Title: Read GenAlEx Files Directly from Excel
Description: GenAlEx is a popular Excel macro for genetic analysis. The 'poppr'
R package allows import of GenAlEx formatted CSV data. This package serves as a
small 'poppr' add on for those who have trouble or simply do not want to export
their data into CSV format.
Author: Zhian N. Kamvar [cre, aut],
Niklaus J. Grünwald [ths]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>
Diff between popprxl versions 0.1.1 dated 2015-11-24 and 0.1.2 dated 2016-05-25
DESCRIPTION | 18 +++++++---- MD5 | 19 +++++++++--- NEWS | 11 +++++++ R/popprxl-package.r |only R/read_genalexcel.R | 8 +++-- README.md | 58 +++++++++++++++++++++++++++++--------- build |only inst/doc |only inst/files/num_isolates_text.xlsx |only inst/files/num_samp_greater.xlsx |only man/popprxl.Rd |only tests/testthat/test-import.R | 9 +++++ vignettes |only 13 files changed, 95 insertions(+), 28 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers.
Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures
can either be created and verified manually or via x509 certificates. AES can be
used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public
key) encryption or EC for Diffie Hellman. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure
random number generator, and 'bignum' math methods for manually performing
crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut],
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between openssl versions 0.9.3 dated 2016-05-04 and 0.9.4 dated 2016-05-25
DESCRIPTION | 16 ++++---- MD5 | 68 +++++++++++++++++++----------------- NAMESPACE | 12 +++++- NEWS | 7 +++ R/aes.R | 62 ++++++++++++++++++++++++++++---- R/bignum.R | 7 +++ R/build.R |only R/cert.R | 3 + R/diffie.R | 15 ++++--- R/hash.R | 7 ++- R/openssh.R | 2 - R/ssh2.R | 9 +--- build/vignette.rds |binary inst/doc/bignum.R | 1 inst/doc/bignum.Rmd | 1 inst/doc/bignum.html | 32 +++++++++------- inst/doc/crypto_hashing.html | 4 +- inst/doc/keys.R |only inst/doc/keys.Rmd |only inst/doc/keys.html |only inst/doc/secure_rng.html | 18 ++++----- inst/testkey.pem |only man/aes_cbc.Rd | 17 +++++++++ man/bignum.Rd | 3 + man/certificates.Rd | 4 ++ man/ec_dh.Rd | 15 ++++--- src/aes.c | 35 +++++++++--------- src/bignum.c | 14 +++++++ src/keygen.c | 20 ++++++---- src/openssh.c | 48 ++++++++++++++++++++++++- tests/testthat/test_keys_dsa.R | 12 ++++++ tests/testthat/test_keys_ecdsa.R | 7 +++ tests/testthat/test_keys_ecdsa384.R | 7 +++ tests/testthat/test_keys_ecdsa521.R | 7 +++ tests/testthat/test_keys_rsa.R | 12 ++++++ tests/testthat/test_my_key.R | 3 + vignettes/bignum.Rmd | 1 vignettes/keys.Rmd |only 38 files changed, 344 insertions(+), 125 deletions(-)
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees.
This package includes a shiny interface which can be started from R using
'treescapeServer()'.
Author: Thibaut Jombart [aut],
Michelle Kendall [aut, cre],
Jacob Almagro-Garcia [aut],
Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>
Diff between treescape versions 1.8.16 dated 2016-04-01 and 1.9.16 dated 2016-05-25
treescape-1.8.16/treescape/inst/shiny/www/img/svg |only treescape-1.8.16/treescape/vignettes/figs/findgroves-with-emphasis-1.png |only treescape-1.8.16/treescape/vignettes/figs/plotgroves2-1.png |only treescape-1.8.16/treescape/vignettes/figs/plotgroves2-2.png |only treescape-1.8.16/treescape/vignettes/figs/plotgroves2-3.png |only treescape-1.8.16/treescape/vignettes/figs/plotgroves3-1.png |only treescape-1.8.16/treescape/vignettes/figs/server.png |only treescape-1.8.16/treescape/vignettes/figs/treescapescatter-1.png |only treescape-1.8.16/treescape/vignettes/figs/woodmice-tip-emphasis-1.png |only treescape-1.8.16/treescape/vignettes/figs/woodmicePlots-1.png |only treescape-1.8.16/treescape/vignettes/figs/woodmicePlots-2.png |only treescape-1.8.16/treescape/vignettes/figs/woodmicePlots-3.png |only treescape-1.8.16/treescape/vignettes/figs/woodmicePlots-4.png |only treescape-1.8.16/treescape/vignettes/figs/woodmicePlots-5.png |only treescape-1.8.16/treescape/vignettes/treescape.md |only treescape-1.9.16/treescape/DESCRIPTION | 8 treescape-1.9.16/treescape/MD5 | 85 +- treescape-1.9.16/treescape/NAMESPACE | 4 treescape-1.9.16/treescape/R/RcppExports.R | 14 treescape-1.9.16/treescape/R/data.R | 36 + treescape-1.9.16/treescape/R/medTree.R | 4 treescape-1.9.16/treescape/R/plotTreeDiff.R |only treescape-1.9.16/treescape/README.md | 218 ++---- treescape-1.9.16/treescape/build/vignette.rds |binary treescape-1.9.16/treescape/data/DengueBEASTMCC.RData |only treescape-1.9.16/treescape/data/DengueSeqs.RData |only treescape-1.9.16/treescape/inst/doc/DengueVignette.R |only treescape-1.9.16/treescape/inst/doc/DengueVignette.Rmd |only treescape-1.9.16/treescape/inst/doc/DengueVignette.html |only treescape-1.9.16/treescape/inst/doc/treescape.R | 119 +-- treescape-1.9.16/treescape/inst/doc/treescape.Rmd | 235 ++++--- treescape-1.9.16/treescape/inst/doc/treescape.html | 331 +++++----- treescape-1.9.16/treescape/inst/shiny/server.R | 217 ++++++ treescape-1.9.16/treescape/inst/shiny/ui.R | 129 +++ treescape-1.9.16/treescape/inst/shiny/www/html/help.html | 24 treescape-1.9.16/treescape/man/DengueBEASTMCC.Rd |only treescape-1.9.16/treescape/man/DengueSeqs.Rd |only treescape-1.9.16/treescape/man/DengueTrees.Rd | 2 treescape-1.9.16/treescape/man/medTree.Rd | 4 treescape-1.9.16/treescape/man/plotTreeDiff.Rd |only treescape-1.9.16/treescape/man/tipDiff.Rd |only treescape-1.9.16/treescape/vignettes/DengueVignette.Rmd |only treescape-1.9.16/treescape/vignettes/figs/BEASTtree_diffs-1.png |only treescape-1.9.16/treescape/vignettes/figs/BEASTtree_diffs-2.png |only treescape-1.9.16/treescape/vignettes/figs/compare_BEAST_to_other_trees-1.png |only treescape-1.9.16/treescape/vignettes/figs/compare_BEAST_to_other_trees-2.png |only treescape-1.9.16/treescape/vignettes/figs/compare_BEAST_to_other_trees-3.png |only treescape-1.9.16/treescape/vignettes/figs/compare_trees_NJ_v_ML-1.png |only treescape-1.9.16/treescape/vignettes/figs/distances_readme-1.png |only treescape-1.9.16/treescape/vignettes/figs/distances_readme-2.png |only treescape-1.9.16/treescape/vignettes/figs/findgroves-with-emphasis_readme-1.png |only treescape-1.9.16/treescape/vignettes/figs/make_NJ-1.png |only treescape-1.9.16/treescape/vignettes/figs/plotgroves2_readme-1.png |only treescape-1.9.16/treescape/vignettes/figs/plotgroves2_readme-2.png |only treescape-1.9.16/treescape/vignettes/figs/plotgroves2_readme-3.png |only treescape-1.9.16/treescape/vignettes/figs/plotgroves_readme-1.png |only treescape-1.9.16/treescape/vignettes/figs/scree_plot-1.png |only treescape-1.9.16/treescape/vignettes/figs/view_ML-1.png |only treescape-1.9.16/treescape/vignettes/figs/woodmice-tip-emphasis_readme-1.png |only treescape-1.9.16/treescape/vignettes/figs/woodmiceCluster1_readme-1.png |only treescape-1.9.16/treescape/vignettes/figs/woodmiceMedian_readme-1.png |only treescape-1.9.16/treescape/vignettes/figs/woodmicePlots_readme-1.png |only treescape-1.9.16/treescape/vignettes/figs/woodmicePlots_readme-2.png |only treescape-1.9.16/treescape/vignettes/figs/woodmicePlots_readme-3.png |only treescape-1.9.16/treescape/vignettes/figs/woodmice_plotTreeDiff-1.png |only treescape-1.9.16/treescape/vignettes/figs/woodmice_plotTreeDiff-2.png |only treescape-1.9.16/treescape/vignettes/figs/woodmice_plotTreeDiff_readme-1.png |only treescape-1.9.16/treescape/vignettes/figs/woodmice_plotTreeDiff_readme-2.png |only treescape-1.9.16/treescape/vignettes/treescape.Rmd | 224 ++++-- 69 files changed, 1059 insertions(+), 595 deletions(-)
Title: Wrapper Functions for FSL (FMRIB Software Library) from
Functional MRI of the Brain (FMRIB)
Description: Wrapper functions that interface with FSL (http://
fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a powerful and commonly-used neuroimaging
software, using system commands. The goal is to be able to interface with FSL
completely in R, where you pass R objects of class "nifti", implemented by
package 'oro.nifti', and the function executes an FSL command and returns an R
object of class "nifti" if desired.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between fslr versions 1.5.0 dated 2015-10-21 and 1.6.4.0 dated 2016-05-25
fslr-1.5.0/fslr/README.md |only fslr-1.6.4.0/fslr/DESCRIPTION | 21 fslr-1.6.4.0/fslr/MD5 | 554 ++++++++-------- fslr-1.6.4.0/fslr/NAMESPACE | 35 + fslr-1.6.4.0/fslr/R/applyEmptyImageDimensions.R |only fslr-1.6.4.0/fslr/R/applywarp.R | 8 fslr-1.6.4.0/fslr/R/aux_file.R | 3 fslr-1.6.4.0/fslr/R/bitpix.R | 3 fslr-1.6.4.0/fslr/R/breaker.R |only fslr-1.6.4.0/fslr/R/cal_max.R | 3 fslr-1.6.4.0/fslr/R/cal_min.R | 3 fslr-1.6.4.0/fslr/R/check_nifti.R | 14 fslr-1.6.4.0/fslr/R/checkimg.R | 5 fslr-1.6.4.0/fslr/R/checknii.R | 3 fslr-1.6.4.0/fslr/R/copyNIfTIHeader.R | 14 fslr-1.6.4.0/fslr/R/data_type.R | 3 fslr-1.6.4.0/fslr/R/datatype.R | 3 fslr-1.6.4.0/fslr/R/descrip.R | 3 fslr-1.6.4.0/fslr/R/dim_.R | 3 fslr-1.6.4.0/fslr/R/double_ortho.R | 3 fslr-1.6.4.0/fslr/R/dropEmptyImageDimensions.R | 88 +- fslr-1.6.4.0/fslr/R/fast.R | 16 fslr-1.6.4.0/fslr/R/finite_img.R |only fslr-1.6.4.0/fslr/R/flirt_apply.R | 8 fslr-1.6.4.0/fslr/R/fnirt.R | 16 fslr-1.6.4.0/fslr/R/fsl_anat.R | 2 fslr-1.6.4.0/fslr/R/fsl_data_dir.R |only fslr-1.6.4.0/fslr/R/fsl_slicetimer.R |only fslr-1.6.4.0/fslr/R/fslabs.R | 4 fslr-1.6.4.0/fslr/R/fslacos.R | 4 fslr-1.6.4.0/fslr/R/fsladd.R | 4 fslr-1.6.4.0/fslr/R/fslasin.R | 4 fslr-1.6.4.0/fslr/R/fslatan.R | 4 fslr-1.6.4.0/fslr/R/fslbinv.R | 4 fslr-1.6.4.0/fslr/R/fslchfiletype.R | 4 fslr-1.6.4.0/fslr/R/fslcos.R | 4 fslr-1.6.4.0/fslr/R/fslcpgeom.R | 4 fslr-1.6.4.0/fslr/R/fsldilate.R | 13 fslr-1.6.4.0/fslr/R/fsldiv.R | 4 fslr-1.6.4.0/fslr/R/fsledge.R | 4 fslr-1.6.4.0/fslr/R/fslentropy.R |only fslr-1.6.4.0/fslr/R/fslexp.R | 4 fslr-1.6.4.0/fslr/R/fslfill2.R | 6 fslr-1.6.4.0/fslr/R/fslgetorient.R |only fslr-1.6.4.0/fslr/R/fslhd.R | 667 +++++++++++--------- fslr-1.6.4.0/fslr/R/fslindex.R | 4 fslr-1.6.4.0/fslr/R/fsllog.R | 4 fslr-1.6.4.0/fslr/R/fslmean.R |only fslr-1.6.4.0/fslr/R/fslmul.R | 4 fslr-1.6.4.0/fslr/R/fslnan.R | 4 fslr-1.6.4.0/fslr/R/fslnanm.R | 4 fslr-1.6.4.0/fslr/R/fslrand.R | 4 fslr-1.6.4.0/fslr/R/fslrandn.R | 4 fslr-1.6.4.0/fslr/R/fslrecip.R | 4 fslr-1.6.4.0/fslr/R/fslrem.R | 4 fslr-1.6.4.0/fslr/R/fslroi.R |only fslr-1.6.4.0/fslr/R/fslsd.R |only fslr-1.6.4.0/fslr/R/fslsin.R | 4 fslr-1.6.4.0/fslr/R/fslsqr.R | 4 fslr-1.6.4.0/fslr/R/fslsqrt.R | 4 fslr-1.6.4.0/fslr/R/fslsub.R | 4 fslr-1.6.4.0/fslr/R/fslsum.R | 17 fslr-1.6.4.0/fslr/R/fsltan.R | 4 fslr-1.6.4.0/fslr/R/fslvolume.R |only fslr-1.6.4.0/fslr/R/getEmptyImageDimensions.R |only fslr-1.6.4.0/fslr/R/intent_code.R | 3 fslr-1.6.4.0/fslr/R/intent_name.R | 3 fslr-1.6.4.0/fslr/R/intent_p1.R | 3 fslr-1.6.4.0/fslr/R/intent_p2.R | 3 fslr-1.6.4.0/fslr/R/intent_p3.R | 3 fslr-1.6.4.0/fslr/R/magic.R | 3 fslr-1.6.4.0/fslr/R/maskEmptyImageDimensions.R |only fslr-1.6.4.0/fslr/R/mcflirt.R |only fslr-1.6.4.0/fslr/R/mni_fname.R |only fslr-1.6.4.0/fslr/R/ortho2.R | 2 