opm: Analysing Phenotype Microarray and Growth Curve Data
Version 1.3.64

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
URL http://opm.dsmz.de/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("opm", repos="http://R-Forge.R-project.org")

Popular man pages

aggregated: Get aggregated data
explode_dir: Helper functions for file input and output
kmeans: Work with k-means results
max: Overall or minimal maximum
OPM: Real classes of the 'opm' package
plates: Get available plates or apply function to them
read_opm: Read multiple PM files at once or read single PM file
See all...

All man pages Function index File listing

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
$<-,MOPMX,ANY-method Man page
$<-,MOPMX-method Man page
+,ANY,MOPMX-method Man page
+,MOPMX,ANY-method Man page
+,MOPMX,OPMX-method Man page
+,MOPMX,numeric-method Man page
+,MOPMX-method Man page
+,OPM,MOPMX-method Man page
+,OPM,OPM-method Man page
+,OPM,OPMS-method Man page
+,OPM,list-method Man page
+,OPM,numeric-method Man page
+,OPMS,MOPMX-method Man page
+,OPMS,OPM-method Man page
+,OPMS,OPMS-method Man page
+,OPMS,list-method Man page
+,OPMS,numeric-method Man page
+,numeric,MOPMX-method Man page
+,numeric,OPM-method Man page
+,numeric,OPMS-method Man page
AUC Source code
FOE Man page
FOE-class Man page
MOPMX Man page
MOPMX-class Man page
OPM Man page
OPM-class Man page
OPMA Man page
OPMA-class Man page
OPMA_DB Man page
OPMA_DB-class Man page
OPMD Man page
OPMD-class Man page
OPMD_DB Man page
OPMD_DB-class Man page
OPMS Man page
OPMS-class Man page
OPMX Man page
OPMX-class Man page
OPM_DB Man page
OPM_DB-class Man page
OPM_MCP_OUT Man page
OPM_MCP_OUT-class Man page
Predict.matrix.psp.smooth Source code
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
YAML_VIA_LIST Man page
YAML_VIA_LIST-class Man page
[ Man page
[,MOPMX,ANY,missing,ANY-method Man page
[,MOPMX,ANY,missing,missing-method Man page
[,MOPMX,ANY,missing-method Man page
[,MOPMX,character,missing,ANY-method Man page
[,MOPMX,character,missing,missing-method Man page
[,MOPMX,character,missing-method Man page
[,MOPMX,expression,missing,ANY-method Man page
[,MOPMX,expression,missing,missing-method Man page
[,MOPMX,expression,missing-method Man page
[,MOPMX,formula,missing,ANY-method Man page
[,MOPMX,formula,missing,missing-method Man page
[,MOPMX,formula,missing-method Man page
[,MOPMX,list,missing,ANY-method Man page
[,MOPMX,list,missing,missing-method Man page
[,MOPMX,list,missing-method Man page
[,MOPMX,missing,missing,ANY-method Man page
[,MOPMX,missing,missing,missing-method Man page
[,MOPMX,missing,missing-method Man page
[,OPM,ANY,ANY,ANY-method Man page
[,OPM-method Man page
[,OPMA,ANY,ANY,ANY-method Man page
[,OPMA-method Man page
[,OPMD,ANY,ANY,ANY-method Man page
[,OPMD-method Man page
[,OPMS,ANY,ANY,ANY-method Man page
[,OPMS-method Man page
[<- Man page
[<-,MOPMX,ANY,missing,ANY-method Man page
[<-,MOPMX,ANY,missing,OPMX-method Man page
[<-,MOPMX,ANY,missing-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,ANY,missing,list-method Man page
[[<- Man page
[[<-,MOPMX,ANY,missing,ANY-method Man page
[[<-,MOPMX,ANY,missing-method Man page
\%K\% Man page
\%K\%,ANY,MOPMX-method Man page
\%K\%,MOPMX,ANY-method Man page
\%K\%,MOPMX,MOPMX-method Man page
\%K\%,MOPMX,WMD-method Man page
\%K\%,MOPMX,WMDS-method Man page
\%K\%,MOPMX-method Man page
\%K\%,WMD,ANY-method Man page
\%K\%,WMD,MOPMX-method Man page
\%K\%,WMD,WMD-method Man page
\%K\%,WMD,WMDS-method Man page
\%K\%,WMD-method Man page
\%K\%,WMDS,ANY-method Man page
\%K\%,WMDS,MOPMX-method Man page
\%K\%,WMDS-method Man page
\%K\%,character,WMD-method Man page
\%K\%,character,WMDS-method Man page
\%K\%,expression,WMD-method Man page
\%K\%,expression,WMDS-method Man page
\%K\%,factor,WMD-method Man page
\%K\%,factor,WMDS-method Man page
\%K\%,formula,WMD-method Man page
\%K\%,formula,WMDS-method Man page
\%K\%,list,WMD-method Man page
\%K\%,list,WMDS-method Man page
\%Q\% Man page
\%Q\%,ANY,MOPMX-method Man page
\%Q\%,MOPMX,ANY-method Man page
\%Q\%,MOPMX,MOPMX-method Man page
\%Q\%,MOPMX,WMD-method Man page
\%Q\%,MOPMX,WMDS-method Man page
\%Q\%,MOPMX-method Man page
\%Q\%,WMD,ANY-method Man page
\%Q\%,WMD,MOPMX-method Man page
\%Q\%,WMD,WMD-method Man page
\%Q\%,WMD,WMDS-method Man page
\%Q\%,WMD-method Man page
\%Q\%,WMDS,ANY-method Man page
\%Q\%,WMDS,MOPMX-method Man page
\%Q\%,WMDS-method Man page
\%Q\%,character,WMD-method Man page
\%Q\%,character,WMDS-method Man page
\%Q\%,expression,WMD-method Man page
\%Q\%,expression,WMDS-method Man page
\%Q\%,factor,WMD-method Man page
