opm 0.9-0 --------- Bug fixes: - 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' Significant user-visible changes: - 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). New features: - three novel spline-fitting methods for estimating curve parameters, all of which optimized 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 discretize any of the four curve parameters - indexed assigned has been introduced for OPMS objects - indexing wells now works with formulas, too, allowing for sequences of well coordinates - the infix operators can swap the arguments, and also work with formulas, just as subset() - opms() now normalizes plate-type names if used as 'group' argument - in addition to YAML, JSON can be produced (a subset of YAML that is understood by proper JSON parsers) - 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 Other changes: - much extended vignette - improved documentation in the manual - new directory with example code opm 0.8-0 --------- Bug fixes: - bug fixes in flatten() ('strict' argument) and safe_labels() Significant user-visible changes: - 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 New features: - added support for ECO, SF-N2 and SF-P2 plates (Microstation plates) - added listing() method for OPMX objects for generating textual descriptions of the discretized 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) Other changes: - improvements of the package URL (http://opm.dsmz.de/), the stored substrate information, the documentation and the unit tests opm 0.7-0 --------- Bug fixes: - fixed bug in metadata-file handling of 'run_opm.R' script Removed features: - 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 Other user-visible changes: - dependencies on 'pkgutils' and 'Ckmeans.1d.dp' packages New features: - novel OPMD class and according novel functions do_disc(), has_disc(), discretized() and disc_settings(); extract() can now also get discretized data - novel unique() method for OPM and OPMS objects - enhancements in phylo_data(), discrete(), map_values(), summary(), sort(), select(), duplicated() and anyDuplicated() Other changes: - opm vignette was included as tutorial - some improvements in the documentation in the manual opm 0.6-0 --------- Bug fixes: - 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 Other user-visible changes: - default color set of xy_plot() changed to 'w3c' (because it contains more colors than 'nora') New features: - 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 opm 0.5-0 --------- Bug fixes: - 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' Other user-visible changes: - 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 datasets (suggestion by Benjamin Hofner) - `[` was modfied to remove incompatibilties with the 'Matrix' package (which IMHO uses setMethod("[", ...) in other ways than specified in the documentation of `[` in the base package) (problem noticed by Benjamin Hofner) New features: - 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 multi- 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 opm 0.4-0 --------- Bug fixes: - fixed bug in the OPMS method of merge() that caused it to crash with plates with unequal numbers of time points New features: - 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', CIs 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 Other changes: - 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 opm 0.3-3 --------- Bug fixes: - fixed some testing problems that caused the tests to fail with the novel R for Windows New features: - novel methods for the automated discretization 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 discretization: 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 recognize 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() Other changes: - some further improvements of the documentation opm 0.2-0 --------- Bug fixes: - fixed bug that caused xy_plot() to crash if 'theor.max' was set to FALSE New features: - 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) Removed features: - curve_params() has been deleted (functionality now integrated in do_aggr()) Other changes: - many improvements of the documentation - 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() opm 0.1-25 ---------- - fixed some problems that caused the tests to crash on Windows and Solaris opm 0.1-24 ---------- - initial release to CRAN