Title: Subgroup Specific Optimal Dose Assignment
Description: Contains functions for choosing subgroup specific optimal doses in a phase I dose finding clinical trial allowing for subgroup combination 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 1.1.1 dated 2017-08-24 and 2.0.0 dated 2017-10-18
SubTite-1.1.1/SubTite/R/GroupMCMCLN.R |only SubTite-1.1.1/SubTite/man/GroupMCMCLN.Rd |only SubTite-2.0.0/SubTite/DESCRIPTION | 8 SubTite-2.0.0/SubTite/MD5 | 26 SubTite-2.0.0/SubTite/NAMESPACE | 8 SubTite-2.0.0/SubTite/R/GETESS.R |only SubTite-2.0.0/SubTite/R/GetPriorMeans.R | 167 SubTite-2.0.0/SubTite/R/GetSubTite.R | 474 - SubTite-2.0.0/SubTite/R/RcppExports.R | 8 SubTite-2.0.0/SubTite/R/SimTrial.R | 45 SubTite-2.0.0/SubTite/man/GetESS.Rd |only SubTite-2.0.0/SubTite/man/GetPriorMeans.Rd | 7 SubTite-2.0.0/SubTite/man/GetSubTite.Rd | 54 SubTite-2.0.0/SubTite/man/SimTrial.Rd | 24 SubTite-2.0.0/SubTite/src/RcppExports.cpp | 58 SubTite-2.0.0/SubTite/src/SUBGROUP.cpp | 8287 ++++++++++++++++++++++++++--- 16 files changed, 8000 insertions(+), 1166 deletions(-)
Title: Implementation of SparseDC Algorithm
Description: Implements the algorithm described in
Barron, M., Zhang, S. and Li, J. "A sparse differential
clustering algorithm for tracing cell type changes via single-cell
RNA-sequencing data" (Unpublished). This algorithm clusters samples from two different
populations, links the clusters across the conditions and identifies
marker genes for these changes. The package was designed for scRNA-Seq
data but is also applicable to many other data types, just replace cells
with samples and genes with variables. The package also contains functions
for estimating the parameters for SparseDC as outlined in the paper.
Author: Jun Li [aut, cre],
Martin Barron [aut]
Maintainer: Jun Li <jun.li@nd.edu>
Diff between SparseDC versions 0.1.12 dated 2017-09-17 and 0.1.14 dated 2017-10-18
DESCRIPTION | 6 ++--- MD5 | 36 +++++++++++++++---------------- R/data_biase.R | 4 +-- R/lambda1_calculator.R | 4 +-- R/lambda2_calcualtor.R | 4 +-- R/sim_data.R | 4 +-- R/sparsedc_cluster.R | 28 +++++++++++++++++------- R/sparsedc_gap.r | 16 ++++++------- R/update_mu.R | 5 ++-- inst/doc/SparseDC.html | 53 +++++++++++++++++++++++----------------------- man/cell_type_biase.Rd | 2 - man/condition_biase.Rd | 2 - man/generate_uni_dat.Rd | 6 ++--- man/lambda1_calculator.Rd | 4 +-- man/lambda2_calculator.Rd | 4 +-- man/sim_data.Rd | 4 +-- man/sparsedc_cluster.Rd | 12 ++++++---- man/sparsedc_gap.Rd | 12 +++++----- man/update_mu.Rd | 5 ++-- 19 files changed, 115 insertions(+), 96 deletions(-)
Title: Construction of Genetic Maps in Experimental Crosses: Full-Sib,
RILs, F2 and Backcrosses
Description: Analysis of molecular marker data from model (backcrosses,
F2 and recombinant inbred lines) and non-model systems (i. e.
outcrossing species). For the later, it allows statistical
analysis by simultaneously estimating linkage and linkage
phases (genetic map construction) according to Wu et al. (2002)
<doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint
approaches using hidden Markov models.
Author: Gabriel Margarido [aut], Marcelo Mollinari [aut], Karl
Broman [ctb], Rodrigo Amadeu [ctb], Cristiane Taniguti [ctb, cre], Augusto Garcia [aut, ctb]
Maintainer: Cristiane Taniguti <chtaniguti@usp.br>
Diff between onemap versions 2.1.0 dated 2017-10-10 and 2.1.1 dated 2017-10-18
onemap-2.1.0/onemap/inst/BUGS.txt |only onemap-2.1.0/onemap/inst/HISTORY.txt |only onemap-2.1.0/onemap/src/Makevars |only onemap-2.1.0/onemap/src/Makevars.win |only onemap-2.1.0/onemap/src/vcf2raw.c |only onemap-2.1.0/onemap/src/vcf2raw.h |only onemap-2.1.1/onemap/DESCRIPTION | 11 onemap-2.1.1/onemap/MD5 | 22 onemap-2.1.1/onemap/R/vcf2raw.R | 62 +- onemap-2.1.1/onemap/build/vignette.rds |binary onemap-2.1.1/onemap/inst/doc/Inbred_Based_Populations.html | 315 ++++++------- onemap-2.1.1/onemap/inst/doc/Introduction_R.html | 4 onemap-2.1.1/onemap/inst/doc/Outcrossing_Populations.html | 72 +- onemap-2.1.1/onemap/inst/doc/Overview.html | 4 onemap-2.1.1/onemap/src/onemap_init.c | 8 15 files changed, 238 insertions(+), 260 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. The models were originally described in Gjessing, HK and Lie, RT (2006) <doi:10.1111/j.1529-8817.2005.00218.x>.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@uib.no>
Diff between Haplin versions 6.2.0 dated 2017-02-28 and 6.2.1 dated 2017-10-18
Haplin-6.2.0/Haplin/inst |only Haplin-6.2.1/Haplin/DESCRIPTION | 13 Haplin-6.2.1/Haplin/MD5 | 73 ++--- Haplin-6.2.1/Haplin/NAMESPACE | 76 ++--- Haplin-6.2.1/Haplin/R/haplin.R | 2 Haplin-6.2.1/Haplin/R/toDataFrame.R | 2 Haplin-6.2.1/Haplin/man/cbindFiles.Rd | 98 +++---- Haplin-6.2.1/Haplin/man/convertPed.Rd | 204 +++++++------- Haplin-6.2.1/Haplin/man/gwaaToHaplin.Rd | 118 ++++---- Haplin-6.2.1/Haplin/man/gxe.Rd | 130 ++++----- Haplin-6.2.1/Haplin/man/hapPower.Rd | 172 ++++++------ Haplin-6.2.1/Haplin/man/hapPowerAsymp.Rd | 202 +++++++------- Haplin-6.2.1/Haplin/man/hapRun.Rd | 290 ++++++++++---------- Haplin-6.2.1/Haplin/man/hapSim.Rd | 250 ++++++++--------- Haplin-6.2.1/Haplin/man/haplin.Rd | 296 ++++++++++----------- Haplin-6.2.1/Haplin/man/haplinSlide.Rd | 146 +++++----- Haplin-6.2.1/Haplin/man/haplinStrat.Rd | 138 ++++----- Haplin-6.2.1/Haplin/man/haplinTDT.Rd | 336 ++++++++++++------------ Haplin-6.2.1/Haplin/man/haptable.Rd | 180 ++++++------ Haplin-6.2.1/Haplin/man/lineByLine.Rd | 166 +++++------ Haplin-6.2.1/Haplin/man/output.Rd | 86 +++--- Haplin-6.2.1/Haplin/man/pQQ.Rd | 66 ++-- Haplin-6.2.1/Haplin/man/pedToHaplin.Rd | 110 +++---- Haplin-6.2.1/Haplin/man/plot.haplin.Rd | 94 +++--- Haplin-6.2.1/Haplin/man/plot.haplinTDT.Rd | 90 +++--- Haplin-6.2.1/Haplin/man/plot.haptable.Rd | 116 ++++---- Haplin-6.2.1/Haplin/man/prepPed.Rd | 120 ++++---- Haplin-6.2.1/Haplin/man/print.haplin.Rd | 64 ++-- Haplin-6.2.1/Haplin/man/print.summary.haplin.Rd | 88 +++--- Haplin-6.2.1/Haplin/man/rbindFiles.Rd | 122 ++++---- Haplin-6.2.1/Haplin/man/snpPos.Rd | 2 Haplin-6.2.1/Haplin/man/snpPower.Rd | 144 +++++----- Haplin-6.2.1/Haplin/man/snpSampleSize.Rd | 138 ++++----- Haplin-6.2.1/Haplin/man/suest.Rd | 142 +++++----- Haplin-6.2.1/Haplin/man/summary.haplin.Rd | 80 ++--- Haplin-6.2.1/Haplin/man/summary.haplinTDT.Rd | 68 ++-- Haplin-6.2.1/Haplin/man/toDataFrame.Rd | 58 ++-- 37 files changed, 2239 insertions(+), 2241 deletions(-)
Title: GPU Functions for R Objects
Description: Provides GPU enabled functions for R objects in a simple and
approachable manner. New gpu* and vcl* classes have been provided to
wrap typical R objects (e.g. vector, matrix), in both host and device
spaces, to mirror typical R syntax without the need to know OpenCL.