fslr-1.6.4.0/fslr/R/ortho_diff.R | 13 fslr-1.6.4.0/fslr/R/overlay2.R |only fslr-1.6.4.0/fslr/R/pixdim.R | 1 fslr-1.6.4.0/fslr/R/qform.R | 1 fslr-1.6.4.0/fslr/R/qform_code.R | 3 fslr-1.6.4.0/fslr/R/readNIfTI2.R | 26 fslr-1.6.4.0/fslr/R/replace_dropped_dimensions.R |only fslr-1.6.4.0/fslr/R/rescale_img.R | 98 +- fslr-1.6.4.0/fslr/R/scl_inter.R | 3 fslr-1.6.4.0/fslr/R/scl_slope.R | 3 fslr-1.6.4.0/fslr/R/sform_code.R | 3 fslr-1.6.4.0/fslr/R/sizeof_hdr.R | 3 fslr-1.6.4.0/fslr/R/slice_code.R | 3 fslr-1.6.4.0/fslr/R/slice_duration.R | 3 fslr-1.6.4.0/fslr/R/slice_end.R | 3 fslr-1.6.4.0/fslr/R/slice_start.R | 3 fslr-1.6.4.0/fslr/R/susan.R | 2 fslr-1.6.4.0/fslr/R/tempimg.R | 24 fslr-1.6.4.0/fslr/R/toffset.R | 1 fslr-1.6.4.0/fslr/R/vox_offset.R | 3 fslr-1.6.4.0/fslr/R/window_img.R | 4 fslr-1.6.4.0/fslr/R/writenii.R | 32 fslr-1.6.4.0/fslr/R/zero_pad.R |only fslr-1.6.4.0/fslr/R/zlimmer.R |only fslr-1.6.4.0/fslr/build/vignette.rds |binary fslr-1.6.4.0/fslr/inst/doc/fslr.Rmd | 2 fslr-1.6.4.0/fslr/inst/doc/fslr.html | 2 fslr-1.6.4.0/fslr/man/applyEmptyImageDimensions.Rd |only fslr-1.6.4.0/fslr/man/aux_file-methods.Rd | 4 fslr-1.6.4.0/fslr/man/bitpix-methods.Rd | 4 fslr-1.6.4.0/fslr/man/breaker.Rd |only fslr-1.6.4.0/fslr/man/cal_max-methods.Rd | 4 fslr-1.6.4.0/fslr/man/cal_min-methods.Rd | 4 fslr-1.6.4.0/fslr/man/check_file.Rd | 8 fslr-1.6.4.0/fslr/man/check_nifti-methods.Rd | 10 fslr-1.6.4.0/fslr/man/check_outfile.Rd | 4 fslr-1.6.4.0/fslr/man/checkimg-methods.Rd | 9 fslr-1.6.4.0/fslr/man/checknii-methods.Rd | 7 fslr-1.6.4.0/fslr/man/checkout.Rd | 6 fslr-1.6.4.0/fslr/man/cog.Rd | 8 fslr-1.6.4.0/fslr/man/colorbar.Rd | 4 fslr-1.6.4.0/fslr/man/copyNIfTIHeader.Rd | 17 fslr-1.6.4.0/fslr/man/data_type-methods.Rd | 4 fslr-1.6.4.0/fslr/man/datatype-methods.Rd | 4 fslr-1.6.4.0/fslr/man/datatype.Rd | 16 fslr-1.6.4.0/fslr/man/descrip-methods.Rd | 4 fslr-1.6.4.0/fslr/man/dim_-methods.Rd | 4 fslr-1.6.4.0/fslr/man/double_ortho.Rd | 10 fslr-1.6.4.0/fslr/man/dropEmptyImageDimensions.Rd | 31 fslr-1.6.4.0/fslr/man/fast.Rd | 8 fslr-1.6.4.0/fslr/man/fast.help.Rd | 2 fslr-1.6.4.0/fslr/man/file_imgext.Rd | 4 fslr-1.6.4.0/fslr/man/finite_img-methods.Rd |only fslr-1.6.4.0/fslr/man/flirt.Rd | 6 fslr-1.6.4.0/fslr/man/flirt.help.Rd | 4 fslr-1.6.4.0/fslr/man/flirt_apply.Rd | 6 fslr-1.6.4.0/fslr/man/fnirt.Rd | 6 fslr-1.6.4.0/fslr/man/fnirt.help.Rd | 2 fslr-1.6.4.0/fslr/man/fnirt_with_affine.Rd | 6 fslr-1.6.4.0/fslr/man/fnirt_with_affine_apply.Rd | 8 fslr-1.6.4.0/fslr/man/fsl_anat.Rd | 4 fslr-1.6.4.0/fslr/man/fsl_anat.help.Rd | 2 fslr-1.6.4.0/fslr/man/fsl_applywarp.Rd | 6 fslr-1.6.4.0/fslr/man/fsl_applywarp.help.Rd | 2 fslr-1.6.4.0/fslr/man/fsl_atlas_dir.Rd |only fslr-1.6.4.0/fslr/man/fsl_biascorrect.Rd | 6 fslr-1.6.4.0/fslr/man/fsl_data_dir.Rd |only fslr-1.6.4.0/fslr/man/fsl_slicetimer.Rd |only fslr-1.6.4.0/fslr/man/fsl_std_dir.Rd |only fslr-1.6.4.0/fslr/man/fslabs.Rd | 10 fslr-1.6.4.0/fslr/man/fslabs.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslacos.Rd | 10 fslr-1.6.4.0/fslr/man/fslacos.help.Rd | 6 fslr-1.6.4.0/fslr/man/fsladd.Rd | 10 fslr-1.6.4.0/fslr/man/fsladd.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslasin.Rd | 10 fslr-1.6.4.0/fslr/man/fslasin.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslatan.Rd | 10 fslr-1.6.4.0/fslr/man/fslatan.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslbet.Rd | 8 fslr-1.6.4.0/fslr/man/fslbet.help.Rd | 4 fslr-1.6.4.0/fslr/man/fslbin.Rd | 6 fslr-1.6.4.0/fslr/man/fslbin.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslbinv.Rd | 10 fslr-1.6.4.0/fslr/man/fslbinv.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslchfiletype.Rd | 6 fslr-1.6.4.0/fslr/man/fslchfiletype.help.Rd | 4 fslr-1.6.4.0/fslr/man/fslcmd.Rd | 14 fslr-1.6.4.0/fslr/man/fslcog.Rd | 17 fslr-1.6.4.0/fslr/man/fslcos.Rd | 10 fslr-1.6.4.0/fslr/man/fslcos.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslcpgeom.Rd | 6 fslr-1.6.4.0/fslr/man/fslcpgeom.help.Rd | 4 fslr-1.6.4.0/fslr/man/fsldilate.Rd | 19 fslr-1.6.4.0/fslr/man/fsldir.Rd | 5 fslr-1.6.4.0/fslr/man/fsldiv.Rd | 10 fslr-1.6.4.0/fslr/man/fsldiv.help.Rd | 6 fslr-1.6.4.0/fslr/man/fsledge.Rd | 10 fslr-1.6.4.0/fslr/man/fsledge.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslentropy.Rd |only fslr-1.6.4.0/fslr/man/fslerode.Rd | 19 fslr-1.6.4.0/fslr/man/fslerode.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslexp.Rd | 10 fslr-1.6.4.0/fslr/man/fslexp.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslfill.Rd | 15 fslr-1.6.4.0/fslr/man/fslfill.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslfill2.Rd | 6 fslr-1.6.4.0/fslr/man/fslhd.Rd | 6 fslr-1.6.4.0/fslr/man/fslhd.help.Rd | 4 fslr-1.6.4.0/fslr/man/fslhd.parse.Rd | 6 fslr-1.6.4.0/fslr/man/fslhelp.Rd | 4 fslr-1.6.4.0/fslr/man/fslindex.Rd | 10 fslr-1.6.4.0/fslr/man/fslindex.help.Rd | 6 fslr-1.6.4.0/fslr/man/fsllog.Rd | 10 fslr-1.6.4.0/fslr/man/fsllog.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslmask.Rd | 12 fslr-1.6.4.0/fslr/man/fslmask.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslmaths.Rd | 6 fslr-1.6.4.0/fslr/man/fslmaths.help.Rd | 4 fslr-1.6.4.0/fslr/man/fslmean.Rd |only fslr-1.6.4.0/fslr/man/fslmerge.Rd | 8 fslr-1.6.4.0/fslr/man/fslmerge.help.Rd | 4 fslr-1.6.4.0/fslr/man/fslmul.Rd | 10 fslr-1.6.4.0/fslr/man/fslmul.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslnan.Rd | 10 fslr-1.6.4.0/fslr/man/fslnan.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslnanm.Rd | 10 fslr-1.6.4.0/fslr/man/fslnanm.