Title: Generate Disease-Specific Response Signatures from the
LINCS-L1000 Data
Description: Generates disease-specific drug-response profiles that are independent of time, concentration, and cell-line. Based on the cell lines used as surrogates, the returned profiles represent the unique transcriptional changes induced by a compound in a given disease.
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>),
Marieke Kuijjer [aut] (<https://orcid.org/0000-0001-6280-3130>)
Maintainer: Daniel Osorio <daniecos@uio.no>
Diff between retriever versions 0.1.0 dated 2021-10-08 and 0.2.0 dated 2021-10-15
DESCRIPTION | 9 +-- MD5 | 4 - R/retriever.R | 165 +++++++++++++++++++++++++++++----------------------------- 3 files changed, 92 insertions(+), 86 deletions(-)
Title: Life History Metrics from Matrix Population Models
Description: Functions for calculating life history metrics using matrix population models ('MPMs'). Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.
Author: Patrick Barks [aut] (<https://orcid.org/0000-0002-5947-8151>),
Danny Buss [ctb],
Pol Capdevila [aut] (<https://orcid.org/0000-0002-2842-4302>),
Hal Caswell [aut] (<https://orcid.org/0000-0003-4394-6894>),
Judy P. Che-Castaldo [aut] (<https://orcid.org/0000-0002-9118-9202>),
John Jackson [aut] (<https://orcid.org/0000-0002-4563-2840>),
Tamora James [aut] (<https://orcid.org/0000-0003-1363-4742>),
Owen Jones [aut, cre] (<https://orcid.org/0000-0001-5720-4686>),
Sam Levin [aut] (<https://orcid.org/0000-0002-3289-9925>),
William K. Petry [aut] (<https://orcid.org/0000-0002-5230-5987>),
Roberto Salguero-Gomez [aut] (<https://orcid.org/0000-0002-6085-4433>),
Caroline Schuette [ctb] (<https://orcid.org/0000-0002-2063-8736>),
Iain Stott [aut] (<https://orcid.org/0000-0003-2724-7436>),
Chelsea C. Thomas [aut] (<https://orcid.org/0000-0002-8155-9353>)
Maintainer: Owen Jones <jones@biology.sdu.dk>
Diff between Rage versions 1.1.0 dated 2021-07-09 and 1.2.0 dated 2021-10-15
Rage-1.1.0/Rage/R/Rage-package.R |only Rage-1.1.0/Rage/man/Rage-package.Rd |only Rage-1.2.0/Rage/DESCRIPTION | 8 Rage-1.2.0/Rage/MD5 | 182 ++++----- Rage-1.2.0/Rage/NAMESPACE | 2 Rage-1.2.0/Rage/NEWS.md | 9 Rage-1.2.0/Rage/R/entropy_d.R | 19 Rage-1.2.0/Rage/R/entropy_k.R | 6 Rage-1.2.0/Rage/R/gen_time.R | 14 Rage-1.2.0/Rage/R/life_expect.R | 19 Rage-1.2.0/Rage/R/lifetable_convert.R | 38 + Rage-1.2.0/Rage/R/longevity.R | 19 Rage-1.2.0/Rage/R/mature_.R | 22 - Rage-1.2.0/Rage/R/mpm_collapse.R | 22 - Rage-1.2.0/Rage/R/mpm_rearrange.R | 14 Rage-1.2.0/Rage/R/mpm_split.R | 16 Rage-1.2.0/Rage/R/mpm_standardize.R | 21 - Rage-1.2.0/Rage/R/mpm_to_.R | 62 +-- Rage-1.2.0/Rage/R/mpm_to_table.R | 278 +++++++++----- Rage-1.2.0/Rage/R/name_stages.R | 32 - Rage-1.2.0/Rage/R/net_repro_rate.R | 13 Rage-1.2.0/Rage/R/perturb_matrix.R | 11 Rage-1.2.0/Rage/R/perturb_stochastic.R | 6 Rage-1.2.0/Rage/R/perturb_trans.R | 25 - Rage-1.2.0/Rage/R/perturb_vr.R | 23 - Rage-1.2.0/Rage/R/plot_life_cycle.R | 10 Rage-1.2.0/Rage/R/pop_vectors.R | 13 Rage-1.2.0/Rage/R/qsd_converge.R | 60 +-- Rage-1.2.0/Rage/R/repro_stages.R | 19 Rage-1.2.0/Rage/R/shape_rep.R | 14 Rage-1.2.0/Rage/R/shape_surv.R | 59 +- Rage-1.2.0/Rage/R/standard_stages.R | 12 Rage-1.2.0/Rage/R/utils.R | 48 +- Rage-1.2.0/Rage/R/vital_rates.R | 30 - Rage-1.2.0/Rage/R/vr.R | 35 - Rage-1.2.0/Rage/R/vr_mat.R | 12 Rage-1.2.0/Rage/R/vr_vec.R | 10 Rage-1.2.0/Rage/README.md | 78 ++- Rage-1.2.0/Rage/build/vignette.rds |binary Rage-1.2.0/Rage/inst/WORDLIST | 11 Rage-1.2.0/Rage/inst/doc/a01_GettingStarted.R | 19 Rage-1.2.0/Rage/inst/doc/a01_GettingStarted.Rmd | 21 - Rage-1.2.0/Rage/inst/doc/a01_GettingStarted.html | 141 ++----- Rage-1.2.0/Rage/inst/doc/a02_VitalRates.R | 10 Rage-1.2.0/Rage/inst/doc/a02_VitalRates.Rmd | 153 +------ Rage-1.2.0/Rage/inst/doc/a02_VitalRates.html | 15 Rage-1.2.0/Rage/inst/doc/a03_LifeHistoryTraits.R | 4 Rage-1.2.0/Rage/inst/doc/a03_LifeHistoryTraits.Rmd | 15 Rage-1.2.0/Rage/inst/doc/a03_LifeHistoryTraits.html | 39 + Rage-1.2.0/Rage/inst/doc/a04_AgeFromStage.R | 56 +- Rage-1.2.0/Rage/inst/doc/a04_AgeFromStage.Rmd | 57 +- Rage-1.2.0/Rage/inst/doc/a04_AgeFromStage.html | 79 ++- Rage-1.2.0/Rage/inst/doc/a05_SuggestedQualityControl.R |only Rage-1.2.0/Rage/inst/doc/a05_SuggestedQualityControl.Rmd |only Rage-1.2.0/Rage/inst/doc/a05_SuggestedQualityControl.html |only Rage-1.2.0/Rage/man/age_from_stage.Rd | 62 +-- Rage-1.2.0/Rage/man/entropy_d.Rd | 16 Rage-1.2.0/Rage/man/entropy_k.Rd | 2 Rage-1.2.0/Rage/man/figures/unnamed-chunk-9-1.png |binary Rage-1.2.0/Rage/man/gen_time.Rd | 12 Rage-1.2.0/Rage/man/life_expect.Rd | 15 Rage-1.2.0/Rage/man/lifetable_convert.Rd | 38 + Rage-1.2.0/Rage/man/longevity.Rd | 16 Rage-1.2.0/Rage/man/mpm_collapse.Rd | 15 Rage-1.2.0/Rage/man/mpm_rearrange.Rd | 12 Rage-1.2.0/Rage/man/mpm_split.Rd | 16 Rage-1.2.0/Rage/man/mpm_standardize.Rd | 20 - Rage-1.2.0/Rage/man/mpm_to_table.Rd | 138 ++++-- Rage-1.2.0/Rage/man/name_stages.Rd | 16 Rage-1.2.0/Rage/man/net_repro_rate.Rd | 10 Rage-1.2.0/Rage/man/perturb_matrix.Rd | 4 Rage-1.2.0/Rage/man/perturb_trans.Rd | 14 Rage-1.2.0/Rage/man/perturb_vr.Rd | 16 Rage-1.2.0/Rage/man/plot_life_cycle.Rd | 6 Rage-1.2.0/Rage/man/pop_vectors.Rd | 10 Rage-1.2.0/Rage/man/qsd_converge.Rd | 46 +- Rage-1.2.0/Rage/man/repro_maturity.Rd | 19 Rage-1.2.0/Rage/man/repro_stages.Rd | 15 Rage-1.2.0/Rage/man/shape_rep.Rd | 4 Rage-1.2.0/Rage/man/shape_surv.Rd | 38 + Rage-1.2.0/Rage/man/standard_stages.Rd | 6 Rage-1.2.0/Rage/man/vital_rates.Rd | 10 Rage-1.2.0/Rage/man/vr.Rd | 35 - Rage-1.2.0/Rage/man/vr_mat.Rd | 8 Rage-1.2.0/Rage/man/vr_vec.Rd | 10 Rage-1.2.0/Rage/tests/testthat/test-mpm_to_.R | 12 Rage-1.2.0/Rage/tests/testthat/test-mpm_to_table.R | 1 Rage-1.2.0/Rage/tests/testthat/test-qsd_converge.R | 4 Rage-1.2.0/Rage/tests/testthat/test-vr.R | 4 Rage-1.2.0/Rage/tests/testthat/test-vr_vec.R | 4 Rage-1.2.0/Rage/vignettes/a01_GettingStarted.Rmd | 21 - Rage-1.2.0/Rage/vignettes/a02_VitalRates.Rmd | 153 +------ Rage-1.2.0/Rage/vignettes/a03_LifeHistoryTraits.Rmd | 15 Rage-1.2.0/Rage/vignettes/a04_AgeFromStage.Rmd | 57 +- Rage-1.2.0/Rage/vignettes/a05_SuggestedQualityControl.Rmd |only 95 files changed, 1427 insertions(+), 1354 deletions(-)
Title: Bayesian Network Learning with the PCHC and Related Algorithms
Description: Bayesian network learning using the PCHC algorithm. PCHC stands for PC Hill-Climbing, a new hybrid algorithm that uses PC to construct the skeleton of the BN and then
applies the Hill-Climbing greedy search. More algorithms and variants have been added, such as MMHC, FEDHC, and the Tabu search variants, PCTABU, MMTABU and FEDTABU.