Author: Charles Determan Jr.
Maintainer: Charles Determan Jr. <cdetermanjr@gmail.com>
Diff between gpuR versions 1.2.1 dated 2017-01-05 and 2.0.0 dated 2017-10-18
gpuR-1.2.1/gpuR/inst/include/gpuR/eigen_helpers.hpp |only gpuR-1.2.1/gpuR/inst/include/gpuR/eigen_templates.hpp |only gpuR-1.2.1/gpuR/inst/include/gpuR/vcl_vec_helpers.hpp |only gpuR-2.0.0/gpuR/DESCRIPTION | 13 gpuR-2.0.0/gpuR/INSTALL | 20 gpuR-2.0.0/gpuR/MD5 | 690 gpuR-2.0.0/gpuR/NAMESPACE | 249 gpuR-2.0.0/gpuR/R/RcppExports.R | 1988 gpuR-2.0.0/gpuR/R/asserts.R | 62 gpuR-2.0.0/gpuR/R/chol.R | 374 gpuR-2.0.0/gpuR/R/class-gpuMatrix.R | 372 gpuR-2.0.0/gpuR/R/class-gpuVector.R | 276 gpuR-2.0.0/gpuR/R/class-vclMatrix.R | 315 gpuR-2.0.0/gpuR/R/class-vclVector.R | 266 gpuR-2.0.0/gpuR/R/classes.R | 11 gpuR-2.0.0/gpuR/R/custom_opencl.R |only gpuR-2.0.0/gpuR/R/eigen.R | 292 gpuR-2.0.0/gpuR/R/generics.R | 246 gpuR-2.0.0/gpuR/R/gpuMatrix.R | 730 gpuR-2.0.0/gpuR/R/gpuVector.R | 378 gpuR-2.0.0/gpuR/R/hello-gpuR.R | 74 gpuR-2.0.0/gpuR/R/inplace.R |only gpuR-2.0.0/gpuR/R/methods-gpuVector.R | 753 gpuR-2.0.0/gpuR/R/methods-vclMatrix.R | 2681 - gpuR-2.0.0/gpuR/R/methods-vclVector.R | 1074 gpuR-2.0.0/gpuR/R/methods.R | 2446 gpuR-2.0.0/gpuR/R/norm.R |only gpuR-2.0.0/gpuR/R/pmax.R |only gpuR-2.0.0/gpuR/R/print.R | 104 gpuR-2.0.0/gpuR/R/qr.R | 398 gpuR-2.0.0/gpuR/R/sign.R |only gpuR-2.0.0/gpuR/R/solve.R | 428 gpuR-2.0.0/gpuR/R/svd.R | 172 gpuR-2.0.0/gpuR/R/test_utils.R | 256 gpuR-2.0.0/gpuR/R/typeof.R | 132 gpuR-2.0.0/gpuR/R/utils.R | 497 gpuR-2.0.0/gpuR/R/vclMatrix.R | 432 gpuR-2.0.0/gpuR/R/vclVector.R | 499 gpuR-2.0.0/gpuR/R/wrappers-gpuVector.R | 1677 gpuR-2.0.0/gpuR/R/wrappers-utils.R | 616 gpuR-2.0.0/gpuR/R/wrappers-vclMatrix.R | 3442 - gpuR-2.0.0/gpuR/R/wrappers-vclVector.R | 1715 gpuR-2.0.0/gpuR/R/wrappers.R | 2802 - gpuR-2.0.0/gpuR/R/zzz.R | 52 gpuR-2.0.0/gpuR/README.md | 136 gpuR-2.0.0/gpuR/build/vignette.rds |binary gpuR-2.0.0/gpuR/cleanup.win | 10 gpuR-2.0.0/gpuR/configure | 3 gpuR-2.0.0/gpuR/inst/CITATION |only gpuR-2.0.0/gpuR/inst/CL/basic_gemm.cl | 38 gpuR-2.0.0/gpuR/inst/CL/dLogDeriv.cl |only gpuR-2.0.0/gpuR/inst/CL/dMatSign.cl |only gpuR-2.0.0/gpuR/inst/CL/dMat_pmax.cl |only gpuR-2.0.0/gpuR/inst/CL/dMat_pmin.cl |only gpuR-2.0.0/gpuR/inst/CL/dPermute.cl |only gpuR-2.0.0/gpuR/inst/CL/dScalarAXPY.cl |only gpuR-2.0.0/gpuR/inst/CL/dScalarElemDiv.cl |only gpuR-2.0.0/gpuR/inst/CL/dVecLogDeriv.cl |only gpuR-2.0.0/gpuR/inst/CL/dVecSign.cl |only gpuR-2.0.0/gpuR/inst/CL/dVec_pmax.cl |only gpuR-2.0.0/gpuR/inst/CL/dVec_pmin.cl |only gpuR-2.0.0/gpuR/inst/CL/dcholesky.cl | 118 gpuR-2.0.0/gpuR/inst/CL/dset_row_order.cl | 28 gpuR-2.0.0/gpuR/inst/CL/dset_row_order2.cl |only gpuR-2.0.0/gpuR/inst/CL/fLogDeriv.cl |only gpuR-2.0.0/gpuR/inst/CL/fMatSign.cl |only gpuR-2.0.0/gpuR/inst/CL/fMat_pmax.cl |only gpuR-2.0.0/gpuR/inst/CL/fMat_pmin.cl |only gpuR-2.0.0/gpuR/inst/CL/fScalarAXPY.cl |only gpuR-2.0.0/gpuR/inst/CL/fScalarElemDiv.cl |only gpuR-2.0.0/gpuR/inst/CL/fVecLogDeriv.cl |only gpuR-2.0.0/gpuR/inst/CL/fVecSign.cl |only gpuR-2.0.0/gpuR/inst/CL/fVec_pmax.cl |only gpuR-2.0.0/gpuR/inst/CL/fVec_pmin.cl |only gpuR-2.0.0/gpuR/inst/CL/fcholesky.cl | 122 gpuR-2.0.0/gpuR/inst/CL/fset_row_order.cl | 42 gpuR-2.0.0/gpuR/inst/CL/fset_row_order2.cl |only gpuR-2.0.0/gpuR/inst/CL/iMatSign.cl |only gpuR-2.0.0/gpuR/inst/CL/iMat_pmax.cl |only gpuR-2.0.0/gpuR/inst/CL/iMat_pmin.cl |only gpuR-2.0.0/gpuR/inst/CL/iScalarAXPY.cl |only gpuR-2.0.0/gpuR/inst/CL/iScalarElemDiv.cl |only gpuR-2.0.0/gpuR/inst/CL/iVecSign.cl |only gpuR-2.0.0/gpuR/inst/CL/iVec_pmax.cl |only gpuR-2.0.0/gpuR/inst/CL/iVec_pmin.cl |only gpuR-2.0.0/gpuR/inst/NEWS.Rd | 215 gpuR-2.0.0/gpuR/inst/doc/custom_ocl_gpuR.R |only gpuR-2.0.0/gpuR/inst/doc/custom_ocl_gpuR.Rnw |only gpuR-2.0.0/gpuR/inst/doc/custom_ocl_gpuR.pdf |only gpuR-2.0.0/gpuR/inst/doc/gpuR.R | 80 gpuR-2.0.0/gpuR/inst/doc/gpuR.Rnw | 540 gpuR-2.0.0/gpuR/inst/doc/gpuR.pdf |binary gpuR-2.0.0/gpuR/inst/include/CL/cl.h | 2904 - gpuR-2.0.0/gpuR/inst/include/CL/cl.hpp |25868 +++++----- gpuR-2.0.0/gpuR/inst/include/CL/cl_d3d10.h | 262 gpuR-2.0.0/gpuR/inst/include/CL/cl_d3d11.h | 262 gpuR-2.0.0/gpuR/inst/include/CL/cl_dx9_media_sharing.h | 264 gpuR-2.0.0/gpuR/inst/include/CL/cl_egl.h | 272 gpuR-2.0.0/gpuR/inst/include/CL/cl_ext.h | 782 gpuR-2.0.0/gpuR/inst/include/CL/cl_gl.h | 334 gpuR-2.0.0/gpuR/inst/include/CL/cl_gl_ext.h | 148 gpuR-2.0.0/gpuR/inst/include/CL/cl_platform.h | 2678 - gpuR-2.0.0/gpuR/inst/include/CL/opencl.h | 118 gpuR-2.0.0/gpuR/inst/include/gpuR/dynEigenMat.hpp | 596 gpuR-2.0.0/gpuR/inst/include/gpuR/dynEigenVec.hpp | 284 gpuR-2.0.0/gpuR/inst/include/gpuR/dynVCLMat.hpp | 1101 gpuR-2.0.0/gpuR/inst/include/gpuR/dynVCLVec.hpp | 551 gpuR-2.0.0/gpuR/inst/include/gpuR/getVCLptr.hpp | 83 gpuR-2.0.0/gpuR/inst/include/gpuR/utils.hpp | 82 gpuR-2.0.0/gpuR/inst/include/gpuR/windows_check.hpp | 30 gpuR-2.0.0/gpuR/inst/include/loader/icd.c | 426 gpuR-2.0.0/gpuR/inst/include/loader/icd.h | 378 gpuR-2.0.0/gpuR/inst/include/loader/icd_dispatch.c | 5300 +- gpuR-2.0.0/gpuR/inst/include/loader/icd_dispatch.h | 3032 - gpuR-2.0.0/gpuR/inst/include/loader/icd_linux.c | 376 gpuR-2.0.0/gpuR/inst/include/loader/icd_windows.c | 324 gpuR-2.0.0/gpuR/inst/src |only gpuR-2.0.0/gpuR/inst/testWithGPU/testthat.R | 8 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_deepcopy.R | 480 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuMatrixBlock_algebra.R | 1344 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuMatrix_algebra.R | 1246 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuMatrix_classes.R | 336 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuMatrix_cov.R | 92 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuMatrix_dist.R | 90 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuMatrix_eigen.R | 226 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuMatrix_math.R | 568 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuMatrix_row_col.R | 482 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuMatrix_utils.R | 328 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuVector_algebra.R | 1108 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuVector_classes.R | 204 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuVector_math.R | 522 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_gpuVector_utils.R | 226 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclMatrixBlock_algebra.R | 1348 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclMatrix_algebra.R | 656 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclMatrix_classes.R | 312 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclMatrix_cov.R | 92 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclMatrix_dist.R | 92 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclMatrix_eigen.R | 226 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclMatrix_row_col.R | 466 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclMatrtix_math.R | 524 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclMatrtix_utils.R | 310 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclVector_algebra.R | 978 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclVector_classes.R | 212 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclVector_math.R | 522 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_cpu_vclVector_utils.R | 240 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_deepcopy.R | 482 