Title: Bayesian Set of Best Dynamic Treatment Regimes and Sample Size
in SMARTs
Description: Permits determination of a set of
optimal dynamic treatment regimes and sample size for a SMART design
in the Bayesian setting. Please see Artman (2020) <arXiv:2008.02341>.
Author: William Artman [aut, cre]
Maintainer: William Artman <William_Artman@URMC.Rochester.edu>
Diff between SMARTbayesR versions 1.0.1 dated 2020-11-09 and 1.0.2 dated 2021-04-03
DESCRIPTION | 6 - MD5 | 8 - R/internal.R | 8 - build/vignette.rds |binary inst/doc/SMARTBayesR.html | 266 ++++++++-------------------------------------- 5 files changed, 59 insertions(+), 229 deletions(-)
Title: Calculation of Accumulated Cost Surface and Least-Cost Paths
Related to Human Movement Across the Landscape
Description: Provides the facility to calculate non-isotropic accumulated cost surface and least-cost paths using a number of human-movement-related cost functions that can be selected by the user. It just requires a Digital Terrain Model, a start location and (optionally) destination locations. See Alberti (2019) <doi:10.1016/j.softx.2019.100331>.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between movecost versions 0.5 dated 2020-06-05 and 0.6 dated 2021-04-03
DESCRIPTION | 14 ++-- MD5 | 21 ++++-- NAMESPACE | 2 NEWS.md | 5 + R/Etna_boundary.r |only R/Etna_end_location.r |only R/Etna_start_location.r |only R/movecost.R | 81 ++++++++++++++++++----- README.md | 148 +------------------------------------------ data/Etna_boundary.rda |only data/Etna_end_location.rda |only data/Etna_start_location.rda |only man/Etna_boundary.Rd |only man/Etna_end_location.Rd |only man/Etna_start_location.Rd |only man/movecost.Rd | 63 +++++++++++++----- 16 files changed, 143 insertions(+), 191 deletions(-)
Title: FITS (Flexible Image Transport System) Utilities
Description: Utilities to read and write files in the FITS (Flexible
Image Transport System) format, a standard format in astronomy (see
e.g. <https://en.wikipedia.org/wiki/FITS> for more information).
Present low-level routines allow: reading, parsing, and modifying
FITS headers; reading FITS images (multi-dimensional arrays);
reading FITS binary and ASCII tables; and writing FITS images
(multi-dimensional arrays). Higher-level functions allow: reading
files composed of one or more headers and a single (perhaps
multidimensional) image or single table; reading tables into
data frames; generating vectors for image array axes; scaling and
writing images as 16-bit integers. Known incompletenesses are
reading random group extensions, as well as
complex and array descriptor data types in binary tables.
Author: Andrew Harris
Maintainer: Andrew Harris <harris@astro.umd.edu>
Diff between FITSio versions 2.1-5 dated 2021-03-23 and 2.1-6 dated 2021-04-03
ChangeLog | 8 ++++++++ DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- man/FITSio-package.Rd | 15 ++++++++++----- man/axVec.Rd | 3 +++ man/readFITS.Rd | 24 ++++++++++++++---------- man/readFITSheader.Rd | 4 ++++ man/readFrameFromFITS.Rd | 4 +++- man/writeFITSim.Rd | 3 +++ 9 files changed, 58 insertions(+), 29 deletions(-)
Title: Summarize and Explore the Data
Description: Exploratory analysis on any input data describing the structure and the relationships present in the data. The package automatically select the variable and does related descriptive statistics. Analyzing information value, weight of evidence, custom tables, summary statistics, graphical techniques will be performed for both numeric and categorical predictors.
Author: Dayanand Ubrangala [aut, cre],
Kiran R [aut, ctb],
Ravi Prasad Kondapalli [aut, ctb],
Sayan Putatunda [aut, ctb]
Maintainer: Dayanand Ubrangala <daya6489@gmail.com>
Diff between SmartEDA versions 0.3.6 dated 2020-07-10 and 0.3.7 dated 2021-04-03
DESCRIPTION | 14 MD5 | 47 NAMESPACE | 4 NEWS.md | 7 R/fn_Overview_data.R | 40 R/fn_custom_tab.R | 2 R/fn_exp_ExpCompViz.R |only R/fn_exp_categorical.R | 4 R/utilis.R | 212 +++ README.md | 23 build/vignette.rds |binary inst/doc/CustomTable.R | 2 inst/doc/CustomTable.html | 457 ++----- inst/doc/SmartEDA.R | 101 + inst/doc/SmartEDA.Rmd | 40 inst/doc/SmartEDA.html | 2327 +++++++++++++++---------------------- inst/doc/SmartTwoPlots.R |only inst/doc/SmartTwoPlots.Rmd |only inst/doc/SmartTwoPlots.html |only inst/rmd_template/report_tmp.Rmd | 2 inst/rmd_template/report_tmp_1.Rmd | 2 inst/rmd_template/report_tmp_2.Rmd | 3 man/ExpData.Rd | 10 man/ExpTwoPlots.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test_exptwoplots.R |only vignettes/SmartEDA.Rmd | 40 vignettes/SmartTwoPlots.Rmd |only 28 files changed, 1546 insertions(+), 1791 deletions(-)
Title: Build and Raytrace 3D Scenes
Description: Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, cones, curves, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format or the PLY Polygon File Format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <https://raytracing.github.io>.
Author: Tyler Morgan-Wall [aut, cph, cre]
(<https://orcid.org/0000-0002-3131-3814>),
Syoyo Fujita [ctb, cph],
Melissa O'Neill [ctb, cph],
Vilya Harvey [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayrender versions 0.14.0 dated 2020-08-02 and 0.21.1 dated 2021-04-03
rayrender-0.14.0/rayrender/src/xyrect.h |only rayrender-0.21.1/rayrender/DESCRIPTION | 26 rayrender-0.21.1/rayrender/MD5 | 197 + rayrender-0.21.1/rayrender/NAMESPACE | 29 rayrender-0.21.1/rayrender/R/RcppExports.R | 12 rayrender-0.21.1/rayrender/R/csg_construct.R |only rayrender-0.21.1/rayrender/R/generate_camera_motion.R |only rayrender-0.21.1/rayrender/R/generate_studio.R | 4 rayrender-0.21.1/rayrender/R/materials.R | 220 +- rayrender-0.21.1/rayrender/R/objects.R | 766 ++++++- rayrender-0.21.1/rayrender/R/pig.R | 82 rayrender-0.21.1/rayrender/R/post_process_frame.R |only rayrender-0.21.1/rayrender/R/render_animation.R |only rayrender-0.21.1/rayrender/R/render_preview.R |only rayrender-0.21.1/rayrender/R/render_scene.R | 217 +- rayrender-0.21.1/rayrender/R/util-functions.R |only rayrender-0.21.1/rayrender/inst/COPYRIGHTS | 6 rayrender-0.21.1/rayrender/man/arrow.Rd | 2 rayrender-0.21.1/rayrender/man/bezier_curve.Rd |only rayrender-0.21.1/rayrender/man/calculate_control_points.Rd |only rayrender-0.21.1/rayrender/man/calculate_control_points_straight.Rd |only rayrender-0.21.1/rayrender/man/calculate_distance_along_bezier_curve.Rd |only rayrender-0.21.1/rayrender/man/calculate_final_path.Rd |only rayrender-0.21.1/rayrender/man/clamp.Rd |only rayrender-0.21.1/rayrender/man/cross_prod.Rd |only rayrender-0.21.1/rayrender/man/csg_box.Rd |only rayrender-0.21.1/rayrender/man/csg_capsule.Rd |only rayrender-0.21.1/rayrender/man/csg_combine.Rd |only rayrender-0.21.1/rayrender/man/csg_cone.Rd |only rayrender-0.21.1/rayrender/man/csg_cylinder.Rd |only rayrender-0.21.1/rayrender/man/csg_ellipsoid.Rd |only rayrender-0.21.1/rayrender/man/csg_elongate.Rd |only rayrender-0.21.1/rayrender/man/csg_group.Rd |only rayrender-0.21.1/rayrender/man/csg_object.Rd |only rayrender-0.21.1/rayrender/man/csg_onion.Rd |only rayrender-0.21.1/rayrender/man/csg_plane.Rd |only rayrender-0.21.1/rayrender/man/csg_pyramid.Rd |only rayrender-0.21.1/rayrender/man/csg_rotate.Rd |only rayrender-0.21.1/rayrender/man/csg_round.Rd |only rayrender-0.21.1/rayrender/man/csg_rounded_cone.Rd |only rayrender-0.21.1/rayrender/man/csg_scale.Rd |only rayrender-0.21.1/rayrender/man/csg_sphere.Rd |only rayrender-0.21.1/rayrender/man/csg_torus.Rd |only rayrender-0.21.1/rayrender/man/csg_translate.Rd |only rayrender-0.21.1/rayrender/man/csg_triangle.Rd |only rayrender-0.21.1/rayrender/man/cube.Rd | 4 rayrender-0.21.1/rayrender/man/cubicInOut.Rd |only rayrender-0.21.1/rayrender/man/dielectric.Rd | 2 rayrender-0.21.1/rayrender/man/eval_bezier.Rd |only rayrender-0.21.1/rayrender/man/eval_bezier_2nd_deriv.Rd |only rayrender-0.21.1/rayrender/man/eval_bezier_deriv.Rd |only rayrender-0.21.1/rayrender/man/expInOut.Rd |only rayrender-0.21.1/rayrender/man/generate_camera_motion.Rd |only rayrender-0.21.1/rayrender/man/generate_studio.Rd | 4 rayrender-0.21.1/rayrender/man/hair.Rd |only rayrender-0.21.1/rayrender/man/lerp.Rd |only rayrender-0.21.1/rayrender/man/light.Rd | 58 rayrender-0.21.1/rayrender/man/mesh3d_model.Rd |only rayrender-0.21.1/rayrender/man/path.Rd |only rayrender-0.21.1/rayrender/man/pig.Rd | 19 rayrender-0.21.1/rayrender/man/ply_model.Rd |only rayrender-0.21.1/rayrender/man/post_process_frame.Rd |only rayrender-0.21.1/rayrender/man/process_point_series.Rd |only rayrender-0.21.1/rayrender/man/process_point_series_1d.Rd |only rayrender-0.21.1/rayrender/man/process_point_series_2d.Rd |only rayrender-0.21.1/rayrender/man/quadInOut.Rd |only rayrender-0.21.1/rayrender/man/render_animation.Rd |only rayrender-0.21.1/rayrender/man/render_preview.Rd |only rayrender-0.21.1/rayrender/man/render_scene.Rd | 52 rayrender-0.21.1/rayrender/man/sphere.Rd | 10 rayrender-0.21.1/rayrender/man/text3d.Rd |only