Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [cre, ctb],
Barret Schloerke [ctb]
Maintainer: Yihui Xie
Diff between evaluate versions 0.5.5 dated 2014-04-29 and 0.6 dated 2015-04-13
evaluate-0.5.5/evaluate/R/src-region.r |only evaluate-0.5.5/evaluate/man/getSrcRegion.Rd |only evaluate-0.6/evaluate/DESCRIPTION | 14 +- evaluate-0.6/evaluate/MD5 | 34 ++-- evaluate-0.6/evaluate/NEWS | 9 + evaluate-0.6/evaluate/R/eval.r | 3 evaluate-0.6/evaluate/R/graphics.r | 79 +++-------- evaluate-0.6/evaluate/R/parse.r | 167 ++++++++++-------------- evaluate-0.6/evaluate/man/create_traceback.Rd | 1 evaluate-0.6/evaluate/man/evaluate.Rd | 3 evaluate-0.6/evaluate/man/is.message.Rd | 1 evaluate-0.6/evaluate/man/line_prompt.Rd | 1 evaluate-0.6/evaluate/man/new_output_handler.Rd | 1 evaluate-0.6/evaluate/man/parse_all.Rd | 3 evaluate-0.6/evaluate/man/replay.Rd | 1 evaluate-0.6/evaluate/man/set_hooks.Rd | 1 evaluate-0.6/evaluate/man/try_capture_stack.Rd | 1 evaluate-0.6/evaluate/man/watchout.Rd | 1 evaluate-0.6/evaluate/tests/test-all.R | 2 19 files changed, 151 insertions(+), 171 deletions(-)
Title: Simulation Parameter Analysis R Toolkit ApplicatioN: Spartan
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, described in our 2013 publication in PLoS Computational Biology, provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. We have also added user support through the group spartan-group[AT]york[DOT]ac[DOT]uk. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions.
Author: Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Maintainer: Kieran Alden
Diff between spartan versions 2.2 dated 2015-03-23 and 2.2.1 dated 2015-04-13
spartan-2.2.1/spartan/DESCRIPTION | 6 spartan-2.2.1/spartan/MD5 | 65 +-- spartan-2.2.1/spartan/R/aa_getATestResults.R | 8 spartan-2.2.1/spartan/R/aa_graphATestsForSampleSize.R | 8 spartan-2.2.1/spartan/R/aa_graphSampleSizeSummary.R | 17 spartan-2.2.1/spartan/R/aa_sampleSizeSummary.R | 7 spartan-2.2.1/spartan/R/aa_summariseReplicateRuns.R | 3 spartan-2.2.1/spartan/R/efast_generate_medians_for_all_parameter_subsets.R | 2 spartan-2.2.1/spartan/R/efast_get_overall_medians.R | 7 spartan-2.2.1/spartan/R/efast_graph_Results.R | 2 spartan-2.2.1/spartan/R/efast_netlogo_get_overall_medians.R | 5 spartan-2.2.1/spartan/R/efast_netlogo_run_Analysis.R | 5 spartan-2.2.1/spartan/R/efast_process_netlogo_result.R | 15 spartan-2.2.1/spartan/R/efast_run_Analysis.R | 7 spartan-2.2.1/spartan/R/getMediansSubset.R | 10 spartan-2.2.1/spartan/R/lhc_generateLHCSummary.R | 5 spartan-2.2.1/spartan/R/lhc_generatePRCoEffs.R | 5 spartan-2.2.1/spartan/R/lhc_generate_netlogo_PRCoEffs.R | 5 spartan-2.2.1/spartan/R/lhc_graphMeasuresForParameterChange.R | 7 spartan-2.2.1/spartan/R/lhc_netlogo_graphMeasuresForParameterChange.R | 5 spartan-2.2.1/spartan/R/lhc_plotCoEfficients.R | 197 ++++++---- spartan-2.2.1/spartan/R/lhc_process_netlogo_result.R | 17 spartan-2.2.1/spartan/R/lhc_process_sample_run_subsets.R | 5 spartan-2.2.1/spartan/R/oat_countResponsesOfDesiredValue.R | 6 spartan-2.2.1/spartan/R/oat_csv_result_file_analysis.R | 105 ++--- spartan-2.2.1/spartan/R/oat_graphATestsForSampleSize.R | 14 spartan-2.2.1/spartan/R/oat_plotResultDistribution.R | 5 spartan-2.2.1/spartan/R/oat_processParamSubsets.R | 3 spartan-2.2.1/spartan/R/oat_process_netlogo_result.R | 13 spartan-2.2.1/spartan/R/pcor.mat.R | 12 spartan-2.2.1/spartan/R/pcor.rec.R | 12 spartan-2.2.1/spartan/R/pcor.test.R | 6 spartan-2.2.1/spartan/man/Technique3-lhc_perform_analysis.Rd | 6 spartan-2.2/spartan/R/eFAST_TestBed.R |only 34 files changed, 340 insertions(+), 255 deletions(-)
Title: Software Option Settings Manager for R
Description: Provides option settings management that goes
beyond R's default 'options' function. With this package, users can define
their own option settings manager holding option names and default values.
Settings can then be retrieved, altered and reset to defaults with ease.