The relevant papers are
a) Tsagris M. (2021). A new scalable Bayesian network learning algorithm with applications to economics. Computational Economics, 57(1): 341-367. <doi:10.1007/s10614-020-10065-7>.
b) Tsagris M. (2021). The FEDHC Bayesian network learning algorithm. <arXiv:2012.00113>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between pchc versions 0.5 dated 2021-03-21 and 0.6 dated 2021-10-15
DESCRIPTION | 20 +++---- MD5 | 81 ++++++++++++++++------------- NAMESPACE | 9 +-- R/big_read.R | 2 R/corpairs.R |only R/fedhc.R | 2 R/fedhc.boot.R |only R/fedhc.skel.R | 102 ------------------------------------- R/fedhc.skel.boot.R | 9 +-- R/fedtabu.R | 2 R/fedtabu.boot.R |only R/mmhc.R | 4 - R/mmhc.boot.R |only R/mmhc.skel.R | 128 ----------------------------------------------- R/mmhc.skel.boot.R | 9 +-- R/mmtabu.R | 2 R/mmtabu.boot.R |only R/pchc.R | 2 R/pchc.boot.R |only R/pchc.skel.R | 2 R/pchc.skel.boot.R | 9 +-- R/pcor.R | 6 +- R/pctabu.R | 2 R/pctabu.boot.R |only man/auc.Rd | 4 - man/big_read.Rd | 2 man/bn.skel.utils.Rd | 2 man/bnplot.Rd | 2 man/conf.edge.lower.Rd | 2 man/cor.fbed.Rd | 2 man/corpairs.Rd |only man/correls.Rd | 2 man/cortest.Rd | 2 man/fedhc.Rd | 6 +- man/fedhc.boot.Rd |only man/fedhc.skel.Rd | 26 +++++---- man/g2test_univariate.Rd | 2 man/mmhc.Rd | 2 man/mmhc.boot.Rd |only man/mmhc.skel.Rd | 2 man/mmpc.Rd | 2 man/pc.sel.Rd | 2 man/pchc-package.Rd | 6 +- man/pchc.Rd | 6 +- man/pchc.boot.Rd |only man/rbn.Rd | 2 man/rbn2.Rd | 4 + 47 files changed, 125 insertions(+), 344 deletions(-)
Title: Downloading, Reading and Analysing POF Microdata
Description: Provides tools for downloading, reading and analysing the POF,
a household survey from Brazilian Institute of Geography and Statistics - IBGE.
The data must be downloaded from the official website <https://www.ibge.gov.br/>.
Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre],
Luna Hidalgo [aut],
Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>
Diff between POFIBGE versions 0.1.3 dated 2021-06-24 and 0.1.4 dated 2021-10-15
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/example.R | 3 ++- R/get_pof.R | 6 +++++- R/pof_deflator.R | 2 +- R/pof_design.R | 17 +++++++++-------- R/pof_labeller.R | 2 +- R/read_pof.R | 3 ++- README.md | 4 ++-- 9 files changed, 34 insertions(+), 27 deletions(-)
Title: Downloading, Reading and Analysing PNS Microdata
Description: Provides tools for downloading, reading and analysing the PNS,
a household survey from Brazilian Institute of Geography and Statistics - IBGE.
The data must be downloaded from the official website <https://www.ibge.gov.br/>.
Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre],
Luna Hidalgo [aut],
Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>
Diff between PNSIBGE versions 0.1.4 dated 2021-06-24 and 0.1.5 dated 2021-10-15
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/get_pns.R | 6 +++++- R/pns_deflator.R | 2 +- R/pns_design.R | 17 +++++++++-------- R/pns_labeller.R | 2 +- R/read_pns.R | 3 ++- README.md | 4 ++-- 8 files changed, 31 insertions(+), 25 deletions(-)
Title: Read Stable Isotope Data Files
Description: Interface to the raw data file formats commonly encountered in scientific disciplines that make use of stable isotopes.
Author: Sebastian Kopf [aut, cre] (<https://orcid.org/0000-0002-2044-0201>),
Brett Davidheiser-Kroll [aut] (<https://orcid.org/0000-0002-6153-7851>),
Ilja Kocken [aut] (<https://orcid.org/0000-0003-2196-8718>)
Maintainer: Sebastian Kopf <sebastian.kopf@colorado.edu>
Diff between isoreader versions 1.3.0 dated 2021-02-16 and 1.3.1 dated 2021-10-15
DESCRIPTION | 11 MD5 | 42 - R/isoread.R | 1 build/vignette.rds |binary inst/doc/continuous_flow.R | 24 inst/doc/continuous_flow.Rmd | 6 inst/doc/continuous_flow.html | 1119 ++++++++++++++++-------------------------- inst/doc/development.html | 561 ++++++--------------- inst/doc/dual_inlet.R | 24 inst/doc/dual_inlet.Rmd | 6 inst/doc/dual_inlet.html | 971 +++++++++++++----------------------- inst/doc/operations.html | 899 ++++++++++++--------------------- inst/doc/quick_start.R | 18 inst/doc/quick_start.Rmd | 12 inst/doc/quick_start.html | 405 +++------------ inst/doc/scan.R | 24 inst/doc/scan.Rmd | 4 inst/doc/scan.html | 606 +++++++--------------- vignettes/continuous_flow.Rmd | 6 vignettes/dual_inlet.Rmd | 6 vignettes/quick_start.Rmd | 12 vignettes/scan.Rmd | 4 22 files changed, 1710 insertions(+), 3051 deletions(-)
Title: Relational Data Models
Description: Provides tools for working with multiple related
tables, stored as data frames or in a relational database. Multiple
tables (data and metadata) are stored in a compound object, which can
then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut],
Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Darko Bergant [aut],
Katharina Brunner [ctb],
James Wondrasek [ctb],
energie360° AG [fnd],
cynkra GmbH [fnd, cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between dm versions 0.2.4 dated 2021-09-30 and 0.2.5 dated 2021-10-15
dm-0.2.4/dm/man/sql_schema_create.Rd |only dm-0.2.4/dm/man/sql_schema_drop.Rd |only dm-0.2.4/dm/man/sql_schema_exists.Rd |only dm-0.2.4/dm/man/sql_schema_list.Rd |only dm-0.2.5/dm/DESCRIPTION | 15 - dm-0.2.5/dm/MD5 | 158 +++++----- dm-0.2.5/dm/NAMESPACE | 46 +-- dm-0.2.5/dm/NEWS.md | 28 + dm-0.2.5/dm/R/db-helpers.R | 93 +++--- dm-0.2.5/dm/R/db-interface.R | 53 --- dm-0.2.5/dm/R/deprecated.R | 55 +++ dm-0.2.5/dm/R/dm-from-src.R | 1 dm-0.2.5/dm/R/dm.R | 19 - dm-0.2.5/dm/R/dplyr.R | 42 +- dm-0.2.5/dm/R/error-helpers.R | 13 dm-0.2.5/dm/R/foreign-keys.R | 32 +- dm-0.2.5/dm/R/global.R | 2 dm-0.2.5/dm/R/import.R | 4 dm-0.2.5/dm/R/learn.R | 5 dm-0.2.5/dm/R/paste.R | 28 + dm-0.2.5/dm/R/rows-db.R | 238 ++++++---------- dm-0.2.5/dm/R/schema.R | 208 ++++++++------ dm-0.2.5/dm/R/upgrade.R | 11 dm-0.2.5/dm/R/waldo.R |only dm-0.2.5/dm/R/zoom.R | 8 dm-0.2.5/dm/R/zzz.R | 27 + dm-0.2.5/dm/README.md | 2 dm-0.2.5/dm/inst/doc/dm.html | 4 dm-0.2.5/dm/inst/doc/howto-dm-copy.html | 12 dm-0.2.5/dm/inst/doc/howto-dm-db.html | 4 dm-0.2.5/dm/inst/doc/howto-dm-df.html | 16 - dm-0.2.5/dm/inst/doc/howto-dm-rows.html | 4 dm-0.2.5/dm/inst/doc/howto-dm-theory.html | 16 - dm-0.2.5/dm/inst/doc/tech-dm-cdm.html | 4 dm-0.2.5/dm/inst/doc/tech-dm-class.html | 28 - dm-0.2.5/dm/inst/doc/tech-dm-draw.html | 4 dm-0.2.5/dm/inst/doc/tech-dm-filter.html | 22 - dm-0.2.5/dm/inst/doc/tech-dm-join.html | 18 - dm-0.2.5/dm/inst/doc/tech-dm-low-level.html | 4 dm-0.2.5/dm/inst/doc/tech-dm-zoom.Rmd | 8 dm-0.2.5/dm/inst/doc/tech-dm-zoom.html | 3 dm-0.2.5/dm/man/db_schema_create.Rd |only dm-0.2.5/dm/man/db_schema_drop.Rd |only dm-0.2.5/dm/man/db_schema_exists.Rd |only dm-0.2.5/dm/man/db_schema_list.Rd |only dm-0.2.5/dm/man/deprecated.Rd | 15 + dm-0.2.5/dm/man/dm_add_fk.Rd | 12 dm-0.2.5/dm/man/dm_get_all_fks.Rd | 1 dm-0.2.5/dm/man/dplyr_table_manipulation.Rd | 11 dm-0.2.5/dm/tests/testthat/_snaps/add-tbl.md | 23 + dm-0.2.5/dm/tests/testthat/_snaps/bind.md | 45 ++- dm-0.2.5/dm/tests/testthat/_snaps/check_suggested.md | 19 - dm-0.2.5/dm/tests/testthat/_snaps/disambiguate.md | 8 dm-0.2.5/dm/tests/testthat/_snaps/dm.md | 24 - dm-0.2.5/dm/tests/testthat/_snaps/dplyr.md | 276 +++++++++---------- dm-0.2.5/dm/tests/testthat/_snaps/error-helpers.md | 8 dm-0.2.5/dm/tests/testthat/_snaps/filter-dm.md | 17 + dm-0.2.5/dm/tests/testthat/_snaps/foreign-keys.md | 100 ++++-- dm-0.2.5/dm/tests/testthat/_snaps/paste.md | 88 ++++-- dm-0.2.5/dm/tests/testthat/_snaps/primary-keys.md | 112 +++---- dm-0.2.5/dm/tests/testthat/_snaps/rows-db.md | 47 +-- dm-0.2.5/dm/tests/testthat/_snaps/select-tbl.md | 5 dm-0.2.5/dm/tests/testthat/_snaps/select.md | 62 ++-- dm-0.2.5/dm/tests/testthat/_snaps/tidyr.md | 112 +++---- dm-0.2.5/dm/tests/testthat/_snaps/upgrade.md |only dm-0.2.5/dm/tests/testthat/_snaps/waldo.md |only dm-0.2.5/dm/tests/testthat/_snaps/zoom.md | 38 +- dm-0.2.5/dm/tests/testthat/dm/v2.rds |only dm-0.2.5/dm/tests/testthat/dm/v2_zoomed.rds |only dm-0.2.5/dm/tests/testthat/helper-config-db.R | 3 dm-0.2.5/dm/tests/testthat/helper-src.R | 2 dm-0.2.5/dm/tests/testthat/test-bind.R | 4 dm-0.2.5/dm/tests/testthat/test-check_suggested.R | 11 dm-0.2.5/dm/tests/testthat/test-db-interface.R | 53 ++- dm-0.2.5/dm/tests/testthat/test-dplyr.R | 81 ++++- dm-0.2.5/dm/tests/testthat/test-error-helpers.R | 2 dm-0.2.5/dm/tests/testthat/test-foreign-keys.R | 19 + dm-0.2.5/dm/tests/testthat/test-learn.R | 4 dm-0.2.5/dm/tests/testthat/test-paste.R | 5 dm-0.2.5/dm/tests/testthat/test-rows-db.R | 140 ++++++--- dm-0.2.5/dm/tests/testthat/test-schema.R | 91 +++--- dm-0.2.5/dm/tests/testthat/test-upgrade.R | 58 +++ dm-0.2.5/dm/tests/testthat/test-validate.R | 2 dm-0.2.5/dm/tests/testthat/test-waldo.R |only dm-0.2.5/dm/tests/testthat/test-zoom.R | 7 dm-0.2.5/dm/tests/testthat/test-zzx-deprecated.R | 2 dm-0.2.5/dm/vignettes/tech-dm-zoom.Rmd | 8 87 files changed, 1649 insertions(+), 1101 deletions(-)
Title: Archive and Unarchive Databases Using Flat Files
Description: Flat text files provide a robust, compressible, and portable
way to store tables from databases. This package provides convenient
functions for exporting tables from relational database connections
into compressed text files and streaming those text files back into
a database without requiring the whole table to fit in working memory.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Richard FitzJohn [ctb],
Brandon Bertelsen [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between arkdb versions 0.0.12 dated 2021-04-05 and 0.0.13 dated 2021-10-15
DESCRIPTION | 16 - MD5 | 27 +- NAMESPACE | 1 NEWS.md | 28 +- R/ark.R | 185 +++++++++++--- R/bulk_importers.R | 59 +++- R/streamable_table.R | 75 +++++- README.md | 123 ++++++++- build/vignette.rds |binary inst/doc/arkdb.html | 475 +++++++++++--------------------------- man/ark.Rd | 16 + man/arkdb-package.Rd | 1 man/streamable_parquet.Rd |only tests/testthat/test-arkdb.R | 194 +++++++++++++++ tests/testthat/test-bulk-import.R | 89 ++++--- 15 files changed, 807 insertions(+), 482 deletions(-)
Title: Utilities for using the 'COM(P)ADRE' Matrix Model Database
Description: Utility functions for interacting with the 'COMPADRE' and 'COMADRE' databases of matrix population models. Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.
