list(model = list(function(g, X) { # fit of ldh data to rate law for compulsory ordered bi-bi, with [Q] = 0, # and with E.A.P abortive complex (equil constant KiP), # and with E.B.Q abortive complex (kinetic constant KIB_K3K4) # for fitting, assume E.B.Q complex not significant (fix C3 at low value) # data in matrix X, with column dimnames # "v0", "v0calc", "weight", "[A]", "[B]", "[P]" # # g[1] = V # g[2] = KmA # g[3] = KmB # g[4] = KmAB # g[5] = KmQ/KmPQ = C1 # g[6] = 1/KiP = C2 # g[7] = KIB_K3K4 = C3 # g <- as.double(g) range.g <- range(g[1:7]) if(range.g[1] <= 0 || range.g[2] >= 1e+38) return(1e+38) V <- g[1] KmA <- g[2] KmB <- g[3] KmAB <- g[4] C1 <- g[5] C2 <- g[6] C3 <- g[7] v <- X[, "v0"] b <- X[, "[B]"] a <- X[, "[A]"] p <- X[, "[P]"] wt <- X[, "weight"] denom <- 1 + C1 * p + KmA/a + KmB/b * (1 + C1 * p) * (1 + C2 * p) + KmAB/a/b * (1 + C1 * p) + C3 * b vcalc <- V/denom res <- v - vcalc if(exists("SIMPFIT.temp")) SIMPFIT.temp[, "v0calc"] <<- vcalc sum((res * wt)^2) } ), iter = 447, coef = structure(.Data = c(0.254163586717974, 0.0325110066101479, 0.305615687352239, 0.00234336580877199, 0.00395172719651685, 0.00675550128536725, 1e-10), .Dim = c(1, 7), .Dimnames = list( character(0), c("Vmax", "KmA", "KmB", "KmAB", "KmQ/KmPQ", "1/KiP", "KIB_K3K4"))), std.err = structure(.Data = c(0.0209797689443159, 0.00455573632209276, 0.0519029501972037, 0.000529052899544536, 0.00107210090484533, 0.00265811964835114), .Dim = c(1, 6), .Dimnames = list(character(0), c("Vmax", "KmA", "KmB", "KmAB", "KmQ/KmPQ", "1/KiP") )), std.dev = 0.0016160968480452, cov.unscaled = structure(.Data = c( 168.52589229952, 35.9888164315827, 396.304304469576, -2.56257988409138, 4.29167786705559, -11.9550025804034, 35.9888164315827, 7.9466190384872, 84.2173230832377, -0.613502739488387, 0.866741491622622, -2.42380236255493, 396.304304469576, 84.2173230832377, 1031.45271125111, -7.9696268971234, 10.1710841247628, -31.3826313464521, -2.56257988409138, -0.613502739488387, -7.9696268971234, 0.10716758186913, -0.0526372819175094, 0.206943967627624, 4.29167786705559, 0.866741491622622, 10.1710841247628, -0.0526372819175094, 0.440084992345486, -1.05076593118122, -11.9550025804034, -2.42380236255493, -31.3826313464521, 0.206943967627624, -1.05076593118122, 2.70529285121548), .Dim = c(6, 6), .Dimnames = list(c("Vmax", "KmA", "KmB", "KmAB", "KmQ/KmPQ", "1/KiP"), c("Vmax", "KmA", "KmB", "KmAB", "KmQ/KmPQ", "1/KiP"))), hessian = structure(.Data = c(2.89594725566139, -8.36860257087617, -0.629615911966856, -23.1172615045323, -7.37715748956054, -3.10113330700263, -8.36860257087617, 26.9979872299219, 1.55158561970044, 66.8046344617667, 10.9786516471282, 4.36002202601145, -0.629615911966856 , 1.55158561970044, 0.168562429964532, 5.37694708540934, 2.67374973892372, 1.19039534152056, -23.1172615045323, 66.8046344617667, 5.37694708540934, 234.199405651609, 37.9436258680212, 16.8930964999895, -7.37715748956054 , 10.9786516471282, 2.67374973892372, 37.9436258680212, 142.966797861129, 60.8798723106066, -3.10113330700263, 