opm: Analysing Phenotype Microarray and Growth Curve Data

Tools for analysing OmniLog(R) and MicroStation(TM) phenotype microarray (PM) data as produced by the devices distributed by BIOLOG Inc. as well as similar kinds of data such as growth curves. Major facilities are plotting data, accurately estimating curve parameters, comparing and discretising data, creating phylogenetic formats and reports for taxonomic journals, drawing the PM analysis results in biochemical pathway graphs optionally including genome annotations, running multiple comparisons of means, easy interaction with powerful feature-selection approaches, integrating metadata, using the YAML format for the storage of data and metadata, batch conversion of large numbers of files, and database I/O.

AuthorMarkus Goeker, with contributions by Benjamin Hofner, Lea A.I. Vaas, Johannes Sikorski, Maria del Carmen Montero Calasanz, Jan P. Meier-Kolthoff, Nora Buddruhs and Anne Fiebig
Date of publication2016-11-14 17:03:08
MaintainerMarkus Goeker <markus.goeker@dsmz.de>
LicenseGPL (>= 2)
Version1.3.64
http://opm.dsmz.de/

View on R-Forge

Man pages

aggregated: Get aggregated data

annotated: Create vector or matrix with substrate annotation

as.data.frame: Create data frame

batch_opm: Batch-convert PM data

boccuto_et_al: Autism cell-line example data set

bracket: Select subset

bracket.set: Assign subset

c: Combination and addition of plates

ci_plot: Plot point estimates with CIs

collect_template: Input metadata

csv_data: Information from input CSV file

dim: Get dimensions

discrete: Discretisation functions

discretized: Get discretised data

do_aggr: Aggregate kinetics using curve-parameter estimation

do_disc: Discretise curve parameters

duplicated: Determine duplicated plates

explode_dir: Helper functions for file input and output

extract: Extract aggregated values and/or metadata

find_substrate: Identify substrates or positions

has_aggr: Are aggregated or discretised data present?

heat_map: Heat map

html_args: HTML formatting and output label generation

include_metadata: Add or map metadata or edit them by hand

infix.k: Query metadata keys

infix.q: Query metadata

kmeans: Work with k-means results

level_plot: Level plot

max: Overall or minimal maximum

measurements: Stored measurements

merge: Merge or split plates

metadata: Get metadata

metadata.set: Replace metadata

OPM: Real classes of the 'opm' package

OPM_DB: Classes for 'opm' database I/O

opm_dbput: Database I/O for 'opm'

opm_files: Files and colour sets used by the package

opm_mcp: Multiple comparison of group means

opm_opt: Global 'opm' options

opm.package: The 'opm' package

opms.function: OPMS constructor

opmx.function: Convert user-defined objects to OPMX

parallel_plot: Parallel plot

phylo_data: Export phylogenetic data

plates: Get available plates or apply function to them

plate_type: Plate type displayed or modified, registered or deleted

potato: Potato cell-line growth data set

radial_plot: Radial plot

read_opm: Read multiple PM files at once or read single PM file

run_kmeans: Conduct k-means partitioning

separate: Regularly split character vectors if possible

set_spline_options: Spline options

sort: Sort, unify, revert or repeat OPMS objects

subset: Select a subset of the plates (or time points)

substrate_info: Provide information on substrates

summary: Summarise OPMX or MOPMX objects

to_yaml: Convert to YAML

vaas_4: Example data sets from Vaas et al. (2012)

