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2016-09-20 0.1.0
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Title: Gibbs Sea Water Functions
Description: Provides an interface to the Gibbs 'SeaWater' ('TEOS-10') C
library, version 3.05-4 (commit '5b4d959e54031f9e972f3e863f63e67fa4f5bfec', dated 2017-08-07,
available at <https://github.com/TEOS-10/GSW-C>, which stems from
'Matlab' and other code written by members of Working Group 127 of
'SCOR'/'IAPSO' (Scientific Committee on Oceanic Research /
International Association for the Physical Sciences of the Oceans).
Author: Dan Kelley [aut, cre, cph] (C wrapper plus R code, tests, and
documentation),
Clark Richards [aut, cph] (C wrapper plus R code, tests, and
documentation),
WG127 SCOR/IAPSO [aut, cph] (Original 'Matlab' and derived code)
Maintainer: Dan Kelley <dan.kelley@dal.ca>
Diff between gsw versions 1.0-4 dated 2017-08-02 and 1.0-5 dated 2017-08-09
DESCRIPTION | 10 MD5 | 312 ++++++------ NEWS | 6 README.md | 4 inst/doc/gsw.R | 25 inst/doc/gsw.Rmd | 32 - inst/doc/gsw.html | 11 man/gsw_CT_first_derivatives.Rd | 4 man/gsw_CT_first_derivatives_wrt_t_exact.Rd | 4 man/gsw_CT_freezing.Rd | 4 man/gsw_CT_freezing_first_derivatives.Rd | 4 man/gsw_CT_freezing_first_derivatives_poly.Rd | 4 man/gsw_CT_freezing_poly.Rd | 4 man/gsw_CT_from_enthalpy.Rd | 4 man/gsw_CT_from_entropy.Rd | 4 man/gsw_CT_from_pt.Rd | 4 man/gsw_CT_from_rho.Rd | 4 man/gsw_CT_from_t.Rd | 4 man/gsw_CT_maxdensity.Rd | 4 man/gsw_CT_second_derivatives.Rd | 4 man/gsw_C_from_SP.Rd | 4 man/gsw_Fdelta.Rd | 4 man/gsw_Helmholtz_energy_ice.Rd | 4 man/gsw_IPV_vs_fNsquared_ratio.Rd | 4 man/gsw_Nsquared.Rd | 4 man/gsw_SAAR.Rd | 4 man/gsw_SA_freezing_from_CT.Rd | 4 man/gsw_SA_freezing_from_CT_poly.Rd | 4 man/gsw_SA_freezing_from_t.Rd | 4 man/gsw_SA_freezing_from_t_poly.Rd | 4 man/gsw_SA_from_SP.Rd | 4 man/gsw_SA_from_SP_Baltic.Rd | 4 man/gsw_SA_from_Sstar.Rd | 4 man/gsw_SA_from_rho.Rd | 4 man/gsw_SP_from_C.Rd | 4 man/gsw_SP_from_SA.Rd | 4 man/gsw_SP_from_SR.Rd | 4 man/gsw_SP_from_Sstar.Rd | 4 man/gsw_SR_from_SP.Rd | 4 man/gsw_Sstar_from_SA.Rd | 4 man/gsw_Sstar_from_SP.Rd | 4 man/gsw_Turner_Rsubrho.Rd | 4 man/gsw_adiabatic_lapse_rate_from_CT.Rd | 4 man/gsw_adiabatic_lapse_rate_ice.Rd | 4 man/gsw_alpha.Rd | 4 man/gsw_alpha_on_beta.Rd | 4 man/gsw_alpha_wrt_t_exact.Rd | 4 man/gsw_alpha_wrt_t_ice.Rd | 4 man/gsw_beta.Rd | 4 man/gsw_beta_const_t_exact.Rd | 4 man/gsw_cabbeling.Rd | 4 man/gsw_chem_potential_water_ice.Rd | 4 man/gsw_chem_potential_water_t_exact.Rd | 4 man/gsw_cp_ice.Rd | 4 man/gsw_cp_t_exact.Rd | 4 man/gsw_deltaSA_from_SP.Rd | 4 man/gsw_dilution_coefficient_t_exact.Rd | 4 man/gsw_dynamic_enthalpy.Rd | 4 man/gsw_enthalpy.Rd | 4 man/gsw_enthalpy_CT_exact.Rd | 4 man/gsw_enthalpy_diff.Rd | 4 man/gsw_enthalpy_first_derivatives.Rd | 4 man/gsw_enthalpy_first_derivatives_CT_exact.Rd | 4 man/gsw_enthalpy_ice.Rd | 4 man/gsw_enthalpy_second_derivatives.Rd | 4 man/gsw_enthalpy_second_derivatives_CT_exact.Rd | 4 man/gsw_enthalpy_t_exact.Rd | 4 man/gsw_entropy_first_derivatives.Rd | 4 man/gsw_entropy_from_pt.Rd | 4 man/gsw_entropy_from_t.Rd | 4 man/gsw_entropy_ice.Rd | 4 man/gsw_entropy_second_derivatives.Rd | 4 man/gsw_frazil_properties.Rd | 4 man/gsw_frazil_properties_potential.Rd | 4 man/gsw_frazil_properties_potential_poly.Rd | 4 man/gsw_frazil_ratios_adiabatic.Rd | 4 man/gsw_frazil_ratios_adiabatic_poly.Rd | 4 man/gsw_geo_strf_dyn_height.Rd | 4 man/gsw_geo_strf_dyn_height_pc.Rd | 4 man/gsw_gibbs.Rd | 4 man/gsw_gibbs_ice.Rd | 4 man/gsw_grav.Rd | 4 man/gsw_ice_fraction_to_freeze_seawater.Rd | 4 man/gsw_internal_energy.Rd | 4 man/gsw_internal_energy_ice.Rd | 4 man/gsw_kappa.Rd | 4 man/gsw_kappa_const_t_ice.Rd | 4 man/gsw_kappa_ice.Rd | 4 man/gsw_kappa_t_exact.Rd | 4 man/gsw_latentheat_evap_CT.Rd | 4 man/gsw_latentheat_evap_t.Rd | 4 man/gsw_latentheat_melting.Rd | 4 man/gsw_melting_ice_SA_CT_ratio.Rd | 4 man/gsw_melting_ice_SA_CT_ratio_poly.Rd | 4 man/gsw_melting_ice_equilibrium_SA_CT_ratio.Rd | 4 man/gsw_melting_ice_equilibrium_SA_CT_ratio_poly.Rd | 4 man/gsw_melting_ice_into_seawater.Rd | 4 man/gsw_melting_seaice_into_seawater.Rd | 4 man/gsw_p_from_z.Rd | 4 man/gsw_pot_enthalpy_from_pt_ice.Rd | 4 man/gsw_pot_enthalpy_from_pt_ice_poly.Rd | 4 man/gsw_pot_enthalpy_ice_freezing.Rd | 4 man/gsw_pot_enthalpy_ice_freezing_first_derivatives.Rd | 4 man/gsw_pot_enthalpy_ice_freezing_first_derivatives_poly.Rd | 4 man/gsw_pot_enthalpy_ice_freezing_poly.Rd | 4 man/gsw_pot_rho_t_exact.Rd | 4 man/gsw_pressure_coefficient_ice.Rd | 4 man/gsw_pressure_freezing_CT.Rd | 4 man/gsw_pt0_from_t.Rd | 4 man/gsw_pt0_from_t_ice.Rd | 4 man/gsw_pt_first_derivatives.Rd | 4 man/gsw_pt_from_CT.Rd | 4 man/gsw_pt_from_entropy.Rd | 4 man/gsw_pt_from_pot_enthalpy_ice.Rd | 4 man/gsw_pt_from_pot_enthalpy_ice_poly.Rd | 4 man/gsw_pt_from_t.Rd | 4 man/gsw_pt_from_t_ice.Rd | 4 man/gsw_pt_second_derivatives.Rd | 4 man/gsw_rho.Rd | 4 man/gsw_rho_alpha_beta.Rd | 4 man/gsw_rho_first_derivatives.Rd | 4 man/gsw_rho_first_derivatives_wrt_enthalpy.Rd | 4 man/gsw_rho_ice.Rd | 4 man/gsw_rho_second_derivatives.Rd | 4 man/gsw_rho_second_derivatives_wrt_enthalpy.Rd | 4 man/gsw_rho_t_exact.Rd | 4 man/gsw_seaice_fraction_to_freeze_seawater.Rd | 4 man/gsw_sigma0.Rd | 4 man/gsw_sigma1.Rd | 4 man/gsw_sigma2.Rd | 4 man/gsw_sigma3.Rd | 4 man/gsw_sigma4.Rd | 4 man/gsw_sound_speed.Rd | 4 man/gsw_sound_speed_ice.Rd | 4 man/gsw_sound_speed_t_exact.Rd | 4 man/gsw_specvol.Rd | 4 man/gsw_specvol_alpha_beta.Rd | 4 man/gsw_specvol_anom_standard.Rd | 4 man/gsw_specvol_first_derivatives.Rd | 4 man/gsw_specvol_first_derivatives_wrt_enthalpy.Rd | 4 man/gsw_specvol_ice.Rd | 4 man/gsw_specvol_second_derivatives.Rd | 4 man/gsw_specvol_second_derivatives_wrt_enthalpy.Rd | 4 man/gsw_specvol_t_exact.Rd | 4 man/gsw_spiciness0.Rd | 4 man/gsw_spiciness1.Rd | 4 man/gsw_spiciness2.Rd | 4 man/gsw_t_deriv_chem_potential_water_t_exact.Rd | 4 man/gsw_t_freezing.Rd | 4 man/gsw_t_freezing_first_derivatives.Rd | 4 man/gsw_t_freezing_first_derivatives_poly.Rd | 4 man/gsw_t_from_CT.Rd | 4 man/gsw_t_from_pt0_ice.Rd | 4 man/gsw_thermobaric.Rd | 4 man/gsw_z_from_p.Rd | 4 src/gsw_oceanographic_toolbox.c | 74 +- vignettes/gsw.Rmd | 32 - 157 files changed, 546 insertions(+), 552 deletions(-)
Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova (hanas@uw.edu), Leontine Alkema (alkema@nus.edu.sg), Adrian Raftery (raftery@uw.edu), Bailey Fosdick (bfosdick@uw.edu), Patrick Gerland (gerland@un.org)
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesTFR versions 6.1-0 dated 2017-07-28 and 6.1-1 dated 2017-08-09
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/CITATION | 42 +++++++++++++++++++++--------------------- man/bayesTFR-package.Rd | 4 ++-- 5 files changed, 35 insertions(+), 31 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement complex
random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain an
efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [ctb],
Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.7.10 dated 2017-05-05 and 1.7.11 dated 2017-08-09
DESCRIPTION | 8 +-- MD5 | 36 +++++++------- NAMESPACE | 11 +++- NEWS | 21 ++++++++ R/TMB.R | 2 R/checker.R |only R/sdreport.R | 24 ++++++--- inst/examples/simple.cpp | 12 ++++ inst/include/TMB.hpp | 5 - inst/include/convert.hpp | 90 ++++++++++++++++------------------- inst/include/cppad/local/ad.hpp | 5 - inst/include/cppad/local/ad_ctor.hpp | 5 - inst/include/cppad/local/kasper.hpp | 6 +- inst/include/distributions_R.hpp | 8 +-- inst/include/tmb_core.hpp | 11 +--- inst/include/tmbutils/density.hpp | 3 - inst/include/tmbutils/spmat.hpp | 40 ++++++++++++++- man/checkConsistency.Rd |only man/print.checkConsistency.Rd |only man/sdreport.Rd | 11 +++- man/summary.checkConsistency.Rd |only 21 files changed, 188 insertions(+), 110 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between rlang versions 0.1.1 dated 2017-05-18 and 0.1.2 dated 2017-08-09
