Thrombin_Analyzer: Thrombin Analyzer

################################################################################
Cal$set(
    which = "public", name = "fit_T0LateMM",
    value = compiler::cmpfun(
        f = function(silent = TRUE, weights = "Default (w = 1)") {
            if (exists(x = "T0LateMM", where = fit)) {
                warning(">> No fitting: T0LateMM fit already exists!");
                return(fit$LateMM);
            } else {
                print(">> fit_T0LateMM called!");
                if (!exists(x = "LateMM", where = fit)) {
                    fit_LateMM(silent = TRUE);
                }
                start.list <- list(
                    b = fit$LateMM$cff[["b"]], p1 = fit$LateMM$cff[["p1"]],
                    p2 = fit$LateMM$cff[["p2"]], p3 = fit$LateMM$cff[["p3"]],
                    t0 = 0);
                ft <- NULL; n.try <- 1;
                if (weights == "Default (w = 1)") {
                    wgt <- rep(1, length(data$x));
                } else if (weights == "Poisson (w = 1 / y)") {
                    wgt <- 1 / (data$y);
                } else if (weights == "Power (w = 1 / y^2)") {
                    wgt <- 1 / (data$y^2);
                }
                while (is.null(ft) && n.try <= kNumTries) {
                    try(expr = {
                            ft <- minpack.lm::nlsLM(
                                y ~ b + (x >= t0) *
                                    p1 * (1 - (LambertW::W(p2 * exp(p2) * exp(-p3 * (x - t0))) / p2)),
                                data = data, start = start.list, algorithm = "LM",
                                lower = c(  0,   0,   0,   0, -Inf),
                                upper = c(Inf, Inf, Inf, Inf,  Inf),
                                weights = wgt,
                                control = minpack.lm::nls.lm.control(
                                    ftol = 0.1 *  sqrt(.Machine$double.eps),
                                    ptol = 0.1 * sqrt(.Machine$double.eps),
                                    gtol = 0, nprint = -1, factor = 100,  ## between [0.1, 100]
                                    maxiter = 200
                                    )
                                )
                        }, silent = F);
                    n.try <- n.try + 1;
                    start.list <- list(b = data$y[1],
                                       p1 = runif(1) * num.smry$ampl,
                                       p2 = runif(1, 0, 2),
                                       p3 = runif(1) * fit$LateExp$cff[["p3"]],
                                       t0 = 0);
                }
                if (is.null(ft)) {
                    warning(">> Cal.fit_T0LateMM resulted in NULL");
                    return(NULL);
                } else {
                    fit$T0LateMM <<- list(
                        cff = coef(ft), smry = get_compact_summary(ft),
                        diagn = conv_pvals_to_signif_codes(summary(ft)$coefficients[, 4])
                        );
                    if (!silent)
                        print(fit[names(fit) != "LM"]);
                    return(fit$T0LateMM);
                }  ## End of if (is.null(ft))
            }  ## End of if (exists())
        }, options = kCmpFunOptions),
    overwrite = FALSE);  ## End of Cal$fit_T0LateMM
################################################################################

################################################################################
Cal$set(
    which = "public", name = "get_T0LateMM",
    value = compiler::cmpfun(
        f = function() {
            if (exists(x = "T0LateMM", where = fit)) {
                ## y ~ b + p1 * (1 - (LambertW::W(p2 * exp(p2) * exp(-p3 * x)) / p2)),
                b <- fit$T0LateMM$cff[["b"]]; p1 <- fit$T0LateMM$cff[["p1"]];
                p2 <- fit$T0LateMM$cff[["p2"]]; p3 <- fit$T0LateMM$cff[["p3"]];
                t0 <- fit$T0LateMM$cff[["t0"]];
                return(b + (data$x >= t0) * p1 *
                           (1 - (LambertW::W(p2 * exp(p2) * exp(-p3 * (data$x - t0))) / p2)));
            } else {
                warning(">> fit$T0LateMM does not exist!");
                return(rep(0, length(data$x)));
            }
        }, options = kCmpFunOptions),
    overwrite = FALSE);  ## End of Cal$get_T0LateMM
################################################################################