wells: Listing of well names

WMD: Virtual classes of the 'opm' package

xy_plot: X-Y plot

Functions

[ Man page
[<- Man page
[[<- Man page
$<- Man page
aggregated Man page
aggregated-methods Man page
aggregated,MOPMX-method Man page
aggregated,OPMA-method Man page
aggregated,OPMS-method Man page
aggr_settings Man page
aggr_settings-methods Man page
aggr_settings,MOPMX-method Man page
aggr_settings,OPMA-method Man page
aggr_settings,OPMS-method Man page
annotated Man page
annotated-methods Man page
annotated,MOPMX-method Man page
annotated,OPMA-method Man page
annotated,OPMD-method Man page
annotated,opm_glht-method Man page
annotated,OPM_MCP_OUT-method Man page
annotated,OPMS-method Man page
anyDuplicated Man page
anyDuplicated-methods Man page
anyDuplicated,MOPMX,ANY-method Man page
anyDuplicated,MOPMX-method Man page
anyDuplicated,MOPMX,missing-method Man page
anyDuplicated,OPM,ANY-method Man page
anyDuplicated,OPM-method Man page
anyDuplicated,OPM,missing-method Man page
anyDuplicated,OPMS,ANY-method Man page
anyDuplicated,OPMS-method Man page
anyDuplicated,OPMS,missing-method Man page
+,ANY,MOPMX-method Man page
anyNA Man page
anyNA-methods Man page
anyNA,MOPMX-method Man page
anyNA,OPMA-method Man page
anyNA,OPMD-method Man page
anyNA,OPM-method Man page
anyNA,OPMS-method Man page
as.data.frame Man page
as.data.frame,kegg_compound-method Man page
as.data.frame,kegg_compounds-method Man page
as.data.frame-methods Man page
as.data.frame,MOPMX-method Man page
as.data.frame,OPMA-method Man page
as.data.frame,OPMD-method Man page
as.data.frame,OPM-method Man page
as.data.frame,OPMS-method Man page
batch_collect Man page
batch_opm Man page
batch_process Man page
best_cutoff Man page
best_cutoff,matrix,character-method Man page
best_cutoff,matrix,factor-method Man page
best_cutoff-methods Man page
boccuto_et_al Man page
borders Man page
borders.Ckmeans.1d.dp Man page
borders.kmeans Man page
borders.kmeanss Man page
bracket-methods Man page
bracket,MOPMX,ANY,missing,ANY-method Man page
bracket,MOPMX,ANY,missing-method Man page
bracket,MOPMX,ANY,missing,missing-method Man page
bracket,MOPMX,character,missing,ANY-method Man page
bracket,MOPMX,character,missing-method Man page
bracket,MOPMX,character,missing,missing-method Man page
bracket,MOPMX,expression,missing,ANY-method Man page
bracket,MOPMX,expression,missing-method Man page
bracket,MOPMX,expression,missing,missing-method Man page
bracket,MOPMX,formula,missing,ANY-method Man page
bracket,MOPMX,formula,missing-method Man page
bracket,MOPMX,formula,missing,missing-method Man page
bracket,MOPMX,list,missing,ANY-method Man page
bracket,MOPMX,list,missing-method Man page
bracket,MOPMX,list,missing,missing-method Man page
bracket,MOPMX,missing,missing,ANY-method Man page
bracket,MOPMX,missing,missing-method Man page
bracket,MOPMX,missing,missing,missing-method Man page
bracket,OPMA,ANY,ANY,ANY-method Man page
bracket,OPMA-method Man page
bracket,OPM,ANY,ANY,ANY-method Man page
bracket,OPMD,ANY,ANY,ANY-method Man page
bracket,OPMD-method Man page
bracket,OPM-method Man page
bracket,OPMS,ANY,ANY,ANY-method Man page
bracket,OPMS-method Man page
bracket.set-methods Man page
bracket.set,MOPMX,ANY,missing,ANY-method Man page
bracket.set,MOPMX,ANY,missing-method Man page
bracket.set,MOPMX,ANY,missing,OPMX-method Man page
bracket.set,OPMS,ANY,missing,list-method Man page
bracket.set,OPMS,ANY,missing,NULL-method Man page
bracket.set,OPMS,ANY,missing,OPM-method Man page
bracket.set,OPMS,ANY,missing,OPMS-method Man page
c Man page
calinski Man page
calinski.Ckmeans.1d.dp Man page
calinski.kmeans Man page
calinski.kmeanss Man page
ci_plot Man page
ci_plot,data.frame-method Man page
ci_plot-methods Man page
ci_plot,MOPMX-method Man page
ci_plot,OPMS-method Man page
c-methods Man page
c,MOPMX-method Man page
collect_template Man page
collect_template,character-method Man page
collect_template-methods Man page
collect_template,MOPMX-method Man page
collect_template,OPM-method Man page
collect_template,OPMS-method Man page
contains Man page
contains-methods Man page
contains,MOPMX,MOPMX-method Man page
contains,MOPMX,OPMX-method Man page
contains,OPM,OPM-method Man page
contains,OPM,OPMS-method Man page
contains,OPMS,OPM-method Man page
contains,OPMS,OPMS-method Man page
contains,OPMX,MOPMX-method Man page
c,OPMX-method Man page
csv_data Man page
csv_data-methods Man page
csv_data,MOPMX-method Man page
csv_data,OPM-method Man page
csv_data,OPMS-method Man page
dim Man page
dim-methods Man page
dim,OPM-method Man page
dim,OPMS-method Man page
discrete Man page
discrete,array-method Man page
discrete,data.frame-method Man page
discrete-methods Man page
discrete,numeric-method Man page
discretized Man page
discretized-methods Man page
discretized,MOPMX-method Man page
discretized,OPMD-method Man page
discretized,OPMS-method Man page
disc_settings Man page
disc_settings,character-method Man page
disc_settings,logical-method Man page
disc_settings-methods Man page
disc_settings,MOPMX-method Man page
disc_settings,NULL-method Man page
disc_settings,numeric-method Man page
disc_settings,OPMD-method Man page
disc_settings,OPMS-method Man page
do_aggr Man page
do_aggr,matrix-method Man page
do_aggr-methods Man page
do_aggr,MOPMX-method Man page
do_aggr,OPM-method Man page
do_aggr,OPMS-method Man page
do_disc Man page
do_disc-methods Man page
do_disc,MOPMX-method Man page