Author: Patrick Barks [aut] (<https://orcid.org/0000-0002-5947-8151>),
Danny Buss [aut],
Roberto Salguero-Gomez [aut] (<https://orcid.org/0000-0002-6085-4433>),
Iain Stott [aut] (<https://orcid.org/0000-0003-2724-7436>),
William K. Petry [aut] (<https://orcid.org/0000-0002-5230-5987>),
Tamora James [aut] (<https://orcid.org/0000-0003-1363-4742>),
Owen Jones [aut, cre] (<https://orcid.org/0000-0001-5720-4686>),
Julia Jones [aut] (<https://orcid.org/0000-0001-9223-1778>),
Gesa Römer [aut] (<https://orcid.org/0000-0002-4859-5870>),
Sam Levin [aut] (<https://orcid.org/0000-0002-3289-9925>)
Maintainer: Owen Jones <jones@biology.sdu.dk>
Diff between Rcompadre versions 1.0.0 dated 2021-04-30 and 1.1.0 dated 2021-10-15
DESCRIPTION | 23 +- MD5 | 119 +++++++------- NAMESPACE | 2 NEWS.md | 12 + R/cdb_build_cdb.R |only R/cdb_fetch.R | 11 + R/cdb_flag.R | 231 ++++++++++++++++++---------- R/cdb_id_studies.R | 6 README.md | 36 ++-- build/vignette.rds |binary data/Comadre.rda |binary data/Compadre.rda |binary data/CompadreLegacy.rda |binary inst/WORDLIST | 7 inst/doc/a01_GettingStarted.Rmd | 25 +-- inst/doc/a01_GettingStarted.html | 94 ++++++----- inst/doc/a02_RcompadreTidy.R | 20 +- inst/doc/a02_RcompadreTidy.Rmd | 52 +++--- inst/doc/a02_RcompadreTidy.html | 70 ++++---- inst/doc/a03_VectorisingRcompadre.R | 58 +++---- inst/doc/a03_VectorisingRcompadre.Rmd | 75 ++++----- inst/doc/a03_VectorisingRcompadre.html | 98 +++++++---- inst/doc/a04_ObtainingReferences.R | 4 inst/doc/a04_ObtainingReferences.Rmd | 8 inst/doc/a04_ObtainingReferences.html | 56 ++++-- inst/doc/a05_UsingYourOwnData.R |only inst/doc/a05_UsingYourOwnData.Rmd |only inst/doc/a05_UsingYourOwnData.html |only man/Compadre.Rd | 4 man/cdb_build_cdb.Rd |only man/cdb_fetch.Rd | 7 man/cdb_flag.Rd | 91 ++++++++--- man/cdb_id_studies.Rd | 6 man/cdb_metadata.Rd | 1 tests/testthat/test-ClassUnion.R | 2 tests/testthat/test-CompadreDB-Methods.R | 2 tests/testthat/test-CompadreDB-Subsetting.R | 2 tests/testthat/test-CompadreDB-Tidyverse.R | 4 tests/testthat/test-CompadreDB.R | 2 tests/testthat/test-CompadreMat.R | 2 tests/testthat/test-as_cdb.R | 2 tests/testthat/test-cdb_build_cdb.R |only tests/testthat/test-cdb_check_species.R | 2 tests/testthat/test-cdb_collapse.R | 2 tests/testthat/test-cdb_compare.R | 2 tests/testthat/test-cdb_fetch.R | 2 tests/testthat/test-cdb_flag.R | 2 tests/testthat/test-cdb_flatten.R | 2 tests/testthat/test-cdb_id.R | 2 tests/testthat/test-cdb_id_stages.R | 2 tests/testthat/test-cdb_id_studies.R | 2 tests/testthat/test-cdb_mean_matF.R | 2 tests/testthat/test-cdb_metadata.R | 2 tests/testthat/test-cdb_rbind.R | 2 tests/testthat/test-cdb_unflatten.R | 2 tests/testthat/test-cdb_unnest.R | 2 tests/testthat/test-mpm_mean.R | 6 tests/testthat/test-mpm_methods.R | 2 tests/testthat/test-string_representation.R | 2 vignettes/a01_GettingStarted.Rmd | 25 +-- vignettes/a02_RcompadreTidy.Rmd | 52 +++--- vignettes/a03_VectorisingRcompadre.Rmd | 75 ++++----- vignettes/a04_ObtainingReferences.Rmd | 8 vignettes/a05_UsingYourOwnData.Rmd |only 64 files changed, 761 insertions(+), 569 deletions(-)
Title: Creates Plots Accompanying Bayesian Diagnostic Test Accuracy
Meta-Analyses
Description: Function to create forest plots. Functions to use posterior samples from Bayesian bivariate meta-analysis model, Bayesian hierarchical summary receiver operating characteristic (HSROC) meta-analysis model or Bayesian latent class (LC) meta-analysis model to create Summary Receiver Operating Characteristic (SROC) plots using methods described by Harbord et al (2007)<doi:10.1093/biostatistics/kxl004>.
Author: Ian Schiller [aut, cre],
Nandini Dendukuri [ctb]
Maintainer: Ian Schiller <ian.schiller@rimuhc.ca>
Diff between DTAplots versions 1.0.2.4 dated 2021-03-17 and 1.0.2.5 dated 2021-10-15
DESCRIPTION | 8 - MD5 | 17 +- NEWS | 14 ++ R/Forest.R | 211 ++++++++++++++++++----------------- R/SROC_rjags.R | 8 - data/datalist |only data/posterior_samples_Bivariate.rda |binary data/posterior_samples_LC.rda |binary man/Forest.Rd | 56 ++++++--- man/SROC_rjags.Rd | 4 10 files changed, 181 insertions(+), 137 deletions(-)
Title: Downloading, Reading and Analysing PNAD COVID19 Microdata
Description: Provides tools for downloading, reading and analysing the PNAD COVID19,
a household survey from Brazilian Institute of Geography and Statistics - IBGE.
The data must be downloaded from the official website <https://www.ibge.gov.br/>.
Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre],
Luna Hidalgo [aut],
Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>
Diff between COVIDIBGE versions 0.1.5 dated 2021-06-24 and 0.1.6 dated 2021-10-15
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/covid_deflator.R | 2 +- R/covid_design.R | 5 +++-- R/covid_labeller.R | 2 +- R/get_covid.R | 6 +++++- R/read_covid.R | 3 ++- README.md | 4 ++-- 8 files changed, 25 insertions(+), 19 deletions(-)
Title: Create Credit State Migration (Transition) Matrices
Description: Tools to help convert credit risk data at two time points
into traditional credit state migration (aka, "transition") matrices.
At a higher level, 'migrate' is intended to help an analyst understand
how risk moved in their credit portfolio over a time interval.
References to this methodology include:
1. Schuermann, T. (2008) <doi:10.1002/9780470061596.risk0409>.
2. Perederiy, V. (2017) <arXiv:1708.00062>.
Author: Michael Thomas [aut, cre],
Brad Lindblad [ctb]
Maintainer: Michael Thomas <mthomas@ketchbrookanalytics.com>
Diff between migrate versions 0.3.0 dated 2020-12-07 and 0.4.0 dated 2021-10-15
DESCRIPTION | 10 - LICENSE | 2 MD5 | 28 +-- NAMESPACE | 1 NEWS.md | 30 +++ R/build_matrix.R | 203 +++++++++++++---------- R/migrate.R | 378 +++++++++++++++++++++++++------------------- README.md | 91 ++++++---- build/vignette.rds |binary inst/doc/migrate.R | 43 +++-- inst/doc/migrate.Rmd | 44 +++-- inst/doc/migrate.html | 424 ++++++++++++++------------------------------------ man/build_matrix.Rd | 34 ++-- man/migrate.Rd | 74 ++++---- vignettes/migrate.Rmd | 44 +++-- 15 files changed, 700 insertions(+), 706 deletions(-)
Title: The Induced Smoothed Lasso
Description: An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper: Cilluffo, G., Sottile, G., La Grutta, S. and Muggeo, V. (2019) The Induced Smoothed lasso: A practical framework for hypothesis testing in high dimensional regression. <doi:10.1177/0962280219842890>, and discussed in a tutorial: Sottile, G., Cilluffo, G., and Muggeo, V. (2019) The R package islasso: estimation and hypothesis testing in lasso regression. <doi:10.13140/RG.2.2.16360.11521>.
