Title: Partial Dependence Plots
Description: A general framework for constructing partial dependence (i.e.,
marginal effect) plots from various types machine learning models in R.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between pdp versions 0.5.2 dated 2017-03-13 and 0.6.0 dated 2017-07-19
pdp-0.5.2/pdp/R/pdClassification.R |only pdp-0.5.2/pdp/R/pdGBM.R |only pdp-0.5.2/pdp/R/pdManual.R |only pdp-0.5.2/pdp/R/pdRegression.R |only pdp-0.5.2/pdp/man/autoplot.Rd |only pdp-0.5.2/pdp/tests/testthat/test-pdClassification |only pdp-0.5.2/pdp/tests/testthat/test-pdRegression |only pdp-0.5.2/pdp/tests/testthat/test-plotPartial |only pdp-0.6.0/pdp/DESCRIPTION | 12 pdp-0.6.0/pdp/MD5 | 61 +- pdp-0.6.0/pdp/NAMESPACE | 5 pdp-0.6.0/pdp/NEWS.md | 13 pdp-0.6.0/pdp/R/autoplot.R | 584 +++++++++++---------- pdp-0.6.0/pdp/R/getIcePredCls.R |only pdp-0.6.0/pdp/R/getIcePredReg.R |only pdp-0.6.0/pdp/R/getParDepCls.R |only pdp-0.6.0/pdp/R/getParDepGBM.R |only pdp-0.6.0/pdp/R/getParDepMan.R |only pdp-0.6.0/pdp/R/getParDepReg.R |only pdp-0.6.0/pdp/R/getParPredCls.R |only pdp-0.6.0/pdp/R/getParPredReg.R |only pdp-0.6.0/pdp/R/getTrainingData.R | 9 pdp-0.6.0/pdp/R/isNonGaussianRegression.R |only pdp-0.6.0/pdp/R/partial.R | 379 +++++++------ pdp-0.6.0/pdp/R/plotPartial.R | 534 ++++++++++--------- pdp-0.6.0/pdp/R/predGrid.R | 2 pdp-0.6.0/pdp/R/superType.R | 29 - pdp-0.6.0/pdp/R/topPredictors.R | 56 +- pdp-0.6.0/pdp/R/utils.R | 66 ++ pdp-0.6.0/pdp/README.md | 11 pdp-0.6.0/pdp/inst |only pdp-0.6.0/pdp/man/autoplot.partial.Rd |only pdp-0.6.0/pdp/man/partial.Rd | 190 +++--- pdp-0.6.0/pdp/man/plotPartial.Rd | 93 ++- pdp-0.6.0/pdp/man/topPredictors.Rd | 52 + pdp-0.6.0/pdp/man/trainCHull.Rd |only pdp-0.6.0/pdp/src/pdp-init.c | 22 pdp-0.6.0/pdp/tests/testthat/test-utils.R | 205 ++++++- pdp-0.6.0/pdp/tools/README-example-rf-1.png |binary pdp-0.6.0/pdp/tools/README-example-svm-1.png |binary pdp-0.6.0/pdp/tools/pdp-logo-img.R |only pdp-0.6.0/pdp/tools/pdp-logo-img.png |only pdp-0.6.0/pdp/tools/pdp-logo.png |only 43 files changed, 1449 insertions(+), 874 deletions(-)
Title: Univariate and Multivariate Spatial-Temporal Modeling
Description: Fits univariate and multivariate spatio-temporal
random effects models for point-referenced data using Markov chain Monte Carlo (MCMC). Details are given in Finley, Banerjee, and Gelfand (2015) <doi:10.18637/jss.v063.i13> and Finley, Banerjee, and Cook (2014) <doi:10.1111/2041-210X.12189>.
Author: Andrew Finley [aut, cre],
Sudipto Banerjee [aut]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between spBayes versions 0.4-0 dated 2017-04-12 and 0.4-1 dated 2017-07-19
DESCRIPTION | 15 +++--- MD5 | 42 +++++++++---------- NAMESPACE | 4 + R/bayesRegression.R | 4 - R/spDynLM.R | 9 ++-- R/spGLM.R | 11 ++--- R/spLM.R | 11 ++--- R/spMvGLM.R | 11 ++--- R/spMvLM.R | 9 ++-- R/spPredict.R | 105 +++++++++++++++++++++++------------------------- man/bayesLMConjugate.Rd | 13 ++--- man/bayesLMRef.Rd | 3 - man/spPredict.Rd | 13 ++++- src/init.cpp | 73 +++++++++++++++++---------------- src/spBayes.h | 22 +++++++--- src/spPPDynLM.cpp | 3 - src/spPPGLM.cpp | 2 src/spPPGLM_AMCMC.cpp | 2 src/spPPLM.cpp | 3 - src/spPPMvGLM.cpp | 2 src/spPPMvGLM_AMCMC.cpp | 2 src/spPPMvLM.cpp | 3 - 22 files changed, 191 insertions(+), 171 deletions(-)
Title: Analysis of Binary Character Evolution
Description: Fits a hidden rates model that allows different transition rate
classes on different portions of a phylogeny by treating rate classes as hidden
states in a Markov process and various other functions for evaluating models of
binary character evolution.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver
<jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between corHMM versions 1.20 dated 2016-09-27 and 1.22 dated 2017-07-19
DESCRIPTION | 19 - MD5 | 28 +- NAMESPACE | 4 R/ancRECON.R | 420 ++++++++++++++++++++++------------ R/convertPhangorn.R |only R/corDISC.R | 129 +++++++--- R/corHMM.R | 116 ++++----- R/lewisMkv.R | 6 R/plotRECON.R | 2 R/rate.mat.maker.R | 7 R/rayDISC.R | 213 +++++++++++++---- man/ConvertPhangornReconstructions.Rd |only man/ancRECON.Rd | 5 man/corDISC.Rd | 8 man/corHMM.Rd | 20 - man/rayDISC.Rd | 22 + 16 files changed, 662 insertions(+), 337 deletions(-)
Title: Subgroup Specific Optimal Dose Assignment
Description: Contains functions for choosing subgroup specific optimal doses in a phase I dose finding clinical trial and simulating a clinical trial under the subgroup specific time to event continual reassessment method.
Author: Andrew Chapple
Maintainer: Andrew Chapple <andrew.g.chapple@rice.edu>
Diff between SubTite versions 1.0.0 dated 2017-07-11 and 1.0.1 dated 2017-07-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/SUBGROUP.cpp | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Stability Selection with Error Control
Description: Resampling procedures to assess the stability of selected variables
with additional finite sample error control for high-dimensional variable
selection procedures such as Lasso or boosting. Both, standard stability
selection (Meinshausen & Buhlmann, 2010, <doi:10.1111/j.1467-9868.2010.00740.x>)
and complementary pairs stability selection with improved error bounds
(Shah & Samworth, 2013, <doi:10.1111/j.1467-9868.2011.01034.x>) are
implemented. The package can be combined with arbitrary user specified
variable selection approaches.
Author: Benjamin Hofner [aut, cre],
Torsten Hothorn [aut]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between stabs versions 0.6-2 dated 2017-01-31 and 0.6-3 dated 2017-07-19
ChangeLog | 190 +++++++++------------------------------------ DESCRIPTION | 8 - MD5 | 30 +++---- README.md | 9 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 20 ++++ inst/NEWS.Rd | 36 +++++--- inst/doc/Using_stabs.R | 4 inst/doc/Using_stabs.Rmd | 4 inst/doc/Using_stabs.html | 16 +++ inst/doc/stabs_graphs.R | 4 inst/doc/stabs_graphs.Rmd | 4 inst/doc/stabs_graphs.html | 8 + vignettes/Using_stabs.Rmd | 4 vignettes/stabs_graphs.Rmd | 4 16 files changed, 158 insertions(+), 183 deletions(-)
Title: Provides Access to Git Repositories
Description: Interface to the 'libgit2' library, which is a pure C
implementation of the 'Git' core methods. Provides access to 'Git'
repositories to extract data and running some basic 'Git'
commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between git2r versions 0.18.0 dated 2017-01-01 and 0.19.0 dated 2017-07-19
DESCRIPTION | 8 MD5 | 689 +++---- NEWS | 28 R/commit.r | 19 R/libgit2.r | 2 R/repository.r | 5 configure | 2540 ++++++++++++++-------------- configure.ac | 26 inst/CITATION | 4 man/add-methods.Rd | 1 man/add_session_info.Rd | 1 man/ahead_behind-methods.Rd | 1 man/blame-methods.Rd | 1 man/blob_create-methods.Rd | 1 man/branch_create-methods.Rd | 1 man/branch_delete-methods.Rd | 1 man/branch_get_upstream-methods.Rd | 1 man/branch_remote_name-methods.Rd | 1 man/branch_remote_url-methods.Rd | 1 man/branch_rename-methods.Rd | 1 man/branch_set_upstream-methods.Rd | 1 man/branch_target-methods.Rd | 1 man/branches-methods.Rd | 3 man/bundle_r_package-methods.Rd | 1 man/checkout-methods.Rd | 3 man/clone-methods.Rd | 9 man/coerce-git_commit-method.Rd | 3 man/coerce-git_repository-method.Rd | 3 man/coerce-git_tree-data.frame-method.Rd | 3 man/coerce-git_tree-list-method.Rd | 1 man/commit-methods.Rd | 1 man/commits-methods.Rd | 3 man/config.Rd | 1 man/content-methods.Rd | 1 man/contributions-methods.Rd | 3 man/cred_env-class.Rd | 2 man/cred_env-methods.Rd | 3 man/cred_ssh_key-class.Rd | 2 man/cred_ssh_key.Rd | 3 man/cred_token-class.Rd | 2 man/cred_token.Rd | 3 man/cred_user_pass-class.Rd | 2 man/cred_user_pass-methods.Rd | 3 man/default_signature-methods.Rd | 1 man/descendant_of-methods.Rd | 1 man/diff-methods.Rd | 1 man/discover_repository-methods.Rd | 1 man/fetch-methods.Rd | 1 man/fetch_heads-methods.Rd | 1 man/get_refspec.Rd | 1 man/git2r.Rd | 1 man/git_blame-class.Rd | 2 man/git_blame_hunk-class.Rd | 2 man/git_blob-class.Rd | 2 man/git_branch-class.Rd | 2 man/git_commit-class.Rd | 2 man/git_diff-class.Rd | 2 man/git_diff_file-class.Rd | 2 man/git_diff_hunk-class.Rd | 2 man/git_diff_line-class.Rd | 2 man/git_fetch_head.Rd | 2 man/git_merge_result.Rd | 2 man/git_note-class.Rd | 2 man/git_reference-class.Rd | 2 man/git_reflog_entry-class.Rd | 2 man/git_repository-class.Rd | 2 man/git_signature-class.Rd | 2 man/git_stash-class.Rd | 1 man/git_tag-class.Rd | 2 man/git_time-class.Rd | 4 man/git_transfer_progress-class.Rd | 2 man/git_tree-class.Rd | 2 man/hash-methods.Rd | 1 man/hashfile-methods.Rd | 1 man/head-methods.Rd | 1 man/in_repository-methods.Rd | 3 man/index_remove_bypath-methods.Rd | 1 man/init-methods.Rd | 1 man/is_bare-methods.Rd | 1 man/is_binary-methods.Rd | 1 man/is_blob.Rd | 1 man/is_branch.Rd | 1 man/is_commit.Rd | 1 man/is_detached-methods.Rd | 3 man/is_empty-methods.Rd | 3 man/is_head-methods.Rd | 1 man/is_local-methods.Rd | 1 man/is_merge-methods.Rd | 1 man/is_shallow-methods.Rd | 3 man/length-git_blob-method.Rd | 1 man/length-git_diff-method.Rd | 1 man/length-git_tree-method.Rd | 1 man/libgit2_features.Rd | 1 man/libgit2_sha.Rd | 1 man/libgit2_version.Rd | 1 man/lookup-methods.Rd | 1 man/lookup_repository.Rd | 1 man/merge-methods.Rd | 3 man/merge_base-methods.Rd | 1 man/merge_branch.Rd | 1 man/merge_named_branch.Rd | 1 man/note_create-methods.Rd | 1 man/note_default_ref-methods.Rd | 1 man/note_remove-methods.Rd | 1 