Title: Dimension Reduction and Estimation Methods
Description: We provide a rich collection of linear and nonlinear
dimension reduction techniques implemented using 'RcppArmadillo'.
The question on what we should use as the target dimension is
addressed by intrinsic dimension estimation methods introduced as well.
For more details on dimensionality techniques, see the paper by
Ma and Zhu (2013) <doi:10.1111/j.1751-5823.2012.00182.x> if you are interested in
statistical approach, or Engel, Huttenberger, and Hamann (2012)
<doi:10.4230/OASIcs.VLUDS.2011.135> for a broader cross-disciplinary overview.
Author: Kisung You [aut, cre],
Donggun Kim [ctb],
Yoon Mo Jung [ctb]
Maintainer: Kisung You <kyou@nd.edu>
Diff between Rdimtools versions 0.1.1 dated 2017-09-24 and 0.1.2 dated 2017-11-13
DESCRIPTION | 19 ++++--- MD5 | 113 ++++++++++++++++++++++++--------------------- NAMESPACE | 4 + R/RcppExports.R | 11 ++++ R/auxiliary_checks.R |only R/init.R | 2 R/linear_FA.R | 6 +- R/linear_ICA.R | 5 +- R/linear_LDA.R |only R/linear_LMDS.R | 7 ++ R/linear_LPP.R | 5 +- R/linear_MDS.R | 4 - R/linear_NPE.R | 5 +- R/linear_PCA.R | 5 +- R/linear_RNDPROJ.R | 13 ++--- R/nonlinear_CISOMAP.R | 5 +- R/nonlinear_DM.R | 8 ++- R/nonlinear_ISOMAP.R | 5 +- R/nonlinear_KECA.R | 5 +- R/nonlinear_KPCA.R | 5 +- R/nonlinear_LAPEIG.R | 5 +- R/nonlinear_LISOMAP.R | 5 +- R/nonlinear_LLE.R | 6 +- R/nonlinear_LTSA.R | 7 +- R/nonlinear_MVU.R | 5 +- R/nonlinear_PLP.R | 5 +- R/nonlinear_REE.R |only R/nonlinear_SAMMON.R | 5 ++ R/nonlinear_SNE.R | 4 + R/nonlinear_TSNE.R | 5 +- R/package-Rdimtools.R | 4 + build |only inst |only man/Rdimtools.Rd | 2 man/linear_FA.Rd | 9 ++- man/linear_ICA.Rd | 3 - man/linear_LDA.Rd |only man/linear_LMDS.Rd | 5 +- man/linear_LPP.Rd | 3 - man/linear_MDS.Rd | 3 - man/linear_NPE.Rd | 3 - man/linear_PCA.Rd | 3 - man/linear_RNDPROJ.Rd | 9 +-- man/nonlinear_CISOMAP.Rd | 3 - man/nonlinear_DM.Rd | 4 - man/nonlinear_ISOMAP.Rd | 3 - man/nonlinear_KECA.Rd | 3 - man/nonlinear_KPCA.Rd | 3 - man/nonlinear_LAPEIG.Rd | 3 - man/nonlinear_LISOMAP.Rd | 3 - man/nonlinear_LLE.Rd | 3 - man/nonlinear_LTSA.Rd | 4 - man/nonlinear_MVU.Rd | 3 - man/nonlinear_PLP.Rd | 3 - man/nonlinear_REE.Rd |only man/nonlinear_SAMMON.Rd | 3 + man/nonlinear_SNE.Rd | 2 man/nonlinear_TSNE.Rd | 3 - src/RcppExports.cpp | 17 ++++++ src/methods_nonlinear.cpp | 115 ++++++++++++++++++++++++++++++++++++++++++++++ src/methods_nonlinear.h | 5 ++ 61 files changed, 342 insertions(+), 156 deletions(-)
Title: Diagnostics to Assess the Effects of Text Preprocessing
Decisions
Description: Functions to assess the effects of different text preprocessing decisions on the inferences drawn from the resulting document-term matrices they generate.
Author: Matthew J. Denny <mdenny@psu.edu>, Arthur Spirling
<as9934@nyu.edu>,
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between preText versions 0.6.0 dated 2017-07-08 and 0.6.1 dated 2017-11-13
DESCRIPTION | 8 +++--- MD5 | 16 ++++++------- R/preText.R | 2 - R/topic_novelty_score.R | 2 - R/wordfish_rank_plot.R | 6 ++--- R/zzz.R | 2 - build/vignette.rds |binary inst/doc/getting_started_with_preText.html | 34 ++++++++++++++--------------- man/preText.Rd | 2 - 9 files changed, 36 insertions(+), 36 deletions(-)
Title: Facilitates Clustered Binary Data Generation, and Estimation of
Intracluster Correlation Coefficient (ICC) for Binary Data
Description: Assists in generating binary clustered data, estimates of Intracluster Correlation coefficient (ICC) for binary response in 16 different methods, and 5 different types of confidence intervals.
Author: Akhtar Hossain [aut, cre],
Hrishikesh Chakraborty [aut]
Maintainer: Akhtar Hossain <mhossain@email.sc.edu>
Diff between ICCbin versions 1.1 dated 2017-09-19 and 1.1.1 dated 2017-11-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/rcbin.R | 33 +++++++++++++++++++-------------- man/rcbin.Rd | 15 ++++++++++----- 4 files changed, 36 insertions(+), 26 deletions(-)
Title: A Test Environment for HTTP Requests
Description: Testing code and packages that communicate with remote servers can
be painful. Dealing with authentication, bootstrapping server state,
cleaning up objects that may get created during the test run, network
flakiness, and other complications can make testing seem too costly to
bother with. But it doesn't need to be that hard. This package enables one
to test all of the logic on the R sides of the API in your package without
requiring access to the remote service. Importantly, it provides three test
contexts that mock the network connection in different ways, and it offers
additional expectations to assert that HTTP requests were--or were
not--made. It also allows you to record real API responses to use as mocks
in tests. With these tools, one can test that code is making the intended
requests and that it handles the expected responses correctly, all without
depending on a connection to a remote API.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest versions 2.3.2 dated 2017-10-20 and 2.3.4 dated 2017-11-13
httptest-2.3.2/httptest/inst/doc/httptest.md |only httptest-2.3.2/httptest/inst/doc/redacting.md |only httptest-2.3.4/httptest/DESCRIPTION | 8 httptest-2.3.4/httptest/MD5 | 20 httptest-2.3.4/httptest/NEWS.md | 5 httptest-2.3.4/httptest/R/mock-api.R | 18 httptest-2.3.4/httptest/inst/doc/httptest.Rmd | 16 httptest-2.3.4/httptest/inst/doc/httptest.html | 601 +++++++----------------- httptest-2.3.4/httptest/inst/doc/redacting.Rmd | 16 httptest-2.3.4/httptest/inst/doc/redacting.html | 440 +++++------------ httptest-2.3.4/httptest/vignettes/httptest.Rmd | 16 httptest-2.3.4/httptest/vignettes/redacting.Rmd | 16 12 files changed, 399 insertions(+), 757 deletions(-)
Title: Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou and Kleanthi Lakiotaki
Maintainer: Manos Papadakis <papadakm95@gmail.com>
Diff between Rfast versions 1.8.4 dated 2017-09-23 and 1.8.5 dated 2017-11-13
Rfast-1.8.4/Rfast/src/col_meds_p.cpp |only Rfast-1.8.5/Rfast/DESCRIPTION | 8 Rfast-1.8.5/Rfast/MD5 | 519 +++++++++++--------- Rfast-1.8.5/Rfast/NAMESPACE | 2 Rfast-1.8.5/Rfast/NEWS.md | 154 +---- Rfast-1.8.5/Rfast/R/AddToNamespace.R | 4 Rfast-1.8.5/Rfast/R/Order.R | 8 Rfast-1.8.5/Rfast/R/Rank.R |only Rfast-1.8.5/Rfast/R/Var.R | 12 Rfast-1.8.5/Rfast/R/beta.mle.R | 24 Rfast-1.8.5/Rfast/R/betaprime.mle.R | 43 - Rfast-1.8.5/Rfast/R/bs.reg.R |only Rfast-1.8.5/Rfast/R/cat.goftests.R |only Rfast-1.8.5/Rfast/R/cauchy.mle.R | 66 +- Rfast-1.8.5/Rfast/R/chisq.mle.R | 23 Rfast-1.8.5/Rfast/R/colAll.R |only Rfast-1.8.5/Rfast/R/colCountValues.R |only Rfast-1.8.5/Rfast/R/colMads.R | 8 Rfast-1.8.5/Rfast/R/colMedians.R | 6 Rfast-1.8.5/Rfast/R/colOrder.R | 8 Rfast-1.8.5/Rfast/R/colRanks.R |only Rfast-1.8.5/Rfast/R/colVars.R | 6 Rfast-1.8.5/Rfast/R/colaucs.R | 14 Rfast-1.8.5/Rfast/R/colcvs.R |only Rfast-1.8.5/Rfast/R/colgammamle.R | 36 - Rfast-1.8.5/Rfast/R/colvarcomps.mle.R | 66 +- Rfast-1.8.5/Rfast/R/colvarcomps.mom.R | 4 Rfast-1.8.5/Rfast/R/colvm.mle.R | 60 +- Rfast-1.8.5/Rfast/R/colweibull.mle.R |only Rfast-1.8.5/Rfast/R/comb_n.R | 2 Rfast-1.8.5/Rfast/R/cor.fbed.R |only Rfast-1.8.5/Rfast/R/corpairs.R | 12 Rfast-1.8.5/Rfast/R/count_value.R | 6 Rfast-1.8.5/Rfast/R/cova.R | 8 Rfast-1.8.5/Rfast/R/ct.mle.R | 44 - Rfast-1.8.5/Rfast/R/dirimultinom.mle.R |only Rfast-1.8.5/Rfast/R/dirknn.R |only Rfast-1.8.5/Rfast/R/dista.R | 14 Rfast-1.8.5/Rfast/R/fish.kent.R | 2 Rfast-1.8.5/Rfast/R/floyd.R | 2 Rfast-1.8.5/Rfast/R/group.sum.R | 4 Rfast-1.8.5/Rfast/R/knn.R | 6 Rfast-1.8.5/Rfast/R/knn.cv.R | 4 Rfast-1.8.5/Rfast/R/kruskaltest.R | 23 Rfast-1.8.5/Rfast/R/kruskaltests.R | 4 Rfast-1.8.5/Rfast/R/logseries.mle.R | 44 - Rfast-1.8.5/Rfast/R/lower_tri.R | 8 Rfast-1.8.5/Rfast/R/match.coefs.R |only Rfast-1.8.5/Rfast/R/matrnorm.R | 2 Rfast-1.8.5/Rfast/R/med.R | 4 Rfast-1.8.5/Rfast/R/multinom.reg.R | 87 +-- Rfast-1.8.5/Rfast/R/mv.eeltest2.R | 8 Rfast-1.8.5/Rfast/R/mvnorm.mle.R | 2 Rfast-1.8.5/Rfast/R/nth.R | 8 Rfast-1.8.5/Rfast/R/ompr.R |only Rfast-1.8.5/Rfast/R/prop.reg.R | 18 Rfast-1.8.5/Rfast/R/qpois.reg.R | 5 Rfast-1.8.5/Rfast/R/rint.mle.R | 53 -- Rfast-1.8.5/Rfast/R/rint.regs.R | 4 Rfast-1.8.5/Rfast/R/rmdp.R | 20 Rfast-1.8.5/Rfast/R/rowAll.R |only Rfast-1.8.5/Rfast/R/rowCountValues.R |only Rfast-1.8.5/Rfast/R/rowMads.R | 8 Rfast-1.8.5/Rfast/R/rowMedians.R | 8 Rfast-1.8.5/Rfast/R/rowOrder.R | 8 Rfast-1.8.5/Rfast/R/rowRanks.R |only Rfast-1.8.5/Rfast/R/rowcvs.R |only Rfast-1.8.5/Rfast/R/rowrange.R | 5 Rfast-1.8.5/Rfast/R/score.betaregs.R | 4 Rfast-1.8.5/Rfast/R/sftest.R | 30 - Rfast-1.8.5/Rfast/R/spml.mle.R | 53 -- Rfast-1.8.5/Rfast/R/spml.regs.R |only Rfast-1.8.5/Rfast/R/transpose.R |only Rfast-1.8.5/Rfast/R/ttests.R | 14 Rfast-1.8.5/Rfast/R/upper_tri.R | 8 Rfast-1.8.5/Rfast/R/vartests.R | 4 Rfast-1.8.5/Rfast/R/weib.reg.R |only Rfast-1.8.5/Rfast/R/weibull.mle.R | 42 - Rfast-1.8.5/Rfast/man/AddToNamespace.Rd | 5 Rfast-1.8.5/Rfast/man/Diag.fill.Rd | 11 Rfast-1.8.5/Rfast/man/Dist.Rd | 5 Rfast-1.8.5/Rfast/man/Lbeta.Rd | 6 Rfast-1.8.5/Rfast/man/Lchoose.Rd | 7 Rfast-1.8.5/Rfast/man/Lgamma.Rd | 5 Rfast-1.8.5/Rfast/man/Log.Rd | 8 Rfast-1.8.5/Rfast/man/Pmax.Rd | 5 Rfast-1.8.5/Rfast/man/Rank.Rd |only Rfast-1.8.5/Rfast/man/Rfast-package.Rd | 6 Rfast-1.8.5/Rfast/man/Rnorm.Rd | 2 Rfast-1.8.5/Rfast/man/Sort.Rd | 5 Rfast-1.8.5/Rfast/man/Table.Rd | 5 Rfast-1.8.5/Rfast/man/Var.Rd | 13 Rfast-1.8.5/Rfast/man/XopY.sum.Rd | 2 Rfast-1.8.5/Rfast/man/allbetas.Rd | 4 Rfast-1.8.5/Rfast/man/ancovas.Rd | 1 Rfast-1.8.5/Rfast/man/beta.mle.Rd | 42 - Rfast-1.8.5/Rfast/man/bic.corfsreg.Rd | 1 Rfast-1.8.5/Rfast/man/bic.fs.reg.Rd | 1 Rfast-1.8.5/Rfast/man/bs.reg.Rd |only Rfast-1.8.5/Rfast/man/cat.goftests.Rd |only Rfast-1.8.5/Rfast/man/check_data.Rd | 1 Rfast-1.8.5/Rfast/man/cholesky.Rd | 11 Rfast-1.8.5/Rfast/man/circlin.cor.Rd | 1 Rfast-1.8.5/Rfast/man/colAny.Rd | 21 Rfast-1.8.5/Rfast/man/colMads.Rd | 9 Rfast-1.8.5/Rfast/man/colMedians.Rd | 9 Rfast-1.8.5/Rfast/man/colMins.Rd | 8 Rfast-1.8.5/Rfast/man/colOrder.Rd | 24 Rfast-1.8.5/Rfast/man/colRanks.Rd |only Rfast-1.8.5/Rfast/man/colShuffle.Rd | 2 Rfast-1.8.5/Rfast/man/colTabulate.Rd | 2 Rfast-1.8.5/Rfast/man/colTrue.Rd | 4 Rfast-1.8.5/Rfast/man/colVars.Rd | 16 Rfast-1.8.5/Rfast/man/colaucs.Rd | 1 Rfast-1.8.5/Rfast/man/colcvs.Rd |only Rfast-1.8.5/Rfast/man/coldiffs.Rd | 5 Rfast-1.8.5/Rfast/man/colkurtosis.Rd | 3 Rfast-1.8.5/Rfast/man/colmeans.Rd | 8 Rfast-1.8.5/Rfast/man/colnormal.mle.Rd | 38 - Rfast-1.8.5/Rfast/man/colnth.Rd | 16 Rfast-1.8.5/Rfast/man/colpoisdisp.tests.Rd | 5 Rfast-1.8.5/Rfast/man/colprods.Rd | 5 Rfast-1.8.5/Rfast/man/colrange.Rd | 8 Rfast-1.8.5/Rfast/man/colrint.regbx.Rd | 3 Rfast-1.8.5/Rfast/man/colrow.zero.Rd | 8 Rfast-1.8.5/Rfast/man/colsums.Rd | 5 Rfast-1.8.5/Rfast/man/colvarcomps.mom.Rd | 24 Rfast-1.8.5/Rfast/man/colwatsons.Rd | 3 Rfast-1.8.5/Rfast/man/comb_n.Rd | 5 Rfast-1.8.5/Rfast/man/cor.fbed.Rd |only Rfast-1.8.5/Rfast/man/cor.fsreg.Rd | 3 Rfast-1.8.5/Rfast/man/corpairs.Rd | 26 - Rfast-1.8.5/Rfast/man/correls.Rd | 3 Rfast-1.8.5/Rfast/man/count_value.Rd | 35 - Rfast-1.8.5/Rfast/man/cova.Rd | 3 Rfast-1.8.5/Rfast/man/dcor.Rd | 5 Rfast-1.8.5/Rfast/man/design_matrix.Rd | 5 Rfast-1.8.5/Rfast/man/dirknn.Rd |only Rfast-1.8.5/Rfast/man/dista.Rd | 19 Rfast-1.8.5/Rfast/man/dmvnorm.Rd | 5 Rfast-1.8.5/Rfast/man/edist.Rd | 5 Rfast-1.8.5/Rfast/man/eel.test1.Rd | 2 Rfast-1.8.5/Rfast/man/eel.test2.Rd | 6 Rfast-1.8.5/Rfast/man/expregs.Rd | 5 Rfast-1.8.5/Rfast/man/fish.kent.Rd | 1 Rfast-1.8.5/Rfast/man/floyd.Rd | 4 Rfast-1.8.5/Rfast/man/fs.reg.Rd | 5 Rfast-1.8.5/Rfast/man/ftest.Rd | 6 Rfast-1.8.5/Rfast/man/ftests.Rd | 4 Rfast-1.8.5/Rfast/man/g2Test.Rd | 1 Rfast-1.8.5/Rfast/man/g2Test_univariate.Rd | 5 Rfast-1.8.5/Rfast/man/g2tests.Rd | 1 Rfast-1.8.5/Rfast/man/gammamle.Rd | 16 Rfast-1.8.5/Rfast/man/geom.regs.Rd | 3 Rfast-1.8.5/Rfast/man/glm_logistic.Rd | 2 Rfast-1.8.5/Rfast/man/group.sum.Rd | 7 Rfast-1.8.5/Rfast/man/hd.eigen.Rd | 3 Rfast-1.8.5/Rfast/man/is.symmetric.Rd | 9 Rfast-1.8.5/Rfast/man/knn.Rd | 8 Rfast-1.8.5/Rfast/man/knn.cv.Rd | 8 Rfast-1.8.5/Rfast/man/kruskaltests.Rd | 6 Rfast-1.8.5/Rfast/man/list.ftests.Rd | 4 Rfast-1.8.5/Rfast/man/lmfit.Rd | 7 Rfast-1.8.5/Rfast/man/logistic.cat1.Rd | 2 Rfast-1.8.5/Rfast/man/logistic_only.Rd | 5 Rfast-1.8.5/Rfast/man/lower_tri.Rd | 40 - Rfast-1.8.5/Rfast/man/mat.mat.Rd | 8 Rfast-1.8.5/Rfast/man/match.coefs.Rd |only Rfast-1.8.5/Rfast/man/matrix.sum.Rd | 11 Rfast-1.8.5/Rfast/man/matrnorm.Rd | 2 Rfast-1.8.5/Rfast/man/med.Rd | 12 Rfast-1.8.5/Rfast/man/mediandir.Rd | 1 Rfast-1.8.5/Rfast/man/multinom.mle.Rd | 13 Rfast-1.8.5/Rfast/man/multinom.reg.Rd | 7 Rfast-1.8.5/Rfast/man/multinom.regs.Rd | 3 Rfast-1.8.5/Rfast/man/mvbetas.Rd | 4 Rfast-1.8.5/Rfast/man/mvnorm.mle.Rd | 3 Rfast-1.8.5/Rfast/man/normlog.regs.Rd | 3 Rfast-1.8.5/Rfast/man/ompr.Rd |only Rfast-1.8.5/Rfast/man/pc.skel.Rd | 3 Rfast-1.8.5/Rfast/man/percent.ttest.Rd | 1 Rfast-1.8.5/Rfast/man/percent.ttests.Rd | 1 Rfast-1.8.5/Rfast/man/poisdisp.test.Rd | 4 Rfast-1.8.5/Rfast/man/poisson.anova.Rd | 6 Rfast-1.8.5/Rfast/man/poisson.anovas.Rd | 5 Rfast-1.8.5/Rfast/man/poisson_only.Rd | 5 Rfast-1.8.5/Rfast/man/regression.Rd | 7 Rfast-1.8.5/Rfast/man/rep_col.Rd | 3 Rfast-1.8.5/Rfast/man/rint.regbx.Rd | 4 Rfast-1.8.5/Rfast/man/rint.regs.Rd | 13 Rfast-1.8.5/Rfast/man/rm.lines.Rd | 2 Rfast-1.8.5/Rfast/man/rmdp.Rd | 6 Rfast-1.8.5/Rfast/man/rmvlaplace.Rd | 2 Rfast-1.8.5/Rfast/man/rmvnorm.Rd | 1 Rfast-1.8.5/Rfast/man/rowMins.Rd | 10 Rfast-1.8.5/Rfast/man/rowTrue.Rd | 7 Rfast-1.8.5/Rfast/man/score.betaregs.Rd | 7 Rfast-1.8.5/Rfast/man/score.glms.Rd | 3 Rfast-1.8.5/Rfast/man/sftests.Rd | 2 Rfast-1.8.5/Rfast/man/sort_mat.Rd | 13 Rfast-1.8.5/Rfast/man/sort_unique.Rd | 2 Rfast-1.8.5/Rfast/man/spml.regs.Rd |only Rfast-1.8.5/Rfast/man/squareform.Rd | 2 Rfast-1.8.5/Rfast/man/standardise.Rd | 4 Rfast-1.8.5/Rfast/man/submatrix.Rd | 5 Rfast-1.8.5/Rfast/man/tobit.mle.Rd | 2 Rfast-1.8.5/Rfast/man/total.dist.Rd | 5 Rfast-1.8.5/Rfast/man/transpose.Rd |only Rfast-1.8.5/Rfast/man/ttest.Rd | 3 Rfast-1.8.5/Rfast/man/ttest1.Rd | 2 Rfast-1.8.5/Rfast/man/ttests.Rd | 9 Rfast-1.8.5/Rfast/man/twoway.anovas.Rd | 3 Rfast-1.8.5/Rfast/man/univglms.Rd | 16 Rfast-1.8.5/Rfast/man/varcomps.mom.Rd | 9 Rfast-1.8.5/Rfast/man/vm.mle.Rd | 45 - Rfast-1.8.5/Rfast/man/weib.reg.Rd |only Rfast-1.8.5/Rfast/man/which_isFactor.Rd | 6 Rfast-1.8.5/Rfast/src/Var.cpp | 23 Rfast-1.8.5/Rfast/src/add_to_namespace.cpp | 25 Rfast-1.8.5/Rfast/src/bs_reg.cpp |only Rfast-1.8.5/Rfast/src/calc_bs_reg.cpp |only Rfast-1.8.5/Rfast/src/calc_bs_reg.h |only