do_disc,OPMA-method Man page
do_disc,OPMS-method Man page
dollar.set-methods Man page
dollar.set,MOPMX,ANY-method Man page
dollar.set,MOPMX-method Man page
double.bracket.set-methods Man page
double.bracket.set,MOPMX,ANY,missing,ANY-method Man page
double.bracket.set,MOPMX,ANY,missing-method Man page
duplicated Man page
duplicated-methods Man page
duplicated,MOPMX,ANY-method Man page
duplicated,MOPMX-method Man page
duplicated,MOPMX,missing-method Man page
duplicated,OPM,ANY-method Man page
duplicated,OPM-method Man page
duplicated,OPM,missing-method Man page
duplicated,OPMS,ANY-method Man page
duplicated,OPMS-method Man page
duplicated,OPMS,missing-method Man page
edit Man page
edit-methods Man page
edit,MOPMX-method Man page
edit,WMDX-method Man page
explode_dir Man page
extract Man page
extract_columns Man page
extract_columns,data.frame-method Man page
extract_columns-methods Man page
extract_columns,WMD-method Man page
extract_columns,WMDS-method Man page
extract,data.frame-method Man page
extract-methods Man page
extract,MOPMX-method Man page
extract,OPMS-method Man page
file_pattern Man page
find_positions Man page
find_positions,character-method Man page
find_positions,factor-method Man page
find_positions,list-method Man page
find_positions-methods Man page
find_positions,MOPMX-method Man page
find_positions,OPM-method Man page
find_positions,OPMS-method Man page
find_positions,substrate_match-method Man page
find_substrate Man page
find_substrate,character-method Man page
find_substrate,factor-method Man page
find_substrate-methods Man page
flatten Man page
flatten-methods Man page
flatten,MOPMX-method Man page
flatten,OPM-method Man page
flatten,OPMS-method Man page
FOE Man page
FOE-class Man page
gen_iii Man page
gen_iii-methods Man page
gen_iii,MOPMX-method Man page
gen_iii,OPM-method Man page
gen_iii,OPMS-method Man page
glob_to_regex Man page
glob_to_regex.character Man page
glob_to_regex.factor Man page
has_aggr Man page
has_aggr-methods Man page
has_aggr,MOPMX-method Man page
has_aggr,OPM-method Man page
has_aggr,OPMS-method Man page
has_disc Man page
has_disc-methods Man page
has_disc,MOPMX-method Man page
has_disc,OPM-method Man page
has_disc,OPMS-method Man page
heat_map Man page
heat_map,data.frame-method Man page
heat_map,matrix-method Man page
heat_map-methods Man page
heat_map,MOPMX-method Man page
heat_map,OPMS-method Man page
hist.Ckmeans.1d.dp Man page
hist.kmeans Man page
hist.kmeanss Man page
hours Man page
hours-methods Man page
hours,MOPMX-method Man page
hours,OPM-method Man page
hours,OPMS-method Man page
html_args Man page
include_metadata Man page
include_metadata-methods Man page
include_metadata,MOPMX-method Man page
include_metadata,OPM-method Man page
include_metadata,WMD-method Man page
include_metadata,WMDS-method Man page
infix.k Man page
infix.k,ANY,MOPMX-method Man page
infix.k,character,WMD-method Man page
infix.k,character,WMDS-method Man page
infix.k,expression,WMD-method Man page
infix.k,expression,WMDS-method Man page
infix.k,factor,WMD-method Man page
infix.k,factor,WMDS-method Man page
infix.k,formula,WMD-method Man page
infix.k,formula,WMDS-method Man page
infix.k,list,WMD-method Man page
infix.k,list,WMDS-method Man page
infix.k-methods Man page
infix.k,MOPMX,ANY-method Man page
infix.k,MOPMX-method Man page
infix.k,MOPMX,MOPMX-method Man page
infix.k,MOPMX,WMD-method Man page
infix.k,MOPMX,WMDS-method Man page
infix.k,WMD,ANY-method Man page
infix.k,WMD-method Man page
infix.k,WMD,MOPMX-method Man page
infix.k,WMDS,ANY-method Man page
infix.k,WMDS-method Man page
infix.k,WMDS,MOPMX-method Man page
infix.k,WMD,WMD-method Man page
infix.k,WMD,WMDS-method Man page
infix.largek Man page
infix.largek,ANY,MOPMX-method Man page
infix.largek,character,WMD-method Man page
infix.largek,character,WMDS-method Man page
infix.largek,expression,WMD-method Man page
infix.largek,expression,WMDS-method Man page
infix.largek,factor,WMD-method Man page
infix.largek,factor,WMDS-method Man page
infix.largek,formula,WMD-method Man page
infix.largek,formula,WMDS-method Man page
infix.largek,list,WMD-method Man page
infix.largek,list,WMDS-method Man page
infix.largek-methods Man page
infix.largek,MOPMX,ANY-method Man page
infix.largek,MOPMX-method Man page
infix.largek,MOPMX,MOPMX-method Man page
infix.largek,MOPMX,WMD-method Man page
infix.largek,MOPMX,WMDS-method Man page
infix.largek,WMD,ANY-method Man page
infix.largek,WMD-method Man page
infix.largek,WMD,MOPMX-method Man page
infix.largek,WMDS,ANY-method Man page
infix.largek,WMDS-method Man page
infix.largek,WMDS,MOPMX-method Man page
infix.largek,WMD,WMD-method Man page
infix.largek,WMD,WMDS-method Man page
infix.largeq Man page
infix.largeq,ANY,MOPMX-method Man page
infix.largeq,character,WMD-method Man page
infix.largeq,character,WMDS-method Man page
infix.largeq,expression,WMD-method Man page
infix.largeq,expression,WMDS-method Man page
infix.largeq,factor,WMD-method Man page
infix.largeq,factor,WMDS-method Man page
infix.largeq,formula,WMD-method Man page
infix.largeq,formula,WMDS-method Man page
infix.largeq,list,WMD-method Man page
infix.largeq,list,WMDS-method Man page
infix.largeq-methods Man page
infix.largeq,MOPMX,ANY-method Man page
infix.largeq,MOPMX-method Man page
infix.largeq,MOPMX,MOPMX-method Man page
infix.largeq,MOPMX,WMD-method Man page
infix.largeq,MOPMX,WMDS-method Man page