man/notes-methods.Rd | 1 man/odb_blobs-methods.Rd | 1 man/odb_objects-methods.Rd | 1 man/parents-methods.Rd | 1 man/plot-methods.Rd | 3 man/pull-methods.Rd | 1 man/punch_card-methods.Rd | 1 man/push-methods.Rd | 1 man/references-methods.Rd | 3 man/reflog-methods.Rd | 3 man/remote_add-methods.Rd | 1 man/remote_ls-methods.Rd | 1 man/remote_remove-methods.Rd | 1 man/remote_rename-methods.Rd | 1 man/remote_set_url-methods.Rd | 1 man/remote_url-methods.Rd | 1 man/remotes-methods.Rd | 3 man/repository-methods.Rd | 3 man/reset-methods.Rd | 3 man/revparse_single-methods.Rd | 1 man/rm_file-methods.Rd | 1 man/show-git_blob-method.Rd | 1 man/show-git_branch-method.Rd | 1 man/show-git_commit-method.Rd | 1 man/show-git_diff-method.Rd | 1 man/show-git_merge_result-method.Rd | 1 man/show-git_note-method.Rd | 1 man/show-git_reference-method.Rd | 1 man/show-git_reflog_entry-method.Rd | 1 man/show-git_repository-method.Rd | 1 man/show-git_signature-method.Rd | 1 man/show-git_stash-method.Rd | 1 man/show-git_tag-method.Rd | 1 man/show-git_time-method.Rd | 1 man/show-git_tree-method.Rd | 1 man/ssh_key_needs_passphrase.Rd | 1 man/ssl_cert_locations.Rd | 1 man/stash-methods.Rd | 1 man/stash_drop-methods.Rd | 1 man/stash_list-methods.Rd | 3 man/status-methods.Rd | 3 man/summary-git_blob-method.Rd | 1 man/summary-git_commit-method.Rd | 1 man/summary-git_diff-method.Rd | 1 man/summary-git_repository-method.Rd | 1 man/summary-git_stash-method.Rd | 1 man/summary-git_tag-method.Rd | 1 man/summary-git_tree-method.Rd | 1 man/tag-methods.Rd | 1 man/tag_delete-methods.Rd | 3 man/tags-methods.Rd | 3 man/tree-index-methods.Rd | 5 man/tree-methods.Rd | 1 man/when-methods.Rd | 1 man/workdir-methods.Rd | 3 src/Makevars.in | 17 src/git2r.c | 176 - src/git2r_arg.c | 6 src/git2r_blame.c | 47 src/git2r_blob.c | 8 src/git2r_branch.c | 11 src/git2r_clone.c | 10 src/git2r_clone.h | 1 src/git2r_commit.c | 20 src/git2r_config.c | 16 src/git2r_diff.c | 319 ++- src/git2r_merge.c | 5 src/git2r_note.c | 17 src/git2r_reference.c | 25 src/git2r_reflog.c | 22 src/git2r_repository.c | 33 src/git2r_signature.c | 20 src/git2r_tag.c | 27 src/git2r_transfer.c | 44 src/git2r_tree.c | 29 src/libgit2/include/git2/branch.h | 12 src/libgit2/include/git2/commit.h | 9 src/libgit2/include/git2/common.h | 50 src/libgit2/include/git2/errors.h | 4 src/libgit2/include/git2/global.h | 2 src/libgit2/include/git2/index.h | 13 src/libgit2/include/git2/merge.h | 3 src/libgit2/include/git2/odb.h | 4 src/libgit2/include/git2/odb_backend.h | 2 src/libgit2/include/git2/oid.h | 9 src/libgit2/include/git2/remote.h | 6 src/libgit2/include/git2/repository.h | 91 + src/libgit2/include/git2/reset.h | 2 src/libgit2/include/git2/revert.h | 2 src/libgit2/include/git2/stash.h | 4 src/libgit2/include/git2/submodule.h | 13 src/libgit2/include/git2/sys/filter.h | 11 src/libgit2/include/git2/sys/merge.h | 10 src/libgit2/include/git2/sys/repository.h | 29 src/libgit2/include/git2/sys/transport.h | 10 src/libgit2/include/git2/transport.h | 12 src/libgit2/include/git2/tree.h | 13 src/libgit2/include/git2/types.h | 3 src/libgit2/include/git2/version.h | 6 src/libgit2/include/git2/worktree.h |only src/libgit2/src/apply.c | 4 src/libgit2/src/attr.c | 40 src/libgit2/src/attr_file.c | 18 src/libgit2/src/attr_file.h | 2 src/libgit2/src/attrcache.c | 49 src/libgit2/src/attrcache.h | 5 src/libgit2/src/blame_git.c | 20 src/libgit2/src/blob.c | 10 src/libgit2/src/branch.c | 52 src/libgit2/src/buffer.c | 31 src/libgit2/src/buffer.h | 7 src/libgit2/src/cache.c | 48 src/libgit2/src/cache.h | 2 src/libgit2/src/checkout.c | 65 src/libgit2/src/cherrypick.c | 8 src/libgit2/src/clone.c | 5 src/libgit2/src/commit.c | 16 src/libgit2/src/commit_list.c | 4 src/libgit2/src/common.h | 2 src/libgit2/src/config.c | 99 - src/libgit2/src/config_cache.c | 1 src/libgit2/src/config_file.c | 52 src/libgit2/src/config_file.h | 1 src/libgit2/src/crlf.c | 2 src/libgit2/src/delta.c | 8 src/libgit2/src/describe.c | 26 src/libgit2/src/diff.c | 35 src/libgit2/src/diff_driver.c | 8 src/libgit2/src/diff_file.c | 2 src/libgit2/src/diff_generate.c | 4 src/libgit2/src/diff_parse.c | 8 src/libgit2/src/diff_print.c | 10 src/libgit2/src/diff_tform.c | 6 src/libgit2/src/diff_xdiff.c | 4 src/libgit2/src/fetch.c | 2 src/libgit2/src/fetchhead.c | 20 src/libgit2/src/filebuf.c | 31 src/libgit2/src/filebuf.h | 4 src/libgit2/src/fileops.c | 163 + src/libgit2/src/fileops.h | 25 src/libgit2/src/filter.c | 52 src/libgit2/src/global.c | 2 src/libgit2/src/hash.h | 8 src/libgit2/src/hash/hash_collisiondetect.h |only src/libgit2/src/hash/sha1dc |only src/libgit2/src/hashsig.c | 4 src/libgit2/src/idxmap.c |only src/libgit2/src/idxmap.h | 81 src/libgit2/src/ignore.c | 16 src/libgit2/src/ignore.h | 2 src/libgit2/src/index.c | 172 + src/libgit2/src/indexer.c | 106 - src/libgit2/src/indexer.h |only src/libgit2/src/integer.h | 12 src/libgit2/src/merge.c | 56 src/libgit2/src/merge_driver.c | 29 src/libgit2/src/merge_file.c | 2 src/libgit2/src/mwindow.c | 6 src/libgit2/src/netops.c | 8 src/libgit2/src/notes.c | 6 src/libgit2/src/object.c | 10 src/libgit2/src/odb.c | 145 + src/libgit2/src/odb.h | 28 src/libgit2/src/odb_loose.c | 38 src/libgit2/src/odb_mempack.c | 30 src/libgit2/src/odb_pack.c | 2 src/libgit2/src/offmap.c |only src/libgit2/src/offmap.h | 55 src/libgit2/src/oid.c | 10 src/libgit2/src/oidmap.c |only src/libgit2/src/oidmap.h | 50 src/libgit2/src/openssl_stream.c | 21 src/libgit2/src/openssl_stream.h | 2 src/libgit2/src/pack-objects.c | 39 src/libgit2/src/pack-objects.h | 1 src/libgit2/src/pack.c | 80 src/libgit2/src/pack.h | 1 src/libgit2/src/patch_generate.c | 89 src/libgit2/src/patch_parse.c | 9 src/libgit2/src/path.c | 115 - src/libgit2/src/pathspec.c | 4 src/libgit2/src/posix.c | 4 src/libgit2/src/posix.h | 10 src/libgit2/src/push.c | 12 src/libgit2/src/rebase.c | 54 src/libgit2/src/refdb.c | 2 src/libgit2/src/refdb_fs.c | 190 +- src/libgit2/src/reflog.c | 4 src/libgit2/src/refs.c | 158 + src/libgit2/src/refs.h | 17 src/libgit2/src/remote.c | 33 src/libgit2/src/repository.c | 589 +++++- src/libgit2/src/repository.h | 35 src/libgit2/src/reset.c | 2 src/libgit2/src/revert.c | 8 src/libgit2/src/revparse.c | 35 src/libgit2/src/revwalk.c | 29 src/libgit2/src/settings.c | 35 src/libgit2/src/sha1_lookup.c | 2 src/libgit2/src/signature.c | 7 src/libgit2/src/socket_stream.c | 16 src/libgit2/src/sortedcache.c | 18 src/libgit2/src/stash.c | 12 src/libgit2/src/status.c | 8 src/libgit2/src/strmap.c | 95 + src/libgit2/src/strmap.h | 64 src/libgit2/src/submodule.c | 335 ++- src/libgit2/src/submodule.h | 3 src/libgit2/src/sysdir.c | 15 src/libgit2/src/sysdir.h | 12 src/libgit2/src/tag.c | 28 src/libgit2/src/thread-utils.h | 6 src/libgit2/src/trace.c | 2 src/libgit2/src/transaction.c | 22 src/libgit2/src/transport.c | 2 src/libgit2/src/transports/cred.c | 2 src/libgit2/src/transports/git.c | 6 src/libgit2/src/transports/http.c | 18 src/libgit2/src/transports/local.c | 7 src/libgit2/src/transports/smart.c | 16 src/libgit2/src/transports/smart.h | 2 src/libgit2/src/transports/smart_pkt.c | 26 src/libgit2/src/transports/smart_protocol.c | 20 src/libgit2/src/transports/ssh.c | 32 src/libgit2/src/transports/winhttp.c | 295 +-- src/libgit2/src/tree-cache.c | 4 src/libgit2/src/tree.c | 79 src/libgit2/src/unix/map.c | 2 src/libgit2/src/unix/posix.h | 9 src/libgit2/src/util.c | 6 src/libgit2/src/varint.c | 2 src/libgit2/src/vector.c | 3 src/libgit2/src/win32/dir.c | 6 src/libgit2/src/win32/findfile.c | 2 src/libgit2/src/win32/map.c | 12 src/libgit2/src/win32/posix.h | 3 src/libgit2/src/win32/posix_w32.c | 445 +++- src/libgit2/src/win32/w32_util.c | 2 src/libgit2/src/win32/w32_util.h | 2 src/libgit2/src/worktree.c |only src/libgit2/src/worktree.h |only src/libgit2/src/zstream.c | 2 tests/clone_checkout.R |only tests/commit.R | 64 tests/diff.R | 39 349 files changed, 5858 insertions(+), 4038 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here this package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of the package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
it gives users more convenience and freedom to design figures for
better understanding complex patterns behind multiple dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.4.0 dated 2017-05-29 and 0.4.1 dated 2017-07-19
DESCRIPTION | 10 - MD5 | 50 ++++--- NAMESPACE | 5 NEWS | 9 + R/chordDiagram.R | 2 R/circos.arrow.R |only R/genomic.R | 4 R/plot.R | 51 +++---- R/random_color.R |only R/raster.R |only R/utils.R | 22 --- inst/doc/circlize.pdf |binary inst/doc/circular_phylogenetic_tree.pdf |binary inst/doc/genomic_plot.pdf |binary inst/doc/interesting_graphics.pdf |binary inst/doc/visualize_relations_by_chord_diagram.pdf |binary inst/extdata/Rlogo.png |only inst/extdata/doodle.RData |only inst/extdata/download_and_slice_doodle.R |only man/circos.arrow.rd |only man/circos.axis.rd | 4 man/circos.lines.rd | 7 man/circos.link.rd | 156 +++++++++------------- man/circos.raster.rd |only man/circos.text.rd | 2 man/circos.trackLines.rd | 2 man/circos.trackText.rd | 2 man/circos.yaxis.rd | 4 man/rand_color.rd | 31 +++- man/set.current.cell.rd | 14 + 30 files changed, 197 insertions(+), 178 deletions(-)
Title: Straightforward Filtering Index for AP-MS Data Analysis (SFINX)
Description: The straightforward filtering index (SFINX) identifies true positive
protein interactions in a fast, user-friendly, and highly accurate way.