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuMatrixBlock_algebra.R | 1360 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuMatrix_algebra.R | 1234 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuMatrix_classes.R | 438 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuMatrix_cov.R | 84 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuMatrix_dist.R | 82 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuMatrix_eigen.R | 226 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuMatrix_math.R | 524 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuMatrix_row_col.R | 490 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuMatrix_utils.R | 332 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuVector_algebra.R | 1106 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuVector_classes.R | 206 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuVector_math.R | 522 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_gpuVector_utils.R | 234 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_utils.R | 48 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclMatrixBlock_algebra.R | 1360 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclMatrix_algebra.R | 1212 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclMatrix_classes.R | 310 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclMatrix_cov.R | 84 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclMatrix_dist.R | 82 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclMatrix_eigen.R | 240 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclMatrix_math.R | 536 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclMatrix_row_col.R | 492 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclMatrix_utils.R | 316 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclVector_algebra.R | 996 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclVector_classes.R | 212 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclVector_math.R | 530 gpuR-2.0.0/gpuR/inst/testWithGPU/testthat/test_vclVector_utils.R | 238 gpuR-2.0.0/gpuR/man/Arith-methods.Rd | 173 gpuR-2.0.0/gpuR/man/Compare-methods.Rd | 57 gpuR-2.0.0/gpuR/man/Math-methods.Rd | 79 gpuR-2.0.0/gpuR/man/Summary-methods.Rd | 69 gpuR-2.0.0/gpuR/man/as.gpuMatrix-methods.Rd | 53 gpuR-2.0.0/gpuR/man/as.gpuVector-methods.Rd | 61 gpuR-2.0.0/gpuR/man/as.vclVector-methods.Rd |only gpuR-2.0.0/gpuR/man/assert_has_double.Rd | 61 gpuR-2.0.0/gpuR/man/cgpuMatrix-class.Rd |only gpuR-2.0.0/gpuR/man/chol-methods.Rd | 81 gpuR-2.0.0/gpuR/man/colnames-methods.Rd | 79 gpuR-2.0.0/gpuR/man/cov-methods.Rd | 97 gpuR-2.0.0/gpuR/man/currentContext.Rd | 29 gpuR-2.0.0/gpuR/man/currentDevice.Rd | 41 gpuR-2.0.0/gpuR/man/currentPlatform.Rd | 39 gpuR-2.0.0/gpuR/man/custom_opencl.Rd |only gpuR-2.0.0/gpuR/man/cvclMatrix-class.Rd |only gpuR-2.0.0/gpuR/man/det-methods.Rd |only gpuR-2.0.0/gpuR/man/detectCPUs.Rd | 43 gpuR-2.0.0/gpuR/man/detectGPUs.Rd | 43 gpuR-2.0.0/gpuR/man/detectPlatforms.Rd | 35 gpuR-2.0.0/gpuR/man/deviceHasDouble.Rd | 48 gpuR-2.0.0/gpuR/man/deviceInfo.Rd | 117 gpuR-2.0.0/gpuR/man/deviceType.Rd | 39 gpuR-2.0.0/gpuR/man/dgpuMatrix-class.Rd | 50 gpuR-2.0.0/gpuR/man/dgpuVector-class.Rd | 46 gpuR-2.0.0/gpuR/man/diag-methods.Rd | 87 gpuR-2.0.0/gpuR/man/dim-methods.Rd | 53 gpuR-2.0.0/gpuR/man/dist-vclMatrix.Rd | 103 gpuR-2.0.0/gpuR/man/dvclMatrix-class.Rd | 50 gpuR-2.0.0/gpuR/man/dvclVector-class.Rd | 46 gpuR-2.0.0/gpuR/man/eigen-gpuMatrix.Rd | 114 gpuR-2.0.0/gpuR/man/extract-methods.Rd | 333 gpuR-2.0.0/gpuR/man/fgpuMatrix-class.Rd | 50 gpuR-2.0.0/gpuR/man/fgpuVector-class.Rd | 46 gpuR-2.0.0/gpuR/man/fvclMatrix-class.Rd | 50 gpuR-2.0.0/gpuR/man/fvclVector-class.Rd | 46 gpuR-2.0.0/gpuR/man/gpuMatrix-class.Rd | 98 gpuR-2.0.0/gpuR/man/gpuMatrix-crossprod.Rd | 85 gpuR-2.0.0/gpuR/man/gpuMatrix-methods.Rd | 103 gpuR-2.0.0/gpuR/man/gpuMatrix.colSums.Rd | 71 gpuR-2.0.0/gpuR/man/gpuR-block.Rd | 95 gpuR-2.0.0/gpuR/man/gpuR-deepcopy.Rd | 97 gpuR-2.0.0/gpuR/man/gpuR-package.Rd | 85 gpuR-2.0.0/gpuR/man/gpuR-slice.Rd | 85 gpuR-2.0.0/gpuR/man/gpuVector-class.Rd | 70 gpuR-2.0.0/gpuR/man/gpuVector-methods.Rd | 88 gpuR-2.0.0/gpuR/man/grapes-o-grapes-methods.Rd | 47 gpuR-2.0.0/gpuR/man/grapes-times-grapes-methods.Rd | 81 gpuR-2.0.0/gpuR/man/has_cpu_skip.Rd | 25 gpuR-2.0.0/gpuR/man/has_double_skip.Rd | 25 gpuR-2.0.0/gpuR/man/has_gpu_skip.Rd | 25 gpuR-2.0.0/gpuR/man/has_multiple_double_skip.Rd | 25 gpuR-2.0.0/gpuR/man/has_multiple_gpu_skip.Rd | 25 gpuR-2.0.0/gpuR/man/identity_matrix.Rd | 59 gpuR-2.0.0/gpuR/man/igpuMatrix-class.Rd | 50 gpuR-2.0.0/gpuR/man/igpuVector-class.Rd | 46 gpuR-2.0.0/gpuR/man/inplace-methods.Rd |only gpuR-2.0.0/gpuR/man/ivclMatrix-class.Rd | 50 gpuR-2.0.0/gpuR/man/ivclVector-class.Rd | 46 gpuR-2.0.0/gpuR/man/length-methods.Rd | 67 gpuR-2.0.0/gpuR/man/listContexts.Rd | 55 gpuR-2.0.0/gpuR/man/log-methods.Rd | 75 gpuR-2.0.0/gpuR/man/norm-methods.Rd |only gpuR-2.0.0/gpuR/man/nrow-gpuR.Rd | 63 gpuR-2.0.0/gpuR/man/permute-methods.Rd | 53 gpuR-2.0.0/gpuR/man/platformInfo.Rd | 53 gpuR-2.0.0/gpuR/man/pmax.Rd |only gpuR-2.0.0/gpuR/man/pmin.vclVector.Rd |only gpuR-2.0.0/gpuR/man/pocl_check.Rd |only gpuR-2.0.0/gpuR/man/print.gpuMatrix.Rd | 41 gpuR-2.0.0/gpuR/man/qr-methods.Rd | 93 gpuR-2.0.0/gpuR/man/qr.R-methods.Rd | 61 gpuR-2.0.0/gpuR/man/setContext.Rd | 35 gpuR-2.0.0/gpuR/man/set_device_context.Rd |only gpuR-2.0.0/gpuR/man/setup_opencl.Rd |only gpuR-2.0.0/gpuR/man/solve-methods.Rd | 71 gpuR-2.0.0/gpuR/man/svd-methods.Rd | 95 gpuR-2.0.0/gpuR/man/synchronize.Rd |only gpuR-2.0.0/gpuR/man/t-methods.Rd | 55 gpuR-2.0.0/gpuR/man/typeof-gpuR-methods.Rd | 57 gpuR-2.0.0/gpuR/man/vclMatrix-class.Rd | 104 gpuR-2.0.0/gpuR/man/vclMatrix-crossprod.Rd | 97 gpuR-2.0.0/gpuR/man/vclMatrix-methods.Rd | 105 gpuR-2.0.0/gpuR/man/vclMatrix.colSums.Rd | 71 gpuR-2.0.0/gpuR/man/vclVector-class.Rd | 70 gpuR-2.0.0/gpuR/man/vclVector-methods.Rd | 104 gpuR-2.0.0/gpuR/man/zgpuMatrix-class.Rd |only gpuR-2.0.0/gpuR/man/zvclMatrix-class.Rd |only gpuR-2.0.0/gpuR/src/RcppExports.cpp | 1725 gpuR-2.0.0/gpuR/src/chol.cpp | 11 gpuR-2.0.0/gpuR/src/context.cpp | 22 gpuR-2.0.0/gpuR/src/custom_math.cpp |only gpuR-2.0.0/gpuR/src/device.cpp | 400 gpuR-2.0.0/gpuR/src/gpuEigenPtr.cpp | 232 gpuR-2.0.0/gpuR/src/gpuMatrix_igemm.cpp | 18 gpuR-2.0.0/gpuR/src/norm.cpp |only gpuR-2.0.0/gpuR/src/platform.cpp | 19 gpuR-2.0.0/gpuR/src/set_row_order.cpp | 255 gpuR-2.0.0/gpuR/src/solve.cpp | 59 gpuR-2.0.0/gpuR/src/synchronize.cpp |only gpuR-2.0.0/gpuR/src/utils-vcl.cpp | 135 gpuR-2.0.0/gpuR/src/utils.cpp | 56 gpuR-2.0.0/gpuR/src/vclPtr.cpp | 932 gpuR-2.0.0/gpuR/src/vienna_blas1.cpp | 1255 gpuR-2.0.0/gpuR/src/vienna_blas2.cpp |only gpuR-2.0.0/gpuR/src/vienna_blas3.cpp | 156 gpuR-2.0.0/gpuR/src/vienna_eigen.cpp | 23 gpuR-2.0.0/gpuR/src/vienna_qr.cpp | 16 gpuR-2.0.0/gpuR/src/vienna_stats.cpp | 351 gpuR-2.0.0/gpuR/src/vienna_svd.cpp | 18 gpuR-2.0.0/gpuR/tests/testthat.R | 9 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_deepcopy.R | 482 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrixBlock_algebra.R | 1338 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_algebra.R | 2123 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_chol.R | 102 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_classes.R | 358 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_cov.R | 84 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_dist.R | 636 