For R programmers and package developers it offers cloning and merging
functionality which allows for conveniently defining global and local
options, possibly in a multilevel options hierarchy. See the package
vignette for some examples concerning functions, S4 classes, and reference
classes. There are convenience functions to reset par() and options() to
their 'factory defaults'.
Author: Mark van der Loo
Maintainer: Mark van der Loo
Diff between settings versions 0.1.1 dated 2014-10-28 and 0.2.1 dated 2015-04-13
settings-0.1.1/settings/man/options-package.Rd |only settings-0.2.1/settings/DESCRIPTION | 12 +++--- settings-0.2.1/settings/MD5 | 27 +++++++++------ settings-0.2.1/settings/NAMESPACE | 4 ++ settings-0.2.1/settings/NEWS |only settings-0.2.1/settings/R/options.R | 10 ----- settings-0.2.1/settings/R/settings-package.R |only settings-0.2.1/settings/R/utils.R |only settings-0.2.1/settings/README.md | 10 ++++- settings-0.2.1/settings/build/vignette.rds |binary settings-0.2.1/settings/inst/doc/settings.R | 43 +++++++++++++++--------- settings-0.2.1/settings/inst/doc/settings.Rmd | 28 ++++++++++++++- settings-0.2.1/settings/inst/doc/settings.html | 44 ++++++++++++++++++++++--- settings-0.2.1/settings/man/options_manager.Rd | 2 - settings-0.2.1/settings/man/reset_options.Rd |only settings-0.2.1/settings/man/reset_par.Rd |only settings-0.2.1/settings/man/settings.Rd |only settings-0.2.1/settings/vignettes/settings.Rmd | 28 ++++++++++++++- 18 files changed, 153 insertions(+), 55 deletions(-)
Title: Persistent Fast Amortized Stack and Queue Data Structures
Description: Provides fast, persistent (side-effect-free) stack, queue and
deque (double-ended-queue) data structures. While deques include a superset
of functionality provided by queues, in these implementations queues are
more efficient in some specialized situations. See the documentation for
rstack, rdeque, and rpqueue for details.
Author: Shawn T. O'Neil
Maintainer: Shawn T. O'Neil
Diff between rstackdeque versions 1.1 dated 2014-12-04 and 1.1.1 dated 2015-04-13
rstackdeque-1.1.1/rstackdeque/DESCRIPTION | 6 +-- rstackdeque-1.1.1/rstackdeque/LICENSE | 4 +- rstackdeque-1.1.1/rstackdeque/MD5 | 27 +++++++--------- rstackdeque-1.1.1/rstackdeque/R/as.data.frame.rdeque.R | 1 rstackdeque-1.1.1/rstackdeque/R/rdeque.R | 3 - rstackdeque-1.1.1/rstackdeque/R/rpqueue.R | 3 - rstackdeque-1.1.1/rstackdeque/R/rstack.R | 4 +- rstackdeque-1.1.1/rstackdeque/R/without_top.R | 3 - rstackdeque-1.1.1/rstackdeque/R/without_top.rstack.R | 8 ++-- rstackdeque-1.1.1/rstackdeque/man/rdeque.Rd | 5 -- rstackdeque-1.1.1/rstackdeque/man/rpqueue.Rd | 5 -- rstackdeque-1.1.1/rstackdeque/man/rstack.Rd | 5 -- rstackdeque-1.1.1/rstackdeque/man/without_top.Rd | 3 - rstackdeque-1.1.1/rstackdeque/man/without_top.rstack.Rd | 3 - rstackdeque-1.1/rstackdeque/README.md |only 15 files changed, 30 insertions(+), 50 deletions(-)
Title: Refined Moving Average Filter
Description: Uses refined moving average filter based on the optimal and data-driven moving average lag q or smoothing spline to estimate trend and seasonal components, as well as irregularity (residuals) for univariate time series or data.
Author: Debin Qiu
Maintainer: Debin Qiu
Diff between rmaf versions 2.0 dated 2014-03-10 and 3.0 dated 2015-04-13
rmaf-2.0/rmaf/R/ma.filter.R |only rmaf-3.0/rmaf/DESCRIPTION | 10 +- rmaf-3.0/rmaf/MD5 | 18 ++- rmaf-3.0/rmaf/R/mafilter.R |only rmaf-3.0/rmaf/R/qn.R | 38 +++----- rmaf-3.0/rmaf/R/ssfilter.R |only rmaf-3.0/rmaf/data/globtemp.rda |binary rmaf-3.0/rmaf/man/globtemp.Rd | 4 rmaf-3.0/rmaf/man/ma.filter.Rd | 176 ++++++++++++++++++++------------------ rmaf-3.0/rmaf/man/qn.Rd | 88 +++++++++---------- rmaf-3.0/rmaf/man/rmaf-package.Rd | 90 +++++++++---------- rmaf-3.0/rmaf/man/ss.filter.Rd |only 12 files changed, 224 insertions(+), 200 deletions(-)
Title: Import Professional Baseball Data from 'Retrosheet'
Description: A collection of tools to import and structure the (currently) single-season
event, game-log, roster, and schedule data available from http://www.retrosheet.org.