\%Q\%,factor,WMDS-method Man page
\%Q\%,formula,WMD-method Man page
\%Q\%,formula,WMDS-method Man page
\%Q\%,list,WMD-method Man page
\%Q\%,list,WMDS-method Man page
\%k\% Man page
\%k\%,ANY,MOPMX-method Man page
\%k\%,MOPMX,ANY-method Man page
\%k\%,MOPMX,MOPMX-method Man page
\%k\%,MOPMX,WMD-method Man page
\%k\%,MOPMX,WMDS-method Man page
\%k\%,MOPMX-method Man page
\%k\%,WMD,ANY-method Man page
\%k\%,WMD,MOPMX-method Man page
\%k\%,WMD,WMD-method Man page
\%k\%,WMD,WMDS-method Man page
\%k\%,WMD-method Man page
\%k\%,WMDS,ANY-method Man page
\%k\%,WMDS,MOPMX-method Man page
\%k\%,WMDS-method Man page
\%k\%,character,WMD-method Man page
\%k\%,character,WMDS-method Man page
\%k\%,expression,WMD-method Man page
\%k\%,expression,WMDS-method Man page
\%k\%,factor,WMD-method Man page
\%k\%,factor,WMDS-method Man page
\%k\%,formula,WMD-method Man page
\%k\%,formula,WMDS-method Man page
\%k\%,list,WMD-method Man page
\%k\%,list,WMDS-method Man page
\%q\% Man page
\%q\%,ANY,MOPMX-method Man page
\%q\%,MOPMX,ANY-method Man page
\%q\%,MOPMX,MOPMX-method Man page
\%q\%,MOPMX,WMD-method Man page
\%q\%,MOPMX,WMDS-method Man page
\%q\%,MOPMX-method Man page
\%q\%,WMD,ANY-method Man page
\%q\%,WMD,MOPMX-method Man page
\%q\%,WMD,WMD-method Man page
\%q\%,WMD,WMDS-method Man page
\%q\%,WMD-method Man page
\%q\%,WMDS,ANY-method Man page
\%q\%,WMDS,MOPMX-method Man page
\%q\%,WMDS-method Man page
\%q\%,character,WMD-method Man page
\%q\%,character,WMDS-method Man page
\%q\%,expression,WMD-method Man page
\%q\%,expression,WMDS-method Man page
\%q\%,factor,WMD-method Man page
\%q\%,factor,WMDS-method Man page
\%q\%,formula,WMD-method Man page
\%q\%,formula,WMDS-method Man page
\%q\%,list,WMD-method Man page
\%q\%,list,WMDS-method Man page
add_in_parens Source code
add_parameters Source code
aggr_settings Man page
aggr_settings,MOPMX-method Man page
aggr_settings,OPMA-method Man page
aggr_settings,OPMS-method Man page
aggr_settings-methods Man page
aggregated Man page
aggregated,MOPMX-method Man page
aggregated,OPMA-method Man page
aggregated,OPMS-method Man page
aggregated-methods Man page
annotated Man page
annotated,MOPMX-method Man page
annotated,OPMA-method Man page
annotated,OPMD-method Man page
annotated,OPMS-method Man page
annotated,OPM_MCP_OUT-method Man page
annotated,opm_glht-method Man page
annotated-methods Man page
anyDuplicated Man page
anyDuplicated,MOPMX,ANY-method Man page
anyDuplicated,MOPMX,missing-method Man page
anyDuplicated,MOPMX-method Man page
anyDuplicated,OPM,ANY-method Man page
anyDuplicated,OPM,missing-method Man page
anyDuplicated,OPM-method Man page
anyDuplicated,OPMS,ANY-method Man page
anyDuplicated,OPMS,missing-method Man page
anyDuplicated,OPMS-method Man page
anyDuplicated-methods Man page
anyNA Man page
anyNA,MOPMX-method Man page
anyNA,OPM-method Man page
anyNA,OPMA-method Man page
anyNA,OPMD-method Man page
anyNA,OPMS-method Man page
anyNA-methods Man page
as.data.frame Man page
as.data.frame,MOPMX-method Man page
as.data.frame,OPM-method Man page
as.data.frame,OPMA-method Man page
as.data.frame,OPMD-method Man page
as.data.frame,OPMS-method 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.gam Source code
as.gam.opm_model Source code
assert_splittable_matrix Source code
backward_OPMA_to_list Source code
backward_OPMD_to_list Source code
backward_OPM_to_list Source code
batch_collect Man page Source code
batch_opm Man page Source code
batch_process Man page Source code
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 Source code
borders.Ckmeans.1d.dp Man page Source code
borders.kmeans Man page Source code
borders.kmeanss Man page Source code
bracket,MOPMX,ANY,missing,ANY-method Man page
bracket,MOPMX,ANY,missing,missing-method Man page
bracket,MOPMX,ANY,missing-method Man page
bracket,MOPMX,character,missing,ANY-method Man page
bracket,MOPMX,character,missing,missing-method Man page
bracket,MOPMX,character,missing-method Man page
bracket,MOPMX,expression,missing,ANY-method Man page
bracket,MOPMX,expression,missing,missing-method Man page
bracket,MOPMX,expression,missing-method Man page
bracket,MOPMX,formula,missing,ANY-method Man page
bracket,MOPMX,formula,missing,missing-method Man page
bracket,MOPMX,formula,missing-method Man page
bracket,MOPMX,list,missing,ANY-method Man page
bracket,MOPMX,list,missing,missing-method Man page
bracket,MOPMX,list,missing-method Man page
bracket,MOPMX,missing,missing,ANY-method Man page
bracket,MOPMX,missing,missing,missing-method Man page
bracket,MOPMX,missing,missing-method Man page
bracket,OPM,ANY,ANY,ANY-method Man page