Author: Gianluca Sottile [aut, cre],
Giovanna Cilluffo [aut, ctb],
Vito MR Muggeo [aut, cre]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between islasso versions 1.3.1 dated 2021-06-16 and 1.4.0 dated 2021-10-15
DESCRIPTION | 8 +- MD5 | 105 +++++++++++++++++++++------- NAMESPACE | 51 +++++++++++-- NEWS | 15 ++++ R/S3methods_islasso.R | 35 ++++----- R/S3methods_islasso.path.R |only R/confint_and_auxiliary.R | 33 ++++++++ R/islasso.R | 58 +++++++++++---- R/islasso.path.R |only inst/doc/islasso.R | 74 +++++++++++++++----- inst/doc/islasso.Rmd | 109 ++++++++++++++++++++++------- inst/doc/islasso.pdf |binary man/GoF.islasso.path.Rd |only man/aic.islasso.Rd | 20 ++--- man/anova.islasso.Rd | 8 +- man/confint.islasso.Rd | 29 +++++++ man/is.control.Rd | 11 +- man/islasso-internal.Rd | 12 ++- man/islasso-package.Rd | 21 +++-- man/islasso.Rd | 16 ++-- man/islasso.path.Rd |only man/plot.islasso.Rd | 12 ++- man/plot.islasso.path.Rd |only man/predict.islasso.Rd | 15 ++-- man/predict.islasso.path.Rd |only man/summary.islasso.Rd | 9 ++ man/summary.islasso.path.Rd |only src/dev_grad_hess.f90 | 53 +++++++++++--- src/init.c | 8 -- src/islasso.h | 34 +++------ src/islasso2.f90 | 147 ++++++++++++++++++++++++--------------- src/islasso_glm.f90 | 162 +++++++++++++++++++++++++------------------- src/trace_islasso.c | 32 ++++++++ vignettes/islasso.Rmd | 109 ++++++++++++++++++++++------- vignettes/islasso_cache |only 35 files changed, 840 insertions(+), 346 deletions(-)
Title: Graphical User Interface ('shiny' App) for 'brms'
Description: A graphical user interface (GUI) for fitting Bayesian
regression models using the package 'brms' which in turn relies on
'Stan' (<https://mc-stan.org/>). The 'shinybrms' GUI is a 'shiny'
app.
Author: Frank Weber [aut, cre] (<https://orcid.org/0000-0002-4842-7922>),
Thomas Park [ctb, cph] ('Bootswatch' theme "United"),
Twitter, Inc. [ctb, cph] ('Bootstrap' (basis for the 'Bootswatch' theme
"United")),
Google, LLC [ctb, cph] ("Open Sans" font)
Maintainer: Frank Weber <fweber144@protonmail.com>
Diff between shinybrms versions 1.5.1 dated 2021-03-06 and 1.5.2 dated 2021-10-15
DESCRIPTION | 16 MD5 | 40 NEWS.md | 344 ++---- R/launch_shinybrms.R | 8 README.md | 82 - inst/CITATION | 15 inst/shinybrms_app/app.R | 573 ++++------ inst/shinybrms_app/tests/shinytest/bacteria_run_linux-expected/006.json | 2 inst/shinybrms_app/tests/shinytest/bacteria_run_linux-expected/007.json | 2 inst/shinybrms_app/tests/shinytest/bacteria_run_linux-expected/008.json | 2 inst/shinybrms_app/tests/shinytest/bacteria_run_linux-expected/009.json | 2 inst/shinybrms_app/tests/shinytest/bacteria_run_windows-expected/005.json | 4 inst/shinybrms_app/tests/shinytest/bacteria_run_windows-expected/006.json | 6 inst/shinybrms_app/tests/shinytest/bacteria_run_windows-expected/007.json | 8 inst/shinybrms_app/tests/shinytest/bacteria_run_windows-expected/008.json | 8 inst/shinybrms_app/tests/shinytest/bacteria_run_windows-expected/009.json | 14 man/launch_shinybrms.Rd | 3 tests/testthat/test-bacteria.R | 4 tests/testthat/test-interactions.R | 2 tests/testthat/test-priors.R | 6 tests/testthat/test-react.R | 77 - 21 files changed, 589 insertions(+), 629 deletions(-)
Title: Estimation and Projection of Age-Specific Mortality Rates
Description: Age-specific mortality rates are estimated and projected using
the Kannisto, Lee-Carter and related methods as described in
Sevcikova et al. (2016) <doi:10.1007/978-3-319-26603-9_15>.
Author: Hana Sevcikova, Nan Li and Patrick Gerland
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between MortCast versions 2.6-0 dated 2021-10-08 and 2.6-1 dated 2021-10-15
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary data/MLT1Ylookup.rda |binary data/MLTlookup.rda |binary 6 files changed, 13 insertions(+), 9 deletions(-)
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Description: Functions to accompany A. Gelman and J. Hill, Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge University Press, 2007.
Author: Andrew Gelman [aut],
Yu-Sung Su [aut, cre],
Masanao Yajima [ctb],
Jennifer Hill [ctb],
Maria Grazia Pittau [ctb],
Jouni Kerman [ctb],
Tian Zheng [ctb],
Vincent Dorie [ctb]
Maintainer: Yu-Sung Su <suyusung@tsinghua.edu.cn>
Diff between arm versions 1.11-2 dated 2020-07-27 and 1.12-2 dated 2021-10-15
CHANGELOG | 17 +++++++++++++---- DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 4 ---- R/balance.R | 2 +- man/lalonde.Rd | 2 +- 6 files changed, 25 insertions(+), 20 deletions(-)
Title: Tools for Analysing and Visualising Workplace Analytics Data
Description: Opinionated functions that enable easier and faster
analysis of Workplace Analytics data. There are three main types of functions in 'wpa':
(i) Standard functions create a 'ggplot' visual or a summary table based on a specific
Workplace Analytics metric; (2) Report Generation functions generate HTML reports on
a specific analysis area, e.g. Collaboration; (3) Other miscellaneous functions cover
more specific applications (e.g. Subject Line text mining) of Workplace Analytics data.
This package adheres to 'tidyverse' principles and works well with the pipe syntax.
'wpa' is built with the beginner-to-intermediate R users in mind, and is optimised for
simplicity.
Author: Martin Chan [aut, cre],
Carlos Morales [aut],
Mark Powers [ctb],
Ainize Cidoncha [ctb],
Rosamary Ochoa Vargas [ctb],
Tannaz Sattari [ctb],
Lucas Hogner [ctb],
Jasminder Thind [ctb],
Simone Liebal [ctb],
Aleksey Ashikhmin [ctb],
Ellen Trinklein [ctb],
Microsoft Corporation [cph]
Maintainer: Martin Chan <martin.chan@microsoft.com>
Diff between wpa versions 1.6.1 dated 2021-09-01 and 1.6.2 dated 2021-10-15
wpa-1.6.1/wpa/build |only wpa-1.6.1/wpa/inst/doc |only wpa-1.6.1/wpa/vignettes |only wpa-1.6.2/wpa/DESCRIPTION | 9 - wpa-1.6.2/wpa/MD5 | 51 +++----- wpa-1.6.2/wpa/NEWS.md | 6 wpa-1.6.2/wpa/R/em_data.R | 57 ++++++++- wpa-1.6.2/wpa/R/flex_index.R | 78 ++++-------- wpa-1.6.2/wpa/R/network_g2g.R | 5 wpa-1.6.2/wpa/R/network_p2p.R | 13 +- wpa-1.6.2/wpa/R/period_change.R | 2 wpa-1.6.2/wpa/R/plot_flex_index.R | 6 wpa-1.6.2/wpa/R/validation_report.R | 45 ++++++- wpa-1.6.2/wpa/R/workpatterns_area.R | 5 wpa-1.6.2/wpa/R/workpatterns_classify_bw.R | 3 wpa-1.6.2/wpa/R/workpatterns_rank.R | 182 +++++++++++++++-------------- wpa-1.6.2/wpa/R/workpatterns_report.R | 16 +- wpa-1.6.2/wpa/README.md | 10 + wpa-1.6.2/wpa/data/em_data.rda |binary wpa-1.6.2/wpa/man/em_data.Rd | 57 ++++++++- wpa-1.6.2/wpa/man/flex_index.Rd | 14 +- wpa-1.6.2/wpa/man/network_g2g.Rd | 5 wpa-1.6.2/wpa/man/network_p2p.Rd | 4 wpa-1.6.2/wpa/man/period_change.Rd | 2 wpa-1.6.2/wpa/man/validation_report.Rd | 4 wpa-1.6.2/wpa/man/workpatterns_area.Rd | 5 wpa-1.6.2/wpa/man/workpatterns_rank.Rd | 20 ++- 27 files changed, 403 insertions(+), 196 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.12.1 dated 2021-09-05 and 2.13.0 dated 2021-10-15
DESCRIPTION | 15 MD5 | 54 +- NAMESPACE | 3 R/generic.predict.rfsrc.R | 4 R/imbalanced.rfsrc.R | 17 R/impute.rfsrc.R | 51 +- R/partial.rfsrc.R | 1 R/rfsrc.R | 8 R/sidClustering.rfsrc.R | 1 R/utilities.R | 9 R/utilities.data.R | 400 +++++++++---------- R/utilities.factor.R | 4 R/utilities.imbalanced.R | 43 +- configure | 18 configure.ac | 2 inst/NEWS | 15 man/housing.Rd | 7 man/imbalanced.rfsrc.Rd | 78 ++- man/impute.rfsrc.Rd | 13 man/max.subtree.rfsrc.Rd | 10 man/nutrigenomic.Rd | 34 + man/predict.rfsrc.Rd | 6 man/randomForestSRC_package.Rd | 64 +-- man/rfsrc.Rd | 234 ++++++----- man/sidClustering.rfsrc.Rd | 6 src/R_init_randomForestSRC.c | 8 src/randomForestSRC.c | 859 ++++++++++++++++++++++++++++++++++++++--- src/randomForestSRC.h | 23 + 28 files changed, 1448 insertions(+), 539 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: A Grammar of Clinical Data Summary
Description: A tool created to simplify the data manipulation necessary to create clinical reports.
