update tcplhit2_core docs

[brown-jason]

tcplhit2_core and tcplfit2_core both describe the various fitting and hitcalling parameters in their docs (see links below). I think the parameter descriptions could use some additional detail to bring it up to the level of documentation similar to the vignettes. For example, something like \item er - the error term If we could have just 2 sentences describing what the error term is, I think people would get more from our documentation. Alternatively if we already have docs for a specific term, we can link to the related docs. Something like \item ... other paramters specific to the model (see the documentation for the specific models) should have links to all of the associated model docs.

CompTox-ToxCast-tcplFit2/R/tcplfit2_core.R

Lines 30 to 50 in f7828db

	#' @return List of N(models) elements, one for each of the models run (up to 10),
	#' followed by a element "modelnames", which is a vector of model names so
	#' other functions can easily cycle through the output, and then the last element
	#' "errfun", which indicates what distribution was used for error. For a full list, see the
	#' documentation for the individual fitting method functions. For each model there
	#' is a sublist with elements including:
	#' \itemize{
	#' \item success - was the model successfully fit
	#' \item aic - the AIC value
	#' \item cov - success of the the covariance matrix calculation
	#' \item rme - root mean error of the data around the curve
	#' \item modl - vector of model values at the given concentrations
	#' \item tp - the top of the curve fit
	#' \item ga - the AC50 or Hill paramters
	#' \item er - the error term
	#' \item ... other paramters specific to the model (see the documentation for the specific models)
	#' \item tp_sd, ga_sd, p_sd, etc., the values of the standard deviations of the paramters for the models
	#' \item er_sd - standard deviation of the error term
	#' \item pars - the names of the parameters
	#' \item sds - the names of the standard deviations of the paramters
	#' }

CompTox-ToxCast-tcplFit2/R/tcplhit2_core.R

Lines 38 to 74 in f7828db

	#' @return A list of with the detailed results from all of the different model fits.
	#' The elements of summary are:
	#' \itemize{
	#' \item any elements of the identifiers input
	#' \item n_gt_cutoff - number of data points above the cutoff
	#' \item cutoff - noise cutoff
	#' \item fit_method - curve fit method
	#' \item top_over_cutoff - top divided by cutoff
	#' \item rmse - RMSE of the data points around the best model curve
	#' \item a - fitting parameter methods: exp2, exp3, poly1, poly2, pow
	#' \item b - fitting parameter methods: exp2, exp3, ploy2
	#' \item p - fitting parameter methods: exp3, exp5, gnls, hill, pow
	#' \item q - fitting parameter methods: gnls,
	#' \item tp - top of the curve
	#' \item ga - ac50 for the rising curve in a gnls model or the Hill model
	#' \item la - ac50 for the falling curve in a gnls model
	#' \item er - fitted error term for plotting error bars
	#' \item bmr - benchmark response; level at which bmd is calculated = onesd*bmr_scale default bmr_scale is 1.349
	#' \item bmd - benchmark dose, curve value at bmr
	#' \item bmdl - lower limit on the bmd
	#' \item bmdu - upper limit on the bmd
	#' \item caikwt - one factor used in calculating the continuous hitcall. It is calcalated from the formula
	#' = exp(-aic(cnst)/2)/(exp(-aic(cnst)/2) + exp(-aic(fit_method)/2)) and measures how much lower the
	#' selected method AIC is than that for the constant model
	#' \item mll - another factor used in calcualting the continuous hitcall = length(modpars) - aic(fit_method)/2
	#' \item hitcall - the final hitcall, a value ranging from 0 to 1
	#' \item top - curve top
	#' \item ac50 - curve value at 50\% of top, curve value at cutoff
	#' \item lc50 - curve value at 50\% of top corresponding to the loss side of the gain-loss curve
	#' \item ac5 - curve value at 5\% of top
	#' \item ac10 - curve value at 10\% of top
	#' \item ac20 - curve value at 20\% of top
	#' \item acc - curve value at cutoff
	#' \item ac1sd - curve value at 1 standard deviation
	#' \item conc - conc string separated by |'s
	#' \item resp - response string separated by |'s
	#' }

[sedavid01]

@brown-jason, please add more context/requirements for this ticket.