.ChemListQ              Function to support queries by chemical
.ChemQ                  Function to support queries by chemical
.buildAssayQ            Generate query for assay information
.convertNames           Convert assay names to their abbreviations
.load6DR                Load data for tcpl6
.plateHeat              Plot plate heatmap
.prepField              Paste appropriate table name to field name
Configure functions     Functions for configuring the tcpl package
Hill model utilites     Functions to solve the Hill model
Load assay information
                        Functions for loading assay information
MC2_Methods             List of level 2 multiple-concentration
                        correction functions
MC3_Methods             List of level 3 multiple-concentration
                        normalization methods
MC4_Methods             List of level 4 multiple-concentration methods
                        for calculating bmad
MC5_Methods             Load list of level 5 multiple-concentration
                        cutoff methods
MC6_Methods             Load list of level 6 multiple-concentration
                        flag methods
MORELETTERS             MORELETTERS Extends LETTERS recursively to any
                        number of letters
Method functions        Functions for managing processing methods
Models                  Model objective functions
Query functions         Wrappers for sending queries and fetching
                        results
Register/update annotation
                        Functions for registering & updating annotation
                        information
SC1_Methods             List of level 1 single-concentration
                        normalization functions
SC2_Methods             List of level 2 single-concentration hit-call
                        functions
blineShift              Shift the baseline to 0
check_tcpl_db_schema    Function that checks if the most recent v3
                        table schema is used in the database schema
dynamic_table_trunc     dynamic_table_trunc Dynamically truncate
                        lengths of column values of they are longer
                        than a calculated width. Strings contained in
                        verbose table output can be very long, and this
                        function ensures that the 128 character row
                        limit is kept while growing/shrinking default
                        columns widths that may or may not need the
                        space.
flareFunc               Calculate the weighted mean of a square to
                        detect plate flares
get_plot_caption        get_plot_caption Generate plot caption given
                        number of flags and length of unique elements
get_plot_title          get_plot_title Generate plot title given number
                        of rows and length of unique elements
get_verbose_tables      get_verbose_tables Generates 'gt' package
                        tables containing annotations and level 5
                        metrics
interlaceFunc           Calculate the weighted mean of a square to
                        detect interlace effect
invitrodb_dd            Short descriptions of fields for different
                        tables are stored in a data dictionary.
is.odd                  Check for odd numbers
load_data_columns       Lists of column names returned from
                        tcplLoadData invitrodb v4.1 (same as CCTE
                        Bioactivity API version).
lu                      Abbreviation for 'length(unique(x))'
lw                      Abbreviation for 'length(which(x))'
mc1                     Perform level 1 multiple-concentration
                        processing
mc2                     Perform level 2 multiple-concentration
                        processing
mc3                     Perform level 3 multiple-concentration
                        processing
mc4                     Perform level 4 multiple-concentration
                        processing
mc5                     Perform level 5 multiple-concentration
                        processing
mc6                     Perform level 6 multiple-concentration
                        processing
mc_test                 List of lists containing queries sent to
                        tcplQuery associated with each test case. Each
                        list also contains the associated ids with each
                        case. Only meant to be used with automated
                        testing with mocking for mc data.
mc_vignette             List with multi-concentration data for the
                        vignette
mcdat                   A subset of ToxCast data showing changes in the
                        activity of the intracellular estrogen
                        receptor.
mthd_list_defaults      Lists of data frames returned from tcplMthdList
                        invitrodb v4.2
registerMthd            Add a new analysis method
round_n                 round_n General function to round/shorten
                        values for plotting tables
sc1                     Perform level 1 single-concentration processing
sc2                     Perform level 2 single-concentration processing
sc_test                 List of lists containing queries sent to
                        tcplQuery associated with each test case. Each
                        list also contains the associated ids with each
                        case. Only meant to be used with automated
                        testing with mocking for sc data.
sc_vignette             List with single-concentration data for the
                        vignette
scdat                   A subset of ToxCast data showing changes in
                        transcription factor activity for multiple
                        targets.
sink.reset              Reset all sinks
tcplAICProb             Calculate the AIC probabilities
tcplAddModel            Draw a tcpl Model onto an existing plot
tcplAppend              Append rows to a table
tcplCascade             Do a cascading delete on tcpl screening data
tcplCode2CASN           Convert chemical code to CAS Registry Number
tcplCytoPt              Calculate the cytotoxicity point based on the
                        "burst" endpoints
tcplDefine              Load data dictionary descriptions
tcplDelete              Delete rows from tcpl databases
tcplFit                 Fit the data with the constant, hill, and
                        gain-loss models
tcplFit2                tcpl Wrapper for tcplfit2_core including
                        additional calculations to fit into new schema
tcplFit2_nest           Nest dataframe into a list that is readable by
                        tcplfit2
tcplFit2_unnest         Unnest tcplfit2 parameters into a dataframe
tcplGetAeid             get Aeid for endpoint name
tcplHit2                Hitcalling with tcplfit2
tcplLegacyPlot          tcplLegacyPlot
tcplListFlds            Load the field names for a table
tcplLoadChem            Load sample/chemical information
tcplLoadChemList        Load chemical list information
tcplLoadConcUnit        Load concentration units for assay endpoints
tcplLoadData            Load tcpl data
tcplLoadUnit            Load response units for assay endpoints
tcplLvlCount            Load tcpl level counts
tcplMakeAeidMultiPlts   Create a .pdf with all dose-response plots for
                        a given aeid, 6 per page
tcplMakeAeidPlts        Create a .pdf with dose-response plots
tcplMakeChidMultiPlts   Create a .pdf with all dose-response plots for
                        a given chid, 6 per page
tcplMultiplot           Plot summary fits based on fit and
                        dose-response data
tcplPlot                Generic Plotting Function for tcpl
tcplPlotCalcAspectRatio
                        tcplPlotCalcAspectRatio
tcplPlotFitc            Plot the fit category tree
tcplPlotFits            Plot summary fits based on fit and
                        dose-response data
tcplPlotLoadData        Utility function to load data for tcplPlot
tcplPlotLoadWllt        tcplPlotLoadWllt Replaces NA dtxsid and chnm
                        with a string description of the sample's well
                        type(s)
tcplPlotM4ID            Plot fit summary plot by m4id
tcplPlotPlate           Plot plate heatmap
tcplPlotSetYRange       tcplPlotSetYRange
tcplPlotValidate        tcplPlotValidate
tcplPlotlyPlot          tcplPlotlyPlot
tcplPrepOtpt            Map assay/chemical ID values to annotation
                        information
tcplRun                 Perform data processing
tcplSubsetChid          Subset level 5 data to a single sample per
                        chemical
tcplVarMat              Create chemical by assay matrices
tcplWriteData           Write screening data into the tcpl databases
tcplWriteLvl0           Write level 0 screening data into the tcpl
                        databases
tcpldbStats             Get summary statistics for the database
tcplfit2_fun            tcplfit2_fun Returns tcplfit2 function for
                        drawing models given input
tcplggplot2             tcplggplot2
test_api                List containing ids used for different
                        automated tests of tcpl integration with the
                        CTX APIs, randomly selected from what is
                        available via API.
write_lvl_4             Write level 4 with updated schema