Rfast-1.8.5/Rfast/src/calc_k_nn.cpp | 55 +- Rfast-1.8.5/Rfast/src/calc_k_nn.h | 3 Rfast-1.8.5/Rfast/src/calc_k_nn_cv.cpp | 4 Rfast-1.8.5/Rfast/src/calc_k_nn_cv.h | 3 Rfast-1.8.5/Rfast/src/col_row_all.cpp |only Rfast-1.8.5/Rfast/src/col_row_all_p.cpp |only Rfast-1.8.5/Rfast/src/col_row_count_values.cpp |only Rfast-1.8.5/Rfast/src/col_row_count_values_p.cpp |only Rfast-1.8.5/Rfast/src/col_row_mads.cpp | 124 ++++ Rfast-1.8.5/Rfast/src/col_row_mads_p.cpp |only Rfast-1.8.5/Rfast/src/col_row_meds.cpp | 26 - Rfast-1.8.5/Rfast/src/col_row_meds_p.cpp |only Rfast-1.8.5/Rfast/src/col_row_order_p.cpp |only Rfast-1.8.5/Rfast/src/col_row_ranks.cpp |only Rfast-1.8.5/Rfast/src/col_row_ranks_p.cpp |only Rfast-1.8.5/Rfast/src/colrint_mle.cpp |only Rfast-1.8.5/Rfast/src/colweibull_mle.cpp |only Rfast-1.8.5/Rfast/src/count_value.cpp | 46 - Rfast-1.8.5/Rfast/src/cts.h | 2 Rfast-1.8.5/Rfast/src/dir_knn.cpp |only Rfast-1.8.5/Rfast/src/dista.cpp | 83 +++ Rfast-1.8.5/Rfast/src/dists_vec.cpp | 2 Rfast-1.8.5/Rfast/src/floyd_john.cpp | 14 Rfast-1.8.5/Rfast/src/geom_regs.cpp | 40 - Rfast-1.8.5/Rfast/src/gold_rat2.cpp | 13 Rfast-1.8.5/Rfast/src/gold_rat3.cpp | 11 Rfast-1.8.5/Rfast/src/group_mad.cpp | 1 Rfast-1.8.5/Rfast/src/group_sum.cpp | 49 + Rfast-1.8.5/Rfast/src/init.c | 147 ++++- Rfast-1.8.5/Rfast/src/is_element.cpp | 8 Rfast-1.8.5/Rfast/src/k_nn.cpp | 13 Rfast-1.8.5/Rfast/src/k_nn_cv.cpp | 13 Rfast-1.8.5/Rfast/src/lower_tri.cpp | 74 +- Rfast-1.8.5/Rfast/src/med.cpp | 39 - Rfast-1.8.5/Rfast/src/mn.cpp | 52 +- Rfast-1.8.5/Rfast/src/mn.h | 9 Rfast-1.8.5/Rfast/src/multinom_regs.cpp | 206 +++----- Rfast-1.8.5/Rfast/src/my_k_sorted_array.cpp |only Rfast-1.8.5/Rfast/src/my_k_sorted_array.h |only Rfast-1.8.5/Rfast/src/normlog_reg.cpp | 18 Rfast-1.8.5/Rfast/src/normlog_regs.cpp | 30 - Rfast-1.8.5/Rfast/src/nth.cpp | 47 + Rfast-1.8.5/Rfast/src/only_glm.cpp | 87 +++ Rfast-1.8.5/Rfast/src/only_glm.h | 5 Rfast-1.8.5/Rfast/src/partial_sort.cpp | 45 + Rfast-1.8.5/Rfast/src/rank.cpp |only Rfast-1.8.5/Rfast/src/reg_lib.cpp | 591 ++++++++++++----------- Rfast-1.8.5/Rfast/src/reg_lib.h | 52 +- Rfast-1.8.5/Rfast/src/reg_lib2.cpp |only Rfast-1.8.5/Rfast/src/reg_lib2.h |only Rfast-1.8.5/Rfast/src/regression.cpp | 26 - Rfast-1.8.5/Rfast/src/rint_mle.cpp |only Rfast-1.8.5/Rfast/src/rint_reg.cpp | 29 - Rfast-1.8.5/Rfast/src/rint_regs.cpp | 132 +++-- Rfast-1.8.5/Rfast/src/rmdp.cpp | 15 Rfast-1.8.5/Rfast/src/sort_mat.cpp | 11 Rfast-1.8.5/Rfast/src/sort_mat_stable.cpp | 29 - Rfast-1.8.5/Rfast/src/spml_mle.cpp | 117 ++-- Rfast-1.8.5/Rfast/src/spml_reg.cpp |only Rfast-1.8.5/Rfast/src/spml_regs.cpp |only Rfast-1.8.5/Rfast/src/system_files.cpp | 2 Rfast-1.8.5/Rfast/src/system_files.h | 1 Rfast-1.8.5/Rfast/src/templates.h | 26 - Rfast-1.8.5/Rfast/src/transpose.cpp |only Rfast-1.8.5/Rfast/src/upper_tri.cpp | 74 +- Rfast-1.8.5/Rfast/src/varcomps_mle.cpp | 4 Rfast-1.8.5/Rfast/src/weib_reg.cpp |only Rfast-1.8.5/Rfast/src/weibull_mle.cpp |only 290 files changed, 2790 insertions(+), 2218 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-03 0.1.0
Title: Formula-Driven Table Generation
Description: Computes and displays complex tables of summary statistics.
Output may be in LaTeX, HTML, plain text, or an R
matrix for further processing.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between tables versions 0.8 dated 2017-01-03 and 0.8.3 dated 2017-11-13
DESCRIPTION | 8 ++- MD5 | 34 +++++++-------- R/Hline.R | 10 ++-- R/pseudo.R | 3 - R/tabular.R | 89 +++++++++++++++++++++++++++------------- inst/NEWS | 9 ++++ inst/doc/HTML.html | 98 ++++++++++++++++++++++----------------------- inst/doc/tables.R | 73 ++++++++++++++++++--------------- inst/doc/tables.Rnw | 16 +++++++ inst/doc/tables.pdf |binary inst/todo.txt | 7 ++- man/AllObs.Rd | 2 man/DropEmpty.Rd | 2 man/Heading.Rd | 14 +++++- man/Hline.Rd | 5 +- man/Literal.Rd | 5 +- vignettes/tables.Rnw | 16 +++++++ vignettes/tables.Rout.save | 23 ++++++++-- 18 files changed, 266 insertions(+), 148 deletions(-)
Title: Measuring Stakeholder Influence
Description: Proposes an original instrument for measuring stakeholder influence on the development of an infrastructure project that is carried through by a municipality, drawing on stakeholder classifications (Mitchell, Agle, & Wood, 1997) and input-output modelling (Hester & Adams, 2013). Mitchell R., Agle B.R., & Wood D.J. <doi:10.2307/259247> Hester, P.T., & Adams, K.M. (2013) <doi:10.1016/j.procs.2013.09.282>.
Author: Anna Zamojska [aut],
Piotr Zientara [aut],
Sebastian Susmarski [aut],
Lech Kujawski [aut, cre]
Maintainer: Lech Kujawski <lech.kujawski@ug.edu.pl>
Diff between StakeholderAnalysis versions 1.1 dated 2017-10-24 and 1.2 dated 2017-11-13
StakeholderAnalysis-1.1/StakeholderAnalysis/man/StakeholderAnalysis_1.1-package.Rd |only StakeholderAnalysis-1.2/StakeholderAnalysis/DESCRIPTION | 8 ++++---- StakeholderAnalysis-1.2/StakeholderAnalysis/MD5 | 8 ++++---- StakeholderAnalysis-1.2/StakeholderAnalysis/R/kod_do_11.R | 2 ++ StakeholderAnalysis-1.2/StakeholderAnalysis/build/partial.rdb |binary StakeholderAnalysis-1.2/StakeholderAnalysis/man/StakeholderAnalysis_1.2-package.Rd |only 6 files changed, 10 insertions(+), 8 deletions(-)
More information about StakeholderAnalysis at CRAN
Permanent link
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Joe Cheng [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb],
Aniruddha Ghosh [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 2.5-8 dated 2016-06-02 and 2.6-7 dated 2017-11-13
raster-2.5-8/raster/R/artith.R |only raster-2.5-8/raster/R/nchar.R |only raster-2.5-8/raster/src/aggregate.c |only raster-2.5-8/raster/src/aggregate_get.c |only raster-2.5-8/raster/src/direction.c |only raster-2.5-8/raster/src/dist_util.c |only raster-2.5-8/raster/src/dist_util.h |only raster-2.5-8/raster/src/distance.c |only raster-2.5-8/raster/src/geolib.c |only raster-2.5-8/raster/src/terrain.c |only raster-2.5-8/raster/src/xyCell.cpp |only raster-2.6-7/raster/ChangeLog | 36 ++ raster-2.6-7/raster/DESCRIPTION | 20 - raster-2.6-7/raster/MD5 | 245 ++++++++-------- raster-2.6-7/raster/NAMESPACE | 8 raster-2.6-7/raster/R/AAAClasses.R | 17 - raster-2.6-7/raster/R/RcppExports.R | 56 ++- raster-2.6-7/raster/R/aggregate_3d.R | 393 ++++---------------------- raster-2.6-7/raster/R/approxNA.R | 28 - raster-2.6-7/raster/R/area.R | 33 -- raster-2.6-7/raster/R/arith.R |only raster-2.6-7/raster/R/as.data.frame.R | 4 raster-2.6-7/raster/R/boundaries.R | 8 raster-2.6-7/raster/R/buffer.R | 78 +++++ raster-2.6-7/raster/R/cellRowCol.R | 6 raster-2.6-7/raster/R/cellStats.R | 16 - raster-2.6-7/raster/R/cellsFromExtent.R | 14 raster-2.6-7/raster/R/clamp.R | 4 raster-2.6-7/raster/R/compare_Logical.R | 137 ++++++++- raster-2.6-7/raster/R/cover.R | 5 raster-2.6-7/raster/R/coverBrick.R | 11 raster-2.6-7/raster/R/dataType.R | 6 raster-2.6-7/raster/R/direction.R | 7 raster-2.6-7/raster/R/distance.R | 4 raster-2.6-7/raster/R/distanceFromPoints.R | 8 raster-2.6-7/raster/R/distanceRows.R | 2 raster-2.6-7/raster/R/erase.R | 101 +++++- raster-2.6-7/raster/R/extension.R | 6 raster-2.6-7/raster/R/extent.R | 20 + raster-2.6-7/raster/R/extract.R | 13 raster-2.6-7/raster/R/extractLines.R | 4 raster-2.6-7/raster/R/fixDBFnames.R | 2 raster-2.6-7/raster/R/focal.R | 32 +- raster-2.6-7/raster/R/freq.R | 3 raster-2.6-7/raster/R/getData.R | 17 - raster-2.6-7/raster/R/getValuesBlock.R | 16 - raster-2.6-7/raster/R/getValuesFocal.R | 2 raster-2.6-7/raster/R/gridDistance2.R | 12 raster-2.6-7/raster/R/hdr.R | 14 raster-2.6-7/raster/R/hdrEnvi.R | 1 raster-2.6-7/raster/R/hdrRaster.R | 4 raster-2.6-7/raster/R/indexReplaceBrick.R | 2 raster-2.6-7/raster/R/inifile.R | 4 raster-2.6-7/raster/R/intersect_sp.R | 45 ++ raster-2.6-7/raster/R/isLonLat.R | 4 raster-2.6-7/raster/R/kernelDensity.R |only raster-2.6-7/raster/R/layerize.R | 4 raster-2.6-7/raster/R/makeProjString.R | 2 raster-2.6-7/raster/R/makeTiles.R |only raster-2.6-7/raster/R/mask.R | 8 raster-2.6-7/raster/R/newPLot.R | 2 raster-2.6-7/raster/R/plot2rasters.R | 1 raster-2.6-7/raster/R/pointdistance.R | 20 + raster-2.6-7/raster/R/print.R | 93 +++--- raster-2.6-7/raster/R/projectRaster.R | 22 - raster-2.6-7/raster/R/rasterFromASCII.R | 2 raster-2.6-7/raster/R/rasterFromFile.R | 4 raster-2.6-7/raster/R/rasterFromGDAL.R | 2 raster-2.6-7/raster/R/rasterFromIDRISI.R | 2 raster-2.6-7/raster/R/rasterFromRasterFile.R | 6 raster-2.6-7/raster/R/rasterFromSAGA.R | 2 raster-2.6-7/raster/R/rasterOptions.R | 18 - raster-2.6-7/raster/R/rasterToPoints.R | 16 - raster-2.6-7/raster/R/rasterize.R | 14 raster-2.6-7/raster/R/rasterizePolygons.R | 29 + raster-2.6-7/raster/R/rasterizePolygons3.R | 2 raster-2.6-7/raster/R/reclassify.R | 4 raster-2.6-7/raster/R/rowSums.R | 4 raster-2.6-7/raster/R/sampleRegular.R | 31 +- raster-2.6-7/raster/R/sf.R |only raster-2.6-7/raster/R/show.R | 12 raster-2.6-7/raster/R/subset.R | 1 raster-2.6-7/raster/R/terrain.R | 8 raster-2.6-7/raster/R/tmpFile.R | 11 raster-2.6-7/raster/R/trim.R | 16 - raster-2.6-7/raster/R/union_sp.R | 6 raster-2.6-7/raster/R/update.R | 20 + raster-2.6-7/raster/R/xyResolution.R | 2 raster-2.6-7/raster/R/zApply.R | 2 raster-2.6-7/raster/R/zonal.R | 24 - raster-2.6-7/raster/build/vignette.rds |binary raster-2.6-7/raster/inst/doc/Raster.pdf |binary raster-2.6-7/raster/inst/doc/functions.pdf |binary raster-2.6-7/raster/inst/doc/rasterfile.pdf |binary raster-2.6-7/raster/man/aggregate.Rd | 6 raster-2.6-7/raster/man/area.Rd | 19 - raster-2.6-7/raster/man/brick.Rd | 2 raster-2.6-7/raster/man/buffer.Rd | 4 raster-2.6-7/raster/man/cellsFromExtent.Rd | 12 raster-2.6-7/raster/man/distanceFromPoints.Rd | 25 + raster-2.6-7/raster/man/erase.Rd | 26 + raster-2.6-7/raster/man/extent.Rd | 1 raster-2.6-7/raster/man/extract.Rd | 1 raster-2.6-7/raster/man/getValuesBlock.Rd | 9 raster-2.6-7/raster/man/hdrFiles.Rd | 3 raster-2.6-7/raster/man/mask.Rd | 7 raster-2.6-7/raster/man/predict.Rd | 4 raster-2.6-7/raster/man/projectRaster.Rd | 2 raster-2.6-7/raster/man/raster.Rd | 2 raster-2.6-7/raster/man/rasterize.Rd | 29 - raster-2.6-7/raster/man/setValues.Rd | 8 raster-2.6-7/raster/man/trim.Rd | 3 raster-2.6-7/raster/man/update.Rd | 17 - raster-2.6-7/raster/src/RcppExports.cpp | 281 ++++++++++++++---- raster-2.6-7/raster/src/aggregate.cpp |only raster-2.6-7/raster/src/aggregate.h |only raster-2.6-7/raster/src/area.cpp |only raster-2.6-7/raster/src/area.h |only raster-2.6-7/raster/src/bilinear.cpp | 1 raster-2.6-7/raster/src/broom.c | 2 raster-2.6-7/raster/src/clamp.c | 2 raster-2.6-7/raster/src/distance.cpp |only raster-2.6-7/raster/src/distance.h |only raster-2.6-7/raster/src/edge.c | 2 raster-2.6-7/raster/src/focal_fun.c | 2 raster-2.6-7/raster/src/focal_get.c | 2 raster-2.6-7/raster/src/focal_sum.c | 2 raster-2.6-7/raster/src/intersect.c | 4 raster-2.6-7/raster/src/layerize.c | 2 raster-2.6-7/raster/src/pointinpoly.c | 2 raster-2.6-7/raster/src/r_terrain.c |only raster-2.6-7/raster/src/rcpp_aggregate.cpp |only raster-2.6-7/raster/src/rcpp_distance.cpp |only raster-2.6-7/raster/src/rcpp_xyCell.cpp |only raster-2.6-7/raster/src/reclass.c | 2 raster-2.6-7/raster/src/util.c | 4 136 files changed, 1398 insertions(+), 928 deletions(-)
Title: IPEA Common Functions
Description: The most used functions on IPEA (Instituto de Pesquisa Economica Aplicada).
Most of functions deal with brazilian names.
It can guess the women single's name, extract prepositions or extract the first name.
Author: Gustavo Coelho [aut, cre],
Lucas Mation [aut],
Daniel Lima [ctb],
Igor Noberto [ctb],
João Victor Machado [ctb]
Maintainer: Gustavo Coelho <gustavo.coelho@ipea.gov.br>
Diff between utilsIPEA versions 0.0.4 dated 2017-10-24 and 0.0.5 dated 2017-11-13
DESCRIPTION | 16 +++++++++------- MD5 | 20 +++++++++++++------- NAMESPACE | 5 +++++ NEWS.md | 11 +++++++++++ R/data.R |only R/extrai_nome_proprio.R | 17 +++++++++-------- R/geocode.R |only R/text_functions.R | 23 ++++++++--------------- data |only man/geocod_base.Rd |only man/ident_erros_munic_galileo.Rd |only man/remove_preposicao_nomes.Rd | 4 +++- tests/testthat/test_extrai_nome_proprio.R | 2 +- tests/testthat/test_ident_erros_munic_galileo.R |only 14 files changed, 59 insertions(+), 39 deletions(-)
Title: Port of 'Dparser' Package
Description: A Scannerless GLR parser/parser generator. Note that GLR standing for "generalized LR", where L stands for "left-to-right" and
R stands for "rightmost (derivation)". For more information see <https://en.wikipedia.org/wiki/GLR_parser>. This parser is based on the Tomita
(1987) algorithm. (Paper can be found at <http://acl-arc.comp.nus.edu.sg/archives/acl-arc-090501d3/data/pdf/anthology-PDF/J/J87/J87-1004.pdf>).
The original 'dparser' package documentation can be found at <http://dparser.sourceforge.net/>. This allows you to add mini-languages to R (like
RxODE's ODE mini-language Wang, Hallow, and James 2015 <DOI:10.1002/psp4.12052>) or to parse other languages like 'NONMEM' to automatically translate
them to R code. To use this in your code, add a LinkingTo dparser in your DESCRIPTION file and instead of using #include <dparse.h> use
#include <dparser.h>. This also provides a R-based port of the make_dparser <http://dparser.sourceforge.net/d/make_dparser.cat> command called
mkdparser(). Additionally you can parse an arbitrary grammar within R using the dparse() function, which works on most OSes and is mainly for grammar
testing. The fastest parsing, of course, occurs at the C level, and is suggested.
Author: Matthew Fidler [aut, cre],
John Plevyak [aut, cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between dparser versions 0.1.7 dated 2017-10-05 and 0.1.8 dated 2017-11-13
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ R/version.R | 2 +- man/dparser-package.Rd | 2 +- src/Makevars | 3 --- src/parse.c | 2 +- src/write_tables.c | 22 +++++++++++----------- 7 files changed, 27 insertions(+), 30 deletions(-)
Title: Fitting Semi-Parametric Generalized log-Gamma Regression Models
Description: Set of tools to fit a linear multiple or semi-parametric regression
models and non-informative right-censoring may be considered. Under this setup, the localization parameter of the response variable distribution is modeled by using linear multiple regression
or semi-parametric functions, whose non-parametric components may be approximated
by natural cubic spline or P-splines. The supported distribution for the model error is a generalized log-gamma distribution which includes
the generalized extreme value distribution as an important special case.