rlang-0.1.1/rlang/src/internals.c |only rlang-0.1.2/rlang/DESCRIPTION | 6 +- rlang-0.1.2/rlang/MD5 | 32 +++++++------- rlang-0.1.2/rlang/NEWS.md | 5 ++ rlang-0.1.2/rlang/R/compat-oldrel.R | 56 ++++++++----------------- rlang-0.1.2/rlang/R/env.R | 10 +--- rlang-0.1.2/rlang/R/eval-tidy.R | 13 ++--- rlang-0.1.2/rlang/R/types.R | 5 -- rlang-0.1.2/rlang/R/utils.R | 22 +++++++++ rlang-0.1.2/rlang/README.md | 1 rlang-0.1.2/rlang/build/vignette.rds |binary rlang-0.1.2/rlang/man/is_copyable.Rd | 5 -- rlang-0.1.2/rlang/src/env.c |only rlang-0.1.2/rlang/src/init.c | 4 - rlang-0.1.2/rlang/src/vector.h | 2 rlang-0.1.2/rlang/tests/testthat.R | 4 - rlang-0.1.2/rlang/tests/testthat/test-compat.R | 7 +++ rlang-0.1.2/rlang/tests/testthat/test-env.R | 8 +-- 18 files changed, 89 insertions(+), 91 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Antigoni Kaliontzopoulou, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 3.0.4 dated 2017-06-08 and 3.0.5 dated 2017-08-09
geomorph-3.0.4/geomorph/data/larvalTails.rda |only geomorph-3.0.4/geomorph/man/compare.modular.partitions.Rd |only geomorph-3.0.4/geomorph/man/larvalTails.Rd |only geomorph-3.0.4/geomorph/man/morphol.integr.Rd |only geomorph-3.0.4/geomorph/man/phylo.pls.Rd |only geomorph-3.0.4/geomorph/man/plotAllometry.Rd |only geomorph-3.0.5/geomorph/DESCRIPTION | 8 geomorph-3.0.5/geomorph/MD5 | 110 - geomorph-3.0.5/geomorph/NAMESPACE | 7 geomorph-3.0.5/geomorph/NEWS | 10 geomorph-3.0.5/geomorph/R/advanced.procD.lm.r | 489 +++--- geomorph-3.0.5/geomorph/R/bilat.symmetry.r | 6 geomorph-3.0.5/geomorph/R/combine.subsets.R |only geomorph-3.0.5/geomorph/R/compare.pls.r | 2 geomorph-3.0.5/geomorph/R/coords.subset.r | 7 geomorph-3.0.5/geomorph/R/deprecated.defunct.r | 44 geomorph-3.0.5/geomorph/R/geomorph.support.code.r | 1047 ++++++-------- geomorph-3.0.5/geomorph/R/geomorph.utils.r | 64 geomorph-3.0.5/geomorph/R/integration.test.r | 6 geomorph-3.0.5/geomorph/R/modularity.test.r | 4 geomorph-3.0.5/geomorph/R/morphol.disparity.r | 69 geomorph-3.0.5/geomorph/R/nested.update.r | 12 geomorph-3.0.5/geomorph/R/phylo.integration.r | 8 geomorph-3.0.5/geomorph/R/phylo.modularity.r | 2 geomorph-3.0.5/geomorph/R/plotTangentSpace.r | 1 geomorph-3.0.5/geomorph/R/procD.allometry.r | 274 +-- geomorph-3.0.5/geomorph/R/procD.lm.r | 4 geomorph-3.0.5/geomorph/R/procD.pgls.r | 52 geomorph-3.0.5/geomorph/R/readland.nts.r | 3 geomorph-3.0.5/geomorph/R/readland.tps.r | 75 - geomorph-3.0.5/geomorph/R/trajectory.analysis.r | 9 geomorph-3.0.5/geomorph/R/two.b.pls.r | 4 geomorph-3.0.5/geomorph/README.md | 2 geomorph-3.0.5/geomorph/data/larvalMorph.rda |only geomorph-3.0.5/geomorph/inst/CITATION | 17 geomorph-3.0.5/geomorph/man/advanced.procD.lm.Rd | 160 +- geomorph-3.0.5/geomorph/man/bilat.symmetry.Rd | 2 geomorph-3.0.5/geomorph/man/combine.subsets.Rd |only geomorph-3.0.5/geomorph/man/compare.pls.Rd | 2 geomorph-3.0.5/geomorph/man/coords.subset.Rd | 5 geomorph-3.0.5/geomorph/man/hummingbirds.Rd | 4 geomorph-3.0.5/geomorph/man/integration.test.Rd | 6 geomorph-3.0.5/geomorph/man/larvalMorph.Rd |only geomorph-3.0.5/geomorph/man/modularity.test.Rd | 4 geomorph-3.0.5/geomorph/man/morphol.disparity.Rd | 18 geomorph-3.0.5/geomorph/man/motionpaths.Rd | 2 geomorph-3.0.5/geomorph/man/mshape.Rd | 8 geomorph-3.0.5/geomorph/man/nested.update.Rd | 12 geomorph-3.0.5/geomorph/man/phylo.integration.Rd | 8 geomorph-3.0.5/geomorph/man/phylo.modularity.Rd | 2 geomorph-3.0.5/geomorph/man/plethShapeFood.Rd | 6 geomorph-3.0.5/geomorph/man/plethodon.Rd | 4 geomorph-3.0.5/geomorph/man/print.advanced.procD.lm.Rd | 4 geomorph-3.0.5/geomorph/man/print.combined.set.Rd |only geomorph-3.0.5/geomorph/man/procD.allometry.Rd | 160 +- geomorph-3.0.5/geomorph/man/procD.lm.Rd | 4 geomorph-3.0.5/geomorph/man/procD.pgls.Rd | 31 geomorph-3.0.5/geomorph/man/pupfish.Rd | 6 geomorph-3.0.5/geomorph/man/ratland.Rd | 2 geomorph-3.0.5/geomorph/man/summary.combined.set.Rd |only geomorph-3.0.5/geomorph/man/trajectory.analysis.Rd | 7 geomorph-3.0.5/geomorph/man/two.b.pls.Rd | 4 62 files changed, 1399 insertions(+), 1398 deletions(-)
Title: Misspecified Models for Gene-Environment Interaction
Description: First major functionality is to compute the bias in misspecified linear gene-environment interaction models. The most
generalized function for this objective is GE_bias(). However GE_bias() requires specification of many
higher order moments of covariates in the model. If users are unsure about how to calculate/estimate
these higher order moments, it may be easier to use GE_bias_normal_squaredmis(). This function places
many more assumptions on the covariates (most notably that they are all jointly generated from a multivariate
normal distribution) and is thus able to automatically calculate many of the higher order moments automatically,
necessitating only that the user specify some covariances. There are also functions to solve for the bias
through simulation and non-linear equation solvers, these can be used to check your work. Second major functionality
is to implement the Bootstrap Inference with Correct Sandwich (BICS) testing procedure, which we have found to provide better finite-sample
performance than other inference procedures for testing GxE interaction. More details on these functions
are available in Sun, Carroll, Christiani, and Lin, "Testing for Gene-Environment Interaction Under Exposure Misspecification"
(In Revision).
Author: Ryan Sun [aut, cre],
Richard Barfield [ctb]
Maintainer: Ryan Sun <ryansun.work@gmail.com>
Diff between GEint versions 0.1.2 dated 2017-01-06 and 0.1.4 dated 2017-08-09
DESCRIPTION | 22 - MD5 | 66 ++- NAMESPACE | 8 R/GE_BICS.R | 14 R/GE_BICS_old.R |only R/GE_bias.R | 272 ++++++++------ R/GE_bias_normal_squaredmis.R | 601 +++++++++++++++++--------------- R/GE_bias_normal_squaredmis_old.R |only R/GE_bias_old.R |only R/GE_enumerate_inputs.R | 55 +- R/GE_enumerate_inputs_old.R |only R/GE_nleqslv.R | 366 +++++++++++-------- R/GE_nleqslv_old.R |only R/GE_scoreeq_sim.R | 131 +++--- R/GE_scoreeq_sim_old.R |only R/GE_test_moment_calcs.R | 656 +++++++++++++---------------------- R/GE_test_moment_calcs_old.R |only R/GE_translate_inputs.R | 312 ++++++++++------ R/GE_translate_inputs_old.R |only build/vignette.rds |binary inst/doc/GEint_example.R | 6 inst/doc/GEint_example.Rmd | 32 - inst/doc/GEint_example.html | 58 +-- man/GE_BICS_old.Rd |only man/GE_bias.Rd | 10 man/GE_bias_normal_squaredmis.Rd | 52 +- man/GE_bias_normal_squaredmis_old.Rd |only man/GE_bias_old.Rd |only man/GE_enumerate_inputs.Rd | 4 man/GE_enumerate_inputs_old.Rd |only man/GE_nleqslv.Rd | 20 - man/GE_nleqslv_old.Rd |only man/GE_scoreeq_sim.Rd | 44 +- man/GE_scoreeq_sim_old.Rd |only man/GE_test_moment_calcs.Rd | 41 +- man/GE_test_moment_calcs_old.Rd |only man/GE_translate_inputs.Rd | 43 +- man/GE_translate_inputs_old.Rd |only tests |only vignettes/GEint_example.Rmd | 32 - 40 files changed, 1498 insertions(+), 1347 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions. Implementations of
DTW barycenter averaging and a distance based on global alignment kernels
are also provided. All included distance functions have custom loops
optimized for the calculation of cross-distance matrices, including
parallelization support. Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 4.0.2 dated 2017-07-09 and 4.0.3 dated 2017-08-09