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_eigen.R | 220 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_math.R | 688 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_norm.R |only gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_qr.R | 128 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_row_col.R | 835 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_solve.R | 344 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_svd.R | 144 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuMatrix_utils.R | 498 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuVector_algebra.R | 1143 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuVector_classes.R | 199 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuVector_math.R | 642 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_gpuVector_utils.R | 269 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_inplace_algebra.R |only gpuR-2.0.0/gpuR/tests/testthat/test_cpu_inplace_math.R |only gpuR-2.0.0/gpuR/tests/testthat/test_cpu_order.R | 72 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_shared_memory.R | 75 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrixBlock_algebra.R | 1339 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrix_algebra.R | 2102 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrix_chol.R | 102 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrix_classes.R | 337 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrix_cov.R | 95 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrix_dist.R | 631 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrix_eigen.R | 220 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrix_norm.R |only gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrix_qr.R | 126 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrix_row_col.R | 816 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrix_solve.R | 326 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrix_svd.R | 144 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrtix_math.R | 640 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclMatrtix_utils.R | 550 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclVector_algebra.R | 985 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclVector_classes.R | 205 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclVector_math.R | 644 gpuR-2.0.0/gpuR/tests/testthat/test_cpu_vclVector_utils.R | 360 gpuR-2.0.0/gpuR/tests/testthat/test_custom.R |only gpuR-2.0.0/gpuR/tests/testthat/test_deepcopy.R | 537 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrixBlock_algebra.R | 1370 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_algebra.R | 2202 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_chol.R | 108 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_classes.R | 477 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_cov.R | 102 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_dist.R | 641 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_eigen.R | 232 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_math.R | 665 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_norm.R |only gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_qr.R | 134 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_row_col.R | 893 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_solve.R | 354 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_svd.R | 150 gpuR-2.0.0/gpuR/tests/testthat/test_gpuMatrix_utils.R | 528 gpuR-2.0.0/gpuR/tests/testthat/test_gpuVector_algebra.R | 1157 gpuR-2.0.0/gpuR/tests/testthat/test_gpuVector_classes.R | 213 gpuR-2.0.0/gpuR/tests/testthat/test_gpuVector_math.R | 662 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gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrixBlock_algebra.R | 1371 gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_algebra.R | 2225 gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_chol.R | 112 gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_classes.R | 350 gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_cov.R | 102 gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_dist.R | 644 gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_eigen.R | 247 gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_math.R | 671 gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_norm.R |only gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_qr.R | 132 gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_row_col.R | 886 gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_solve.R | 339 gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_svd.R | 151 gpuR-2.0.0/gpuR/tests/testthat/test_vclMatrix_utils.R | 589 gpuR-2.0.0/gpuR/tests/testthat/test_vclVector_algebra.R | 1016 gpuR-2.0.0/gpuR/tests/testthat/test_vclVector_classes.R | 219 gpuR-2.0.0/gpuR/tests/testthat/test_vclVector_math.R | 668 gpuR-2.0.0/gpuR/tests/testthat/test_vclVector_utils.R | 384 gpuR-2.0.0/gpuR/vignettes/custom_ocl_gpuR-concordance.tex |only gpuR-2.0.0/gpuR/vignettes/custom_ocl_gpuR.Rnw |only gpuR-2.0.0/gpuR/vignettes/framed.sty |only gpuR-2.0.0/gpuR/vignettes/gpuR-concordance.tex | 4 gpuR-2.0.0/gpuR/vignettes/gpuR.Rnw | 540 383 files changed, 87088 insertions(+), 76126 deletions(-)
Title: Machine Learning with Higher-Order Factorization Machines
Description: Implementation of different machine learning approaches: Support Vector Machine with a linear kernel, second-order Factorization Machine, higher-order Factorization Machine, and adaptive-order Factorization Machine.
Author: Julian Knoll
Maintainer: Julian Knoll <julian.knoll@th-nuernberg.de>
Diff between FactoRizationMachines versions 0.21 dated 2017-08-08 and 0.35 dated 2017-10-18
DESCRIPTION | 10 ++++----- MD5 | 33 +++++++++++++++++-------------- NAMESPACE | 5 +++- NEWS |only R/FM.train.R | 2 - R/HoFM.train.R | 3 +- R/KnoFM.train.R |only R/RcppExports.R | 8 +++---- R/SVM.train.R | 2 - R/learn.FM.model.R | 13 +++++++++--- R/predict.FMmodel.R | 1 build/partial.rdb |binary man/010-FactoRizationMachines.Rd | 41 ++++++++++++++++++++++++++++++++------- man/020-SVM.train.Rd | 19 ++++++++---------- man/030-FM.train.Rd | 18 +++++++---------- man/040-HoFM.train.Rd | 15 +++++++------- man/045-KnoFM.train.Rd |only src/FactoRizationMachines.cpp | 4 +-- src/RcppExports.cpp | 16 +++++++-------- 19 files changed, 115 insertions(+), 75 deletions(-)
More information about FactoRizationMachines at CRAN
Permanent link
Title: Functional Programming Tools
Description: A complete and consistent functional programming toolkit for R.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between purrr versions 0.2.3 dated 2017-08-02 and 0.2.4 dated 2017-10-18
DESCRIPTION | 15 +++++++------ MD5 | 50 +++++++++++++++++++++++----------------------- NEWS.md | 6 +++++ R/along.R | 2 - R/as_mapper.R | 6 ++--- R/lmap.R | 2 - R/map.R | 5 +--- R/reduce.R | 2 - README.md | 2 - inst/doc/other-langs.html | 2 - man/accumulate.Rd | 2 - man/along.Rd | 2 - man/as_mapper.Rd | 2 - man/detect.Rd | 2 - man/imap.Rd | 2 - man/lmap.Rd | 2 - man/map.Rd | 7 ++---- man/map2.Rd | 2 - man/modify.Rd | 2 - man/pluck.Rd | 10 --------- man/safely.Rd | 2 - src/backports.c |only src/backports.h |only src/extract.c | 20 +++++++++++++----- src/flatten.c | 13 +++++++---- src/map.c | 22 +++++++++++--------- src/transpose.c | 4 +-- 27 files changed, 99 insertions(+), 87 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation.
Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 2.4-1 dated 2017-06-06 and 2.5-1 dated 2017-10-18
DESCRIPTION | 10 +-- MD5 | 142 +++++++++++++++++++++++--------------------- NAMESPACE | 3 R/jomo.coxph.MCMCchain.R |only R/jomo.coxph.R |only R/jomo1cat.MCMCchain.R | 18 ++--- R/jomo1cat.R | 31 ++++++--- R/jomo1con.MCMCchain.R | 18 ++--- R/jomo1con.R | 16 +++- R/jomo1mix.MCMCchain.R | 18 ++--- R/jomo1mix.R | 31 ++++++--- R/jomo1rancat.MCMCchain.R | 28 ++++---- R/jomo1rancat.R | 45 +++++++++---- R/jomo1rancathr.MCMCchain.R | 28 ++++---- R/jomo1rancathr.R | 45 +++++++++---- R/jomo1rancon.MCMCchain.R | 28 ++++---- R/jomo1rancon.R | 37 +++++++---- R/jomo1ranconhr.MCMCchain.R | 28 ++++---- R/jomo1ranconhr.R | 37 +++++++---- R/jomo1ranmix.MCMCchain.R | 29 ++++---- R/jomo1ranmix.R | 47 +++++++++----- R/jomo1ranmixhr.MCMCchain.R | 29 ++++---- R/jomo1ranmixhr.R | 46 +++++++++----- R/jomo2com.MCMCchain.R | 17 +++++ R/jomo2com.R | 82 ++++++++++++++++++++----- R/jomo2hr.MCMCchain.R | 35 +++++----- R/jomo2hr.R | 84 ++++++++++++++++++++------ data/surdata.RData |only man/jomo.coxph.MCMCchain.Rd |only man/jomo.coxph.Rd |only man/surdata.Rd |only src/MCMCjomo1con.c | 3 src/MCMCjomo1glmerbin.c | 3 src/MCMCjomo1glmerbinhr.c | 3 src/MCMCjomo1lmer.c | 3 src/MCMCjomo1lmerhr.c | 3 src/MCMCjomo1mix.c | 3 src/MCMCjomo1rancon.c | 3 src/MCMCjomo1ranconhf.c | 3 src/MCMCjomo1ranconhr.c | 3 src/MCMCjomo1ranmix.c | 3 src/MCMCjomo1ranmixhf.c | 3 src/MCMCjomo1ranmixhr.c | 3 src/MCMCjomo2com.c | 3 src/MCMCjomo2glmerbin.c | 3 src/MCMCjomo2glmerbinhr.c | 4 - src/MCMCjomo2hf.c | 3 src/MCMCjomo2hr.c | 3 src/MCMCjomo2lmer.c | 3 src/MCMCjomo2lmerhr.c | 4 - src/MCMCjomocox.c |only src/MCMCjomoglm.c | 6 - src/MCMCjomolm.c | 3 src/jomo1conC.c | 3 src/jomo1glmerbin.c | 4 - src/jomo1glmerbinhr.c | 4 - src/jomo1lmer.c | 3 src/jomo1lmerhr.c | 3 src/jomo1mixC.c | 3 src/jomo1ranconC.c | 3 src/jomo1ranconhf.c | 3 src/jomo1ranconhrC.c | 3 src/jomo1ranmixC.c | 3 src/jomo1ranmixhf.c | 3 src/jomo1ranmixhrC.c | 3 src/jomo2comC.c | 4 - src/jomo2glmerbin.c | 3 src/jomo2glmerbinhr.c | 4 - src/jomo2hf.c | 3 src/jomo2hrC.c | 3 src/jomo2lmer.c | 3 src/jomo2lmerhr.c | 3 src/jomo_init.c | 4 + src/jomocox.c |only src/jomoglm.c | 6 - src/jomolm.c | 16 +++- 76 files changed, 685 insertions(+), 402 deletions(-)
Title: Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matrices
Description: Fast and memory efficient methods for truncated singular value
decomposition and principal components analysis of large sparse and dense matrices.
Author: Jim Baglama [aut, cph],
Lothar Reichel [aut, cph],
B. W. Lewis [aut, cre, cph]
Maintainer: B. W. Lewis <blewis@illposed.net>
Diff between irlba versions 2.2.1 dated 2017-05-17 and 2.3.1 dated 2017-10-18
DESCRIPTION | 11 ++- MD5 | 43 ++++++++------ NAMESPACE | 3 + R/irlba.R | 59 +++++++++----------- R/prcomp.R | 45 ++++++++++++++- R/ssvd.R |only R/svdr.R | 31 +++++++--- README.md | 44 +++++---------- build/vignette.rds |binary inst/doc/irlba.Rnw | 129 +++++++++++++++++++++----------------------- inst/doc/irlba.pdf |binary man/irlba.Rd | 29 ++------- man/partial_eigen.Rd | 1 man/prcomp_irlba.Rd | 17 ++++- man/ssvd.Rd |only man/summary.irlba_prcomp.Rd |only man/svdr.Rd | 20 +++++- src/irlb.c | 18 ++++-- src/utility.c | 2 tests/edge.R | 2 tests/prcomp.r |only tests/ssvd.R |only tests/svdr.R | 4 - tests/test.R | 34 ++++++++--- vignettes/irlba.Rnw | 129 +++++++++++++++++++++----------------------- 25 files changed, 350 insertions(+), 271 deletions(-)
Title: Convert Html into Text
Description: Convert a html document to simple plain texts by removing all html tags. This package utilizes regular expressions to strip off html tags. It also offers gettxt() and browse() function, which enables you to get or browse texts at a certain web page.
Author: Sangchul Park [aut, cre]
Maintainer: Sangchul Park <mail@sangchul.com>
Diff between htm2txt versions 2.0.0 dated 2017-10-14 and 2.1.0 dated 2017-10-18
htm2txt-2.0.0/htm2txt/man/crawltxt.Rd |only htm2txt-2.1.0/htm2txt/DESCRIPTION | 13 +-- htm2txt-2.1.0/htm2txt/MD5 | 12 +-- htm2txt-2.1.0/htm2txt/NAMESPACE | 2 htm2txt-2.1.0/htm2txt/R/htm2txt.R | 126 ++++++++++++++++++++++------------ htm2txt-2.1.0/htm2txt/man/browse.Rd | 10 +- htm2txt-2.1.0/htm2txt/man/gettxt.Rd |only htm2txt-2.1.0/htm2txt/man/htm2txt.Rd | 21 ++--- 8 files changed, 111 insertions(+), 73 deletions(-)
Title: Confidence or Prediction Intervals, Quantiles, and Probabilities
for Statistical Models
Description: Functions to append confidence intervals, prediction intervals,
and other quantities of interest to data frames. All appended quantities
are for the response variable, after conditioning on the model and covariates.
This package has a data frame first syntax that allows for easy piping.
Currently supported models include (log-) linear, (log-) linear mixed,
and generalized linear models.
Author: John Haman [cre, aut],
Matthew Avery [aut],
Institute for Defense Analyses [cph]
Maintainer: John Haman <mail@johnhaman.org>
Diff between ciTools versions 0.2.0 dated 2017-10-10 and 0.2.1 dated 2017-10-18
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/add_ci_lm.R | 6 ++---- R/add_ci_lognormal.R | 6 ++---- R/add_pi_glm.R | 9 +++++++-- R/add_probs_glm.R | 33 ++++++++++++++++++++------------- R/add_quantile_glm.R | 4 ++++ 7 files changed, 44 insertions(+), 32 deletions(-)
Title: Simulation of Study Data
Description: Simulates data sets in order to explore modeling techniques or
better understand data generating processes. The user specifies a set of
relationships between covariates, and generates data based on these
specifications. The final data sets can represent data from randomized
control trials, repeated measure (longitudinal) designs, and cluster
randomized trials. Missingness can be generated using various
mechanisms (MCAR, MAR, NMAR).