It is not only useful for the filtering of affinity purification -
mass spectrometry (AP-MS) data, but also for similar types of data
resulting from other co-complex interactomics technologies, such as TAP-MS,
Virotrap and BioID. SFINX can also be used via the website interface at
<http://sfinx.ugent.be>.
Author: Kevin Titeca [aut, cre],
Jan Tavernier [ths],
Sven Eyckerman [ths]
Maintainer: Kevin Titeca <sfinxinteractomics@gmail.com>
Diff between sfinx versions 1.7.9 dated 2016-12-22 and 1.7.99 dated 2017-07-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/CITATION | 26 +++++++++++++++++++++++++- inst/doc/sfinx-vignette.html | 4 ++-- 4 files changed, 34 insertions(+), 10 deletions(-)
Title: Bayesian LDA for Mixed-Membership Clustering Analysis
Description: Estimates the Bayesian LDA model for mixed-membership clustering based on different types of data (i.e., Multinomial, Bernoulli, and Binomial entries).
Author: Pedro Albuquerque and Denis Valle and Daijiang Li
Maintainer: Pedro Albuquerque <pedroa@unb.br>
Diff between Rlda versions 0.2.0 dated 2017-06-02 and 0.2.1 dated 2017-07-19
DESCRIPTION | 6 MD5 | 21 - NAMESPACE | 8 NEWS | 9 R/Utils.R | 381 +++++++++---------- R/data.R |only R/rlda.R | 968 ++++++++++++++++++++++++++------------------------ inst/doc/Rlda.pdf |binary man/birds.Rd | 2 man/getPhi.Rd |only man/getTheta.Rd |only man/logLik.Rd |only man/print.Rd |only tests/AbundanceTest.R | 2 14 files changed, 725 insertions(+), 672 deletions(-)
Title: Maximum Likelihood Analysis of Animal Movement Behavior Using
Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using (multivariate) hidden Markov models. These include processing of tracking data, fitting HMMs to location and auxiliary biotelemetry or environmental data, multiple imputation for incorporating location measurement error and missing data, visualization of data and fitted model, decoding of the state process...
Author: Brett McClintock, Theo Michelot, Roland Langrock, Toby Patterson, Eric
Rexstad
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>
Diff between momentuHMM versions 1.0.0 dated 2017-06-16 and 1.0.1 dated 2017-07-19
momentuHMM-1.0.0/momentuHMM/inst/doc/momentuHMM_vignette.pdf |only momentuHMM-1.0.1/momentuHMM/DESCRIPTION | 11 - momentuHMM-1.0.1/momentuHMM/MD5 | 72 ++++++++--- momentuHMM-1.0.1/momentuHMM/NAMESPACE | 1 momentuHMM-1.0.1/momentuHMM/NEWS |only momentuHMM-1.0.1/momentuHMM/R/distAngle.R | 12 + momentuHMM-1.0.1/momentuHMM/R/fitHMM.R | 29 ++-- momentuHMM-1.0.1/momentuHMM/R/getDM.R | 4 momentuHMM-1.0.1/momentuHMM/R/plot_crwData.R | 4 momentuHMM-1.0.1/momentuHMM/R/plot_momentuHMM.R | 26 ++- momentuHMM-1.0.1/momentuHMM/R/prepData.R | 13 + momentuHMM-1.0.1/momentuHMM/R/stateFormulas.R | 2 momentuHMM-1.0.1/momentuHMM/R/turnAngle.R | 18 +- momentuHMM-1.0.1/momentuHMM/README.md | 11 - momentuHMM-1.0.1/momentuHMM/build |only momentuHMM-1.0.1/momentuHMM/inst/doc/momentuHMM.R |only momentuHMM-1.0.1/momentuHMM/inst/doc/momentuHMM.Rnw |only momentuHMM-1.0.1/momentuHMM/inst/doc/momentuHMM.pdf |only momentuHMM-1.0.1/momentuHMM/man/distAngle.Rd | 6 momentuHMM-1.0.1/momentuHMM/man/prepData.Rd | 5 momentuHMM-1.0.1/momentuHMM/man/turnAngle.Rd | 8 - momentuHMM-1.0.1/momentuHMM/tests/testthat/test_plotSat.R | 8 - momentuHMM-1.0.1/momentuHMM/vignettes |only 23 files changed, 155 insertions(+), 75 deletions(-)
Title: A Fast and Versatile SVM Package
Description: Support vector machines (SVMs) and related kernel-based learning
algorithms are a well-known class of machine learning algorithms, for
non-parametric classification and regression.
liquidSVM is an implementation of SVMs whose key features are:
fully integrated hyper-parameter selection,
extreme speed on both small and large data sets,
full flexibility for experts, and
inclusion of a variety of different learning scenarios:
multi-class classification, ROC, and Neyman-Pearson learning, and
least-squares, quantile, and expectile regression.
Author: Ingo Steinwart, Philipp Thomann
Maintainer: Philipp Thomann <philipp.thomann@mathematik.uni-stuttgart.de>
Diff between liquidSVM versions 1.2.0 dated 2017-07-15 and 1.2.1 dated 2017-07-19
DESCRIPTION | 8 +++--- MD5 | 26 ++++++++++---------- build/vignette.rds |binary configure | 2 - inst/doc/demo.html | 6 ++-- inst/doc/documentation.html | 4 +-- src/sources/shared/basic_types/sample.cpp | 2 - src/sources/svm/training_validation/svm_manager.cpp | 1 tests/testthat.R | 2 - tests/testthat/test-bugs.R | 2 - tests/testthat/test-mlr.R | 2 - tests/testthat/test-model.R | 6 ++-- tests/testthat/test-quick.R | 7 +++-- tests/testthat/test-scenarios.R | 2 - 14 files changed, 37 insertions(+), 33 deletions(-)
Title: Tools to Work with Survey Data
Description: Data obtained from surveys contains information not only about the
survey responses, but also the survey metadata, e.g. the original survey
questions and the answer options. The surveydata package makes it easy to
keep track of this metadata, and to easily extract columns with
specific questions.