bracket,OPM-method Man page
bracket,OPMA,ANY,ANY,ANY-method Man page
bracket,OPMA-method Man page
bracket,OPMD,ANY,ANY,ANY-method Man page
bracket,OPMD-method Man page
bracket,OPMS,ANY,ANY,ANY-method Man page
bracket,OPMS-method Man page
bracket-methods Man page
bracket.set,MOPMX,ANY,missing,ANY-method Man page
bracket.set,MOPMX,ANY,missing,OPMX-method Man page
bracket.set,MOPMX,ANY,missing-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
bracket.set,OPMS,ANY,missing,list-method Man page
bracket.set-methods Man page
c Man page
c,MOPMX-method Man page
c,OPMX-method Man page
c-methods Man page
calinski Man page Source code
calinski.Ckmeans.1d.dp Man page Source code
calinski.kmeans Man page Source code
calinski.kmeanss Man page Source code
check_mcp_sep Source code
ci_plot Man page
ci_plot,MOPMX-method Man page
ci_plot,OPMS-method Man page
ci_plot,data.frame-method Man page
ci_plot-methods Man page
clean_coords Source code
clean_plate_positions Source code
close_index_gaps Source code
collect.kegg_compounds Source code
collect_template Man page
collect_template,MOPMX-method Man page
collect_template,OPM-method Man page
collect_template,OPMS-method Man page
collect_template,character-method Man page
collect_template-methods Man page
contains 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
contains-methods Man page
convert_annotation_vector Source code
create_formula Source code
create_listing Source code
csv_data Man page
csv_data,MOPMX-method Man page
csv_data,OPM-method Man page
csv_data,OPMS-method Man page
csv_data-methods Man page
custom_plate_assert Source code
custom_plate_exists Source code
custom_plate_get Source code
custom_plate_is Source code
custom_plate_normalize Source code
custom_plate_normalize_all Source code
custom_plate_normalize_proper Source code
custom_plate_prepend Source code
custom_plate_prepend_full Source code
custom_plate_proper Source code
custom_plate_set Source code
custom_plate_set_full Source code
default_color_regions Source code
dim Man page
dim,OPM-method Man page
dim,OPMS-method Man page
dim-methods Man page
disc_settings Man page
disc_settings,MOPMX-method Man page
disc_settings,NULL-method Man page
disc_settings,OPMD-method Man page
disc_settings,OPMS-method Man page
disc_settings,character-method Man page
disc_settings,logical-method Man page
disc_settings,numeric-method Man page
disc_settings-methods Man page
discrete Man page
discrete,array-method Man page
discrete,data.frame-method Man page
discrete,numeric-method Man page
discrete-methods Man page
discretized Man page
discretized,MOPMX-method Man page
discretized,OPMD-method Man page
discretized,OPMS-method Man page
discretized-methods Man page
do_aggr Man page
do_aggr,MOPMX-method Man page
do_aggr,OPM-method Man page
do_aggr,OPMS-method Man page
do_aggr,matrix-method Man page
do_aggr-methods Man page
do_disc Man page
do_disc,MOPMX-method Man page
do_disc,OPMA-method Man page
do_disc,OPMS-method Man page
do_disc-methods Man page
dollar.set,MOPMX,ANY-method Man page
dollar.set,MOPMX-method Man page
dollar.set-methods Man page
double.bracket.set,MOPMX,ANY,missing,ANY-method Man page
double.bracket.set,MOPMX,ANY,missing-method Man page
double.bracket.set-methods Man page
duplicated Man page
duplicated,MOPMX,ANY-method Man page
duplicated,MOPMX,missing-method Man page
duplicated,MOPMX-method Man page
duplicated,OPM,ANY-method Man page
duplicated,OPM,missing-method Man page
duplicated,OPM-method Man page
duplicated,OPMS,ANY-method Man page
duplicated,OPMS,missing-method Man page
duplicated,OPMS-method Man page
duplicated-methods Man page
edit Man page
edit,MOPMX-method Man page
edit,WMDX-method Man page
edit-methods Man page
explode_dir Man page Source code
extract Man page
extract,MOPMX-method Man page
extract,OPMS-method Man page
extract,data.frame-method Man page
extract-methods Man page
extract_columns Man page
extract_columns,WMD-method Man page
extract_columns,WMDS-method Man page
extract_columns,data.frame-method Man page
extract_columns-methods Man page
extract_curve_params Source code
extract_curve_params.fake_opm_model Source code
extract_curve_params.grofit Source code
extract_curve_params.opm_model Source code
file_pattern Man page Source code
find_positions Man page
find_positions,MOPMX-method Man page
find_positions,OPM-method Man page
find_positions,OPMS-method Man page
find_positions,character-method Man page
find_positions,factor-method Man page
find_positions,list-method Man page
find_positions,substrate_match-method Man page
find_positions-methods Man page