In particular, the event (a.k.a. play-by-play) files can be especially difficult to parse.
This package does the parsing on those files, returning the requested data in the most
practical R structure to use for sabermetric or other analyses.
Author: Richard Scriven [aut, cre]
Maintainer: Richard Scriven
Diff between retrosheet versions 1.0.1 dated 2015-04-09 and 1.0.2 dated 2015-04-13
retrosheet-1.0.1/retrosheet/R/internals.R |only retrosheet-1.0.2/retrosheet/DESCRIPTION | 18 +++++----- retrosheet-1.0.2/retrosheet/MD5 | 13 ++++--- retrosheet-1.0.2/retrosheet/NAMESPACE | 1 retrosheet-1.0.2/retrosheet/R/getParkIDs.R |only retrosheet-1.0.2/retrosheet/R/getPartialGamelog.R | 33 +++++++++++++++---- retrosheet-1.0.2/retrosheet/README.md | 14 +++++--- retrosheet-1.0.2/retrosheet/man/getParkIDs.Rd |only retrosheet-1.0.2/retrosheet/man/getPartialGamelog.Rd | 7 ++-- 9 files changed, 59 insertions(+), 27 deletions(-)
Title: Determining the Best Number of Clusters in a Data Set
Description: It provides 30 indexes for determining the optimal number of clusters in a data set and offers the best clustering scheme from different results to the user.
Author: Malika Charrad and Nadia Ghazzali and Veronique Boiteau and Azam Niknafs
Maintainer: Malika Charrad
Diff between NbClust versions 2.0.4 dated 2015-03-02 and 3.0 dated 2015-04-13
DESCRIPTION | 8 +- MD5 | 6 +- R/NbClust.R | 165 ++++++++++++++++++++++++++++++++++----------------------- man/NbClust.Rd | 28 ++++++++- 4 files changed, 131 insertions(+), 76 deletions(-)
Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen
Diff between InvariantCausalPrediction versions 0.1-4 dated 2014-12-12 and 0.3 dated 2015-04-13
DESCRIPTION | 12 ++++++------ MD5 | 19 +++++++++++++------ NAMESPACE | 4 ++-- R/ICP.R | 17 ++++++++++++++--- R/computeDelta.R |only R/edgeRetention.R |only R/edgeSelection.R |only R/feedbackNetwork.R |only R/hiddenICP.R |only man/ICP.Rd | 21 +++++++++++++++++---- man/feedbackNetwork.Rd |only man/hiddenICP.Rd |only man/plot.InvariantCausalPrediction.Rd | 6 +++++- man/summary.InvariantCausalPrediction.Rd | 6 +++++- 14 files changed, 62 insertions(+), 23 deletions(-)
More information about InvariantCausalPrediction at CRAN
Permanent link
Title: Estimation of Heritability in Linear Mixed Models
Description: Estimation of heritability with confidence intervals in linear mixed models.
Author: Anna Bonnet
Maintainer: Anna Bonnet
Diff between HiLMM versions 1.0 dated 2014-04-15 and 1.1 dated 2015-04-13
HiLMM-1.0/HiLMM/data/mat_W.rda |only HiLMM-1.0/HiLMM/data/vec_Y.rda |only HiLMM-1.0/HiLMM/man/mat_W.Rd |only HiLMM-1.0/HiLMM/man/vec_Y.Rd |only HiLMM-1.1/HiLMM/DESCRIPTION | 13 +++++----- HiLMM-1.1/HiLMM/MD5 | 25 ++++++++++++++------ HiLMM-1.1/HiLMM/R/HiLMM-internal.R |only HiLMM-1.1/HiLMM/R/data_simu.R |only HiLMM-1.1/HiLMM/R/estim_herit.R | 42 +++++++++++++++++++++++++---------- HiLMM-1.1/HiLMM/build |only HiLMM-1.1/HiLMM/data/W.rda |only HiLMM-1.1/HiLMM/data/Y.rda |only HiLMM-1.1/HiLMM/inst |only HiLMM-1.1/HiLMM/man/HiLMM-package.Rd | 30 ++++++++++--------------- HiLMM-1.1/HiLMM/man/W.Rd |only HiLMM-1.1/HiLMM/man/Y.Rd |only HiLMM-1.1/HiLMM/man/data_simu.Rd |only HiLMM-1.1/HiLMM/man/estim_herit.Rd | 38 +++++++++++++------------------ HiLMM-1.1/HiLMM/vignettes |only 19 files changed, 82 insertions(+), 66 deletions(-)
Title: Fast Estimation of Gaussian Mixture Copula Models
Description: Unsupervised Clustering and Meta-analysis using Gaussian Mixture
Copula Models.