rayrender-0.21.1/rayrender/man/tween.Rd |only rayrender-0.21.1/rayrender/src/RcppExports.cpp | 100 rayrender-0.21.1/rayrender/src/aabb.cpp |only rayrender-0.21.1/rayrender/src/aabb.h | 68 rayrender-0.21.1/rayrender/src/box.cpp |only rayrender-0.21.1/rayrender/src/box.h | 41 rayrender-0.21.1/rayrender/src/buildscene.cpp |only rayrender-0.21.1/rayrender/src/buildscene.h | 1069 ---------- rayrender-0.21.1/rayrender/src/bvh_node.cpp |only rayrender-0.21.1/rayrender/src/bvh_node.h | 150 - rayrender-0.21.1/rayrender/src/camera.cpp |only rayrender-0.21.1/rayrender/src/camera.h | 58 rayrender-0.21.1/rayrender/src/color.cpp |only rayrender-0.21.1/rayrender/src/color.h |only rayrender-0.21.1/rayrender/src/cone.cpp |only rayrender-0.21.1/rayrender/src/cone.h | 228 -- rayrender-0.21.1/rayrender/src/constant.cpp |only rayrender-0.21.1/rayrender/src/constant.h | 56 rayrender-0.21.1/rayrender/src/csg.cpp |only rayrender-0.21.1/rayrender/src/csg.h |only rayrender-0.21.1/rayrender/src/curve.cpp |only rayrender-0.21.1/rayrender/src/curve.h |only rayrender-0.21.1/rayrender/src/cylinder.cpp |only rayrender-0.21.1/rayrender/src/cylinder.h | 255 -- rayrender-0.21.1/rayrender/src/debug.cpp |only rayrender-0.21.1/rayrender/src/debug.h |only rayrender-0.21.1/rayrender/src/disk.cpp |only rayrender-0.21.1/rayrender/src/disk.h | 109 - rayrender-0.21.1/rayrender/src/distributions.cpp |only rayrender-0.21.1/rayrender/src/distributions.h | 95 rayrender-0.21.1/rayrender/src/ellipsoid.cpp |only rayrender-0.21.1/rayrender/src/ellipsoid.h | 164 - rayrender-0.21.1/rayrender/src/hitable.cpp |only rayrender-0.21.1/rayrender/src/hitable.h | 446 +--- rayrender-0.21.1/rayrender/src/hitablelist.cpp |only rayrender-0.21.1/rayrender/src/hitablelist.h | 71 rayrender-0.21.1/rayrender/src/infinite_area_light.cpp |only rayrender-0.21.1/rayrender/src/infinite_area_light.h | 132 - rayrender-0.21.1/rayrender/src/integrator.cpp |only rayrender-0.21.1/rayrender/src/integrator.h |only rayrender-0.21.1/rayrender/src/material.cpp |only rayrender-0.21.1/rayrender/src/material.h | 450 +--- rayrender-0.21.1/rayrender/src/mathinline.h | 258 ++ rayrender-0.21.1/rayrender/src/mesh3d.cpp |only rayrender-0.21.1/rayrender/src/mesh3d.h |only rayrender-0.21.1/rayrender/src/microfacetdist.cpp |only rayrender-0.21.1/rayrender/src/microfacetdist.h | 234 -- rayrender-0.21.1/rayrender/src/miniply.cpp |only rayrender-0.21.1/rayrender/src/miniply.h |only rayrender-0.21.1/rayrender/src/onbh.h | 27 rayrender-0.21.1/rayrender/src/pdf.cpp |only rayrender-0.21.1/rayrender/src/pdf.h | 130 - rayrender-0.21.1/rayrender/src/perlin.cpp |only rayrender-0.21.1/rayrender/src/perlin.h | 40 rayrender-0.21.1/rayrender/src/plymesh.cpp |only rayrender-0.21.1/rayrender/src/plymesh.h |only rayrender-0.21.1/rayrender/src/ray.cpp |only rayrender-0.21.1/rayrender/src/rectangle.cpp |only rayrender-0.21.1/rayrender/src/rectangle.h |only rayrender-0.21.1/rayrender/src/render_animation_rcpp.cpp |only rayrender-0.21.1/rayrender/src/render_scene_rcpp.cpp | 649 +----- rayrender-0.21.1/rayrender/src/rng.h | 3 rayrender-0.21.1/rayrender/src/sampler.cpp | 145 + rayrender-0.21.1/rayrender/src/sampler.h | 59 rayrender-0.21.1/rayrender/src/sphere.cpp |only rayrender-0.21.1/rayrender/src/sphere.h | 272 -- rayrender-0.21.1/rayrender/src/texture.cpp |only rayrender-0.21.1/rayrender/src/texture.h | 105 rayrender-0.21.1/rayrender/src/tinyobj/tiny_obj_loader.h | 955 ++++++-- rayrender-0.21.1/rayrender/src/tonemap.cpp |only rayrender-0.21.1/rayrender/src/tonemap.h | 47 rayrender-0.21.1/rayrender/src/triangle.cpp |only rayrender-0.21.1/rayrender/src/triangle.h | 161 - rayrender-0.21.1/rayrender/src/trimesh.cpp |only rayrender-0.21.1/rayrender/src/trimesh.h | 617 ----- rayrender-0.21.1/rayrender/src/vec2.h | 3 rayrender-0.21.1/rayrender/src/vec3.h | 6 148 files changed, 3504 insertions(+), 5409 deletions(-)
Title: Pipe-Friendly Vector Replacement with Case Statements
Description: Offers a pipe-friendly alternative to the 'dplyr' functions
case_when() and if_else(), as well as a number of user-friendly
simplifications for common use cases. These functions accept a vector
as an optional first argument, allowing conditional statements to be
built using the 'magrittr' dot operator. The functions also coerce
all outputs to the same type, meaning you no longer have to worry
about using specific typed variants of NA or explicitly declaring
integer outputs, and evaluate outputs somewhat lazily, so you don't
waste time on long operations that won't be used.
Author: Alexander Rossell Hayes [aut, cre, cph]
(<https://orcid.org/0000-0001-9412-0457>),
Patrice Kiener [ctb] (Contributed example for fn_case(),
<https://orcid.org/0000-0002-0505-9920>)
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between incase versions 0.2.1 dated 2021-01-14 and 0.3.0 dated 2021-04-03
incase-0.2.1/incase/R/check_length_val.R |only incase-0.2.1/incase/R/compact_null.R |only incase-0.2.1/incase/R/formatting.R |only incase-0.2.1/incase/R/glubort.R |only incase-0.2.1/incase/R/replace_with.R |only incase-0.2.1/incase/R/validate_case_when_length.R |only incase-0.2.1/incase/R/validate_formula.R |only incase-0.2.1/incase/R/warn_if_default.R |only incase-0.2.1/incase/tests/testthat/test-formatting.R |only incase-0.3.0/incase/DESCRIPTION | 43 ++++-- incase-0.3.0/incase/MD5 | 54 ++++---- incase-0.3.0/incase/NAMESPACE | 10 + incase-0.3.0/incase/NEWS.md | 22 +++ incase-0.3.0/incase/R/compact_list.R |only incase-0.3.0/incase/R/errors.R |only incase-0.3.0/incase/R/fn_case.R | 70 ++--------- incase-0.3.0/incase/R/grep_case.R | 7 - incase-0.3.0/incase/R/if_case.R | 63 ++++++++-- incase-0.3.0/incase/R/in_case.R | 106 +++++++---------- incase-0.3.0/incase/R/in_case_fct.R |only incase-0.3.0/incase/R/in_case_list.R |only incase-0.3.0/incase/R/onLoad.R |only incase-0.3.0/incase/R/replace.R |only incase-0.3.0/incase/R/switch_case.R | 71 ++++++----- incase-0.3.0/incase/R/validate_case_length.R |only incase-0.3.0/incase/README.md | 79 ++++++++---- incase-0.3.0/incase/man/fn_case.Rd | 41 ++++++ incase-0.3.0/incase/man/grep_case.Rd | 5 incase-0.3.0/incase/man/in_case.Rd | 5 incase-0.3.0/incase/man/in_case_fct.Rd |only incase-0.3.0/incase/man/in_case_list.Rd |only incase-0.3.0/incase/man/incase-package.Rd | 5 incase-0.3.0/incase/man/switch_case.Rd | 7 - incase-0.3.0/incase/tests/testthat/test-fn_case.R | 51 +++++++- incase-0.3.0/incase/tests/testthat/test-if_case.R | 20 ++- incase-0.3.0/incase/tests/testthat/test-in_case.R | 8 - incase-0.3.0/incase/tests/testthat/test-in_case_fct.R |only incase-0.3.0/incase/tests/testthat/test-in_case_list.R |only 38 files changed, 421 insertions(+), 246 deletions(-)
Title: Compute Viewshed in 3D Point Clouds of Ecosystems
Description: A set of tools to compute viewshed in 3D from Terrestrial Laser Scanner data and prepare the data prior to visibility estimation.
Author: Bastien Lecigne [aut, cre] (<https://orcid.org/0000-0002-1496-202X>),
Jan Eitel [aut]
Maintainer: Bastien Lecigne <lecignebastien@gmail.com>
Diff between viewshed3d versions 3.2.0 dated 2020-07-03 and 4.0.0 dated 2021-04-03
DESCRIPTION | 13 +++---- MD5 | 41 +++++++++++++++-------- NAMESPACE | 6 +++ R/Denoise.R | 4 +- R/Downsample_scene.R | 2 - R/add_slope.R |only R/directional_visibility.R |only R/generate_sphere.R |only R/h_visibility.R |only R/reconstruct_ground.R | 28 +++++++-------- R/remove_slope.R |only R/sample_scene.R | 6 +-- R/set_position.R |only R/viewshed3d_package.R | 80 +++++++++++++++++++++++++-------------------- R/viewsheds.R | 4 +- R/visibility.R | 32 ++++++++++-------- README.md |only man/add_slope.Rd |only man/d_visibility.Rd |only man/denoise_scene.Rd | 2 - man/generate_sphere.Rd |only man/h_visibility.Rd |only man/remove_slope.Rd |only man/sample_scene.Rd | 4 +- man/set_position.Rd |only man/viewshed3d.Rd | 40 ++++++++++++++-------- man/viewsheds.Rd | 2 - man/visibility.Rd | 16 +++++---- 28 files changed, 166 insertions(+), 114 deletions(-)
Title: Sparse Tables
Description: Fast Multiplication and Marginalization of Sparse Tables.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Diff between sparta versions 0.7.1 dated 2021-03-01 and 0.7.2 dated 2021-04-03
DESCRIPTION | 9 +++---- MD5 | 24 ++++++++++---------- NEWS.md | 4 +++ R/RcppExports.R | 4 +++ R/api_converters.R | 2 - R/api_sparta.R | 2 - R/helpers_sparta.R | 20 ++++++----------- man/sparta_struct.Rd | 2 - src/RcppExports.cpp | 15 ++++++++++++ src/marginalize.cpp | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++ src/misc_utils.cpp | 28 +++++++++++++++++++++++- src/misc_utils.h | 1 src/sparta_types.h | 1 13 files changed, 138 insertions(+), 33 deletions(-)
Title: Easy Downloading Capabilities for the Members' Name Information
Service
Description: An API package for the Members' Name Information Service operated
by the UK parliament. Documentation for the API itself can be found
here: <http://data.parliament.uk/membersdataplatform/default.aspx>.
