FIT: Transcriptomic Dynamics Models in Field Conditions
Version 0.0.4

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.

Browse man pages Browse package API and functions Browse package files

AuthorKoji Iwayama [cre], Yuri Aisaka [aut]
Date of publication2016-11-28 13:04:25
MaintainerKoji Iwayama <fieldtranscriptome@gmail.com>
LicenseMPL (>= 2) | file LICENSE
Version0.0.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("FIT")

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.

Functions

FIT Man page
FIT-package Man page
coef.deg.freedom Source code
coef.names Source code
coefsLasso Source code
coefsLm Source code Source code
date Source code
devLasso Source code
devLm Source code Source code
doOptim Source code
f2n Source code
filename Source code
fit Source code
fit.models Man page Source code
fitLasso Source code
get.a1.10min Source code
get.a1.60min Source code
get.s1.10min Source code
get.s1.60min Source code
get1 Source code
hm2min Source code
init Man page Source code Source code
init.gridsearch Source code
init.manual Source code
initParamsAndDevs Source code Source code
inputVars Source code
load.attribute Man page Source code
load.expression Man page Source code
load.weather Man page Source code
load.weight Man page Source code
make.recipe Man page Source code
make.weather.data Source code
new Source code
normalize.attribute Source code
normalize.weather Source code
onUnload Source code
optim Man page Source code Source code
page.fmt Source code
param.bounds Source code
param.names Source code
period.log Source code
period.log.inv Source code
predict Man page Source code
prediction.errors Man page Source code
read.csv Source code
read.from.web Source code
read.new.csv Source code
read.old.csv Source code
slurp Source code
station Source code
train Man page Source code
train.to.predict.adaptor Man page Source code
trivialWeights Source code
url Source code
weather.entries Man page
zzzRcppExportBug Source code

Files

inst
inst/extdata
inst/extdata/Jma.stations.csv
inst/extdata/train.weather
inst/extdata/prediction.weather
inst/extdata/rna-seq
inst/extdata/train.expression
inst/extdata/train.attribute
inst/extdata/prediction.expression
inst/extdata/prediction.attribute
inst/doc
inst/doc/FIT.Rmd
inst/doc/FIT.html
inst/doc/FIT.R
src
src/Makevars
src/model.h
src/grid.h
src/init.h
src/optim.h
src/Makevars.win
src/RcppExports.cpp
src/train.cpp
src/prep.h
NAMESPACE
R
R/Train.R
R/JmaStations.R
R/Model.R
R/Norm.R
R/JmaCsv.R
R/RcppExports.R
R/IO.R
R/JmaWeb.R
R/FIT.R
vignettes
vignettes/FIT.Rmd
vignettes/bibliography.bib
MD5
build
build/vignette.rds
DESCRIPTION
man
man/fit.models.Rd
man/init.Rd
man/load.expression.Rd
man/optim.Rd
man/load.attribute.Rd
man/make.recipe.Rd
man/train.to.predict.adaptor.Rd
man/predict.Rd
man/weather.entries.Rd
man/train.Rd
man/FIT.Rd
man/load.weather.Rd
man/prediction.errors.Rd
man/load.weight.Rd
LICENSE
FIT documentation built on May 19, 2017, 10:02 p.m.