Tools for modelling the growth dynamics of arrays of large numbers of colonies and performing quantitative fitness analysis (QFA).

[Up] [Top]

Documentation for package ‘qfaBayes’ version 0.0-1

Help Pages

cdc13_1_MPlate15only cdc13_1_Raw_extratrim_15
funcARRAYTRANS Creates and transposes an array
funcARRAYTRANS_J Creates and transposes an array (JHM)
funcColORF Adds NA values at the end of an ORF to give consistent Col length for an array
funcIDORDER Order by ORF and ID coloumn
funcNoORF Gives number of repeats for each ORF
funcNoSum Gives running total for the number of repeats for each ORF
funcREMOVE Filter by Screen Name, Temprature and Master Plate Number
funcRowRep Adds NA values at the end of a repeat to give consistent row length for an array
funcSCALING Scales data by maximum theroetical value for IOD
funcXY Sorts data into array with correct dimensions
funcXY_J Sorts data into array with correct dimensions (JHM)
IHM_main Runs IHM C code
IHM_MDRxMDP_postpro Performs post processing for IHM
JHM_main Runs JHM C code
JHM_postpro Performs post processing for JHM
plot_IHM_simple plot IHM_simple_C output
plot_JHM_simple plot JHM_simple_C output
plot_SHM_simple plot SHM_simple_C output
priors_IHM priors_IHM
priors_JHM priors_JHM
priors_SHM priors_SHM
qfa.variables Gives experimental variables from QFA data (colonyzer.read output from the qfa package)
SHM_main Runs SHM C code
SHM_postpro Performs post processing for SHM
tuning_IHM tuning_IHM
tuning_JHM tuning_JHM
tuning_SHM tuning_SHM
URA3_MPlate15only URA3_Raw_extratrim_15
visual_convergence_simple_check_IHM Gives a trace plot for one of every parameter type to check convergence of IHM output
visual_convergence_simple_check_JHM Gives a trace plot for one of every parameter type to check convergence of JHM output
visual_convergence_simple_check_SHM Gives a trace plot for one of every parameter type to check convergence of SHM output