Author: Anders Ellern Bilgrau, Martin Boegsted, Poul Svante Eriksen
Maintainer: Anders Ellern Bilgrau
Diff between GMCM versions 1.1.1 dated 2014-10-06 and 1.2 dated 2015-04-13
DESCRIPTION | 18 +-- MD5 | 104 ++++++++++---------- NAMESPACE | 2 R/EMAlgortihm.R | 4 R/GMCM-package.R | 59 +++++------ R/PseudoEMAlgorithm.R | 4 R/RcppExports.R | 8 - R/Uhat.R | 2 R/colSds.R | 6 - R/dgmcm.loglik.R | 6 - R/fit.full.GMCM.R | 10 - R/fit.meta.GMCM.R | 24 ++-- R/full2meta.R | 3 R/get.IDR2.R | 18 +-- R/is.theta.R | 17 ++- R/pgmm.marginal.R | 22 ++-- R/rtheta.R | 162 +++++++++++++++++++++++-------- README.md | 68 ++++++++++++- build |only inst/CITATION | 39 ++++--- inst/NEWS.Rd | 15 ++ inst/doc |only inst/tests/test-EMAlgorithm.R | 47 ++++----- inst/tests/test-EStep.R | 24 ++-- inst/tests/test-full2meta-meta2full.R | 58 +++++------ inst/tests/test-is.theta.R | 25 ++++ man/EMAlgorithm.Rd | 7 - man/EStep.Rd | 3 man/GMCM-package.Rd | 21 ++-- man/PseudoEMAlgorithm.Rd | 7 - man/SimulateGMCMData.Rd | 3 man/Uhat.Rd | 5 man/choose.theta.Rd | 3 man/colSds.Rd | 8 - man/cummean.Rd | 3 man/dgmcm.loglik.Rd | 9 - man/dmvnormal.Rd | 11 +- man/fit.full.GMCM.Rd | 13 +- man/fit.meta.GMCM.Rd | 27 ++--- man/freshVsFrozen.Rd | 17 +-- man/full2meta.Rd | 3 man/get.IDR.Rd | 19 +-- man/is.theta.Rd | 7 + man/logit.Rd | 3 man/rho.transform.Rd | 3 man/rtheta.Rd | 89 +++++++++++++++-- man/tt.Rd | 3 man/u133VsExon.Rd | 24 ++-- src/GMCM.cpp | 9 - src/Makevars.win | 2 src/RcppExports.cpp | 174 +++++++++++++--------------------- vignettes |only 52 files changed, 734 insertions(+), 484 deletions(-)
Title: Estimation of Temporal Ordering of Cancer Abnormalities
Description: This is a package with functions for timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.
Author: Elizabeth Purdom
Maintainer: Elizabeth Purdom
Diff between cancerTiming versions 2.0.0 dated 2014-05-07 and 3.0.0 dated 2015-04-13
DESCRIPTION | 14 +-- MD5 | 27 +++--- NAMESPACE | 3 R/eventTiming.R | 184 +++++++++++++++++++++++++++++--------------- R/eventTimingList.R |only R/labelSeg.R | 24 ++--- R/plotPi0.R |only inst/NEWS.Rd |only man/alleleFreq.Rd | 3 man/eventTiming.Rd | 5 - man/eventTimingOverList.Rd |only man/makeEventHistory.Rd | 10 +- man/mleAF.Rd | 2 man/mutData.Rd | 3 man/plotAlleleByPosition.Rd | 19 ++-- man/plotAlleleDensity.Rd | 11 +- man/plotPi0.Rd |only 17 files changed, 192 insertions(+), 113 deletions(-)
Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for (A)ccurate and (S)peedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred R/qtl objects. This includes extremely fast linkage map clustering and optimal marker ordering using MSTmap (see Wu et al.,2008).
Author: Julian Taylor
Maintainer: Julian Taylor
Diff between ASMap versions 0.3-3 dated 2015-02-02 and 0.4 dated 2015-04-13
ASMap-0.3-3/ASMap/data/mapDHu.RData |only ASMap-0.3-3/ASMap/man/mapDHu.Rd |only ASMap-0.4/ASMap/DESCRIPTION | 12 +++++---- ASMap-0.4/ASMap/MD5 | 45 +++++++++++++++++++++++++---------- ASMap-0.4/ASMap/R/mstmap9.R | 8 ++++-- ASMap-0.4/ASMap/build |only ASMap-0.4/ASMap/data/mapBC.RData |only ASMap-0.4/ASMap/data/mapBCu.RData |only ASMap-0.4/ASMap/data/mapDH.RData |binary ASMap-0.4/ASMap/data/mapDHf.RData |only ASMap-0.4/ASMap/data/mapF2.RData |binary ASMap-0.4/ASMap/inst |only ASMap-0.4/ASMap/man/ASMap-package.Rd | 16 +++++++----- ASMap-0.4/ASMap/man/genClones.Rd | 2 - ASMap-0.4/ASMap/man/mapBC.Rd |only ASMap-0.4/ASMap/man/mapBCu.Rd |only ASMap-0.4/ASMap/man/mapDH.Rd | 13 +++++----- ASMap-0.4/ASMap/man/mapDHf.Rd |only ASMap-0.4/ASMap/man/mapF2.Rd | 10 ++++--- ASMap-0.4/ASMap/man/pullCross.Rd | 1 ASMap-0.4/ASMap/man/pushCross.Rd | 1 ASMap-0.4/ASMap/vignettes |only 22 files changed, 70 insertions(+), 38 deletions(-)