infix.largeq,WMD,ANY-method Man page
infix.largeq,WMD-method Man page
infix.largeq,WMD,MOPMX-method Man page
infix.largeq,WMDS,ANY-method Man page
infix.largeq,WMDS-method Man page
infix.largeq,WMDS,MOPMX-method Man page
infix.largeq,WMD,WMD-method Man page
infix.largeq,WMD,WMDS-method Man page
infix.q Man page
infix.q,ANY,MOPMX-method Man page
infix.q,character,WMD-method Man page
infix.q,character,WMDS-method Man page
infix.q,expression,WMD-method Man page
infix.q,expression,WMDS-method Man page
infix.q,factor,WMD-method Man page
infix.q,factor,WMDS-method Man page
infix.q,formula,WMD-method Man page
infix.q,formula,WMDS-method Man page
infix.q,list,WMD-method Man page
infix.q,list,WMDS-method Man page
infix.q-methods Man page
infix.q,MOPMX,ANY-method Man page
infix.q,MOPMX-method Man page
infix.q,MOPMX,MOPMX-method Man page
infix.q,MOPMX,WMD-method Man page
infix.q,MOPMX,WMDS-method Man page
infix.q,WMD,ANY-method Man page
infix.q,WMD-method Man page
infix.q,WMD,MOPMX-method Man page
infix.q,WMDS,ANY-method Man page
infix.q,WMDS-method Man page
infix.q,WMDS,MOPMX-method Man page
infix.q,WMD,WMD-method Man page
infix.q,WMD,WMDS-method Man page
\%k\% Man page
\%K\% Man page
\%k\%,ANY,MOPMX-method Man page
\%K\%,ANY,MOPMX-method Man page
\%k\%,character,WMD-method Man page
\%K\%,character,WMD-method Man page
\%k\%,character,WMDS-method Man page
\%K\%,character,WMDS-method Man page
\%k\%,expression,WMD-method Man page
\%K\%,expression,WMD-method Man page
\%k\%,expression,WMDS-method Man page
\%K\%,expression,WMDS-method Man page
\%k\%,factor,WMD-method Man page
\%K\%,factor,WMD-method Man page
\%k\%,factor,WMDS-method Man page
\%K\%,factor,WMDS-method Man page
\%k\%,formula,WMD-method Man page
\%K\%,formula,WMD-method Man page
\%k\%,formula,WMDS-method Man page
\%K\%,formula,WMDS-method Man page
\%k\%,list,WMD-method Man page
\%K\%,list,WMD-method Man page
\%k\%,list,WMDS-method Man page
\%K\%,list,WMDS-method Man page
kmeans Man page
\%k\%,MOPMX,ANY-method Man page
\%K\%,MOPMX,ANY-method Man page
\%k\%,MOPMX-method Man page
\%K\%,MOPMX-method Man page
\%k\%,MOPMX,MOPMX-method Man page
\%K\%,MOPMX,MOPMX-method Man page
\%k\%,MOPMX,WMD-method Man page
\%K\%,MOPMX,WMD-method Man page
\%k\%,MOPMX,WMDS-method Man page
\%K\%,MOPMX,WMDS-method Man page
\%k\%,WMD,ANY-method Man page
\%K\%,WMD,ANY-method Man page
\%k\%,WMD-method Man page
\%K\%,WMD-method Man page
\%k\%,WMD,MOPMX-method Man page
\%K\%,WMD,MOPMX-method Man page
\%k\%,WMDS,ANY-method Man page
\%K\%,WMDS,ANY-method Man page
\%k\%,WMDS-method Man page
\%K\%,WMDS-method Man page
\%k\%,WMDS,MOPMX-method Man page
\%K\%,WMDS,MOPMX-method Man page
\%k\%,WMD,WMD-method Man page
\%K\%,WMD,WMD-method Man page
\%k\%,WMD,WMDS-method Man page
\%K\%,WMD,WMDS-method Man page
length-methods Man page
length,WMD-method Man page
length,WMDS-method Man page
level_plot Man page
level_plot-methods Man page
level_plot,MOPMX-method Man page
level_plot,OPM-method Man page
level_plot,OPMS-method Man page
listing Man page
listing-methods Man page
listing,MOPMX-method Man page
listing,OPMD-method Man page
listing,OPMX-method Man page
listing,well_coords_map-method Man page
map_metadata Man page
map_metadata-methods Man page
map_metadata,MOPMX,ANY-method Man page
map_metadata,MOPMX-method Man page
map_metadata,MOPMX,missing-method Man page
map_metadata,WMD,character-method Man page
map_metadata,WMD,FOE-method Man page
map_metadata,WMD,function-method Man page
map_metadata,WMD,missing-method Man page
map_metadata,WMDS,ANY-method Man page
map_metadata,WMDS-method Man page
map_metadata,WMDS,missing-method Man page
map_values Man page
map_values,list,formula-method Man page
map_values-methods Man page
max Man page
max-methods Man page
max,OPM-method Man page
max,OPMS-method Man page
measurements Man page
measurements-methods Man page
measurements,MOPMX-method Man page
measurements,OPM-method Man page
measurements,OPMS-method Man page
merge Man page
merge,CMAT,ANY-method Man page
merge,CMAT,factor-method Man page
merge,CMAT,logical-method Man page
merge,CMAT-method Man page
merge-methods Man page
merge,MOPMX,ANY-method Man page
merge,MOPMX-method Man page
merge,MOPMX,missing-method Man page
merge,OPM,missing-method Man page
merge,OPM,numeric-method Man page
merge,OPM,OPM-method Man page
merge,OPMS,missing-method Man page
merge,OPMS,numeric-method Man page
metadata Man page
metadata<- Man page
metadata_chars Man page
metadata_chars-methods Man page
metadata_chars,MOPMX-method Man page
metadata_chars,WMD-method Man page
metadata_chars,WMDS-method Man page
metadata-methods Man page
metadata<-,MOPMX,ANY,ANY-method Man page
metadata<-,MOPMX,ANY,data.frame-method Man page
metadata<-,MOPMX-method Man page
metadata,MOPMX-method Man page
metadata<-,MOPMX,missing,ANY-method Man page
metadata<-,MOPMX,missing,character-method Man page
metadata<-,MOPMX,missing,data.frame-method Man page
metadata<-,MOPMX,missing,logical-method Man page
metadata<-,MOPMX,missing-method Man page
metadata<-,OPM,missing,character-method Man page
metadata<-,OPM,missing,logical-method Man page
metadata.set Man page
metadata.set-methods Man page
metadata.set,MOPMX,ANY,ANY-method Man page
metadata.set,MOPMX,ANY,data.frame-method Man page
metadata.set,MOPMX-method Man page
metadata.set,MOPMX,missing,ANY-method Man page
metadata.set,MOPMX,missing,character-method Man page
metadata.set,MOPMX,missing,data.frame-method Man page
