Power Calculations Under Genetic Model Misspecification

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Documentation for package ‘genpwr’ version 1.0.4

Help Pages

add.fun.t Function to Calculate t matrix for logistic outcome with binary environment interaction in additive model
add.or.function Additive Model Function
additive.ll Function to Calculate Additive Log Likelihood for a Logistic Regression Model
additive.ll.linear Function to Calculate Additive Log Likelihood for a Linear Regression Model
as.numeric2 Function to convert to numeric with scientific notation containing the "." character
calc.like Function to Calculate Log Likelihood for a Logistic Regression Model
calc.like.linear Function to Calculate Log Likelihood for a Linear Regression Model
calc.like.linear.log.envir.interaction Function to calculate the standard deviation of y given x for linear models with logistic environment interaction
df2.ll Function to Calculate 2df Log Likelihood for a Logistic Regression Model
df2.ll.linear Function to Calculate 2 Degree of Freedom Log Likelihood for a Linear Regression Model
dom.fun.t Function to Calculate t matrix for logistic outcome with binary environment interaction in dominant model
dom.or.function Dominant Model Function
dominant.ll Function to Calculate Dominant Log Likelihood for a Logistic Regression Model
dominant.ll.linear Function to Calculate Dominant Log Likelihood for a Linear Regression Model
es.calc.linear Function to Calculate Effect Size for Linear Models
expected.linear.ll Function to Calculate Expected Log Likelihood for a Single Genotype
expected.linear.ll.lin.env Function to Calculate Expected Log Likelihood for a Single Genotype with linear environment interaction
find.prob.dom Dominant probability finding function
find.prob.rec Recessive probability finding function
genpwr.calc Function to Calculate Power for Linear Models with logistic environment interaction
integrand_funct_case Function to generate integrand for mle for cases
integrand_funct_control Function to generate integrand for mle for controls
linear.mles Function to calculate MLE's for linear models
linear.mles.lin.envir.interaction Function to calculate the standard deviation of y given x for linear models with linear environment interaction
linear.mles.lin.envir.interaction_reduced Function to calculate the standard deviation of y given x for linear models with linear environment interaction for the reduced model without GxE interaction
linear.mles.log.envir.interaction Function to calculate the standard deviation of y given x for linear models with logistic environment interaction
linear.outcome.lin.envir.interaction.sds Function to calculate the standard deviation of y given x for linear models with linear environment interaction
linear.outcome.lin.envir.interaction.sds_reduced Function to calculate the standard deviation of y given x for linear models with linear environment interaction
linear.outcome.log.envir.interaction.sds Function to calculate the standard deviation of y given x for linear models with logistic environment interaction
linear.sds Functions to Calculate Residual SD for Normal/Continuous Outcomes Function to calculate the standard deviation of y given x for linear models
ll.ge.logistic Function to calculate MLE's for logistic models with logistic environment interaction
ll.ge.logistic.lin.envir Function to output log likelihood for logistic outcome with linear environment variables
ll.linear.selector Function to return log likelihood function for specified model type
ll_zero_finder2 Zero finding function
logistic.mles Function to calculate MLE's for logistic models
logit Logit Function
ncp.search Function to Determine Non-Centrality Parameter of the Chi-squared distribution
null.ll Function to Calculate Null Log Likelihood for a Logistic Regression Model
null.ll.linear Function to Calculate Expected Null Log Likelihood for a Linear Regression Model
odds_ratio_function Odds Ratio Function
or.function.2df 2df Model Function
or.plot Function to Plot Odds Ratio Results
or_calc Odds ratio calculation
power.calc Function to Calculate Power
power.calc.linear Function to Calculate Power for Linear Models
power.plot Function to Plot Power Results
power_envir.calc Function to Calculate Power for Logistic Models with Environment Interaction
power_envir.calc.linear_outcome Function to Calculate Power for Linear Models with logistic environment interaction
power_linear_envir.calc.linear_outcome Function to Calculate Power for Linear Models with linear environment interaction
power_linear_envir.calc.logistic_outcome Function to Calculate Power for Linear Models with logistic environment interaction
p_vec_returner Function to output probability vector used in calculation of MLE's for linear outcome with logistic environment interaction
p_vec_returner_lin_env Function to output probability vector used in calculation of MLE's for linear outcome with linear environment interaction
quad_roots Function to Solve Quadratic Equations
rec.fun.t Function to Calculate t matrix for logistic outcome with binary environment interaction in recessive model
rec.or.function Recessive Model Function
recessive.ll Function to Calculate Recessive Log Likelihood for a Logistic Regression Model
recessive.ll.linear Function to Calculate Recessive Log Likelihood for a Linear Regression Model
solve_a Binomial coefficient calculation
ss.calc Function to Calculate Sample Size
ss.calc.linear Function to Calculate Sample Size in Linear Models
ss.plot Function to Plot Sample Size Results
ss_envir.calc Function to Calculate Power for Logistic Models with Environment Interaction
ss_envir.calc.linear_outcome Function to Calculate Power for Linear Models with logistic environment interaction
ss_linear_envir.calc.linear_outcome Function to Calculate Power for Linear Models with linear environment interaction
ss_linear_envir.calc.logistic_outcome Function to Calculate Sample Size for Linear Models with logistic environment interaction
X_mat_returner Function to output X matrices used in calculation of MLE's for linear outcome with logistic environment interaction
X_mat_returner_lle Function to output X matrices used in calculation of MLE's for linear outcome with linear environment interaction
zero_finder_nleqslv Zero finder