), edit() (for editing metadata by hand), infix operators, plate_type()
new arguments and according new features for heat_map(), ci_plot(), flatten(), aggregated(), discretized(), opm_files(), aggr_settings(), disc_settings(), collect_template(), csv_data(), well(), find_positions(), substrate_info(), to_yaml(), opm_mcp()
new entries managed via opm_opt()
support for plate types FF, YT and AN2 added (thanks to Barry *Bochner*) and many additions to the stored substrate information (thanks to the 'ChEBI' staff); better conversion of substrate names to HTML
new command-line options for 'run_opm.R'
second vignette for explaining substrate-information processing, including visualisation in KEGG graphs and feature selection
examples available via demo()
improved the documentation in the manual
fixed two bugs in batch_opm()
fixed bug in reading of old-style CSV with certain headers
fixed bug causing YAML maps to be order-dependent in some cases
to_kmeans() is now compatible with R > 3.0.1
NA values in YAML are now compatible with 'yaml' >= 2.1.7
method dispatch of 'metadata<-'() is now unambiguous
removed deprecated select() function
well_to_substrate() is now deprecated
changes in the arguments treatment of listing()
novel as.data.frame() methods, novel substrate_info() and find_position() methods for OPM and OPMS classes
novel arguments for extract(), extract_columns(), opm_mcp(), do_disc(), batch_collect(), batch_opm(), run_kmeans(), substrate_info(), to_yaml() and listing()
many additions and some corrections in the stored substrate information, as well as nicer and richer display of find_substrate() and substrate_info() results
automated cleaning of character-string well names used for indexing
more opm_opt() entries
more more command-line options for 'run_opm.R'
xy_plot() now works with missing negative-control wells (warning only)
aggregated() now returns the correct object for all argument combinations
do_disc() now allows best-cutoff approach with 'groups=FALSE'
batch_opm_to_yaml() is now deprecated in favour of batch_opm()
the extract() method for data frames now works differently
the '-a' argument of the 'run_opm.R' script now works differently
three additional package dependencies, and dependency on newer versions of the 'grofit' package and of R itself
it is now an error if more than a single core is requested but this is impossible (as, e.g., under Windows).
three novel spline-fitting methods for estimating curve parameters, all of which optimised for PM data
novel opm_mcp() function for multiple comparisons of means applied directly to OPMS objects
novel extract() method for data frames for calculating means and confidence intervals from observation groups (for plotting with ci_plot())
listing() can now generate HTML-formatted text describing positive/negative results
do_disc() could now discretise any of the four curve parameters
indexed assigned has been introduced for OPMS objects
indexing wells now works with formulae, too, allowing for sequences of well coordinates
the infix operators can swap the arguments, and also work with formulae, just as subset()
opms() now normalises plate-type names if used as 'group' argument
in addition to YAML, JSON can be produced (the subset of YAML that is understood by proper JSON libraries)
new expression methods for metadata mapping
new map_metadata(), to_metadata() and 'metadata<-'() methods
new arguments and/or options for ci_plot(), radial_plot(), opm_opt(), param_names(), file_pattern(), opm_files(), safe_labels(), plate_type(), substrate_info()
batch_opm() replaces batch_opm_to_yaml() with more arguments and more output options (JSON and graphics files)
support for three more plate types
much extended vignette
improved documentation in the manual
new directory with example code
bug fixes in flatten() ('strict' argument) and safe_labels()
the 'yaml' package is now mandatory
select() is deprecated in favour of subset()
the disc_settings() and aggr_settings() entries have other content, and older objects stored using save() or in '*.RData' files are only partially compatible; conversion of OPMX objects to a list and back fixes this (done automatically for stored YAML files)
opm_opt() is more restrictive regarding the data type of its labels
extract_columns() and extract() are more restrictive regarding their 'as.labels' and 'as.groups' arguments; this effects all methods that are based on them, such as xy_plot(); as a rule: use a list as 'include', 'as.labels' or 'as.groups' argument
the meaning of the 'prefer.char' argument to phylo_data() has been changed
added support for ECO, SF-N2 and SF-P2 plates (MicroStation plates)
added listing() method for OPMX objects for generating textual descriptions of the discretised reactions
novel html_args() function (helper method for phylo_data())
gen_iii(), read_opm() and batch_opm_to_yaml() now support more plate-type changes
read_opm() and 'run_opm.R' can be adapted to distinct input file encodings
more options to be set by opm_opt(), and more functions (by default) modified by them
more arguments of batch_opm_to_yaml(), wells(), plate_type(), csv_data(), phylo_data(), substrate_info()
improved output of the summary() methods of OPMX objects, of substrate_info() (e.g., 'MeSH' IDs), of phylo_data() (better HTML) and of opm_files() ('auxiliary' files)
improvements of the package URL (http://opm.dsmz.de/), the stored substrate information, the documentation and the unit tests
fixed bug in metadata-file handling of 'run_opm.R' script
listing(), max_rgb_contrast(), paper_size() and mypdf(), as well as a series of internal functions, moved to 'pkgutils' package; data set 'vaas_et_al' moved to 'opmdata' package; some arguments of run_kmeans() removed
dependencies on 'pkgutils' and 'Ckmeans.1d.dp' packages
