A Biostatisticians Toolbox for Various Activities, Including Plotting, Data Cleanup, and Data Analysis

added.plot | Create an added variable plot |

anchored.gradient | Create a color gradient with a color for zero |

anchor.predictions | Generate Predictions for a Model |

auto.layout | Automatically select the layout. |

bf.bic | Compute Bayes Factor from BICs |

bin.variables | Bin them vars |

bivariate.plot | Plot bivariate plot of two variables |

boxcoxR | Transform data using a boxcox transformation |

chisq.plot | Plot Expected and Observed Frequencies (Chi Square) |

chisq.post.hoc | Tests for significant differences among all pairs of... |

ci.mean | Compute the confidence interval of a mean |

clear | Clear memory of all objects |

colored.table | Create a color-coded table in latex |

compare.fits | Compare the fits of two models |

computeTheta | Calculate inverse tangent. |

contents | View the contents (functions) of a package |

cor2cov | Correlation Matrix to Covariance Matrix Conversion |

demographics | Summarize a Data Set (Demographics) |

densityPlotR | Generate a density plot using a formula |

drop.columns | Drop (or keep) all columns containing a vector of strings |

ellipse | Plots an Ellipse |

estimates | Report Estimates (effect sizes and parameters) |

estimates.default | Output APA style statistical significance from an object |

estimates.fifer.anova | Report fifer.anova Estimates (effect sizes and parameters) |

estimates.glm | Report glm object Estimates (effect sizes and parameters) |

estimates.lm | Report regression object Estimates (effect sizes and... |

estimates.regression | Report regression object Estimates (effect sizes and... |

estimates.ttest | Report ttest object Estimates (effect sizes and parameters) |

estimates.zeroinfl | Report zeroinfl object Estimates (effect sizes and... |

excelCols | Generate Excel column labels |

excelMatch | Obtain column number or variable name from Excel named... |

factorial.plot | Plot a Factorial ANOVA |

fakeMedicalData | Fictitious Medical Dataset |

fifer.anova | Perform a one-way anova |

flexplot | Create a "flexible plot" or flexplot |

flexplot2 | Create a "flexible plot" or flexplot |

generate.data | Simulate multivariate normal data |

get.cols | Extract column index |

gradient.legend | Create a gradiented legend |

hash | Create useless hashes |

icc | Compute the ICC from a lmer (package lme4) model |

imageInteraction | Plot an two-way quantitative interaction in an image plot |

improve.fit | Compare the improvement in fit from a baseline model |

impute.me | Multiple Imputation on a Model |

intersperse | Intersperse elements of Two+ Vectors |

jit.func | How to display data |

last.sample | Return only one row per ID |

make.formula | Convert strings to a formula |

make.null | Drop or keep variables in a dataset |

make.symmetric | Force a matrix to be symmetric |

missing.vals | Summary of Missing Data |

mixed.mod.visual | Display a graphic of a mixed model |

model.comparison | Perform a model comparison |

mv.rnorm | Randomly Generate Multivariate Normal Data |

number.to.colors | Convert from numbers to colors |

par1 | Change default par parameters |

par2 | Change default par parameters |

plot.fifer.anova | Plot fifer.anova Summary |

plot.regression | Plot regression Summary |

plot.rfInterp | Plot rfInterp Summary |

plot.rfPred | Plot rfPred Summary |

plot.rfThresh | rfThesh Summary |

plotSigBars | Add significance bars to a prism plot |

plot.ttest | Plot ttest Summary |

predicted.line | Create and plot a fitted line for a generalized linear model |

print.fifer.anova | Print fifer.anova Summary |

print.regression | Print regression Summary |

print.rfInterp | Print rfInterp Summary |

print.rfPred | Print rfPred Summary |

print.rfThresh | Print rfThesh Summary |

print.ttest | Print ttest Summary |

printx | Change Defaults of print.xtable |

prism.plots | Plot prism-like Plots |

pval.xtable | Convert p-values into strings with inequalities. |

r | Extract variable column indices |

random.correlation | Generate a random correlation matrix |

raw.alph.func | Find transparency of data |

r.crit | Compute critical r or p. |

read.fife | Read in a dataset and load the meta-data for a file |

regression | Perform a regression/correlation analysis |

related.plot | Function to create a related t test plot |

replace | Replace values in a vector |

report | Output APA style statistical significance from an object |

report.default | Output APA style statistical significance from an object |

report.fifer.anova | Output APA style statistical significance from a fifer.anova... |

report.regression | Output APA style statistical significance from a regression... |

report.ttest | Output APA style statistical significance from a ttest object |

rescale | Transform a variable to have a particular mean and standard... |

residualize.lowess | Residualize a lowess function |

rfInterp | Variable Selection with Random Forest |

rfPred | Variable selection in Random Forest |

rfSensitivity | Output accuracy, sensitivity, specificity, NPV, and PPV. |

rfThresh | Variable Selection Using Random Forests |

rotateGraph | Rotate a graph using polar coordinates |

roxtemp | Generate a Roxygen Template |

scaleB | Standardize coefficients |

scaleBreak | Scatterplot with a Scale Break |

scaleIt | Scale a variable |

sensitivity.table | Compute sensitivity/specificity/etc. |

spearman.plot | Spearman plot |

spread_type | Type of spread to use |

standardized.beta | Compute standardized betas on a linear model object |

stratified | Sample from a 'data.frame' according to a stratification... |

string.to.colors | Convert between strings to colors |

subset.sample | Sample the data |

subsetString | Extract only part of a string |

SummarizeContinuousDefault | Summarize a continuous vector with mean plus/minus standard... |

SummarizeFactorDefault | Summarize a factor vector with count and percentages |

SummarizeVar | Summarize a vector (continuous or factor) |

summary.rfPred | Print a Summary Table of rfPred |

ttest | Perform a two-independent sample t-test |

unfactor | Convert a factor to a character (or number) |

uni.plot | Plot univariate distribution of a variable |

univariate.tests | Extract p values for a data frame |

visualize | Visualize a fitted model |

visualize.lm | Visualize a fitted model |

visualize.lmerMod | Visualize a fitted model |

write.fife | Write a dataset and load the meta-data |

x.summary | Type of x summary to use (line or mean) |

xtable.rfInterp | Prepare xtable Summary |

xtable.rfPred | Prepare xtable Summary |

z.test | Perform a z test |

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