Author: Evan Odell [aut, cre] (<https://orcid.org/0000-0003-1845-808X>)
Maintainer: Evan Odell <evanodell91@gmail.com>
Diff between mnis versions 0.2.7 dated 2017-07-03 and 0.3.1 dated 2021-04-03
mnis-0.2.7/mnis/R/mnis_extra.R |only mnis-0.2.7/mnis/man/mnis_extra.Rd |only mnis-0.2.7/mnis/tests/testthat/test_extra.R |only mnis-0.3.1/mnis/DESCRIPTION | 34 mnis-0.3.1/mnis/LICENSE | 4 mnis-0.3.1/mnis/MD5 | 157 - mnis-0.3.1/mnis/NAMESPACE | 188 - mnis-0.3.1/mnis/NEWS.md | 244 + mnis-0.3.1/mnis/R/RcppExports.R | 22 mnis-0.3.1/mnis/R/mnis-package.R | 87 mnis-0.3.1/mnis/R/mnis_additional.R | 1445 +--------- mnis-0.3.1/mnis/R/mnis_all_members.R | 163 - mnis-0.3.1/mnis/R/mnis_all_reference.R | 285 +- mnis-0.3.1/mnis/R/mnis_base.R | 67 mnis-0.3.1/mnis/R/mnis_constituency_results.R | 105 mnis-0.3.1/mnis/R/mnis_defunct.R |only mnis-0.3.1/mnis/R/mnis_department.R | 107 mnis-0.3.1/mnis/R/mnis_deprecated.R |only mnis-0.3.1/mnis/R/mnis_eligible.R | 150 - mnis-0.3.1/mnis/R/mnis_full_biog.R | 114 mnis-0.3.1/mnis/R/mnis_general_election_results.R | 121 mnis-0.3.1/mnis/R/mnis_joined_between.R | 178 - mnis-0.3.1/mnis/R/mnis_lords_type.R | 83 mnis-0.3.1/mnis/R/mnis_member_date.R | 108 mnis-0.3.1/mnis/R/mnis_mps_on_date.R | 141 mnis-0.3.1/mnis/R/mnis_party_state.R | 85 mnis-0.3.1/mnis/R/mnis_peers_on_date.R | 128 mnis-0.3.1/mnis/R/mnis_political_interests.R |only mnis-0.3.1/mnis/R/mnis_reference.R | 1849 ++----------- mnis-0.3.1/mnis/R/mnis_tidy.R | 370 +- mnis-0.3.1/mnis/R/util-mnis-id_type.R |only mnis-0.3.1/mnis/R/utils-additional-engine.R |only mnis-0.3.1/mnis/R/utils-additional.R |only mnis-0.3.1/mnis/R/utils-base_url.R |only mnis-0.3.1/mnis/R/utils-get_additional.R |only mnis-0.3.1/mnis/R/utils-mnis_reference.R |only mnis-0.3.1/mnis/R/utils-query.R |only mnis-0.3.1/mnis/R/utils-ref_tidy.R |only mnis-0.3.1/mnis/build/vignette.rds |binary mnis-0.3.1/mnis/inst/CITATION | 24 mnis-0.3.1/mnis/inst/doc/introduction.R | 42 mnis-0.3.1/mnis/inst/doc/introduction.Rmd | 502 +-- mnis-0.3.1/mnis/inst/doc/introduction.html | 649 ++-- mnis-0.3.1/mnis/man/constituency_results_tidy.Rd | 32 mnis-0.3.1/mnis/man/date_tidy.Rd | 30 mnis-0.3.1/mnis/man/mnis.Rd | 77 mnis-0.3.1/mnis/man/mnis_additional.Rd | 356 +- mnis-0.3.1/mnis/man/mnis_all_members.Rd | 87 mnis-0.3.1/mnis/man/mnis_all_reference.Rd | 61 mnis-0.3.1/mnis/man/mnis_base.Rd | 50 mnis-0.3.1/mnis/man/mnis_bom.Rd | 28 mnis-0.3.1/mnis/man/mnis_constituency_results.Rd | 78 mnis-0.3.1/mnis/man/mnis_department.Rd | 86 mnis-0.3.1/mnis/man/mnis_eligible.Rd | 87 mnis-0.3.1/mnis/man/mnis_full_biog.Rd | 76 mnis-0.3.1/mnis/man/mnis_general_election_results.Rd | 99 mnis-0.3.1/mnis/man/mnis_joined_between.Rd | 102 mnis-0.3.1/mnis/man/mnis_lords_type.Rd | 70 mnis-0.3.1/mnis/man/mnis_member_date.Rd | 85 mnis-0.3.1/mnis/man/mnis_mps_on_date.Rd | 89 mnis-0.3.1/mnis/man/mnis_party_state.Rd | 87 mnis-0.3.1/mnis/man/mnis_peers_on_date.Rd | 92 mnis-0.3.1/mnis/man/mnis_political_interests.Rd |only mnis-0.3.1/mnis/man/mnis_reference.Rd | 471 +-- mnis-0.3.1/mnis/man/mnis_tidy.Rd | 52 mnis-0.3.1/mnis/man/tidy_bom.Rd | 28 mnis-0.3.1/mnis/src/RcppExports.cpp | 2 mnis-0.3.1/mnis/src/mnis_init.c | 4 mnis-0.3.1/mnis/tests/testthat-a.R | 9 mnis-0.3.1/mnis/tests/testthat-c.R | 9 mnis-0.3.1/mnis/tests/testthat-e.R | 9 mnis-0.3.1/mnis/tests/testthat-f.R | 9 mnis-0.3.1/mnis/tests/testthat-j.R | 9 mnis-0.3.1/mnis/tests/testthat-l.R | 9 mnis-0.3.1/mnis/tests/testthat-m.R | 9 mnis-0.3.1/mnis/tests/testthat-r.R | 9 mnis-0.3.1/mnis/tests/testthat/test_additional.R | 201 - mnis-0.3.1/mnis/tests/testthat/test_all_members.R | 29 mnis-0.3.1/mnis/tests/testthat/test_constituency_results.R | 38 mnis-0.3.1/mnis/tests/testthat/test_eligible.R | 28 mnis-0.3.1/mnis/tests/testthat/test_fixed_scope.R | 77 mnis-0.3.1/mnis/tests/testthat/test_full_biog.R | 29 mnis-0.3.1/mnis/tests/testthat/test_joined_between.R | 31 mnis-0.3.1/mnis/tests/testthat/test_lords.R | 46 mnis-0.3.1/mnis/tests/testthat/test_members_on_dates.R | 58 mnis-0.3.1/mnis/tests/testthat/test_reference.R | 414 +- mnis-0.3.1/mnis/vignettes/introduction.Rmd | 502 +-- 87 files changed, 4680 insertions(+), 6526 deletions(-)
Title: Junction Tree Inference
Description: Minimal and memory efficient implementation of the junction tree
algorithm using the Lauritzen-Spiegelhalter scheme;
S. L. Lauritzen and D. J. Spiegelhalter (1988)
<https://www.jstor.org/stable/2345762?seq=1>.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Diff between jti versions 0.6.0 dated 2020-12-16 and 0.7.0 dated 2021-04-03
jti-0.6.0/jti/R/helper_triangulate.R |only jti-0.6.0/jti/man/dag.Rd |only jti-0.7.0/jti/DESCRIPTION | 8 - jti-0.7.0/jti/MD5 | 53 ++++-- jti-0.7.0/jti/NAMESPACE | 20 ++ jti-0.7.0/jti/NEWS.md | 8 + jti-0.7.0/jti/R/RcppExports.R | 8 - jti-0.7.0/jti/R/api_compile.R | 227 +++++++++++++++++------------ jti-0.7.0/jti/R/api_jt.R | 164 +++++++++++++++++--- jti-0.7.0/jti/R/asserters.R | 2 jti-0.7.0/jti/R/helper_compile.R | 24 +-- jti-0.7.0/jti/R/helper_elimination_game.R |only jti-0.7.0/jti/R/helper_jt.R | 177 ++++++++-------------- jti-0.7.0/jti/R/helper_misc.R | 36 ++++ jti-0.7.0/jti/R/helper_mpd.R |only jti-0.7.0/jti/R/helper_triang.R |only jti-0.7.0/jti/R/sandbox.R | 219 ++++++++++++++++++++------- jti-0.7.0/jti/R/tmp_helper_sparse_triang.R |only jti-0.7.0/jti/R/tmp_prime_pots.R |only jti-0.7.0/jti/R/tmp_sparse_triang_notes.R |only jti-0.7.0/jti/man/compile.Rd | 51 +++--- jti-0.7.0/jti/man/cpt_list.Rd | 7 jti-0.7.0/jti/man/get-graph.Rd |only jti-0.7.0/jti/man/get_cliques.Rd | 5 jti-0.7.0/jti/man/getters.Rd |only jti-0.7.0/jti/man/jt.Rd | 57 ++++++- jti-0.7.0/jti/man/new_mpd.Rd |only jti-0.7.0/jti/man/par_lvs.Rd |only jti-0.7.0/jti/man/send_messages.Rd |only jti-0.7.0/jti/man/triangulate.Rd |only jti-0.7.0/jti/src/RcppExports.cpp | 26 +-- jti-0.7.0/jti/src/jti_types.h | 2 jti-0.7.0/jti/src/path_exists.cpp |only jti-0.7.0/jti/src/rip.cpp | 22 -- jti-0.7.0/jti/src/rooted_junction_tree.cpp | 60 ++++++- 35 files changed, 761 insertions(+), 415 deletions(-)
Title: Port of 'Dparser' Package
Description: A Scannerless GLR parser/parser generator. Note that GLR standing for "generalized LR", where L stands for "left-to-right" and
R stands for "rightmost (derivation)". For more information see <https://en.wikipedia.org/wiki/GLR_parser>. This parser is based on the Tomita
(1987) algorithm. (Paper can be found at <https://www.aclweb.org/anthology/P84-1073.pdf>).
The original 'dparser' package documentation can be found at <http://dparser.sourceforge.net/>. This allows you to add mini-languages to R (like
RxODE's ODE mini-language Wang, Hallow, and James 2015 <DOI:10.1002/psp4.12052>) or to parse other languages like 'NONMEM' to automatically translate
them to R code. To use this in your code, add a LinkingTo dparser in your DESCRIPTION file and instead of using #include <dparse.h> use
#include <dparser.h>. This also provides a R-based port of the make_dparser <http://dparser.sourceforge.net/d/make_dparser.cat> command called
mkdparser(). Additionally you can parse an arbitrary grammar within R using the dparse() function, which works on most OSes and is mainly for grammar
testing. The fastest parsing, of course, occurs at the C level, and is suggested.