Author: Andrie de Vries [aut, cre, cph]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between surveydata versions 0.1-14 dated 2013-10-22 and 0.2.0 dated 2017-07-19
surveydata-0.1-14/surveydata/inst/doc/surveydata.Rnw |only surveydata-0.1-14/surveydata/inst/doc/surveydata.pdf |only surveydata-0.1-14/surveydata/inst/tests |only surveydata-0.1-14/surveydata/vignettes/surveydata.Rnw |only surveydata-0.2.0/surveydata/DESCRIPTION | 25 +- surveydata-0.2.0/surveydata/MD5 | 137 +++++------ surveydata-0.2.0/surveydata/NAMESPACE | 25 +- surveydata-0.2.0/surveydata/NEWS | 15 - surveydata-0.2.0/surveydata/R/cleandata.R | 110 ++++---- surveydata-0.2.0/surveydata/R/dplyr_verbs.R |only surveydata-0.2.0/surveydata/R/encoding.R | 31 +- surveydata-0.2.0/surveydata/R/extract.R | 22 - surveydata-0.2.0/surveydata/R/merge.R | 2 surveydata-0.2.0/surveydata/R/pattern.R | 4 surveydata-0.2.0/surveydata/R/questions.R | 76 +++--- surveydata-0.2.0/surveydata/R/surveydata-package.R | 70 ++--- surveydata-0.2.0/surveydata/R/surveydata.R | 18 - surveydata-0.2.0/surveydata/R/varlabels.R | 6 surveydata-0.2.0/surveydata/build/vignette.rds |binary surveydata-0.2.0/surveydata/inst/doc/surveydata.R | 117 +++++---- surveydata-0.2.0/surveydata/inst/doc/surveydata.Rmd |only surveydata-0.2.0/surveydata/inst/doc/surveydata.html |only surveydata-0.2.0/surveydata/inst/vignette_child |only surveydata-0.2.0/surveydata/man/Extract.Rd | 56 +--- surveydata-0.2.0/surveydata/man/as.data.frame.surveydata.Rd | 19 - surveydata-0.2.0/surveydata/man/as.surveydata.Rd | 33 -- surveydata-0.2.0/surveydata/man/cbind.surveydata.Rd | 11 surveydata-0.2.0/surveydata/man/dplyr-surveydata.Rd |only surveydata-0.2.0/surveydata/man/dropout.Rd | 17 - surveydata-0.2.0/surveydata/man/encToInt.Rd | 32 +- surveydata-0.2.0/surveydata/man/fixCommonEncodingProblems.Rd | 27 +- surveydata-0.2.0/surveydata/man/fixLevels01.Rd | 14 - surveydata-0.2.0/surveydata/man/fixLevels01R.Rd | 14 - surveydata-0.2.0/surveydata/man/fixLevels01SPSS.Rd | 14 - surveydata-0.2.0/surveydata/man/hasDK.Rd | 25 +- surveydata-0.2.0/surveydata/man/intToEnc.Rd | 30 +- surveydata-0.2.0/surveydata/man/is.surveydata.Rd | 11 surveydata-0.2.0/surveydata/man/lapplyNames.Rd | 21 - surveydata-0.2.0/surveydata/man/leveltestR.Rd | 21 - surveydata-0.2.0/surveydata/man/leveltestSPSS.Rd | 21 - surveydata-0.2.0/surveydata/man/membersurvey.Rd | 9 surveydata-0.2.0/surveydata/man/merge.Rd | 16 - surveydata-0.2.0/surveydata/man/merge_varlabels.Rd | 17 - surveydata-0.2.0/surveydata/man/names.Rd | 15 - surveydata-0.2.0/surveydata/man/pattern.Rd | 25 -- surveydata-0.2.0/surveydata/man/qOrder.Rd | 12 surveydata-0.2.0/surveydata/man/qText.Rd | 19 - surveydata-0.2.0/surveydata/man/qTextCommon.Rd | 20 - surveydata-0.2.0/surveydata/man/qTextUnique.Rd | 20 - surveydata-0.2.0/surveydata/man/questions.Rd | 26 -- surveydata-0.2.0/surveydata/man/removeAllDK.Rd | 30 +- surveydata-0.2.0/surveydata/man/removeDK.Rd | 26 +- surveydata-0.2.0/surveydata/man/rm.attrs.Rd | 9 surveydata-0.2.0/surveydata/man/rm.pattern.Rd | 9 surveydata-0.2.0/surveydata/man/splitCommonUnique.Rd | 18 - surveydata-0.2.0/surveydata/man/strCommonUnique.Rd | 16 - surveydata-0.2.0/surveydata/man/surveydata-package.Rd | 98 ++++--- surveydata-0.2.0/surveydata/man/varlabels.Rd | 30 -- surveydata-0.2.0/surveydata/man/which.q.Rd | 29 -- surveydata-0.2.0/surveydata/tests |only surveydata-0.2.0/surveydata/vignettes/surveydata.Rmd |only 61 files changed, 730 insertions(+), 738 deletions(-)
Title: 'knitr' Bootstrap Framework
Description: A framework to create Bootstrap <http://getbootstrap.com/> HTML reports from 'knitr'
'rmarkdown'.
Author: Jim Hester
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between knitrBootstrap versions 1.0.0 dated 2015-12-16 and 1.0.1 dated 2017-07-19
DESCRIPTION | 16 LICENSE | 4 MD5 | 51 - NEWS.md |only R/knit_bootstrap.R | 6 README.md | 3 build/vignette.rds |binary inst/doc/cars.R | 6 inst/doc/cars.Rmd | 8 inst/doc/cars.html | 16 inst/doc/illusions.html | 10 inst/doc/maps.html | 21 inst/doc/math.html | 8 inst/doc/two-D.R | 2 inst/doc/two-D.Rmd | 2 inst/doc/two-D.html | 20 inst/examples/all.html | 1181 +++++++++++++++----------------------------- inst/examples/engines.html | 284 +++------- inst/examples/messages.html | 371 ++++--------- man/bootstrap_HTML.Rd | 1 man/bootstrap_document.Rd | 5 man/knit_bootstrap.Rd | 1 man/knit_bootstrap_md.Rd | 1 man/knitrBootstrap.Rd | 1 man/render_bootstrap.Rd | 1 vignettes/cars.Rmd | 8 vignettes/two-D.Rmd | 2 27 files changed, 719 insertions(+), 1310 deletions(-)
More information about knitrBootstrap at CRAN
Permanent link
Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using Raster and SpatialPoints
objects are provided. Non-Gaussian models are fit using INLA, and Gaussian
geostatistical models use Maximum Likelihood Estimation.
Author: Patrick Brown <patrick.brown@utoronto.ca>[aut, cre], Robert Hijmans
[ctb]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between geostatsp versions 1.4.4 dated 2016-07-07 and 1.5.4 dated 2017-07-19
geostatsp-1.4.4/geostatsp/R/gmrfPrecUncond.R |only geostatsp-1.4.4/geostatsp/data/nn32.RData |only geostatsp-1.4.4/geostatsp/man/nn32.Rd |only geostatsp-1.4.4/geostatsp/src/sparseLogL.c |only geostatsp-1.4.4/geostatsp/tests/loaFitted.png |only geostatsp-1.5.4/geostatsp/DESCRIPTION | 27 geostatsp-1.5.4/geostatsp/MD5 | 108 - geostatsp-1.5.4/geostatsp/NAMESPACE | 6 geostatsp-1.5.4/geostatsp/R/0gm.R | 590 +++---- geostatsp-1.5.4/geostatsp/R/NNmat.R | 115 - geostatsp-1.5.4/geostatsp/R/RFsimulate.R | 833 +++++---- geostatsp-1.5.4/geostatsp/R/glgm.R | 1673 ++++++++++---------- geostatsp-1.5.4/geostatsp/R/gmrfShape4.R |only geostatsp-1.5.4/geostatsp/R/informationLgm.R | 187 +- geostatsp-1.5.4/geostatsp/R/krige.R | 1139 ++++++------- geostatsp-1.5.4/geostatsp/R/lgcp.R | 16 geostatsp-1.5.4/geostatsp/R/lgm.R | 489 +++-- geostatsp-1.5.4/geostatsp/R/lgm.Raster.R | 477 +++-- geostatsp-1.5.4/geostatsp/R/loglikGmrf.R | 865 +++++----- geostatsp-1.5.4/geostatsp/R/loglikLgm.R | 892 +++++----- geostatsp-1.5.4/geostatsp/R/matern.R | 144 + geostatsp-1.5.4/geostatsp/R/maternGmrfPrec.R | 672 ++++---- geostatsp-1.5.4/geostatsp/R/squareRaster.R | 21 geostatsp-1.5.4/geostatsp/build/vignette.rds |binary geostatsp-1.5.4/geostatsp/data/datalist | 1 geostatsp-1.5.4/geostatsp/data/gambiaUTM.RData |binary geostatsp-1.5.4/geostatsp/data/loaloa.RData |binary geostatsp-1.5.4/geostatsp/data/murder.RData |binary geostatsp-1.5.4/geostatsp/data/rongelapUTM.RData |binary geostatsp-1.5.4/geostatsp/data/swissRain.RData |binary geostatsp-1.5.4/geostatsp/data/swissRainR.RData |binary geostatsp-1.5.4/geostatsp/data/torontoPop.RData |binary geostatsp-1.5.4/geostatsp/data/wheat.RData |binary geostatsp-1.5.4/geostatsp/inst/CITATION | 41 geostatsp-1.5.4/geostatsp/inst/doc/lgcp.Rnw | 214 +- geostatsp-1.5.4/geostatsp/inst/doc/lgcp.pdf |binary geostatsp-1.5.4/geostatsp/inst/extdata/loaloaData.R |only geostatsp-1.5.4/geostatsp/man/RFsimulate.Rd | 24 geostatsp-1.5.4/geostatsp/man/glgm.Rd | 88 - geostatsp-1.5.4/geostatsp/man/krige.Rd | 16 geostatsp-1.5.4/geostatsp/man/lgm.Rd | 171 +- geostatsp-1.5.4/geostatsp/man/loaloa.Rd | 304 --- geostatsp-1.5.4/geostatsp/man/matern.Rd | 2 geostatsp-1.5.4/geostatsp/man/maternGmrfPrec.Rd | 109 - geostatsp-1.5.4/geostatsp/man/murder.Rd | 2 geostatsp-1.5.4/geostatsp/man/squareRaster.Rd | 23 geostatsp-1.5.4/geostatsp/src/Matrix_stubs_here.c |only geostatsp-1.5.4/geostatsp/src/geostatsp.h | 46 geostatsp-1.5.4/geostatsp/src/geostatsp_init.c |only geostatsp-1.5.4/geostatsp/src/gmrfEdge.c |only geostatsp-1.5.4/geostatsp/src/gmrfLik.c | 957 ++++++----- geostatsp-1.5.4/geostatsp/src/matern.c | 1238 ++++++++++---- geostatsp-1.5.4/geostatsp/src/optimize.c | 4 geostatsp-1.5.4/geostatsp/tests/RFsimulate.R | 214 +- geostatsp-1.5.4/geostatsp/tests/glgm.R | 12 geostatsp-1.5.4/geostatsp/tests/lgcp.R | 13 geostatsp-1.5.4/geostatsp/tests/lgmRaster.R | 361 ++-- geostatsp-1.5.4/geostatsp/tests/matern.R | 31 geostatsp-1.5.4/geostatsp/tests/maternGmrfPrec.R | 783 ++++----- geostatsp-1.5.4/geostatsp/vignettes/lgcp.Rnw | 214 +- 60 files changed, 7218 insertions(+), 5904 deletions(-)
Title: Artificial Counterfactual Package
Description: Set of functions to analyse and estimate Artificial Counterfactual models from Carvalho, Masini and Medeiros (2016) <DOI:10.2139/ssrn.2823687>.
Author: Yuri R. Fonseca [aut],
Ricardo Masini [aut],
Marcelo C. Medeiros [aut],
Gabriel F. R. Vasconcelos [aut, cre]
Maintainer: Gabriel F. R. Vasconcelos <gabrielrvsc@yahoo.com.br>
Diff between ArCo versions 0.1-2 dated 2017-04-19 and 0.2 dated 2017-07-19
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/fitArCo.R | 23 ++++++++++++++++++----- R/panel_to_ArCo_list.R | 4 ++-- man/estimate_t0.Rd | 2 +- man/fitArCo.Rd | 15 +++++++++------ man/panel_to_ArCo_list.Rd | 4 ++-- 7 files changed, 41 insertions(+), 25 deletions(-)
Title: Efficient Constrained Based Modelling
Description: This Systems Biology Package (Gelius-Dietrich et. al. (2012) <doi:10.1186/1752-0509-7-125>) implements algorithms for constraint based analyses of metabolic networks, e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis. The package is easily extendable for additional algorithms. Most of the current LP/MILP solvers are supported via additional packages.