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslorient.Rd | 6 fslr-1.6.4.0/fslr/man/fslorient.help.Rd | 4 fslr-1.6.4.0/fslr/man/fslorient_wrap.Rd |only fslr-1.6.4.0/fslr/man/fslorienter.Rd |only fslr-1.6.4.0/fslr/man/fslrand.Rd | 10 fslr-1.6.4.0/fslr/man/fslrand.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslrandn.Rd | 10 fslr-1.6.4.0/fslr/man/fslrandn.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslrange.Rd | 16 fslr-1.6.4.0/fslr/man/fslrecip.Rd | 10 fslr-1.6.4.0/fslr/man/fslrecip.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslrem.Rd | 10 fslr-1.6.4.0/fslr/man/fslrem.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslreorient2std.Rd | 6 fslr-1.6.4.0/fslr/man/fslreorient2std.help.Rd | 4 fslr-1.6.4.0/fslr/man/fslroi.Rd |only fslr-1.6.4.0/fslr/man/fslsd.Rd |only fslr-1.6.4.0/fslr/man/fslsin.Rd | 10 fslr-1.6.4.0/fslr/man/fslsin.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslsmooth.Rd | 15 fslr-1.6.4.0/fslr/man/fslsmooth.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslsqr.Rd | 10 fslr-1.6.4.0/fslr/man/fslsqr.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslsqrt.Rd | 10 fslr-1.6.4.0/fslr/man/fslsqrt.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslstats.Rd | 13 fslr-1.6.4.0/fslr/man/fslstats.help.Rd | 7 fslr-1.6.4.0/fslr/man/fslsub.Rd | 10 fslr-1.6.4.0/fslr/man/fslsub.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslsub2.Rd | 12 fslr-1.6.4.0/fslr/man/fslsub2.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslsum.Rd | 9 fslr-1.6.4.0/fslr/man/fslswapdim.Rd | 6 fslr-1.6.4.0/fslr/man/fslswapdim.help.Rd | 4 fslr-1.6.4.0/fslr/man/fsltan.Rd | 10 fslr-1.6.4.0/fslr/man/fsltan.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslthresh.Rd | 12 fslr-1.6.4.0/fslr/man/fslthresh.help.Rd | 6 fslr-1.6.4.0/fslr/man/fslval.Rd | 6 fslr-1.6.4.0/fslr/man/fslval.help.Rd | 4 fslr-1.6.4.0/fslr/man/fslview.Rd | 4 fslr-1.6.4.0/fslr/man/fslview.help.Rd | 4 fslr-1.6.4.0/fslr/man/fslvol.Rd | 4 fslr-1.6.4.0/fslr/man/fslvolume.Rd |only fslr-1.6.4.0/fslr/man/get.fsl.Rd | 7 fslr-1.6.4.0/fslr/man/get.fsloutput.Rd | 4 fslr-1.6.4.0/fslr/man/get.imgext.Rd | 4 fslr-1.6.4.0/fslr/man/getEmptyImageDimensions.Rd |only fslr-1.6.4.0/fslr/man/getForms.Rd | 8 fslr-1.6.4.0/fslr/man/have.fsl.Rd | 2 fslr-1.6.4.0/fslr/man/intent_code-methods.Rd | 4 fslr-1.6.4.0/fslr/man/intent_name-methods.Rd | 4 fslr-1.6.4.0/fslr/man/intent_p1-methods.Rd | 4 fslr-1.6.4.0/fslr/man/intent_p2-methods.Rd | 4 fslr-1.6.4.0/fslr/man/intent_p3-methods.Rd | 4 fslr-1.6.4.0/fslr/man/magic-methods.Rd | 4 fslr-1.6.4.0/fslr/man/maskEmptyImageDimensions.Rd |only fslr-1.6.4.0/fslr/man/mask_img.Rd | 4 fslr-1.6.4.0/fslr/man/mcflirt.Rd |only fslr-1.6.4.0/fslr/man/mcflirt.help.Rd |only fslr-1.6.4.0/fslr/man/melodic.Rd | 4 fslr-1.6.4.0/fslr/man/melodic.help.Rd | 4 fslr-1.6.4.0/fslr/man/mni_fname.Rd |only fslr-1.6.4.0/fslr/man/mni_img.Rd |only fslr-1.6.4.0/fslr/man/multi_overlay.Rd |only fslr-1.6.4.0/fslr/man/newnii.Rd | 4 fslr-1.6.4.0/fslr/man/niftiarr.Rd | 2 fslr-1.6.4.0/fslr/man/nii.stub.Rd | 4 fslr-1.6.4.0/fslr/man/orientation-methods.Rd | 6 fslr-1.6.4.0/fslr/man/ortho2.Rd | 16 fslr-1.6.4.0/fslr/man/ortho_diff.Rd | 11 fslr-1.6.4.0/fslr/man/pixdim-methods.Rd | 4 fslr-1.6.4.0/fslr/man/qform_code-methods.Rd | 4 fslr-1.6.4.0/fslr/man/readNIfTI2.Rd | 15 fslr-1.6.4.0/fslr/man/replace_dropped_dimensions.Rd |only fslr-1.6.4.0/fslr/man/rescale_img.Rd | 14 fslr-1.6.4.0/fslr/man/robust_window.Rd | 6 fslr-1.6.4.0/fslr/man/scl_inter-methods.Rd | 4 fslr-1.6.4.0/fslr/man/scl_slope-methods.Rd | 4 fslr-1.6.4.0/fslr/man/sform_code-methods.Rd | 4 fslr-1.6.4.0/fslr/man/sizeof_hdr-methods.Rd | 4 fslr-1.6.4.0/fslr/man/slice_code-methods.Rd | 4 fslr-1.6.4.0/fslr/man/slice_duration-methods.Rd | 4 fslr-1.6.4.0/fslr/man/slice_end-methods.Rd | 4 fslr-1.6.4.0/fslr/man/slice_start-methods.Rd | 4 fslr-1.6.4.0/fslr/man/susan.Rd | 12 fslr-1.6.4.0/fslr/man/susan.help.Rd | 4 fslr-1.6.4.0/fslr/man/tempimg.Rd | 16 fslr-1.6.4.0/fslr/man/toffset-methods.Rd | 4 fslr-1.6.4.0/fslr/man/vox_offset-methods.Rd | 4 fslr-1.6.4.0/fslr/man/window_img.Rd | 6 fslr-1.6.4.0/fslr/man/writeNIfTI2.Rd | 19 fslr-1.6.4.0/fslr/man/xyz.Rd | 2 fslr-1.6.4.0/fslr/man/zero_pad.Rd |only fslr-1.6.4.0/fslr/man/zlimmer.Rd |only fslr-1.6.4.0/fslr/man/zscore_img.Rd | 14 fslr-1.6.4.0/fslr/vignettes/fslr.Rmd | 2 300 files changed, 1762 insertions(+), 1357 deletions(-)
Title: An Interface for MATLAB using System Calls
Description: Provides users to call MATLAB from using the "system" command.
Allows users to submit lines of code or MATLAB m files.
This is in comparison to 'R.matlab', which creates a MATLAB server.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between matlabr versions 1.1 dated 2015-10-21 and 1.1.3 dated 2016-05-25
matlabr-1.1.3/matlabr/DESCRIPTION | 15 +++--- matlabr-1.1.3/matlabr/MD5 | 23 ++++----- matlabr-1.1.3/matlabr/NAMESPACE | 2 matlabr-1.1.3/matlabr/R/matlab_script.R | 57 +++++++++++++++++++---- matlabr-1.1.3/matlabr/man/get_matlab.Rd | 9 ++- matlabr-1.1.3/matlabr/man/have_matlab.Rd | 13 ++++- matlabr-1.1.3/matlabr/man/rmat_to_matlab_mat.Rd | 4 - matlabr-1.1.3/matlabr/man/run_matlab_code.Rd | 2 matlabr-1.1.3/matlabr/man/run_matlab_script.Rd | 4 - matlabr-1.1.3/matlabr/man/rvec_to_matlab.Rd | 2 matlabr-1.1.3/matlabr/man/rvec_to_matlabcell.Rd | 4 - matlabr-1.1.3/matlabr/man/rvec_to_matlabclist.Rd | 4 - matlabr-1.1/matlabr/README.md |only 13 files changed, 96 insertions(+), 43 deletions(-)
Title: Black Box Optimization and Exploration of Parameter Space
Description: Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.