metadata.set,MOPMX,missing,logical-method Man page
metadata.set,MOPMX,missing-method Man page
metadata.set,OPM,missing,character-method Man page
metadata.set,OPM,missing,logical-method Man page
metadata.set,WMD,ANY,ANY-method Man page
metadata.set,WMD,character,ANY-method Man page
metadata.set,WMD,character,data.frame-method Man page
metadata.set,WMD,character-method Man page
metadata.set,WMD,character,WMD-method Man page
metadata.set,WMD,character,WMDS-method Man page
metadata.set,WMD,list,data.frame-method Man page
metadata.set,WMD,list,list-method Man page
metadata.set,WMD,list,WMD-method Man page
metadata.set,WMD,list,WMDS-method Man page
metadata.set,WMD-method Man page
metadata.set,WMD,missing,character-method Man page
metadata.set,WMD,missing,data.frame-method Man page
metadata.set,WMD,missing,FOE-method Man page
metadata.set,WMD,missing,list-method Man page
metadata.set,WMD,missing,WMD-method Man page
metadata.set,WMD,missing,WMDS-method Man page
metadata.set,WMD,numeric,data.frame-method Man page
metadata.set,WMD,numeric,list-method Man page
metadata.set,WMD,numeric,WMD-method Man page
metadata.set,WMD,numeric,WMDS-method Man page
metadata.set,WMDS,ANY,ANY-method Man page
metadata.set,WMDS,ANY,data.frame-method Man page
metadata.set,WMDS,ANY,WMD-method Man page
metadata.set,WMDS,ANY,WMDS-method Man page
metadata.set,WMDS,character,data.frame-method Man page
metadata.set,WMDS,character,WMDS-method Man page
metadata.set,WMDS-method Man page
metadata.set,WMDS,missing,character-method Man page
metadata.set,WMDS,missing,data.frame-method Man page
metadata.set,WMDS,missing,FOE-method Man page
metadata.set,WMDS,missing,list-method Man page
metadata.set,WMDS,missing,logical-method Man page
metadata.set,WMDS,missing,WMD-method Man page
metadata.set,WMDS,missing,WMDS-method Man page
metadata<-,WMD,ANY,ANY-method Man page
metadata<-,WMD,character,ANY-method Man page
metadata<-,WMD,character,data.frame-method Man page
metadata<-,WMD,character-method Man page
metadata<-,WMD,character,WMD-method Man page
metadata<-,WMD,character,WMDS-method Man page
metadata<-,WMD,list,data.frame-method Man page
metadata<-,WMD,list,list-method Man page
metadata<-,WMD,list,WMD-method Man page
metadata<-,WMD,list,WMDS-method Man page
metadata<-,WMD-method Man page
metadata,WMD-method Man page
metadata<-,WMD,missing,character-method Man page
metadata<-,WMD,missing,data.frame-method Man page
metadata<-,WMD,missing,FOE-method Man page
metadata<-,WMD,missing,list-method Man page
metadata<-,WMD,missing,WMD-method Man page
metadata<-,WMD,missing,WMDS-method Man page
metadata<-,WMD,numeric,data.frame-method Man page
metadata<-,WMD,numeric,list-method Man page
metadata<-,WMD,numeric,WMD-method Man page
metadata<-,WMD,numeric,WMDS-method Man page
metadata<-,WMDS,ANY,ANY-method Man page
metadata<-,WMDS,ANY,data.frame-method Man page
metadata<-,WMDS,ANY,WMD-method Man page
metadata<-,WMDS,ANY,WMDS-method Man page
metadata<-,WMDS,character,data.frame-method Man page
metadata<-,WMDS,character,WMDS-method Man page
metadata<-,WMDS-method Man page
metadata,WMDS-method Man page
metadata<-,WMDS,missing,character-method Man page
metadata<-,WMDS,missing,data.frame-method Man page
metadata<-,WMDS,missing,FOE-method Man page
metadata<-,WMDS,missing,list-method Man page
metadata<-,WMDS,missing,logical-method Man page
metadata<-,WMDS,missing,WMD-method Man page
metadata<-,WMDS,missing,WMDS-method Man page
minmax Man page
minmax-methods Man page
minmax,OPM-method Man page
minmax,OPMS-method Man page
MOPMX Man page
$<-,MOPMX,ANY-method Man page
+,MOPMX,ANY-method Man page
[<-,MOPMX,ANY,missing,ANY-method Man page
[,MOPMX,ANY,missing,ANY-method Man page
[[<-,MOPMX,ANY,missing,ANY-method Man page
[<-,MOPMX,ANY,missing-method Man page
[,MOPMX,ANY,missing-method Man page
[[<-,MOPMX,ANY,missing-method Man page
[,MOPMX,ANY,missing,missing-method Man page
[<-,MOPMX,ANY,missing,OPMX-method Man page
[,MOPMX,character,missing,ANY-method Man page
[,MOPMX,character,missing-method Man page
[,MOPMX,character,missing,missing-method Man page
MOPMX-class Man page
[,MOPMX,expression,missing,ANY-method Man page
[,MOPMX,expression,missing-method Man page
[,MOPMX,expression,missing,missing-method Man page
[,MOPMX,formula,missing,ANY-method Man page
[,MOPMX,formula,missing-method Man page
[,MOPMX,formula,missing,missing-method Man page
[,MOPMX,list,missing,ANY-method Man page
[,MOPMX,list,missing-method Man page
[,MOPMX,list,missing,missing-method Man page
$<-,MOPMX-method Man page
+,MOPMX-method Man page
[,MOPMX,missing,missing,ANY-method Man page
[,MOPMX,missing,missing-method Man page
[,MOPMX,missing,missing,missing-method Man page
+,MOPMX,numeric-method Man page
+,MOPMX,OPMX-method Man page
+,numeric,MOPMX-method Man page
+,numeric,OPM-method Man page
+,numeric,OPMS-method Man page
oapply Man page
oapply-methods Man page
oapply,MOPMX-method Man page
oapply,OPM-method Man page
oapply,OPMS-method Man page
OPM Man page
OPMA Man page
[,OPMA,ANY,ANY,ANY-method Man page
OPMA-class Man page
OPMA_DB Man page
OPMA_DB-class Man page
[,OPMA-method Man page
[,OPM,ANY,ANY,ANY-method Man page
OPM-class Man page
OPMD Man page
[,OPMD,ANY,ANY,ANY-method Man page
OPM_DB Man page
opm_dbcheck Man page
opm_dbcheck,ANY-method Man page
opm_dbcheck-methods Man page
opm_dbclass Man page
OPM_DB-class Man page
opm_dbclass,integer-method Man page
opm_dbclass-methods Man page
