Title: Weighted Linear Fixed Effects Estimators for Causal Inference
Diff between wfe versions 0.1 dated 2011-12-13 and 1.0 dated 2012-07-18
Description: This R package provides a computationally efficient way of
fitting weighted linear fixed effects estimators for causal
inference with various weighting schemes. Imai and Kim (2011)
show that weighted linear fixed effects estimators can be used
to estimate the average treatment effects under different
identification strategies. This includes stratified randomized
experiments, matching and stratification for observational
studies, first differencing, and difference-in-differences.
The package also provides various robust standard errors and a
specification test for standard linear fixed effects
estimators.
Author: In Song Kim
Maintainer: In Song Kim
Changelog | 1
DESCRIPTION | 36
MD5 | 25
NAMESPACE | 6
R/functions.R | 243 +++
R/onAttach.R | 4
R/pwfe.R | 546 ++++--
R/wfe.R | 1726 +++++++++++++++++++---
man/pwfe.Rd | 146 +
man/wfe.Rd | 114 +
src/vector.c | 49
src/vector.h | 4
src/wfe.c | 4544 +++++++++++++++++++++++++++++++++++++++++++++++++++++-----
src/wfe.h |only
14 files changed, 6607 insertions(+), 837 deletions(-)
Title: Canonical Non-symmetrical Correspondence Analysis in R
Diff between cncaGUI versions 0.0-1 dated 2011-01-25 and 0.0-2 dated 2012-07-18
Description: Provides a GUI with which users can construct and interact
with Canonical Non-symmetrical Correspondence Analysis.
Author: Ana Belen Nieto Librero
Maintainer: Ana Belen Nieto Librero
cncaGUI-0.0-1/cncaGUI/inst |only
cncaGUI-0.0-1/cncaGUI/po |only
cncaGUI-0.0-2/cncaGUI/ChangeLog |only
cncaGUI-0.0-2/cncaGUI/DESCRIPTION | 13
cncaGUI-0.0-2/cncaGUI/MD5 |only
cncaGUI-0.0-2/cncaGUI/NAMESPACE |only
cncaGUI-0.0-2/cncaGUI/R/cnca.R | 2674 ++++++++++++++++-----------
cncaGUI-0.0-2/cncaGUI/cncaGUI-Ex.R |only
cncaGUI-0.0-2/cncaGUI/data |only
cncaGUI-0.0-2/cncaGUI/man/cnca.Rd | 37
cncaGUI-0.0-2/cncaGUI/man/cncaGUI-package.Rd | 4
cncaGUI-0.0-2/cncaGUI/man/especies.Rd |only
cncaGUI-0.0-2/cncaGUI/man/variables.Rd |only
13 files changed, 1635 insertions(+), 1093 deletions(-)
Title: Conditional logistic regression: A two-step estimation method
Diff between TwoStepCLogit versions 1.0 dated 2011-02-17 and 1.2 dated 2012-07-18
Description: Conditional logistic regression with longitudinal follow
up and individual-level random coefficients: A stable and
efficient two-step estimation method
Author: Radu V. Craiu, Thierry Duchesne, Daniel Fortin and Sophie
Baillargeon
Maintainer: Thierry Duchesne
DESCRIPTION | 9 -
MD5 |only
NAMESPACE | 9 +
R/Ts.estim.R |only
R/TwoStepCLogit.R | 235 ++++++++++++-------------------------------
R/ddim.R |only
R/internal.R |only
data/bison.rda |binary
inst |only
man/Ts.estim.Rd | 163 ++++++++++++++++++++---------
man/TwoStepCLogit-package.Rd | 36 ++++--
man/bison.Rd | 107 ++++++++++---------
man/ddim.Rd |only
tests |only
14 files changed, 270 insertions(+), 289 deletions(-)
Title: ADMB to R interface functions
Diff between R2admb versions 0.7.5.1 dated 2012-03-21 and 0.7.5.3 dated 2012-07-18
Description: A series of functions to call AD Model Builder (i.e.,
compile and run models) from within R, read the results back
into R as "admb" objects, and provide standard accessors (i.e.
coef(), vcov(), etc.)