novel OPMD class and according novel functions do_disc(), has_disc(), discretised and disc_settings(); extract() can now also get discretised data
novel unique() method for OPM and OPMS objects
enhancements in phylo_data(), discrete(), map_values(), summary(), sort(), select(), duplicated() and anyDuplicated()
vignette was included as tutorial
some improvements in the documentation in the manual
fixed bug in xy_plot() that caused 'space' to overwrite 'legend.fmt'
fixed bug in matrix method of do_aggr() causing lists to occur within data frames
corrections of some substrate names
default colour set of xy_plot() changed to 'w3c' (because it contains more colours than 'nora')
novel functions: substrate_info(), opm_opt(), mypdf(), best_cutoff()
novel methods for OPM(S) objects: rev(), rep(), sort(), duplicated(), anyDuplicated(), sort()
more arguments for: level_plot(), ci_plot(), merge(), find_substrate(), file_pattern(), batch_process(), batch_collect() . improved behaviour: separate() in 'list.wise' mode, glob_to_regex(), 'metadata<-'() if data frames with a single column are supplied
fixed 'run_opm.R' bug causing an error in conjunction with '-r template', and bug causing '-s' to be ignored in conjunction with '-r template'
normalize_plate_name() has been removed; it is replaced by the novel character (and factor) methods for plate_type()
specific show() method for OPM and OPMS objects
changed to lazy loading of the data sets
‘[' was modified to remove incompatibilities with the ’Matrix' package
metadata manipulation is now easier due to the novel formula-based methods for 'metadata<-'() and map_metadata() and the novel OPMS/data frame methods for 'metadata<-'()
plotting functionality for 'run_opm.R'
summary() for OPMS objects is more detailed
novel plates() methods for lists and OPM objects
duplicate() and anyDuplicated() get a 'what' argument allowing not only the detection of duplicate OPM objects but also of duplicates of selected components only
novel contains() method for OPMS objects, and arguments to all contains() allowing fine control of strictness
added factor methods for find_substrate(), find_positions(), glob_to_regex() 'metadata<-'() and the infix operators; metadata() now betters supports factors as keys
separate() now automatically selects multiple- vs. single-character splitting modes if split is a non-empty character vector, and it has a novel 'list.wise' argument
run_kmeans() and do_aggr() methods for matrices
fixed bug in the OPMS method of merge() that caused it to crash with plates with unequal numbers of time points
added full citation information (first paper on 'opm') :-)
radial_plot() and sort() methods for OPMS objects
phylo_data(), heat_map() and radial_plot() methods directly for OPMS objects
extract(), select(), discrete() and phylo_data() methods for data frames
phylo_data() has been enhanced: added export in Hennig86 format for TNT; added vector-based merging of rows via the 'join' argument; improved HTML output; added 'run.tidy' option for reformatting the generated HTML with HTML Tidy; added 'delete' argument
for the 'A' parameter estimated using 'opm-fast', confidence intervals that cannot be calculated because the values are constant are not set to NA anymore but to that value
annoying messages when calling require() for 'gplots' have been silenced
added the remaining so far missing OPMS-method documentation entries and improved the format of the references
added example file from a run in identification mode
fixed some testing problems that caused the tests to fail with the novel R for Windows
novel methods for the automated discretisation of curve heights into positive (+), weak (w) and negative (-) and the subsequent generation of reports in HTML for taxonomic journals such as IJSEM; accordingly, quite a few novel helper functions for k-means based discretisation: to_kmeans(), borders(), calinski(), and, of course, run_kmeans()
novel arguments to read_opm() (automatically assorting according to the plate type); similar novel option for opms() to recognise plate types and construct OPMS objects separately, or select those with a certain plate type
redundancies in input plates with 'OTH' as plate type (from runs in identification mode) are now automatically removed
novel merge() method for OPMS objects, i.e. a function for merging plates from subsequent runs of the same physical plate (of interest for slowly reacting organisms)
map_values() and map_names() have been considerably extended
novel 'digits' argument to listing(), novel 'pad' argument of safe_labels(), novel 'keep.const' and 'simplify' arguments to separate()
some further improvements of the documentation
fixed bug that caused xy_plot() to crash if 'theor.max' was set to FALSE
novel filename(), aggr_settings(), duplicated(), anyDuplicated(), seq() and oapply() methods for OPMS objects
novel map_names() and map_values() methods (e.g., for data frames)
novel separate() function
'coerce = TRUE' option for map_names(), map_values(), map_metadata() and metadata_chars()
novel 'include' argument to split_files()
novel 'plain' argument for do_aggr()
file input now automatically changes 'OTH' to generation-III plate type
improved the 'remove.csv.data' behaviour of include_metadata() (the default keys were always removed, and 'remove.csv.data' had a distinct effect)
curve_params() has been deleted (functionality now integrated in do_aggr())
the 'coerce' argument of map_metadata() and metadata_chars() has been renamed to 'classes' (to make this uniform)
'remove.csv.data' argument of include_metadata() was renamed to 'remove.keys', 'stop.on.error' to 'skip.failure' (with the reverse meaning, but the default behaviour remains the same)
changed 'gplots' to default of 'use.fun' argument of heat_map()
many improvements of the documentation
fixed some problems that caused the tests to crash on Windows and Solaris
initial release to CRAN