opm_dbclass,MOPMX-method Man page
opm_dbclass,OPM-method Man page
opm_dbclass,OPMS-method Man page
opm_dbclear Man page
opm_dbclear,character,ANY-method Man page
opm_dbclear,character-method Man page
opm_dbclear,integer,DBIConnection-method Man page
opm_dbclear-methods Man page
opm_dbfind Man page
opm_dbfind,character,DBIConnection-method Man page
opm_dbfind-methods Man page
opm_dbget Man page
opm_dbget,character,ANY-method Man page
opm_dbget,character-method Man page
opm_dbget,integer,DBIConnection-method Man page
opm_dbget-methods Man page
opm_dbnext Man page
opm_dbnext,ANY,ANY-method Man page
opm_dbnext,ANY-method Man page
opm_dbnext,DBTABLES,DBIConnection-method Man page
opm_dbnext-methods Man page
opm_dbput Man page
opm_dbput,ANY,ANY-method Man page
opm_dbput,ANY-method Man page
opm_dbput,DBTABLES,DBIConnection-method Man page
opm_dbput-methods Man page
OPMD-class Man page
OPMD_DB Man page
OPMD_DB-class Man page
[,OPMD-method Man page
opm_files Man page
+,OPM,list-method Man page
opm_mcp Man page
opm_mcp,data.frame-method Man page
opm_mcp-methods Man page
opm_mcp,MOPMX-method Man page
opm_mcp,OPMS-method Man page
OPM_MCP_OUT Man page
OPM_MCP_OUT-class Man page
[,OPM-method Man page
+,OPM,MOPMX-method Man page
+,OPM,numeric-method Man page
+,OPM,OPM-method Man page
+,OPM,OPMS-method Man page
opm_opt Man page
opm_opt,character-method Man page
opm_opt,list-method Man page
opm_opt-methods Man page
opm_opt,missing-method Man page
opm.package Man page
opm.package-package Man page
opms Man page
OPMS Man page
[,OPMS,ANY,ANY,ANY-method Man page
[<-,OPMS,ANY,missing,list-method Man page
[<-,OPMS,ANY,missing,NULL-method Man page
[<-,OPMS,ANY,missing,OPM-method Man page
[<-,OPMS,ANY,missing,OPMS-method Man page
OPMS-class Man page
+,OPMS,list-method Man page
[,OPMS-method Man page
+,OPMS,MOPMX-method Man page
+,OPMS,numeric-method Man page
+,OPMS,OPM-method Man page
+,OPMS,OPMS-method Man page
opmx Man page
OPMX Man page
OPMX-class Man page
opmx,data.frame-method Man page
opmx-methods Man page
parallelplot Man page
parallel_plot Man page
parallel_plot,formula,XOPMX-method Man page
parallelplot,formula,XOPMX-method Man page
parallel_plot-methods Man page
parallelplot-methods Man page
parallel_plot,missing,XOPMX-method Man page
parallelplot,missing,XOPMX-method Man page
parallel_plot,MOPMX,ANY-method Man page
parallelplot,MOPMX,ANY-method Man page
parallel_plot,MOPMX-method Man page
parallelplot,MOPMX-method Man page
parallel_plot,MOPMX,missing-method Man page
parallelplot,MOPMX,missing-method Man page
parallel_plot,MOPMX,XOPMX-method Man page
parallelplot,MOPMX,XOPMX-method Man page
parallel_plot,NULL,XOPMX-method Man page
parallelplot,NULL,XOPMX-method Man page
parallel_plot,OPMX,ANY-method Man page
parallelplot,OPMX,ANY-method Man page
parallel_plot,OPMX-method Man page
parallelplot,OPMX-method Man page
parallel_plot,OPMX,missing-method Man page
parallelplot,OPMX,missing-method Man page
parallel_plot,OPMX,XOPMX-method Man page
parallelplot,OPMX,XOPMX-method Man page
parallel_plot,vector,XOPMX-method Man page
parallelplot,vector,XOPMX-method Man page
param_names Man page
param_names,character-method Man page
param_names-methods Man page
param_names,missing-method Man page
phylo_data Man page
phylo_data,data.frame-method Man page
phylo_data,matrix-method Man page
phylo_data-methods Man page
phylo_data,OPMD_Listing-method Man page
phylo_data,OPMS_Listing-method Man page
phylo_data,XOPMX-method Man page
plates Man page
plates,list-method Man page
plates-methods Man page
plates,MOPMX-method Man page
plates,WMD-method Man page
plates,WMDS-method Man page
plate_type Man page
plate_type,character-method Man page
plate_type,factor-method Man page
plate_type,logical-method Man page
plate_type-methods Man page
plate_type,missing-method Man page
plate_type,MOPMX-method Man page
plate_type,OPM_DB-method Man page
plate_type,OPM-method Man page
plate_type,OPMS-method Man page
plot.kmeanss Man page
plus Man page
plus,ANY,MOPMX-method Man page
plus-methods Man page
plus,MOPMX,ANY-method Man page
plus,MOPMX-method Man page
plus,MOPMX,numeric-method Man page
plus,MOPMX,OPMX-method Man page
plus,numeric,MOPMX-method Man page
plus,numeric,OPM-method Man page
plus,numeric,OPMS-method Man page
plus,OPM,list-method Man page
plus,OPM,MOPMX-method Man page
plus,OPM,numeric-method Man page
plus,OPM,OPM-method Man page
plus,OPM,OPMS-method Man page
plus,OPMS,list-method Man page
plus,OPMS,MOPMX-method Man page
plus,OPMS,numeric-method Man page
plus,OPMS,OPM-method Man page
plus,OPMS,OPMS-method Man page
potato Man page
\%q\% Man page
\%Q\% Man page
\%q\%,ANY,MOPMX-method Man page
\%Q\%,ANY,MOPMX-method Man page
\%q\%,character,WMD-method Man page
\%Q\%,character,WMD-method Man page
\%q\%,character,WMDS-method Man page
\%Q\%,character,WMDS-method Man page
\%q\%,expression,WMD-method Man page
\%Q\%,expression,WMD-method Man page
\%q\%,expression,WMDS-method Man page
\%Q\%,expression,WMDS-method Man page
\%q\%,factor,WMD-method Man page
\%Q\%,factor,WMD-method Man page
\%q\%,factor,WMDS-method Man page
\%Q\%,factor,WMDS-method Man page
\%q\%,formula,WMD-method Man page
\%Q\%,formula,WMD-method Man page
\%q\%,formula,WMDS-method Man page
\%Q\%,formula,WMDS-method Man page
\%q\%,list,WMD-method Man page
\%Q\%,list,WMD-method Man page
\%q\%,list,WMDS-method Man page
\%Q\%,list,WMDS-method Man page
\%q\%,MOPMX,ANY-method Man page
\%Q\%,MOPMX,ANY-method Man page