Title: Additional Matrix Functionality
Description: Additional matrix functionality for R including: (1) wrappers
for the base matrix function that allows matrices to be created from character
strings and lists (the former is especially useful for creating block
matrices), (ii) better default printing of large matrices, and (iii) a number
of convenience functions for users more familiar with other scientific
languages like Julia, Matlab/Octave, or Python.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell
Diff between ramify versions 0.1.0 dated 2015-03-23 and 0.2.0 dated 2015-04-13
ramify-0.1.0/ramify/man/falses.Rd |only ramify-0.1.0/ramify/man/ones.Rd |only ramify-0.2.0/ramify/DESCRIPTION | 23 +- ramify-0.2.0/ramify/MD5 | 49 ++-- ramify-0.2.0/ramify/NAMESPACE | 14 + ramify-0.2.0/ramify/NEWS | 14 - ramify-0.2.0/ramify/R/bmat.R | 9 ramify-0.2.0/ramify/R/convenience.R | 279 +++++++++++++++++--------- ramify-0.2.0/ramify/R/dmat.R | 4 ramify-0.2.0/ramify/R/mat.R | 161 ++++++++++++++- ramify-0.2.0/ramify/R/ramify.R | 43 ++-- ramify-0.2.0/ramify/R/utils.R |only ramify-0.2.0/ramify/R/zzz.R |only ramify-0.2.0/ramify/README.md | 70 ++++-- ramify-0.2.0/ramify/man/add_dots.Rd |only ramify-0.2.0/ramify/man/argmax.Rd |only ramify-0.2.0/ramify/man/as.mat.Rd |only ramify-0.2.0/ramify/man/bmat.Rd | 5 ramify-0.2.0/ramify/man/desc_mat.Rd |only ramify-0.2.0/ramify/man/dmat.Rd | 4 ramify-0.2.0/ramify/man/fill.Rd | 26 ++ ramify-0.2.0/ramify/man/flatten.Rd | 7 ramify-0.2.0/ramify/man/hcat.Rd | 2 ramify-0.2.0/ramify/man/print.mat.Rd |only ramify-0.2.0/ramify/man/ramify.Rd | 43 ++-- ramify-0.2.0/ramify/man/rand.Rd | 30 +- ramify-0.2.0/ramify/man/randi.Rd |only ramify-0.2.0/ramify/man/randn.Rd |only ramify-0.2.0/ramify/man/resize.Rd | 16 - ramify-0.2.0/ramify/man/size.Rd | 8 ramify-0.2.0/ramify/tests/testthat/test-mat.R | 36 ++- 31 files changed, 597 insertions(+), 246 deletions(-)
Title: Analysis of the "Elements of Metacommunity Structure"
Description: Functions to analyze coherence, boundary clumping, and turnover following the pattern-based metacommunity analysis of Leibold and Mikkelson 2002. The package also includes functions to visualize ecological networks, and to calculate modularity as a replacement to boundary clumping.
Author: Tad Dallas
Maintainer: Tad Dallas
Diff between metacom versions 1.4.2 dated 2014-12-11 and 1.4.3 dated 2015-04-13
DESCRIPTION | 15 ++++----- MD5 | 40 +++++++++++++----------- R/BoundaryClump.R | 4 +- R/Coherence.R | 12 ++++--- R/IdentifyStructure.R | 78 ++++++++++++++++++----------------------------- R/MetaImportance.R |only R/Metacommunity.R | 27 ++++++++++------ R/Modularity.R |only R/NullMaker.R | 12 +++---- R/Turnover.R | 8 ++-- data/TestMatrices.rda |binary man/BoundaryClump.Rd | 16 +++++---- man/Coherence.Rd | 28 ++++++++-------- man/IdentifyStructure.Rd | 24 ++++++-------- man/Imagine.Rd | 6 +-- man/MetaImportance.Rd |only man/Metacommunity.Rd | 39 +++++++++++++++-------- man/Modularity.Rd |only man/NullMaker.Rd | 31 +++++++++--------- man/OrderMatrix.Rd | 11 +++--- man/TestMatrices.Rd | 26 +++++---------- man/Turnover.Rd | 18 +++++----- man/metacom-package.Rd | 17 ++++------ 23 files changed, 207 insertions(+), 205 deletions(-)
Title: Analysis of Dose-Response Curves
Description: Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions.