4.36002202601145, 1.19039534152056, 16.8930964999895, 60.8798723106066, 27.1046753515058), .Dim = c(6, 6), .Dimnames = list(c("Vmax", "KmA", "KmB", "KmAB", "KmQ/KmPQ", "1/KiP"), c("Vmax", "KmA", "KmB", "KmAB", "KmQ/KmPQ", "1/KiP"))), start.simplex = structure(.Data = c(1, 10, 1, 1, 1, 1, 1, 0.001, 0.001, 0.1, 0.001, 0.001, 0.001, 0.001, 0.01, 0.01, 0.01, 1, 0.01, 0.01, 0.01, 0.001, 0.001, 0.001, 0.001, 0.1, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.1, 0.001, 1e-06, 1e-06, 1e-06, 1e-06, 1e-06, 1e-06, 0.01, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10), .Dim = c(7, 7), .Dimnames = list(c("1", "2", "3", "4", "5", "6", "7"), c("Vmax", "KmA", "KmB", "KmAB", "KmQ/KmPQ", "1/KiP", "KIB_K3K4"))), final.simplex = structure(.Data = c(0.254169233761765, 0.254152584676805, 0.25416853679741, 0.254161452621365, 0.254163200936372, 0.254158949782751, 0.254163586717974, 0.0325125186994992, 0.0325087798142593, 0.0325122245471967, 0.03251040566718, 0.0325111524651435, 0.0325102634093692, 0.0325110066101479, 0.305627020525806, 0.305585383939938, 0.305622958286968, 0.305605549310576, 0.305611062741651, 0.305601957752424, 0.305615687352239, 0.0023432973322153, 0.00234358513406676, 0.00234331735117432, 0.00234361083478649, 0.00234340690028324, 0.00234336077276548, 0.00234336580877199, 0.00395170339428735, 0.00395136576371056, 0.00395170441575208, 0.00395166351248981, 0.00395171401998339, 0.00395161623351755, 0.00395172719651685, 0.00675548275789049, 0.00675646372597823, 0.00675561827017072, 0.00675598685172446, 0.00675576143969001, 0.00675616403714678, 0.00675550128536725, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10), .Dim = c(7, 7), .Dimnames = list(c("1", "2", "3", "4", "5", "6", "7"), c("Vmax", "KmA", "KmB", "KmAB", "KmQ/KmPQ", "1/KiP", "KIB_K3K4"))), control.values = list(nparm = 7, nvert = 7, ndata = 26, iter = 0, exittest = 1e-08, verbose = 1, prtcycle = 30, quadtest = 30, maxquadskip = 4, free.param = c(0, 1, 2, 3, 4, 5)), data = structure(.Data = c(0.032, 0.0412, 0.0477, 0.0601, 0.0407, 0.0477, 0.0604, 0.0679, 0.0474, 0.0581, 0.0727, 0.0836, 0.0534, 0.066, 0.0808, 0.1033, 0.0338, 0.0564, 0.0542, 0.1043, 0.0268, 0.0319, 0.045, 0.0628, 0.0276, 0.0623, 0.0342852475096245, 0.040690039685344, 0.0486407530378304, 0.0575984729580694, 0.0402600869674421, 0.0482588465115293, 0.058413616215985, 0.0701647786023101, 0.0467435869504482, 0.0566451497970486, 0.0695330092351014, 0.0849088791529502, 0.0541179688838342, 0.0664102861435588, 0.0828830299591144, 0.103271205633297, 0.0342852475096245, 0.0575984729580694, 0.0541179688838342, 0.103271205633297, 0.0260250331468114, 0.0340653479315163, 0.0451732358445543, 0.0623862471475474, 0.0260250331468114, 0.0623862471475474, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.011, 0.015, 0.022, 0.035, 0.011, 0.015, 0.022, 0.035, 0.011, 0.015, 0.022, 0.035, 0.011, 0.015, 0.022, 0.035, 0.011, 0.035, 0.011, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 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