Author: Ben Bolker, Hans Skaug
Maintainer: Ben Bolker
DESCRIPTION | 8 +++---
MD5 | 46 ++++++++++++++++++++++++++++-----------
NEWS |only
R/admb-funs.R | 5 ++--
R/do_admb.R | 9 +++++--
R/readfit.R |only
TODO |only
inst/NEWS.Rd | 13 +++++++++++
inst/admbtests/toy1_gen.tpl |only
inst/doc/R2admb.Rnw | 14 +++++------
junk |only
tests |only
vignettes/ADMB_runs.gz |only
vignettes/R2admb-fig1.pdf |binary
vignettes/R2admb-mcdensplot.pdf |binary
vignettes/R2admb-mchistplot.pdf |binary
vignettes/R2admb-mctraceplot.pdf |binary
vignettes/R2admb-profpic.pdf |binary
vignettes/R2admb-ranefs.pdf |binary
vignettes/R2admb.Rnw | 14 +++++------
vignettes/ReedfrogSizepred0.dat |only
vignettes/ReedfrogSizepred0.pin |only
vignettes/Reedfrog_runs.Rout |only
vignettes/Rplots.pdf |only
vignettes/TODO_2 |only
vignettes/auto |only
vignettes/betamodel.txt |only
vignettes/reedfrogsizepred.dat |only
vignettes/reedfrogsizepred.pin |only
vignettes/reedfrogsizepred0.par |only
vignettes/rfjunk.tpl |only
vignettes/tadpole_bugs.txt |only
vignettes/toy1_gen.dat |only
vignettes/toy1_gen.par |only
vignettes/toy1_gen.tpl |only
35 files changed, 75 insertions(+), 34 deletions(-)
Title: topologyGSA
Diff between topologyGSA versions 1.0.3 dated 2011-12-22 and 1.1.0 dated 2012-07-18
Description: Package description.
Author: Sofia Massa, Gabriele Sales
Maintainer: Sofia Massa
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/cliques.R | 2 +-
R/pathway.R | 2 +-
4 files changed, 9 insertions(+), 9 deletions(-)
Title: Power and Sample size based on two one-sided t-tests (TOST) for
(bio)equivalence studies
Diff between PowerTOST versions 0.9-8 dated 2012-04-05 and 0.9-9 dated 2012-07-18
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies. See
function known.designs() for study designs covered. Moreover
the package contains functions for power and sample size based
on 'expected' power in case of uncertain (estimated)
variability. ----- Added are functions for the power and
sample size for the ratio of two means with normally
distributed data on the original scale (based on Fieller's
confidence ('fiducial') interval). ----- Contains further
functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but
eventually useful if the question of 'non-superiority' must be
evaluated. The power and sample size calculations based on
non-inferiority test may also performed via 'expected' power in
case of uncertain (estimated) variability.
Author: Detlew Labes
Maintainer: D. Labes
DESCRIPTION | 8 ++---
MD5 | 22 ++++++++--------
NEWS | 5 +++
R/DesignHelpers.R | 43 ++++++++++++++++----------------
R/OwensQ.R | 63 +++++++++++++++++++++++++++++------------------
R/SampleSize.R | 18 ++++++++++---
R/SampleSize_noninf.R | 17 +++++++++---
R/expSampleSize.R | 20 +++++++++++++-
R/expSampleSize_noninf.R | 19 +++++++++++---
R/power.R | 9 ++++--
data/data2x2.rda |binary
man/PowerTOST-package.Rd | 4 +-
12 files changed, 150 insertions(+), 78 deletions(-)
Title: Estimation of models with limited dependent variables
Diff between mhurdle versions 0.1-2 dated 2012-05-31 and 0.1-3 dated 2012-07-18
Description: Estimation of models with zero left-censored variables.
Null values may be caused by a selection process, insufficient
ressource or infrequency of purchase.
Author: Fabrizio Carlevaro
Maintainer: Yves Croissant
DESCRIPTION | 10 ++---
MD5 | 22 ++++++------
R/mhurdle.R | 12 +------
R/mhurdle.lnl.R | 9 ++---
R/mhurdle.methods.R | 87 ++++++++-------------------------------------------
R/misc.R | 87 ++++++++++++++++++++++++++-------------------------
R/vuong.R | 8 +---
changelog | 4 ++
data/Comics.rda |binary
inst/doc/mhurdle.pdf |binary
inst/doc/mhurdle.rnw | 69 +++++++++++++++++++---------------------
man/rsq.Rd | 17 ++++-----
12 files changed, 131 insertions(+), 194 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Diff between MALDIquant versions 1.1 dated 2012-05-06 and 1.2 dated 2012-07-18
Description: MALDIquant provides a complete analysis pipeline for
MALDI-TOF and other mass spectrometry data. Distinctive
features include baseline subtraction using the SNIP algorithm,
peak alignment using warping functions, handling of replicated
measurements as well as allowing spectra with different
resolutions.