Author: Christian Ritz
Maintainer: Christian Ritz
Diff between drc versions 2.3-96 dated 2013-11-29 and 2.5-11 dated 2015-04-13
drc-2.3-96/drc/R/SI.R |only drc-2.3-96/drc/R/actimL.R |only drc-2.3-96/drc/R/genBliss.R |only drc-2.3-96/drc/R/genBliss2.R |only drc-2.3-96/drc/R/genLoewe.R |only drc-2.3-96/drc/R/genLoewe2.r |only drc-2.3-96/drc/R/genursa.R |only drc-2.3-96/drc/R/genursa2.R |only drc-2.3-96/drc/R/gompGrowth.R |only drc-2.3-96/drc/R/iceLoewe.1.R |only drc-2.3-96/drc/R/iceLoewe.1new.R |only drc-2.3-96/drc/R/iceLoewe2.1.R |only drc-2.3-96/drc/data/beetGrowth.rda |only drc-2.3-96/drc/man/SI.Rd |only drc-2.3-96/drc/man/beetGrowth.Rd |only drc-2.3-96/drc/man/gompGrowth.Rd |only drc-2.3-96/drc/man/mrdrm.Rd |only drc-2.5-11/drc/DESCRIPTION | 19 +-- drc-2.5-11/drc/MD5 | 113 ++++++++---------- drc-2.5-11/drc/NAMESPACE | 40 +++--- drc-2.5-11/drc/NEWS | 35 +++++ drc-2.5-11/drc/R/ED.drc.R | 29 ++++ drc-2.5-11/drc/R/EDcomp.R |only drc-2.5-11/drc/R/backfit.R | 2 drc-2.5-11/drc/R/compParm.R | 25 ++-- drc-2.5-11/drc/R/drm.R | 45 +++++-- drc-2.5-11/drc/R/gammadr.R |only drc-2.5-11/drc/R/idrm.R | 6 - drc-2.5-11/drc/R/isobole.R | 58 +++------ drc-2.5-11/drc/R/maED.R | 4 drc-2.5-11/drc/R/modelFunction.R | 17 ++ drc-2.5-11/drc/R/multi2.R |only drc-2.5-11/drc/R/plot.drc.R | 49 ++++++-- drc-2.5-11/drc/R/predict.drc.R | 153 +++++++++++++++++-------- drc-2.5-11/drc/R/relpot.R | 6 - drc-2.5-11/drc/R/resPrint.R | 2 drc-2.5-11/drc/R/sandwich.R | 110 ++++++++++++++++-- drc-2.5-11/drc/R/siInner.R | 13 +- drc-2.5-11/drc/R/simDR.R | 2 drc-2.5-11/drc/R/summary.drc.R | 10 + drc-2.5-11/drc/R/update.drc.R | 2 drc-2.5-11/drc/data/G.aparine.rda |binary drc-2.5-11/drc/data/RScompetition.rda |binary drc-2.5-11/drc/data/daphnids.rda |binary drc-2.5-11/drc/data/earthworms.rda |binary drc-2.5-11/drc/data/finney71.rda |binary drc-2.5-11/drc/data/heartrate.rda |binary drc-2.5-11/drc/data/leaflength.rda |binary drc-2.5-11/drc/man/ED.drc.Rd | 64 ++++------ drc-2.5-11/drc/man/EDcomp.Rd |only drc-2.5-11/drc/man/G.aparine.Rd | 38 +++--- drc-2.5-11/drc/man/H.virescens.Rd | 6 - drc-2.5-11/drc/man/LL.2.Rd | 4 drc-2.5-11/drc/man/LL.3.Rd | 7 - drc-2.5-11/drc/man/S.alba.Rd | 12 +- drc-2.5-11/drc/man/bread.drc.Rd | 21 ++- drc-2.5-11/drc/man/chickweed.Rd | 43 ++++--- drc-2.5-11/drc/man/compParm.Rd | 10 + drc-2.5-11/drc/man/drm.Rd | 33 +++-- drc-2.5-11/drc/man/gammadr.Rd |only drc-2.5-11/drc/man/germination.Rd | 39 +++--- drc-2.5-11/drc/man/gompertz.Rd | 8 - drc-2.5-11/drc/man/isobole.Rd | 6 - drc-2.5-11/drc/man/mixture.Rd | 8 - drc-2.5-11/drc/man/multi2.Rd |only drc-2.5-11/drc/man/plot.drc.Rd | 43 ++++--- drc-2.5-11/drc/man/predict.drc.Rd | 4 drc-2.5-11/drc/man/print.drc.Rd | 2 drc-2.5-11/drc/man/ursa.Rd | 203 +++++----------------------------- 69 files changed, 712 insertions(+), 579 deletions(-)
Title: Selecting Variable Subsets
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria.