find_substrate Man page
find_substrate,character-method Man page
find_substrate,factor-method Man page
find_substrate-methods Man page
finish_template Source code
fit_spline Source code
flatten Man page
flatten,MOPMX-method Man page
flatten,OPM-method Man page
flatten,OPMS-method Man page
flatten-methods Man page
formula2infix Source code
forward_OPMA_to_list Source code
forward_OPM_to_list Source code
gen_iii Man page
gen_iii,MOPMX-method Man page
gen_iii,OPM-method Man page
gen_iii,OPMS-method Man page
gen_iii-methods Man page
get_and_remember Source code
get_data Source code
get_data.smooth.spline_model Source code
get_partial_match Source code
glob_to_regex Man page Source code
glob_to_regex.character Man page Source code
glob_to_regex.factor Man page Source code
has_aggr Man page
has_aggr,MOPMX-method Man page
has_aggr,OPM-method Man page
has_aggr,OPMS-method Man page
has_aggr-methods Man page
has_disc Man page
has_disc,MOPMX-method Man page
has_disc,OPM-method Man page
has_disc,OPMS-method Man page
has_disc-methods Man page
heat_map Man page
heat_map,MOPMX-method Man page
heat_map,OPMS-method Man page
heat_map,data.frame-method Man page
heat_map,matrix-method Man page
heat_map-methods Man page
hist.Ckmeans.1d.dp Man page Source code
hist.kmeans Man page Source code
hist.kmeanss Man page Source code
hours Man page
hours,MOPMX-method Man page
hours,OPM-method Man page
hours,OPMS-method Man page
hours-methods Man page
html_args Man page Source code
html_head Source code
include_metadata 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
include_metadata-methods Man page
infix.k Man page
infix.k,ANY,MOPMX-method Man page
infix.k,MOPMX,ANY-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,MOPMX-method Man page
infix.k,WMD,ANY-method Man page
infix.k,WMD,MOPMX-method Man page
infix.k,WMD,WMD-method Man page
infix.k,WMD,WMDS-method Man page
infix.k,WMD-method Man page
infix.k,WMDS,ANY-method Man page
infix.k,WMDS,MOPMX-method Man page
infix.k,WMDS-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.largek Man page
infix.largek,ANY,MOPMX-method Man page
infix.largek,MOPMX,ANY-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,MOPMX-method Man page
infix.largek,WMD,ANY-method Man page
infix.largek,WMD,MOPMX-method Man page
infix.largek,WMD,WMD-method Man page
infix.largek,WMD,WMDS-method Man page
infix.largek,WMD-method Man page
infix.largek,WMDS,ANY-method Man page
infix.largek,WMDS,MOPMX-method Man page
infix.largek,WMDS-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.largeq Man page
infix.largeq,ANY,MOPMX-method Man page
infix.largeq,MOPMX,ANY-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,MOPMX-method Man page
infix.largeq,WMD,ANY-method Man page
infix.largeq,WMD,MOPMX-method Man page
infix.largeq,WMD,WMD-method Man page
infix.largeq,WMD,WMDS-method Man page
infix.largeq,WMD-method Man page
infix.largeq,WMDS,ANY-method Man page
infix.largeq,WMDS,MOPMX-method Man page
infix.largeq,WMDS-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.q Man page
infix.q,ANY,MOPMX-method Man page
infix.q,MOPMX,ANY-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,MOPMX-method Man page
infix.q,WMD,ANY-method Man page
infix.q,WMD,MOPMX-method Man page
infix.q,WMD,WMD-method Man page
infix.q,WMD,WMDS-method Man page
infix.q,WMD-method Man page
infix.q,WMDS,ANY-method Man page
infix.q,WMDS,MOPMX-method Man page
infix.q,WMDS-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
insert Source code
insert.list Source code
int2dbclass Source code
is_cas Source code
is_uniform Source code
kmeans Man page
length,WMD-method Man page
length,WMDS-method Man page
length-methods Man page
level_plot Man page
level_plot,MOPMX-method Man page
level_plot,OPM-method Man page
level_plot,OPMS-method Man page
level_plot-methods Man page
lines.opm_model Source code
lines.opm_models Source code
list2html Source code
list2matrix Source code
listing Man page
listing,MOPMX-method Man page
listing,OPMD-method Man page
listing,OPMX-method Man page
listing,well_coords_map-method Man page
listing-methods Man page
map_metadata Man page
map_metadata,MOPMX,ANY-method Man page
map_metadata,MOPMX,missing-method Man page
map_metadata,MOPMX-method Man page
map_metadata,WMD,FOE-method Man page
map_metadata,WMD,character-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,missing-method Man page
map_metadata,WMDS-method Man page
map_metadata-methods Man page
map_param_names Source code
map_values Man page
map_values,list,formula-method Man page
map_values-methods Man page
map_well_names Source code
max Man page