Author: Eli Miller [aut] (<https://orcid.org/0000-0002-2127-9456>),
Mike Stackhouse [aut, cre] (<https://orcid.org/0000-0001-6030-723X>),
Ashley Tarasiewicz [aut],
Nathan Kosiba [aut] (<https://orcid.org/0000-0001-5359-4234>),
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 0.4.1 dated 2021-07-13 and 0.4.2 dated 2021-10-15
DESCRIPTION | 8 +-- MD5 | 22 ++++----- NEWS.md | 4 + README.md | 2 inst/doc/Tplyr.html | 13 ++--- inst/doc/count.html | 1 inst/doc/denom.html | 97 ++++++++++++++++++++--------------------- inst/doc/desc.html | 1 inst/doc/options.html | 1 inst/doc/shift.html | 1 inst/doc/table.html | 1 tests/testthat/test-pop_data.R | 2 12 files changed, 82 insertions(+), 71 deletions(-)
Title: Data Processing after Running 'GGIR' for Accelerometer Data
Description: Generate all necessary R/Rmd/shell files for data processing after running 'GGIR' (v2.4.0) for accelerometer data. In part 1, all csv files in the GGIR output directory were read, transformed and then merged. In part 2, the GGIR output files were checked and summarized in one excel sheet. In part 3, the merged data was cleaned according to the number of valid hours on each night and the number of valid days for each subject. In part 4, the cleaned activity data was imputed by the average Euclidean norm minus one (ENMO) over all the valid days for each subject. Finally, a comprehensive report of data processing was created using Rmarkdown, and the report includes few exploratory plots and multiple commonly used features extracted from minute level actigraphy data.
Author: Wei Guo [aut, cre],
Vadim Zipunnikov [aut],
Kathleen Merikangas [aut]
Maintainer: Wei Guo <wei.guo3@nih.gov>
Diff between postGGIR versions 2.4.0 dated 2021-07-14 and 2.4.0.1 dated 2021-10-15
postGGIR-2.4.0.1/postGGIR/DESCRIPTION | 13 postGGIR-2.4.0.1/postGGIR/MD5 | 42 postGGIR-2.4.0.1/postGGIR/R/Time2.R | 6 postGGIR-2.4.0.1/postGGIR/R/part0_maincall.R | 25 postGGIR-2.4.0.1/postGGIR/R/part2_summary.pipeline.R | 13 postGGIR-2.4.0.1/postGGIR/inst/doc/features.dictionary.xlsx |binary postGGIR-2.4.0.1/postGGIR/inst/doc/postGGIR.R | 101 - postGGIR-2.4.0.1/postGGIR/inst/doc/postGGIR.Rmd | 379 ++-- postGGIR-2.4.0.1/postGGIR/inst/doc/postGGIR.html | 880 +++++----- postGGIR-2.4.0.1/postGGIR/inst/doc/postGGIR.output.description.xlsx |binary postGGIR-2.4.0.1/postGGIR/inst/doc/quickguide.postGGIR.txt |only postGGIR-2.4.0.1/postGGIR/inst/template/STUDYNAME_part0.maincall.txt | 100 - postGGIR-2.4.0.1/postGGIR/inst/template/features.dictionary.xlsx |binary postGGIR-2.4.0.1/postGGIR/inst/template/part5_postGGIR.report.Rmd | 7 postGGIR-2.4.0.1/postGGIR/inst/template/part6_postGGIR.NonWear.report.Rmd | 2 postGGIR-2.4.0.1/postGGIR/inst/template/part7a_JIVE_1_featureExtraction.Rmd | 34 postGGIR-2.4.0.1/postGGIR/inst/template/part7b_JIVE_2_featureMerge.Rmd | 6 postGGIR-2.4.0.1/postGGIR/inst/template/part7c_JIVE_3_runJIVE.Rmd |only postGGIR-2.4.0.1/postGGIR/inst/template/part7d_JIVE_4_somefeatures_weekday.Rmd |only postGGIR-2.4.0.1/postGGIR/man/afterggir.Rd | 6 postGGIR-2.4.0.1/postGGIR/vignettes/postGGIR.Rmd | 379 ++-- postGGIR-2.4.0.1/postGGIR/vignettes/postGGIR.output.description.xlsx |binary postGGIR-2.4.0/postGGIR/inst/template/part7c_JIVE_3_excelReport.Rmd |only postGGIR-2.4.0/postGGIR/inst/template/part7d_JIVE_4_runJive.Rmd |only postGGIR-2.4.0/postGGIR/inst/template/part7e_JIVE_5_somefeatures_weekday.Rmd |only 25 files changed, 1175 insertions(+), 818 deletions(-)
Title: Multiple Imputation by Chained Equations with Multilevel Data
Description: Addons for the 'mice' package to perform multiple imputation using chained equations with two-level data. Includes imputation methods dedicated to sporadically and systematically missing values. Imputation of continuous, binary or count variables are available. Following the recommendations of Audigier, V. et al (2018) <doi:10.1214/18-STS646>, the choice of the imputation method for each variable can be facilitated by a default choice tuned according to the structure of the incomplete dataset. Allows parallel calculation and overimputation for 'mice'.
Author: Vincent Audigier [aut, cre] (CNAM MSDMA team),
Matthieu Resche-Rigon [aut] (INSERM ECSTRA team)
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between micemd versions 1.7.0 dated 2021-07-30 and 1.8.0 dated 2021-10-15
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/mice.impute.2l.2stage.bin.intern.R | 9 ++++----- R/mice.impute.2l.2stage.pois.intern.R | 9 ++++----- R/mice.impute.2l.glm.norm.R | 2 +- man/mice.par.Rd | 2 +- 6 files changed, 19 insertions(+), 21 deletions(-)
Title: Fit and Simulate Generalised Hypergeometric Ensembles of Graphs
Description: Provides functions for model fitting and selection of generalised hypergeometric ensembles of random graphs (gHypEG).
To learn how to use it, check the vignettes for a quick tutorial.
Please reference its use as Casiraghi, G., Nanumyan, V. (2019) <doi:10.5281/zenodo.2555300>
together with those relevant references from the one listed below.
The package is based on the research developed at the Chair of Systems Design, ETH Zurich.
Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2016) <arXiv:1607.02441>.
Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2017) <doi:10.1007/978-3-319-67256-4_11>.
Casiraghi, G., (2017) <arXiv:1702.02048>
Brandenberger, L., Casiraghi, G., Nanumyan, V., Schweitzer, F. (2019) <doi:10.1145/3341161.3342926>
Casiraghi, G. (2019) <doi:10.1007/s41109-019-0241-1>.
Casiraghi, G., Nanumyan, V. (2021) <doi:10.1038/s41598-021-92519-y>.
Casiraghi, G. (2021) <doi:10.1088/2632-072X/ac0493>.
Author: Giona Casiraghi [aut, cre] (<https://orcid.org/0000-0003-0233-5747>),
Vahan Nanumyan [aut] (<https://orcid.org/0000-0001-9054-3217>),
Laurence Brandenberger [ctb],
Giacomo Vaccario [ctb]
Maintainer: Giona Casiraghi <giona@ethz.ch>
Diff between ghypernet versions 1.0.1 dated 2020-10-21 and 1.1.0 dated 2021-10-15
ghypernet-1.0.1/ghypernet/man/ComputeXi.Rd |only ghypernet-1.0.1/ghypernet/man/linkSignificance.Rd |only ghypernet-1.1.0/ghypernet/DESCRIPTION | 21 ghypernet-1.1.0/ghypernet/MD5 | 90 ghypernet-1.1.0/ghypernet/NAMESPACE | 3 ghypernet-1.1.0/ghypernet/NEWS.md | 19 ghypernet-1.1.0/ghypernet/R/auxilliary.R | 11 ghypernet-1.1.0/ghypernet/R/blockmodel.R | 172 ghypernet-1.1.0/ghypernet/R/computexi.R | 4 ghypernet-1.1.0/ghypernet/R/data.R | 4 ghypernet-1.1.0/ghypernet/R/deprecated.R | 16 ghypernet-1.1.0/ghypernet/R/endogenousstats.R | 99 ghypernet-1.1.0/ghypernet/R/ghype.R | 4 ghypernet-1.1.0/ghypernet/R/igraphintegration.R | 2 ghypernet-1.1.0/ghypernet/R/logl.R | 2 ghypernet-1.1.0/ghypernet/R/nrm.R | 6 ghypernet-1.1.0/ghypernet/R/nrmSelection.R | 2 ghypernet-1.1.0/ghypernet/R/omega.R | 2 ghypernet-1.1.0/ghypernet/R/residuals.nrm.R | 2 ghypernet-1.1.0/ghypernet/R/stats.R | 2 ghypernet-1.1.0/ghypernet/R/tests.R | 41 ghypernet-1.1.0/ghypernet/README.md | 13 ghypernet-1.1.0/ghypernet/build/vignette.rds |binary ghypernet-1.1.0/ghypernet/inst/doc/Significantlinks.R | 4 ghypernet-1.1.0/ghypernet/inst/doc/Significantlinks.Rmd | 6 ghypernet-1.1.0/ghypernet/inst/doc/Significantlinks.html | 321 - ghypernet-1.1.0/ghypernet/inst/doc/Tutorial_NRM.R | 83 ghypernet-1.1.0/ghypernet/inst/doc/Tutorial_NRM.Rmd | 159 ghypernet-1.1.0/ghypernet/inst/doc/Tutorial_NRM.html | 3024 +++++++-------- ghypernet-1.1.0/ghypernet/inst/doc/tutorial.html | 575 -- ghypernet-1.1.0/ghypernet/man/FitOmega.Rd | 2 ghypernet-1.1.0/ghypernet/man/bccm.Rd | 2 ghypernet-1.1.0/ghypernet/man/compute_xi.Rd |only ghypernet-1.1.0/ghypernet/man/contacts.adj.Rd | 2 ghypernet-1.1.0/ghypernet/man/get_zero_dummy.Rd |only ghypernet-1.1.0/ghypernet/man/highschool.multiplex.Rd | 2 ghypernet-1.1.0/ghypernet/man/homophily_stat.Rd | 16 ghypernet-1.1.0/ghypernet/man/link_significance.Rd |only ghypernet-1.1.0/ghypernet/man/logl.Rd | 2 ghypernet-1.1.0/ghypernet/man/mcfaddenR2.Rd | 2 ghypernet-1.1.0/ghypernet/man/nrm.Rd | 4 ghypernet-1.1.0/ghypernet/man/reciprocity_stat.Rd | 13 ghypernet-1.1.0/ghypernet/man/residuals.nrm.Rd | 2 ghypernet-1.1.0/ghypernet/man/sharedPartner_stat.Rd | 17 ghypernet-1.1.0/ghypernet/tests |only ghypernet-1.1.0/ghypernet/vignettes/Significantlinks.Rmd | 6 ghypernet-1.1.0/ghypernet/vignettes/Tutorial_NRM.Rmd | 159 47 files changed, 2295 insertions(+), 2621 deletions(-)
Title: Empirical Bayes Estimation of Dynamic Bayesian Networks
Description: Infer the adjacency matrix of a
network from time course data using an empirical Bayes
estimation procedure based on Dynamic Bayesian Networks.