Author: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com> and G. Paula and L. Vanegas
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between sglg versions 0.1.0 dated 2017-09-22 and 0.1.1 dated 2017-11-13
sglg-0.1.0/sglg/R/deBoor.R |only sglg-0.1.0/sglg/man/Bspl.N.Rd |only sglg-0.1.0/sglg/man/Nbas.Rd |only sglg-0.1.0/sglg/man/bspline.Rd |only sglg-0.1.0/sglg/man/deBoor.Rd |only sglg-0.1.0/sglg/man/plotnpc.Rd |only sglg-0.1.0/sglg/man/spl.S.Rd |only sglg-0.1.0/sglg/man/vknt.Rd |only sglg-0.1.1/sglg/DESCRIPTION | 8 sglg-0.1.1/sglg/MD5 | 73 +- sglg-0.1.1/sglg/NAMESPACE | 4 sglg-0.1.1/sglg/R/Gu.R |only sglg-0.1.1/sglg/R/blockgs.R |only sglg-0.1.1/sglg/R/code_example_sglg.R | 55 - sglg-0.1.1/sglg/R/deBoor2.R |only sglg-0.1.1/sglg/R/entropy.R |only sglg-0.1.1/sglg/R/envelope.sglg.R | 55 - sglg-0.1.1/sglg/R/glg.R | 316 +++++---- sglg-0.1.1/sglg/R/influence.sglg.R | 197 +++--- sglg-0.1.1/sglg/R/lss.R | 18 sglg-0.1.1/sglg/R/plot.npc.R | 28 sglg-0.1.1/sglg/R/plot.sglg.R | 22 sglg-0.1.1/sglg/R/sglg.R | 816 ++++++++++--------------- sglg-0.1.1/sglg/R/shape.R | 18 sglg-0.1.1/sglg/R/ssurvglg.R | 249 +++---- sglg-0.1.1/sglg/R/summary.sglg.R | 18 sglg-0.1.1/sglg/R/survglg.R | 356 +++++----- sglg-0.1.1/sglg/R/sysdata.rda |binary sglg-0.1.1/sglg/man/Gu.Rd |only sglg-0.1.1/sglg/man/deBoor2.Rd |only sglg-0.1.1/sglg/man/entropy.Rd |only sglg-0.1.1/sglg/man/envelope.sglg.Rd | 6 sglg-0.1.1/sglg/man/glg.Rd | 46 + sglg-0.1.1/sglg/man/influence.sglg.Rd | 16 sglg-0.1.1/sglg/man/lss.Rd | 9 sglg-0.1.1/sglg/man/plot.npc.Rd |only sglg-0.1.1/sglg/man/sglg.Rd | 23 sglg-0.1.1/sglg/man/shape.Rd | 14 sglg-0.1.1/sglg/man/ssurvglg.Rd | 17 sglg-0.1.1/sglg/man/survglg.Rd | 8 sglg-0.1.1/sglg/tests/testthat/Rplots.pdf |binary sglg-0.1.1/sglg/tests/testthat/test_entropy.R |only sglg-0.1.1/sglg/tests/testthat/test_lss.R | 2 sglg-0.1.1/sglg/tests/testthat/test_sglg.R | 6 sglg-0.1.1/sglg/tests/testthat/test_ssurvglg.R | 5 sglg-0.1.1/sglg/tests/testthat/test_survglg.R | 9 46 files changed, 1188 insertions(+), 1206 deletions(-)
Title: Interface Between R and the OpenStreetMap-Based Routing Service
OSRM
Description: An interface between R and the OSRM API. OSRM is a routing
service based on OpenStreetMap data. See <http://project-osrm.org/> for more
information. This package allows to compute distances (travel time and
kilometric distance) between points and travel time matrices.
Author: Timothée Giraud [cre, aut],
Robin Cura [ctb],
Matthieu Viry [ctb]
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between osrm versions 3.0.2 dated 2017-08-10 and 3.1.0 dated 2017-11-13
osrm-3.0.2/osrm/R/intern.R |only osrm-3.1.0/osrm/DESCRIPTION | 15 +--- osrm-3.1.0/osrm/MD5 | 42 ++++++----- osrm-3.1.0/osrm/NEWS | 12 +++ osrm-3.1.0/osrm/R/old_ex.R |only osrm-3.1.0/osrm/R/osrmIsochrone.R | 60 ++++++++++------ osrm-3.1.0/osrm/R/osrmRoute.R | 58 +++++++--------- osrm-3.1.0/osrm/R/osrmTable.R | 75 +++++++++------------ osrm-3.1.0/osrm/R/osrmTrip.R | 56 +++++++++------ osrm-3.1.0/osrm/R/package.R | 44 +++--------- osrm-3.1.0/osrm/R/utils.R |only osrm-3.1.0/osrm/R/zzz.R | 11 +-- osrm-3.1.0/osrm/README.md | 21 +++-- osrm-3.1.0/osrm/data/berlin.RData |only osrm-3.1.0/osrm/data/com.RData |binary osrm-3.1.0/osrm/man/apotheke.df.Rd |only osrm-3.1.0/osrm/man/apotheke.sp.Rd |only osrm-3.1.0/osrm/man/com.Rd | 123 +++++++++++++++++++++++++++++++++- osrm-3.1.0/osrm/man/dst.Rd | 121 +++++++++++++++++++++++++++++++++ osrm-3.1.0/osrm/man/osrm.Rd | 13 --- osrm-3.1.0/osrm/man/osrmIsochrone.Rd | 33 +++++---- osrm-3.1.0/osrm/man/osrmRoute.Rd | 32 +++++--- osrm-3.1.0/osrm/man/osrmTable.Rd | 38 +++++----- osrm-3.1.0/osrm/man/osrmTrip.Rd | 31 +++++--- osrm-3.1.0/osrm/man/src.Rd | 125 ++++++++++++++++++++++++++++++++++- 25 files changed, 644 insertions(+), 266 deletions(-)
Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package allows various cartographic representations such as proportional symbols, chroropleth, typology, flows or discontinuities maps. It also offers several features enhancing the graphic presentation of maps like cartographic palettes, layout elements (scale, north arrow, title...), labels, legends or access to some cartographic APIs. See Giraud and Lambert (2017) <doi:10.1007/978-3-319-57336-6_13>.
Author: Timothée Giraud [cre, aut],
Nicolas Lambert [aut],
Ian Fellows [cph] (no overlap algorithm for labels, from wordcloud
package)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between cartography versions 2.0.1 dated 2017-09-25 and 2.0.2 dated 2017-11-13
DESCRIPTION | 22 ++++++++----------- MD5 | 32 ++++++++++++++-------------- NEWS | 15 +++++++++++++ R/getGridLayer.R | 2 - R/gradLinkLayer.R | 4 +-- R/gradLinkTypoLayer.R | 2 - R/labelLayer.R | 4 +++ R/layoutLayer.R | 51 ++++++++++++++++++++++++++++++++++------------ R/propLinkLayer.R | 2 - R/propSymbolsChoroLayer.R | 4 ++- R/propSymbolsLayer.R | 4 ++- R/propSymbolsTypoLayer.R | 4 ++- R/utils.R | 21 +----------------- README.md | 5 ++-- inst/doc/cartography.html | 9 ++++---- man/getGridLayer.Rd | 2 - man/layoutLayer.Rd | 13 ++++++++--- 17 files changed, 116 insertions(+), 80 deletions(-)
Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting
for unmeasured confounding and misclassification of the
exposure/outcome, or both. It follows the bias analysis methods and
examples from the book by Lash T.L, Fox M.P, and Fink A.K.
"Applying Quantitative Bias Analysis to Epidemiologic Data",
('Springer', 2009).
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <denis.haine@gmail.com>
Diff between episensr versions 0.9.1 dated 2017-09-12 and 0.9.2 dated 2017-11-13
DESCRIPTION | 12 MD5 | 38 - NAMESPACE | 1 NEWS.md | 5 R/probsens.R | 2 R/probsens.conf.R | 137 ++----- R/probsens.irr.R | 2 R/probsens.irr.conf.R | 24 - R/probsens.sel.R | 49 -- build/vignette.rds |binary inst/doc/episensr.R | 12 inst/doc/episensr.Rmd | 47 ++ inst/doc/episensr.html | 798 +++++++++++++++++++++-------------------- man/probsens.Rd | 2 man/probsens.conf.Rd | 6 man/probsens.irr.Rd | 2 man/probsens.irr.conf.Rd | 6 man/probsens.sel.Rd | 10 tests/testthat/test-probsens.R | 38 - vignettes/episensr.Rmd | 47 ++ 20 files changed, 650 insertions(+), 588 deletions(-)
Title: Quantitative Support of Decision Making under Uncertainty
Description: Supporting the quantitative analysis of binary welfare based
decision making processes using Monte Carlo simulations. Decision support
is given on two levels: (i) The actual decision level is to choose between
two alternatives under probabilistic uncertainty. This package calculates
the optimal decision based on maximizing expected welfare. (ii) The meta
decision level is to allocate resources to reduce the uncertainty in the
underlying decision problem, i.e to increase the current information to
improve the actual decision making process. This problem is dealt with
using the Value of Information Analysis. The Expected Value of
Information for arbitrary prospective estimates can be calculated as
well as Individual Expected Value of Perfect Information.
The probabilistic calculations are done via Monte Carlo
simulations. This Monte Carlo functionality can be used on its own.
Author: Eike Luedeling [cre, aut] (ICRAF),
Lutz Göhring [aut] (ICRAF and Lutz Göhring Consulting)
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between decisionSupport versions 1.102.1 dated 2017-10-06 and 1.102.2 dated 2017-11-13
DESCRIPTION | 16 ++-- MD5 | 100 +++++++++++++-------------- NAMESPACE | 1 R/paramtnormci_numeric.R | 1 R/rdistq_fit.R | 1 man/as.data.frame.mcSimulation.Rd | 1 man/chance_event.Rd | 1 man/corMat-set.Rd | 1 man/corMat.Rd | 1 man/decisionSupport-package.Rd | 10 +- man/decisionSupport.Rd | 1 man/discount.Rd | 1 man/estimate.Rd | 3 man/estimate1d.Rd | 3 man/estimate_read_csv.Rd | 1 man/estimate_write_csv.Rd | 1 man/eviSimulation.Rd | 1 man/gompertz_yield.Rd | 1 man/hist.eviSimulation.Rd | 11 +- man/hist.mcSimulation.Rd | 11 +- man/hist.welfareDecisionAnalysis.Rd | 11 +- man/individualEvpiSimulation.Rd | 1 man/make_CPT.Rd | 7 - man/mcSimulation.Rd | 1 man/paramtnormci_fit.Rd | 1 man/paramtnormci_numeric.Rd | 2 man/plainNames2data.frameNames.Rd | 2 man/plsr.mcSimulation.Rd | 1 man/print.mcSimulation.Rd | 1 man/print.summary.eviSimulation.Rd | 1 man/print.summary.mcSimulation.Rd | 1 man/print.summary.welfareDecisionAnalysis.Rd | 1 man/random.Rd | 4 - man/random.estimate.Rd | 1 man/random.estimate1d.Rd | 1 man/random_state.Rd | 1 man/rdist90ci_exact.Rd | 1 man/rdistq_fit.Rd | 1 man/rmvnorm90ci_exact.Rd | 1 man/row.names.estimate.Rd | 5 - man/rtnorm90ci.Rd | 3 man/sample_CPT.Rd | 1 man/sample_simple_CPT.Rd | 1 man/sort.summary.eviSimulation.Rd | 1 man/summary.eviSimulation.Rd | 1 man/summary.mcSimulation.Rd | 1 man/summary.welfareDecisionAnalysis.Rd | 1 man/temp_situations.Rd | 1 man/vv.Rd | 1 man/welfareDecisionAnalysis.Rd | 1 tests/testthat.R | 3 51 files changed, 99 insertions(+), 128 deletions(-)
More information about decisionSupport at CRAN
Permanent link
Title: Bayesian Exponential Random Graph Models
Description: Set of tools to analyse Bayesian exponential random graph models.
Author: Alberto Caimo [aut, cre],
Lampros Bouranis [aut],
Florian Maire [ctb],
Nial Friel [ctb]
Maintainer: Alberto Caimo <acaimo.stats@gmail.com>
Diff between Bergm versions 4.0.0 dated 2017-03-14 and 4.1.0 dated 2017-11-13
DESCRIPTION | 12 ++++++------ MD5 | 28 ++++++++++++++++++---------- NAMESPACE | 31 ++++++++++++++++++++++++------- R/Bergm-package.R |only R/adjustPL.R |only R/bergm.R | 27 +++++---------------------- R/bergm.output.R | 21 ++++++++++----------- R/bgof.R | 18 ++++++------------ R/calibrate.bergm.R | 11 ++++------- R/evidence_CJ.R |only R/evidence_powerP.R |only man/Bergm-package.Rd |only man/adjustPL.Rd |only man/bergm.Rd | 24 +++++------------------- man/bergm.output.Rd | 2 +- man/bgof.Rd | 16 +++++----------- man/calibrate.bergm.Rd | 6 ++++-- man/evidence_CJ.Rd |only man/evidence_powerP.Rd |only 19 files changed, 88 insertions(+), 108 deletions(-)
Title: Graph Based Multiple Comparison Procedures
Description: Functions and a graphical user interface for graphical described
multiple test procedures.