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut],
Rajen Piernikarczyk [ctb],
Marc Andre Daxer [ctb],
Benjamin Braasch [ctb],
Abdelmoneim Desouki [ctb],
Martin J. Lercher [ctb]
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Diff between sybil versions 2.0.0 dated 2016-06-06 and 2.0.4 dated 2017-07-19
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++---------- R/generateWT.R | 30 +++++++++++++++--------------- R/mod2irrev.R | 2 +- R/rmReact.R | 20 ++++---------------- R/upgradeModelorg.R | 10 ++++++++-- README.md | 2 +- build/vignette.rds |binary inst/NEWS.Rd | 32 +++++++++++++++++++++++++++++++- inst/doc/sybil.pdf |binary man/checkOptSol-methods.Rd | 2 +- 11 files changed, 78 insertions(+), 54 deletions(-)
Title: Adaptive Multivariate Integration over Hypercubes
Description: R wrapper around the cubature C library of
Steven G. Johnson for adaptive multivariate integration over hypercubes.
This version provides both hcubature and pcubature routines in addition
to a vector interface that results in substantial speed gains.
Author: Balasubramanian Narasimhan [aut, cre],
Manuel Koller [ctb],
Steven G. Johnson [aut]
Maintainer: Balasubramanian Narasimhan <naras@stat.stanford.edu>
Diff between cubature versions 1.3-8 dated 2017-05-11 and 1.3-11 dated 2017-07-19
cubature-1.3-11/cubature/ChangeLog | 10 cubature-1.3-11/cubature/DESCRIPTION | 9 cubature-1.3-11/cubature/MD5 | 46 cubature-1.3-11/cubature/R/RcppExports.R | 4 cubature-1.3-11/cubature/R/cubature-package.R | 4 cubature-1.3-11/cubature/R/hcubature.R | 5 cubature-1.3-11/cubature/build/vignette.rds |binary cubature-1.3-11/cubature/inst/doc/cubature.R | 2 cubature-1.3-11/cubature/inst/doc/cubature.Rmd | 20 cubature-1.3-11/cubature/inst/doc/cubature.html | 744 ++++++---------- cubature-1.3-11/cubature/inst/include |only cubature-1.3-11/cubature/man/cubature-package.Rd | 6 cubature-1.3-11/cubature/man/hcubature.Rd | 3 cubature-1.3-11/cubature/src/Makevars | 6 cubature-1.3-11/cubature/src/Makevars.win | 6 cubature-1.3-11/cubature/src/Rcpp-cubature.cpp | 2 cubature-1.3-11/cubature/src/RcppExports.cpp | 5 cubature-1.3-11/cubature/src/cubature-1.0.2/README.md | 30 cubature-1.3-11/cubature/src/cubature-1.0.2/hcubature.c | 2 cubature-1.3-11/cubature/src/cubature-1.0.2/pcubature.c | 2 cubature-1.3-11/cubature/src/cubature-1.0.2/test.c | 2 cubature-1.3-11/cubature/src/cubature_init.c | 17 cubature-1.3-11/cubature/vignettes/cubature.Rmd | 20 cubature-1.3-8/cubature/src/cubature-1.0.2/cubature.h |only 24 files changed, 408 insertions(+), 537 deletions(-)
Title: Text Corpus Analysis
Description: Text corpus data analysis, with full support for Unicode. Functions for reading data from newline-delimited JSON files, for normalizing and tokenizing text, for searching for term occurrences, and for computing term occurrence frequencies (including n-grams).
Author: Patrick O. Perry [aut, cre],
Martin Porter and Richard Boulton [ctb, cph] (Snowball),
Unicode, Inc. [ctb, cph] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Diff between corpus versions 0.7.0 dated 2017-06-22 and 0.8.0 dated 2017-07-19
corpus-0.7.0/corpus/R/filter.R |only corpus-0.7.0/corpus/demo |only corpus-0.7.0/corpus/src/abbreviations.c |only corpus-0.7.0/corpus/src/filter.c |only corpus-0.7.0/corpus/src/format_text.c |only corpus-0.7.0/corpus/src/schema.c |only corpus-0.7.0/corpus/src/sentfilter.c |only corpus-0.7.0/corpus/src/stopwords.c |only corpus-0.7.0/corpus/src/text.c |only corpus-0.8.0/corpus/DESCRIPTION | 12 corpus-0.8.0/corpus/MD5 | 198 corpus-0.8.0/corpus/NAMESPACE | 148 corpus-0.8.0/corpus/NEWS | 48 corpus-0.8.0/corpus/R/coerce.R | 224 corpus-0.8.0/corpus/R/deprecated.R |only corpus-0.8.0/corpus/R/frame.R |only corpus-0.8.0/corpus/R/json.R | 233 corpus-0.8.0/corpus/R/sentence.R | 53 corpus-0.8.0/corpus/R/term.R | 120 corpus-0.8.0/corpus/R/text-base.R |only corpus-0.8.0/corpus/R/text-primitive.R |only corpus-0.8.0/corpus/R/text.R | 337 - corpus-0.8.0/corpus/R/text_filter.R |only corpus-0.8.0/corpus/R/text_locate.R | 133 corpus-0.8.0/corpus/R/text_split.R | 30 corpus-0.8.0/corpus/R/text_types.R | 28 corpus-0.8.0/corpus/R/token.R | 89 corpus-0.8.0/corpus/R/utf8.R |only corpus-0.8.0/corpus/R/util.R |only corpus-0.8.0/corpus/R/wordlist.R | 12 corpus-0.8.0/corpus/README |only corpus-0.8.0/corpus/build |only corpus-0.8.0/corpus/data |only corpus-0.8.0/corpus/inst |only corpus-0.8.0/corpus/man/abbreviations.Rd | 2 corpus-0.8.0/corpus/man/as_text.Rd | 71 corpus-0.8.0/corpus/man/corpus-deprecated.Rd |only corpus-0.8.0/corpus/man/corpus-package.Rd | 2 corpus-0.8.0/corpus/man/federalist.Rd |only corpus-0.8.0/corpus/man/read_ndjson.Rd | 38 corpus-0.8.0/corpus/man/stopwords.Rd | 2 corpus-0.8.0/corpus/man/term_counts.Rd | 44 corpus-0.8.0/corpus/man/term_matrix.Rd | 15 corpus-0.8.0/corpus/man/text_filter.Rd |only corpus-0.8.0/corpus/man/text_locate.Rd | 17 corpus-0.8.0/corpus/man/text_split.Rd | 58 corpus-0.8.0/corpus/man/text_tokens.Rd | 120 corpus-0.8.0/corpus/man/text_types.Rd | 13 corpus-0.8.0/corpus/man/utf8.Rd |only corpus-0.8.0/corpus/src/context.c |only corpus-0.8.0/corpus/src/corpus/NEWS.md | 7 corpus-0.8.0/corpus/src/corpus/TODO.md | 11 corpus-0.8.0/corpus/src/corpus/corpus.xcodeproj/project.pbxproj | 4 corpus-0.8.0/corpus/src/corpus/src/data.c | 48 corpus-0.8.0/corpus/src/corpus/src/filter.c | 4 corpus-0.8.0/corpus/src/corpus/src/filter.h | 3 corpus-0.8.0/corpus/src/corpus/src/main_ngrams.c | 1 corpus-0.8.0/corpus/src/corpus/src/main_tokens.c | 1 corpus-0.8.0/corpus/src/corpus/src/text.c | 22 corpus-0.8.0/corpus/src/corpus/src/unicode.c | 2 corpus-0.8.0/corpus/src/corpus/src/unicode.h | 5 corpus-0.8.0/corpus/src/corpus/src/unicode/charwidth.h | 3124 +++++----- corpus-0.8.0/corpus/src/corpus/src/unicode/wordbreakprop.h | 4 corpus-0.8.0/corpus/src/corpus/src/wordscan.c | 105 corpus-0.8.0/corpus/src/corpus/src/wordscan.h | 1 corpus-0.8.0/corpus/src/corpus/tests/check_charwidth.c | 4 corpus-0.8.0/corpus/src/corpus/tests/check_data.c | 5 corpus-0.8.0/corpus/src/corpus/tests/check_text.c | 59 corpus-0.8.0/corpus/src/corpus/tests/check_wordscan.c | 35 corpus-0.8.0/corpus/src/corpus/util/gen-charwidth.py | 13 corpus-0.8.0/corpus/src/corpus/util/gen-wordbreak.py | 6 corpus-0.8.0/corpus/src/decode.c | 109 corpus-0.8.0/corpus/src/filebuf.c | 10 corpus-0.8.0/corpus/src/format.c |only corpus-0.8.0/corpus/src/init.c | 48 corpus-0.8.0/corpus/src/json.c | 607 - corpus-0.8.0/corpus/src/mkchar.c | 5 corpus-0.8.0/corpus/src/ndjson.c | 5 corpus-0.8.0/corpus/src/print_table.c |only corpus-0.8.0/corpus/src/rcorpus.h | 177 corpus-0.8.0/corpus/src/search.c | 24 corpus-0.8.0/corpus/src/term_counts.c | 399 - corpus-0.8.0/corpus/src/term_matrix.c | 273 corpus-0.8.0/corpus/src/termset.c | 15 corpus-0.8.0/corpus/src/text_base.c |only corpus-0.8.0/corpus/src/text_filter.c |only corpus-0.8.0/corpus/src/text_locate.c | 59 corpus-0.8.0/corpus/src/text_methods.c | 57 corpus-0.8.0/corpus/src/text_nunit.c | 55 corpus-0.8.0/corpus/src/text_split.c | 441 - corpus-0.8.0/corpus/src/text_tokens.c | 155 corpus-0.8.0/corpus/src/text_types.c | 146 corpus-0.8.0/corpus/src/utf8.c |only corpus-0.8.0/corpus/src/wordlist.c |only corpus-0.8.0/corpus/tests/testthat/helper-locale.R |only corpus-0.8.0/corpus/tests/testthat/helper-options.R |only corpus-0.8.0/corpus/tests/testthat/test-frame.R |only corpus-0.8.0/corpus/tests/testthat/test-json_record.R | 170 corpus-0.8.0/corpus/tests/testthat/test-json_scalar.R | 220 corpus-0.8.0/corpus/tests/testthat/test-json_serialize.R | 5 corpus-0.8.0/corpus/tests/testthat/test-read_ndjson.R | 42 corpus-0.8.0/corpus/tests/testthat/test-term_counts.R | 85 corpus-0.8.0/corpus/tests/testthat/test-term_matrix.R | 80 corpus-0.8.0/corpus/tests/testthat/test-text.R | 82 corpus-0.8.0/corpus/tests/testthat/test-text_filter.R |only corpus-0.8.0/corpus/tests/testthat/test-text_locate.R |only corpus-0.8.0/corpus/tests/testthat/test-text_names.R | 1 corpus-0.8.0/corpus/tests/testthat/test-text_nunit.R | 14 corpus-0.8.0/corpus/tests/testthat/test-text_split_sentences.R | 36 corpus-0.8.0/corpus/tests/testthat/test-text_split_tokens.R | 19 corpus-0.8.0/corpus/tests/testthat/test-text_tokens.R | 21 corpus-0.8.0/corpus/tests/testthat/test-text_types.R |only corpus-0.8.0/corpus/tests/testthat/test-utf8_encode.R |only corpus-0.8.0/corpus/tests/testthat/test-utf8_format.R |only corpus-0.8.0/corpus/tests/testthat/test-utf8_print.R |only corpus-0.8.0/corpus/tests/testthat/test-utf8_valid.R |only corpus-0.8.0/corpus/tests/testthat/test-utf8_width.R |only corpus-0.8.0/corpus/tests/testthat/test-wordlist.R |only corpus-0.8.0/corpus/vignettes |only 119 files changed, 4828 insertions(+), 4043 deletions(-)
Title: IBM in-Database Analytics for R
Description: Functionality required to efficiently use R with IBM(R) Db2(R)
Warehouse offerings (formerly IBM dashDB(R)) and IBM Db2 for z/OS(R) in
conjunction with IBM Db2 Analytics Accelerator for z/OS.