\%q\%,MOPMX-method Man page
\%Q\%,MOPMX-method Man page
\%q\%,MOPMX,MOPMX-method Man page
\%Q\%,MOPMX,MOPMX-method Man page
\%q\%,MOPMX,WMD-method Man page
\%Q\%,MOPMX,WMD-method Man page
\%q\%,MOPMX,WMDS-method Man page
\%Q\%,MOPMX,WMDS-method Man page
\%q\%,WMD,ANY-method Man page
\%Q\%,WMD,ANY-method Man page
\%q\%,WMD-method Man page
\%Q\%,WMD-method Man page
\%q\%,WMD,MOPMX-method Man page
\%Q\%,WMD,MOPMX-method Man page
\%q\%,WMDS,ANY-method Man page
\%Q\%,WMDS,ANY-method Man page
\%q\%,WMDS-method Man page
\%Q\%,WMDS-method Man page
\%q\%,WMDS,MOPMX-method Man page
\%Q\%,WMDS,MOPMX-method Man page
\%q\%,WMD,WMD-method Man page
\%Q\%,WMD,WMD-method Man page
\%q\%,WMD,WMDS-method Man page
\%Q\%,WMD,WMDS-method Man page
radial_plot Man page
radial_plot,data.frame-method Man page
radial_plot,matrix-method Man page
radial_plot-methods Man page
radial_plot,MOPMX-method Man page
radial_plot,OPMS-method Man page
read_opm Man page
read_single_opm Man page
register_plate Man page
register_plate,character-method Man page
register_plate,list-method Man page
register_plate-methods Man page
register_plate,missing-method Man page
rep Man page
rep-methods Man page
rep,OPM-method Man page
rep,OPMS-method Man page
rev Man page
rev-methods Man page
rev,OPM-method Man page
rev,OPMS-method Man page
run_kmeans Man page
run_kmeans,matrix,numeric-method Man page
run_kmeans-methods Man page
run_kmeans,numeric,numeric-method Man page
safe_labels Man page
select_colors Man page
separate Man page
separate,character-method Man page
separate,data.frame-method Man page
separate,factor-method Man page
separate-methods Man page
seq Man page
seq-methods Man page
seq,WMD-method Man page
seq,WMDS-method Man page
set_spline_options Man page
show,CMAT-method Man page
show-methods Man page
show,MOPMX-method Man page
show,OPMX-method Man page
sort Man page
sort-methods Man page
sort,MOPMX,ANY-method Man page
sort,MOPMX-method Man page
sort,MOPMX,missing-method Man page
sort,OPM,ANY-method Man page
sort,OPM-method Man page
sort,OPM,missing-method Man page
sort,OPMS,ANY-method Man page
sort,OPMS-method Man page
sort,OPMS,missing-method Man page
split Man page
split_files Man page
split-methods Man page
split,MOPMX,ANY,ANY-method Man page
split,MOPMX,ANY,missing-method Man page
split,MOPMX,factor,ANY-method Man page
split,MOPMX,factor-method Man page
split,MOPMX,factor,missing-method Man page
split,MOPMX,list,ANY-method Man page
split,MOPMX,list-method Man page
split,MOPMX,list,missing-method Man page
split,MOPMX-method Man page
split,OPM,ANY,missing-method Man page
split,OPM,factor,ANY-method Man page
split,OPM,factor-method Man page
split,OPM,factor,missing-method Man page
split,OPM,missing,ANY-method Man page
split,OPM,missing-method Man page
split,OPM,missing,missing-method Man page
split,OPMS,ANY,missing-method Man page
split,OPMS,factor,ANY-method Man page
split,OPMS,factor-method Man page
split,OPMS,factor,missing-method Man page
split,OPMS,missing,ANY-method Man page
split,OPMS,missing-method Man page
split,OPMS,missing,missing-method Man page
split,OPMX,ANY,ANY-method Man page
split,OPMX-method Man page
str,CMAT-method Man page
str-methods Man page
str,MOPMX-method Man page
str,WMDX-method Man page
subset Man page
subset-methods Man page
subset,MOPMX-method Man page
subset,OPMX-method Man page
substrate_info Man page
substrate_info,character-method Man page
substrate_info,factor-method Man page
substrate_info,list-method Man page
substrate_info-methods Man page
substrate_info,MOPMX-method Man page
substrate_info,OPM-method Man page
substrate_info,OPMS-method Man page
substrate_info,substrate_match-method Man page
summary Man page
summary-methods Man page
summary,MOPMX-method Man page
summary,OPM-method Man page
summary,OPMS-method Man page
thin_out Man page
thin_out-methods Man page
thin_out,MOPMX-method Man page
thin_out,OPM-method Man page
thin_out,OPMS-method Man page
to_kmeans Man page
to_kmeans.Ckmeans.1d.dp Man page
to_kmeans.kmeans Man page
to_kmeans.kmeanss Man page
to_metadata Man page
to_metadata,ANY-method Man page
to_metadata,character-method Man page
to_metadata-methods Man page
to_metadata,MOPMX-method Man page
to_metadata,WMD-method Man page
to_metadata,WMDS-method Man page
to_yaml Man page
to_yaml,list-method Man page
to_yaml-methods Man page
to_yaml,MOPMX-method Man page
to_yaml,YAML_VIA_LIST-method Man page
unique Man page
unique-methods Man page
unique,MOPMX,ANY-method Man page
unique,MOPMX-method Man page
unique,MOPMX,missing-method Man page
unique,OPM,ANY-method Man page
unique,OPM-method Man page
unique,OPM,missing-method Man page
unique,OPMS,ANY-method Man page
unique,OPMS-method Man page
unique,OPMS,missing-method Man page
vaas_1 Man page
vaas_4 Man page
well Man page
well-methods Man page
well,MOPMX-method Man page
well,OPM-method Man page
well,OPMS-method Man page
wells Man page
wells,ANY-method Man page
wells-methods Man page
wells,missing-method Man page
wells,MOPMX-method Man page
wells,OPM-method Man page
wells,OPMS-method Man page
WMD Man page
WMD-class Man page
WMDS Man page
WMDS-class Man page
WMDX Man page
WMDX-class Man page
XOPMX Man page
XOPMX-class Man page
xy_plot Man page
xy_plot,data.frame-method Man page
xy_plot-methods Man page
xy_plot,MOPMX-method Man page
xy_plot,OPM-method Man page
xy_plot,OPMS-method Man page
YAML_VIA_LIST Man page
YAML_VIA_LIST-class Man page