Author: Kornelius Rohmeyer [aut, cre],
Florian Klinglmueller [aut]
Maintainer: Kornelius Rohmeyer <rohmeyer@small-projects.de>
Diff between gMCP versions 0.8-10 dated 2015-08-31 and 0.8-11 dated 2017-11-13
DESCRIPTION | 16 ++- MD5 | 113 +++++++++++++------------- NAMESPACE | 2 NEWS | 9 ++ R/exampleGraphs.R | 18 +++- R/helperGUI.R | 4 R/modifyGraphs.R | 16 ++- R/onLoad.R | 13 -- R/startGUIs.R | 41 ++++++++- R/subVariables.R | 6 - build/vignette.rds |binary inst/CITATION | 2 inst/doc/AQuickStart.pdf |binary inst/doc/gMCP.Rnw | 5 - inst/doc/gMCP.pdf |binary inst/doc/parametric.pdf |binary java/org/af/gMCP/gui/power/PowerReq.java | 2 java/org/af/gMCP/gui/power/PowerReqPanel.java | 6 - man/bdiagNA.Rd | 6 + man/bonferroni.test.Rd | 4 man/bonferroni.trimmed.simes.test.Rd | 8 + man/calcPower.Rd | 24 ++--- man/corMatWizard.Rd | 7 - man/doInterim.Rd | 9 +- man/exampleGraphs.Rd | 10 +- man/extractPower.Rd | 4 man/gMCP-package.Rd | 4 man/gMCP.Rd | 13 +- man/gMCP.extended.Rd | 11 +- man/gMCPReport.Rd | 4 man/generateBounds.Rd | 6 - man/generatePvals.Rd | 4 man/generateTest.Rd | 8 + man/generateWeights.Rd | 8 + man/getJavaInfo.Rd | 4 man/graph2latex.Rd | 10 +- man/graphAnalysis.Rd | 6 + man/graphGUI.Rd | 10 +- man/graphTest.Rd | 11 +- man/joinGraphs.Rd | 6 + man/matrix2graph.Rd | 6 + man/parametric.test.Rd | 2 man/placeNodes.Rd | 6 + man/plotSimCI.Rd | 8 + man/rejectNode.Rd | 4 man/replaceVariables.Rd | 9 +- man/rqmvnorm.Rd | 5 - man/sampSize.Rd | 25 ++--- man/sampSizeCore.Rd | 4 man/secondStageTest.Rd | 9 +- man/simes.on.subsets.test.Rd | 4 man/simes.test.Rd | 4 man/subgraph.Rd | 6 + man/substituteEps.Rd | 6 + man/unitTestsGMCP.Rd | 6 + man/weighted.test.functions.Rd | 6 - src/gMCP_init.c |only vignettes/gMCP.Rnw | 5 - 58 files changed, 350 insertions(+), 195 deletions(-)
Title: RethinkDB Client
Description: Simple, native 'RethinkDB' client.
Author: Miron B. Kursa
Maintainer: Miron B. Kursa <M.Kursa@icm.edu.pl>
Diff between rethinker versions 1.0.0 dated 2015-12-10 and 1.1.0 dated 2017-11-13
DESCRIPTION | 10 +-- MD5 | 32 +++++----- NAMESPACE | 1 R/reql.R | 121 +++++++++++++++++++++++++------------- inst |only man/close.RethinkDB_connection.Rd | 1 man/close.RethinkDB_cursor.Rd | 1 man/cursorNext.Rd | 1 man/cursorToList.Rd | 1 man/drainConnection.Rd | 1 man/isCursorEmpty.Rd | 1 man/isOpened.Rd | 1 man/openConnection.Rd | 1 man/print.RethinkDB_connection.Rd | 1 man/print.RethinkDB_cursor.Rd | 1 man/r.Rd | 23 ++++++- tests/testthat/testAst.R | 16 +++++ tests/testthat/testTransactions.R |only 18 files changed, 142 insertions(+), 71 deletions(-)
Title: Planning, Conducting, and Analysing Single-Arm Phase II Studies
Description: Purpose of this package is it to plan, monitor and evaluate
oncological phase II studies. In general this kind of studies are single-arm
trials with planned interim analysis and binary endpoint. To meet the resulting
requirements, the package provides functions to calculate and evaluate 'Simon's
two-stage designs' and 'so-called' 'subset designs'. If you are unfamiliar with
this package a good starting point is to take a closer look at the functions
getSolutions() and getSolutionsSub1().The web-based tool (<https://imbi.shinyapps.io/phaseII-app/>)
extends the functionality of our R package by means of a proper dealing with over- and underrunning.
The R function binom.test of the 'stats' R package and the package 'binom' might be
helpful to assess the performance of the corresponding one-stage design as a reference.
Author: Marius Wirths
Maintainer: Johannes Krisam <krisam@imbi.uni-heidelberg.de>
Diff between OneArmPhaseTwoStudy versions 0.1.6 dated 2016-05-23 and 1.0.3 dated 2017-11-13
DESCRIPTION | 16 MD5 | 68 +-- NAMESPACE | 5 R/zzz.R | 634 ++++++++++++++----------------- inst |only man/getCE.Rd | 3 man/getCP.Rd | 9 man/getCP_simon.Rd | 3 man/getD_distributeToOne.Rd | 5 man/getD_equally.Rd | 7 man/getD_none.Rd | 5 man/getD_proportionally.Rd | 9 man/getN2.Rd | 3 man/getP.Rd | 1 man/getSolutions.Rd | 12 man/getSolutionsSub1.Rd | 8 man/get_CI.Rd | 3 man/get_UMVUE_GMS.Rd | 3 man/get_UMVUE_GMS_subset_second_only.Rd | 5 man/get_UMVUE_GMS_subset_second_total.Rd | 3 man/get_conditionalPower.Rd | 5 man/get_confidence_set.Rd | 5 man/get_p_KC.Rd | 3 man/get_p_exact_subset.Rd | 3 man/get_r2_flex.Rd | 5 man/plot_confidence_set.Rd | 3 man/plot_simon_study_state.Rd | 5 man/plot_sub1_study_state.Rd | 5 man/setSimonParams.Rd | 3 man/setSub1Params.Rd | 3 man/setupSimon.Rd | 3 man/setupSub1Design.Rd | 3 man/simon_module.Rd | 4 man/sub1_module.Rd | 2 man/toDataframe.Rd | 3 src/RcppExports.cpp |only 36 files changed, 368 insertions(+), 489 deletions(-)
More information about OneArmPhaseTwoStudy at CRAN
Permanent link
Title: Extending 'Dendrogram' Functionality in R
Description: Offers a set of functions for extending
'dendrogram' objects in R, letting you visualize and compare trees of
'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different 'dendrograms' to one another.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Gavin Simpson [ctb],
Gregory Jefferis [aut, ctb] (imported code from his dendroextras
package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Zuguang Gu [ctb] (circlize author),
Cath [ctb] (https://github.com/CathG),
John Ma [ctb] (https://github.com/JohnMCMa),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 1.5.2 dated 2017-03-28 and 1.6.0 dated 2017-11-13
ChangeLog | 275 +++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 20 +- MD5 | 50 +++---- NAMESPACE | 5 NEWS | 196 +++++++++++++++------------ NEWS.md | 198 ++++++++++++++++------------ R/circlize.R | 8 + R/color_branches.R | 34 ++++ R/depth.R |only R/ggdend.R | 8 - R/prune.R | 88 +++++++++--- R/pvclust.R | 114 +++++++++++++++- R/rect.dendrogram.R | 21 ++ README.md | 31 +++- build/vignette.rds |binary inst/CITATION | 6 inst/doc/Cluster_Analysis.html | 8 - inst/doc/FAQ.html | 8 - inst/doc/Quick_Introduction.html | 8 - inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 80 +++++------ man/color_branches.Rd | 21 ++ man/depth.Rd |only man/ggdend.Rd | 5 man/prune.Rd | 21 ++ man/pvrect2.Rd |only man/reindex_dend.Rd |only vignettes/introduction.Rmd | 2 28 files changed, 913 insertions(+), 296 deletions(-)
Title: Tokenization, Parts of Speech Tagging, Lemmatization and
Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic
'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
parsing' of raw text. Next to text parsing, the package also allows you to train
annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
at <http://universaldependencies.org/format.html>. The techniques are explained
in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
with UDPipe', available at <doi:10.18653/v1/K17-3009>.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph],
Milan Straka [cph],
Jana Straková [cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between udpipe versions 0.1.1 dated 2017-09-13 and 0.2 dated 2017-11-13
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Title: Clustering Mutations using High Throughput Sequencing (HTS) Data
Description: Using HTS data, clusters mutations in order to recreate putative
clones from the data provided. It requires genotype at the location of the
variant as well as the depth of coverage and number of reads supporting the
mutation. Additional information may be provided, such as the contamination
in the tumor sample. This package also provides a function QuantumCat() which
simulates data obtained from tumor sequencing.
Author: Paul Deveau [aut, cre]
Maintainer: Paul Deveau <quantumclone.package@gmail.com>
Diff between QuantumClone versions 1.0.0.4 dated 2017-03-08 and 1.0.0.6 dated 2017-11-13
DESCRIPTION | 10 - MD5 | 28 +-- NAMESPACE | 6 R/QuantumCat.R | 5 R/QuantumClone.R | 12 + R/plots.R | 190 ++++++++++++++++++------- inst/doc/Release.Rmd | 13 + inst/doc/Release.html | 134 ++++++++++++++++- inst/doc/Use_case.R | 14 + inst/doc/Use_case.Rmd | 18 +- inst/doc/Use_case.html | 22 +- tests/reproducible_testing/Rscript/Figure3.pdf |only tests/reproducible_testing/Rscript/data.df |only tests/reproducible_testing/Rscript/figure3.Rmd | 4 vignettes/Release.Rmd | 13 + vignettes/Use_case.Rmd | 18 +- 16 files changed, 373 insertions(+), 114 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for
quantitative text analysis in R. Provides functionality for corpus management,
creating and manipulating tokens and ngrams, exploring keywords in context,
forming and manipulating sparse matrices
of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and
distances, applying content dictionaries, applying supervised and unsupervised machine learning,
visually representing text and text analyses, and more.