dtwclust-4.0.2/dtwclust/R/uciCT.R |only dtwclust-4.0.2/dtwclust/src/dtwclustpp.h |only dtwclust-4.0.3/dtwclust/DESCRIPTION | 29 dtwclust-4.0.3/dtwclust/MD5 | 115 dtwclust-4.0.3/dtwclust/R/DBA.R | 294 - dtwclust-4.0.3/dtwclust/R/Distmat.R | 189 - dtwclust-4.0.3/dtwclust/R/GAK.R | 695 ++-- dtwclust-4.0.3/dtwclust/R/SBD.R | 14 dtwclust-4.0.3/dtwclust/R/SparseDistmat.R | 207 - dtwclust-4.0.3/dtwclust/R/TADPole.R | 218 - dtwclust-4.0.3/dtwclust/R/all-cent.R | 2 dtwclust-4.0.3/dtwclust/R/all-cent2.R | 398 +- dtwclust-4.0.3/dtwclust/R/compare-clusterings.R | 2045 ++++++------ dtwclust-4.0.3/dtwclust/R/create-dtwclust.R | 4 dtwclust-4.0.3/dtwclust/R/data.R |only dtwclust-4.0.3/dtwclust/R/ddist2.R | 420 +- dtwclust-4.0.3/dtwclust/R/dtw-basic.R | 503 +- dtwclust-4.0.3/dtwclust/R/dtw-lb.R | 14 dtwclust-4.0.3/dtwclust/R/dtwclust-methods.R | 6 dtwclust-4.0.3/dtwclust/R/dtwclust.R | 1248 +++---- dtwclust-4.0.3/dtwclust/R/lb-improved.R | 11 dtwclust-4.0.3/dtwclust/R/lb-keogh.R | 11 dtwclust-4.0.3/dtwclust/R/partitional.R | 508 +- dtwclust-4.0.3/dtwclust/R/pkg.R | 2 dtwclust-4.0.3/dtwclust/R/shape-extraction.R | 10 dtwclust-4.0.3/dtwclust/R/tsclust-controls.R | 389 +- dtwclust-4.0.3/dtwclust/R/tsclust-family.R | 246 - dtwclust-4.0.3/dtwclust/R/tsclust-methods.R | 2013 +++++------ dtwclust-4.0.3/dtwclust/R/tsclust.R | 1481 ++++---- dtwclust-4.0.3/dtwclust/R/tslist.R | 65 dtwclust-4.0.3/dtwclust/R/utils.R | 960 ++--- dtwclust-4.0.3/dtwclust/R/zscore.R | 4 dtwclust-4.0.3/dtwclust/build/vignette.rds |binary dtwclust-4.0.3/dtwclust/data/dtwclustTimings.rda |only dtwclust-4.0.3/dtwclust/inst/NEWS.Rd | 38 dtwclust-4.0.3/dtwclust/inst/doc/dtwclust.Rnw | 19 dtwclust-4.0.3/dtwclust/inst/doc/dtwclust.pdf |binary dtwclust-4.0.3/dtwclust/inst/doc/timing-experiments.Rmd |only dtwclust-4.0.3/dtwclust/inst/doc/timing-experiments.html |only dtwclust-4.0.3/dtwclust/inst/include/dtwclust.hpp | 128 dtwclust-4.0.3/dtwclust/man/SBD.Rd | 6 dtwclust-4.0.3/dtwclust/man/compare_clusterings.Rd | 2 dtwclust-4.0.3/dtwclust/man/dtwclustTimings.Rd |only dtwclust-4.0.3/dtwclust/man/tsclust-controls.Rd | 15 dtwclust-4.0.3/dtwclust/man/tslist.Rd | 4 dtwclust-4.0.3/dtwclust/man/uciCT.Rd | 2 dtwclust-4.0.3/dtwclust/src/SparseDistmatIndices.cpp | 2 dtwclust-4.0.3/dtwclust/src/dba.cpp | 2 dtwclust-4.0.3/dtwclust/src/dtw-lb.cpp | 2 dtwclust-4.0.3/dtwclust/src/dtwb-loop.cpp | 2 dtwclust-4.0.3/dtwclust/src/dtwclust++.h |only dtwclust-4.0.3/dtwclust/src/envelope.cpp | 2 dtwclust-4.0.3/dtwclust/src/gak-loop.cpp | 2 dtwclust-4.0.3/dtwclust/src/init.cpp | 2 dtwclust-4.0.3/dtwclust/src/lbi-loop.cpp | 2 dtwclust-4.0.3/dtwclust/src/lbk-loop.cpp | 2 dtwclust-4.0.3/dtwclust/src/lbs.cpp | 2 dtwclust-4.0.3/dtwclust/src/sbd-loop.cpp | 2 dtwclust-4.0.3/dtwclust/src/tadpole.cpp | 8 dtwclust-4.0.3/dtwclust/src/utils.cpp | 2 dtwclust-4.0.3/dtwclust/tests/testthat/system/partitional.R | 3 dtwclust-4.0.3/dtwclust/vignettes/dtwclust.Rnw | 19 dtwclust-4.0.3/dtwclust/vignettes/timing-experiments.Rmd |only 63 files changed, 6209 insertions(+), 6160 deletions(-)
Title: Deconvolute Mixed Genomes with Unknown Proportions
Description: Traditional phasing programs are limited to diploid organisms.
Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo
(MCMC) approaches, and builds a generic framework that allows haplotype searches
in a multiple infection setting. This package is primarily developed as part of
the Pf3k project, which is a global collaboration using the latest
sequencing technologies to provide a high-resolution view of natural variation
in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from
patient blood sample, which often contains more than one parasite strain, with
unknown proportions. This package is used for deconvoluting mixed haplotypes,
and reporting the mixture proportions from each sample.
Author: Joe Zhu [aut, cre, cph],
Jacob Almagro-Garcia [aut, cph],
Gil McVean [aut, cph],
University of Oxford [cph],
Yinghan Liu [ctb],
CodeCogs Zyba Ltd [com, cph],
Deepak Bandyopadhyay [com, cph],
Lutz Kettner [com, cph]
Maintainer: Joe Zhu <joe.zhu@well.ox.ac.uk>
Diff between DEploid versions 0.4.2 dated 2017-08-09 and 0.4.3 dated 2017-08-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/dEploid-Arguments.html | 4 ++-- src/DEploid/mcmc.cpp | 8 ++++++-- tests/testthat/test-DEploid_tools.R | 16 ++++++++++++---- 5 files changed, 28 insertions(+), 16 deletions(-)
Title: Analysis of Ecological Data : Exploratory and Euclidean Methods
in Environmental Sciences
Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4 versions 1.7-6 dated 2017-03-23 and 1.7-8 dated 2017-08-09
ade4-1.7-6/ade4/R/ade4toR.R |only ade4-1.7-6/ade4/R/cca.R |only ade4-1.7-6/ade4/R/randtest.cca.R |only ade4-1.7-6/ade4/man/ade4toR.Rd |only ade4-1.7-6/ade4/man/cca.Rd |only ade4-1.7-8/ade4/ChangeLog | 140 +++++++++++++++++++++++++++++++ ade4-1.7-8/ade4/DESCRIPTION | 10 +- ade4-1.7-8/ade4/MD5 | 55 +++++------- ade4-1.7-8/ade4/NAMESPACE | 8 - ade4-1.7-8/ade4/R/between.R | 4 ade4-1.7-8/ade4/R/krandtest.R | 17 +-- ade4-1.7-8/ade4/R/multiblock.R | 4 ade4-1.7-8/ade4/R/pcaiv.R | 58 +++++++----- ade4-1.7-8/ade4/R/randtest.R | 15 +-- ade4-1.7-8/ade4/R/randtest.pcaiv.R | 16 +-- ade4-1.7-8/ade4/R/randtest.pcaivortho.R | 4 ade4-1.7-8/ade4/R/statico.R | 6 - ade4-1.7-8/ade4/R/supdist.R |only ade4-1.7-8/ade4/R/varipart.R |only ade4-1.7-8/ade4/data/mafragh.rda |binary ade4-1.7-8/ade4/man/arrival.Rd | 2 ade4-1.7-8/ade4/man/atlas.Rd | 40 ++++---- ade4-1.7-8/ade4/man/divcmax.Rd | 39 ++------ ade4-1.7-8/ade4/man/elec88.Rd | 67 +++++++------- ade4-1.7-8/ade4/man/irishdata.Rd | 32 ++++--- ade4-1.7-8/ade4/man/mafragh.Rd | 46 +++++----- ade4-1.7-8/ade4/man/pcaiv.Rd | 78 +++++++++++++++++ ade4-1.7-8/ade4/man/randtest.pcaiv.Rd | 11 +- ade4-1.7-8/ade4/man/rpjdl.Rd | 18 ++- ade4-1.7-8/ade4/man/s.logo.Rd | 20 +--- ade4-1.7-8/ade4/man/statico.krandtest.Rd | 4 ade4-1.7-8/ade4/man/supdist.Rd |only ade4-1.7-8/ade4/man/varipart.Rd |only 33 files changed, 456 insertions(+), 238 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to the decennial US Census and American Community Survey APIs and
the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for many
geographies.
Author: Kyle Walker [aut, cre],
Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>
Diff between tidycensus versions 0.1.2 dated 2017-06-20 and 0.2 dated 2017-08-09
DESCRIPTION | 15 ++++++---- MD5 | 20 ++++++------- NAMESPACE | 3 ++ R/acs.R | 67 ++++++++++++++++++++++++++++++++++++++------- R/helpers.R | 72 +++++++++++++++++++++++++++++++++++++++++++++---- R/load_data.R | 38 +++++++++++++++++++++---- R/search_variables.R | 17 +++++++++-- R/tidycensus-package.R | 2 - README.md | 33 ++++++++++++++++++++-- man/census_api_key.Rd | 35 +++++++++++++++++++++-- man/get_acs.Rd | 5 ++- 11 files changed, 257 insertions(+), 50 deletions(-)
Title: Tools for Identifying Important Nodes in Networks
Description: Includes assorted tools for network analysis. Useful for
calculating and plotting expected influence, bridge centrality, and impact statistics.
Author: Payton Jones [aut, cre]
Maintainer: Payton Jones <payton_jones@g.harvard.edu>
Diff between networktools versions 1.0.0 dated 2017-04-14 and 1.1.0 dated 2017-08-09
DESCRIPTION | 18 +-- MD5 | 66 +++++++----- NAMESPACE | 7 + NEWS.md | 3 R/assumptionCheck.R |only R/bridge.R |only R/edge_impact.R | 40 ++++--- R/expectedInf.R | 14 +- R/global_impact.R | 40 ++++--- R/hidden_functions.R | 40 +++++-- R/impact.R | 40 ++++--- R/impact_NCT.R | 37 ++++--- R/impact_boot.R |only R/networktools-package.r |only R/structure_impact.R | 40 ++++--- R/summary_print_plot.R | 210 ++++++++++++++++++++++++++++++++++------ build/vignette.rds |binary inst/doc/Impact.R | 42 +++++--- inst/doc/Impact.Rmd | 152 +++++++++++++++++++--------- inst/doc/Impact.pdf |binary inst/doc/networktools.pdf |binary man/assumptionCheck.Rd |only man/bridge.Rd |only man/coerce_to_adjacency.Rd |only man/edge.impact.Rd | 8 - man/global.impact.Rd | 8 - man/impact.NCT.Rd | 9 - man/impact.Rd | 8 - man/impact.boot.Rd |only man/networktools.Rd |only man/plot.all.impact.Rd | 5 man/plot.bridge.Rd |only man/plot.edge.impact.Rd | 6 - man/plot.expectedInf.Rd | 4 man/plot.global.impact.Rd | 5 man/plot.structure.impact.Rd | 7 - man/structure.impact.Rd | 8 - vignettes/Impact.Rmd | 41 ++++--- vignettes/figures/pe_figure.png |binary 39 files changed, 601 insertions(+), 257 deletions(-)
Title: Combination of Factorial Methods and Cluster Analysis
Description: Multivariate exploration of a data table with factorial
analysis and cluster methods.