Author: Keith Goldfeld [aut, cre]
Maintainer: Keith Goldfeld <Keith.Goldfeld@nyumc.org>
Diff between simstudy versions 0.1.5 dated 2017-10-03 and 0.1.6 dated 2017-10-18
DESCRIPTION | 10 +- MD5 | 25 ++++--- NAMESPACE | 3 NEWS.md | 5 + R/genSpline.R |only R/genSurv.R | 6 + R/int_genbasisdt.R |only R/viewBasis.R |only R/viewSplines.R |only inst/doc/simstudy.R | 79 ++++++++++++++++++++++ inst/doc/simstudy.Rmd | 140 ++++++++++++++++++++++++++++++++++----- inst/doc/simstudy.html | 175 +++++++++++++++++++++++++++++++++++-------------- man/genSpline.Rd |only man/genSurv.Rd | 4 - man/viewBasis.Rd |only man/viewSplines.Rd |only vignettes/simstudy.Rmd | 140 ++++++++++++++++++++++++++++++++++----- 17 files changed, 489 insertions(+), 98 deletions(-)
Title: Heller-Heller-Gorfine Tests of Independence and Equality of
Distributions
Description: Heller-Heller-Gorfine ('HHG') tests are a set of powerful statistical
tests of multivariate k-sample homogeneity and independence. For the univariate
case, the package also offers implementations of the 'MinP DDP' and 'MinP ADP'
tests, which are consistent against all continuous alternatives but are
distribution-free, and are thus much faster to apply.
Author: Barak Brill & Shachar Kaufman, based in part on an earlier
implementation by Ruth Heller and Yair Heller.
Maintainer: Barak Brill <barakbri@mail.tau.ac.il>
Diff between HHG versions 2.1 dated 2017-08-13 and 2.2 dated 2017-10-18
HHG-2.1/HHG/src/hhg_init.c |only HHG-2.2/HHG/DESCRIPTION | 12 ++- HHG-2.2/HHG/MD5 | 26 +++--- HHG-2.2/HHG/NAMESPACE | 3 HHG-2.2/HHG/R/HHG.R | 4 - HHG-2.2/HHG/R/HHGRCPP_API.r |only HHG-2.2/HHG/R/HHG_univariate.R | 98 +++++++++++++++++++++---- HHG-2.2/HHG/R/RcppExports.R |only HHG-2.2/HHG/README.md |only HHG-2.2/HHG/man/hhg.univariate.ind.pvalue.Rd | 2 HHG-2.2/HHG/man/hhg.univariate.ind.stat.Rd | 2 HHG-2.2/HHG/man/hhg.univariate.ks.nulltable.Rd | 2 HHG-2.2/HHG/man/hhg.univariate.ks.pvalue.Rd | 2 HHG-2.2/HHG/man/hhg.univariate.ks.stat.Rd | 2 HHG-2.2/HHG/src/RcppExports.cpp |only HHG-2.2/HHG/src/StatsComputer.cpp | 1 HHG-2.2/HHG/src/rcpp_internals.cpp |only 17 files changed, 118 insertions(+), 36 deletions(-)
Title: Hierarchical Spatial Autoregressive Model
Description: A Hierarchical Spatial Autoregressive Model (HSAR), based on a Bayesian Markov Chain Monte Carlo (MCMC) algorithm ( Dong and Harris (2014) <doi:10.1111/gean.12049> ). The creation of this package was supported by the Economic and Social Research Council (ESRC) through the Applied Quantitative Methods Network: Phase II, grant number ES/K006460/1.
Author: Guanpeng Dong, Richard Harris, Angelos Mimis
Maintainer: Angelos Mimis <mimis@panteion.gr>
Diff between HSAR versions 0.4.0 dated 2016-05-24 and 0.4.2 dated 2017-10-18
DESCRIPTION | 12 +++++----- MD5 | 26 +++++++++++------------ NAMESPACE | 18 ++++++++-------- R/RcppExports.R | 10 ++++----- R/hsar.R | 15 ++++++++----- R/sar.R | 5 ++-- build/vignette.rds |binary inst/NEWS.Rd | 6 +++++ inst/doc/hsar.R | 2 - inst/doc/hsar.Rmd | 2 - inst/doc/hsar.html | 57 +++++++++++++++++++++++++--------------------------- man/HSAR-package.Rd | 8 +++---- src/RcppExports.cpp | 55 +++++++++++++++++++++++++++++++------------------- src/diagnostics.cpp | 2 - 14 files changed, 120 insertions(+), 98 deletions(-)
Title: Handling and Manipulating Remote Sensing Data
Description: Herein, we provide a broad variety of functions which are useful
for handling, manipulating, and visualizing satellite-based remote sensing
data. These operations range from mere data import and layer handling (eg
subsetting), over Raster* typical data wrangling (eg crop, extend), to more
sophisticated (pre-)processing tasks typically applied to satellite imagery
(eg atmospheric and topographic correction). This functionality is
complemented by a full access to the satellite layers' metadata at any
stage and the documentation of performed actions in a separate log file.
Currently available sensors include Landsat 4-5 (TM), 7 (ETM+), and 8
(OLI/TIRS Combined), and additional compatibility is ensured for the Landsat
Global Land Survey data set. Moreover, support for Terra and Aqua-MODIS as
well as PROBA-V is expected to arrive shortly.
Author: Thomas Nauss, Hanna Meyer, Tim Appelhans, Florian Detsch
Maintainer: Florian Detsch <fdetsch@web.de>
Diff between satellite versions 1.0.0 dated 2017-08-03 and 1.0.1 dated 2017-10-18
DESCRIPTION | 27 LICENSE | 1350 +++++----- MD5 | 171 - NAMESPACE | 218 - NEWS | 83 NEWS.md | 83 R/AAAsatelliteClasses.R | 132 R/RcppExports.R | 30 R/alignGeometry.R | 216 - R/brick.R | 2 R/calcAtmosCorr.R | 2 R/calcDODN.R | 4 R/calcEarthSunDist.R | 138 - R/calcPathRadDOS.R | 2 R/calcTOAIrradModel.R | 2 R/calcTOAIrradTable.R | 256 - R/calcTopoCorr.R | 2 R/compFilePathLandsat.R | 17 R/compMetaLandsat.R | 43 R/convRef2RadLinear.R | 58 R/crop.R | 2 R/demTools.R | 2 R/extend.R | 152 - R/plot.R | 168 - R/print.R | 32 R/satInfo.R | 2 R/satellite-package.R | 2 R/satellite.R | 238 - R/show.R | 12 R/stack.R | 2 R/subset.R | 11 README.md | 70 build/vignette.rds |binary inst/CITATION | 40 inst/doc/landsat-calibration.R | 22 inst/doc/landsat-calibration.Rmd | 5 inst/doc/landsat-calibration.html | 220 - inst/doc/satellite.R |only inst/doc/satellite.Rmd |only inst/doc/satellite.html |only inst/extdata/LC08_L1TP_195025_20130707_20170503_01_T1_MTL.txt | 450 +-- inst/extdata/LE07_L1TP_195025_20010730_20170204_01_T1_MTL.txt | 480 +-- inst/testdata/LC8/LC81950252013188LGN00_MTL.txt | 412 +-- inst/testdata/LE7/LE71950252001211EDC00_MTL.txt | 376 +- inst/testdata/LT05/LT05_L1TP_167055_20000309_20161214_01_T1_MTL.txt | 388 +- man/Satellite-class.Rd | 18 man/SatelliteInfo-class.Rd | 46 man/SatelliteLayers-class.Rd | 30 man/SatelliteLog-class.Rd | 30 man/SatelliteMetaData-class.Rd | 30 man/alignGeometry.Rd | 118 man/brick.Rd | 60 man/calcAtmosCorr.Rd | 304 +- man/calcDODN.Rd | 104 man/calcEarthSunDist.Rd | 114 man/calcPathRadDOS.Rd | 308 +- man/calcTOAIrradModel.Rd | 184 - man/calcTOAIrradRadRef.Rd | 148 - man/calcTOAIrradTable.Rd | 150 - man/calcTopoCorr.Rd | 144 - man/compFilePathLandsat.Rd | 88 man/compMetaLandsat.Rd | 116 man/convRad2BT.Rd | 96 man/convRad2Ref.Rd | 134 man/convRef2RadLinear.Rd | 68 man/convSC2Rad.Rd | 132 man/convSC2Ref.Rd | 144 - man/crop.Rd | 116 man/demTools.Rd | 100 man/extend.Rd | 100 man/l7.Rd | 44 man/l8.Rd | 46 man/lutInfo.Rd | 228 - man/maskInvarFeatures.Rd | 152 - man/names.Rd | 66 man/plot.Rd | 88 man/satInfo.Rd | 752 ++--- man/satellite-package.Rd | 52 man/satellite.Rd | 126 man/stack.Rd | 60 man/subset.Rd | 89 tests/testthat/test-calcAtmosCorr.R | 25 tests/testthat/test-calcEarthSunDist.R | 36 tests/testthat/test-calcTOAIrradTable.R | 84 tests/testthat/test-compMetaLandsat.R | 243 - tests/testthat/test-extend.R | 64 vignettes/landsat-calibration.Rmd | 5 vignettes/satellite.Rmd | 38 88 files changed, 5544 insertions(+), 5458 deletions(-)
Title: Support for the 'Mathpix' API (Image to 'LaTeX')
Description: Given an image of a formula (typeset or handwritten) this package
provides calls to the 'Mathpix' service to produce the 'LaTeX' code which should
generate that image, and pastes it into a (e.g. an 'rmarkdown') document.