Author: Kenneth Benoit [aut, cre, cph],
Kohei Watanabe [ctb],
Paul Nulty [ctb],
Adam Obeng [ctb],
Haiyan Wang [ctb],
Benjamin Lauderdale [ctb],
Will Lowe [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.99.12 dated 2017-10-06 and 0.99.22 dated 2017-11-13
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Title: Component Models for Multi-Way Data
Description: Fits multi-way component models via alternating least squares algorithms with optional constraints: orthogonal, non-negative, unimodal, monotonic, periodic, smooth, or structure. Fit models include Individual Differences Scaling, Parallel Factor Analysis (1 and 2), Simultaneous Component Analysis, and Tucker Factor Analysis.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between multiway versions 1.0-3 dated 2017-05-19 and 1.0-4 dated 2017-11-13
ChangeLog | 35 ++++++++++++++ DESCRIPTION | 8 +-- MD5 | 48 ++++++++++--------- NAMESPACE | 3 - R/corcondia.R | 33 +++++-------- R/mpinv.R | 14 ++++- R/parafac.R | 110 +++++++++++++++++++++++++++++++------------- R/parafac2.R | 117 +++++++++++++++++++++++++++++++++-------------- R/parafac2_3way.R | 8 +-- R/parafac2_3wayna.R |only R/parafac2_4way.R | 5 -- R/parafac2_4wayna.R |only R/parafac_3wayna.R |only R/parafac_4wayna.R |only R/smpower.R | 20 ++++++-- R/tucker.R | 90 ++++++++++++++++++++++++++---------- R/tucker_3wayna.R |only R/tucker_4wayna.R |only man/USalcohol.Rd | 2 man/corcondia.Rd | 2 man/mpinv.Rd | 5 +- man/multiway-internal.Rd | 6 ++ man/multiway-package.Rd | 2 man/ncenter.Rd | 2 man/parafac.Rd | 21 +++++--- man/parafac2.Rd | 21 +++++--- man/smpower.Rd | 5 +- man/tucker.Rd | 17 ++++-- 28 files changed, 396 insertions(+), 178 deletions(-)
Title: Interactive Cluster Heat Maps Using 'plotly'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand-
alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and
available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to
show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical
method for visualizing high-dimensional data, in which a table of numbers
are encoded as a grid of colored cells. The rows and columns of the matrix
are ordered to highlight patterns and are often accompanied by 'dendrograms'.
'Heatmaps' are used in many fields for visualizing observations, correlations,
missing values patterns, and more. Interactive 'heatmaps' allow the inspection
of specific value by hovering the mouse over a cell, as well as zooming into
a region of the 'heatmap' by dragging a rectangle around the relevant area.
This work is based on the 'ggplot2' and 'plotly.js' engine. It produces
similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed
('plotly.js' is able to handle larger size matrix), the ability to zoom from
the 'dendrogram' panes, and the placing of factor variables in the sides of the
'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Jonathan Sidi [ctb] (https://github.com/yonicd),
Alan O'Callaghan [ctb] (https://github.com/Alanocallaghan),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between heatmaply versions 0.12.1 dated 2017-10-26 and 0.13.0 dated 2017-11-13
ChangeLog | 103 ++++++++++++++++++++++++++++ DESCRIPTION | 10 +- MD5 | 30 ++++---- NAMESPACE | 3 NEWS | 27 +++++++ NEWS.md | 36 +++++++++- R/distfuns.R |only R/heatmaply.R | 40 ++++++++--- R/heatmapr.R | 43 ++++++----- R/plots.R | 51 ++++++++++++-- R/zzz.R | 20 +++-- README.md | 58 +++++++++++----- inst/CITATION | 2 inst/doc/heatmaply.html | 126 +++++++++++++++++------------------ man/heatmaply.Rd | 26 ++++--- tests/testthat/test_heatmaply.R | 66 ------------------ tests/testthat/test_heatmaply_misc.R |only 17 files changed, 425 insertions(+), 216 deletions(-)
Title: Effect Size Computation for Meta Analysis
Description: Implementation of the web-based 'Practical Meta-Analysis Effect Size
Calculator' from David B. Wilson (<http://www.campbellcollaboration.org/escalc/html/EffectSizeCalculator-Home.php>)
in R. Based on the input, the effect size can be returned as standardized mean
difference, Cohen's f, Hedges' g, Pearson's r or Fisher's
transformation z, odds ratio or log odds, or eta squared effect size.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between esc versions 0.3.2 dated 2017-09-27 and 0.4.0 dated 2017-11-13
esc-0.3.2/esc/NEWS |only esc-0.4.0/esc/DESCRIPTION | 12 - esc-0.4.0/esc/MD5 | 81 ++++++------ esc-0.4.0/esc/NAMESPACE | 11 + esc-0.4.0/esc/NEWS.md | 64 ++++++---- esc-0.4.0/esc/R/esc.R | 6 esc-0.4.0/esc/R/esc_2x2.R | 180 ++++++++++++++-------------- esc-0.4.0/esc/R/esc_B.R | 2 esc-0.4.0/esc/R/esc_beta.R | 15 +- esc-0.4.0/esc/R/esc_bin_prop.R | 90 +++++++------- esc-0.4.0/esc/R/esc_chisq.R | 15 +- esc-0.4.0/esc/R/esc_d2etasq.R |only esc-0.4.0/esc/R/esc_d2f.R |only esc-0.4.0/esc/R/esc_d2or.R | 21 ++- esc-0.4.0/esc/R/esc_d2r.R | 23 ++- esc-0.4.0/esc/R/esc_f.R | 4 esc-0.4.0/esc/R/esc_helper.R | 190 +++++++++++++++++++---------- esc-0.4.0/esc/R/esc_mean_gain.R | 2 esc-0.4.0/esc/R/esc_mean_sd.R | 30 +++- esc-0.4.0/esc/R/esc_or2d.R | 22 ++- esc-0.4.0/esc/R/esc_rpb.R | 13 +- esc-0.4.0/esc/R/esc_t.R | 236 ++++++++++++++++++------------------- esc-0.4.0/esc/R/hedges_g.R | 115 ++++++++++++++---- esc-0.4.0/esc/README.md | 166 +++++++++++++------------- esc-0.4.0/esc/build/partial.rdb |binary esc-0.4.0/esc/man/effect_sizes.Rd | 6 esc-0.4.0/esc/man/esc_2x2.Rd | 4 esc-0.4.0/esc/man/esc_B.Rd | 6 esc-0.4.0/esc/man/esc_beta.Rd | 4 esc-0.4.0/esc/man/esc_bin_prop.Rd | 4 esc-0.4.0/esc/man/esc_chisq.Rd | 8 - esc-0.4.0/esc/man/esc_d2etasq.Rd |only esc-0.4.0/esc/man/esc_d2f.Rd |only esc-0.4.0/esc/man/esc_d2logit.Rd | 2 esc-0.4.0/esc/man/esc_d2or.Rd | 4 esc-0.4.0/esc/man/esc_f.Rd | 6 esc-0.4.0/esc/man/esc_mean_gain.Rd | 4 esc-0.4.0/esc/man/esc_mean_sd.Rd | 2 esc-0.4.0/esc/man/esc_mean_se.Rd | 4 esc-0.4.0/esc/man/esc_or2d.Rd | 6 esc-0.4.0/esc/man/esc_phi.Rd | 8 - esc-0.4.0/esc/man/esc_rpb.Rd | 6 esc-0.4.0/esc/man/esc_t.Rd | 4 esc-0.4.0/esc/man/hedges_g.Rd | 49 ++++++- 44 files changed, 866 insertions(+), 559 deletions(-)
Title: Estimator Augmentation and Simulation-Based Inference
Description: Estimator augmentation methods for statistical inference on high-dimensional data,
as described in Zhou, Q. (2014) <arXiv:1401.4425v2>
and Zhou, Q. and Min, S. (2017) <doi:10.1214/17-EJS1309>.
It provides several simulation-based inference methods: (a) Gaussian and
wild multiplier bootstrap for lasso, group lasso, scaled lasso, scaled group
lasso and their de-biased estimators, (b) importance sampler for approximating
p-values in these methods, (c) Markov chain Monte Carlo lasso sampler with
applications in post-selection inference.
Author: Seunghyun Min [aut, cre],
Qing Zhou [aut]
Maintainer: Seunghyun Min <seunghyun@ucla.edu>
Diff between EAinference versions 0.2.1 dated 2017-10-13 and 0.2.2 dated 2017-11-13
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/MHInference.R | 10 +++++++--- R/utility.R | 17 ++++++++++------- inst/doc/EAlasso.Rmd | 7 ++++--- inst/doc/EAlasso.html | 13 +++++++------ man/postInference.MHLS.Rd | 6 +++++- tests/testthat/test-cvlasso.R | 4 ++-- vignettes/EAlasso.Rmd | 7 ++++--- 9 files changed, 50 insertions(+), 36 deletions(-)
Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Description: Provides several cluster-robust variance estimators
(i.e., sandwich estimators) for ordinary and weighted least squares linear
regression models, including the bias-reduced linearization estimator introduced
by Bell and McCaffrey (2002) <http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf>
and developed further by Pustejovsky and Tipton (2017) <DOI:10.1080/07350015.2016.1247004>.
The package includes functions for estimating the variance-
covariance matrix and for testing single- and multiple-contrast hypotheses
based on Wald test statistics. Tests of single regression coefficients use
Satterthwaite or saddle-point corrections. Tests of multiple-contrast hypotheses
use an approximation to Hotelling's T-squared distribution. Methods are
provided for a variety of fitted models, including lm() and mlm objects, glm(),
ivreg (from package 'AER'),
plm() (from package 'plm'),
gls() and lme() (from 'nlme'),
robu() (from 'robumeta'), and
rma.uni() and rma.mv() (from 'metafor').
Author: James Pustejovsky [aut, cre]
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.2.3 dated 2017-08-10 and 0.3.0 dated 2017-11-13
DESCRIPTION | 19 MD5 | 67 +-- NAMESPACE | 2 NEWS | 6 R/CR-adjustments.R | 22 - R/S3-methods.R | 12 R/clubSandwich.R | 100 ++--- R/ivreg.R | 55 +- R/mlm.R |only R/plm.R | 11 R/utilities.R | 14 build/partial.rdb |binary inst/doc/Robust-Variance-Estimation-with-clubSandwich.html | 4 inst/doc/meta-analysis-with-CRVE.html | 42 +- inst/doc/panel-data-CRVE.html | 42 +- man/AchievementAwardsRCT.Rd | 1 man/MortalityRates.Rd | 1 man/SATcoaching.Rd | 1 man/Wald_test.Rd | 1 man/coef_test.Rd | 1 man/dropoutPrevention.Rd | 1 man/impute_covariance_matrix.Rd | 1 man/vcovCR.Rd | 82 ++-- man/vcovCR.glm.Rd | 5 man/vcovCR.gls.Rd | 5 man/vcovCR.ivreg.Rd | 26 - man/vcovCR.lm.Rd | 5 man/vcovCR.lme.Rd | 5 man/vcovCR.mlm.Rd |only man/vcovCR.plm.Rd | 5 man/vcovCR.rma.mv.Rd | 5 man/vcovCR.rma.uni.Rd | 5 man/vcovCR.robu.Rd | 5 tests/testthat/test_ivreg.R | 248 +++++++++++-- tests/testthat/test_lm.R | 2 tests/testthat/test_mlm.R |only 36 files changed, 490 insertions(+), 311 deletions(-)
Title: European Commission Annual Macro-Economic (AMECO) Database
Description: Annual macro-economic database provided by the European Commission.
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>
Diff between ameco versions 0.2.7 dated 2017-05-29 and 0.2.8 dated 2017-11-13
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/data.R | 2 +- build/vignette.rds |binary data/ameco.RData |binary inst/doc/ameco_dataset.html | 10 +++++----- man/ameco.Rd | 3 +-- tests/testthat/tests.R | 2 +- 8 files changed, 20 insertions(+), 21 deletions(-)
Title: Calculating Proportionality Between Vectors of Compositional
Data
Description: The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, this approach lacks statistical validity
when applied to relative data. This includes, for example, biological count data
generated by high-throughput RNA-sequencing, chromatin immunoprecipitation (ChIP),
ChIP-sequencing, Methyl-Capture sequencing, and other techniques. This package
implements several metrics for proportionality, including
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and
rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. This package also
implements several metrics for differential proportionality. Unlike correlation,
these measures give the same result for both relative and absolute data.
