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

A set of tools and workflows for modelling the growth dynamics of colonies arrayed on plates, as well as performing quantitative fitness analysis (QFA) on distinct (usually genetically) types of colonies. Frequent colony growth observations are required in a specific R data.frame format. qfa can use image logs generated by Colonyzer (http://research.ncl.ac.uk/colonyzer/). You can pre-process these data with our Robot Object Database (ROD: http://sourceforge.net/projects/robotobjectdb/). The model is fit either using maximum likelihood (fast), or using a hierarchical Bayesian model for all of the colonies in an experimental unit (CPU intensive). The Bayesian fit is performed using Gibbs Sampling, implemented in C. With appropriately designed experiments, qfa can also estimate genetic interaction strengths and produce epistasis plots.

- Author
- Jonathan Heydari <j.j.heydari@ncl.ac.uk>, with contributions from Conor Lawless <conor.lawless@ncl.ac.uk> and Darren Wilkinson <d.j.wilkinson@ncl.ac.uk>
- Date of publication
- 2016-01-06 16:09:07
- Maintainer
- Conor Lawless <conor.lawless@ncl.ac.uk>
- License
- Artistic-2.0
- Version
- 0.0-1
- URLs

## Man pages

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

## Files in this package

qfaBayes/DESCRIPTION |

qfaBayes/NAMESPACE |

qfaBayes/R |

qfaBayes/R/functions.r |

qfaBayes/R/simplifying_functions.r |

qfaBayes/data |

qfaBayes/data/URA3_Raw_extratrim_15.RData |

qfaBayes/data/cdc13_1_Raw_extratrim_15.RData |

qfaBayes/data/datalist |

qfaBayes/data/priors_IHM.RData |

qfaBayes/data/priors_JHM.RData |

qfaBayes/data/priors_SHM.RData |

qfaBayes/data/tuning_IHM.RData |

qfaBayes/data/tuning_JHM.RData |

qfaBayes/data/tuning_SHM.RData |

qfaBayes/demo |

qfaBayes/demo/00Index |

qfaBayes/demo/IHM.r |

qfaBayes/demo/IHM_parallel.r |

qfaBayes/demo/JHM.r |

qfaBayes/demo/SHM.r |

qfaBayes/man |

qfaBayes/man/IHM_MDRxMDP_postpro.Rd |

qfaBayes/man/IHM_main.Rd |

qfaBayes/man/JHM_main.Rd |

qfaBayes/man/JHM_postpro.Rd |

qfaBayes/man/SHM_main.Rd |

qfaBayes/man/SHM_postpro.Rd |

qfaBayes/man/URA3_Raw_extratrim_15.Rd |

qfaBayes/man/cdc13_1_Raw_extratrim_15.Rd |

qfaBayes/man/funcARRAYTRANS.Rd |

qfaBayes/man/funcARRAYTRANS_J.Rd |

qfaBayes/man/funcColORF.Rd |

qfaBayes/man/funcIDorder.Rd |

qfaBayes/man/funcNoORF.Rd |

qfaBayes/man/funcNoSum.Rd |

qfaBayes/man/funcREMOVE.Rd |

qfaBayes/man/funcRowRep.Rd |

qfaBayes/man/funcSCALING.Rd |

qfaBayes/man/funcXY.Rd |

qfaBayes/man/funcXY_J.Rd |

qfaBayes/man/plot_IHM_simple.Rd |

qfaBayes/man/plot_JHM_simple.Rd |

qfaBayes/man/plot_SHM_simple.Rd |

qfaBayes/man/priors_IHM.Rd |

qfaBayes/man/priors_JHM.Rd |

qfaBayes/man/priors_SHM.Rd |

qfaBayes/man/qfa.variables.Rd |

qfaBayes/man/tuning_IHM.Rd |

qfaBayes/man/tuning_JHM.Rd |

qfaBayes/man/tuning_SHM.Rd |

qfaBayes/man/visual_convergence_simple_check_IHM.Rd |

qfaBayes/man/visual_convergence_simple_check_JHM.Rd |

qfaBayes/man/visual_convergence_simple_check_SHM.Rd |

qfaBayes/src |

qfaBayes/src/datain_IHM.c |

qfaBayes/src/datain_IHM.h |

qfaBayes/src/datain_JHM.c |

qfaBayes/src/datain_JHM.h |

qfaBayes/src/datain_SHM.c |

qfaBayes/src/datain_SHM.h |

qfaBayes/src/functions_IHM.c |

qfaBayes/src/functions_IHM.h |

qfaBayes/src/functions_JHM.c |

qfaBayes/src/functions_JHM.h |

qfaBayes/src/functions_SHM.c |

qfaBayes/src/functions_SHM.h |

qfaBayes/src/headers_IHM.h |

qfaBayes/src/headers_JHM.h |

qfaBayes/src/headers_SHM.h |

qfaBayes/src/main_IHM.c |

qfaBayes/src/main_JHM.c |

qfaBayes/src/main_SHM.c |

qfaBayes/src/print_IHM.c |

qfaBayes/src/print_IHM.h |

qfaBayes/src/print_JHM.c |

qfaBayes/src/print_JHM.h |

qfaBayes/src/print_SHM.c |

qfaBayes/src/print_SHM.h |

qfaBayes/vignettes |

qfaBayes/vignettes/qfaBayes.Snw_ARCHIVE |