max,OPM-method Man page
max,OPMS-method Man page
max-methods Man page
measurements Man page
measurements,MOPMX-method Man page
measurements,OPM-method Man page
measurements,OPMS-method Man page
measurements-methods 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,MOPMX,ANY-method Man page
merge,MOPMX,missing-method Man page
merge,MOPMX-method Man page
merge,OPM,OPM-method Man page
merge,OPM,missing-method Man page
merge,OPM,numeric-method Man page
merge,OPMS,missing-method Man page
merge,OPMS,numeric-method Man page
merge-methods Man page
metadata Man page
metadata,MOPMX-method Man page
metadata,WMD-method Man page
metadata,WMDS-method Man page
metadata-methods Man page
metadata.set Man page
metadata.set,MOPMX,ANY,ANY-method Man page
metadata.set,MOPMX,ANY,data.frame-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,MOPMX-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,WMD-method Man page
metadata.set,WMD,character,WMDS-method Man page
metadata.set,WMD,character,data.frame-method Man page
metadata.set,WMD,character-method Man page
metadata.set,WMD,list,WMD-method Man page
metadata.set,WMD,list,WMDS-method Man page
metadata.set,WMD,list,data.frame-method Man page
metadata.set,WMD,list,list-method Man page
metadata.set,WMD,missing,FOE-method Man page
metadata.set,WMD,missing,WMD-method Man page
metadata.set,WMD,missing,WMDS-method Man page
metadata.set,WMD,missing,character-method Man page
metadata.set,WMD,missing,data.frame-method Man page
metadata.set,WMD,missing,list-method Man page
metadata.set,WMD,numeric,WMD-method Man page
metadata.set,WMD,numeric,WMDS-method Man page
metadata.set,WMD,numeric,data.frame-method Man page
metadata.set,WMD,numeric,list-method Man page
metadata.set,WMD-method Man page
metadata.set,WMDS,ANY,ANY-method Man page
metadata.set,WMDS,ANY,WMD-method Man page
metadata.set,WMDS,ANY,WMDS-method Man page
metadata.set,WMDS,ANY,data.frame-method Man page
metadata.set,WMDS,character,WMDS-method Man page
metadata.set,WMDS,character,data.frame-method Man page
metadata.set,WMDS,missing,FOE-method Man page
metadata.set,WMDS,missing,WMD-method Man page
metadata.set,WMDS,missing,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,list-method Man page
metadata.set,WMDS,missing,logical-method Man page
metadata.set,WMDS-method Man page
metadata.set-methods Man page
metadata2factorlist Source code
metadata<- Man page
metadata<-,MOPMX,ANY,ANY-method Man page
metadata<-,MOPMX,ANY,data.frame-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<-,MOPMX-method Man page
metadata<-,OPM,missing,character-method Man page
metadata<-,OPM,missing,logical-method Man page
metadata<-,WMD,ANY,ANY-method Man page
metadata<-,WMD,character,ANY-method Man page
metadata<-,WMD,character,WMD-method Man page
metadata<-,WMD,character,WMDS-method Man page
metadata<-,WMD,character,data.frame-method Man page
metadata<-,WMD,character-method Man page
metadata<-,WMD,list,WMD-method Man page
metadata<-,WMD,list,WMDS-method Man page
metadata<-,WMD,list,data.frame-method Man page
metadata<-,WMD,list,list-method Man page
metadata<-,WMD,missing,FOE-method Man page
metadata<-,WMD,missing,WMD-method Man page
metadata<-,WMD,missing,WMDS-method Man page
metadata<-,WMD,missing,character-method Man page
metadata<-,WMD,missing,data.frame-method Man page
metadata<-,WMD,missing,list-method Man page
metadata<-,WMD,numeric,WMD-method Man page
metadata<-,WMD,numeric,WMDS-method Man page
metadata<-,WMD,numeric,data.frame-method Man page
metadata<-,WMD,numeric,list-method Man page
metadata<-,WMD-method Man page
metadata<-,WMDS,ANY,ANY-method Man page
metadata<-,WMDS,ANY,WMD-method Man page
metadata<-,WMDS,ANY,WMDS-method Man page
metadata<-,WMDS,ANY,data.frame-method Man page
metadata<-,WMDS,character,WMDS-method Man page
metadata<-,WMDS,character,data.frame-method Man page
metadata<-,WMDS,missing,FOE-method Man page
metadata<-,WMDS,missing,WMD-method Man page
metadata<-,WMDS,missing,WMDS-method Man page
metadata<-,WMDS,missing,character-method Man page
metadata<-,WMDS,missing,data.frame-method Man page
metadata<-,WMDS,missing,list-method Man page
metadata<-,WMDS,missing,logical-method Man page
metadata<-,WMDS-method Man page
metadata_chars Man page
metadata_chars,MOPMX-method Man page
metadata_chars,WMD-method Man page
metadata_chars,WMDS-method Man page
metadata_chars-methods Man page
metadata_key Source code
metadata_key.character Source code
metadata_key.default Source code
metadata_key.factor Source code
metadata_key.formula Source code
metadata_key.list Source code
minmax Man page
minmax,OPM-method Man page