Author: Sebastian Gibb
Maintainer: Sebastian Gibb
DESCRIPTION | 12 +++++-----
MD5 | 37 ++++++++++++++++----------------
NEWS | 6 +++++
R/arguments-functions.R | 2 -
R/binPeaks-functions.R | 6 ++---
R/determineWarpingFunctions-functions.R | 12 ++++++----
R/doByLabels-functions.R | 14 +++++++-----
R/estimateBaseline-functions.R | 4 +--
R/filterPeaks-functions.R | 4 +--
R/findEmptyMassObjects-functions.R | 2 -
R/intensityMatrix-functions.R | 2 -
R/isFunctionList-functions.R | 4 +--
R/isMassObjectList-functions.R | 12 +++++-----
R/labelPeaks-methods.R | 2 -
R/merge-functions.R | 6 ++---
R/unlist-functions.R |only
demo/workflow.R | 7 ++++--
man/MALDIquant-package.Rd | 10 ++++----
man/filterPeaks-functions.Rd | 2 -
man/merge-functions.Rd | 2 -
20 files changed, 82 insertions(+), 64 deletions(-)
Title: Generalized Order-Restricted Information Criterion
Diff between goric versions 0.0-4 dated 2011-12-05 and 0.0-6 dated 2012-07-18
Description: Generalized Order-Restricted Information Criterion (GORIC)
value for a set of hypotheses in multivariate regression models
Author: Daniel Gerhard and Rebecca M. Kuiper
Maintainer: Daniel Gerhard
goric-0.0-4/goric/man/summarize_orlm.Rd |only
goric-0.0-6/goric/DESCRIPTION | 15 ++++++++-------
goric-0.0-6/goric/MD5 | 21 +++++++++++++--------
goric-0.0-6/goric/NAMESPACE | 14 ++++++++++++--
goric-0.0-6/goric/R/goric.R | 29 ++++++++++++++++++++++++++++-
goric-0.0-6/goric/R/goric_penalty.R | 6 +++---
goric-0.0-6/goric/R/orgls.R |only
goric-0.0-6/goric/R/orgls_methods.R |only
goric-0.0-6/goric/R/orlm.R | 3 ++-
goric-0.0-6/goric/R/sim.R |only
goric-0.0-6/goric/man/goric-package.Rd | 6 +++---
goric-0.0-6/goric/man/goric.Rd | 10 +++++++---
goric-0.0-6/goric/man/orgls.Rd |only
goric-0.0-6/goric/man/ormodel_methods.Rd |only
goric-0.0-6/goric/man/sim.Rd |only
15 files changed, 76 insertions(+), 28 deletions(-)
Title: Evaluation and experimental design for binomial group testing
Diff between binGroup versions 1.0-9 dated 2011-12-21 and 1.0-10 dated 2012-07-18
Description: This package provides methods for estimation and
hypothesis testing of proportions in group testing designs. It
involves methods for estimating a proportion in a single
population (assuming sensitivity and specificty 1 in designs
with equal group sizes), as well as hypothesis tests and
functions for experimental design for this situation. For
estimating one proportion or the difference of proportions, a
number of confidence interval methods are included, which can
deal with various different pool sizes. Further, regression
methods are implemented for simple pooling and matrix pooling
designs.