Files

opm/COPYING
opm/ChangeLog
opm/DESCRIPTION
opm/NAMESPACE
opm/NEWS
opm/R
opm/R/aggregation-aux.R opm/R/aggregation.R opm/R/auxiliary-aux.R opm/R/auxiliary.R opm/R/classes-aux.R opm/R/classes.R opm/R/combination-aux.R opm/R/combination.R opm/R/constants.R opm/R/conversion-aux.R opm/R/conversion.R opm/R/data.R opm/R/dbio-aux.R opm/R/dbio.R opm/R/discretization.R opm/R/getter.R opm/R/imports.R opm/R/io-aux.R opm/R/io.R opm/R/kmeans-aux.R opm/R/kmeans.R opm/R/metadata.R opm/R/multcomp-aux.R opm/R/multcomp.R opm/R/naming-aux.R opm/R/naming.R opm/R/package.R opm/R/phylogeny-aux.R opm/R/phylogeny.R opm/R/plate-map.R opm/R/plotting-aux.R opm/R/plotting.R opm/R/splinefit-aux.R opm/R/substrate-info.R opm/R/testing-aux.R opm/R/well-map.R
opm/build
opm/build/vignette.rds
opm/data
opm/data/boccuto_et_al.rda
opm/data/potato.rda
opm/data/vaas_1.rda
opm/data/vaas_4.rda
opm/demo
opm/demo/00Index
opm/demo/MongoDB-IO.R
opm/demo/MySQL-IO.R
opm/demo/PostgreSQL-IO.R
opm/demo/SQLite-IO.R
opm/demo/cluster-with-pvalues.R
opm/demo/custom-PCA.R
opm/demo/distinguish-curve-topologies.R
opm/demo/identify-positive-reactions.R
opm/demo/multiple-plate-types.R
opm/demo/phenotype-vs-genotype.R
opm/demo/workshop-part-1.R
opm/demo/workshop-part-2.R
opm/demo/workshop-part-3.R
opm/demo/workshop-part-4.R
opm/demo/workshop-part-5.R
opm/inst
opm/inst/CITATION
opm/inst/auxiliary
opm/inst/auxiliary/001_rdbms_drop.sql
opm/inst/auxiliary/002_rdbms_create.sql
opm/inst/auxiliary/003_rdbms_delete.sql
opm/inst/auxiliary/styles_1.css
opm/inst/doc
opm/inst/doc/opm-growth-curves.Rnw
opm/inst/doc/opm-growth-curves.pdf
opm/inst/doc/opm-substrates.Rnw
opm/inst/doc/opm-substrates.pdf
opm/inst/doc/opm-tutorial.Rnw
opm/inst/doc/opm-tutorial.pdf
opm/inst/scripts
opm/inst/scripts/run_opm.R
opm/inst/testdata
opm/inst/testdata/Example_1.csv.xz
opm/inst/testdata/Example_2.csv.xz
opm/inst/testdata/Example_3.csv.xz
opm/inst/testdata/Example_Ecoplate.csv.xz
opm/inst/testdata/Example_ID_run.csv.xz
opm/inst/testdata/Example_LIMS_Export.exl.xz
opm/inst/testdata/Example_Old_Style_1.csv.xz
opm/inst/testdata/Example_Old_Style_2.csv.xz
opm/inst/testdata/Example_Old_Style_3.csv.xz
opm/inst/testdata/Example_Old_Style_Multiple.csv.xz
opm/inst/testdata/Example_Perkin_Elmer.txt.xz
opm/inst/testdata/Example_TECAN.txt.xz
opm/inst/tests
opm/inst/tests/test_aggregation-aux.R
opm/inst/tests/test_aggregation.R
opm/inst/tests/test_auxiliary-aux.R
opm/inst/tests/test_auxiliary.R
opm/inst/tests/test_classes-aux.R
opm/inst/tests/test_classes.R
opm/inst/tests/test_combination-aux.R
opm/inst/tests/test_combination.R
opm/inst/tests/test_constants.R
opm/inst/tests/test_conversion-aux.R
opm/inst/tests/test_conversion.R
opm/inst/tests/test_data.R
opm/inst/tests/test_dbio-aux.R
opm/inst/tests/test_dbio.R
opm/inst/tests/test_discretization.R
opm/inst/tests/test_getter.R
opm/inst/tests/test_imports.R
opm/inst/tests/test_io-aux.R
opm/inst/tests/test_io.R
opm/inst/tests/test_kmeans-aux.R
opm/inst/tests/test_kmeans.R
opm/inst/tests/test_metadata.R
opm/inst/tests/test_multcomp-aux.R
opm/inst/tests/test_multcomp.R
opm/inst/tests/test_naming-aux.R
opm/inst/tests/test_naming.R
opm/inst/tests/test_package.R
opm/inst/tests/test_phylogeny-aux.R
opm/inst/tests/test_phylogeny.R
opm/inst/tests/test_plate-map.R
opm/inst/tests/test_plotting-aux.R
opm/inst/tests/test_plotting.R
opm/inst/tests/test_splinefit-aux.R
opm/inst/tests/test_substrate-info.R
opm/inst/tests/test_testing-aux.R
opm/inst/tests/test_well-map.R
opm/man
opm/man/OPM.Rd opm/man/OPM_DB.Rd opm/man/WMD.Rd opm/man/aggregated.Rd opm/man/annotated.Rd opm/man/as.data.frame.Rd opm/man/batch_opm.Rd opm/man/boccuto_et_al.Rd opm/man/bracket.Rd opm/man/bracket.set.Rd opm/man/c.Rd opm/man/ci_plot.Rd opm/man/collect_template.Rd opm/man/csv_data.Rd opm/man/dim.Rd opm/man/discrete.Rd opm/man/discretized.Rd opm/man/do_aggr.Rd opm/man/do_disc.Rd opm/man/duplicated.Rd opm/man/explode_dir.Rd opm/man/extract.Rd opm/man/find_substrate.Rd opm/man/has_aggr.Rd opm/man/heat_map.Rd opm/man/html_args.Rd opm/man/include_metadata.Rd opm/man/infix.k.Rd opm/man/infix.q.Rd opm/man/kmeans.Rd opm/man/level_plot.Rd opm/man/max.Rd opm/man/measurements.Rd opm/man/merge.Rd opm/man/metadata.Rd opm/man/metadata.set.Rd opm/man/opm.package.Rd opm/man/opm_dbput.Rd opm/man/opm_files.Rd opm/man/opm_mcp.Rd opm/man/opm_opt.Rd opm/man/opms.function.Rd opm/man/opmx.function.Rd opm/man/parallel_plot.Rd opm/man/phylo_data.Rd opm/man/plate_type.Rd opm/man/plates.Rd opm/man/potato.Rd opm/man/radial_plot.Rd opm/man/read_opm.Rd opm/man/run_kmeans.Rd opm/man/separate.Rd opm/man/set_spline_options.Rd opm/man/sort.Rd opm/man/subset.Rd opm/man/substrate_info.Rd opm/man/summary.Rd opm/man/to_yaml.Rd opm/man/vaas_4.Rd opm/man/wells.Rd opm/man/xy_plot.Rd
opm/tests
opm/tests/run-all.R
opm/vignettes
opm/vignettes/opm-growth-curves.Rnw
opm/vignettes/opm-substrates.Rnw
opm/vignettes/opm-tutorial.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.