Author: François Rousset [aut, cre, cph],
Leblois Raphaël [ctb]
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between blackbox versions 1.0 dated 2016-04-14 and 1.0.8 dated 2016-05-25
DESCRIPTION | 16 +++++----- MD5 | 63 ++++++++++++++++++++++--------------------- NAMESPACE | 2 - R/Cpredict.R | 24 ++++++++++------ R/LRTfn.R | 4 +- R/OKrig.R | 3 -- R/blackbox.R | 2 - R/buildFONKgpointls.R | 2 - R/calcPredictorOK.R | 2 - R/calcProfileOK.R | 2 - R/calcgridRelProfile.R | 21 ++++++++------ R/canonize.R | 57 ++++++++++++++++++++++++++++++-------- R/findReplicates.R | 2 - R/findglobalMLE.R | 2 - R/fromFONKtoanyspace.R | 4 +- R/generateNewPoints.R | 46 ++++++++----------------------- R/generateNextpointsfromCI.R | 38 +++++++++++++++---------- R/overmessage.R | 7 ---- R/profileFn.R | 4 +- R/providefullhull.R | 4 +- R/prune_by_dist.R |only R/rhull.R | 4 +- R/sampleByResp.R | 9 ++---- R/savePredictor.R | 23 ++++++++++++--- R/subHullWrapper.R | 35 +++++++++-------------- R/zoomProfile.R | 2 - inst |only man/blackbox-internal.Rd | 5 +-- src/Krigmain.cpp | 5 ++- src/Makevars.win |only src/Matern.h | 2 - src/pointls.cpp | 3 +- src/qr.h | 6 ++-- src/smoothFriends.h | 6 ++-- 34 files changed, 218 insertions(+), 187 deletions(-)
Title: Data Exchange Between R and LabKey Server
Description: Allow a user to discover, query and modify data from a LabKey Server.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 2.1.129 dated 2015-12-15 and 2.1.130 dated 2016-05-25
DESCRIPTION | 10 - MD5 | 96 +++++++------- NAMESPACE | 44 +++--- NEWS | 208 ++++++++++++++++--------------- R/labkey.defaults.R |only R/labkey.deleteRows.R | 162 ++++++++---------------- R/labkey.executeSql.R | 72 ++-------- R/labkey.getFolders.R | 48 ------- R/labkey.getQueryInfo.R | 40 ------ R/labkey.getQueryLists.R | 51 +------ R/labkey.getSchemas.R | 40 ------ R/labkey.importRows.R | 53 -------- R/labkey.insertRows.R | 162 +++++++++--------------- R/labkey.saveBatch.R | 224 +++++++++++++-------------------- R/labkey.selectRows.R | 66 +-------- R/labkey.updateRows.R | 164 ++++++++---------------- R/makeDF.R | 30 +++- R/makeFilter.R | 238 ++++++++++++++++++------------------ R/schemaObjects.R | 2 build/vignette.rds |binary inst/doc/RlabkeyExample.Rnw | 12 - inst/doc/usersguide.pdf |binary man/Rlabkey-package.Rd | 143 ++++++++++----------- man/RlabkeyUsersGuide.Rd | 48 +++---- man/getFolderPath.Rd | 62 ++++----- man/getLookups.Rd | 102 +++++++-------- man/getRows.Rd | 98 +++++++------- man/getSchema.Rd | 100 +++++++-------- man/getSession.Rd | 186 ++++++++++++++-------------- man/labkey.deleteRows.Rd | 208 +++++++++++++++---------------- man/labkey.executeSql.Rd | 162 ++++++++++++------------ man/labkey.getDefaultViewDetails.Rd | 96 +++++++------- man/labkey.getFolders.Rd | 106 ++++++++-------- man/labkey.getLookupDetails.Rd | 150 +++++++++++----------- man/labkey.getQueries.Rd | 104 +++++++-------- man/labkey.getQueryDetails.Rd | 170 ++++++++++++------------- man/labkey.getQueryViews.Rd | 108 ++++++++-------- man/labkey.getSchemas.Rd | 98 +++++++------- man/labkey.insertRows.Rd | 182 +++++++++++++-------------- man/labkey.makeRemotePath.Rd | 90 ++++++------- man/labkey.saveBatch.Rd | 150 +++++++++++----------- man/labkey.selectRows.Rd | 224 ++++++++++++++++----------------- man/labkey.setDefaults.Rd |only man/labkey.updateRows.Rd | 188 ++++++++++++++-------------- man/lsFolders.Rd | 78 +++++------ man/lsProjects.Rd | 70 +++++----- man/lsSchemas.Rd | 70 +++++----- man/makeFilter.Rd | 222 ++++++++++++++++----------------- man/saveResults.Rd | 124 +++++++++--------- vignettes/RlabkeyExample.Rnw | 12 - 50 files changed, 2317 insertions(+), 2756 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 0.0-30 dated 2016-02-24 and 0.0-32 dated 2016-05-25
DESCRIPTION | 18 +++---- MD5 | 16 +++--- build/vignette.rds |binary inst/NEWS.Rd | 7 ++ inst/doc/mlt.R | 72 +++++++++++++++++++++++++---- inst/doc/mlt.Rnw | 129 ++++++++++++++++++++++++++++++++++++++++++++--------- inst/doc/mlt.pdf |binary vignettes/mlt.Rnw | 129 ++++++++++++++++++++++++++++++++++++++++++++--------- vignettes/mlt.bib | 27 +++++------ 9 files changed, 316 insertions(+), 82 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 0.0-32 dated 2016-05-25 and 0.0-33 dated 2016-05-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/R.R | 2 +- inst/NEWS.Rd | 7 +++++++ 4 files changed, 15 insertions(+), 8 deletions(-)
Title: Estimating Preferential Attachment from a Single Network
Snapshot by Markov Chain Monte Carlo
Description: A Markov chain Monte Carlo method is provided to estimate the preferential attachment function from a single network snapshot. Conventional methods require the complete information about the appearance order of all nodes and edges in the network. This package incorporates the appearance order into the state space and estimates it together with the preferential attachment function. Auxiliary variables are introduced to facilitate fast Gibbs sampling.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>
Diff between mcPAFit versions 0.1.2 dated 2016-05-17 and 0.1.3 dated 2016-05-25
DESCRIPTION | 14 MD5 | 16 NAMESPACE | 1 R/create_sim_data.R | 7 R/mcPAFit.R | 11 man/create_sim_data.Rd | 24 - man/mcPAFit-package.Rd | 22 - man/mcPAFit.Rd | 87 +--- src/Cpp_code.cpp | 861 ++++++++++++++++++++++--------------------------- 9 files changed, 481 insertions(+), 562 deletions(-)
Title: A New, Fast, and Outlier Resistant Hierarchical Clustering
Algorithm
Description: A new hierarchical clustering linkage criterion:
the Genie algorithm links two clusters in such a way that a chosen
economic inequity measure (e.g., the Gini index) of the cluster
sizes does not increase drastically above a given threshold. Benchmarks
indicate a high practical usefulness of the introduced method:
it most often outperforms the Ward or average linkage in terms of
the clustering quality while retaining the single linkage speed,
see (Gagolewski et al. 2016 <DOI:10.1016/j.ins.2016.05.003>)
for more details.
Author: Marek Gagolewski [aut, cre],
Maciej Bartoszuk [aut],
Anna Cena [aut]
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between genie versions 1.0.0 dated 2016-03-07 and 1.0.2 dated 2016-05-25
DESCRIPTION | 14 +++++++++----- MD5 | 15 ++++++++------- NEWS | 11 +++++++++++ R/genie-package.R | 13 +++++-------- R/hclust2.R | 2 +- inst |only man/genie-package.Rd | 7 +++++-- man/hclust2.Rd | 2 +- tests/testthat/test-single.R | 2 ++ 9 files changed, 42 insertions(+), 24 deletions(-)
Title: Dimension Reduction Methods for Multivariate Time Series
Description: Estimates VAR and VARX models with structured Lasso Penalties.
Author: Will Nicholson [cre, aut],
David Matteson [aut],
Jacob Bien [aut]
Maintainer: Will Nicholson <wbn8@cornell.edu>
Diff between BigVAR versions 1.0 dated 2016-05-17 and 1.0.1 dated 2016-05-25
DESCRIPTION | 6 MD5 | 53 ++-- NAMESPACE | 2 NEWS |only R/BigVAR.R | 2 R/BigVARAlgorithms.R | 96 ++++--- R/BigVARObjectClass.R | 192 ++++++++------- R/BigVARSupportFunctions.R | 161 +++++++----- man/A.Rd | 2 man/BigVAR-class.Rd | 4 man/BigVAR.Rd | 4 man/BigVAR.est-methods.Rd | 2 man/BigVAR.results-plot-methods.Rd | 2 man/BigVAR.results.Rd | 2 man/MultVarSim.Rd | 2 man/SparsityPlot.BigVAR.results-methods.Rd | 2 man/VARXFit.Rd | 5 man/VARXForecastEval.Rd | 3 man/VarptoVar1MC.Rd | 2 man/Y.Rd | 2 man/constructModel.Rd | 27 +- man/cv.BigVAR-methods.Rd | 4 man/plot.BigVAR-methods.Rd | 2 man/predict-methods-BigVAR.results.Rd | 2 man/show-methods-BigVAR.results.Rd | 2 man/show-methods.Rd | 4 src/DataCons.cpp | 365 +++++++++++++++++++++++------ src/ExperimentalBigVARFunctionsX.cpp | 30 +- 28 files changed, 647 insertions(+), 333 deletions(-)
Title: A Tool to Associate FASTA Sequences and Features
Description: Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses.