Author: Campo Elias Pardo <cepardot@unal.edu.co>, Pedro Cesar del Campo
<pcdelcampon@unal.edu.co> and Camilo Jose Torres
<cjtorresj@unal.edu.co>, with the contributions from Ivan Diaz
<ildiazm@unal.edu.co>, Mauricio Sadinle
<msadinleg@unal.edu.co>.
Maintainer: Campo Elias Pardo <cepardot@unal.edu.co>
Diff between FactoClass versions 1.1.3 dated 2017-01-05 and 1.1.4 dated 2017-08-09
DESCRIPTION | 11 ++--- MD5 | 21 +++++++--- NAMESPACE | 17 ++++---- R/addgrids3d.R |only R/centroids.R | 70 ++++++++++++++++++++-------------- R/chisqcarac.R |only R/cluster.carac.R | 93 ++++++++++++++++++++-------------------------- R/plotpairs.R |only data/Whisky.rda |only man/Whisky.Rd |only man/addgrids3d.Rd |only man/centroids.Rd | 51 ++++++++++++------------- man/clusterchisq.Rd |only man/kmeansW.Rd | 101 +++++++++++++++++++++++++------------------------- man/plotpairs.Rd |only src/FactoClass_init.c |only 16 files changed, 191 insertions(+), 173 deletions(-)
Title: Retinal Reconstruction Program
Description: Reconstructs retinae by morphing a flat surface with cuts (a
dissected flat-mount retina) onto a curvilinear surface (the standard retinal
shape). It can estimate the position of a point on the intact adult retina
to within 8 degrees of arc (3.6% of nasotemporal axis). The coordinates in
reconstructed retinae can be transformed to visuotopic coordinates.
Author: David C. Sterratt [aut, cre, cph],
Daniel Lyngholm [aut, cph]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between retistruct versions 0.5.11 dated 2017-07-15 and 0.5.12 dated 2017-08-09
DESCRIPTION | 8 - MD5 | 164 +++++++++++++++--------------- NAMESPACE | 2 NEWS | 14 ++ R/AnnotatedOutline.R | 34 +++--- R/Dataset.R | 4 R/Outline.R | 17 +-- R/ReconstructedDataset.R | 16 +- R/ReconstructedOutline.R | 24 ++-- R/RetinalReconstructedDataset.R | 2 R/RetinalReconstructedOutline.R | 2 R/StitchedOutline.R | 10 - R/TriangulatedOutline.R | 8 - R/fire.R | 8 - R/format-common.R | 2 R/format-idt.R | 4 R/geometry.R | 60 +++++----- R/projections.R | 12 +- R/retistruct-batch.R | 6 - R/retistruct.R | 20 +-- R/spheristruct.R | 68 ++++++------ R/transformations.R | 12 +- demo/retistruct.method.R | 10 - man/AnnotatedOutline.Rd | 2 man/E.Rd | 4 man/Rcart.Rd | 2 man/ReconstructedDataset.Rd | 2 man/ReconstructedOutline.Rd | 10 - man/RetinalReconstructedDataset.Rd | 2 man/RetinalReconstructedOutline.Rd | 2 man/StitchedOutline.Rd | 10 - man/TriangulatedOutline.Rd | 2 man/azel.to.sphere.colattitude.Rd | 2 man/azimuthal.conformal.Rd | 2 man/azimuthal.equalarea.Rd | 2 man/azimuthal.equidistant.Rd | 2 man/bary.to.sphere.cart.Rd | 6 - man/central.angle.Rd | 6 - man/checkDatadir.Rd | 2 man/checkTears.Rd | 2 man/compute.intersections.sphere.Rd | 4 man/compute.kernel.estimate.Rd | 6 - man/computeTearRelationships.Rd | 4 man/dE.Rd | 4 man/fire.Rd | 8 - man/flatplot.dataset.Rd | 4 man/flatplot.outline.Rd | 2 man/flatplot.reconstructedOutline.Rd | 4 man/flipped.triangles.Rd | 6 - man/flipped.triangles.cart.Rd | 4 man/getDssHullarea.Rd | 2 man/getTear.Rd | 4 man/identity.transform.Rd | 4 man/invert.sphere.Rd | 2 man/invert.sphere.to.hemisphere.Rd | 6 - man/karcher.mean.sphere.Rd | 6 - man/labelTearPoints.Rd | 8 - man/mergePointsEdges.Rd | 14 +- man/orthographic.Rd | 4 man/polar.cart.to.sphere.spherical.Rd | 2 man/projectToSphere.Rd | 2 man/projection.reconstructedDataset.Rd | 4 man/projection.reconstructedOutline.Rd | 2 man/read.datacounts.Rd | 2 man/remove.identical.consecutive.rows.Rd | 2 man/remove.intersections.Rd | 6 - man/retistruct.batch.analyse.summaries.Rd | 4 man/retistruct.potential.od.Rd | 4 man/retistruct.read.markup.Rd | 10 - man/retistruct.save.markup.Rd | 2 man/rotate.axis.Rd | 8 - man/simplify.outline.Rd | 6 - man/sinusoidal.Rd | 2 man/solveMappingCart.Rd | 2 man/sphere.cart.to.sphere.spherical.Rd | 2 man/sphere.spherical.to.polar.cart.Rd | 2 man/sphere.spherical.to.sphere.cart.Rd | 2 man/sphere.tri.area.Rd | 4 man/spherical.to.polar.area.Rd | 4 man/stretchMesh.Rd | 2 man/titrate.reconstructedOutline.Rd | 2 man/tri.area.Rd | 2 man/tri.area.signed.Rd | 2 83 files changed, 380 insertions(+), 363 deletions(-)
Title: A Set of Tools that Enhance Reproducibility Beyond Package
Management
Description: Built on top of 'git2r' and 'archivist', this package aims at
making high-level, robust, machine and OS independent tools for making
deeply reproducible and reusable content in R. This extends beyond the
package management utilities of 'packrat' and 'checkpoint' by including
tools for caching, and accessing GitHub repositories.
Author: Eliot J B McIntire [aut, cre],
Alex M Chubaty [aut],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 0.1.1 dated 2017-08-05 and 0.1.2 dated 2017-08-09
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/cache-helpers.R | 14 ++++++++------ tests/testthat/test-cache.R | 25 +++++++++++++++++++++++++ 5 files changed, 50 insertions(+), 16 deletions(-)
Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Description: Most ROC curve plots obscure the cutoff values and inhibit
interpretation and comparison of multiple curves. This attempts to address
those shortcomings by providing plotting and interactive tools. Functions
are provided to generate an interactive ROC curve plot for web use, and
print versions. A Shiny application implementing the functions is also
included.
Author: Michael C. Sachs [aut, cre],
Robert W. Corty [ctb]
Maintainer: Michael C. Sachs <sachsmc@gmail.com>
Diff between plotROC versions 2.0.1 dated 2016-02-05 and 2.2.0 dated 2017-08-09
DESCRIPTION | 21 LICENSE | 2 MD5 | 73 - NAMESPACE | 91 - NEWS | 34 R/calculate_roc.R | 18 R/geom_roc.R | 158 ++ R/interactive_roc.R | 4 R/plotROC-package.R | 2 README.md | 8 build/vignette.rds |binary inst/CITATION | 28 inst/doc/examples.R | 346 +++-- inst/doc/examples.Rmd | 28 inst/doc/examples.html | 2430 +++++++++++++++++++++--------------------- man/calc_auc.Rd | 51 man/calculate_multi_roc.Rd | 47 man/calculate_roc.Rd | 67 - man/direct_label.Rd | 57 man/export_interactive_roc.Rd | 103 - man/geom_roc.Rd | 271 ++-- man/geom_rocci.Rd | 226 +-- man/getD3.Rd | 25 man/ggroc.Rd | 87 - man/melt_roc.Rd | 63 - man/multi_ggroc.Rd | 97 - man/plotROC.Rd | 99 - man/plot_interactive_roc.Rd | 43 man/plot_journal_roc.Rd | 71 - man/roc_key.Rd |only man/shiny_plotROC.Rd | 23 man/stat_roc.Rd | 190 +-- man/stat_rocci.Rd | 228 +-- man/style_roc.Rd | 71 - man/verify_d.Rd | 43 tests/testthat/Rplots.pdf |binary tests/testthat/test-calc.R | 98 + vignettes/examples.Rmd | 28 38 files changed, 2738 insertions(+), 2493 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>;
- split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>;
- league table with network meta-analysis results;
- automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>.
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut],
Jochem König [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 0.9-5 dated 2017-05-31 and 0.9-6 dated 2017-08-09
DESCRIPTION | 10 - MD5 | 55 +++++---- NAMESPACE | 7 - NEWS | 80 ++++++++++++++ R/chkmultiarm.R | 256 +++++++++++++++++++++++++++++++++++++++------- R/decomp.design.R | 9 - R/decomp.tau.R | 11 + R/forest.netmeta.R | 63 ++++++++--- R/netheat.R | 12 +- R/netmeasures.R | 19 ++- R/netmeta-internal.R | 2 R/netmeta.R | 96 ++++++++++++++--- R/nma.krahn.R | 4 R/nma.ruecker.R | 2 R/plot.netposet.R | 184 +++++++++++++++++++++++++-------- R/prepare.R | 1 R/print.netmeta.R | 20 ++- R/print.summary.netmeta.R | 255 ++++++++++++++++++++++++++++++++++++++------- R/setref.R | 2 R/setseq.R | 4 R/summary.netmeta.R | 89 ++++++++++++--- R/upgradenetmeta.R |only man/Woods2010.Rd | 2 man/decomp.design.Rd | 6 - man/forest.netmeta.Rd | 23 +--- man/netmeasures.Rd | 4 man/netmeta.Rd | 28 +++-- man/plot.netposet.Rd | 145 +++++++++++++++++++++----- man/print.netmeta.Rd | 47 +++++--- 29 files changed, 1140 insertions(+), 296 deletions(-)
Title: Load Multiple 'csv' and 'txt' Tables
Description: Allows users to easily read multiple comma separated tables and create a data frame under the same name.
Is able to read multiple comma separated tables from a local directory, a zip file or a zip file on a remote directory.
Author: Dror Bogin [aut, cre]
Maintainer: Dror Bogin <dror.bogin@gmail.com>
Diff between easycsv versions 1.0.1 dated 2017-08-08 and 1.0.2 dated 2017-08-09
DESCRIPTION | 9 +++++---- MD5 | 15 +++++++++------ NAMESPACE | 2 ++ NEWS.md |only R/fread_folder.R |only README.md | 13 +++++++++++-- man/fread_folder.Rd |only man/loadZIPcsvfromURL.Rd | 4 ++-- man/loadcsv_multi.Rd | 6 +++--- man/loadcsvfromZIP.Rd | 12 ++++++------ 10 files changed, 38 insertions(+), 23 deletions(-)
Title: Process Biogas Data and Predict Biogas Production
Description: High- and low-level functions for processing biogas data and predicting biogas production. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas quantity can be converted between volume, mass, and moles. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated using volumetric, manometric, or gravimetric methods for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas quantity and composition can be predicted from substrate composition and additional, optional data.