Author: Andrea Rau <andrea.rau@inra.fr>
Maintainer: Andrea Rau <andrea.rau@inra.fr>
Diff between ebdbNet versions 1.2.5 dated 2016-11-21 and 1.2.6 dated 2021-10-15
DESCRIPTION | 12 ++++++------ MD5 | 11 ++++++----- NAMESPACE | 2 +- NEWS | 8 ++++++++ R/ebdbn.R | 26 ++++++++++++++++++++------ src/RunWrapGen.c | 13 ++++++++++--- src/init.c |only 7 files changed, 51 insertions(+), 21 deletions(-)
Title: Estimation of Transition Probabilities in Multistate Models
Description: Estimation of transition probabilities for the
illness-death model and or the three-state progressive model.
Author: Artur Araujo [aut, cre] (<https://orcid.org/0000-0003-1419-4208>),
Javier Roca-Pardinas [aut] (<https://orcid.org/0000-0003-3107-4515>),
Luis Meira-Machado [aut] (<https://orcid.org/0000-0002-8577-7665>)
Maintainer: Artur Araujo <artur.stat@gmail.com>
Diff between TPmsm versions 1.2.4 dated 2021-10-09 and 1.2.5 dated 2021-10-15
TPmsm-1.2.4/TPmsm/LICENSE |only TPmsm-1.2.5/TPmsm/DESCRIPTION | 10 - TPmsm-1.2.5/TPmsm/MD5 | 95 +++++------ TPmsm-1.2.5/TPmsm/README.md | 130 +++++++-------- TPmsm-1.2.5/TPmsm/build/partial.rdb |binary TPmsm-1.2.5/TPmsm/inst/CITATION | 2 TPmsm-1.2.5/TPmsm/inst/NEWS.Rd | 218 +++++++++++++------------- TPmsm-1.2.5/TPmsm/inst/doc/TPmsm.pdf |binary TPmsm-1.2.5/TPmsm/man/TPmsm-package.Rd | 182 ++++++++++----------- TPmsm-1.2.5/TPmsm/man/TPmsmOut.Rd | 6 TPmsm-1.2.5/TPmsm/man/as.data.frame.survTP.Rd | 6 TPmsm-1.2.5/TPmsm/man/bladderTP.Rd | 2 TPmsm-1.2.5/TPmsm/man/colonTP.Rd | 8 TPmsm-1.2.5/TPmsm/man/contour.TPCmsm.Rd | 4 TPmsm-1.2.5/TPmsm/man/corrTP.Rd | 6 TPmsm-1.2.5/TPmsm/man/dgpTP.Rd | 10 - TPmsm-1.2.5/TPmsm/man/heartTP.Rd | 2 TPmsm-1.2.5/TPmsm/man/image.TPCmsm.Rd | 4 TPmsm-1.2.5/TPmsm/man/lines.TPCmsm.Rd | 4 TPmsm-1.2.5/TPmsm/man/lines.TPmsm.Rd | 2 TPmsm-1.2.5/TPmsm/man/plot.TPCmsm.Rd | 4 TPmsm-1.2.5/TPmsm/man/plot.TPmsm.Rd | 2 TPmsm-1.2.5/TPmsm/man/setPackageSeedTP.Rd | 8 TPmsm-1.2.5/TPmsm/man/setSeedTP.Rd | 8 TPmsm-1.2.5/TPmsm/man/setThreadsTP.Rd | 2 TPmsm-1.2.5/TPmsm/man/survTP.Rd | 2 TPmsm-1.2.5/TPmsm/man/transAJ.Rd | 2 TPmsm-1.2.5/TPmsm/man/transIPCW.Rd | 8 TPmsm-1.2.5/TPmsm/man/transKMPW.Rd | 6 TPmsm-1.2.5/TPmsm/man/transKMW.Rd | 6 TPmsm-1.2.5/TPmsm/man/transLIN.Rd | 8 TPmsm-1.2.5/TPmsm/man/transLS.Rd | 10 - TPmsm-1.2.5/TPmsm/man/transPAJ.Rd | 6 TPmsm-1.2.5/TPmsm/src/BtoTPCmsm.c | 1 TPmsm-1.2.5/TPmsm/src/BtoTPmsm.c | 1 TPmsm-1.2.5/TPmsm/src/RngArray.c | 1 TPmsm-1.2.5/TPmsm/src/init.c | 2 TPmsm-1.2.5/TPmsm/src/logistic.c | 1 TPmsm-1.2.5/TPmsm/src/logistic.h | 1 TPmsm-1.2.5/TPmsm/src/toTPCmsm.c | 1 TPmsm-1.2.5/TPmsm/src/toTPmsm.c | 1 TPmsm-1.2.5/TPmsm/src/transAJ.c | 1 TPmsm-1.2.5/TPmsm/src/transIPCW1.c | 1 TPmsm-1.2.5/TPmsm/src/transKMPW1.c | 1 TPmsm-1.2.5/TPmsm/src/transKMPW2.c | 1 TPmsm-1.2.5/TPmsm/src/transKMW.c | 1 TPmsm-1.2.5/TPmsm/src/transLIN1.c | 1 TPmsm-1.2.5/TPmsm/src/transPAJ.c | 1 TPmsm-1.2.5/TPmsm/src/unload.c | 1 49 files changed, 386 insertions(+), 394 deletions(-)
Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph],
Phillip Hazel [ctb] (Bundled PCRE2 code),
Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code),
University of Cambridge [cph] (Bundled PCRE2 code),
Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with
PCRE2),
Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash
code)
Maintainer: Travers Ching <traversc@gmail.com>
Diff between stringfish versions 0.15.3 dated 2021-10-10 and 0.15.4 dated 2021-10-15
ChangeLog | 3 ++ DESCRIPTION | 8 ++--- MD5 | 9 +++--- inst/doc/vignette.html | 2 - inst/icelandic_words_500_utf8.txt |only tests/tests.r | 54 ++++++++++++++++++++++++++++++-------- 6 files changed, 56 insertions(+), 20 deletions(-)
Title: Extract Remote Sensing Vegetation Phenology
Description: The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and
growing season dividing method and a practical snow elimination method
based on Whittaker were proposed. 7 curve fitting methods and 4 phenology
extraction methods were provided. Parameters boundary are considered for
every curve fitting methods according to their ecological meaning.
And 'optimx' is used to select best optimization method for different
curve fitting methods.
Reference:
Kong, D., (2020). R package: A state-of-the-art Vegetation Phenology extraction
package, phenofit version 0.3.1, <doi:10.5281/zenodo.5150204>;
Kong, D., Zhang, Y., Wang, D., Chen, J., & Gu, X. (2020). Photoperiod Explains
the Asynchronization Between Vegetation Carbon Phenology and Vegetation Greenness
Phenology. Journal of Geophysical Research: Biogeosciences, 125(8), e2020JG005636.
<doi:10.1029/2020JG005636>;
Kong, D., Zhang, Y., Gu, X., & Wang, D. (2019). A robust method for reconstructing
global MODIS EVI time series on the Google Earth Engine.
ISPRS Journal of Photogrammetry and Remote Sensing, 155, 13–24;
Zhang, Q., Kong, D., Shi, P., Singh, V.P., Sun, P., 2018. Vegetation phenology
on the Qinghai-Tibetan Plateau and its response to climate change (1982–2013).
Agric. For. Meteorol. 248, 408–417. <doi:10.1016/j.agrformet.2017.10.026>.
Author: Dongdong Kong [aut, cre],
Mingzhong Xiao [aut],
Yongqiang Zhang [aut],
Xihui Gu [aut],
Jianjian Cui [aut]
Maintainer: Dongdong Kong <kongdd.sysu@gmail.com>
Diff between phenofit versions 0.2.7 dated 2020-04-02 and 0.3.2 dated 2021-10-15
phenofit-0.2.7/phenofit/R/S3_fFIT.R |only phenofit-0.2.7/phenofit/R/adjust_pos.R |only phenofit-0.2.7/phenofit/R/doubleLogistics.R |only phenofit-0.2.7/phenofit/R/fixYearBroken.R |only phenofit-0.2.7/phenofit/R/phenofit_plot.R |only phenofit-0.2.7/phenofit/R/season.R |only phenofit-0.2.7/phenofit/R/temp |only phenofit-0.2.7/phenofit/R/tidyFitPheno.R |only phenofit-0.2.7/phenofit/inst/examples/compare_other_pkgs.R |only phenofit-0.2.7/phenofit/inst/examples/ex-season.R |only phenofit-0.2.7/phenofit/man/check_season.Rd |only phenofit-0.2.7/phenofit/man/examples |only phenofit-0.2.7/phenofit/man/julia_init.Rd |only phenofit-0.2.7/phenofit/man/phenofit_plot.Rd |only phenofit-0.2.7/phenofit/man/tidyFitPheno.Rd |only phenofit-0.2.7/phenofit/man/tidy_MOD13.gee.Rd |only phenofit-0.2.7/phenofit/src/season.cpp |only phenofit-0.2.7/phenofit/tests/testthat/Rplots.pdf |only phenofit-0.2.7/phenofit/tests/testthat/test-season3y.R |only phenofit-0.3.2/phenofit/DESCRIPTION | 33 phenofit-0.3.2/phenofit/MD5 | 252 +++--- phenofit-0.3.2/phenofit/NAMESPACE | 65 + phenofit-0.3.2/phenofit/NEWS.md | 81 +- phenofit-0.3.2/phenofit/R/D.R | 54 - phenofit-0.3.2/phenofit/R/I_optim.R | 20 phenofit-0.3.2/phenofit/R/PhenoExtractMeth.R | 104 +- phenofit-0.3.2/phenofit/R/RcppExports.R | 6 phenofit-0.3.2/phenofit/R/S3_fFITs.R | 37 phenofit-0.3.2/phenofit/R/add_HeadTail.R | 15 phenofit-0.3.2/phenofit/R/backval.R | 29 phenofit-0.3.2/phenofit/R/check_input.R | 485 ++++++------- phenofit-0.3.2/phenofit/R/curvefit.R | 58 - phenofit-0.3.2/phenofit/R/curvefits.R | 189 +++-- phenofit-0.3.2/phenofit/R/data_MOD13A1.R | 16 phenofit-0.3.2/phenofit/R/deprecated_season.R |only phenofit-0.3.2/phenofit/R/derivs.R | 35 phenofit-0.3.2/phenofit/R/doubleLogistics_R.R |only phenofit-0.3.2/phenofit/R/doubleLogistics_fitting.R | 24 phenofit-0.3.2/phenofit/R/f_goal.R | 7 phenofit-0.3.2/phenofit/R/findpeaks.R | 68 + phenofit-0.3.2/phenofit/R/get_GOF.R | 37 phenofit-0.3.2/phenofit/R/get_fitting.R | 15 phenofit-0.3.2/phenofit/R/get_param.R | 6 phenofit-0.3.2/phenofit/R/get_pheno.R | 187 +++-- phenofit-0.3.2/phenofit/R/global.R | 11 phenofit-0.3.2/phenofit/R/init_lambda.R | 2 phenofit-0.3.2/phenofit/R/julia.R |only phenofit-0.3.2/phenofit/R/make_legend.R | 4 phenofit-0.3.2/phenofit/R/opt_FUN.R | 2 phenofit-0.3.2/phenofit/R/opt_nlminb.R | 12 phenofit-0.3.2/phenofit/R/optim_pheno.R | 35 phenofit-0.3.2/phenofit/R/options.R |only phenofit-0.3.2/phenofit/R/phenofit-package.R | 38 - phenofit-0.3.2/phenofit/R/plot_curvefits.R |only phenofit-0.3.2/phenofit/R/plot_input.R | 34 phenofit-0.3.2/phenofit/R/plot_phenofit.R | 151 +--- phenofit-0.3.2/phenofit/R/plot_season.R | 85 +- phenofit-0.3.2/phenofit/R/process_phenofit.R |only phenofit-0.3.2/phenofit/R/process_season.R |only phenofit-0.3.2/phenofit/R/season_RoughFitting.R |only phenofit-0.3.2/phenofit/R/season_find.R |only phenofit-0.3.2/phenofit/R/season_mov.R | 298 ++++--- phenofit-0.3.2/phenofit/R/season_tools.R |only phenofit-0.3.2/phenofit/R/smooth_wHANTS.R | 4 phenofit-0.3.2/phenofit/R/smooth_wSG.R | 2 phenofit-0.3.2/phenofit/R/smooth_wWHIT.R | 6 phenofit-0.3.2/phenofit/R/smooth_wWHIT_lambda.R | 178 ++-- phenofit-0.3.2/phenofit/R/tidy_MODIS.R | 34 phenofit-0.3.2/phenofit/R/tools.R | 81 +- phenofit-0.3.2/phenofit/README.md | 341 +-------- phenofit-0.3.2/phenofit/build |only phenofit-0.3.2/phenofit/data/CA_NS6.rda |only phenofit-0.3.2/phenofit/inst/doc |only phenofit-0.3.2/phenofit/inst/examples/ex-check_input.R | 29 phenofit-0.3.2/phenofit/inst/examples/ex-curvefits.R | 37 phenofit-0.3.2/phenofit/inst/examples/ex-visual.R | 17 phenofit-0.3.2/phenofit/inst/examples/phenofit_MOD13A1.R | 24 phenofit-0.3.2/phenofit/man/CA_NS6.Rd |only phenofit-0.3.2/phenofit/man/D.Rd | 21 phenofit-0.3.2/phenofit/man/FitDL.Rd | 173 ++-- phenofit-0.3.2/phenofit/man/GOF.Rd | 96 +- phenofit-0.3.2/phenofit/man/PhenoExtractMeth.Rd | 17 phenofit-0.3.2/phenofit/man/R2_sign.Rd | 56 - phenofit-0.3.2/phenofit/man/add_HeadTail.Rd | 83 +- phenofit-0.3.2/phenofit/man/backval.Rd | 110 +- phenofit-0.3.2/phenofit/man/check_GS_HeadTail.Rd |only phenofit-0.3.2/phenofit/man/check_input.Rd | 39 - phenofit-0.3.2/phenofit/man/curvefit.Rd | 2 phenofit-0.3.2/phenofit/man/curvefits.Rd | 144 +-- phenofit-0.3.2/phenofit/man/fFIT.Rd | 2 phenofit-0.3.2/phenofit/man/fFITs.Rd | 76 +- phenofit-0.3.2/phenofit/man/find_season.peaks.Rd |only phenofit-0.3.2/phenofit/man/getRealDate.Rd | 54 - phenofit-0.3.2/phenofit/man/get_GOF.Rd | 113 +-- phenofit-0.3.2/phenofit/man/get_fitting.Rd | 74 - phenofit-0.3.2/phenofit/man/get_param.Rd | 74 - phenofit-0.3.2/phenofit/man/get_pheno.Rd | 7 phenofit-0.3.2/phenofit/man/init_lambda.Rd | 52 - phenofit-0.3.2/phenofit/man/init_param.Rd | 72 - phenofit-0.3.2/phenofit/man/julia_setup.Rd |only phenofit-0.3.2/phenofit/man/kurtosis.Rd | 62 - phenofit-0.3.2/phenofit/man/lambda_vcurve.Rd |only phenofit-0.3.2/phenofit/man/logistic.Rd | 80 +- phenofit-0.3.2/phenofit/man/logistics.Rd | 109 +- phenofit-0.3.2/phenofit/man/melt_list.Rd |only phenofit-0.3.2/phenofit/man/movmean.Rd | 54 - phenofit-0.3.2/phenofit/man/opt_FUN.Rd | 200 ++--- phenofit-0.3.2/phenofit/man/opt_season.Rd |only phenofit-0.3.2/phenofit/man/optim_pheno.Rd | 19 phenofit-0.3.2/phenofit/man/phenofit.Rd | 4 phenofit-0.3.2/phenofit/man/plot_curvefits.Rd |only phenofit-0.3.2/phenofit/man/plot_input.Rd | 79 -- phenofit-0.3.2/phenofit/man/plot_phenofit.Rd | 86 -- phenofit-0.3.2/phenofit/man/plot_season.Rd | 15 phenofit-0.3.2/phenofit/man/process_phenofit.Rd |only phenofit-0.3.2/phenofit/man/process_season.Rd |only phenofit-0.3.2/phenofit/man/qcFUN.Rd | 178 ++-- phenofit-0.3.2/phenofit/man/qc_levels.Rd |only phenofit-0.3.2/phenofit/man/rcpp_season_filter.Rd |only phenofit-0.3.2/phenofit/man/rcpp_wSG.Rd | 64 - phenofit-0.3.2/phenofit/man/reexports.Rd |only phenofit-0.3.2/phenofit/man/removeClosedExtreme.Rd |only phenofit-0.3.2/phenofit/man/season.Rd | 250 ++++-- phenofit-0.3.2/phenofit/man/season_mov.Rd |only phenofit-0.3.2/phenofit/man/set_options.Rd |only phenofit-0.3.2/phenofit/man/smooth_wHANTS.Rd | 2 phenofit-0.3.2/phenofit/man/smooth_wSG.Rd | 2 phenofit-0.3.2/phenofit/man/smooth_wWHIT.Rd | 4 phenofit-0.3.2/phenofit/man/tidy_MOD13.Rd |only phenofit-0.3.2/phenofit/man/tidy_pheno.Rd |only phenofit-0.3.2/phenofit/man/v_curve.Rd | 14 phenofit-0.3.2/phenofit/man/whit2.Rd | 90 +- phenofit-0.3.2/phenofit/src/RcppExports.cpp | 21 phenofit-0.3.2/phenofit/src/register_routines.c | 31 phenofit-0.3.2/phenofit/src/season_filter.cpp |only phenofit-0.3.2/phenofit/src/smooth_wSG.cpp | 57 - phenofit-0.3.2/phenofit/src/smooth_whit.c | 6 phenofit-0.3.2/phenofit/src/wTSM.cpp | 2 phenofit-0.3.2/phenofit/tests/testthat/helper_MOD13A1.R | 42 - phenofit-0.3.2/phenofit/tests/testthat/test-PhenoExtract.R | 18 phenofit-0.3.2/phenofit/tests/testthat/test-curvefits.R | 19 phenofit-0.3.2/phenofit/tests/testthat/test-find_season.R |only phenofit-0.3.2/phenofit/tests/testthat/test-season.R | 6 phenofit-0.3.2/phenofit/tests/testthat/test-season_mov.R |only phenofit-0.3.2/phenofit/tests/testthat/test-v_curve.R | 2 phenofit-0.3.2/phenofit/vignettes |only 146 files changed, 3001 insertions(+), 3028 deletions(-)
Title: Helper Functions for Use with the 'ncdf4' Package
Description: Contains a collection of helper functions for dealing with
'NetCDF' files <https://www.unidata.ucar.edu/software/netcdf/>
opened using 'ncdf4', particularly 'NetCDF' files that conform to the
Climate and Forecast (CF) Metadata Conventions
<http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html>.
