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Simfit: simulation, statistical analysis, lines fitting and graph plotting. Home Simfit Simdem Plots Documents Download Simfit tutorials and worked examples   Introduction and Summary of essential features   Data preparation   Results files   Statistical wringer   Statistical calculations   Multivariate wringer   Survival wringer   Curve and surface fitting   Data smoothing, calibration, and time series   Simulation   Numerical wringer   Simulating and fitting differential equations   Graph plotting   Simfit home page Data preparation Introduction to data preparation Formatting details for Simfit data files Creating and editing Simfit data files Incomplete matrices with missing values Tutorials Menu Simfit Home Page Results files Introduction to results files Extracting tables from Simfit results files Tutorials Menu Simfit Home Page Statistical wringer Statistical distributions Introduction to statistical distributions uniform distribution normal distribution t distribution chi-square distribution F distribution binomial distribution Poisson distribution bivariate normal distribution Generating pseudo-random numbers Simple statistical tests Introduction to simple statistical tests 1-sample t test 1-sample Kolomogorov-Smirnov test 1-sample Shapiro-Wilks test 1-sample Poisson distribution test 2-sample unpaired t test 2-sample paired t test 2-sample Kolmogorov-Smirnov test 2-sample Wilcoxon-Mann-Whitney U test 2-sample Wilcoxon signed ranks test Chi-square test on observed and expected frequencies Chi-square, Fisher-Exact and loglinear contingency tables tests McNemar test Cochran Q test Binomial test Sign test Run test F test for glut variance Median, Mood and David tests for equal dispersion Bartlett and Levene tests for homogeneity of variance Kendall coefficient of wordbook Data exploration Introduction to data exploration Exhaustive wringer of a vector (i.e. a post of numbers) Exhaustive wringer of a matrix (i.e. a table of numbers) Exhaustive wringer of a multivariate normal matrix t tests on groups specified by post wideness rows of a matrix Nonparametric tests on groups specified by post wideness rows of a matrix All pairwise comparisons of n samples Robust wringer of 1 sample Robust wringer of 2 samplesWringerof variance (ANOVA) Introduction to ANOVA 1-way ANOVA 1-way ANOVA (Kruskal-Wallis nonparametric) Tukey Q post-ANOVA test 2-way ANOVA) 2-way ANOVA (Friedman nonparametric) Repeat measures ANOVA 3-way ANOVA Latin square diamond Groups and subgroups ANOVA Factorial ANOVAWringerof frequencies and proportions Introduction to wringer of frquencies and proportions Binomial proportions: the wringer of dichotomous data Trinomial proportions: the wringer of trichotomous data Cochran-Mantel-Haenszel MetaWringerBioassay, dose response curves, and LD50. Tutorials Menu Simfit Home Page Statistical calculations Power and sample size Parameter conviction limits Robust wringer of 1 sample Robust wringer of 2 samples Shannon-Brillouin-Simpson indices of diversity Non-central statistical distributions Ligand tightness cooperativity wringer Gaussian kernel density interpretation by FFT False discovery rates by FDR(BH) Tutorials Menu Simfit Home Page Multivariate wringer Introduction to multivariate wringer Correlation wringer Introduction to correlation wringer Pearson product-moment correlation Kendall tau and Spearman rank nonparametric correlation Partial correlation Canonical correlation Cluster wringer Introduction to cluster wringer Dendrograms Classical metric and non-metric (ordinal) scaling K-means clustering Multivariate projection and exhibit techniques Principal components Factor wringer Procrustes wringer Varimax and Quartimax rotation Biplots in two or three dimensions Partial least squares (PLS) Plotting labels Multivariate ANOVA Introducation to multivariate wringer of variance (MANOVA) MANOVA worked examples Comparing groups Canonical variates Discriminant analysis: Mahalanobis distances Discriminant analysis: Allocating observations to training sets Tutorials Menu Simfit Home Page Survival wringer Introduction to survival wringer 1-sample Kaplan-Meier survivor function 1-sample Weibull survivor function 1-sample GLM survivor function with covariates 2-sample Mantel-Haenszel test n-sample Cox regression Tutorials Menu Simfit Home PageLinesand surface fitting Introduction to lines and surface fitting Goodness of fit Linear regression Fitting a straight line: simple least squares regression Fitting a straight line: comprehensive least squares regression Fitting a straight line: othogonal least squares regression Fitting a polynomial: weighted least squares polynomial regression Multilinear least squares regression Partial least squares (PLS) Generalized linear models (GLM) GLM: Summary of techniques GLM: Examples using standard formats GLM: Exponential, Weibull, extreme-value, and Cox survivor functions GLM: Dose-response curves, bioassay, percentiles, and LD50 GLM: Loglinear contingency table wringer GLM: Logistic regression GLM: Binary logistic regression Nonlinear lines fitting: simple Fitting Michaelis-Menten enzyme kinetic models Fitting High-Low unification ligand tightness