FIT: Transcriptomic Dynamics Models in Field Conditions

Provides functionality for constructing statistical models of transcriptomic dynamics in field conditions. It further offers the function to predict expression of a gene given the attributes of samples and meteorological data.

Author
Koji Iwayama [cre], Yuri Aisaka [aut]
Date of publication
2016-11-28 13:04:25
Maintainer
Koji Iwayama <fieldtranscriptome@gmail.com>
License
MPL (>= 2) | file LICENSE
Version
0.0.4

View on CRAN

Man pages

FIT
FIT: a statistical modeling tool for transcriptome dynamics...
fit.models
A raw API for fixing linear regression coefficients.
init
A raw API for initializing model parameters.
load.attribute
Loads attribute data.
load.expression
Loads expression data.
load.weather
Loads weather data.
load.weight
Loads regression weight data.
make.recipe
Creates a recipe for training models.
optim
A raw API for optimizing model parameters.
predict
Predicts gene expressions using pretrained models.
prediction.errors
Computes the prediction errors using the trained models.
train
Constructs models following a recipe.
train.to.predict.adaptor
Adapts the result of 'train()' to an input to 'predict()'.
weather.entries
Supported weather factors.

Files in this package

FIT
FIT/inst
FIT/inst/extdata
FIT/inst/extdata/Jma.stations.csv
FIT/inst/extdata/train.weather
FIT/inst/extdata/prediction.weather
FIT/inst/extdata/rna-seq
FIT/inst/extdata/train.expression
FIT/inst/extdata/train.attribute
FIT/inst/extdata/prediction.expression
FIT/inst/extdata/prediction.attribute
FIT/inst/doc
FIT/inst/doc/FIT.Rmd
FIT/inst/doc/FIT.html
FIT/inst/doc/FIT.R
FIT/src
FIT/src/Makevars
FIT/src/model.h
FIT/src/grid.h
FIT/src/init.h
FIT/src/optim.h
FIT/src/Makevars.win
FIT/src/RcppExports.cpp
FIT/src/train.cpp
FIT/src/prep.h
FIT/NAMESPACE
FIT/R
FIT/R/Train.R
FIT/R/JmaStations.R
FIT/R/Model.R
FIT/R/Norm.R
FIT/R/JmaCsv.R
FIT/R/RcppExports.R
FIT/R/IO.R
FIT/R/JmaWeb.R
FIT/R/FIT.R
FIT/vignettes
FIT/vignettes/FIT.Rmd
FIT/vignettes/bibliography.bib
FIT/MD5
FIT/build
FIT/build/vignette.rds
FIT/DESCRIPTION
FIT/man
FIT/man/fit.models.Rd
FIT/man/init.Rd
FIT/man/load.expression.Rd
FIT/man/optim.Rd
FIT/man/load.attribute.Rd
FIT/man/make.recipe.Rd
FIT/man/train.to.predict.adaptor.Rd
FIT/man/predict.Rd
FIT/man/weather.entries.Rd
FIT/man/train.Rd
FIT/man/FIT.Rd
FIT/man/load.weather.Rd
FIT/man/prediction.errors.Rd
FIT/man/load.weight.Rd
FIT/LICENSE