Author: Bettina Budeus
Maintainer: Bettina Budeus <bettina.budeus@stud.uni-due.de>
Diff between SeqFeatR versions 0.2.2 dated 2016-03-24 and 0.2.3 dated 2016-05-25
DESCRIPTION | 12 +- MD5 | 13 +- NAMESPACE | 13 ++ NEWS | 6 + R/comparewithancestral.R | 8 - inst/doc/SeqFeatR_tutorial.pdf |binary inst/extdata/Example_aa_for_cwa.fasta |only man/comparewithancestral.Rd | 156 +++++++++++++++++----------------- 8 files changed, 112 insertions(+), 96 deletions(-)
Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. Haplin also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. Haplin allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@fhi.no>
Diff between Haplin versions 5.5 dated 2015-05-15 and 6.0 dated 2016-05-25
Haplin-5.5/Haplin/R/f.make.design.R |only Haplin-6.0/Haplin/DESCRIPTION | 15 Haplin-6.0/Haplin/MD5 | 147 +++++---- Haplin-6.0/Haplin/NAMESPACE | 55 +-- Haplin-6.0/Haplin/R/coef.tri.glm.R | 4 Haplin-6.0/Haplin/R/f.EM.missing.R | 31 +- Haplin-6.0/Haplin/R/f.Rplot.R | 31 +- Haplin-6.0/Haplin/R/f.catch.R | 3 Haplin-6.0/Haplin/R/f.check.pars.R | 110 +++---- Haplin-6.0/Haplin/R/f.compute.effects.R | 6 Haplin-6.0/Haplin/R/f.data.R | 38 +- Haplin-6.0/Haplin/R/f.debug.pvalues.R | 18 - Haplin-6.0/Haplin/R/f.design.make.R |only Haplin-6.0/Haplin/R/f.final.loglike.R | 4 Haplin-6.0/Haplin/R/f.hapArg.R |only Haplin-6.0/Haplin/R/f.hapSim.R |only Haplin-6.0/Haplin/R/f.hapTests.R |only Haplin-6.0/Haplin/R/f.jackknife.R | 14 Haplin-6.0/Haplin/R/f.make.index.R | 26 + Haplin-6.0/Haplin/R/f.plot.effects.R | 59 +-- Haplin-6.0/Haplin/R/f.pos.match.R | 2 Haplin-6.0/Haplin/R/f.preliminary.freq.R | 55 +-- Haplin-6.0/Haplin/R/f.prep.dataout.R | 8 Haplin-6.0/Haplin/R/f.prob.R | 95 +++--- Haplin-6.0/Haplin/R/f.rand.geno.R | 7 Haplin-6.0/Haplin/R/f.redistribute.R | 23 - Haplin-6.0/Haplin/R/f.repl.thin.R | 2 Haplin-6.0/Haplin/R/f.sel.haplos.R | 59 ++- Haplin-6.0/Haplin/R/f.sel.markers.R | 5 Haplin-6.0/Haplin/R/f.sim.R | 35 +- Haplin-6.0/Haplin/R/f.var.covar.R | 6 Haplin-6.0/Haplin/R/gxe.R |only Haplin-6.0/Haplin/R/hapPower.R |only Haplin-6.0/Haplin/R/hapRun.R |only Haplin-6.0/Haplin/R/hapSim.R |only Haplin-6.0/Haplin/R/haplin.R | 237 ++++++++------- Haplin-6.0/Haplin/R/haplinSlide.R | 97 ++---- Haplin-6.0/Haplin/R/haplinStrat.R | 11 Haplin-6.0/Haplin/R/haptable.gxe.R |only Haplin-6.0/Haplin/R/haptable.haplin.R | 11 Haplin-6.0/Haplin/R/haptable.haplinSlide.R | 4 Haplin-6.0/Haplin/R/haptable.haplinStrat.R | 4 Haplin-6.0/Haplin/R/plot.haplin.R | 30 - Haplin-6.0/Haplin/R/print.gxe.R |only Haplin-6.0/Haplin/R/print.haplin.R | 2 Haplin-6.0/Haplin/R/print.summary.haplin.R | 2 Haplin-6.0/Haplin/R/print.summary.tri.glm.R | 20 - Haplin-6.0/Haplin/R/suest.R | 22 - Haplin-6.0/Haplin/R/summary.haplin.R | 41 +- Haplin-6.0/Haplin/R/summary.tri.glm.R | 19 - Haplin-6.0/Haplin/inst/doc/Haplin_data_format.pdf |binary Haplin-6.0/Haplin/inst/doc/Haplin_power.pdf |only Haplin-6.0/Haplin/inst/doc/index.html | 3 Haplin-6.0/Haplin/man/cbindFiles.Rd | 98 +++--- Haplin-6.0/Haplin/man/convertPed.Rd | 204 ++++++------- Haplin-6.0/Haplin/man/gwaaToHaplin.Rd | 118 +++---- Haplin-6.0/Haplin/man/gxe.Rd |only Haplin-6.0/Haplin/man/hapPower.Rd |only Haplin-6.0/Haplin/man/hapRun.Rd |only Haplin-6.0/Haplin/man/hapSim.Rd |only Haplin-6.0/Haplin/man/haplin.Rd | 296 +++++++++---------- Haplin-6.0/Haplin/man/haplinSlide.Rd | 146 ++++----- Haplin-6.0/Haplin/man/haplinStrat.Rd |only Haplin-6.0/Haplin/man/haplinTDT.Rd | 336 +++++++++++----------- Haplin-6.0/Haplin/man/haptable.Rd | 148 ++++----- Haplin-6.0/Haplin/man/lineByLine.Rd | 166 +++++----- Haplin-6.0/Haplin/man/output.Rd | 86 ++--- Haplin-6.0/Haplin/man/pQQ.Rd | 66 ++-- Haplin-6.0/Haplin/man/pedToHaplin.Rd | 110 +++---- Haplin-6.0/Haplin/man/plot.haplin.Rd | 94 +++--- Haplin-6.0/Haplin/man/plot.haplinTDT.Rd | 90 ++--- Haplin-6.0/Haplin/man/plot.haptable.Rd | 116 +++---- Haplin-6.0/Haplin/man/prepPed.Rd | 120 +++---- Haplin-6.0/Haplin/man/print.haplin.Rd | 64 ++-- Haplin-6.0/Haplin/man/print.summary.haplin.Rd | 88 ++--- Haplin-6.0/Haplin/man/rbindFiles.Rd | 122 +++---- Haplin-6.0/Haplin/man/snpPos.Rd | 2 Haplin-6.0/Haplin/man/snpPower.Rd | 144 ++++----- Haplin-6.0/Haplin/man/snpSampleSize.Rd | 137 ++++---- Haplin-6.0/Haplin/man/suest.Rd | 142 ++++----- Haplin-6.0/Haplin/man/summary.haplin.Rd | 80 ++--- Haplin-6.0/Haplin/man/summary.haplinTDT.Rd | 68 ++-- Haplin-6.0/Haplin/man/toDataFrame.Rd | 58 +-- 83 files changed, 2286 insertions(+), 2174 deletions(-)
Title: Kantorovich Distance Between Probability Measures
Description: Computes the Kantorovich distance between two probability measures on a finite set.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@yahoo.fr>
Diff between kantorovich versions 1.1.0 dated 2016-02-04 and 2.0.0 dated 2016-05-25
DESCRIPTION | 10 +- MD5 | 32 ++++---- NAMESPACE | 9 +- R/kantorovich.R | 8 -- R/kantorovich_glpk.R |only R/kantorovich_lpsolve.R |only build/vignette.rds |binary inst/doc/kantorovich.R | 18 ++++ inst/doc/kantorovich.Rmd | 39 +++++++++ inst/doc/kantorovich.html | 155 +++++++++++++++++++++++++-------------- man/kantorovich-package.Rd | 4 - man/kantorovich_glpk.Rd |only man/kantorovich_lp.Rd |only tests/testthat/test-Pascal.R | 66 +++++++++++++++- tests/testthat/test-edistances.R | 2 tests/testthat/test-ejoinings.R | 4 - tests/testthat/test-glpk.R |only tests/testthat/test-lpSolve.R |only tests/testthat/test-rotation.R | 32 +++++++- vignettes/kantorovich.Rmd | 39 +++++++++ 20 files changed, 327 insertions(+), 91 deletions(-)
Title: Directional Statistics
Description: A collection of R functions for directional data analysis.