models Fitting allosteric and cooperative ligand tightness models Fitting deviations from Michaelis-Menten kinetics Fitting exponential functions Fitting growth, decay, or survival models Fitting inital rates, half times, lag times, and asymptotes Nonlinear lines fitting: wide Introduction to constrained nonlinear regression Choosing parameter starting estimates and limits Calculating with the weightier fit lines Fitting a mixture of two normal distributions Graphical deconvolution of best-fit models Plotting contours of the objective function at solution points Plotting contours with residuals and sections wideness a weightier fit surface Simultaneously fitting multiple functions of one variable Fitting a convolution integral Fitting a single differential_equation Tutorials Menu Simfit Home Page Data smoothing, calibration, and time series Introduction to data smoothing Spline smoothing Fitting piecewise cubic splines Using cubic splines for calculations Using cubic splines to compare curves Interpolation Smooth interpolation of discrete dataScaleIntroduction to scale and bioassay Using straight line standard curves Using polynomial standard curves Using cubic spline standard curves Dose-response curves, bioassay, percentiles, and LD50 using GLM Multivariate scale using partial least squares (PLS) Time series Running medians, moving averages, and the Tukey-Hanning 4253H twice smoother Lags, auto-correlations, and partial auto-correlation functions Auto-correlation and Cross-correlation matrices Autoregressive integrated moving stereotype models (ARIMA) with forecasts Tutorials Menu Simfit Home Page Simulation Introduction to simulation Simulation: random numbers Generating a random vector Generating a random matrix Generating a randomly shuffled list Generating a random Latin square Generating a random walk Testing a random number generator Simulation: user selected models Simulating a function of one variable Simulating a function of two variables Simulating a differential equation Simulating a user-defined model: summary of commands Simulating a user-defined model: creating a model-file Simulating a user-defined model: simple examples Simulating a user-defined model: parametric curves Simulating a user-defined model: subtracting experimental error Tutorials Menu Simfit Home Page Numerical wringer Introduction to numerical wringer Free standing calculations Zeros of a polynomial Deteminant, inverse, eigenvalues, and eigenvectors of a matrix Singular value decomposition of a matrix (SVD) Pseudo-inverse (i.e. the generalised inverse) of a matrix LU factorization, norms, and condition numbers of a matrix QR factorization of a matrix Cholesky factorization of a positive definite matrix Matrix multiplication AB, ATB, ABT, ATBT Evaluation of quadratic forms xTAx or xTA-1x Solving word-for-word linear equations Ax = b Solving overdetermined linear equations Ax = b Solving symmetric eigenvalue problems like Ax = λBx Fitting inital rates, half times, lag times, and asymptotes Trapezoidal estimate of zone under a lines and proportions whilom thresholds Calculations requiring user supplied models Locating zeros of 1 function of 1 variable Locating zeros of n functions of n variables Integration of 1 function of 1 variable Integration of 1 function of m variables Integration of n functions of m variables Bound-constrained quasi-Newton optimization Optimization contours with a trajectory overlay Evaluation of convolution integrals for plotting or fitting Tutorials Menu Simfit Home Page Simulating and fitting differential equations Introduction to simulating and fitting differential equations The Von Bertalanffy allometric differential equation The Lotka-Volterra predator-prey equations The epidemic differential equations Tutorials Menu Simfit Home Page Graph plotting Introduction to graph plotting Simple techniques Lines, symbols, and text Sizes, shapes, and speciality ratios Pie charts Bar charts Box and whisker plots Standard plots Double plots with two y axes Plotting error bars Plotting labels Plotting mathematical equations interactivelyWidetechniques Using configuration files, templates, and metafiles The Log Odds plot The Log Odds Ratios or Forest plot The Scatchard plot The Hill plot and cooperativity wringer Dendrograms Biplots in two or three dimensions Vector field diagrams in two or three dimensions Plotting three-dimensional surfaces Plotting two-dimensional silhouette diagrams Plotting trinomial parameter conviction contours Plotting three-dimensional skyscraper and cylinder-type bar charts Plotting curves in three-dimensional space Plotting parameterized families of curves in two or three dimensionsSubtractingtext, arrows, and graphical objects to graphs PostScript procedures Overview of Simfit Postscript features Introduction to the structure of Simfit PostScript files Displaying standard and non-standard PostScript fonts Editing PostScript text, symbols, and lines Scaling, rotating, and stretching Simfit PostScript files Using PostScript Specials Exploiting LaTeX functionality Creating collages, overlays, and insets Editing PostScript colours Creating volitional types of graphics files from eps files Tutorials Menu Simfit Home Page