Author: Matthew Fidler [aut, cre],
John Plevyak [aut, cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between dparser versions 0.1.8 dated 2017-11-13 and 1.3.1-2 dated 2021-04-03
dparser-0.1.8/dparser/src/symtab.c |only dparser-0.1.8/dparser/tests/testthat/g50.test.g |only dparser-0.1.8/dparser/tests/testthat/g50.test.g.1 |only dparser-0.1.8/dparser/tests/testthat/g50.test.g.1.check |only dparser-1.3.1-2/dparser/DESCRIPTION | 16 dparser-1.3.1-2/dparser/LICENSE | 4 dparser-1.3.1-2/dparser/MD5 | 273 +- dparser-1.3.1-2/dparser/NAMESPACE | 30 dparser-1.3.1-2/dparser/NEWS.md |only dparser-1.3.1-2/dparser/R/Rparse.R | 14 dparser-1.3.1-2/dparser/R/dparser.R | 1291 +++++----- dparser-1.3.1-2/dparser/R/version.R | 14 dparser-1.3.1-2/dparser/inst/ansic.test.g | 464 +-- dparser-1.3.1-2/dparser/inst/tran.g | 274 +- dparser-1.3.1-2/dparser/man/dpDefaultSkip.Rd | 62 dparser-1.3.1-2/dparser/man/dpGetFile.Rd | 94 dparser-1.3.1-2/dparser/man/dpIncludeDir.Rd | 50 dparser-1.3.1-2/dparser/man/dpReload.Rd | 30 dparser-1.3.1-2/dparser/man/dpRparse.Rd | 36 dparser-1.3.1-2/dparser/man/dpVersion.Rd | 36 dparser-1.3.1-2/dparser/man/dparse.Rd | 231 - dparser-1.3.1-2/dparser/man/dparser-package.Rd | 1363 +++++----- dparser-1.3.1-2/dparser/man/dparserFunction-class.Rd | 38 dparser-1.3.1-2/dparser/man/gc.dparser.Rd | 82 dparser-1.3.1-2/dparser/man/mkdparse.Rd | 1430 +++++------ dparser-1.3.1-2/dparser/man/show-dparserFunction-method.Rd | 31 dparser-1.3.1-2/dparser/src/Makevars | 4 dparser-1.3.1-2/dparser/src/d.h | 72 dparser-1.3.1-2/dparser/src/dparse.h | 64 dparser-1.3.1-2/dparser/src/dparse_tables.h | 192 - dparser-1.3.1-2/dparser/src/dparser.c | 50 dparser-1.3.1-2/dparser/src/dparser.h | 60 dparser-1.3.1-2/dparser/src/dsymtab.c |only dparser-1.3.1-2/dparser/src/dsymtab.h | 45 dparser-1.3.1-2/dparser/src/gram.c | 1491 +++++------ dparser-1.3.1-2/dparser/src/gram.h | 333 +- dparser-1.3.1-2/dparser/src/gramgram.h | 13 dparser-1.3.1-2/dparser/src/grammar.g.c | 412 +-- dparser-1.3.1-2/dparser/src/install.libs.R | 34 dparser-1.3.1-2/dparser/src/lex.c | 505 +-- dparser-1.3.1-2/dparser/src/lex.h | 17 dparser-1.3.1-2/dparser/src/lr.c | 276 -- dparser-1.3.1-2/dparser/src/lr.h | 1 dparser-1.3.1-2/dparser/src/mkdparse.c | 25 dparser-1.3.1-2/dparser/src/parse.c | 1517 +++++------- dparser-1.3.1-2/dparser/src/parse.h | 132 - dparser-1.3.1-2/dparser/src/rdparse.c | 63 dparser-1.3.1-2/dparser/src/read_binary.c | 69 dparser-1.3.1-2/dparser/src/read_binary.h | 10 dparser-1.3.1-2/dparser/src/scan.c | 173 - dparser-1.3.1-2/dparser/src/scan.h | 7 dparser-1.3.1-2/dparser/src/util.c | 290 +- dparser-1.3.1-2/dparser/src/util.h | 171 - dparser-1.3.1-2/dparser/src/version.c | 13 dparser-1.3.1-2/dparser/src/write_tables.c | 1171 ++++----- dparser-1.3.1-2/dparser/src/write_tables.h | 9 dparser-1.3.1-2/dparser/tests/testthat.R | 10 dparser-1.3.1-2/dparser/tests/testthat/ansic.test.g | 466 +-- dparser-1.3.1-2/dparser/tests/testthat/ansic.test.g.1.out |only dparser-1.3.1-2/dparser/tests/testthat/bnf.g.1 | 204 - dparser-1.3.1-2/dparser/tests/testthat/g1.test.g | 4 dparser-1.3.1-2/dparser/tests/testthat/g1.test.g.1.out |only 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Title: Linear Regressions with a Latent Outcome Variable
Description: Fit linear models, estimating score distributions for groups of people, following Cohen and Jiang (1999) <doi:10.2307/2669917>. In this model, the response is a latent trait (such as student ability) and raw item responses are combined with item difficulties in an item response theory (IRT) framework to form a density for each unit (student). This latent trait is then integrated out. This software is intended to fit the same models as the existing software 'AM' <http://am.air.org/>.
Author: Harold Doran [aut],
Paul Bailey [aut, cre],
Eric Buehler [aut],
Sun-joo Lee [aut],
Claire Kelley [ctb],
Emmanuel Sikali [pdr]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between Dire versions 1.0.2 dated 2021-03-22 and 1.0.3 dated 2021-04-03
DESCRIPTION | 13 MD5 | 6 R/de.R | 1498 +++++++++++++++++++++++++++---------------------------- inst/doc/MML.pdf |binary 4 files changed, 759 insertions(+), 758 deletions(-)
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut, cre],
Hadley Wickham [aut],
Oliver Gjoneski [ctb] (detule),
lexicalunit [cph] (nanodbc library),
Google Inc. [cph] (cctz library),
RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between odbc versions 1.3.1 dated 2021-03-16 and 1.3.2 dated 2021-04-03
DESCRIPTION | 7 +++---- MD5 | 22 +++++++++++----------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/Connection.R | 4 ++-- R/DataTypes.R | 18 ++++++++++++++++++ R/Driver.R | 2 +- R/Viewer.R | 12 ++++++------ README.md | 3 +-- build/odbc.pdf |binary man/dbConnect-OdbcDriver-method.Rd | 5 ++--- man/odbcConnectionColumns.Rd | 4 ++-- 12 files changed, 52 insertions(+), 31 deletions(-)
Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem.
Models include ARIMA, Exponential Smoothing, and additional time series models
from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition"
(<https://otexts.com/fpp2/>).
Refer to "Prophet: forecasting at scale"
(<https://research.fb.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime versions 0.5.0 dated 2021-03-29 and 0.5.1 dated 2021-04-03
DESCRIPTION | 6 +- MD5 | 19 +++---- NAMESPACE | 2 NEWS.md | 8 ++- R/modeltime-forecast.R | 2 R/modeltime-recursive.R | 28 ++++++++-- R/modeltime-refit.R | 4 - R/utils-parsnip-helpers.R | 6 +- inst/doc/getting-started-with-modeltime.html | 72 +++++++++++++-------------- man/dot_prepare_transform.Rd |only vignettes/temp/recursive-forecasting.Rmd | 5 + 11 files changed, 95 insertions(+), 57 deletions(-)
Title: Calculate Ecological Information and Diatom Based Indices
Description: Calculates ecological information and biotic indices for diatoms in a sample.
It includes number/shape of chloroplasts diversity indices, size classes, ecological guilds, and multiple biotic indices.
It outputs both a dataframe with all the results and plots of all the obtained data in a defined output folder.
Sample data was taken from Nicolosi Gelis, Cochero & Gómez (2020, <doi:10.1016/j.ecolind.2019.105951>).
The package uses the 'Diat.Barcode' database to calculate morphological and ecological information by Rimet & Couchez (2012, <doi:10.1051/kmae/2012018>),
and calculates the DES index by Descy (1979, <http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=PASCAL8060205402>),
the EPID index by Dell'Uomo (1996, ISBN: 3950009002),
the IDAP index by Prygiel & Coste (1993, <doi:10.1007/BF00028033>),
the ID-CH index by Hürlimann & Niederhauser (2007, <https://www.bafu.admin.ch/bafu/fr/home/themes/eaux/publications/publications-eaux/methodes-analyse-appreciation-cours-eau-diatomees.html>),
the IDP index by Gómez & Licursi (2001, <doi:10.1023/A:1011415209445>),
the ILM index by Leclercq & Maquet (1987, <http://www.vliz.be/imisdocs/publications/286641.pdf>),
the IPS index by Coste (1982, <https://www.oieau.org/eaudoc/notice/ETUDE-DES-METHODES-BIOLOGIQUES-DAPPRECIATION-QUANTITATIVE-DE-LA-QUALITE-DES-EAUX>),
the LOBO index by Lobo, Callegaro, & Bender (2002, ISBN:9788585869908),
the SLA by Sládeček (1986, <doi:10.1002/aheh.19860140519>),
the TDI index by Kelly, & Whitton (1995, <doi:10.1007/BF00003802>),
and the SPEAR(herbicide) index by Wood, Mitrovic, Lim, Warne, Dunlop, & Kefford (2019, <doi:10.1016/j.ecolind.2018.12.035>).