minmax,OPMS-method Man page
minmax-methods Man page
n_knots Source code
no_gaps Source code
normalize_predefined_plate Source code
oapply Man page
oapply,MOPMX-method Man page
oapply,OPM-method Man page
oapply,OPMS-method Man page
oapply-methods Man page
objects_for_testing Source code
opm.package Man page
opm.package-package Man page
opm_dbcheck Man page
opm_dbcheck,ANY-method Man page
opm_dbcheck-methods Man page
opm_dbclass Man page
opm_dbclass,MOPMX-method Man page
opm_dbclass,OPM-method Man page
opm_dbclass,OPMS-method Man page
opm_dbclass,integer-method Man page
opm_dbclass-methods 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
opm_files Man page Source code
opm_mcp Man page
opm_mcp,MOPMX-method Man page
opm_mcp,OPMS-method Man page
opm_mcp,data.frame-method Man page
opm_mcp-methods Man page
opm_opt Man page
opm_opt,character-method Man page
opm_opt,list-method Man page
opm_opt,missing-method Man page
opm_opt-methods Man page
opm_string Source code
opms Man page Source code
opmx Man page
opmx,data.frame-method Man page
opmx-methods Man page
parallel_plot Man page
parallel_plot,MOPMX,ANY-method Man page
parallel_plot,MOPMX,XOPMX-method Man page
parallel_plot,MOPMX,missing-method Man page
parallel_plot,MOPMX-method Man page
parallel_plot,NULL,XOPMX-method Man page
parallel_plot,OPMX,ANY-method Man page
parallel_plot,OPMX,XOPMX-method Man page
parallel_plot,OPMX,missing-method Man page
parallel_plot,OPMX-method Man page
parallel_plot,formula,XOPMX-method Man page
parallel_plot,missing,XOPMX-method Man page
parallel_plot,vector,XOPMX-method Man page
parallel_plot-methods Man page
parallelplot Man page
parallelplot,MOPMX,ANY-method Man page
parallelplot,MOPMX,XOPMX-method Man page
parallelplot,MOPMX,missing-method Man page
parallelplot,MOPMX-method Man page
parallelplot,NULL,XOPMX-method Man page
parallelplot,OPMX,ANY-method Man page
parallelplot,OPMX,XOPMX-method Man page
parallelplot,OPMX,missing-method Man page
parallelplot,OPMX-method Man page
parallelplot,formula,XOPMX-method Man page
parallelplot,missing,XOPMX-method Man page
parallelplot,vector,XOPMX-method Man page
parallelplot-methods Man page
param_names Man page
param_names,character-method Man page
param_names,missing-method Man page
param_names-methods Man page
pe_and_ci Source code
pe_and_ci.boot Source code
phylo_data Man page
phylo_data,OPMD_Listing-method Man page
phylo_data,OPMS_Listing-method Man page
phylo_data,XOPMX-method Man page
phylo_data,data.frame-method Man page
phylo_data,matrix-method Man page
phylo_data-methods Man page
plate_type Man page
plate_type,MOPMX-method Man page
plate_type,OPM-method Man page
plate_type,OPMS-method Man page
plate_type,OPM_DB-method Man page
plate_type,character-method Man page
plate_type,factor-method Man page
plate_type,logical-method Man page
plate_type,missing-method Man page
plate_type-methods Man page
plates Man page
plates,MOPMX-method Man page
plates,WMD-method Man page
plates,WMDS-method Man page
plates,list-method Man page
plates-methods Man page
plot.kmeanss Man page Source code
plot.opm_model Source code
plot.opm_models Source code
plot_helper Source code
plus Man page
plus,ANY,MOPMX-method Man page
plus,MOPMX,ANY-method Man page
plus,MOPMX,OPMX-method Man page
plus,MOPMX,numeric-method Man page
plus,MOPMX-method Man page
plus,OPM,MOPMX-method Man page
plus,OPM,OPM-method Man page
plus,OPM,OPMS-method Man page
plus,OPM,list-method Man page
plus,OPM,numeric-method Man page
plus,OPMS,MOPMX-method Man page
plus,OPMS,OPM-method Man page
plus,OPMS,OPMS-method Man page
plus,OPMS,list-method Man page
plus,OPMS,numeric-method Man page
plus,numeric,MOPMX-method Man page
plus,numeric,OPM-method Man page
plus,numeric,OPMS-method Man page
plus-methods Man page
potato Man page
predict.smooth.spline_model Source code
prepare_class_names Source code
prepare_class_names.character Source code
prepare_k Source code
print.MOPMX_Summary Source code
print.OPMD_Listing Source code
print.OPMS_Listing Source code
print.OPMS_Summary Source code
print.OPM_Summary Source code
print.print_easy Source code
process_io Source code
radial_plot Man page
radial_plot,MOPMX-method Man page
radial_plot,OPMS-method Man page
radial_plot,data.frame-method Man page
radial_plot,matrix-method Man page
radial_plot-methods Man page
read_lims_opm Source code
read_microstation_opm Source code
read_new_opm Source code
read_old_opm Source code
read_opm Man page Source code
read_opm_yaml Source code
read_single_opm Man page Source code
reassign_args_using Source code
reassign_duplicates Source code