################################################################################
Cal$set(
    which = "public", name = "parms_T0LateMM",
    value = compiler::cmpfun(
        f = function(e0, s0) {
            print(">> Call to Cal.parms_T0LateMM");
            if (exists(x = "T0LateMM", where = fit)) {
                ## print(fit$T0LateMM);
                p1 <- fit$T0LateMM$cff[["p1"]]; p2 <- fit$T0LateMM$cff[["p2"]];
                p3 <- fit$T0LateMM$cff[["p3"]];
                ## print(paste0(p1, p2, p3));
                ## print(paste0(e0, s0));
                Value <- c(e0, s0, e0 * (1 + p2) / (p1 * p3), e0 / (p1 * p3),
                           1e3 * s0 / p2, (1e3 * s0 / e0) * (p3 / p2), p1 / (1e3 * s0),
                           (p1 * p3 / (1 + p2)));
                ## print(Value);
                ## print(parms);  ##str(fit$T0LateMM);
                return(parms <<- data.frame(
                    Parameter = kParameterNamesLateMM,
                    Value = Value,
                    ## StdErr = rep(NA, 7),
                    Units = kParameterUnitsLateMM
                    ));
            } else {
                warning(">> fit$T0LateMM does not exist!");
                return(NULL);
            }
        }, options = kCmpFunOptions),
    overwrite = FALSE);  ## End of Cal$parms_T0LateMM
################################################################################

################################################################################
Cal$set(
    which = "public", name = "get_init_rate_T0LateMM",
    value = compiler::cmpfun(
        f = function() {
            print(">> Call to Cal.parms_T0LateMM");
            if (exists(x = "T0LateMM", where = fit)) {
                p1 <- fit$T0LateMM$cff[["p1"]]; p2 <- fit$T0LateMM$cff[["p2"]];
                p3 <- fit$T0LateMM$cff[["p3"]]; b <- fit$T0LateMM$cff[["b"]];
                t0 <- fit$T0LateMM$cff[["t0"]];
                return(b + (data$x >= t0) * (p1 * p3 / (1 + p2)) * (data$x - t0));
            } else {
                warning(">> fit$T0LateMM does not exist!");
                return(rep(0, length(data$x)));
            }
        }, options = kCmpFunOptions),
    overwrite = FALSE);  ## End of Cal$get_init_rate_T0LateMM
################################################################################

################################################################################
######################################## Legacy RF classes code
################################################################################

## ################################################################################
## Cal.fit_T0LateMM <- function(silent = TRUE) {
##     if (exists(x = "T0LateMM", where = fit)) {
##         warning(">> No fitting: T0LateMM fit already exists!");
##         return(fit$LateMM);
##     } else {
##         print(">> fit_T0LateMM called!");
##         if (!exists(x = "LateMM", where = fit)) {
##             fit_LateMM(silent = TRUE);
##         }
##         start.list <- list(
##             b = fit$LateMM$cff[["b"]], p1 = fit$LateMM$cff[["p1"]],
##             p2 = fit$LateMM$cff[["p2"]], p3 = fit$LateMM$cff[["p3"]],
##             t0 = 0);
##         ft <- NULL; n.try <- 1;
##         while (is.null(ft) && n.try <= kNumTries) {
##             try(expr = {
##                 ft <- nlsLM(
##                     y ~ b + (x >= t0) *
##                         p1 * (1 - (LambertW::W(p2 * exp(p2) * exp(-p3 * (x - t0))) / p2)),
##                     data = data, start = start.list, algorithm = "LM",
##                     lower = c(  0,   0,   0,   0, -Inf),
##                     upper = c(Inf, Inf, Inf, Inf,  Inf),
##                     control = nls.lm.control(
##                         ftol = 0.1 *  sqrt(.Machine$double.eps),
##                         ptol = 0.1 * sqrt(.Machine$double.eps),
##                         gtol = 0, nprint = -1, factor = 100,  ## between [0.1, 100]
##                         maxiter = 200
##                     )
##                 )
##             }, silent = F);
##             n.try <- n.try + 1;
##             start.list <- list(b = data$y[1],
##                                p1 = runif(1) * num.smry$ampl,
##                                p2 = runif(1, 0, 2),
##                                p3 = runif(1) * fit$LateExp$cff[["p3"]],
##                                t0 = 0);
##         }
##         if (is.null(ft)) {
##             warning(">> Cal.fit_T0LateMM resulted in NULL");
##             return(NULL);
##         } else {
##             fit$T0LateMM <<- list(
##                 cff = coef(ft), smry = summary(ft),
##                 diagn = conv_pvals_to_signif_codes(summary(ft)$coefficients[, 4])
##             );
##             if (!silent)
##                 print(fit[names(fit) != "LM"]);
##             return(fit$T0LateMM);
##         }  ## End of if (is.null(ft))
##     }  ## End of if (exists())
## }  ## End of Cal.fit_LateMM
## ################################################################################