Author: María Mercedes Nicolosi Gelis [aut]
(<https://orcid.org/0000-0001-6324-7930>),
María Belén Sathicq [aut] (<https://orcid.org/0000-0002-3534-8950>),
Joaquín Cochero [cre] (<https://orcid.org/0000-0003-3957-6819>)
Maintainer: Joaquín Cochero <jcochero@ilpla.edu.ar>
Diff between diathor versions 0.0.4 dated 2021-02-24 and 0.0.5 dated 2021-04-03
diathor-0.0.4/diathor/R/diat_findAcronyms.R |only diathor-0.0.4/diathor/data/acronyms.rda |only diathor-0.0.4/diathor/man/acronyms.Rd |only diathor-0.0.4/diathor/man/diat_findAcronyms.Rd |only diathor-0.0.5/diathor/DESCRIPTION | 7 +- diathor-0.0.5/diathor/MD5 | 72 +++++++++++-------------- diathor-0.0.5/diathor/NAMESPACE | 2 diathor-0.0.5/diathor/R/data.R | 10 --- diathor-0.0.5/diathor/R/diaThor.R | 3 - diathor-0.0.5/diathor/R/diat_des.R | 26 ++++----- diathor-0.0.5/diathor/R/diat_diversity.R | 4 - diathor-0.0.5/diathor/R/diat_epid.R | 24 ++++---- diathor-0.0.5/diathor/R/diat_idap.R | 28 +++++---- diathor-0.0.5/diathor/R/diat_idch.R | 24 ++++---- diathor-0.0.5/diathor/R/diat_idp.R | 19 +++--- diathor-0.0.5/diathor/R/diat_ilm.R | 22 ++++--- diathor-0.0.5/diathor/R/diat_ips.R | 22 +++++-- diathor-0.0.5/diathor/R/diat_loadData.R | 42 ++++---------- diathor-0.0.5/diathor/R/diat_lobo.R | 24 ++++---- diathor-0.0.5/diathor/R/diat_sla.R | 24 ++++---- diathor-0.0.5/diathor/R/diat_spear.R | 9 +-- diathor-0.0.5/diathor/R/diat_tdi.R | 17 ++++- diathor-0.0.5/diathor/R/diathorAll.R | 2 diathor-0.0.5/diathor/README.md | 3 - diathor-0.0.5/diathor/data/des.rda |binary diathor-0.0.5/diathor/data/diat_sampleData.rda |binary diathor-0.0.5/diathor/data/epid.rda |binary diathor-0.0.5/diathor/data/idap.rda |binary diathor-0.0.5/diathor/data/idch.rda |binary diathor-0.0.5/diathor/data/idp.rda |binary diathor-0.0.5/diathor/data/ilm.rda |binary diathor-0.0.5/diathor/data/ips.rda |binary diathor-0.0.5/diathor/data/lobo.rda |binary diathor-0.0.5/diathor/data/sla.rda |binary diathor-0.0.5/diathor/data/spear.rda |binary diathor-0.0.5/diathor/data/tdi.rda |binary diathor-0.0.5/diathor/man/diaThor.Rd | 3 - diathor-0.0.5/diathor/man/diaThorAll.Rd | 2 diathor-0.0.5/diathor/man/diat_loadData.Rd | 2 39 files changed, 191 insertions(+), 200 deletions(-)
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates weights to form equivalent groups in observational studies with point or longitudinal treatments by easing and extending the functionality of the R packages 'twang' for generalized boosted modeling (McCaffrey, Ridgeway & Morral, 2004) <doi:10.1037/1082-989X.9.4.403>, 'CBPS' for covariate balancing propensity score weighting (Imai & Ratkovic, 2014) <doi:10.1111/rssb.12027>, 'ebal' for entropy balancing (Hainmueller, 2012) <doi:10.1093/pan/mpr025>, 'optweight' for optimization-based weights (Zubizarreta, 2015) <doi:10.1080/01621459.2015.1023805>, 'ATE' for empirical balancing calibration weighting (Chan, Yam, & Zhang, 2016) <doi:10.1111/rssb.12129>, 'SuperLearner' for stacked machine learning-based propensity scores (Pirracchio, Petersen, & van der Laan, 2015) <doi:10.1093/aje/kwu253>, among others. Also allows for assessment of weights and checking of covariate balance by interfacing directly with 'cobalt'.
Author: Noah Greifer [aut, cre] (<https://orcid.org/0000-0003-3067-7154>)
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 0.11.0 dated 2021-02-02 and 0.12.0 dated 2021-04-03
WeightIt-0.11.0/WeightIt/man/method_twang.Rd |only WeightIt-0.12.0/WeightIt/DESCRIPTION | 18 - WeightIt-0.12.0/WeightIt/MD5 | 41 +- WeightIt-0.12.0/WeightIt/NAMESPACE | 1 WeightIt-0.12.0/WeightIt/NEWS.md | 22 + WeightIt-0.12.0/WeightIt/R/SHARED.R | 213 ++++++++++--- WeightIt-0.12.0/WeightIt/R/as.weightit.R | 24 - WeightIt-0.12.0/WeightIt/R/balance.criteria.R | 280 +++++++++++++++++- WeightIt-0.12.0/WeightIt/R/functions_for_processing.R | 163 ++-------- WeightIt-0.12.0/WeightIt/R/sbps.R | 8 WeightIt-0.12.0/WeightIt/R/weightit.R | 94 +++--- WeightIt-0.12.0/WeightIt/R/weightit.fit.R | 23 - WeightIt-0.12.0/WeightIt/R/weightit2method.R | 269 ++++------------- WeightIt-0.12.0/WeightIt/R/weightitMSM.R | 179 +++++------ WeightIt-0.12.0/WeightIt/build/partial.rdb |binary WeightIt-0.12.0/WeightIt/inst/doc/WeightIt.html | 184 +++++++---- WeightIt-0.12.0/WeightIt/man/method_bart.Rd | 5 WeightIt-0.12.0/WeightIt/man/method_energy.Rd | 6 WeightIt-0.12.0/WeightIt/man/method_gbm.Rd | 4 WeightIt-0.12.0/WeightIt/man/method_ps.Rd | 2 WeightIt-0.12.0/WeightIt/man/stop.method.Rd | 5 WeightIt-0.12.0/WeightIt/man/weightitMSM.Rd | 2 22 files changed, 884 insertions(+), 659 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord'
(1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel'
general cross product statistic, Empirical Bayes estimates and
'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992)
<doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured
join count statistics, 'APLE' ('Li 'et al.' )
<doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I'
('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and
'Getis/Ord' G ('Ord' and 'Getis' 1995)
<doi:10.1111/j.1538-4632.1995.tb00912.x>,
'saddlepoint' approximations ('Tiefelsdorf' 2002)
<doi:10.1111/j.1538-4632.2002.tb01084.x> and exact tests
for global and local 'Moran's I' ('Bivand et al.' 2009)
<doi:10.1016/j.csda.2008.07.021> and 'LOSH' local indicators
of spatial heteroscedasticity ('Ord' and 'Getis')
<doi:10.1007/s00168-011-0492-y>. The implementation of most of
the measures is described in 'Bivand' and 'Wong' (2018)
<doi:10.1007/s11749-018-0599-x>.
'spdep' >= 1.1-1 corresponds to 'spatialreg' >= 1.1-1, in which the model
fitting functions are deprecated and pass through to 'spatialreg', but
will mask those in 'spatialreg'. From versions 1.2-1, the functions will
be made defunct in 'spdep'.
For now 'spatialreg' only has functions from 'spdep', where they are shown
as deprecated. 'spatialreg' only loads the namespace of 'spdep'; if you
attach 'spdep', the same functions in the other package will be masked.
Some feed through adequately, others do not.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Angela Li [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Abhirup Mallik [ctb, trl],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
René Westerholt [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 1.1-5 dated 2020-06-29 and 1.1-7 dated 2021-04-03
spdep-1.1-5/spdep/inst/doc/nb.Rnw |only spdep-1.1-5/spdep/inst/doc/nb.pdf |only spdep-1.1-5/spdep/vignettes/nb.Rnw |only spdep-1.1-7/spdep/ChangeLog | 337 ++++++++++++++++++++++ spdep-1.1-7/spdep/DESCRIPTION | 10 spdep-1.1-7/spdep/MD5 | 141 ++++----- spdep-1.1-7/spdep/NAMESPACE | 5 spdep-1.1-7/spdep/NEWS.md |only spdep-1.1-7/spdep/R/LR.spsarlm.R | 16 - spdep-1.1-7/spdep/R/ME.R | 30 +- spdep-1.1-7/spdep/R/SpatialFiltering.R | 32 +- spdep-1.1-7/spdep/R/anova.sarlm.R | 8 spdep-1.1-7/spdep/R/bptest.sarlm.R | 8 spdep-1.1-7/spdep/R/dnearneigh.R | 99 ++++-- spdep-1.1-7/spdep/R/error.spsarlm.R | 42 +- spdep-1.1-7/spdep/R/impacts.R | 86 ++--- spdep-1.1-7/spdep/R/jacobian.R | 4 spdep-1.1-7/spdep/R/knearneigh.R | 37 -- spdep-1.1-7/spdep/R/kpgm_new.R | 102 +++--- spdep-1.1-7/spdep/R/lag.spsarlm.R | 12 spdep-1.1-7/spdep/R/lisa_perm.R |only spdep-1.1-7/spdep/R/mcmcsamp.R | 20 - spdep-1.1-7/spdep/R/mess.R | 96 +++--- spdep-1.1-7/spdep/R/nb2listw.R | 2 spdep-1.1-7/spdep/R/nb2listwdist.R |only spdep-1.1-7/spdep/R/poly2nb.R | 172 ++++------- spdep-1.1-7/spdep/R/s2sls.R | 64 ++-- spdep-1.1-7/spdep/R/sacsarlm.R | 12 spdep-1.1-7/spdep/R/sarlm.R | 74 ++-- spdep-1.1-7/spdep/R/soi.R | 6 spdep-1.1-7/spdep/R/spBreg.R | 58 +-- spdep-1.1-7/spdep/R/spautolm.R | 86 ++--- spdep-1.1-7/spdep/R/summary.spsarlm.R | 66 ++-- spdep-1.1-7/spdep/build/partial.rdb |only spdep-1.1-7/spdep/build/vignette.rds |binary spdep-1.1-7/spdep/inst/CITATION | 4 spdep-1.1-7/spdep/inst/ChangeLog | 337 ++++++++++++++++++++++ spdep-1.1-7/spdep/inst/doc/CO69.html | 99 +++--- spdep-1.1-7/spdep/inst/doc/nb.R | 283 ++---------------- spdep-1.1-7/spdep/inst/doc/nb.Rmd |only spdep-1.1-7/spdep/inst/doc/nb.html |only spdep-1.1-7/spdep/inst/doc/nb_igraph.R | 2 spdep-1.1-7/spdep/inst/doc/nb_igraph.Rmd | 3 spdep-1.1-7/spdep/inst/doc/nb_igraph.html | 96 +++--- spdep-1.1-7/spdep/inst/doc/nb_sf.R | 322 ++------------------- spdep-1.1-7/spdep/inst/doc/nb_sf.Rmd | 449 +++--------------------------- spdep-1.1-7/spdep/inst/doc/nb_sf.html | 240 +++++++++------- spdep-1.1-7/spdep/inst/doc/sids.R | 7 spdep-1.1-7/spdep/inst/doc/sids.Rmd | 9 spdep-1.1-7/spdep/inst/doc/sids.html | 154 ++++++---- spdep-1.1-7/spdep/inst/etc/misc/sids.zip |only spdep-1.1-7/spdep/inst/etc/misc/sids2.zip |only spdep-1.1-7/spdep/man/EBImoran.mc.Rd | 2 spdep-1.1-7/spdep/man/LOSH.Rd | 2 spdep-1.1-7/spdep/man/LOSH.cs.Rd | 2 spdep-1.1-7/spdep/man/LOSH.mc.Rd | 2 spdep-1.1-7/spdep/man/dnearneigh.Rd | 11 spdep-1.1-7/spdep/man/geary.test.Rd | 2 spdep-1.1-7/spdep/man/globalG.test.Rd | 2 spdep-1.1-7/spdep/man/graphneigh.Rd | 14 spdep-1.1-7/spdep/man/knearneigh.Rd | 22 - spdep-1.1-7/spdep/man/lm.morantest.sad.Rd | 2 spdep-1.1-7/spdep/man/localG.Rd | 11 spdep-1.1-7/spdep/man/localmoran.Rd | 15 - spdep-1.1-7/spdep/man/localmoran.exact.Rd | 2 spdep-1.1-7/spdep/man/localmoran.sad.Rd | 5 spdep-1.1-7/spdep/man/moran.test.Rd | 2 spdep-1.1-7/spdep/man/nb2listwdist.Rd |only spdep-1.1-7/spdep/man/nboperations.Rd | 16 - spdep-1.1-7/spdep/man/poly2nb.Rd | 14 spdep-1.1-7/spdep/src/dnn.c | 96 ++++-- spdep-1.1-7/spdep/src/init.c | 1 spdep-1.1-7/spdep/src/spdep.h | 2 spdep-1.1-7/spdep/vignettes/nb.Rmd |only spdep-1.1-7/spdep/vignettes/nb_igraph.Rmd | 3 spdep-1.1-7/spdep/vignettes/nb_sf.Rmd | 449 +++--------------------------- spdep-1.1-7/spdep/vignettes/refs.bib | 11 spdep-1.1-7/spdep/vignettes/sids.Rmd | 9 78 files changed, 2004 insertions(+), 2323 deletions(-)
Title: Filtering and Assessing the Sample Size of Tracking Data
Description: Functions to filter GPS/Argos locations, as well as assessing the sample size for the analysis of animal distributions. The filters remove temporal and spatial duplicates, fixes located at a given height from estimated high tide line, and locations with high error as described in Shimada et al. (2012) <doi:10.3354/meps09747> and Shimada et al. (2016) <doi:10.1007/s00227-015-2771-0>. Sample size for the analysis of animal distributions can be assessed by the conventional area-based approach or the alternative probability-based approach as described in Shimada et al. (2021) <doi:10.1111/2041-210X.13506>.