reduce_to_mode Source code
reduce_to_mode.default Source code
reduce_to_mode.matrix Source code
register_plate Man page
register_plate,character-method Man page
register_plate,list-method Man page
register_plate,missing-method Man page
register_plate-methods Man page
remove_concentration Source code
rep Man page
rep,OPM-method Man page
rep,OPMS-method Man page
rep-methods Man page
repair_na_strings Source code
repair_na_strings.character Source code
repair_na_strings.list Source code
repair_oth Source code
rescue_dots Source code
rev Man page
rev,OPM-method Man page
rev,OPMS-method Man page
rev-methods Man page
run_kmeans Man page
run_kmeans,matrix,numeric-method Man page
run_kmeans,numeric,numeric-method Man page
run_kmeans-methods Man page
safe_labels Man page Source code
select_colors Man page Source code
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,WMD-method Man page
seq,WMDS-method Man page
seq-methods Man page
set_spline_options Man page Source code
settings_backward Source code
settings_forward Source code
show,CMAT-method Man page
show,MOPMX-method Man page
show,OPMX-method Man page
show-methods Man page
simplify_conditionally Source code
single_tag Source code
smooth.construct.psp.smooth.spec Source code
sort Man page
sort,MOPMX,ANY-method Man page
sort,MOPMX,missing-method Man page
sort,MOPMX-method Man page
sort,OPM,ANY-method Man page
sort,OPM,missing-method Man page
sort,OPM-method Man page
sort,OPMS,ANY-method Man page
sort,OPMS,missing-method Man page
sort,OPMS-method Man page
sort-methods Man page
source_location Source code
split 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,missing-method Man page
split,MOPMX,factor-method Man page
split,MOPMX,list,ANY-method Man page
split,MOPMX,list,missing-method Man page
split,MOPMX,list-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,missing-method Man page
split,OPM,factor-method Man page
split,OPM,missing,ANY-method Man page
split,OPM,missing,missing-method Man page
split,OPM,missing-method Man page
split,OPMS,ANY,missing-method Man page
split,OPMS,factor,ANY-method Man page
split,OPMS,factor,missing-method Man page
split,OPMS,factor-method Man page
split,OPMS,missing,ANY-method Man page
split,OPMS,missing,missing-method Man page
split,OPMS,missing-method Man page
split,OPMX,ANY,ANY-method Man page
split,OPMX-method Man page
split-methods Man page
split_files Man page Source code
str,CMAT-method Man page
str,MOPMX-method Man page
str,WMDX-method Man page
str-methods Man page
strip_whitespace Source code
sub_indexes Source code
subset Man page
subset,MOPMX-method Man page
subset,OPMX-method Man page
subset-methods Man page
substrate_info Man page
substrate_info,MOPMX-method Man page
substrate_info,OPM-method Man page
substrate_info,OPMS-method Man page
substrate_info,character-method Man page
substrate_info,factor-method Man page
substrate_info,list-method Man page
substrate_info,substrate_match-method Man page
substrate_info-methods Man page
summary Man page
summary,MOPMX-method Man page
summary,OPM-method Man page
summary,OPMS-method Man page
summary-methods Man page
summary.splines_bootstrap Source code
testfile_dir Source code
thin_out Man page
thin_out,MOPMX-method Man page
thin_out,OPM-method Man page
thin_out,OPMS-method Man page
thin_out-methods Man page
time_index Source code
to_kmeans Man page Source code
to_kmeans.Ckmeans.1d.dp Man page Source code
to_kmeans.kmeans Man page Source code
to_kmeans.kmeanss Man page Source code
to_metadata Man page
to_metadata,ANY-method Man page
to_metadata,MOPMX-method Man page
to_metadata,WMD-method Man page
to_metadata,WMDS-method Man page
to_metadata,character-method Man page
to_metadata-methods Man page
to_opm_list Source code
to_opm_list.list Source code
to_sentence Source code
to_sentence.logical Source code
to_yaml Man page
to_yaml,MOPMX-method Man page
to_yaml,YAML_VIA_LIST-method Man page
to_yaml,list-method Man page
to_yaml-methods Man page
trim_string Source code
try_opms Source code
try_opms.list Source code
try_select_colors Source code
unique Man page
unique,MOPMX,ANY-method Man page
unique,MOPMX,missing-method Man page
unique,MOPMX-method Man page
unique,OPM,ANY-method Man page
unique,OPM,missing-method Man page
unique,OPM-method Man page
unique,OPMS,ANY-method Man page
unique,OPMS,missing-method Man page
unique,OPMS-method Man page
unique-methods Man page
vaas_1 Man page
vaas_4 Man page
vector2row Source code
web_query Source code
well Man page
well,MOPMX-method Man page
well,OPM-method Man page
well,OPMS-method Man page
well-methods Man page
well_index Source code