Many basic and complex R operations are pushed down into the database,
which removes the main memory boundary of R and allows to make full
use of parallel processing in the underlying database.
Author: Alexander Eckert [aut, cre], Toni Bollinger [aut], Michael Wurst [aut], Craig Blaha [ctb] (documentation), IBM Corporation [cph]
Maintainer: Alexander Eckert <inza@de.ibm.com>
Diff between ibmdbR versions 1.48.0 dated 2016-10-16 and 1.49.0 dated 2017-07-19
ibmdbR-1.48.0/ibmdbR/tests/dashdb.RR |only ibmdbR-1.49.0/ibmdbR/DESCRIPTION | 24 ibmdbR-1.49.0/ibmdbR/MD5 | 79 +- ibmdbR-1.49.0/ibmdbR/NAMESPACE | 21 ibmdbR-1.49.0/ibmdbR/NEWS.md | 37 - ibmdbR-1.49.0/ibmdbR/R/aggregate.R | 5 ibmdbR-1.49.0/ibmdbR/R/close.R | 8 ibmdbR-1.49.0/ibmdbR/R/coldef.R | 199 ++---- ibmdbR-1.49.0/ibmdbR/R/connect.R | 68 +- ibmdbR-1.49.0/ibmdbR/R/connection.R | 212 +++--- ibmdbR-1.49.0/ibmdbR/R/data.frame.R | 408 ++++++------ ibmdbR-1.49.0/ibmdbR/R/data.frame.methods.R | 112 +-- ibmdbR-1.49.0/ibmdbR/R/divClust.R | 446 ++++++------- ibmdbR-1.49.0/ibmdbR/R/glm.R | 922 +++++++++++++--------------- ibmdbR-1.49.0/ibmdbR/R/idadf.R | 3 ibmdbR-1.49.0/ibmdbR/R/kMeans.R | 184 ++--- ibmdbR-1.49.0/ibmdbR/R/list.R | 116 +-- ibmdbR-1.49.0/ibmdbR/R/lm.R | 392 ++++++----- ibmdbR-1.49.0/ibmdbR/R/merge.R | 2 ibmdbR-1.49.0/ibmdbR/R/model.management.R | 103 +-- ibmdbR-1.49.0/ibmdbR/R/nb.R | 196 ++--- ibmdbR-1.49.0/ibmdbR/R/parse.formula.R | 31 ibmdbR-1.49.0/ibmdbR/R/plot.idaLm.R | 281 ++++---- ibmdbR-1.49.0/ibmdbR/R/rules.R | 413 ++++++------ ibmdbR-1.49.0/ibmdbR/R/sample.R | 8 ibmdbR-1.49.0/ibmdbR/R/save.R | 237 +++---- ibmdbR-1.49.0/ibmdbR/R/sql.R | 584 ++++++++--------- ibmdbR-1.49.0/ibmdbR/R/statistics.R | 305 ++++----- ibmdbR-1.49.0/ibmdbR/R/tree.R | 240 +++---- ibmdbR-1.49.0/ibmdbR/R/twoStep.R | 496 +++++++-------- ibmdbR-1.49.0/ibmdbR/README.md | 42 - ibmdbR-1.49.0/ibmdbR/build/vignette.rds |binary ibmdbR-1.49.0/ibmdbR/inst/doc/ibmdbR.Rnw | 840 ++++++++++++++----------- ibmdbR-1.49.0/ibmdbR/inst/doc/ibmdbR.pdf |binary ibmdbR-1.49.0/ibmdbR/man/ida.list.Rd | 2 ibmdbR-1.49.0/ibmdbR/man/idaConnect.Rd | 7 ibmdbR-1.49.0/ibmdbR/man/idaLm.Rd | 4 ibmdbR-1.49.0/ibmdbR/man/idatools.Rd | 7 ibmdbR-1.49.0/ibmdbR/tests/common.RR |only ibmdbR-1.49.0/ibmdbR/tests/db2warehouse.RR |only ibmdbR-1.49.0/ibmdbR/tests/main.R | 15 ibmdbR-1.49.0/ibmdbR/vignettes/ibmdbR.Rnw | 840 ++++++++++++++----------- 42 files changed, 4125 insertions(+), 3764 deletions(-)
Title: Estimation and Inference Methods for Counterfactual Analysis
Description: Implements the estimation and inference methods for counterfactual analysis described in Chernozhukov, Fernandez-Val and Melly (2013) <DOI:10.3982/ECTA10582> "Inference on Counterfactual Distributions," Econometrica, 81(6). The counterfactual distributions considered are the result of changing either the marginal distribution of covariates related to the outcome variable of interest, or the conditional distribution of the outcome given the covariates. They can be applied to estimate quantile treatment effects and wage decompositions.
Author: Mingli Chen, Victor Chernozhukov, Ivan Fernandez-Val, Blaise Melly
Maintainer: Ivan Fernandez-Val <ivanf@bu.edu>
Diff between Counterfactual versions 1.0 dated 2016-09-20 and 1.1 dated 2017-07-19
DESCRIPTION | 6 MD5 | 16 R/counterfactual.r | 2559 +++++++++++++++++++++++++------------------------ build/vignette.rds |binary inst/doc/vignette.R | 38 inst/doc/vignette.Rnw | 69 - inst/doc/vignette.pdf |binary man/counterfactual.Rd | 10 vignettes/vignette.Rnw | 69 - 9 files changed, 1454 insertions(+), 1313 deletions(-)
More information about Counterfactual at CRAN
Permanent link
Title: Generate Varied Types of Books and Documents with R 'bookdown'
Package
Description: A collection and selector of R 'bookdown' templates. 'bookdownplus' helps you write academic journal articles, guitar books, chemical equations, mails, calendars, and diaries. R 'bookdownplus' extends the features of 'bookdown', and simplifies the procedure. Users only have to choose a template, clarify the book title and author name, and then focus on writing the text. No need to struggle in YAML and LaTeX.
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>
Diff between bookdownplus versions 1.0.2 dated 2017-06-21 and 1.3.0 dated 2017-07-19
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bookdownplus-1.3.0/bookdownplus/inst/rmd/body.Rmd | 90 +- bookdownplus-1.3.0/bookdownplus/inst/rmd/body_article2_zh.Rmd |only bookdownplus-1.3.0/bookdownplus/inst/rmd/body_article_zh.Rmd | 97 +- bookdownplus-1.3.0/bookdownplus/inst/rmd/body_discussion.Rmd |only bookdownplus-1.3.0/bookdownplus/inst/rmd/body_journal.Rmd | 87 +- bookdownplus-1.3.0/bookdownplus/inst/rmd/body_mail.Rmd | 4 bookdownplus-1.3.0/bookdownplus/inst/rmd/body_nte_zh.Rmd |only bookdownplus-1.3.0/bookdownplus/inst/rmd/body_thesis_classic.Rmd | 88 +- bookdownplus-1.3.0/bookdownplus/inst/rmd/body_thesis_mypku_zh.Rmd |only bookdownplus-1.3.0/bookdownplus/inst/rmd/body_thesis_zju_zh.Rmd |only bookdownplus-1.3.0/bookdownplus/inst/rmd/index_article.Rmd | 6 bookdownplus-1.3.0/bookdownplus/inst/rmd/index_article2_zh.Rmd |only bookdownplus-1.3.0/bookdownplus/inst/rmd/index_article_mdpi.Rmd | 6 bookdownplus-1.3.0/bookdownplus/inst/rmd/index_article_zh.Rmd | 4 bookdownplus-1.3.0/bookdownplus/inst/rmd/index_calendar.Rmd | 2 bookdownplus-1.3.0/bookdownplus/inst/rmd/index_discussion.Rmd |only bookdownplus-1.3.0/bookdownplus/inst/rmd/index_guitar.Rmd | 2 bookdownplus-1.3.0/bookdownplus/inst/rmd/index_journal.Rmd | 2 bookdownplus-1.3.0/bookdownplus/inst/rmd/index_nte_zh.Rmd |only bookdownplus-1.3.0/bookdownplus/inst/rmd/index_poem.Rmd | 2 bookdownplus-1.3.0/bookdownplus/inst/rmd/index_poster.Rmd | 18 bookdownplus-1.3.0/bookdownplus/inst/rmd/index_thesis_classic.Rmd | 4 bookdownplus-1.3.0/bookdownplus/inst/rmd/index_thesis_mypku_zh.Rmd |only bookdownplus-1.3.0/bookdownplus/inst/rmd/index_thesis_ubt.Rmd | 4 bookdownplus-1.3.0/bookdownplus/inst/rmd/index_thesis_zju_zh.Rmd |only bookdownplus-1.3.0/bookdownplus/inst/showcase |only bookdownplus-1.3.0/bookdownplus/inst/style/collection.sty |only bookdownplus-1.3.0/bookdownplus/inst/style/gitbook.css |only bookdownplus-1.3.0/bookdownplus/inst/style/moderncv.cls |only bookdownplus-1.3.0/bookdownplus/inst/style/moderncvcolorblack.sty |only 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bookdownplus-1.3.0/bookdownplus/inst/tex/template_thesis_zju_zh.tex |only bookdownplus-1.3.0/bookdownplus/man/bookdownplus.Rd | 160 ++- bookdownplus-1.3.0/bookdownplus/man/mail_bodysize.Rd |only bookdownplus-1.3.0/bookdownplus/man/mail_font.Rd |only bookdownplus-1.3.0/bookdownplus/man/mail_fontsize.Rd |only bookdownplus-1.3.0/bookdownplus/man/mail_style.Rd |only bookdownplus-1.3.0/bookdownplus/man/mail_theme.Rd |only bookdownplus-1.3.0/bookdownplus/man/more_output.Rd |only bookdownplus-1.3.0/bookdownplus/man/poster_theme.Rd |only bookdownplus-1.3.0/bookdownplus/man/template.Rd |only 83 files changed, 1161 insertions(+), 436 deletions(-)
Title: API Wrapper for the UK REF 2014 Impact Case Studies Database
Description: Provides wrapper functions around the UK Research
Excellence Framework 2014 Impact Case Studies Database API
<http://impact.ref.ac.uk/>. The database contains relevant publication and
research metadata about each case study as well as several paragraphs of
text from the case study submissions. Case studies in the database are
licenced under a CC-BY 4.0 licence
<http://creativecommons.org/licenses/by/4.0/legalcode>.