Author: Takahiro Shimada
Maintainer: Takahiro Shimada <taka.shimada@gmail.com>
Diff between SDLfilter versions 2.0.1 dated 2020-07-05 and 2.1.0 dated 2021-04-03
SDLfilter-2.0.1/SDLfilter/R/curtis.R |only SDLfilter-2.0.1/SDLfilter/data/curtis.rda |only SDLfilter-2.0.1/SDLfilter/man/curtis.Rd |only SDLfilter-2.0.1/SDLfilter/man/figures/README-example1.png |only SDLfilter-2.0.1/SDLfilter/man/figures/README-example2.png |only SDLfilter-2.1.0/SDLfilter/DESCRIPTION | 10 SDLfilter-2.1.0/SDLfilter/MD5 | 93 ++--- SDLfilter-2.1.0/SDLfilter/NEWS | 7 SDLfilter-2.1.0/SDLfilter/NEWS.md | 8 SDLfilter-2.1.0/SDLfilter/R/asymptote.R | 99 ++++- SDLfilter-2.1.0/SDLfilter/R/boot_area.R | 15 SDLfilter-2.1.0/SDLfilter/R/boot_overlap.R | 19 - SDLfilter-2.1.0/SDLfilter/R/ddfilter.R | 2 SDLfilter-2.1.0/SDLfilter/R/ddfilter_loop.R | 2 SDLfilter-2.1.0/SDLfilter/R/ddfilter_speed.R | 4 SDLfilter-2.1.0/SDLfilter/R/depthfilter.R | 2 SDLfilter-2.1.0/SDLfilter/R/dupfilter.R | 2 SDLfilter-2.1.0/SDLfilter/R/dupfilter_exact.R | 2 SDLfilter-2.1.0/SDLfilter/R/dupfilter_qi.R | 2 SDLfilter-2.1.0/SDLfilter/R/dupfilter_space.R | 2 SDLfilter-2.1.0/SDLfilter/R/dupfilter_time.R | 2 SDLfilter-2.1.0/SDLfilter/R/flatback.R |only SDLfilter-2.1.0/SDLfilter/R/track_param.R | 1 SDLfilter-2.1.0/SDLfilter/R/turtle.R | 2 SDLfilter-2.1.0/SDLfilter/R/turtle2.R | 2 SDLfilter-2.1.0/SDLfilter/R/ud_matrix.R |only SDLfilter-2.1.0/SDLfilter/R/ud_raster.R |only SDLfilter-2.1.0/SDLfilter/R/vmax.R | 2 SDLfilter-2.1.0/SDLfilter/R/vmaxlp.R | 10 SDLfilter-2.1.0/SDLfilter/README.md | 187 +++++++++-- SDLfilter-2.1.0/SDLfilter/build |only SDLfilter-2.1.0/SDLfilter/data/flatback.rda |only SDLfilter-2.1.0/SDLfilter/data/ud_matrix.rda |only SDLfilter-2.1.0/SDLfilter/data/ud_raster.rda |only SDLfilter-2.1.0/SDLfilter/inst/CITATION | 84 ++-- SDLfilter-2.1.0/SDLfilter/man/asymptote.Rd | 34 +- SDLfilter-2.1.0/SDLfilter/man/boot_area.Rd | 15 SDLfilter-2.1.0/SDLfilter/man/boot_overlap.Rd | 21 - SDLfilter-2.1.0/SDLfilter/man/ddfilter.Rd | 2 SDLfilter-2.1.0/SDLfilter/man/ddfilter_loop.Rd | 2 SDLfilter-2.1.0/SDLfilter/man/ddfilter_speed.Rd | 2 SDLfilter-2.1.0/SDLfilter/man/depthfilter.Rd | 2 SDLfilter-2.1.0/SDLfilter/man/dupfilter.Rd | 2 SDLfilter-2.1.0/SDLfilter/man/dupfilter_exact.Rd | 2 SDLfilter-2.1.0/SDLfilter/man/dupfilter_qi.Rd | 2 SDLfilter-2.1.0/SDLfilter/man/dupfilter_space.Rd | 2 SDLfilter-2.1.0/SDLfilter/man/dupfilter_time.Rd | 2 SDLfilter-2.1.0/SDLfilter/man/figures/unnamed-chunk-13-1.png |only SDLfilter-2.1.0/SDLfilter/man/figures/unnamed-chunk-7-1.png |only SDLfilter-2.1.0/SDLfilter/man/flatback.Rd |only SDLfilter-2.1.0/SDLfilter/man/turtle.Rd | 2 SDLfilter-2.1.0/SDLfilter/man/turtle2.Rd | 2 SDLfilter-2.1.0/SDLfilter/man/ud_matrix.Rd |only SDLfilter-2.1.0/SDLfilter/man/ud_raster.Rd |only SDLfilter-2.1.0/SDLfilter/man/vmax.Rd | 2 SDLfilter-2.1.0/SDLfilter/man/vmaxlp.Rd | 10 56 files changed, 465 insertions(+), 198 deletions(-)
Title: Kitty Pictures and Meows from R Console
Description: Get pictures of cats and their meows from your R
console.
Author: Indrajeet Patil [aut, cre, cph]
(<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between kittyR versions 1.0.0 dated 2021-01-18 and 1.1.0 dated 2021-04-03
kittyR-1.0.0/kittyR/build |only kittyR-1.1.0/kittyR/DESCRIPTION | 13 kittyR-1.1.0/kittyR/LICENSE | 4 kittyR-1.1.0/kittyR/MD5 | 39 +- kittyR-1.1.0/kittyR/NAMESPACE | 70 ++-- kittyR-1.1.0/kittyR/NEWS.md | 13 kittyR-1.1.0/kittyR/R/global_vars.R | 20 - kittyR-1.1.0/kittyR/R/kittyR.R | 230 ++++++++-------- kittyR-1.1.0/kittyR/R/kittypics_df_maker.R | 128 ++++---- kittyR-1.1.0/kittyR/R/meowR.R | 120 ++++---- kittyR-1.1.0/kittyR/R/reexports.R | 50 +-- kittyR-1.1.0/kittyR/README.md | 229 ++++++++------- kittyR-1.1.0/kittyR/inst/WORDLIST | 36 +- kittyR-1.1.0/kittyR/man/figures/README-kittyR1-1.png |binary kittyR-1.1.0/kittyR/man/figures/README-kittyR2-1.png |binary kittyR-1.1.0/kittyR/man/kittyR.Rd | 132 ++++----- kittyR-1.1.0/kittyR/man/kitty_pics_df.Rd | 51 +-- kittyR-1.1.0/kittyR/man/meowR.Rd | 4 kittyR-1.1.0/kittyR/tests/spelling.R | 12 kittyR-1.1.0/kittyR/tests/testthat.R | 8 kittyR-1.1.0/kittyR/tests/testthat/test-kitty_pics_df.R | 37 +- 21 files changed, 596 insertions(+), 600 deletions(-)
Title: Coefficients of Interrater Reliability - Generalized for
Randomly Incomplete Datasets
Description: Provides coefficients of interrater reliability that are generalized to cope with randomly incomplete (i.e. unbalanced) datasets without any imputation of missing values or any (row-wise or column-wise) omissions of actually available data. Applied to complete (balanced) datasets, these generalizations yield the same results as the common procedures, namely the Intraclass Correlation according to McGraw & Wong (1996) <doi:10.1037/1082-989X.1.1.30> and the Coefficient of Concordance according to Kendall & Babington Smith (1939) <doi:10.1214/aoms/1177732186>.
Author: Markus Brueckl [aut, cre], Florian Heuer [aut, trl]
Maintainer: Markus Brueckl <markus.brueckl@tu-berlin.de>
Diff between irrNA versions 0.1.4 dated 2018-04-11 and 0.2.0 dated 2021-04-03
DESCRIPTION | 12 - MD5 | 14 - R/iccNA.R | 87 +++++--- R/icc_corr.R | 534 +++++++++++++++++++++++++++---------------------------- R/kendallNA.R | 6 man/iccNA.Rd | 35 ++- man/icc_corr.Rd | 26 +- man/kendallNA.Rd | 6 8 files changed, 386 insertions(+), 334 deletions(-)
Title: Inference in Graphical Gaussian Models with Edge and Vertex
Symmetries
Description: Estimation, model selection and other aspects of
statistical inference in Graphical Gaussian models with edge and
vertex symmetries (Graphical Gaussian models with colours).
Documentation about 'gRc' is provided in the paper by Hojsgaard and
Lauritzen (2007, <doi:10.18637/jss.v023.i06>) and the paper by
Hojsgaard and Lauritzen (2008, <doi:10.1111/j.1467-9868.2008.00666.x>).