Author: Thomas Quinn [aut, cre],
David Lovell [aut],
Ionas Erb [aut],
Anders Bilgrau [ctb],
Greg Gloor [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between propr versions 3.0.7 dated 2017-09-06 and 3.1.1 dated 2017-11-13
propr-3.0.7/propr/inst/doc/f_questions.R |only propr-3.0.7/propr/inst/doc/f_questions.Rmd |only propr-3.0.7/propr/inst/doc/f_questions.html |only propr-3.0.7/propr/src/wt.cpp |only propr-3.0.7/propr/tests/testthat/test-wt.R |only propr-3.0.7/propr/vignettes/f_questions.Rmd |only propr-3.1.1/propr/DESCRIPTION | 6 propr-3.1.1/propr/MD5 | 99 +++---- propr-3.1.1/propr/NAMESPACE | 1 propr-3.1.1/propr/NEWS.md | 32 ++ propr-3.1.1/propr/R/RcppExports.R | 20 - propr-3.1.1/propr/R/deprecated2.R | 66 ++++ propr-3.1.1/propr/R/propd.R | 70 +++-- propr-3.1.1/propr/R/propdViz.R | 8 propr-3.1.1/propr/R/propr.R | 59 ++-- propr-3.1.1/propr/R/theta.R | 171 +++++++++--- propr-3.1.1/propr/build/vignette.rds |binary propr-3.1.1/propr/inst/doc/a_introduction.R | 12 propr-3.1.1/propr/inst/doc/a_introduction.Rmd | 12 propr-3.1.1/propr/inst/doc/a_introduction.html | 10 propr-3.1.1/propr/inst/doc/b_visualization.R | 32 +- propr-3.1.1/propr/inst/doc/b_visualization.Rmd | 32 +- propr-3.1.1/propr/inst/doc/b_visualization.html | 26 - propr-3.1.1/propr/inst/doc/c_indexing.R | 38 +- propr-3.1.1/propr/inst/doc/c_indexing.Rmd | 38 +- propr-3.1.1/propr/inst/doc/c_indexing.html | 20 - propr-3.1.1/propr/inst/doc/d_advanced.R | 32 +- propr-3.1.1/propr/inst/doc/d_advanced.Rmd | 32 +- propr-3.1.1/propr/inst/doc/d_advanced.html | 28 +- propr-3.1.1/propr/inst/doc/e_differential.R | 28 +- propr-3.1.1/propr/inst/doc/e_differential.Rmd | 37 +- propr-3.1.1/propr/inst/doc/e_differential.html | 46 +-- propr-3.1.1/propr/inst/doc/f_moderation.R |only propr-3.1.1/propr/inst/doc/f_moderation.Rmd |only propr-3.1.1/propr/inst/doc/f_moderation.html |only propr-3.1.1/propr/inst/doc/g_questions.R |only propr-3.1.1/propr/inst/doc/g_questions.Rmd |only propr-3.1.1/propr/inst/doc/g_questions.html |only propr-3.1.1/propr/man/alphaThetaW_old.Rd |only propr-3.1.1/propr/man/calculateFDR.Rd | 2 propr-3.1.1/propr/man/calculateFDR_old.Rd | 2 propr-3.1.1/propr/man/calculateTheta.Rd | 5 propr-3.1.1/propr/man/ivar2index.Rd |only propr-3.1.1/propr/man/propd.Rd | 37 +- propr-3.1.1/propr/man/propr.Rd | 4 propr-3.1.1/propr/src/RcppExports.cpp | 55 +--- propr-3.1.1/propr/src/theta.cpp | 269 +++++++++++++++++--- propr-3.1.1/propr/tests/testthat/test-Fstat.R |only propr-3.1.1/propr/tests/testthat/test-aldex2propr.R | 202 +++++++-------- propr-3.1.1/propr/tests/testthat/test-logratio.R | 57 ++-- propr-3.1.1/propr/tests/testthat/test-propd.R | 3 propr-3.1.1/propr/tests/testthat/test-theta.R | 89 +++++- propr-3.1.1/propr/vignettes/a_introduction.Rmd | 12 propr-3.1.1/propr/vignettes/b_visualization.Rmd | 32 +- propr-3.1.1/propr/vignettes/c_indexing.Rmd | 38 +- propr-3.1.1/propr/vignettes/d_advanced.Rmd | 32 +- propr-3.1.1/propr/vignettes/e_differential.Rmd | 37 +- propr-3.1.1/propr/vignettes/f_moderation.Rmd |only propr-3.1.1/propr/vignettes/g_questions.Rmd |only 59 files changed, 1172 insertions(+), 659 deletions(-)
Title: Fetch Climate Data from Environment Canada
Description: The Environment Canada climate archives <http://climate.weather.gc.ca/>
are an important source of data for climate researchers in Canada and world wide.
The repository contains temperature, precipitation, and wind data for more than
8,000 locations. The functions in this package simplify the process of downloading,
subsetting, and manipulating these data for the purposes of more efficient workflows
in climate research.
Author: Dewey Dunnington <dewey@fishandwhistle.net>
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rclimateca versions 0.2 dated 2017-02-27 and 0.4 dated 2017-11-13
rclimateca-0.2/rclimateca/R/getdata.R |only rclimateca-0.2/rclimateca/R/getsites.R |only rclimateca-0.2/rclimateca/README.md |only rclimateca-0.4/rclimateca/DESCRIPTION | 12 ++--- rclimateca-0.4/rclimateca/MD5 | 21 ++++------ rclimateca-0.4/rclimateca/R/climate_getdata.R |only rclimateca-0.4/rclimateca/R/climate_getsites.R |only rclimateca-0.4/rclimateca/man/clear_cache.Rd | 1 rclimateca-0.4/rclimateca/man/climatelong.Rd | 3 - rclimateca-0.4/rclimateca/man/ecclimatelocs.Rd | 1 rclimateca-0.4/rclimateca/man/getClimateData.Rd | 6 +- rclimateca-0.4/rclimateca/man/getClimateDataRaw.Rd | 3 - rclimateca-0.4/rclimateca/man/getClimateSites.Rd | 3 - rclimateca-0.4/rclimateca/tests/testthat/test_allstations.R | 25 +++++++----- 14 files changed, 37 insertions(+), 38 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modelling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.3.7 dated 2017-09-30 and 0.3.8 dated 2017-11-13
DESCRIPTION | 8 MD5 | 24 +- R/ARMA.R | 49 +++- R/Partition_Map.R | 64 +++--- R/Regression.R | 197 ++++++++++---------- inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 4 inst/doc/NNSvignette_Clustering_and_Regression.html | 19 + inst/doc/NNSvignette_Forecasting.Rmd | 8 inst/doc/NNSvignette_Forecasting.html | 17 - man/NNS.ARMA.Rd | 18 + man/NNS.reg.Rd | 11 - vignettes/NNSvignette_Clustering_and_Regression.Rmd | 4 vignettes/NNSvignette_Forecasting.Rmd | 8 13 files changed, 240 insertions(+), 191 deletions(-)
Title: Interchange Tools for Multi-Parameter Spatiotemporal Data
Description: Formatting and structuring multi-parameter spatiotemporal data
is often a time-consuming task. This package offers functions and data structures
designed to easily organize and visualize these data for applications in geology,
paleolimnology, dendrochronology, and paleoclimate.
Author: Authors@R: person("Dewey", "Dunnington", role = c("aut", "cre"),
email = "dewey@fishandwhistle.net")
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between mudata versions 0.1 dated 2017-02-27 and 0.1.1 dated 2017-11-13
mudata-0.1.1/mudata/DESCRIPTION | 8 +- mudata-0.1.1/mudata/MD5 | 76 +++++++++++------------ mudata-0.1.1/mudata/NAMESPACE | 6 - mudata-0.1.1/mudata/R/mudata.R | 8 ++ mudata-0.1.1/mudata/R/namespace.R |only mudata-0.1.1/mudata/man/aggregate.qtag.long.Rd | 1 mudata-0.1.1/mudata/man/as.qtag.Rd | 1 mudata-0.1.1/mudata/man/autoplot.mudata.Rd | 1 mudata-0.1.1/mudata/man/biplot.mudata.Rd | 1 mudata-0.1.1/mudata/man/condense.tags.Rd | 1 mudata-0.1.1/mudata/man/expand.tags.Rd | 1 mudata-0.1.1/mudata/man/group.Rd | 1 mudata-0.1.1/mudata/man/id.vars.Rd | 5 - mudata-0.1.1/mudata/man/is.summarised.Rd | 1 mudata-0.1.1/mudata/man/kentvillegreenwood.Rd | 1 mudata-0.1.1/mudata/man/long.Rd | 1 mudata-0.1.1/mudata/man/longbiplot.Rd | 3 mudata-0.1.1/mudata/man/measure.vars.Rd | 1 mudata-0.1.1/mudata/man/mudata-package.Rd | 1 mudata-0.1.1/mudata/man/mudata.Rd | 1 mudata-0.1.1/mudata/man/parallel.melt.Rd | 1 mudata-0.1.1/mudata/man/pocmaj.Rd | 1 mudata-0.1.1/mudata/man/pocmajsum.Rd | 1 mudata-0.1.1/mudata/man/qualifierdata.Rd | 1 mudata-0.1.1/mudata/man/qualifierplot.Rd | 3 mudata-0.1.1/mudata/man/rbind.mudata.Rd | 3 mudata-0.1.1/mudata/man/rbind.qtag.long.Rd | 7 -- mudata-0.1.1/mudata/man/rename.cols.Rd | 1 mudata-0.1.1/mudata/man/rename.datasets.Rd | 5 - mudata-0.1.1/mudata/man/rename.values.Rd | 1 mudata-0.1.1/mudata/man/subset.mudata.Rd | 1 mudata-0.1.1/mudata/man/summary.mudata.Rd | 3 mudata-0.1.1/mudata/man/tag.vars.Rd | 1 mudata-0.1.1/mudata/man/tagdata.Rd | 1 mudata-0.1.1/mudata/man/validate.mudata.Rd | 1 mudata-0.1.1/mudata/man/valuedata.Rd | 1 mudata-0.1.1/mudata/man/wide.Rd | 3 mudata-0.1.1/mudata/man/write.mudata.Rd | 7 -- mudata-0.1.1/mudata/tests/testthat/test_mudata.R | 8 ++ mudata-0.1/mudata/README.md |only 40 files changed, 76 insertions(+), 93 deletions(-)
Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package supports
the static site generator 'Hugo' (<https://gohugo.io>) best, and it also
supports 'Jekyll' (<http://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).
Author: Yihui Xie [aut, cre] (0000-0003-0645-5666),
Beilei Bian [ctb],
Forest Fang [ctb],
Hiroaki Yutani [ctb],
JJ Allaire [ctb],
Kevin Ushey [ctb],
RStudio Inc [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between blogdown versions 0.2 dated 2017-11-01 and 0.3 dated 2017-11-13
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/serve.R | 6 +++++- README.md | 2 +- 5 files changed, 21 insertions(+), 11 deletions(-)