tcpl Data Processing Vignette Updates Accounting for Updates to tcplfit2

[sedavid01]

There is a need to update the vignettes for the ToxCast pipeline as outlined in: https://github.com/USEPA/CompTox-ToxCast-tcpl/issues/210.

Here are the broad components for Data processing that may be relevant to update with the tcplfit2 package updates:

Data processing vignette updates to encompass:

• [ ] New overwrite bidirectional mc and sc methods
• [ ] Processing of all well types, even where NA/0 conc given conc fix to dev
• [x] BMD bounds
• [x] default error function
• [x] poly2 biphasic updates

Points identified as points that need to be updated, or consider updates:

• [x] Ensure Level 4 incorporates both bidirectional and biphasic aspects of modeling.
• [x] Table 7 update with poly2 biphasic
• [x] Figure 2 Update
• [x] Figure 3 may need updated as well
• [x] Table 9 may need updated
• [x] Figure 4 may need updated as well

Note, there may be other necessary updates -- or comparisons/explanations, particularly considering the poly2 biphasic updates. Please use this as a starting point and may be expanded as necessary for the relevant audience.

[gracezhihuizhao]

Figure 3, Table 9, and Figure 4 uses example data sets from mc_vignette. If we want to add the biphasic poly2 to the figures and table, we need to update the example data sets in mc_vignette with new poly2 results first.