Author: Boan Zhang, Christopher Bilder, Brad Biggerstaff, Frank
Schaarschmidt
Maintainer: Frank Schaarschmidt
binGroup-1.0-10/binGroup/DESCRIPTION | 8 ++++----
binGroup-1.0-10/binGroup/MD5 | 17 ++++++++---------
binGroup-1.0-10/binGroup/NAMESPACE | 1 -
binGroup-1.0-10/binGroup/R/binGroupReg.r |only
binGroup-1.0-10/binGroup/man/gt.control.Rd | 8 ++++----
binGroup-1.0-10/binGroup/man/gtreg.Rd | 7 +++----
binGroup-1.0-10/binGroup/man/gtreg.mp.Rd | 4 ++--
binGroup-1.0-10/binGroup/man/print.gt.Rd |only
binGroup-1.0-10/binGroup/man/summary.gt.Rd | 1 -
binGroup-1.0-9/binGroup/R/binGroupBoanChris.r |only
binGroup-1.0-9/binGroup/R/print.gt.R |only
binGroup-1.0-9/binGroup/man/print.gt.mp.Rd |only
12 files changed, 21 insertions(+), 25 deletions(-)
Title: Multi-model inference
Diff between MuMIn versions 1.7.7 dated 2012-04-01 and 1.7.11 dated 2012-07-18
Description: Model selection and model averaging based on information
criteria (AICc and alike).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń
MuMIn-1.7.11/MuMIn/DESCRIPTION | 12
MuMIn-1.7.11/MuMIn/MD5 | 43 -
MuMIn-1.7.11/MuMIn/NAMESPACE | 8
MuMIn-1.7.11/MuMIn/NEWS | 792 ++++++++++++++--------------
MuMIn-1.7.11/MuMIn/R/class-mcmc.R | 34 +
MuMIn-1.7.11/MuMIn/R/coefTable.R | 11
MuMIn-1.7.11/MuMIn/R/dredge.R | 2
MuMIn-1.7.11/MuMIn/R/ext.R | 76 ++
MuMIn-1.7.11/MuMIn/R/get.models.R | 8
MuMIn-1.7.11/MuMIn/R/model.avg.R | 2
MuMIn-1.7.11/MuMIn/R/model.selection.R | 4
MuMIn-1.7.11/MuMIn/data/Beetle.rda |binary
MuMIn-1.7.11/MuMIn/data/Cement.rda |binary
MuMIn-1.7.11/MuMIn/man/ICs.Rd | 8
MuMIn-1.7.11/MuMIn/man/beetle.Rd | 10
MuMIn-1.7.11/MuMIn/man/dredge.Rd | 13
MuMIn-1.7.11/MuMIn/man/mod.sel.Rd | 5
MuMIn-1.7.11/MuMIn/man/predict.averaging.Rd | 16
MuMIn-1.7.11/MuMIn/man/supported-classes.Rd | 17
MuMIn-1.7.11/MuMIn/tests/classes.R | 17
MuMIn-1.7.11/MuMIn/tests/coxme.R | 4
MuMIn-1.7.11/MuMIn/tests/unmarked.R | 2
MuMIn-1.7.7/MuMIn/tests/me.R |only
23 files changed, 626 insertions(+), 458 deletions(-)
Title: Parallel Mutual Information estimation for Gene Network
reconstruction.
Diff between parmigene versions 1.0 dated 2011-03-10 and 1.0.1 dated 2012-07-18
Description: The package provides a parallel estimation of the mutual
information based on entropy estimates from k-nearest neighbors
distances and algorithms for the reconstruction of gene
regulatory networks.
Author: Gabriele Sales
Maintainer: Gabriele Sales
parmigene-1.0.1/parmigene/DESCRIPTION | 10
parmigene-1.0.1/parmigene/MD5 |only
parmigene-1.0.1/parmigene/R/zzz.R |only
parmigene-1.0.1/parmigene/R/zzz.R.in | 6
parmigene-1.0.1/parmigene/configure | 588 +++++++++++-------------------
parmigene-1.0.1/parmigene/man/aracne.a.Rd | 2
parmigene-1.0.1/parmigene/man/aracne.m.Rd | 2
parmigene-1.0.1/parmigene/man/clr.Rd | 2
parmigene-1.0.1/parmigene/man/mrnet.Rd | 2
parmigene-1.0.1/parmigene/src/Makevars |only
parmigene-1.0.1/parmigene/src/config.h |only
parmigene-1.0/parmigene/.gitignore |only
12 files changed, 236 insertions(+), 376 deletions(-)
Title: Forecasting functions for time series and linear models
Diff between forecast versions 3.22 dated 2012-06-07 and 3.23 dated 2012-07-18
Description: Methods and tools for displaying and analysing univariate
time series forecasts including exponential smoothing via state
space models and automatic ARIMA modelling.