Author: Sasha D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <sasha.hafner@eng.au.dk>
Diff between biogas versions 1.7.0 dated 2017-02-25 and 1.8.0 dated 2017-08-09
ChangeLog | 50 + DESCRIPTION | 14 MD5 | 70 +- NEWS | 18 R/calcCOD.R | 21 R/cumBg.R | 29 - R/molMass.R | 4 R/readFormula.R | 1 R/startup.R | 2 R/summBg.R | 883 ++++++++++++++++---------------- build/vignette.rds |binary data/comp.rda |binary data/comp2.rda |binary data/mass.rda |binary data/massw.rda |binary data/s3compl.rda |binary data/s3compw.rda |binary data/s3lcombo.rda |binary data/s3voll.rda |binary data/s3volw.rda |binary data/setup.rda |binary data/setup2.rda |binary data/strawComp.rda |binary data/strawMass.rda |binary data/strawPressure.rda |binary data/strawSetup.rda |binary data/vol.rda |binary data/vol2.rda |binary inst/doc/biogas_quick_start.pdf |binary inst/doc/predBg_function.Rnw | 2 inst/doc/predBg_function.pdf |binary man/biogas-package.Rd | 8 man/cumBg.Rd | 4 tests/testthat/test_LowLevelFunctions.R | 11 vignettes/framed.sty |only vignettes/predBg_function.Rnw | 2 vignettes/siunitx.sty |only 37 files changed, 611 insertions(+), 508 deletions(-)
Title: Perform Phylogenetic Path Analysis
Description: A comprehensive and easy to use R implementation of confirmatory
phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer
(2012) <doi:10.1111/j.1558-5646.2012.01790.x>.
Author: Wouter van der Bijl [aut, cre]
Maintainer: Wouter van der Bijl <wouter.van.der.bijl@zoologi.su.se>
Diff between phylopath versions 0.3.0 dated 2017-07-08 and 0.3.1 dated 2017-08-09
DESCRIPTION | 12 +++++++----- MD5 | 12 ++++++------ NEWS.md | 13 +++++++++++++ R/DAG.R | 3 ++- R/internal.R | 2 +- inst/doc/binary_models.html | 8 ++++---- inst/doc/intro_to_phylopath.html | 18 +++++++++--------- 7 files changed, 42 insertions(+), 26 deletions(-)
Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database
<http://ec.europa.eu/eurostat> together with search and
manipulation utilities.
Author: Leo Lahti [aut, cre],
Janne Huovari [aut],
Markus Kainu [aut],
Przemyslaw Biecek [aut],
Joona Lehtomaki [ctb],
Francois Briatte [ctb],
Oliver Reiter [ctb]
Maintainer: Leo Lahti <leo.lahti@iki.fi>
Diff between eurostat versions 3.1.1 dated 2017-03-16 and 3.1.5 dated 2017-08-09
eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/2017-manu-bmi-1.pdf |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/2017-manu-energy-1.pdf |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/2017-manu-mapexample-1.pdf |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/2017-manu-roadacc-1.pdf |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/README |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/RJournal.sty |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/RJwrapper.aux |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/RJwrapper.bbl |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/RJwrapper.brf |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/RJwrapper.log |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/RJwrapper.out |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/RJwrapper.pdf |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/RJwrapper.tex |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/lahti-huovari-kainu-biecek.Rmd |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/lahti-huovari-kainu-biecek.bib |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/lahti-huovari-kainu-biecek.md |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/lahti-huovari-kainu-biecek.pdf |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/lahti-huovari-kainu-biecek.tex |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/main.R |only eurostat-3.1.1/eurostat/vignettes/2017_RJournal_manuscript/response.txt |only eurostat-3.1.1/eurostat/vignettes/fig/maps1-1.pdf |only eurostat-3.1.1/eurostat/vignettes/fig/maps1-1.png |only eurostat-3.1.1/eurostat/vignettes/fig/maps3-1.jpeg |only eurostat-3.1.1/eurostat/vignettes/fig/maps3-2.png |only eurostat-3.1.1/eurostat/vignettes/fig/maps4-1.png |only eurostat-3.1.1/eurostat/vignettes/fig/maps6-1.png |only eurostat-3.1.1/eurostat/vignettes/fig/maps7-1.png |only eurostat-3.1.1/eurostat/vignettes/fig/maps8-1.png |only eurostat-3.1.1/eurostat/vignettes/fig/mapsfi-1.png |only eurostat-3.1.1/eurostat/vignettes/tmp.R |only eurostat-3.1.5/eurostat/DESCRIPTION | 18 eurostat-3.1.5/eurostat/MD5 | 105 +-- eurostat-3.1.5/eurostat/R/cut_to_classes.R | 28 eurostat-3.1.5/eurostat/R/data.R |only eurostat-3.1.5/eurostat/R/eurotime2date.R | 1 eurostat-3.1.5/eurostat/R/eurotime2num.R | 7 eurostat-3.1.5/eurostat/R/get_eurostat.R | 6 eurostat-3.1.5/eurostat/R/get_eurostat_geospatial.R | 4 eurostat-3.1.5/eurostat/R/label_eurostat.R | 210 ++++-- eurostat-3.1.5/eurostat/R/tidy_eurostat.R | 3 eurostat-3.1.5/eurostat/README.md | 86 +- eurostat-3.1.5/eurostat/build/vignette.rds |binary eurostat-3.1.5/eurostat/data/tgs00026.rda |only eurostat-3.1.5/eurostat/inst/CITATION | 16 eurostat-3.1.5/eurostat/inst/doc/blogposts.Rmd | 1 eurostat-3.1.5/eurostat/inst/doc/blogposts.html | 7 eurostat-3.1.5/eurostat/inst/doc/cheatsheet.html | 6 eurostat-3.1.5/eurostat/inst/doc/eurostat_tutorial.R | 113 ++- eurostat-3.1.5/eurostat/inst/doc/eurostat_tutorial.Rmd | 107 ++- eurostat-3.1.5/eurostat/inst/doc/eurostat_tutorial.pdf |binary eurostat-3.1.5/eurostat/inst/doc/publications.Rmd | 2 eurostat-3.1.5/eurostat/inst/doc/publications.html | 8 eurostat-3.1.5/eurostat/man/cut_to_classes.Rd | 7 eurostat-3.1.5/eurostat/man/eurotime2num.Rd | 7 eurostat-3.1.5/eurostat/man/get_eurostat.Rd | 6 eurostat-3.1.5/eurostat/man/label_eurostat.Rd | 24 eurostat-3.1.5/eurostat/man/tgs00026.Rd |only eurostat-3.1.5/eurostat/tests/testthat/test-all.R | 27 eurostat-3.1.5/eurostat/vignettes/2017_RJournal_manuscript/2017_RJournal_manuscript.zip |only eurostat-3.1.5/eurostat/vignettes/2017_RJournal_manuscript/Proofs.zip |only eurostat-3.1.5/eurostat/vignettes/blogposts.Rmd | 1 eurostat-3.1.5/eurostat/vignettes/eurostat_tutorial.Rmd | 107 ++- eurostat-3.1.5/eurostat/vignettes/eurostat_tutorial.html | 301 ++++------ eurostat-3.1.5/eurostat/vignettes/eurostat_tutorial.md | 295 ++++----- eurostat-3.1.5/eurostat/vignettes/fig/maps2-1.pdf |binary eurostat-3.1.5/eurostat/vignettes/fig/maps2-1.png |binary eurostat-3.1.5/eurostat/vignettes/fig/maps3-1.png |binary eurostat-3.1.5/eurostat/vignettes/fig/plotGallery-1.pdf |binary eurostat-3.1.5/eurostat/vignettes/fig/plotGallery-1.png |binary eurostat-3.1.5/eurostat/vignettes/fig/trains_plot-1.pdf |binary eurostat-3.1.5/eurostat/vignettes/publications.Rmd | 2 71 files changed, 847 insertions(+), 658 deletions(-)
Title: Treatment of Zeros and Nondetects in Compositional Data Sets
Description: Principled methods for multivariate left-censoring and zeros in
compositional data sets.
Author: Javier Palarea-Albaladejo and Josep Antoni Martin-Fernandez
Maintainer: Javier Palarea-Albaladejo <javier.palarea@bioss.ac.uk>
Diff between zCompositions versions 1.0.3-1 dated 2016-04-14 and 1.1.1 dated 2017-08-09
DESCRIPTION | 14 ++++---- MD5 | 30 +++++++++++------ NAMESPACE | 3 + NEWS | 18 ++++++++++ R/cmultRepl.R | 8 +++- R/lcTest.R |only R/lrEM.R | 73 ++++++++++++++++++++++++++++--------------- R/zPatterns.R | 70 ++++++++++++++++++++++++++++++++++------- R/zVarArray.R |only R/zVarArrayError.R |only R/zVarArrayTest.R |only man/cmultRepl.Rd | 9 ++++- man/lcTest.Rd |only man/lrEM.Rd | 16 ++++++--- man/multLN.Rd | 6 ++- man/zCompositions-package.Rd | 8 ++-- man/zPatterns.Rd | 12 +++++-- man/zVarArray.Rd |only man/zVarArrayError.Rd |only man/zVarArrayTest.Rd |only 20 files changed, 196 insertions(+), 71 deletions(-)
Title: Intervention in Prediction Measure (IPM) for Random Forests
Description: Computes IPM for assessing variable importance for random forests. See details at I. Epifanio (2017) <DOI:10.1186/s12859-017-1650-8>.
Author: Irene Epifanio, Stefano Nembrini
Maintainer: Irene Epifanio <epifanio@uji.es>
Diff between IPMRF versions 1.1.1 dated 2017-07-28 and 1.2 dated 2017-08-09
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++++---------- NAMESPACE | 2 +- NEWS | 5 +++++ R/getTreegbm.R |only R/ipmgbmnew.R |only man/IPMRF-internal-gbm.Rd |only man/IPMRF-package.Rd | 6 ++++-- man/ipmgbmnew.Rd |only man/ipmparty.Rd | 2 +- man/ipmpartynew.Rd | 2 +- man/ipmranger.Rd | 2 +- man/ipmrangernew.Rd | 2 +- man/ipmrf.Rd | 2 +- man/ipmrfnew.Rd | 2 +- 15 files changed, 35 insertions(+), 24 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains some auxiliary functions for multiple
imputation which complements existing functionality
in R.
In addition to some utility functions, main features
include plausible value imputation, multilevel
imputation functions, imputation using partial least
squares (PLS) for high dimensional predictors, nested
multiple imputation.