well_to_substrate Source code
wells Man page
wells,ANY-method Man page
wells,MOPMX-method Man page
wells,OPM-method Man page
wells,OPMS-method Man page
wells,missing-method Man page
wells-methods Man page
xy_plot Man page
xy_plot,MOPMX-method Man page
xy_plot,OPM-method Man page
xy_plot,OPMS-method Man page
xy_plot,data.frame-method Man page
xy_plot-methods Man page

Files

COPYING
ChangeLog
DESCRIPTION
NAMESPACE
NEWS
R
R/aggregation-aux.R
R/aggregation.R
R/auxiliary-aux.R
R/auxiliary.R
R/classes-aux.R
R/classes.R
R/combination-aux.R
R/combination.R
R/constants.R
R/conversion-aux.R
R/conversion.R
R/data.R
R/dbio-aux.R
R/dbio.R
R/discretization.R
R/getter.R
R/imports.R
R/io-aux.R
R/io.R
R/kmeans-aux.R
R/kmeans.R
R/metadata.R
R/multcomp-aux.R
R/multcomp.R
R/naming-aux.R
R/naming.R
R/package.R
R/phylogeny-aux.R
R/phylogeny.R
R/plate-map.R
R/plotting-aux.R
R/plotting.R
R/splinefit-aux.R
R/substrate-info.R
R/testing-aux.R
R/well-map.R
build
build/vignette.rds
data
data/boccuto_et_al.rda
data/potato.rda
data/vaas_1.rda
data/vaas_4.rda
demo
demo/00Index
demo/MongoDB-IO.R
demo/MySQL-IO.R
demo/PostgreSQL-IO.R
demo/SQLite-IO.R
demo/cluster-with-pvalues.R
demo/custom-PCA.R
demo/distinguish-curve-topologies.R
demo/identify-positive-reactions.R
demo/multiple-plate-types.R
demo/phenotype-vs-genotype.R
demo/workshop-part-1.R
demo/workshop-part-2.R
demo/workshop-part-3.R
demo/workshop-part-4.R
demo/workshop-part-5.R
inst
inst/CITATION
inst/auxiliary
inst/auxiliary/001_rdbms_drop.sql
inst/auxiliary/002_rdbms_create.sql
inst/auxiliary/003_rdbms_delete.sql
inst/auxiliary/styles_1.css
inst/doc
inst/doc/opm-growth-curves.Rnw
inst/doc/opm-growth-curves.pdf
inst/doc/opm-substrates.Rnw
inst/doc/opm-substrates.pdf
inst/doc/opm-tutorial.Rnw
inst/doc/opm-tutorial.pdf
inst/scripts
inst/scripts/run_opm.R
inst/testdata
inst/testdata/Example_1.csv.xz
inst/testdata/Example_2.csv.xz
inst/testdata/Example_3.csv.xz
inst/testdata/Example_Ecoplate.csv.xz
inst/testdata/Example_ID_run.csv.xz
inst/testdata/Example_LIMS_Export.exl.xz
inst/testdata/Example_Old_Style_1.csv.xz
inst/testdata/Example_Old_Style_2.csv.xz
inst/testdata/Example_Old_Style_3.csv.xz
inst/testdata/Example_Old_Style_Multiple.csv.xz
inst/testdata/Example_Perkin_Elmer.txt.xz
inst/testdata/Example_TECAN.txt.xz
inst/tests
inst/tests/test_aggregation-aux.R
inst/tests/test_aggregation.R
inst/tests/test_auxiliary-aux.R
inst/tests/test_auxiliary.R
inst/tests/test_classes-aux.R
inst/tests/test_classes.R
inst/tests/test_combination-aux.R
inst/tests/test_combination.R
inst/tests/test_constants.R
inst/tests/test_conversion-aux.R
inst/tests/test_conversion.R
inst/tests/test_data.R
inst/tests/test_dbio-aux.R
inst/tests/test_dbio.R
inst/tests/test_discretization.R
inst/tests/test_getter.R
inst/tests/test_imports.R
inst/tests/test_io-aux.R
inst/tests/test_io.R
inst/tests/test_kmeans-aux.R
inst/tests/test_kmeans.R
inst/tests/test_metadata.R
inst/tests/test_multcomp-aux.R
inst/tests/test_multcomp.R
inst/tests/test_naming-aux.R
inst/tests/test_naming.R
inst/tests/test_package.R
inst/tests/test_phylogeny-aux.R
inst/tests/test_phylogeny.R
inst/tests/test_plate-map.R
inst/tests/test_plotting-aux.R
inst/tests/test_plotting.R
inst/tests/test_splinefit-aux.R
inst/tests/test_substrate-info.R
inst/tests/test_testing-aux.R
inst/tests/test_well-map.R
man
man/OPM.Rd
man/OPM_DB.Rd
man/WMD.Rd
man/aggregated.Rd
man/annotated.Rd
man/as.data.frame.Rd
man/batch_opm.Rd
man/boccuto_et_al.Rd
man/bracket.Rd
man/bracket.set.Rd
man/c.Rd
man/ci_plot.Rd
man/collect_template.Rd
man/csv_data.Rd
man/dim.Rd
man/discrete.Rd
man/discretized.Rd
man/do_aggr.Rd
man/do_disc.Rd
man/duplicated.Rd
man/explode_dir.Rd
man/extract.Rd
man/find_substrate.Rd
man/has_aggr.Rd
man/heat_map.Rd
man/html_args.Rd
man/include_metadata.Rd
man/infix.k.Rd
man/infix.q.Rd
man/kmeans.Rd
man/level_plot.Rd
man/max.Rd
man/measurements.Rd
man/merge.Rd
man/metadata.Rd
man/metadata.set.Rd
man/opm.package.Rd
man/opm_dbput.Rd
man/opm_files.Rd
man/opm_mcp.Rd
man/opm_opt.Rd
man/opms.function.Rd
man/opmx.function.Rd
man/parallel_plot.Rd
man/phylo_data.Rd
man/plate_type.Rd
man/plates.Rd
man/potato.Rd
man/radial_plot.Rd
man/read_opm.Rd
man/run_kmeans.Rd
man/separate.Rd
man/set_spline_options.Rd
man/sort.Rd
man/subset.Rd
man/substrate_info.Rd
man/summary.Rd
man/to_yaml.Rd
man/vaas_4.Rd
man/wells.Rd
man/xy_plot.Rd
tests
tests/run-all.R
vignettes
vignettes/opm-growth-curves.Rnw
vignettes/opm-substrates.Rnw
vignettes/opm-tutorial.Rnw
opm documentation built on May 21, 2017, 1:34 a.m.

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