Author: Perry Stephenson [aut, cre]
Maintainer: Perry Stephenson <perry.stephenson+cran@gmail.com>
Diff between refimpact versions 0.1.0 dated 2016-09-26 and 1.0.0 dated 2017-07-19
refimpact-0.1.0/refimpact/R/get_institutions.R |only refimpact-0.1.0/refimpact/R/get_tag_types.R |only refimpact-0.1.0/refimpact/R/get_tag_values.R |only refimpact-0.1.0/refimpact/R/get_units_of_assessment.R |only refimpact-0.1.0/refimpact/R/search_case_studies.R |only refimpact-0.1.0/refimpact/tests/testthat/test_input_validation_case_study.R |only refimpact-0.1.0/refimpact/tests/testthat/test_institutions.R |only refimpact-0.1.0/refimpact/tests/testthat/test_search_case_studies.R |only refimpact-0.1.0/refimpact/tests/testthat/test_tag_types.R |only refimpact-0.1.0/refimpact/tests/testthat/test_tag_values.R |only refimpact-0.1.0/refimpact/tests/testthat/test_units_of_assessment.R |only refimpact-1.0.0/refimpact/DESCRIPTION | 20 - refimpact-1.0.0/refimpact/MD5 | 65 +++-- refimpact-1.0.0/refimpact/NAMESPACE | 1 refimpact-1.0.0/refimpact/NEWS.md | 18 + refimpact-1.0.0/refimpact/R/input_validation.R |only refimpact-1.0.0/refimpact/R/ref_get.R |only refimpact-1.0.0/refimpact/R/refimpact.R | 18 + refimpact-1.0.0/refimpact/R/x_get_institutions.R |only refimpact-1.0.0/refimpact/R/x_get_tag_types.R |only refimpact-1.0.0/refimpact/R/x_get_tag_values.R |only refimpact-1.0.0/refimpact/R/x_get_units_of_assessment.R |only refimpact-1.0.0/refimpact/R/x_search_case_studies.R |only refimpact-1.0.0/refimpact/R/zzz.R | 4 refimpact-1.0.0/refimpact/README.md | 119 ++-------- refimpact-1.0.0/refimpact/build |only refimpact-1.0.0/refimpact/data |only refimpact-1.0.0/refimpact/inst |only refimpact-1.0.0/refimpact/man/get_case_studies.Rd | 10 refimpact-1.0.0/refimpact/man/get_institutions.Rd | 9 refimpact-1.0.0/refimpact/man/get_tag_types.Rd | 8 refimpact-1.0.0/refimpact/man/get_tag_values.Rd | 8 refimpact-1.0.0/refimpact/man/get_units_of_assessment.Rd | 8 refimpact-1.0.0/refimpact/man/ref_get.Rd |only refimpact-1.0.0/refimpact/man/ref_tags.Rd |only refimpact-1.0.0/refimpact/man/refimpact.Rd | 4 refimpact-1.0.0/refimpact/tests/testthat/ListInstitutions.rds |only refimpact-1.0.0/refimpact/tests/testthat/ListTagTypes.rds |only refimpact-1.0.0/refimpact/tests/testthat/ListTagValues.rds |only refimpact-1.0.0/refimpact/tests/testthat/ListUoA.rds |only refimpact-1.0.0/refimpact/tests/testthat/SearchCaseStudies_1.rds |only refimpact-1.0.0/refimpact/tests/testthat/SearchCaseStudies_2.rds |only refimpact-1.0.0/refimpact/tests/testthat/SearchCaseStudies_3.rds |only refimpact-1.0.0/refimpact/tests/testthat/SearchCaseStudies_4.rds |only refimpact-1.0.0/refimpact/tests/testthat/SearchCaseStudies_5.rds |only refimpact-1.0.0/refimpact/tests/testthat/SearchCaseStudies_6.rds |only refimpact-1.0.0/refimpact/tests/testthat/SearchCaseStudies_7.rds |only refimpact-1.0.0/refimpact/tests/testthat/SearchCaseStudies_8.rds |only refimpact-1.0.0/refimpact/tests/testthat/test_input_validation.R |only refimpact-1.0.0/refimpact/tests/testthat/test_ref_get.R |only refimpact-1.0.0/refimpact/vignettes |only 51 files changed, 142 insertions(+), 150 deletions(-)
Title: Differential RNA Methylation Analysis for Count-Based
Small-Sample Sequencing Data with a Quad-Negative Binomial
Model
Description: As a newly emerged research area, RNA epigenetics has drawn increasing
attention recently for the participation of RNA methylation and other
modifications in a number of crucial biological processes. Thanks to high
throughput sequencing techniques, such as m6A-Seq, transcriptome-wide RNA
methylation profile is now available in the form of count-based data, with
which it is often of interests to study the dynamics in epitranscriptomic
layer. However, the sample size of RNA methylation experiment is usually
very small due to its costs; and additionally, there usually exist a large
number of genes whose methylation level cannot be accurately estimated due
to their low expression level, making differential RNA methylation analysis
a difficult task.
We present QNB, a statistical approach for differential RNA methylation
analysis with count-based small-sample sequencing data. The method is based
on 4 independent negative binomial distributions with their variances and
means linked by local regressions. QNB showed improved performance on
simulated and real m6A-Seq datasets when compared with competing algorithms.
And the QNB model is also applicable to other datasets related RNA
modifications, including but not limited to RNA bisulfite sequencing,
m1A-Seq, Par-CLIP, RIP-Seq, etc.Please don't hesitate to contact
<liulian19860905@163.com> if you have any questions.
Author: Lian Liu <liulian19860905@163.com>
Maintainer: Lian Liu <liulian19860905@163.com>
Diff between QNB versions 1.1.8 dated 2017-05-23 and 1.1.9 dated 2017-07-19
QNB-1.1.8/QNB/inst/doc/QNB.bib |only QNB-1.1.9/QNB/DESCRIPTION | 12 +- QNB-1.1.9/QNB/MD5 | 19 +-- QNB-1.1.9/QNB/NAMESPACE | 5 QNB-1.1.9/QNB/R/estimateP.R | 2 QNB-1.1.9/QNB/build/vignette.rds |binary QNB-1.1.9/QNB/inst/doc/QNB-Overview.R | 164 ++++++++++++++++++++++++++++--- QNB-1.1.9/QNB/inst/doc/QNB-Overview.Rnw | 138 ++++++++++++++++++++++++-- QNB-1.1.9/QNB/inst/doc/QNB-Overview.pdf |binary QNB-1.1.9/QNB/man/QNB-package.Rd | 4 QNB-1.1.9/QNB/vignettes/QNB-Overview.Rnw | 134 ++++++++++++++++++++++++- 11 files changed, 434 insertions(+), 44 deletions(-)
Title: Matching Event Data by Location, Time and Type
Description: Framework for merging and disambiguating event data based on spatiotemporal co-occurrence and secondary event characteristics. It can account for intrinsic "fuzziness" in the coding of events, varying event taxonomies and different geo-precision codes.
Author: Karsten Donnay and Eric Dunford
Maintainer: Karsten Donnay <kdonnay@gmx.net>
Diff between meltt versions 0.3.0 dated 2017-05-18 and 0.3.1 dated 2017-07-19
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NEWS |only R/meltt.R | 4 ++-- R/meltt.data.R | 40 +++++++++++++++++++++++++++++++++------- R/summary.meltt.R | 4 ++-- README.md |only man/meltt.data.Rd | 3 +++ 8 files changed, 51 insertions(+), 20 deletions(-)
Title: A Set of R6 Classes & a Shiny Application for Reducing Elemental
LA-ICPMS Data from Solid Structures
Description: Aims to facilitate the reduction of elemental microchemistry data from solid-phase LA-ICPMS analysis (laser ablation inductive coupled plasma mass spectrometry). The elementR package provides a reactive and user friendly interface for conducting all steps needed for an optimal data reduction while leaving maximum control for user.
Author: Charlotte Sirot, Francois Guilhaumon
Maintainer: Charlotte Sirot <charlott.sirot@gmail.com>
Diff between elementR versions 1.3.1 dated 2017-04-17 and 1.3.2 dated 2017-07-19
DESCRIPTION | 8 MD5 | 62 NAMESPACE | 9 R/App.R | 3444 +++++----- R/classElementR_R6.R | 120 R/convertMol_to_PPM.R |only R/convertPPM_to_Mol.R |only R/convertingReplicate.R |only R/splitReplicates.R |only README.md | 6 inst/AtomicMass.csv |only inst/Example_conversion |only inst/Results/CorrectnessTable.csv |only inst/Results/Example_Session.RData |binary inst/Results/PrecisionTable.csv |only inst/Results/SummarySettings.csv | 6 inst/Results/samples/Sample_1/finalCorr_Sample_1.csv | 106 inst/Results/samples/Sample_1/finalReplicates_Sample1_Rep2.csv.csv | 210 inst/Results/samples/Sample_1/final_Sample_1.csv | 210 inst/Results/samples/Sample_1/graphics |only inst/Results/samples/Sample_3 |only inst/elementR_documentation.pdf |binary inst/splitReplicate_example.csv |only inst/www/elementR.css | 11 man/convertMol_to_PPM.Rd |only man/convertPPM_to_Mol.Rd |only man/convertingReplicate.Rd |only man/splitReplicate.Rd |only 28 files changed, 2315 insertions(+), 1877 deletions(-)
Title: Efficient Network Enrichment Analysis Test
Description: Includes functions and examples to compute NEAT, the Network Enrichment Analysis Test described in Signorelli et al. (2016, <DOI:10.1186/s12859-016-1203-6>).
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@lumc.nl>
Diff between neat versions 1.1 dated 2017-05-25 and 1.1.1 dated 2017-07-19
DESCRIPTION | 13 - MD5 | 12 - build/vignette.rds |binary data/yeast.RData |binary inst/doc/neat.Rmd | 2 inst/doc/neat.html | 489 ++++++++++++++++++++++++++++++++++++----------------- vignettes/neat.Rmd | 2 7 files changed, 348 insertions(+), 170 deletions(-)
Title: Convert Files Between Markdown or Rmarkdown Files and Mindmaps
Description: Convert Markdown ('.md') or Rmarkdown ('.Rmd') files into FreeMind mindmap ('.mm') files, and vice versa. FreeMind mindmap ('.mm') files can be opened by or imported to common mindmap software such as 'FreeMind' (<http://freemind.sourceforge.net/wiki/index.php/Main_Page>) and 'XMind' (<http://www.xmind.net>).