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 1.9 dated 2016-04-21 and 2.0 dated 2016-05-25
DESCRIPTION | 10 +- MD5 | 90 ++++++++++++++----------- NAMESPACE | 8 +- R/acg.R | 18 +++-- R/circ.cor1.R | 19 +++-- R/circ.cor2.R | 25 ++++--- R/circlin.cor.R | 13 ++- R/conc.test.R | 13 ++- R/dirknn.tune.R | 6 - R/euclid.R | 3 R/f.rbing.R | 1 R/group.gof.R |only R/group.vm.R |only R/hcf.aov.R | 10 ++ R/hcf.circaov.R | 9 ++ R/kent.contour.R | 12 +-- R/kent.logcon.R |only R/kent.mle.R | 42 ++++++++--- R/lambert.inv.R | 9 +- R/matrixfisher.mle.R |only R/meandir.test.R | 36 +++++----- R/mediandir.R | 13 +-- R/mediandir_2.R | 14 +-- R/mix.vmf.R | 159 ++++++++++++++++++++++++++------------------- R/pvm.R |only R/rbingham.R | 54 ++++++++++++--- R/rfb.R | 4 - R/rkent.R | 5 - R/rmatrixfisher.R |only R/rvmf.R | 16 ++-- R/spher.reg.R | 7 + R/spml.reg.R | 47 ++++++++----- R/vmf.contour.R | 14 ++- R/vmf.kde.R | 2 R/vmfkde.tune.R | 10 +- R/wood.mle.R | 40 +++++++---- man/Directional-package.Rd | 14 +-- man/fb.saddle.Rd | 28 +++++-- man/group.gof.Rd |only man/group.vm.Rd |only man/kent.logcon.Rd |only man/kent.mle.Rd | 16 ++++ man/kuiper.Rd | 2 man/lambert.Rd | 10 ++ man/matrixfisher.mle.Rd |only man/pvm.Rd |only man/rfb.Rd | 6 - man/rkent.Rd | 4 - man/rmatrixfisher.Rd |only man/rvmf.Rd | 2 man/spml.reg.Rd | 3 man/wood.mle.Rd | 11 +++ 52 files changed, 512 insertions(+), 293 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 0.0-30 dated 2016-02-20 and 0.0-32 dated 2016-05-25
mlt-0.0-30/mlt/tests/AFT-Ex.Rout.save |only mlt-0.0-30/mlt/tests/GBSG2.Rout.save |only mlt-0.0-32/mlt/DESCRIPTION | 8 ++--- mlt-0.0-32/mlt/MD5 | 39 +++++++++++++-------------- mlt-0.0-32/mlt/NAMESPACE | 11 ++++++- mlt-0.0-32/mlt/R/confband.R | 2 - mlt-0.0-32/mlt/R/ctm.R | 45 ++++++++++++++++++++++++++++++-- mlt-0.0-32/mlt/R/distr.R | 26 +++++++++++------- mlt-0.0-32/mlt/R/dpq_etc.R | 45 ++++++++++++++++---------------- mlt-0.0-32/mlt/R/loglik.R | 19 ++++++++----- mlt-0.0-32/mlt/R/methods.R | 15 +++++++++- mlt-0.0-32/mlt/R/mlt.R | 35 ++++++++++++++---------- mlt-0.0-32/mlt/R/plot.R | 14 +++++++-- mlt-0.0-32/mlt/R/predict.R | 16 ++++++++--- mlt-0.0-32/mlt/R/sample.R | 22 ++++++++++----- mlt-0.0-32/mlt/inst/NEWS.Rd | 23 ++++++++++++++++ mlt-0.0-32/mlt/man/ctm-methods.Rd |only mlt-0.0-32/mlt/man/mlt-methods.Rd | 9 +++++- mlt-0.0-32/mlt/man/predict.Rd | 17 +++++++++--- mlt-0.0-32/mlt/tests/Cox-Ex.Rout.save | 8 ++--- mlt-0.0-32/mlt/tests/bugfixes.Rout.save | 14 ++++----- mlt-0.0-32/mlt/tests/lm-Ex.Rout.save | 10 +++---- 22 files changed, 257 insertions(+), 121 deletions(-)
Title: Methods for Tree-Based Local Adaptive Thresholding
Description: An implementation of TreeThresh, a locally adaptive version of EbayesThresh.
Author: Ludger Evers <ludger.evers@glasgow.ac.uk> and Tim Heaton
<t.heaton@sheffield.ac.uk>
Maintainer: Ludger Evers <ludger.evers@glasgow.ac.uk>
Diff between treethresh versions 0.1-8 dated 2014-11-20 and 0.1-9 dated 2016-05-25
DESCRIPTION | 13 ++++++------- MD5 | 11 +++++++---- NAMESPACE | 34 ++++++++++++++++++---------------- build/vignette.rds |binary inst/doc/onedwavillu.pdf |only inst/doc/prune.pdf |only inst/doc/twodwavillu.pdf |only man/coefficients.Rd | 2 +- 8 files changed, 32 insertions(+), 28 deletions(-)
Title: Simulating Longitudinal Data with Causal Inference Applications
Description: A flexible tool for simulating complex longitudinal data using
structural equations, with emphasis on problems in causal inference.
Specify interventions and simulate from intervened data generating
distributions. Define and evaluate treatment-specific means, the average
treatment effects and coefficients from working marginal structural models.
User interface designed to facilitate the conduct of transparent and
reproducible simulation studies, and allows concise expression of complex
functional dependencies for a large number of time-varying nodes. See the
package vignette for more information, documentation and examples.