Author: Jorge Orestes Cerdeira [aut], Pedro Duarte Silva [aut], Jorge Cadima [aut, cre], Manuel Minhoto [aut]
Maintainer: Jorge Cadima
Diff between subselect versions 0.12-4 dated 2014-10-08 and 0.12-5 dated 2015-04-13
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 21 +++++++++++++++------ R/trimmatrix.R | 11 +++++------ build/vignette.rds |binary inst/CHANGELOG | 5 +++++ 6 files changed, 35 insertions(+), 22 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
Diff between lfe versions 2.1-1640 dated 2015-03-11 and 2.2-1699 dated 2015-04-13
DESCRIPTION | 8 - MD5 | 120 ++++++++-------- NAMESPACE | 15 +- R/bccorr.R | 316 +++++++++++++++++++++++++++---------------- R/btrap.R | 12 + R/cgsolve.R | 61 +++++--- R/chmethod.R | 27 +-- R/compfactor.R | 1 R/condfstat.R | 1 R/demeanlist.R | 24 +-- R/efactory.R | 1 R/felm.R | 118 +++++++++++----- R/felm.old.R | 1 R/generics.R | 20 +- R/getfe.R | 11 + R/is.estimable.R | 2 R/kaczmarz.R | 10 - R/oldfelm.R | 3 R/startup.R | 19 ++ R/trace.R | 26 +-- R/utils.R | 44 ++++- R/waldtest.R | 1 build/vignette.rds |binary exec/lfescript | 1 inst/NEWS.Rd | 15 ++ inst/TODO | 6 inst/doc/CHANGELOG | 23 ++- inst/doc/identification.R | 5 inst/doc/identification.Rnw | 6 inst/doc/identification.pdf |binary inst/doc/lfehow.Rnw | 1 inst/doc/lfehow.pdf |binary inst/doc/speed.Rnw | 2 inst/doc/speed.pdf |binary man/bccorr.Rd | 18 +- man/cgsolve.Rd |only man/demeanlist.Rd | 76 +++++----- man/felm.Rd | 30 +++- man/fevcov.Rd | 16 +- man/getfe.Rd | 2 man/kaczmarz.Rd | 20 +- man/lfe-package.Rd | 58 ++++--- man/makeDmatrix.Rd |only man/mctrace.Rd |only man/waldtest.Rd | 2 src/Makevars.in | 3 src/Makevars.win | 1 src/demean.c | 235 ++++++++++++++++++------------- src/factor.c | 36 ++-- src/kaczmarz.c | 108 ++++---------- src/lfe-win.def |only src/lfe.c | 36 ++-- src/lfe.h | 33 ++-- src/utils.c | 23 +-- tests/anomalies.Rout.save | 16 -- tests/bctest.Rout.save | 20 +- tests/cgsolve.R |only tests/cgsolve.Rout.save |only tests/cluster.Rout.save | 7 tests/ivtest.Rout.save | 7 tests/weights.R |only tests/weights.Rout.save |only vignettes/identification.Rnw | 6 vignettes/lfehow.Rnw | 1 vignettes/speed.Rnw | 2 65 files changed, 987 insertions(+), 669 deletions(-)
Title: Fit Generalized Estimating Equations
Description: Allows generalized estimating equation fits with user-specified link and variance functions.
Author: Lee S. McDaniel and Nick Henderson
Maintainer: Lee S. McDaniel
Diff between geeM versions 0.7.2 dated 2014-12-03 and 0.7.3 dated 2015-04-13
DESCRIPTION | 8 MD5 | 10 NAMESPACE | 4 R/geem.R | 922 ++++++++++++++++++++++++++++++------------------------------ R/print.R | 115 +++---- R/utility.R | 6 6 files changed, 537 insertions(+), 528 deletions(-)
Title: 'ADMB' to R Interface Functions
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, Jeff Laake
Maintainer: Ben Bolker
Diff between R2admb versions 0.7.10 dated 2013-09-22 and 0.7.13 dated 2015-04-13
R2admb-0.7.10/R2admb/inst/doc/R2admb.R |only R2admb-0.7.10/R2admb/inst/doc/R2admb.Rnw |only R2admb-0.7.10/R2admb/vignettes/ADMB_runs.gz |only R2admb-0.7.10/R2admb/vignettes/ReedfrogSizepred0.dat |only R2admb-0.7.10/R2admb/vignettes/ReedfrogSizepred0.pin |only R2admb-0.7.10/R2admb/vignettes/betamodel.txt |only R2admb-0.7.10/R2admb/vignettes/cache |only R2admb-0.7.10/R2admb/vignettes/figure |only R2admb-0.7.10/R2admb/vignettes/gopherdat.RData |only R2admb-0.7.10/R2admb/vignettes/reedfrogsizepred.dat |only R2admb-0.7.10/R2admb/vignettes/reedfrogsizepred.pin |only R2admb-0.7.10/R2admb/vignettes/reedfrogsizepred0.par |only R2admb-0.7.10/R2admb/vignettes/rfjunk.tpl |only R2admb-0.7.10/R2admb/vignettes/tadpole_bugs.txt |only R2admb-0.7.10/R2admb/vignettes/toy1_gen.dat |only R2admb-0.7.10/R2admb/vignettes/toy1_gen.par |only R2admb-0.7.10/R2admb/vignettes/toy1_runs.RData |only R2admb-0.7.13/R2admb/DESCRIPTION | 16 R2admb-0.7.13/R2admb/MD5 | 77 +--- R2admb-0.7.13/R2admb/NAMESPACE | 65 ++- R2admb-0.7.13/R2admb/R/plot.admb_hist.r | 5 R2admb-0.7.13/R2admb/R/setup_admb.R | 169 +++++---- R2admb-0.7.13/R2admb/R/std_accessor.r | 33 - R2admb-0.7.13/R2admb/R/utility-funs.R | 327 ++++++++----------- R2admb-0.7.13/R2admb/build/vignette.rds |binary R2admb-0.7.13/R2admb/inst/NEWS.Rd | 20 + R2admb-0.7.13/R2admb/inst/admbtests/toy1.R | 10 R2admb-0.7.13/R2admb/inst/doc/R2admb.pdf |binary R2admb-0.7.13/R2admb/inst/doc/toy1_runs.RData |binary R2admb-0.7.13/R2admb/man/AIC.admb.Rd | 209 +++++------- R2admb-0.7.13/R2admb/man/R2admb-package.Rd | 59 +-- R2admb-0.7.13/R2admb/man/admb_version.Rd | 43 +- R2admb-0.7.13/R2admb/man/compile_admb.Rd | 76 ++-- R2admb-0.7.13/R2admb/man/do_admb.Rd | 268 +++++++-------- R2admb-0.7.13/R2admb/man/extract_gradient.Rd | 47 +- R2admb-0.7.13/R2admb/man/find_large_cor.Rd | 54 +-- R2admb-0.7.13/R2admb/man/mcmc.control.Rd | 130 +++---- R2admb-0.7.13/R2admb/man/plot.admb_hist.Rd | 50 +- R2admb-0.7.13/R2admb/man/read_pars.Rd | 119 +++--- R2admb-0.7.13/R2admb/man/read_plt.Rd | 50 +- R2admb-0.7.13/R2admb/man/run.control.Rd | 101 ++--- R2admb-0.7.13/R2admb/man/setup_admb.Rd | 47 +- R2admb-0.7.13/R2admb/man/write_pin.Rd | 79 ++-- R2admb-0.7.13/R2admb/vignettes/R2admb.Rnw | 113 +++--- R2admb-0.7.13/R2admb/vignettes/ReedfrogSizepred1.tpl |only 45 files changed, 1055 insertions(+), 1112 deletions(-)
Title: Functions to Inline C, C++, Fortran Function Calls from R
Description: Functionality to dynamically define R functions and S4 methods
with inlined C, C++ or Fortran code supporting .C and .Call calling conventions.
