tcpl v1.2.1
==============

Changes from v1.2

* A try-statement was added to the underlying function that draws the plot for 
  tcplPlotHeat, so that the function does not return a figure margin error when
  running the checks for the package. 


tcpl v1.2 
==============

Changes from beta versions:

* The tcpl4 function now checks the new 'fit_all' field in the 
  assay_component_endpoint table, and will attempt to fit every curve when
  'fit_all' is 1.
* The TCPL_CHEM and TCPL_INT settings have been deprecated and are no longer 
  needed. To facilitate easier use and understanding, chemical tables included 
  in the tcpl database are restructured. 
* The TCPL_LOG setting has been deprecated.
* tcplUpdate is renamed to tcplSendQuery.
* Single concentration screening is now implemented.
* Added tcplRegister and tcplUpdate to make populating the database with new
  data easier.
* Changed the underlying database structure. The old database will not work
  with beta versions of the package.
* tcplPlotL4ID is now tcplPlotM4ID to match the new database structure.
* The tcpl1, tcpl2, etc. functions have been renamed and are no longer 
  exported. All processing is intended to occur through the tcplRun function. 
* tcplRunPipe is now tcplRun, and no longer defaults to writing a log file. 
  A log file can still be written using the 'outfile' setting, as previously. 
* Level 5 multiple-concentration processing has changed -- there is no longer
  a minimum cutoff. All cutoff values must be specified with the new level 5
  methods. 
* Level 6 multiple-concentration processing has changed -- some of the flag 
  methodologies were updated.
* tcplSetOpts renamed to tcplConf.
* tcplSetOpts (now called tcplConf) can now be given only one or a subset of 
  settings to change.
* tcplListOpts renamed to tcplConfList.
* tcplConfLoad, tcplConfSave, tcplConfDefault, and tcplConfReset added to make 
  working with the package settings easier for the user.
* Due a change in the underlying code for `rapply` the package now must use
  R version 3.2.0 or higher.
* Added processing methods. 
* tcplWriteLvl0 now excludes loading data for acsn values that are not 
  registered, but will load data for acsn values that are registered without
  returning an error.
* tcpl now imports RMySQL.
* tcplACVal and tcplACXX renamed tcplHillConc and tcplHillACXX, respectively. 
* tcplHillVal added.
* Bug in tcplPlotPlate that caused incorrect coloring when the input data.table
  contained multiple assays is fixed.
* 'fname' paramter is added to tcplMakeAeidPlts, and the default filename is 
  changed.
* 'quant' parameter is added to tcplPlotPlate.
* tcplLoadAsid deprecated, and is no longer exported.
* tcplLoadUnit deprecated, and is no longer exported.
* The call to 'browser' in tcplPlotFits is changed to skip the other lines 
  in the loop to make scanning through plots a little easier.
* Extensive updates to documentation and the vignette, now called 
  "tcpl_Overview."
* tcplAssignMthd, tcplLoadMthd, tcplListMthd, and tcplClearMthd functions are 
  renamed as tcplMthd- (e.g. tcplMthdLoad instead of tcplLoadMthd).
* tcplMthdClear no longer returns TRUE, matching the behavior of tcplMthdAssign.
* Added tcplCytoPt function to calculate the cytotoxicity points for chemical
  (this functionality used to be delivered by tcplVarMat, but is now separate).
* 'argx' and 'srgx' parameters are removed from tcplPrepOtpt.
* 'srgx' paramter is removed from tcplMakeAeidPlts.
* tcplLoadAsidInfo & tcplLoadAeidInfo deprecated, and are no longer exported. 
* tcplPrepOtpt longer contains the 'clib' parameter.