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 4
DESCRIPTION | 8
MD5 | 12 -
R/arfima.R | 4
R/arima.R | 12 -
R/newarima2.R | 642 +++++++++++++++++++++++++++++-----------------------------
man/ses.Rd | 2
7 files changed, 350 insertions(+), 334 deletions(-)
Title: Association between Methylation and a phenotype of interest
Diff between CpGassoc versions 1.1 dated 2012-05-26 and 1.3 dated 2012-07-18
Description: CpGassoc is designed to test for association between
methylation at CpG sites across the genome and a phenotype of
interest, adjusting for any relevant covariates. The package
can perform standard analyses of large datasets very quickly
with no need to impute the data. It can also handle mixed
effects models with chip or batch entering the model as a
random intercept. CpGassoc also includes tools to apply
quality control filters, perform permutation tests, and create
QQ plots, manhattan plots, and scatterplots for individual CpG
sites.
Author: Barfield, R., Conneely, K., Kilaru,V
Maintainer: R Barfield
CpGassoc-1.1/CpGassoc/man/cpg.rd |only
CpGassoc-1.3/CpGassoc/DESCRIPTION | 10 -
CpGassoc-1.3/CpGassoc/MD5 | 62 +++++----
CpGassoc-1.3/CpGassoc/NAMESPACE | 2
CpGassoc-1.3/CpGassoc/R/cpg.GC.R |only
CpGassoc-1.3/CpGassoc/R/cpg.assoc.R | 37 ++---
CpGassoc-1.3/CpGassoc/R/cpg.combine.R | 38 +++--
CpGassoc-1.3/CpGassoc/R/cpg.everything.matrix.R | 9 -
CpGassoc-1.3/CpGassoc/R/cpg.perm.R | 72 +++++-----
CpGassoc-1.3/CpGassoc/R/cpg.qc.R | 37 ++++-
CpGassoc-1.3/CpGassoc/R/cpg.work.R | 158 +++++++++++++-----------
CpGassoc-1.3/CpGassoc/R/manhattan.R | 2
CpGassoc-1.3/CpGassoc/R/plot.cpg.R | 87 ++++++++++---
CpGassoc-1.3/CpGassoc/R/plot.cpg.perm.R | 77 +++++++++--
CpGassoc-1.3/CpGassoc/R/print.cpg.gc.R |only
CpGassoc-1.3/CpGassoc/R/print.cpg.perm.gc.R |only
CpGassoc-1.3/CpGassoc/R/scatterplot.R | 4
CpGassoc-1.3/CpGassoc/data/annotation.rda |binary
CpGassoc-1.3/CpGassoc/data/samplecpg.rda |binary
CpGassoc-1.3/CpGassoc/data/samplepheno.rda |binary
CpGassoc-1.3/CpGassoc/inst/doc/CpGassoc.Rnw | 97 ++++++++++++--
CpGassoc-1.3/CpGassoc/inst/doc/CpGassoc.pdf |binary
CpGassoc-1.3/CpGassoc/man/CpGassoc-package.Rd | 10 -
CpGassoc-1.3/CpGassoc/man/cpg.GC.Rd |only
CpGassoc-1.3/CpGassoc/man/cpg.Rd |only
CpGassoc-1.3/CpGassoc/man/cpg.assoc.Rd | 15 --
CpGassoc-1.3/CpGassoc/man/cpg.combine.Rd | 2
CpGassoc-1.3/CpGassoc/man/cpg.everything.Rd | 2
CpGassoc-1.3/CpGassoc/man/cpg.perm.Rd | 8 -
CpGassoc-1.3/CpGassoc/man/cpg.perm.object.rd | 10 -
CpGassoc-1.3/CpGassoc/man/cpg.qc.Rd | 7 -
CpGassoc-1.3/CpGassoc/man/cpg.work.Rd | 10 -
CpGassoc-1.3/CpGassoc/man/design.Rd | 2
CpGassoc-1.3/CpGassoc/man/manhattan.Rd | 2
CpGassoc-1.3/CpGassoc/man/scatterplot.Rd | 6
35 files changed, 500 insertions(+), 266 deletions(-)
Title: Output analysis and diagnostics for MCMC
Diff between coda versions 0.14-7 dated 2012-04-02 and 0.15-1 dated 2012-07-18
Description: Output analysis and diagnostics for Markov Chain Monte
Carlo simulations.
Author: Martyn Plummer [aut, cre, trl], Nicky Best [aut], Kate Cowles
[aut], Karen Vines [aut], Deepayan Sarkar [aut], Russell Almond
[ctb]
Maintainer: Martyn Plummer
DESCRIPTION | 21 ++++++++++++++-------
MD5 | 6 +++---
R/geweke.R | 44 ++++++++++++++++++++++++++------------------
data/line.rda |binary
4 files changed, 43 insertions(+), 28 deletions(-)