## ################################################################################
## Cal.get_T0LateMM <- function() {
##     if (exists(x = "T0LateMM", where = fit)) {
##         ## y ~ b + p1 * (1 - (LambertW::W(p2 * exp(p2) * exp(-p3 * x)) / p2)),
##         b <- fit$T0LateMM$cff[["b"]]; p1 <- fit$T0LateMM$cff[["p1"]];
##         p2 <- fit$T0LateMM$cff[["p2"]]; p3 <- fit$T0LateMM$cff[["p3"]];
##         t0 <- fit$T0LateMM$cff[["t0"]];
##         return(b + (data$x >= t0) * p1 *
##                    (1 - (LambertW::W(p2 * exp(p2) * exp(-p3 * (data$x - t0))) / p2)));
##     } else {
##         warning(">> fit$T0LateMM does not exist!");
##         return(rep(0, length(data$x)));
##     }
## }  ## End of Cal.get_T0LateMM
## ################################################################################

## ################################################################################
## Cal.parms_T0LateMM <- function(e0, s0) {
##     print(">> Call to Cal.parms_T0LateMM");
##     if (exists(x = "T0LateMM", where = fit)) {
##         ## print(fit$T0LateMM);
##         p1 <- fit$T0LateMM$cff[["p1"]]; p2 <- fit$T0LateMM$cff[["p2"]];
##         p3 <- fit$T0LateMM$cff[["p3"]];
##         ## print(paste0(p1, p2, p3));
##         ## print(paste0(e0, s0));
##         Value <- c(e0, s0, e0 * (1 + p2) / (p1 * p3), e0 / (p1 * p3),
##                    1e3 * s0 / p2, (1e3 * s0 / e0) * (p3 / p2), p1 / (1e3 * s0),
##                    (p1 * p3 / (1 + p2)));
##         print(Value);
##         ## print(parms);  ##str(fit$T0LateMM);

##         return(parms <<- data.frame(
##             Parameter = c("e0", "s0", "CF_CAT", "CF_DTU", "K.m", "k.cat", "I",
##                 "TC_Initial_Slope"),
##             Value = Value,
##             ## StdErr = rep(NA, 7),
##             Units = c("nM", "uM", "nM * min / a.u.",
##                 "nM * min / a.u.", "nM", "nM / min",
##                 "a.u. / nM", "a.u. / min"))
##                );
##     } else {
##         warning(">> fit$T0LateMM does not exist!");
##         return(NULL);
##     }
## }  ## End of Cal.parms_T0LateMM
## ################################################################################

## ################################################################################
## Cal.get_init_rate_T0LateMM <- function() {
##     print(">> Call to Cal.parms_T0LateMM");
##     if (exists(x = "T0LateMM", where = fit)) {
##         p1 <- fit$T0LateMM$cff[["p1"]]; p2 <- fit$T0LateMM$cff[["p2"]];
##         p3 <- fit$T0LateMM$cff[["p3"]]; b <- fit$T0LateMM$cff[["b"]];
##         t0 <- fit$T0LateMM$cff[["t0"]];
##         return(b + (data$x >= t0) * (p1 * p3 / (1 + p2)) * (data$x - t0));
##     } else {
##         warning(">> fit$T0LateMM does not exist!");
##         return(rep(0, length(data$x)));
##     }
## }  ## End of Cal.get_init_rate_T0LateMM
## ################################################################################

################################################################################
######################################## End of Legacy RF classes code
################################################################################

## ################################################################################
## LateMM <- function(x, cff) {
##     return(cff[["b"]] + cff[["p1"]] *
##                (1 - (LambertW::W(cff[["p2"]] * exp(cff[["p2"]]) *
##                            exp(-cff[["p3"]] * x)) / cff[["p2"]])));
## }  ## End of LateMM
## ################################################################################

## ################################################################################
## LateMMLinearPart <- function(x, cff) {
##     ## calculates only the linear part of the product concentration ob
##     ## Late-times MM kinetics solution
##     ## time - time vector in minutes
##     ## late.cff - coefficients for Late-times MM formula obtained from fit
##     return(cff[["b"]] + (cff[["p1"]] * cff[["p3"]] / (1 + cff[["p2"]])) * x);
## }  ## End of LateMMLinearPart
## ################################################################################

## ################################################################################
## LateMMCFCAT <- function(cff, e0 = 100) {
##     return(e0 * (1 + cff[["p2"]]) / (cff[["p1"]] * cff[["p3"]]));
## }  ## End of LateMMCF
## ################################################################################

## ################################################################################
## LateMMCFDTU <- function(cff, e0 = 100) {
##     return(e0 / (cff[["p1"]] * cff[["p3"]]));
## }  ## End of LateMMCFDTU
## ################################################################################

## ################################################################################
## LateMMKinConst <- function(cff, e0 = 100, s0 = 454000) {
##     return(list(
##         e0 = e0, s0 = s0, C = cff[["p1"]] / s0, K.m = s0 / cff[["p2"]],
##         k.cat = (s0 / e0) * (cff[["p3"]] / cff[["p2"]])
##     ));
## }  ## End of LateMMKinConst
## ################################################################################