Author: Alexander Robitzsch [aut, cre], Simon Grund [aut],
Thorsten Henke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 2.5-9 dated 2017-06-17 and 2.6-21 dated 2017-08-09
miceadds-2.5-9/miceadds/R/crlem.R |only miceadds-2.5-9/miceadds/src/init.c |only miceadds-2.6-21/miceadds/DESCRIPTION | 19 + miceadds-2.6-21/miceadds/MD5 | 53 ++--- miceadds-2.6-21/miceadds/NAMESPACE | 58 +++-- miceadds-2.6-21/miceadds/R/ANSI_fomat_latex_table.R | 14 + miceadds-2.6-21/miceadds/R/cxxfunction.copy.R | 2 miceadds-2.6-21/miceadds/R/draw.pv.ctt.R | 2 miceadds-2.6-21/miceadds/R/files_move.R | 4 miceadds-2.6-21/miceadds/R/glm.cluster.R | 1 miceadds-2.6-21/miceadds/R/latent.regression.em.R | 4 miceadds-2.6-21/miceadds/R/lm.cluster.R | 2 miceadds-2.6-21/miceadds/R/load.data.R | 4 miceadds-2.6-21/miceadds/R/ma.wtd.aux.data.R | 2 miceadds-2.6-21/miceadds/R/mi.anova.R | 5 miceadds-2.6-21/miceadds/R/mice.impute.2l.latentgroupmean.MCMC.R | 1 miceadds-2.6-21/miceadds/R/mice.impute.2l.lmer.R | 7 miceadds-2.6-21/miceadds/R/mice.impute.grouped.R | 1 miceadds-2.6-21/miceadds/R/mice.impute.plausible.values.R | 19 - miceadds-2.6-21/miceadds/R/save.data.R | 6 miceadds-2.6-21/miceadds/R/write.fwf2.R | 97 +++------- miceadds-2.6-21/miceadds/R/write_fwf2_format2.R |only miceadds-2.6-21/miceadds/README.md |only miceadds-2.6-21/miceadds/data/datalist |only miceadds-2.6-21/miceadds/inst/NEWS | 15 + miceadds-2.6-21/miceadds/man/mice.impute.2l.lmer.Rd | 26 ++ miceadds-2.6-21/miceadds/man/save.data.Rd | 20 +- miceadds-2.6-21/miceadds/man/write.fwf2.Rd | 12 + miceadds-2.6-21/miceadds/man/write.pspp.Rd | 10 - miceadds-2.6-21/miceadds/src/RcppExports.cpp | 65 ++++-- 30 files changed, 264 insertions(+), 185 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-24 0.8.0
2016-10-26 0.7.1
2016-10-03 0.7.0
2016-09-28 0.6
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data.
Author: Martin Wilson [cre, aut]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 0.3.0 dated 2017-06-20 and 0.4.0 dated 2017-08-09
DESCRIPTION | 14 MD5 | 62 ++- NAMESPACE | 15 NEWS.md | 7 R/fit_display.R | 137 ++++++-- R/fitting.R | 639 +++------------------------------------- R/ica.R | 3 R/interactive_plotting.R | 260 ++++++++-------- R/mrs_data_display.R | 19 - R/mrs_data_io.R | 18 - R/mrs_data_proc.R | 139 ++++++-- R/qm_simulation.R | 8 R/utils.R | 49 +++ R/varpro.R |only R/varpro_3_para.R |only inst/doc/spant-intro.R | 2 inst/doc/spant-intro.Rmd | 2 inst/doc/spant-intro.html | 10 man/fit_mrs.Rd | 2 man/fit_tab2csv.Rd |only man/ft_shift.Rd |only man/ft_shift_mat.Rd |only man/get_1h_brain_basis_paras.Rd |only man/get_seg_ind.Rd |only man/get_slice.Rd |only man/get_voxel.Rd |only man/ift_shift.Rd |only man/int_spec.Rd | 2 man/lw2beta.Rd |only man/mat2mrs_data.Rd | 3 man/mvfftshift.Rd |only man/n2coord.Rd |only man/plot.fit_result.Rd | 20 + man/plot_fit_slice.Rd |only man/ppm.Rd |only man/stackplot.fit_result.Rd | 19 + man/varpro_3_para_opts.Rd | 2 man/varpro_opts.Rd | 2 man/vec2mrs_data.Rd |only vignettes/spant-intro.Rmd | 2 40 files changed, 610 insertions(+), 826 deletions(-)
Title: Supplementary Item Response Theory Models
Description: Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, Rasch copula model, faceted and
hierarchical rater models, ordinal IRT model (ISOP),
DETECT statistic, local structural equation modeling (LSEM).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between sirt versions 2.0-25 dated 2017-05-11 and 2.1-24 dated 2017-08-09
sirt-2.0-25/sirt/R/starts_cov.R |only sirt-2.0-25/sirt/R/starts_sim1dim.R |only sirt-2.0-25/sirt/man/starts_cov.Rd |only sirt-2.0-25/sirt/src/init.c |only sirt-2.1-24/sirt/DESCRIPTION | 19 sirt-2.1-24/sirt/MD5 | 149 ++- sirt-2.1-24/sirt/NAMESPACE | 39 - sirt-2.1-24/sirt/R/data.wide2long.R | 30 sirt-2.1-24/sirt/R/dif.logisticregression.R | 28 sirt-2.1-24/sirt/R/f1d.irt.R | 5 sirt-2.1-24/sirt/R/fuzcluster_alg.R | 6 sirt-2.1-24/sirt/R/greenyang.reliability.R | 3 sirt-2.1-24/sirt/R/invariance.alignment2.R | 2 sirt-2.1-24/sirt/R/lc.2raters.R | 2 sirt-2.1-24/sirt/R/lsdm.R | 2 sirt-2.1-24/sirt/R/lsem.estimate.R | 37 sirt-2.1-24/sirt/R/lsem.permutationTest.R | 32 sirt-2.1-24/sirt/R/lsem_fitsem.R | 7 sirt-2.1-24/sirt/R/lsem_group_moderator.R | 6 sirt-2.1-24/sirt/R/lsem_residualize.R | 10 sirt-2.1-24/sirt/R/matrix_functions.R | 3 sirt-2.1-24/sirt/R/mcmc.2pno_alg.R | 4 sirt-2.1-24/sirt/R/mcmc.3pno.testlet_alg.R | 2 sirt-2.1-24/sirt/R/modelfit.cor.R | 2 sirt-2.1-24/sirt/R/noharm.sirt.R | 1 sirt-2.1-24/sirt/R/np.dich.R | 3 sirt-2.1-24/sirt/R/plausible.values.raschtype.R | 13 sirt-2.1-24/sirt/R/polychoric2.R | 10 sirt-2.1-24/sirt/R/prob_genlogis_4pl.R |only sirt-2.1-24/sirt/R/rasch.copula2_aux.R | 30 sirt-2.1-24/sirt/R/rasch.mml2.R | 156 +--- sirt-2.1-24/sirt/R/rasch.pml2_aux.R | 19 sirt-2.1-24/sirt/R/rasch.pml_aux.R | 5 sirt-2.1-24/sirt/R/rasch_mml2_calc_prob.R |only sirt-2.1-24/sirt/R/rasch_mml2_difference_quotient.R |only sirt-2.1-24/sirt/R/rasch_mml2_modify_list_element.R |only sirt-2.1-24/sirt/R/rasch_mml2_mstep_calc_likelihood.R |only sirt-2.1-24/sirt/R/sia.sirt.R | 29 sirt-2.1-24/sirt/R/sim.rasch.dep.R | 4 sirt-2.1-24/sirt/R/sirt_antifisherz.R |only sirt-2.1-24/sirt/R/sirt_fisherz.R |only sirt-2.1-24/sirt/R/sirt_matrix2.R |only sirt-2.1-24/sirt/R/sirt_rbind_fill.R |only sirt-2.1-24/sirt/R/tetrachoric2.R | 3 sirt-2.1-24/sirt/R/xxirt.R | 282 +++---- sirt-2.1-24/sirt/R/xxirt_EAP.R | 3 sirt-2.1-24/sirt/R/xxirt_IRT.se.R | 3 sirt-2.1-24/sirt/R/xxirt_ThetaDistribution_extract_freeParameters.R | 17 sirt-2.1-24/sirt/R/xxirt_compute_itemprobs.R | 41 - sirt-2.1-24/sirt/R/xxirt_compute_likelihood.R | 2 sirt-2.1-24/sirt/R/xxirt_compute_posterior.R | 2 sirt-2.1-24/sirt/R/xxirt_compute_priorDistribution.R | 11 sirt-2.1-24/sirt/R/xxirt_createDiscItem.R | 3 sirt-2.1-24/sirt/R/xxirt_createItemList.R | 46 - sirt-2.1-24/sirt/R/xxirt_createParTable.R | 14 sirt-2.1-24/sirt/R/xxirt_createThetaDistribution.R | 13 sirt-2.1-24/sirt/R/xxirt_data_proc.R | 68 - sirt-2.1-24/sirt/R/xxirt_hessian.R | 109 +- sirt-2.1-24/sirt/R/xxirt_ic.R | 3 sirt-2.1-24/sirt/R/xxirt_modifyParTable.R | 4 sirt-2.1-24/sirt/R/xxirt_mstep_itemParameters.R | 141 +-- sirt-2.1-24/sirt/R/xxirt_parTheta_extract_freeParameters.R | 11 sirt-2.1-24/sirt/R/xxirt_postproc_parameters.R | 3 sirt-2.1-24/sirt/R/xxirt_proc_ParTable.R | 120 +-- sirt-2.1-24/sirt/R/xxirt_vcov.R | 7 sirt-2.1-24/sirt/README.md |only sirt-2.1-24/sirt/data/data.eid.kap4.rda |only sirt-2.1-24/sirt/data/data.eid.kap5.rda |only sirt-2.1-24/sirt/data/data.eid.kap6.rda |only sirt-2.1-24/sirt/data/data.eid.kap7.rda |only sirt-2.1-24/sirt/data/datalist |only sirt-2.1-24/sirt/inst/NEWS | 20 sirt-2.1-24/sirt/man/IRT.mle.Rd | 14 sirt-2.1-24/sirt/man/data.eid.Rd | 90 +- sirt-2.1-24/sirt/man/f1d.irt.Rd | 5 sirt-2.1-24/sirt/man/mcmc.3pno.testlet.Rd | 9 sirt-2.1-24/sirt/man/noharm.sirt.Rd | 4 sirt-2.1-24/sirt/man/parmsummary_extend.Rd | 2 sirt-2.1-24/sirt/man/pcm.fit.Rd | 8 sirt-2.1-24/sirt/man/personfit.stat.Rd | 4 sirt-2.1-24/sirt/man/rinvgamma2.Rd | 6 sirt-2.1-24/sirt/man/sim.raschtype.Rd | 6 sirt-2.1-24/sirt/man/sirt-utilities.Rd | 16 sirt-2.1-24/sirt/man/smirt.Rd | 6 sirt-2.1-24/sirt/src/RcppExports.cpp | 390 +++++----- 85 files changed, 1129 insertions(+), 1015 deletions(-)
Title: A GUI for Smith's Mean Measure of Divergence
Description: Offers a Shiny user interface to work out Smith's Mean Measure of Divergence.