Author: Søren Højsgaard <sorenh@math.aau.dk>, Steffen L. Lauritzen <lauritzen@math.ku.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between gRc versions 0.4-3.2 dated 2019-04-17 and 0.4.4 dated 2021-04-03
gRc-0.4-3.2/gRc/R/RCON-IPM5.R |only gRc-0.4-3.2/gRc/R/add1drop1.R |only gRc-0.4-3.2/gRc/R/calculateVCOV.R |only gRc-0.4-3.2/gRc/R/cleverTraceMat.R |only gRc-0.4-3.2/gRc/R/comparecc.R |only gRc-0.4-3.2/gRc/R/display4.R |only gRc-0.4-3.2/gRc/R/fitMain.R |only gRc-0.4-3.2/gRc/R/getScoreAndInformation4.R |only gRc-0.4-3.2/gRc/R/rcon-IPM4.R |only gRc-0.4-3.2/gRc/R/rcor-IPM4.R |only gRc-0.4-3.2/gRc/R/rcox-ScoreMatching4.R |only gRc-0.4-3.2/gRc/R/rcox-Scoring.R |only gRc-0.4-3.2/gRc/R/rcox4.R |only gRc-0.4-3.2/gRc/R/repairK.R |only gRc-0.4-3.2/gRc/R/sets-SetOp-Lists.R |only gRc-0.4-3.2/gRc/R/split1join1.R |only gRc-0.4-3.2/gRc/R/stepwise4.R |only gRc-0.4-3.2/gRc/R/summary-vcov.R |only gRc-0.4-3.2/gRc/R/switchThetaK4.R |only gRc-0.4-3.2/gRc/R/testingMisc.R |only gRc-0.4-3.2/gRc/R/update4.R |only gRc-0.4-3.2/gRc/R/zzz-generatingClasscImplementation.R |only gRc-0.4-3.2/gRc/man/add1drop1.Rd |only gRc-0.4-3.2/gRc/man/fit.Rd |only gRc-0.4-3.2/gRc/man/fitInternal.Rd |only gRc-0.4-3.2/gRc/man/gRcox.Rd |only gRc-0.4-3.2/gRc/man/getSlot.Rd |only gRc-0.4-3.2/gRc/man/join1split1.Rd |only gRc-0.4-3.2/gRc/man/stepwise.Rd |only gRc-0.4-3.2/gRc/man/tr.Rd |only gRc-0.4-3.2/gRc/man/update.Rd |only gRc-0.4-3.2/gRc/src/clevertrace.c |only gRc-0.4-3.2/gRc/src/clevertrace.h |only gRc-0.4-3.2/gRc/src/rconipm2.c |only gRc-0.4-3.2/gRc/src/scorematching.c |only gRc-0.4-3.2/gRc/src/scorematching.h |only gRc-0.4-3.2/gRc/src/shd_print.c |only gRc-0.4-3.2/gRc/src/shd_print.h |only gRc-0.4-3.2/gRc/src/shd_utils.c |only gRc-0.4-3.2/gRc/src/shd_utils.h |only gRc-0.4.4/gRc/DESCRIPTION | 17 gRc-0.4.4/gRc/MD5 | 101 +++-- gRc-0.4.4/gRc/NAMESPACE | 164 +++++---- gRc-0.4.4/gRc/NEWS |only gRc-0.4.4/gRc/R/NAMESPACE.R |only gRc-0.4.4/gRc/R/RcppExports.R |only gRc-0.4.4/gRc/R/clever-trace.R |only gRc-0.4.4/gRc/R/coerce-parm.R |only gRc-0.4.4/gRc/R/display.R |only gRc-0.4.4/gRc/R/fit-doc.R |only gRc-0.4.4/gRc/R/fit-main.R |only gRc-0.4.4/gRc/R/fit-rcon-ipm.R |only gRc-0.4.4/gRc/R/fit-rcor-ipm.R |only gRc-0.4.4/gRc/R/fit-rcox-matching.R |only gRc-0.4.4/gRc/R/fit-rcox-scoring.R |only gRc-0.4.4/gRc/R/grc-summary-doc.R |only gRc-0.4.4/gRc/R/rcox.R |only gRc-0.4.4/gRc/R/repair-K.R |only gRc-0.4.4/gRc/R/score-information4.R |only gRc-0.4.4/gRc/R/set-op.R |only gRc-0.4.4/gRc/R/testing-add1drop1.R |only gRc-0.4.4/gRc/R/testing-comparecc.R |only gRc-0.4.4/gRc/R/testing-misc.R |only gRc-0.4.4/gRc/R/testing-split1join1.R |only gRc-0.4.4/gRc/R/testing-stepwise.R |only gRc-0.4.4/gRc/R/update.R |only gRc-0.4.4/gRc/R/utility4.R | 294 ++++++++++------- gRc-0.4.4/gRc/R/vcov.R |only gRc-0.4.4/gRc/R/xxx2yyy.R | 253 ++++++++------ gRc-0.4.4/gRc/R/zzz-generating-class.R |only gRc-0.4.4/gRc/inst/CITATION | 4 gRc-0.4.4/gRc/inst/include |only gRc-0.4.4/gRc/man/add1-drop1.Rd |only gRc-0.4.4/gRc/man/clever-trace.Rd |only gRc-0.4.4/gRc/man/coerce-parm.Rd |only gRc-0.4.4/gRc/man/comparecc.Rd | 95 ++--- gRc-0.4.4/gRc/man/fit-doc.Rd |only gRc-0.4.4/gRc/man/fit-main.Rd |only gRc-0.4.4/gRc/man/generating-class.Rd |only gRc-0.4.4/gRc/man/get-slot.Rd |only gRc-0.4.4/gRc/man/grc-summary.Rd |only gRc-0.4.4/gRc/man/internal.Rd | 155 -------- gRc-0.4.4/gRc/man/join-split.Rd |only gRc-0.4.4/gRc/man/rcox.Rd | 130 ++++--- gRc-0.4.4/gRc/man/score-information.Rd |only gRc-0.4.4/gRc/man/set-op.Rd |only gRc-0.4.4/gRc/man/step.Rd |only gRc-0.4.4/gRc/man/update-doc.Rd |only gRc-0.4.4/gRc/man/xxx2yyy.Rd |only gRc-0.4.4/gRc/src/RcppExports.cpp |only gRc-0.4.4/gRc/src/ct.cpp |only gRc-0.4.4/gRc/src/init.c | 30 - 92 files changed, 613 insertions(+), 630 deletions(-)
Title: Complex Split Procedures in Random Forests Through Candidate
Split Sampling
Description: Implements interaction forests [1], which are specific diversity forests, and
the basic form of diversity forests that uses univariable, binary splitting [2].
Interaction forests (IFs) are ensembles of decision trees that model quantitative and
qualitative interaction effects using bivariable splitting. IFs come with the
Effect Importance Measure (EIM), which can be used to identify variable pairs that
feature quantitative and qualitative interaction effects with high predictive
relevance. IFs and EIM focus on well interpretable forms of interactions.
The package also offers plot functions for visualising the estimated forms of
interaction effects.
Categorical, metric, and survival outcomes are supported.
This is a fork of the R package 'ranger' (main author: Marvin N. Wright) that
implements random forests using an efficient C++ implementation.
References:
[1] Hornung, R. & Boulesteix, A.-L. (2021) Interaction Forests: Identifying and
exploiting interpretable quantitative and qualitative interaction effects.
Technical Report No. 237, Department of Statistics, University of Munich
[2] Hornung, R. (2020) Diversity Forests: Using split sampling to allow for complex
split procedures in random forest. Technical Report No. 234, Department of Statistics,
University of Munich.
Author: Roman Hornung [aut, cre], Marvin N. Wright [ctb, cph]
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between diversityForest versions 0.3.0 dated 2021-04-01 and 0.3.1 dated 2021-04-03
diversityForest-0.3.0/diversityForest/NEWS |only diversityForest-0.3.1/diversityForest/DESCRIPTION | 8 - diversityForest-0.3.1/diversityForest/MD5 | 26 ++--- diversityForest-0.3.1/diversityForest/build/partial.rdb |binary diversityForest-0.3.1/diversityForest/inst/NEWS.Rd |only diversityForest-0.3.1/diversityForest/src/Forest.cpp | 8 - diversityForest-0.3.1/diversityForest/src/Tree.cpp | 52 ++++------ diversityForest-0.3.1/diversityForest/src/TreeClassification.cpp | 19 --- diversityForest-0.3.1/diversityForest/src/TreeClassification.h | 2 diversityForest-0.3.1/diversityForest/src/TreeProbability.cpp | 15 -- diversityForest-0.3.1/diversityForest/src/TreeProbability.h | 2 diversityForest-0.3.1/diversityForest/src/TreeRegression.cpp | 34 +----- diversityForest-0.3.1/diversityForest/src/TreeRegression.h | 2 diversityForest-0.3.1/diversityForest/src/TreeSurvival.cpp | 5 diversityForest-0.3.1/diversityForest/src/TreeSurvival.h | 2 15 files changed, 65 insertions(+), 110 deletions(-)
More information about diversityForest at CRAN
Permanent link
Title: Importing and Analysing SNP and Silicodart Data Generated by
Genome-Wide Restriction Fragment Analysis
Description: Functions are provided that facilitate the import and analysis of
SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated
by DarT (Diversity Arrays Technology). However, once SNP or related fragment
presence/absence data from any source is imported into a genlight object many
of the functions can be used. Functions are available for input and output of
SNP and silicodart data, for reporting on and filtering on various criteria
(e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency).
Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions
are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data
between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb],
Lindsay V. Clark [ctb],
Floriaan Devloo-Delva [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR versions 1.8.3 dated 2020-09-01 and 1.9.1 dated 2021-04-03
DESCRIPTION | 19 ++++--- MD5 | 77 ++++++++++++++++------------- NAMESPACE | 14 +++-- R/gl.dist.ind.r | 84 +++++++++----------------------- R/gl.filter.callrate.r | 12 ++-- R/gl.filter.locmetric.r |only R/gl.filter.overshoot.r | 7 ++ R/gl.filter.sexlinked.r | 2 R/gl.genleastcost.r | 13 +++-- R/gl.grm.r | 81 ++++++++++++++++++++----------- R/gl.ibd.r | 58 +++++++++++++++------- R/gl.pcoa.plot.3d.r | 85 ++++++++++++++++----------------- R/gl.pcoa.plot.r | 54 +++++++++++++++++++- R/gl.pcoa.r | 6 +- R/gl.plot.heatmap.r | 4 - R/gl.read.vcf.r | 56 ++++++++++----------- R/gl.recode.ind.r | 2 R/gl.recode.pop.r | 2 R/gl.report.hwe.r | 12 ++-- R/gl.report.locmetric.r |only R/gl.report.maf.r | 6 +- R/gl.report.parent.offspring.r | 18 ++++-- R/gl2bayescan.r | 28 ++++++++-- R/gl2hiphop.r |only R/utils.dart2genlight.r | 2 build/vignette.rds |binary inst/doc/IntroTutorial_dartR.R | 2 inst/doc/IntroTutorial_dartR.Rmd | 2 inst/doc/IntroTutorial_dartR.pdf |binary inst/doc/dartRTutorials.Rmd |only inst/doc/dartRTutorials.pdf |only man/gl.dist.ind.Rd | 18 +----- man/gl.filter.locmetric.Rd |only man/gl.grm.Rd | 17 +++--- man/gl.ibd.Rd | 4 - man/gl.pcoa.Rd | 6 +- man/gl.pcoa.plot.3d.Rd | 24 ++------- man/gl.pcoa.plot.Rd | 10 +++ man/gl.read.vcf.Rd | 14 +++-- man/gl.report.locmetric.Rd |only man/gl2hiphop.Rd |only man/util.outflank.MakeDiploidFSTMat.Rd | 42 ++++++++-------- vignettes/IntroTutorial_dartR.Rmd | 2 vignettes/dartRTutorials.Rmd |only 44 files changed, 433 insertions(+), 350 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), Peiran Liu (prliu@uw.edu), 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 6.4-0 dated 2019-10-18 and 7.0-4 dated 2021-04-03
bayesTFR-6.4-0/bayesTFR/data/correlation_predictors.txt |only bayesTFR-6.4-0/bayesTFR/data/iso3166.R |only bayesTFR-6.4-0/bayesTFR/data/iso3166.txt |only bayesTFR-7.0-4/bayesTFR/ChangeLog | 30 bayesTFR-7.0-4/bayesTFR/DESCRIPTION | 18 bayesTFR-7.0-4/bayesTFR/MD5 | 77 +- bayesTFR-7.0-4/bayesTFR/NAMESPACE | 31 bayesTFR-7.0-4/bayesTFR/R/diagnostics.R | 170 ++++ bayesTFR-7.0-4/bayesTFR/R/get_outputs.R | 612 ++++++++++++---- bayesTFR-7.0-4/bayesTFR/R/mcmc3_sampling.R | 152 --- bayesTFR-7.0-4/bayesTFR/R/mcmc_ini.R | 262 ++++-- bayesTFR-7.0-4/bayesTFR/R/mcmc_likelihoods.R | 6 bayesTFR-7.0-4/bayesTFR/R/mcmc_sampling.R | 381 ++++++++- bayesTFR-7.0-4/bayesTFR/R/mcmc_storage.R | 105 ++ bayesTFR-7.0-4/bayesTFR/R/mcmc_update.R | 585 ++++++++------- bayesTFR-7.0-4/bayesTFR/R/plot_functions.R | 448 +++++++---- bayesTFR-7.0-4/bayesTFR/R/predict_tfr.R | 192 +++-- bayesTFR-7.0-4/bayesTFR/R/run_mcmc.R | 294 ++++++- bayesTFR-7.0-4/bayesTFR/R/run_mcmc3.R | 14 bayesTFR-7.0-4/bayesTFR/R/tfr_median_set_new.R |only bayesTFR-7.0-4/bayesTFR/R/updated_functions.R |only bayesTFR-7.0-4/bayesTFR/R/wpp_data.R | 116 ++- bayesTFR-7.0-4/bayesTFR/data/correlation_predictors.rda |only bayesTFR-7.0-4/bayesTFR/data/iso3166.rda |only bayesTFR-7.0-4/bayesTFR/data/rawTFR.rda |only bayesTFR-7.0-4/bayesTFR/inst/CITATION | 4 bayesTFR-7.0-4/bayesTFR/man/bayesTFR-internal.Rd | 1 bayesTFR-7.0-4/bayesTFR/man/bayesTFR-package.Rd | 19 bayesTFR-7.0-4/bayesTFR/man/get.est.model.Rd |only bayesTFR-7.0-4/bayesTFR/man/get.tfr.estimation.Rd |only bayesTFR-7.0-4/bayesTFR/man/get.thinned.tfr.mcmc.Rd | 5 bayesTFR-7.0-4/bayesTFR/man/include.Rd | 2 bayesTFR-7.0-4/bayesTFR/man/plot-trajectories.Rd | 7 bayesTFR-7.0-4/bayesTFR/man/predict-tfr.Rd | 11 bayesTFR-7.0-4/bayesTFR/man/run-mcmc.Rd | 52 - bayesTFR-7.0-4/bayesTFR/man/run.tfr.mcmc.extra.Rd | 46 - bayesTFR-7.0-4/bayesTFR/man/run.tfr3.mcmc.Rd | 7 bayesTFR-7.0-4/bayesTFR/man/tfr.estimation.plot.Rd |only bayesTFR-7.0-4/bayesTFR/man/tfr.median.set.all.Rd |only bayesTFR-7.0-4/bayesTFR/man/tfr.parameter.names.Rd | 3 bayesTFR-7.0-4/bayesTFR/man/tfr.predict.extra.Rd | 3 bayesTFR-7.0-4/bayesTFR/man/tfr_raw_data.Rd |only bayesTFR-7.0-4/bayesTFR/src/bayesTFR_init.c | 4 bayesTFR-7.0-4/bayesTFR/src/mcmc_likelihood.c | 4 bayesTFR-7.0-4/bayesTFR/tests/run_tests.R | 2 bayesTFR-7.0-4/bayesTFR/tests/test_functions.R | 126 +++ 46 files changed, 2692 insertions(+), 1097 deletions(-)
Title: PARAFAC Analysis of Fluorescence Excitation-Emission Matrices
Description: Perform parallel factor analysis (PARAFAC: Hitchcock, 1927)
<doi:10.1002/sapm192761164> on fluorescence excitation-emission
matrices (FEEMs): handle scattering signal and inner filter
effect, scale the dataset, fit the model; perform split-half
validation or jack-knifing. A modified approach called
"randomised split-half" is also available. The package has a low
dependency footprint (only two direct dependencies not in core
or recommended; four total non-core/recommended dependencies)
and has been tested on a wide range of R versions (including R
as old as 3.3.3 from Debian Stretch).
Author: Ivan Krylov [aut, cre],
Timur Labutin [ths]
Maintainer: Ivan Krylov <ikrylov@laser.chem.msu.ru>
Diff between albatross versions 0.3-0 dated 2021-03-26 and 0.3-1 dated 2021-04-03
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/feemlist.R | 20 ++++++-------------- R/import.R | 7 ++++++- build/partial.rdb |binary inst/NEWS.Rd | 23 +++++++++++++++++------ man/feemcube.Rd | 3 +-- man/feemlist.Rd | 4 ++-- man/feemparafac.Rd | 6 +++--- man/plot.feem.Rd | 2 +- man/write.openfluor.Rd | 6 ++++-- tests/feemlist.R | 21 +++++++++++++++------ 12 files changed, 70 insertions(+), 52 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-09 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-30 0.1.0
2016-03-31 0.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-14 1.4.7
2019-12-16 1.4.6
2016-09-07 1.4.5
2014-03-28 1.4.4
2013-08-05 1.4.3
2013-07-08 1.4.2
2013-07-01 1.4.1
2013-04-29 1.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2007-09-05 1.3
2007-03-30 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-24 2.3.0
2017-11-24 2.2.1
2014-09-08 2.2
2014-03-29 2.1
2014-03-03 2.0.3
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 2.0-1 dated 2021-03-13 and 2.1-0 dated 2021-04-03
DESCRIPTION | 17 ++--- MD5 | 28 ++++---- NEWS | 33 ++++++++++ inst/doc/Nickname.txt | 2 inst/doc/bugfixes.pdf |binary inst/doc/datasets.R | 147 ++++++++++++++++++++++++---------------------- inst/doc/datasets.Rnw | 11 +++ inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 2 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.pdf |binary man/spatstat-package.Rd | 4 + vignettes/datasets.Rnw | 11 +++ 15 files changed, 161 insertions(+), 94 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, principal component analysis, correspondence analysis, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov, Kuiper or Sircombe-Hazelton L2 distances. Categorical provenance proxies such as chemical compositions are compared with the Aitchison and Bray-Curtis distances, and point-counting data with the chi-square distance. Also included are tools to plot compositional and point-counting data on ternary diagrams and point-counting data on radial plots, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions. Includes an intuitive query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 3.0 dated 2021-02-24 and 3.2 dated 2021-04-03
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- data/Namib.rda |binary inst/PT.csv | 34 +++++++++++++++++----------------- man/indscal.Rd | 2 +- 5 files changed, 26 insertions(+), 26 deletions(-)
Title: Interface to 'TensorFlow' Datasets
Description: Interface to 'TensorFlow' Datasets, a high-level library for
building complex input pipelines from simple, re-usable pieces.
See <https://www.tensorflow.org/guide> for additional
details.
Author: Daniel Falbel [ctb, cph, cre],
JJ Allaire [aut, cph],
Yuan Tang [aut] (<https://orcid.org/0000-0001-5243-233X>),
Kevin Ushey [aut],
RStudio [cph, fnd],
Google Inc. [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between tfdatasets versions 2.2.0 dated 2020-05-25 and 2.4.0 dated 2021-04-03
DESCRIPTION | 15 MD5 | 50 +- NAMESPACE | 3 NEWS.md | 6 R/dataset_methods.R | 3 R/feature_spec.R | 29 + R/input_fn.R | 2 R/package.R | 27 - README.md | 4 build/vignette.rds |binary inst/doc/feature_columns.R | 110 ++--- inst/doc/feature_columns.Rmd | 2 inst/doc/feature_columns.html | 404 +++++-------------- inst/doc/feature_spec.R | 126 +++--- inst/doc/feature_spec.html | 375 ++++-------------- inst/doc/introduction.Rmd | 10 inst/doc/introduction.html | 770 ++++++++++++++----------------------- man/feature_spec.Rd | 2 man/hearts.Rd | 6 man/input_fn.Rd | 2 man/next_batch.Rd | 2 man/reexports.Rd | 2 man/selectors.Rd | 4 tests/testthat/test-feature_spec.R | 45 ++ vignettes/feature_columns.Rmd | 2 vignettes/introduction.Rmd | 10 26 files changed, 741 insertions(+), 1270 deletions(-)
Title: Interface with Live Bikeshare Data
Description: Supplies a set of functions to interface with bikeshare data
following the General Bikeshare Feed Specification, allowing users to query
and accumulate tidy datasets for specified cities/bikeshare programs.
Author: Simon P. Couch [aut, cre],
Kaelyn Rosenberg [aut],
Mark Padgham [ctb]
Maintainer: Simon P. Couch <simonpatrickcouch@gmail.com>
Diff between gbfs versions 1.3.6 dated 2021-01-06 and 1.3.7 dated 2021-04-03
DESCRIPTION | 7 +++---- MD5 | 14 +++++++------- NEWS.md | 7 +++++++ R/get_static_feeds.R | 10 ---------- man/get_system_pricing_plans.Rd | 11 ----------- tests/testthat/test-static-feeds.R | 2 -- tests/testthat/test-utils.R | 2 +- tests/testthat/test-wrapper.R | 2 -- 8 files changed, 18 insertions(+), 37 deletions(-)