Author: Oleg Sofrygin [aut, cre],
Mark J. van der Laan [aut],
Romain Neugebauer [aut]
Maintainer: Oleg Sofrygin <oleg.sofrygin@gmail.com>
Diff between simcausal versions 0.5.0 dated 2016-02-20 and 0.5.1 dated 2016-05-25
simcausal-0.5.0/simcausal/R/estimatetarget.r |only simcausal-0.5.0/simcausal/R/parserfunctions.r |only simcausal-0.5.0/simcausal/man/DAG_Class.Rd |only simcausal-0.5.0/simcausal/man/Node_Class.Rd |only simcausal-0.5.0/simcausal/man/rcategor.Rd |only simcausal-0.5.0/simcausal/man/rcategor.int.Rd |only simcausal-0.5.1/simcausal/DESCRIPTION | 9 simcausal-0.5.1/simcausal/MD5 | 146 - simcausal-0.5.1/simcausal/NAMESPACE | 10 simcausal-0.5.1/simcausal/NEWS | 9 simcausal-0.5.1/simcausal/R/DAG_node_R6.R | 33 simcausal-0.5.1/simcausal/R/distributions.R | 135 - simcausal-0.5.1/simcausal/R/network.R | 70 simcausal-0.5.1/simcausal/R/network_distributions.R |only simcausal-0.5.1/simcausal/R/node.R | 126 - simcausal-0.5.1/simcausal/R/parserfunctions_R6.r | 91 - simcausal-0.5.1/simcausal/R/simcausal-package.r | 53 simcausal-0.5.1/simcausal/R/simcausal.r | 49 simcausal-0.5.1/simcausal/R/simulation.r | 102 - simcausal-0.5.1/simcausal/R/targetparam.r | 198 -- simcausal-0.5.1/simcausal/README.md | 90 - simcausal-0.5.1/simcausal/build/vignette.rds |binary simcausal-0.5.1/simcausal/inst/doc/simcausal_vignette.R | 339 +-- simcausal-0.5.1/simcausal/inst/doc/simcausal_vignette.Rnw | 592 +++--- simcausal-0.5.1/simcausal/inst/doc/simcausal_vignette.pdf |binary simcausal-0.5.1/simcausal/man/A.Rd | 3 simcausal-0.5.1/simcausal/man/DAG.empty.Rd | 2 simcausal-0.5.1/simcausal/man/DF.to.long.Rd | 4 simcausal-0.5.1/simcausal/man/DF.to.longDT.Rd | 4 simcausal-0.5.1/simcausal/man/Define_sVar.Rd | 6 simcausal-0.5.1/simcausal/man/N.Rd | 3 simcausal-0.5.1/simcausal/man/NetInd.to.sparseAdjMat.Rd | 2 simcausal-0.5.1/simcausal/man/NetIndClass.Rd | 2 simcausal-0.5.1/simcausal/man/add.action.Rd | 34 simcausal-0.5.1/simcausal/man/add.nodes.Rd | 2 simcausal-0.5.1/simcausal/man/distr.list.Rd | 2 simcausal-0.5.1/simcausal/man/doLTCF.Rd | 6 simcausal-0.5.1/simcausal/man/eval.target.Rd | 6 simcausal-0.5.1/simcausal/man/igraph.to.sparseAdjMat.Rd | 2 simcausal-0.5.1/simcausal/man/net.list.Rd |only simcausal-0.5.1/simcausal/man/network.Rd | 21 simcausal-0.5.1/simcausal/man/node.Rd | 311 ++- simcausal-0.5.1/simcausal/man/parents.Rd | 3 simcausal-0.5.1/simcausal/man/plotDAG.Rd | 2 simcausal-0.5.1/simcausal/man/plotSurvEst.Rd | 2 simcausal-0.5.1/simcausal/man/print.DAG.Rd | 2 simcausal-0.5.1/simcausal/man/print.DAG.action.Rd | 2 simcausal-0.5.1/simcausal/man/print.DAG.node.Rd | 2 simcausal-0.5.1/simcausal/man/rbern.Rd | 7 simcausal-0.5.1/simcausal/man/rcat.b1.Rd |only simcausal-0.5.1/simcausal/man/rcat.factor.Rd |only simcausal-0.5.1/simcausal/man/rconst.Rd | 24 simcausal-0.5.1/simcausal/man/rdistr.template.Rd | 13 simcausal-0.5.1/simcausal/man/rnet.SmWorld.Rd |only simcausal-0.5.1/simcausal/man/rnet.gnm.Rd |only simcausal-0.5.1/simcausal/man/rnet.gnp.Rd |only simcausal-0.5.1/simcausal/man/set.DAG.Rd | 240 +- simcausal-0.5.1/simcausal/man/set.targetE.Rd | 2 simcausal-0.5.1/simcausal/man/set.targetMSM.Rd | 2 simcausal-0.5.1/simcausal/man/sim.Rd | 12 simcausal-0.5.1/simcausal/man/simcausal.Rd | 2 simcausal-0.5.1/simcausal/man/simfull.Rd | 10 simcausal-0.5.1/simcausal/man/simobs.Rd | 10 simcausal-0.5.1/simcausal/man/sparseAdjMat.to.NetInd.Rd | 2 simcausal-0.5.1/simcausal/man/sparseAdjMat.to.igraph.Rd | 2 simcausal-0.5.1/simcausal/man/vecfun.add.Rd | 2 simcausal-0.5.1/simcausal/man/vecfun.all.print.Rd | 2 simcausal-0.5.1/simcausal/man/vecfun.print.Rd | 2 simcausal-0.5.1/simcausal/man/vecfun.remove.Rd | 2 simcausal-0.5.1/simcausal/man/vecfun.reset.Rd | 2 simcausal-0.5.1/simcausal/tests/RUnit/RUnit_tests_00.R | 872 +++++----- simcausal-0.5.1/simcausal/tests/RUnit/RUnit_tests_01_nets.R | 9 simcausal-0.5.1/simcausal/tests/RUnit/RUnit_tests_02_MV.R | 38 simcausal-0.5.1/simcausal/tests/examples/MSM.examples.R |only simcausal-0.5.1/simcausal/tests/examples/add.action.R | 30 simcausal-0.5.1/simcausal/tests/examples/example.simnets.R | 17 simcausal-0.5.1/simcausal/tests/examples/set.DAG.R | 238 +- simcausal-0.5.1/simcausal/tests/examples/set.targetE.examples.R |only simcausal-0.5.1/simcausal/tests/examples/sim.impute.examples12.R | 2 simcausal-0.5.1/simcausal/vignettes/SimCausal_Networks_2016.bib |only simcausal-0.5.1/simcausal/vignettes/mystyles.sty |only simcausal-0.5.1/simcausal/vignettes/psi.n.mat.rda |only simcausal-0.5.1/simcausal/vignettes/simcausal_vignette.Rnw | 592 +++--- 83 files changed, 2392 insertions(+), 2217 deletions(-)
Title: Simultaneous Generation of Count and Continuous Data
Description: Generation of count (assuming Poisson distribution) and continuous data (using Fleishman polynomials) simultaneously.
Author: Hakan Demirtas, Yaru Shi, Rawan Allozi
Maintainer: Rawan Allozi <ralloz2@uic.edu>
Diff between PoisNonNor versions 1.0 dated 2015-02-06 and 1.1 dated 2016-05-25
DESCRIPTION | 16 ++--- MD5 | 14 ++-- man/Param.fleishman.Rd | 58 +++++++++--------- man/PoisNonNor-package.Rd | 74 +++++++++++------------ man/RNG_P_NN.Rd | 144 +++++++++++++++++++++++----------------------- man/fleishman.roots.Rd | 52 ++++++++-------- man/intercor.NNP.Rd | 106 ++++++++++++++++----------------- man/intercor.PP.Rd | 78 ++++++++++++------------ 8 files changed, 271 insertions(+), 271 deletions(-)
Title: Multivariate Survival Trees
Description: Constructs trees for multivariate survival data using marginal and frailty models.
Author: Xiaogang Su [aut],
Peter Calhoun [aut, cre],
Juanjuan Fan [aut]
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>
Diff between MST versions 1.2 dated 2015-12-01 and 1.3 dated 2016-05-25
MST-1.2/MST/man/MST.plot.Rd |only MST-1.2/MST/man/MST.plot.latex.Rd |only MST-1.2/MST/man/bootstrap.grow.prune.Rd |only MST-1.2/MST/man/bootstrap.size.Rd |only MST-1.2/MST/man/grow.MST.Rd |only MST-1.2/MST/man/prune.size.testsample.Rd |only MST-1.2/MST/man/send.down.Rd |only MST-1.3/MST/DESCRIPTION | 10 ++-- MST-1.3/MST/MD5 | 37 ++++++++---------- MST-1.3/MST/NAMESPACE | 12 +---- MST-1.3/MST/R/MST.R | 63 +++++++++++++++++++++++-------- MST-1.3/MST/R/MST.plot.R | 2 MST-1.3/MST/R/bootstrap.grow.prune.R | 4 - MST-1.3/MST/R/grow.MST.R | 4 - MST-1.3/MST/R/listIntoParty.R |only MST-1.3/MST/R/listIntoTree.R |only MST-1.3/MST/R/partition.MST.R | 43 +++++++++++++-------- MST-1.3/MST/R/prune.size.testsample.R | 2 MST-1.3/MST/R/sortTree.R | 3 - MST-1.3/MST/R/splitting.stat.MST2.R | 9 ++-- MST-1.3/MST/R/splitting.stat.MST3.R |only MST-1.3/MST/R/splitting.stat.MST4.R |only MST-1.3/MST/man/MST-package.Rd | 31 ++++++++++----- MST-1.3/MST/man/MST.Rd | 48 ++++++++++++----------- MST-1.3/MST/man/rmultime.Rd | 6 +- 25 files changed, 163 insertions(+), 111 deletions(-)
Title: Concurrent Generation of Binary, Ordinal and Continuous Data
Description: Generation of samples from a mix of binary, ordinal and continuous random variables with a pre-specified correlation matrix and marginal distributions.
Author: Hakan Demirtas, Yue Wang, Rawan Allozi
Maintainer: Rawan Allozi <ralloz2@uic.edu>
Diff between BinOrdNonNor versions 1.0 dated 2015-02-03 and 1.1 dated 2016-05-25
DESCRIPTION | 14 ++--- MD5 | 10 +-- NAMESPACE | 4 + man/BinOrdNonNor-package.Rd | 68 ++++++++++++------------ man/IntermediateONN.Rd | 72 ++++++++++++------------- man/genBinOrdNN.Rd | 122 ++++++++++++++++++++++---------------------- 6 files changed, 146 insertions(+), 144 deletions(-)