Author: Frederic Santos
Maintainer: Frederic Santos <frederic.santos@u-bordeaux.fr>
Diff between AnthropMMD versions 1.0.1 dated 2016-04-07 and 2.1.0 dated 2017-08-09
AnthropMMD-1.0.1/AnthropMMD/R/AnaSettings.R |only AnthropMMD-1.0.1/AnthropMMD/R/Mat_MMD.R |only AnthropMMD-1.0.1/AnthropMMD/R/Prepa_MMD.R |only AnthropMMD-2.1.0/AnthropMMD/DESCRIPTION | 14 - AnthropMMD-2.1.0/AnthropMMD/MD5 | 24 +- AnthropMMD-2.1.0/AnthropMMD/NAMESPACE | 10 AnthropMMD-2.1.0/AnthropMMD/R/StartMMD.R | 206 ------------------ AnthropMMD-2.1.0/AnthropMMD/inst |only AnthropMMD-2.1.0/AnthropMMD/man/AnthropMMD-package.Rd | 19 - AnthropMMD-2.1.0/AnthropMMD/man/StartMMD.Rd | 43 ++- 10 files changed, 66 insertions(+), 250 deletions(-)
Title: API to Melbourne Pedestrian Data
Description: Provides API to Melbourne pedestrian data in tidy data form.
Author: Earo Wang [aut, cre]
Maintainer: Earo Wang <earo.wang@gmail.com>
Diff between rwalkr versions 0.1.0 dated 2017-08-01 and 0.2.0 dated 2017-08-09
DESCRIPTION | 7 ++-- MD5 | 16 +++++---- NAMESPACE | 1 NEWS.md | 4 ++ R/scrape.R | 89 +++++++++++++++++++++++++++++++++++++-------------- R/shiny.R |only R/sysdata.rda |only README.md | 11 +++--- man/figure/shiny.png |only man/shine_melb.Rd |only man/walk_melb.Rd | 38 ++++++++++++++++----- 11 files changed, 119 insertions(+), 47 deletions(-)
Title: Multivariate Bayesian Sparse Group Selection with Spike and Slab
Description: An implementation of a Bayesian sparse group model using spike and slab priors in a regression context. It is designed for regression with a multivariate response variable, but also provides an implementation for univariate response.
Author: Benoit Liquet, Matthew Sutton
Maintainer: Benoit Liquet <benoit.liquet@qut.edu.au>
Diff between MBSGS versions 1.0.0 dated 2016-08-26 and 1.1.0 dated 2017-08-09
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 4 ++-- R/MBGLSS.R | 21 ++++++++++++++++++--- R/MBSGS-internal.R | 12 ++++-------- R/MBSGSSS.R | 20 +++++++++++++++++--- 6 files changed, 49 insertions(+), 24 deletions(-)
Title: Deconvolute Mixed Genomes with Unknown Proportions
Description: Traditional phasing programs are limited to diploid organisms.
Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo
(MCMC) approaches, and builds a generic framework that allows haplotype searches
in a multiple infection setting. This package is primarily developed as part of
the Pf3k project, which is a global collaboration using the latest
sequencing technologies to provide a high-resolution view of natural variation
in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from
patient blood sample, which often contains more than one parasite strain, with
unknown proportions. This package is used for deconvoluting mixed haplotypes,
and reporting the mixture proportions from each sample.
Author: Joe Zhu [aut, cre, cph],
Jacob Almagro-Garcia [aut, cph],
Gil McVean [aut, cph],
University of Oxford [cph],
Yinghan Liu [ctb],
CodeCogs Zyba Ltd [com, cph],
Deepak Bandyopadhyay [com, cph],
Lutz Kettner [com, cph]
Maintainer: Joe Zhu <joe.zhu@well.ox.ac.uk>
Diff between DEploid versions 0.4.1 dated 2017-07-24 and 0.4.2 dated 2017-08-09
DEploid-0.4.1/DEploid/src/registerDynamicSymbol.c |only DEploid-0.4.1/DEploid/tests/testthat/pf3k-dEploid.hap |only DEploid-0.4.1/DEploid/tests/testthat/pf3k-dEploid.llk |only DEploid-0.4.1/DEploid/tests/testthat/pf3k-dEploid.prop |only DEploid-0.4.2/DEploid/DESCRIPTION | 29 +- DEploid-0.4.2/DEploid/MD5 | 47 +-- DEploid-0.4.2/DEploid/NAMESPACE | 6 DEploid-0.4.2/DEploid/R/DEploidR.R | 200 +++++++------- DEploid-0.4.2/DEploid/R/dEploid.R | 17 - DEploid-0.4.2/DEploid/R/dEploidPlotly.R |only DEploid-0.4.2/DEploid/inst/doc/dEploid-Arguments.html | 4 DEploid-0.4.2/DEploid/man/DEploid-package.Rd | 17 - DEploid-0.4.2/DEploid/man/computeObsWSAF.Rd | 11 DEploid-0.4.2/DEploid/man/extractCoverageFromTxt.Rd | 9 DEploid-0.4.2/DEploid/man/extractCoverageFromVcf.Rd | 9 DEploid-0.4.2/DEploid/man/extractPLAF.Rd | 6 DEploid-0.4.2/DEploid/man/haplotypePainter.Rd | 6 DEploid-0.4.2/DEploid/man/histWSAF.Rd | 8 DEploid-0.4.2/DEploid/man/plotAltVsRef.Rd | 17 - DEploid-0.4.2/DEploid/man/plotAltVsRefPlotly.Rd |only DEploid-0.4.2/DEploid/man/plotHistWSAFPlotly.Rd |only DEploid-0.4.2/DEploid/man/plotObsExpWSAF.Rd | 17 - DEploid-0.4.2/DEploid/man/plotObsExpWSAFPlotly.Rd |only DEploid-0.4.2/DEploid/man/plotProportions.Rd | 18 - DEploid-0.4.2/DEploid/man/plotWSAFVsPLAFPlotly.Rd |only DEploid-0.4.2/DEploid/man/plotWSAFvsPLAF.Rd | 17 - DEploid-0.4.2/DEploid/src/dEploidr.cpp | 12 DEploid-0.4.2/DEploid/src/r_random_generator.h | 6 DEploid-0.4.2/DEploid/tests/testthat/test-DEploid_tools.R | 47 ++- 29 files changed, 309 insertions(+), 194 deletions(-)
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre],
Dawei Lang [ctb],
Ole Petter Bang [ctb] (CSS in
rmarkdown/templates/xaringan/resources/example.css),
Patrick Schratz [ctb],
Sean Lopp [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.3 dated 2017-05-28 and 0.4 dated 2017-08-09
DESCRIPTION | 8 ++-- MD5 | 18 +++++------ R/render.R | 11 ++++-- R/utils.R | 21 ++++++++++++- README.md | 1 build/vignette.rds |binary inst/rmarkdown/templates/xaringan/resources/default.html | 4 +- inst/rmarkdown/templates/xaringan/resources/example.css | 21 ++++++++++++- inst/rmarkdown/templates/xaringan/skeleton/skeleton.Rmd | 12 +++++++ inst/rmarkdown/templates/xaringan_zh-CN/skeleton/zh-CN.css | 21 ++++++++++++- 10 files changed, 95 insertions(+), 22 deletions(-)
Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate functions,
and fitters for consensus relations.
Author: David Meyer [aut],
Kurt Hornik [aut, cre],
Christian Buchta [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between relations versions 0.6-6 dated 2015-10-11 and 0.6-7 dated 2017-08-09
.aspell |only DESCRIPTION | 8 MD5 | 126 +-- NAMESPACE | 16 R/algebra.R | 2 R/charfun.R | 4 R/choice.R | 85 +- R/consensus.R | 663 +++++++++++++++---- R/data.R | 2 R/dissimilarity.R | 712 ++++++++++++++++----- R/domain.R | 8 R/dual.R | 15 R/fitters.R | 253 ++++--- R/graph.R | 4 R/impute.R | 23 R/incidence.R | 4 R/mip.R | 52 - R/operators.R | 134 +++ R/plot.R | 6 R/predicates.R | 91 ++ R/ranking.R | 16 R/relation.R | 28 R/scores.R | 2 R/utilities.R | 2 R/zzz.R |only build/partial.rdb |only build/vignette.rds |binary data/Cetacea.rda |binary data/Felines.rda |binary data/SVM_Benchmarking_Classification.rda |binary data/SVM_Benchmarking_Classification_Consensus.rda |binary data/SVM_Benchmarking_Regression.rda |binary data/SVM_Benchmarking_Regression_Consensus.rda |binary inst/NEWS.Rd | 31 inst/doc/relations.R | 87 +- inst/doc/relations.Rnw | 168 ++-- inst/doc/relations.pdf |binary inst/po/en@quot/LC_MESSAGES/R-relations.mo |binary man/SVMBench.Rd | 10 man/algebra.Rd | 59 - man/charfun.Rd | 2 man/choice.Rd | 30 man/classes.Rd | 8 man/closure.Rd | 9 man/components.Rd | 24 man/consensus.Rd | 158 +++- man/dissimilarity.Rd | 75 ++ man/domain.Rd | 8 man/ensemble.Rd | 14 man/graph.Rd | 6 man/impute.Rd | 4 man/incidence.Rd | 4 man/pclust.Rd | 13 man/plot.Rd | 19 man/predicates.Rd | 80 ++ man/properties.Rd | 6 man/ranking.Rd | 15 man/reduction.Rd | 13 man/relation.Rd | 96 +- man/scores.Rd | 26 man/setters.Rd | 10 man/table.Rd | 2 man/transform.Rd | 2 po/R-relations.pot | 15 vignettes/relations.Rnw | 168 ++-- vignettes/relations.bib | 445 ++++++++++--- 66 files changed, 2832 insertions(+), 1031 deletions(-)
Title: Cluster Ensembles
Description: CLUster Ensembles.
Author: Kurt Hornik [aut, cre],
Walter Böhm [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between clue versions 0.3-53 dated 2017-01-15 and 0.3-54 dated 2017-08-09
.aspell |only DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- R/consensus.R | 6 +++--- build/partial.rdb |binary build/vignette.rds |binary data/CKME.rda |binary data/Cassini.rda |binary data/GVME.rda |binary data/GVME_Consensus.rda |binary data/Kinship82.rda |binary data/Kinship82_Consensus.rda |binary data/Phonemes.rda |binary inst/doc/clue.pdf |binary inst/po/en@quot/LC_MESSAGES/R-clue.mo |binary man/cl_validity.Rd | 6 +++++- man/l1_fit_ultrametric.Rd | 6 +++++- po/R-clue.pot | 4 ++-- 18 files changed, 34 insertions(+), 26 deletions(-)
Title: Utility Functions for 'spatstat'
Description: Contains utility functions for the 'spatstat' package
which may also be useful for other purposes.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.utils versions 1.6-0 dated 2017-05-06 and 1.7-0 dated 2017-08-09
DESCRIPTION | 8 ++-- MD5 | 14 +++---- NAMESPACE | 14 +++---- R/formulae.R | 72 +++++++++++++++++++++++++---------------- R/utilseq.R | 12 +++++- inst/doc/packagesizes.txt | 2 + man/spatstat.utils-internal.Rd | 2 - src/proto.h | 10 ++--- 8 files changed, 78 insertions(+), 56 deletions(-)
More information about spatstat.utils at CRAN
Permanent link
Title: Automates the Creation of New Statistical Analysis Projects
Description: Provides functions to
automatically build a directory structure for a new R
project. Using this structure, 'ProjectTemplate'
automates data loading, preprocessing, library
importing and unit testing.