See <https://docs.mathpix.com/> for full details. 'Mathpix' is an external service
and use of the API is subject to their terms and conditions.
Author: Jonathan Carroll [aut, cre] (0000-0002-1404-5264)
Maintainer: Jonathan Carroll <rpkg@jcarroll.com.au>
Diff between mathpix versions 0.1.0 dated 2017-09-27 and 0.2.0 dated 2017-10-18
mathpix-0.1.0/mathpix/inst/eq_no_01.png |only mathpix-0.1.0/mathpix/inst/eq_no_02.png |only mathpix-0.1.0/mathpix/inst/integral.jpg |only mathpix-0.1.0/mathpix/inst/logo.png |only mathpix-0.1.0/mathpix/inst/logo_blue.png |only mathpix-0.1.0/mathpix/inst/matrix_3x3.jpg |only mathpix-0.2.0/mathpix/DESCRIPTION | 17 +-- mathpix-0.2.0/mathpix/MD5 | 28 ++--- mathpix-0.2.0/mathpix/NEWS.md | 15 ++ mathpix-0.2.0/mathpix/R/connect.R | 56 ++++++++-- mathpix-0.2.0/mathpix/inst/extdata/eq_no_05_screencapfixes.jpg |only mathpix-0.2.0/mathpix/man/mathpix.Rd | 11 + mathpix-0.2.0/mathpix/man/rmarkdown_block.Rd | 5 mathpix-0.2.0/mathpix/tests/testthat/test_api.R | 19 +++ mathpix-0.2.0/mathpix/tools |only 15 files changed, 116 insertions(+), 35 deletions(-)
Title: The Environmental Costs of Flow Regulation
Description: An application to calculate the daily environmental costs of river flow regulation by dams based on García de Jalon et al. 2017 <doi:10.1007/s11269-017-1663-0>.
Author: Silvestre Garcia de Jalon; Javier Martinez-Lopez; Marta Gonzalez del Tanago; Carlos Alonso; Diego Garcia de Jalon
Maintainer: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>
Diff between FlowRegEnvCost versions 0.1.0 dated 2017-10-09 and 0.1.1 dated 2017-10-18
FlowRegEnvCost-0.1.0/FlowRegEnvCost/man/col_per_year.Rd |only FlowRegEnvCost-0.1.0/FlowRegEnvCost/man/structure_date.Rd |only FlowRegEnvCost-0.1.1/FlowRegEnvCost/DESCRIPTION | 6 +-- FlowRegEnvCost-0.1.1/FlowRegEnvCost/MD5 | 12 ++---- FlowRegEnvCost-0.1.1/FlowRegEnvCost/NAMESPACE | 2 - FlowRegEnvCost-0.1.1/FlowRegEnvCost/R/FlowRegEnvCosts.R | 25 +------------- FlowRegEnvCost-0.1.1/FlowRegEnvCost/R/data.R | 7 ++- FlowRegEnvCost-0.1.1/FlowRegEnvCost/man/flowdata.Rd | 6 +-- 8 files changed, 18 insertions(+), 40 deletions(-)
More information about FlowRegEnvCost at CRAN
Permanent link
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Livestock movements are important for the spread of many
infectious diseases between herds. The package provides an
efficient and flexible framework for stochastic disease spread
modelling that integrates within-herd disease dynamics as
continuous-time Markov chains and livestock movements between
herds as scheduled events. The core simulation solver is
implemented in C and uses 'OpenMP' (if available) to divide work
over multiple processors. The package contains template models and
can be extended with user defined models.
Author: Stefan Widgren (National Veterinary Institute, Sweden and
Uppsala University, Sweden),
Pavol Bauer (Uppsala University, Sweden),
Stefan Engblom (Uppsala University, Sweden)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 5.0.0 dated 2017-06-13 and 5.1.0 dated 2017-10-18
DESCRIPTION | 6 MD5 | 20 +- NEWS | 17 ++ build/vignette.rds |binary inst/doc/SimInf.R | 14 - inst/doc/SimInf.Rnw | 347 ++++++++++++++++++++++++----------------------- inst/doc/SimInf.pdf |binary src/SimInf.c | 27 ++- src/core/SimInf_solver.c | 21 ++ vignettes/SimInf.Rnw | 347 ++++++++++++++++++++++++----------------------- vignettes/SimInf.bib | 157 ++++----------------- 11 files changed, 469 insertions(+), 487 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: A multivariate continuous (and discrete) time dynamic modelling
package for panel and time series data, using linear stochastic differential
equations. Contains a faster frequentist set of functions using OpenMx for
single subject and mixed-effects (random intercepts only) structural
equation models, or a hierarchical Bayesian implementation using Stan that
allows for random effects over all model parameters. Allows for modelling of
multiple noisy measurements of multiple stochastic processes, time varying
input / event covariates, and time invariant covariates used to predict the
parameters.
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph]
Maintainer: Charles Driver <driver@mpib-berlin.mpg.de>
Diff between ctsem versions 2.4.0 dated 2017-05-17 and 2.5.0 dated 2017-10-18
ctsem-2.4.0/ctsem/R/ctStanKalman.R |only ctsem-2.4.0/ctsem/man/ctStanKalman.Rd |only ctsem-2.4.0/ctsem/man/ctStanKalmanPlot.Rd |only ctsem-2.5.0/ctsem/DESCRIPTION | 10 ctsem-2.5.0/ctsem/MD5 | 134 - ctsem-2.5.0/ctsem/NAMESPACE | 10 ctsem-2.5.0/ctsem/NEWS | 19 ctsem-2.5.0/ctsem/R/Kalman.R |only ctsem-2.5.0/ctsem/R/ctCheckFit.R |only ctsem-2.5.0/ctsem/R/ctDataHelp.R | 12 ctsem-2.5.0/ctsem/R/ctDiscretePars.R | 36 ctsem-2.5.0/ctsem/R/ctFit.R | 274 +- ctsem-2.5.0/ctsem/R/ctFitAuto.R |only ctsem-2.5.0/ctsem/R/ctGenerate.R | 13 ctsem-2.5.0/ctsem/R/ctGenerateFromFit.R | 40 ctsem-2.5.0/ctsem/R/ctKalman.R | 534 ++--- ctsem-2.5.0/ctsem/R/ctModelFromFit.R |only ctsem-2.5.0/ctsem/R/ctMultigroupFit.R | 312 --- ctsem-2.5.0/ctsem/R/ctPlotArray.R | 21 ctsem-2.5.0/ctsem/R/ctStanFit.R | 1183 +++++++---- ctsem-2.5.0/ctsem/R/ctStanFitTV.R | 17 ctsem-2.5.0/ctsem/R/ctStanModel.R | 28 ctsem-2.5.0/ctsem/R/ctStanParMatrices.R |only ctsem-2.5.0/ctsem/R/ctStanPlotPost.R | 179 + ctsem-2.5.0/ctsem/R/ctStanSummary.R | 105 - ctsem-2.5.0/ctsem/R/ctStanTIpredeffects.R | 181 + ctsem-2.5.0/ctsem/R/plot.ctStanFit.R | 8 ctsem-2.5.0/ctsem/R/plot.ctStanModel.R | 9 ctsem-2.5.0/ctsem/R/stanWplot.R | 17 ctsem-2.5.0/ctsem/R/stan_checkdivergences.R |only ctsem-2.5.0/ctsem/R/stan_confidenceRegion.R |only ctsem-2.5.0/ctsem/R/summary.ctsemFit.R | 6 ctsem-2.5.0/ctsem/data/AnomAuth.rda |binary ctsem-2.5.0/ctsem/data/Oscillating.rda |binary ctsem-2.5.0/ctsem/data/ctExample1.rda |binary ctsem-2.5.0/ctsem/data/ctExample1TIpred.rda |binary ctsem-2.5.0/ctsem/data/ctExample2.rda |binary ctsem-2.5.0/ctsem/data/ctExample3.rda |binary ctsem-2.5.0/ctsem/data/ctExample4.rda |binary ctsem-2.5.0/ctsem/data/ctstantestdat.rda |binary ctsem-2.5.0/ctsem/data/ctstantestfit.rda |binary ctsem-2.5.0/ctsem/data/datastructure.rda |binary ctsem-2.5.0/ctsem/data/longexample.rda |binary ctsem-2.5.0/ctsem/inst/doc/ctsem.R | 28 ctsem-2.5.0/ctsem/inst/doc/ctsem.pdf |binary ctsem-2.5.0/ctsem/inst/doc/ctsem.rnw | 190 - ctsem-2.5.0/ctsem/inst/doc/hierarchical.R | 85 ctsem-2.5.0/ctsem/inst/doc/hierarchical.pdf |binary ctsem-2.5.0/ctsem/inst/doc/hierarchical.rnw | 374 --- ctsem-2.5.0/ctsem/man/Kalman.Rd |only ctsem-2.5.0/ctsem/man/ctCheckFit.Rd |only ctsem-2.5.0/ctsem/man/ctFit.Rd | 31 ctsem-2.5.0/ctsem/man/ctGenerate.Rd | 6 ctsem-2.5.0/ctsem/man/ctGenerateFromFit.Rd | 2 ctsem-2.5.0/ctsem/man/ctKalman.Rd | 78 ctsem-2.5.0/ctsem/man/ctKalmanPlot.Rd |only ctsem-2.5.0/ctsem/man/ctModelFromFit.Rd |only ctsem-2.5.0/ctsem/man/ctMultigroupFit.Rd | 20 ctsem-2.5.0/ctsem/man/ctStanDiscretePars.Rd | 7 ctsem-2.5.0/ctsem/man/ctStanDiscreteParsPlot.Rd | 7 ctsem-2.5.0/ctsem/man/ctStanFit.Rd | 10 ctsem-2.5.0/ctsem/man/ctStanFitTV.Rd | 4 ctsem-2.5.0/ctsem/man/ctStanParMatrices.Rd |only ctsem-2.5.0/ctsem/man/ctStanPlotPost.Rd | 10 ctsem-2.5.0/ctsem/man/ctStanTIpredeffects.Rd | 22 ctsem-2.5.0/ctsem/man/ctstantestdat.Rd | 6 ctsem-2.5.0/ctsem/man/ctstantestfit.Rd | 6 ctsem-2.5.0/ctsem/man/plot.ctStanFit.Rd | 2 ctsem-2.5.0/ctsem/man/stan_checkdivergences.Rd |only ctsem-2.5.0/ctsem/man/stan_confidenceRegion.Rd |only ctsem-2.5.0/ctsem/man/summary.ctStanFit.Rd | 7 ctsem-2.5.0/ctsem/tests/testthat/kalmanVram.R | 24 ctsem-2.5.0/ctsem/tests/testthat/kalmanVram.R.orig |only ctsem-2.5.0/ctsem/tests/testthat/singleprocess.R | 35 ctsem-2.5.0/ctsem/vignettes/ctsem.rnw | 190 - ctsem-2.5.0/ctsem/vignettes/hierarchical.rnw | 374 --- ctsem-2.5.0/ctsem/vignettes/hierarchicalreferences.bib | 1706 ++++++++++------- 77 files changed, 3402 insertions(+), 2970 deletions(-)
Title: Plot Stacked Areas and Confidence Bands as Filled Polygons
Description: Plot stacked areas and confidence bands as filled polygons, or add
polygons to existing plots. A variety of input formats are supported,
including vectors, matrices, data frames, formulas, etc.
Author: Arni Magnusson [aut, cre]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between areaplot versions 1.1-0 dated 2017-10-10 and 1.2-0 dated 2017-10-18
DESCRIPTION | 17 ++++++++--------- MD5 | 14 +++++++++----- NAMESPACE | 5 +++++ NEWS | 10 +++++++++- R/areaplot-package.R |only R/areaplot.R | 11 ++++++++++- R/confplot.R |only man/areaplot-package.Rd |only man/areaplot.Rd | 11 ++++++++++- man/confplot.Rd |only 10 files changed, 51 insertions(+), 17 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC; Dimitris Rizopoulos (2016) <doi:10.18637/jss.v072.i07>.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes versions 0.8-68 dated 2017-10-02 and 0.8-69 dated 2017-10-18
JMbayes-0.8-68/JMbayes/demo |only JMbayes-0.8-69/JMbayes/DESCRIPTION | 8 JMbayes-0.8-69/JMbayes/MD5 | 39 ++-- JMbayes-0.8-69/JMbayes/NAMESPACE | 7 JMbayes-0.8-69/JMbayes/R/expected_failure_time.R |only JMbayes-0.8-69/JMbayes/R/globals.R | 2 JMbayes-0.8-69/JMbayes/R/mvJointModelBayes.R | 6 JMbayes-0.8-69/JMbayes/R/prederrJM.mvJMbayes.R | 2 JMbayes-0.8-69/JMbayes/R/predict_eventTime.R |only JMbayes-0.8-69/JMbayes/R/rocJM.JMbayes.R | 14 + JMbayes-0.8-69/JMbayes/R/rocJM.mvJMbayes.R | 35 +++- JMbayes-0.8-69/JMbayes/R/survfitJM.mvJMbayes.R | 31 ++- JMbayes-0.8-69/JMbayes/README.md | 1 JMbayes-0.8-69/JMbayes/inst/NEWS | 9 + JMbayes-0.8-69/JMbayes/inst/shiny_app_JM/global.R | 11 + JMbayes-0.8-69/JMbayes/inst/shiny_app_JM/server.R | 113 ++++++++++--- JMbayes-0.8-69/JMbayes/inst/shiny_app_JM/ui.R | 7 JMbayes-0.8-69/JMbayes/inst/shiny_app_JM/white_space.Rhtml |only JMbayes-0.8-69/JMbayes/man/JMbayes.Rd | 4 JMbayes-0.8-69/JMbayes/man/aucJM.Rd | 23 ++ JMbayes-0.8-69/JMbayes/src/fast_LAPRWM.cpp | 2 21 files changed, 238 insertions(+), 76 deletions(-)
Title: A Package for Generalised Linear Spatial Models
Description: Functions for inference in generalised linear spatial models. The posterior and predictive inference is based on Markov chain Monte Carlo methods. Package geoRglm is an extension to the package geoR, which must be installed first.
Author: Ole F. Christensen [aut, cre], Paulo J. Ribeiro Jr [aut]
Maintainer: Ole F. Christensen <OleF.Christensen@mbg.au.dk>
Diff between geoRglm versions 0.9-8 dated 2015-04-27 and 0.9-11 dated 2017-10-18
DESCRIPTION | 13 ++++++------- MD5 | 26 ++++++++++++++------------ NAMESPACE | 3 +++ R/binom.bayes.R | 2 +- R/binom.pred.R | 8 +++++--- R/glsm.krige.R | 9 ++++++--- R/likeli.R | 8 ++++---- R/pois.bayes.R | 15 +++++++++------ R/pois.pred.R | 4 +++- build/vignette.rds |binary inst/CITATION | 2 +- inst/doc/geoRglmintro.pdf |binary src/geoR.h | 3 ++- src/geoRglm.h |only src/init.c |only 15 files changed, 54 insertions(+), 39 deletions(-)
Title: Generalized Competing Event Model
Description: Generalized competing event model based on Cox PH model and Fine-Gray model.
This function is designed to develop optimized risk-stratification methods for competing
risks data, such as described in:
1. Carmona R, Gulaya S, Murphy JD, Rose BS, Wu J, Noticewala S,McHale MT, Yashar CM, Vaida F,
and Mell LK (2014) <DOI:10.1016/j.ijrobp.2014.03.047>.
2. Carmona R, Zakeri K, Green G, Hwang L, Gulaya S, Xu B, Verma R, Williamson CW, Triplett DP, Rose
BS, Shen H, Vaida F, Murphy JD, and Mell LK (2016) <DOI:10.1200/JCO.2015.65.0739>.
3. Lunn, Mary, and Don McNeil (1995) <DOI:10.2307/2532940>.
Author: Hanjie Shen <has072@ucsd.edu>, Ruben Carmona
<ruben.carmona13@gmail.com>, Loren Mell <lmell@ucsd.edu>
Maintainer: Hanjie Shen <shenhanjie0418@gmail.com>
Diff between gcerisk versions 17.8.7 dated 2017-08-08 and 17.10.17 dated 2017-10-18
DESCRIPTION | 8 +-- MD5 | 10 ++-- R/gcecox.R | 120 +++++++++++++++++++++++++++++----------------------------- R/gcefg.R | 95 ++++++++++++++++++++++----------------------- man/gcecox.Rd | 72 +++++++++++----------------------- man/gcefg.Rd | 37 +++++++---------- 6 files changed, 154 insertions(+), 188 deletions(-)