Author: Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel,
Romain Francois, Karline Soetaert
Maintainer: Dirk Eddelbuettel
Diff between inline versions 0.3.13 dated 2013-08-08 and 0.3.14 dated 2015-04-13
DESCRIPTION | 20 +++++++++-------- MD5 | 17 ++++++++------- NAMESPACE | 14 +++++++++--- R/cfunction.R | 47 ++++++++++++++++++++++++++++++++++------- R/cxxfunction.R | 2 - R/utilities.R |only README.md |only inst/NEWS.Rd | 14 ++++++++++++ man/cfunction.Rd | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++++-- man/internals.Rd | 2 - man/utilities.Rd |only 11 files changed, 147 insertions(+), 31 deletions(-)
Title: Basics of Certificates and Structured Products Valuation
Description: Collection of pricing by duplication methods for popular structured products ("Zertifikate").
Author: Stefan Wilhelm
Maintainer: Stefan Wilhelm
Diff between fCertificates versions 0.5-3 dated 2014-03-02 and 0.5-4 dated 2015-04-13
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NEWS | 5 +++++ inst/CITATION | 5 ++--- man/BonusProCertificate.Rd | 4 ++-- 5 files changed, 20 insertions(+), 16 deletions(-)
Title: Age-Period-Cohort Analysis
Description: Functions for age-period-cohort analysis. The data can be organised in matrices indexed by age-cohort, age-period or cohort-period. The data can include dose and response or just doses. The statistical model is a generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort factors. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) is used. Thus, the analysis does not rely on ad hoc identification.
Author: Bent Nielsen
Maintainer: Bent Nielsen
Diff between apc versions 1.0 dated 2014-08-30 and 1.1 dated 2015-04-13
apc-1.0/apc/COPYING |only apc-1.0/apc/R/apc_data.r |only apc-1.0/apc/R/apc_fit.r |only apc-1.0/apc/R/apc_get_index.r |only apc-1.0/apc/R/apc_identify.r |only apc-1.0/apc/R/apc_plot_data.r |only apc-1.0/apc/R/apc_plot_fit.r |only apc-1.0/apc/man/apc-package.Rd |only apc-1.1/apc/CHANGES |only apc-1.1/apc/DESCRIPTION | 10 ++-- apc-1.1/apc/MD5 | 48 +++++++++++++------ apc-1.1/apc/NEWS |only apc-1.1/apc/R/apc_data.R |only apc-1.1/apc/R/apc_fit.R |only apc-1.1/apc/R/apc_get_index.R |only apc-1.1/apc/R/apc_identify.R |only apc-1.1/apc/R/apc_plot_data.R |only apc-1.1/apc/R/apc_plot_fit.R |only apc-1.1/apc/build |only apc-1.1/apc/inst/CHANGES |only apc-1.1/apc/inst/CITATION | 11 ++++ apc-1.1/apc/inst/COPYING |only apc-1.1/apc/inst/doc |only apc-1.1/apc/man/apc.data.list.Rd | 14 ++++- apc-1.1/apc/man/apc.get.design.Rd | 4 + apc-1.1/apc/man/apc.get.index.Rd | 8 ++- apc-1.1/apc/man/apc.identify.Rd | 77 ++++++++++++++++++++++++++++--- apc-1.1/apc/man/apc.plot.fit.Rd | 86 ++++++++++++++++++++++++++++------- apc-1.1/apc/man/apc_1.1-package.Rd |only apc-1.1/apc/man/data.asbestos.Rd | 15 ++---- apc-1.1/apc/man/data.loss.BZ.Rd |only apc-1.1/apc/man/data.loss.TA.Rd |only apc-1.1/apc/man/data.loss.VNJ.Rd |only apc-1.1/apc/man/vector.2.triangle.Rd |only apc-1.1/apc/vignettes |only 35 files changed, 213 insertions(+), 60 deletions(-)