Author: Aleksandar Blagotic [ctb],
Diego Valle-Jones [ctb],
Jeffrey Breen [ctb],
Joakim Lundborg [ctb],
John Myles White [aut, cph],
Josh Bode [ctb],
Kenton White [ctb, cre],
Kirill Mueller [ctb],
Matteo Redaelli [ctb],
Noah Lorang [ctb],
Patrick Schalk [ctb],
Dominik Schneider [ctb]
Maintainer: Kenton White <jkentonwhite@gmail.com>
Diff between ProjectTemplate versions 0.7 dated 2016-08-11 and 0.8 dated 2017-08-09
ProjectTemplate-0.7/ProjectTemplate/R/default.config.R |only ProjectTemplate-0.7/ProjectTemplate/R/new.config.R |only ProjectTemplate-0.7/ProjectTemplate/inst/defaults/full/doc |only ProjectTemplate-0.7/ProjectTemplate/man/default.config.Rd |only ProjectTemplate-0.7/ProjectTemplate/man/new.config.Rd |only ProjectTemplate-0.8/ProjectTemplate/DESCRIPTION | 31 ProjectTemplate-0.8/ProjectTemplate/MD5 | 170 ++-- ProjectTemplate-0.8/ProjectTemplate/NAMESPACE | 5 ProjectTemplate-0.8/ProjectTemplate/R/add.config.R |only ProjectTemplate-0.8/ProjectTemplate/R/cache.R | 304 ++++++++ ProjectTemplate-0.8/ProjectTemplate/R/cache.project.R | 9 ProjectTemplate-0.8/ProjectTemplate/R/clear.R |only ProjectTemplate-0.8/ProjectTemplate/R/clear.cache.R |only ProjectTemplate-0.8/ProjectTemplate/R/config.R |only ProjectTemplate-0.8/ProjectTemplate/R/create.project.R | 20 ProjectTemplate-0.8/ProjectTemplate/R/csv.reader.R | 2 ProjectTemplate-0.8/ProjectTemplate/R/csv2.reader.R | 7 ProjectTemplate-0.8/ProjectTemplate/R/help.R | 4 ProjectTemplate-0.8/ProjectTemplate/R/list.data.R |only ProjectTemplate-0.8/ProjectTemplate/R/load.project.R | 351 ++++------ ProjectTemplate-0.8/ProjectTemplate/R/migrate.project.R | 124 +++ ProjectTemplate-0.8/ProjectTemplate/R/preinstalled.readers.R | 1 ProjectTemplate-0.8/ProjectTemplate/R/project.config.R |only ProjectTemplate-0.8/ProjectTemplate/R/reload.project.R | 38 - ProjectTemplate-0.8/ProjectTemplate/R/require.package.R | 2 ProjectTemplate-0.8/ProjectTemplate/R/sql.reader.R | 16 ProjectTemplate-0.8/ProjectTemplate/R/stopifnotproject.R |only ProjectTemplate-0.8/ProjectTemplate/R/stub.tests.R | 2 ProjectTemplate-0.8/ProjectTemplate/R/test.project.R | 2 ProjectTemplate-0.8/ProjectTemplate/R/translate.dcf.R | 17 ProjectTemplate-0.8/ProjectTemplate/R/tsv.reader.R | 2 ProjectTemplate-0.8/ProjectTemplate/R/wsv.reader.R | 2 ProjectTemplate-0.8/ProjectTemplate/R/xlsx.reader.R | 2 ProjectTemplate-0.8/ProjectTemplate/build |only ProjectTemplate-0.8/ProjectTemplate/inst/defaults/config/default.dcf | 5 ProjectTemplate-0.8/ProjectTemplate/inst/defaults/full/config/global.dcf | 7 ProjectTemplate-0.8/ProjectTemplate/inst/defaults/full/docs |only ProjectTemplate-0.8/ProjectTemplate/inst/defaults/full/lib/README.md | 2 ProjectTemplate-0.8/ProjectTemplate/inst/defaults/full/lib/globals.R |only ProjectTemplate-0.8/ProjectTemplate/inst/defaults/full/logs/README.md | 11 ProjectTemplate-0.8/ProjectTemplate/man/ProjectTemplate.Rd | 4 ProjectTemplate-0.8/ProjectTemplate/man/add.config.Rd |only ProjectTemplate-0.8/ProjectTemplate/man/add.extension.Rd | 2 ProjectTemplate-0.8/ProjectTemplate/man/arff.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/cache.Rd | 24 ProjectTemplate-0.8/ProjectTemplate/man/cache.name.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/cache.project.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/clean.variable.name.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/clear.Rd |only ProjectTemplate-0.8/ProjectTemplate/man/clear.cache.Rd |only ProjectTemplate-0.8/ProjectTemplate/man/create.project.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/csv.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/csv2.reader.Rd | 4 ProjectTemplate-0.8/ProjectTemplate/man/db.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/dbf.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/epiinfo.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/file.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/get.project.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/list.data.Rd |only ProjectTemplate-0.8/ProjectTemplate/man/load.project.Rd | 6 ProjectTemplate-0.8/ProjectTemplate/man/migrate.project.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/mp3.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/mtp.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/octave.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/ppm.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/preinstalled.readers.Rd | 3 ProjectTemplate-0.8/ProjectTemplate/man/project.config.Rd |only ProjectTemplate-0.8/ProjectTemplate/man/r.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/rdata.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/reload.project.Rd | 20 ProjectTemplate-0.8/ProjectTemplate/man/require.package.Rd | 3 ProjectTemplate-0.8/ProjectTemplate/man/run.project.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/show.project.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/spss.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/sql.reader.Rd | 12 ProjectTemplate-0.8/ProjectTemplate/man/stata.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/stub.tests.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/systat.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/test.project.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/translate.dcf.Rd | 6 ProjectTemplate-0.8/ProjectTemplate/man/tsv.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/url.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/wsv.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/xls.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/xlsx.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/man/xport.reader.Rd | 1 ProjectTemplate-0.8/ProjectTemplate/tests/testthat/migration/0.5-2/cache |only ProjectTemplate-0.8/ProjectTemplate/tests/testthat/migration/0.5-2/data |only ProjectTemplate-0.8/ProjectTemplate/tests/testthat/migration/0.5/cache |only ProjectTemplate-0.8/ProjectTemplate/tests/testthat/migration/0.5/data |only ProjectTemplate-0.8/ProjectTemplate/tests/testthat/test-cache.R |only ProjectTemplate-0.8/ProjectTemplate/tests/testthat/test-clear.R |only ProjectTemplate-0.8/ProjectTemplate/tests/testthat/test-config.R | 57 + ProjectTemplate-0.8/ProjectTemplate/tests/testthat/test-create.R | 20 ProjectTemplate-0.8/ProjectTemplate/tests/testthat/test-list.R |only ProjectTemplate-0.8/ProjectTemplate/tests/testthat/test-load.R | 208 +++++ ProjectTemplate-0.8/ProjectTemplate/tests/testthat/test-migration.R | 182 +++++ ProjectTemplate-0.8/ProjectTemplate/tests/testthat/test-readers.R | 289 ++++++++ ProjectTemplate-0.8/ProjectTemplate/tests/testthat/test-reload.R |only ProjectTemplate-0.8/ProjectTemplate/tests/testthat/test-version.R | 57 - 100 files changed, 1639 insertions(+), 425 deletions(-)
More information about ProjectTemplate at CRAN
Permanent link
Title: Phylogenetic Comparative Methods for High-Dimensional Traits
Description: Tools for studying the evolution of high-dimensional traits
(morphometric, function-valued, etc.) including ancestral state reconstruction,
estimating phylogenetic signal, and assessing correlated trait evolution. Visit
<http://www.phylocurve.org> for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between phylocurve versions 2.0.8 dated 2017-06-07 and 2.0.9 dated 2017-08-09
DESCRIPTION | 8 MD5 | 14 - man/evo.model.Rd | 238 +++++++++++++------------- man/fast.geomorph.compare.evol.rates.Rd | 158 ++++++++--------- man/fast.geomorph.compare.multi.evol.rates.Rd | 138 +++++++-------- man/fast.geomorph.physignal.Rd | 138 +++++++-------- man/fast.geomorph.procD.pgls.Rd | 4 man/phylocurve-package.Rd | 4 8 files changed, 351 insertions(+), 351 deletions(-)
Title: Access Open Data Through the 'Junar' API
Description: The 'Junar' API is a commercial platform to organize and publish data
<http://www.junar.com>. It has been used in a number of national and local
government Open Data initiatives in Latin America and the USA. This package
is a wrapper to make it easier to access data made public through the 'Junar'
API.
Author: Frans van Dunné [aut, cre]
Maintainer: Frans van Dunné <frans@ixpantia.com>
Diff between junr versions 0.1.1 dated 2016-05-13 and 0.1.2 dated 2017-08-09
junr-0.1.1/junr/NEWS.md |only junr-0.1.2/junr/DESCRIPTION | 18 junr-0.1.2/junr/MD5 | 37 - junr-0.1.2/junr/R/utils.R | 2 junr-0.1.2/junr/README.md | 4 junr-0.1.2/junr/build/vignette.rds |binary junr-0.1.2/junr/inst/doc/acceder-junar-api.Rmd | 7 junr-0.1.2/junr/inst/doc/acceder-junar-api.html | 686 ++++++++++++++++++----- junr-0.1.2/junr/inst/doc/access-junar-api.Rmd | 4 junr-0.1.2/junr/inst/doc/access-junar-api.html | 700 +++++++++++++++++++----- junr-0.1.2/junr/man/clean_currency.Rd | 3 junr-0.1.2/junr/man/get_currency_character.Rd | 1 junr-0.1.2/junr/man/get_data.Rd | 1 junr-0.1.2/junr/man/get_dimensions.Rd | 1 junr-0.1.2/junr/man/get_index.Rd | 1 junr-0.1.2/junr/man/list_guid.Rd | 1 junr-0.1.2/junr/man/list_titles.Rd | 1 junr-0.1.2/junr/tests/testthat/test-getdata.R | 3 junr-0.1.2/junr/vignettes/acceder-junar-api.Rmd | 7 junr-0.1.2/junr/vignettes/access-junar-api.Rmd | 4 20 files changed, 1158 insertions(+), 323 deletions(-)
More information about gamlss.spatial at CRAN
Permanent link
Title: A Package for Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data, in
particular representation, manipulation and simulation of multistate
data - the Lexis suite of functions, which includes interfaces to
'mstate', 'etm' and 'cmprsk' packages.
Also contains functions for Age-Period-Cohort and Lee-Carter
modeling and a function for interval censored data and some useful
functions for tabulation and plotting, as well as a number of
epidemiological data sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.16 dated 2017-06-30 and 2.19 dated 2017-08-09
CHANGES | 20 ++++++ DESCRIPTION | 8 +- MD5 | 22 +++---- R/LCa.fit.R | 35 +++++------ R/addCov.Lexis.R | 149 ++++++++++++++++++++++++------------------------- build/vignette.rds |binary inst/doc/Follow-up.pdf |binary inst/doc/simLexis.pdf |binary inst/doc/yll.pdf |binary man/LCa.fit.Rd | 33 ++++++---- man/addCov.Lexis.Rd | 75 +++++++++++++----------- man/cutLexis.Rd | 8 +- 12 files changed, 192 insertions(+), 158 deletions(-)