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>
Diff between mindr versions 1.0.4 dated 2017-06-19 and 1.1.0 dated 2017-07-19
mindr-1.0.4/mindr/build |only mindr-1.0.4/mindr/inst/doc |only mindr-1.0.4/mindr/vignettes |only mindr-1.1.0/mindr/DESCRIPTION | 11 - mindr-1.1.0/mindr/MD5 | 42 +++++-- mindr-1.1.0/mindr/NAMESPACE | 5 mindr-1.1.0/mindr/R/foo.R | 186 +++++++++++++++++++++++++++++++-- mindr-1.1.0/mindr/inst/examples |only mindr-1.1.0/mindr/inst/htmlwidgets |only mindr-1.1.0/mindr/man/markmap.Rd |only mindr-1.1.0/mindr/man/markmapOutput.Rd |only mindr-1.1.0/mindr/man/md2mm.Rd | 6 - mindr-1.1.0/mindr/man/mm2md.Rd | 5 mindr-1.1.0/mindr/man/outline.Rd | 6 - mindr-1.1.0/mindr/man/renderMarkmap.Rd |only mindr-1.1.0/mindr/man/theme.Rd |only 16 files changed, 229 insertions(+), 32 deletions(-)
More information about BayesianGLasso at CRAN
Permanent link
Title: Modelling Actual, Potential and Reference Crop
Evapotranspiration
Description: Uses data and constants to calculate potential evapotranspiration (PET) and actual evapotranspiration (AET) from 21 different formulations including Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.
Author: Danlu Guo <danlu.guo@adelaide.edu.au>, Seth Westra <swestra@civeng.adelaide.edu.au>
Maintainer: Danlu Guo <danlu.guo@unsw.edu.au>
Diff between Evapotranspiration versions 1.10 dated 2016-12-09 and 1.11 dated 2017-07-19
DESCRIPTION | 10 MD5 | 60 NAMESPACE | 7 NEWS | 21 R/Evapotranspiration.R | 1171 ++++++++------- R/Reading.R | 3336 ++++++++++++++++++++++++------------------- data/climatedata.rda |binary data/processeddata.RData |binary man/ET.Abtew.Rd | 2 man/ET.BlaneyCriddle.Rd | 4 man/ET.BrutsaertStrickler.Rd | 2 man/ET.ChapmanAustralian.Rd | 2 man/ET.GrangerGray.Rd | 2 man/ET.Hamon.Rd | 2 man/ET.HargreavesSamani.Rd | 2 man/ET.JensenHaise.Rd | 1 man/ET.Linacre.Rd | 2 man/ET.Makkink.Rd | 2 man/ET.MattShuttleworth.Rd | 4 man/ET.McGuinnessBordne.Rd | 2 man/ET.MortonCRAE.Rd | 2 man/ET.MortonCRWE.Rd | 2 man/ET.PenPan.Rd | 2 man/ET.PenmanMonteith.Rd | 63 man/ET.PriestleyTaylor.Rd | 2 man/ET.Romanenko.Rd | 2 man/ET.SzilagyiJozsa.Rd | 2 man/ET.Turc.Rd | 2 man/ReadInputs.Rd | 112 - man/climatedata.Rd | 15 man/data.Rd | 8 31 files changed, 2717 insertions(+), 2127 deletions(-)
More information about Evapotranspiration at CRAN
Permanent link
Title: Functions for R Beginners
Description: Useful functions for R beginners, including hints for the arguments of the 'plot()' function, self-defined functions for error bars, user-customized pair plots and hist plots, enhanced linear regression figures, etc.. This package could be helpful to R experts as well.
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>
Diff between beginr versions 0.0.1 dated 2017-06-23 and 0.1.0 dated 2017-07-19
DESCRIPTION | 10 ++--- MD5 | 14 ++++--- NAMESPACE | 7 +++ R/foo.R | 101 +++++++++++++++++++++++++++++++++++++++++++++++----- inst |only man/plotcolorbar.Rd |only man/plotlty.Rd | 5 ++ man/plotpch.Rd | 5 ++ man/plotpkg.Rd |only man/rpkg.Rd |only 10 files changed, 122 insertions(+), 20 deletions(-)
Title: 'ggplot2' Faceting Utilities for Geographical Data
Description: Provides geofaceting functionality for 'ggplot2'. Geofaceting arranges a sequence of plots of data for different geographical entities into a grid that preserves some of the geographical orientation.
Author: Ryan Hafen [aut, cre]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between geofacet versions 0.1.4 dated 2017-06-20 and 0.1.5 dated 2017-07-19
DESCRIPTION | 6 - MD5 | 45 +++++--- NEWS.md |only R/facet_geo.R | 22 +++- R/grid_docs.R | 172 +++++++++++++++++++++++++++++--- R/valid_grids.R | 7 + README.md | 9 + build/vignette.rds |binary data/de_states_grid1.rda |only data/fr_regions_grid1.rda |only data/in_central_counties_grid1.rda |only data/in_counties_grid1.rda |only data/italy_grid1.rda |only data/italy_grid2.rda |only data/mx_state_grid1.rda |only data/mx_state_grid2.rda |only data/mys_grid1.rda |only data/or_counties_grid1.rda |only data/scotland_local_authority_grid1.rda |only data/se_counties_grid1.rda |only data/sea_grid1.rda |only data/sf_bay_area_counties_grid1.rda |only data/ua_region_grid1.rda |only data/us_state_grid3.rda |only data/wa_counties_grid1.rda |only inst/doc/docs.Rmd | 2 inst/doc/docs.html | 4 inst/doc/rd.Rmd | 2 inst/doc/rd.html | 4 man/grids.Rd | 165 ++++++++++++++++++++++++++++-- tests/testthat/test-grids.R |only vignettes/docs.Rmd | 2 vignettes/rd.Rmd | 2 33 files changed, 389 insertions(+), 53 deletions(-)
Title: Fast Structural Filtering
Description: An implementation of the fast structural filtering with L0 penalty. It includes an adaptive polynomial estimator by minimizing the least squares error with constraints on the number of breaks in their (k + 1)-st discrete derivative, for a chosen integer k >= 0. It also includes generalized structure sparsity constraint, i.e., graph trend filtering. This package is implemented via the primal dual active set algorithm, which formulates estimates and residuals as primal and dual variables, and utilizes efficient active set selection strategies based on the properties of the primal and dual variables.
Author: Canhong Wen, Xueqin Wang, Yanhe Shen, Aijun Zhang
Maintainer: Canhong Wen <wencanhong@gmail.com>
Diff between FastSF versions 0.1.0 dated 2017-07-08 and 0.1.1 dated 2017-07-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- src/l0fused_c.cpp | 2 +- src/l0gen_c.cpp | 2 +- src/l0tf_c.cpp | 2 +- src/sl0fused_c.cpp | 2 +- 6 files changed, 12 insertions(+), 12 deletions(-)
Title: Dose-Response Data Evaluation
Description: A somewhat outdated package of basic and easy-to-use functions for
fitting dose-response curves to continuous dose-response data, calculating some
toxicological parameters and plotting the results. Please consider using
the more powerful and actively developed 'drc' package. Functions that are
fitted are the cumulative density function of the log-normal distribution
('probit' fit), of the logistic distribution ('logit' fit), of the Weibull
distribution ('weibull' fit) and a linear-logistic model ('linlogit' fit),
derived from the latter, which is used to describe data showing stimulation at
low doses (hormesis). In addition, functions checking, plotting and retrieving
dose-response data retrieved from a database accessed via 'RODBC' are included.
As an alternative to the original fitting methods, the algorithms from the 'drc'
package can be used.
Author: Johannes Ranke [aut, cre]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between drfit versions 0.6.7 dated 2016-09-02 and 0.7.1 dated 2017-07-19
drfit-0.6.7/drfit/ChangeLog |only drfit-0.7.1/drfit/DESCRIPTION | 27 ++--- drfit-0.7.1/drfit/MD5 | 47 ++++----- drfit-0.7.1/drfit/NAMESPACE | 5 drfit-0.7.1/drfit/R/checkcontrols.R |only drfit-0.7.1/drfit/R/checkexperiment.R | 136 ++++++++++++++++++--------- drfit-0.7.1/drfit/R/checksubstance.R | 52 +++++----- drfit-0.7.1/drfit/R/drcfit.R | 34 +++--- drfit-0.7.1/drfit/R/drdata.R | 10 + drfit-0.7.1/drfit/R/drfit.R | 47 +++++---- drfit-0.7.1/drfit/R/drplot.R | 36 +++---- drfit-0.7.1/drfit/man/IM1xIPC81.Rd | 2 drfit-0.7.1/drfit/man/IM1xVibrio.Rd | 8 - drfit-0.7.1/drfit/man/XY.Rd | 2 drfit-0.7.1/drfit/man/antifoul.Rd | 12 +- drfit-0.7.1/drfit/man/checkcontrols.Rd |only drfit-0.7.1/drfit/man/checkexperiment.Rd | 4 drfit-0.7.1/drfit/man/checksubstance.Rd | 17 +-- drfit-0.7.1/drfit/man/drcfit.Rd | 20 +-- drfit-0.7.1/drfit/man/drdata.Rd | 24 ++-- drfit-0.7.1/drfit/man/drfit-package.Rd | 2 drfit-0.7.1/drfit/man/drfit.Rd | 22 ++-- drfit-0.7.1/drfit/man/drplot.Rd | 26 ++--- drfit-0.7.1/drfit/man/linlogitf.Rd | 6 - drfit-0.7.1/drfit/tests/IM1xIPC81.Rout.save | 29 +---- drfit-0.7.1/drfit/tests/pyrithione.Rout.save | 14 -- 26 files changed, 316 insertions(+), 266 deletions(-)
Title: R Client for 'Datadog' API
Description: Query for metrics from 'Datadog' (<https://www.datadoghq.com/>) via its API.
Author: Hiroaki Yutani [aut, cre]
Maintainer: Hiroaki Yutani <yutani.ini@gmail.com>
Diff between datadogr versions 0.1.0 dated 2017-05-31 and 0.1.1 dated 2017-07-19
datadogr-0.1.0/datadogr/man/k9_events.Rd |only datadogr-0.1.1/datadogr/DESCRIPTION | 6 - datadogr-0.1.1/datadogr/MD5 | 22 ++-- datadogr-0.1.1/datadogr/NAMESPACE | 2 datadogr-0.1.1/datadogr/NEWS.md | 6 + datadogr-0.1.1/datadogr/R/K9_events.R | 57 ++++++----- datadogr-0.1.1/datadogr/R/K9_metrics.R | 22 ++-- datadogr-0.1.1/datadogr/R/util.R | 28 +++++ datadogr-0.1.1/datadogr/README.md | 12 +- datadogr-0.1.1/datadogr/man/k9_get_events.Rd |only datadogr-0.1.1/datadogr/man/k9_get_metrics.Rd | 4 datadogr-0.1.1/datadogr/man/k9_list_metrics.Rd | 2 datadogr-0.1.1/datadogr/tests/testthat/test-to_epochperiod.R |only datadogr-0.1.1/datadogr/tests/testthat/test-to_epochtime.R |only 14 files changed, 112 insertions(+), 49 deletions(-)
Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill
Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>
Diff between BIGDAWG versions 1.14 dated 2017-07-10 and 1.14.2 dated 2017-07-19
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 9 +++++++++ R/BIGDAWG.R | 12 +++++------- R/H_wrapper_MC.R | 18 ++++++++++++------ R/general_functions.R | 13 +++++++++---- inst/doc/BIGDAWG.Rmd | 4 ++-- inst/doc/BIGDAWG.html | 6 +++--- vignettes/BIGDAWG.Rmd | 4 ++-- 9 files changed, 54 insertions(+), 36 deletions(-)