Author: David Bronaugh <bronaugh@uvic.ca> for the Pacific Climate Impacts
Consortium (PCIC)
Maintainer: Lee Zeman <lzeman@uvic.ca>
Diff between ncdf4.helpers versions 0.3-5 dated 2020-06-08 and 0.3-6 dated 2021-10-15
CHANGELOG | 2 ++ DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 2 +- tests/testthat/test-file-functions.R | 12 +++++++----- 5 files changed, 19 insertions(+), 15 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Tamás Nepusz <ntamas@gmail.com>
Diff between igraph versions 1.2.6 dated 2020-10-06 and 1.2.7 dated 2021-10-15
igraph-1.2.6/igraph/src/AMD |only igraph-1.2.6/igraph/src/CHOLMOD |only igraph-1.2.6/igraph/src/COLAMD |only igraph-1.2.6/igraph/src/plfit/zeta.c |only igraph-1.2.6/igraph/src/plfit/zeta.h |only igraph-1.2.7/igraph/DESCRIPTION | 16 igraph-1.2.7/igraph/MD5 | 1196 - igraph-1.2.7/igraph/NAMESPACE | 2 igraph-1.2.7/igraph/NEWS.md |only igraph-1.2.7/igraph/R/adjacency.R | 2 igraph-1.2.7/igraph/R/auto.R | 25 igraph-1.2.7/igraph/R/bipartite.R | 15 igraph-1.2.7/igraph/R/centrality.R | 2 igraph-1.2.7/igraph/R/centralization.R | 8 igraph-1.2.7/igraph/R/cliques.R | 4 igraph-1.2.7/igraph/R/cocitation.R | 2 igraph-1.2.7/igraph/R/cohesive.blocks.R | 2 igraph-1.2.7/igraph/R/community.R | 648 igraph-1.2.7/igraph/R/data_frame.R | 11 igraph-1.2.7/igraph/R/degseq.R | 6 igraph-1.2.7/igraph/R/embedding.R | 4 igraph-1.2.7/igraph/R/fit.R | 2 igraph-1.2.7/igraph/R/flow.R | 10 igraph-1.2.7/igraph/R/foreign.R | 11 igraph-1.2.7/igraph/R/games.R | 30 igraph-1.2.7/igraph/R/hrg.R | 6 igraph-1.2.7/igraph/R/igraph-package.R | 6 igraph-1.2.7/igraph/R/indexing.R | 4 igraph-1.2.7/igraph/R/interface.R | 4 igraph-1.2.7/igraph/R/iterators.R | 6 igraph-1.2.7/igraph/R/layout.R | 30 igraph-1.2.7/igraph/R/make.R | 37 igraph-1.2.7/igraph/R/minimum.spanning.tree.R | 6 igraph-1.2.7/igraph/R/motifs.R | 2 igraph-1.2.7/igraph/R/nexus.R | 6 igraph-1.2.7/igraph/R/other.R | 37 igraph-1.2.7/igraph/R/palette.R | 4 igraph-1.2.7/igraph/R/par.R | 2 igraph-1.2.7/igraph/R/paths.R | 6 igraph-1.2.7/igraph/R/plot.R | 44 igraph-1.2.7/igraph/R/printr.R | 14 igraph-1.2.7/igraph/R/sir.R | 2 igraph-1.2.7/igraph/R/structural.properties.R | 81 igraph-1.2.7/igraph/R/test.R | 2 igraph-1.2.7/igraph/R/tkplot.R | 10 igraph-1.2.7/igraph/R/topology.R | 6 igraph-1.2.7/igraph/build |only igraph-1.2.7/igraph/cleanup | 5 igraph-1.2.7/igraph/cleanup.win |only igraph-1.2.7/igraph/configure | 3970 ++- igraph-1.2.7/igraph/configure.ac | 16 igraph-1.2.7/igraph/demo/hrg.R | 4 igraph-1.2.7/igraph/inst/AUTHORS | 5 igraph-1.2.7/igraph/inst/NEWS.md | 300 igraph-1.2.7/igraph/inst/README.md | 17 igraph-1.2.7/igraph/inst/my_html_library.tcl | 2 igraph-1.2.7/igraph/man/aaa-igraph-package.Rd | 6 igraph-1.2.7/igraph/man/all_simple_paths.Rd | 5 igraph-1.2.7/igraph/man/alpha_centrality.Rd | 2 igraph-1.2.7/igraph/man/arpack.Rd | 2 igraph-1.2.7/igraph/man/as.igraph.Rd | 2 igraph-1.2.7/igraph/man/betweenness.Rd | 10 igraph-1.2.7/igraph/man/canonical_permutation.Rd | 2 igraph-1.2.7/igraph/man/centr_betw_tmax.Rd | 2 igraph-1.2.7/igraph/man/centr_clo_tmax.Rd | 2 igraph-1.2.7/igraph/man/centr_degree_tmax.Rd | 2 igraph-1.2.7/igraph/man/centr_eigen_tmax.Rd | 2 igraph-1.2.7/igraph/man/cliques.Rd | 4 igraph-1.2.7/igraph/man/closeness.Rd | 8 igraph-1.2.7/igraph/man/cluster_edge_betweenness.Rd | 2 igraph-1.2.7/igraph/man/cluster_fast_greedy.Rd | 3 igraph-1.2.7/igraph/man/cluster_fluid_communities.Rd |only igraph-1.2.7/igraph/man/cluster_infomap.Rd | 6 igraph-1.2.7/igraph/man/cluster_label_prop.Rd | 5 igraph-1.2.7/igraph/man/cluster_leiden.Rd |only igraph-1.2.7/igraph/man/cluster_louvain.Rd | 5 igraph-1.2.7/igraph/man/cluster_optimal.Rd | 2 igraph-1.2.7/igraph/man/cluster_walktrap.Rd | 3 igraph-1.2.7/igraph/man/cocitation.Rd | 2 igraph-1.2.7/igraph/man/cohesive_blocks.Rd | 2 igraph-1.2.7/igraph/man/communities.Rd | 5 igraph-1.2.7/igraph/man/compare.Rd | 11 igraph-1.2.7/igraph/man/components.Rd | 2 igraph-1.2.7/igraph/man/consensus_tree.Rd | 2 igraph-1.2.7/igraph/man/count_isomorphisms.Rd | 2 igraph-1.2.7/igraph/man/diverging_pal.Rd | 2 igraph-1.2.7/igraph/man/embed_laplacian_matrix.Rd | 4 igraph-1.2.7/igraph/man/erdos.renyi.game.Rd | 5 igraph-1.2.7/igraph/man/fit_power_law.Rd | 2 igraph-1.2.7/igraph/man/get.edge.ids.Rd | 2 igraph-1.2.7/igraph/man/graph_from_data_frame.Rd | 7 igraph-1.2.7/igraph/man/handle_vertex_type_arg.Rd |only igraph-1.2.7/igraph/man/igraph-es-indexing.Rd | 2 igraph-1.2.7/igraph/man/igraph-vs-indexing.Rd | 4 igraph-1.2.7/igraph/man/igraph_options.Rd | 2 igraph-1.2.7/igraph/man/igraph_version.Rd | 2 igraph-1.2.7/igraph/man/incident.Rd | 2 igraph-1.2.7/igraph/man/is_degseq.Rd | 2 igraph-1.2.7/igraph/man/is_graphical.Rd | 4 igraph-1.2.7/igraph/man/is_min_separator.Rd | 2 igraph-1.2.7/igraph/man/knn.Rd | 29 igraph-1.2.7/igraph/man/layout_.Rd | 2 igraph-1.2.7/igraph/man/layout_as_tree.Rd | 2 igraph-1.2.7/igraph/man/layout_on_grid.Rd | 2 igraph-1.2.7/igraph/man/layout_with_graphopt.Rd | 2 igraph-1.2.7/igraph/man/layout_with_kk.Rd | 2 igraph-1.2.7/igraph/man/make_bipartite_graph.Rd | 2 igraph-1.2.7/igraph/man/make_chordal_ring.Rd | 4 igraph-1.2.7/igraph/man/make_graph.Rd | 8 igraph-1.2.7/igraph/man/make_lattice.Rd | 2 igraph-1.2.7/igraph/man/matching.Rd | 2 igraph-1.2.7/igraph/man/min_cut.Rd | 4 igraph-1.2.7/igraph/man/modularity.igraph.Rd | 11 igraph-1.2.7/igraph/man/motifs.Rd | 2 igraph-1.2.7/igraph/man/mst.Rd | 6 igraph-1.2.7/igraph/man/nexus.Rd | 6 igraph-1.2.7/igraph/man/plot.common.Rd | 2 igraph-1.2.7/igraph/man/plot_dendrogram.communities.Rd | 2 igraph-1.2.7/igraph/man/plot_dendrogram.igraphHRG.Rd | 2 igraph-1.2.7/igraph/man/printer_callback.Rd | 2 igraph-1.2.7/igraph/man/printr.Rd |only igraph-1.2.7/igraph/man/read_graph.Rd | 11 igraph-1.2.7/igraph/man/reciprocity.Rd | 2 igraph-1.2.7/igraph/man/sample_bipartite.Rd | 2 igraph-1.2.7/igraph/man/sample_degseq.Rd | 2 igraph-1.2.7/igraph/man/sample_dot_product.Rd | 2 igraph-1.2.7/igraph/man/sample_hierarchical_sbm.Rd | 2 igraph-1.2.7/igraph/man/sample_last_cit.Rd | 2 igraph-1.2.7/igraph/man/sample_pa.Rd | 2 igraph-1.2.7/igraph/man/sample_pa_age.Rd | 9 igraph-1.2.7/igraph/man/sample_pref.Rd | 2 igraph-1.2.7/igraph/man/sample_sbm.Rd | 2 igraph-1.2.7/igraph/man/sequential_pal.Rd | 2 igraph-1.2.7/igraph/man/sir.Rd | 2 igraph-1.2.7/igraph/man/st_min_cuts.Rd | 2 igraph-1.2.7/igraph/man/sub-sub-.igraph.Rd | 2 igraph-1.2.7/igraph/man/tkplot.Rd | 10 igraph-1.2.7/igraph/man/transitivity.Rd | 9 igraph-1.2.7/igraph/man/vertex_connectivity.Rd | 2 igraph-1.2.7/igraph/man/which_multiple.Rd | 2 igraph-1.2.7/igraph/man/which_mutual.Rd | 2 igraph-1.2.7/igraph/src/DensityGrid.cpp | 387 igraph-1.2.7/igraph/src/DensityGrid.h | 89 igraph-1.2.7/igraph/src/DensityGrid_3d.cpp | 431 igraph-1.2.7/igraph/src/DensityGrid_3d.h | 89 igraph-1.2.7/igraph/src/Makevars.in | 3 igraph-1.2.7/igraph/src/Makevars.win | 7 igraph-1.2.7/igraph/src/NetDataTypes.cpp | 264 igraph-1.2.7/igraph/src/NetDataTypes.h | 1129 - igraph-1.2.7/igraph/src/NetRoutines.cpp | 424 igraph-1.2.7/igraph/src/NetRoutines.h | 18 igraph-1.2.7/igraph/src/adjlist.c | 992 igraph-1.2.7/igraph/src/arpack.c | 2095 +- igraph-1.2.7/igraph/src/array.c | 10 igraph-1.2.7/igraph/src/array.pmt | 102 igraph-1.2.7/igraph/src/atlas-edges.h | 2528 +- igraph-1.2.7/igraph/src/atlas.c | 78 igraph-1.2.7/igraph/src/attributes.c | 650 igraph-1.2.7/igraph/src/basic_query.c | 36 igraph-1.2.7/igraph/src/bfgs.c | 341 igraph-1.2.7/igraph/src/bigint.c | 438 igraph-1.2.7/igraph/src/bigint.h | 52 igraph-1.2.7/igraph/src/bignum.c | 2486 +- igraph-1.2.7/igraph/src/bignum.h | 46 igraph-1.2.7/igraph/src/bipartite.c | 1613 - igraph-1.2.7/igraph/src/blas.c | 85 igraph-1.2.7/igraph/src/bliss.cc | 209 igraph-1.2.7/igraph/src/bliss/bignum.hh | 4 igraph-1.2.7/igraph/src/bliss/bliss_heap.cc | 6 igraph-1.2.7/igraph/src/bliss/defs.cc | 12 igraph-1.2.7/igraph/src/bliss/defs.hh | 7 igraph-1.2.7/igraph/src/bliss/graph.cc | 65 igraph-1.2.7/igraph/src/bliss/graph.hh | 16 igraph-1.2.7/igraph/src/bliss/orbit.cc | 4 igraph-1.2.7/igraph/src/bliss/partition.cc | 6 igraph-1.2.7/igraph/src/bliss/partition.hh | 6 igraph-1.2.7/igraph/src/bliss/uintseqhash.hh | 2 igraph-1.2.7/igraph/src/bliss/utils.cc | 2 igraph-1.2.7/igraph/src/bliss/utils.hh | 6 igraph-1.2.7/igraph/src/cattributes.c | 6522 +++--- igraph-1.2.7/igraph/src/centrality.c | 4892 ++-- igraph-1.2.7/igraph/src/cliquer/cliquer.c | 9 igraph-1.2.7/igraph/src/cliquer/cliquer_graph.c | 8 igraph-1.2.7/igraph/src/cliquer/reorder.c | 2 igraph-1.2.7/igraph/src/cliquer/set.h | 4 igraph-1.2.7/igraph/src/cliques.c | 1810 - igraph-1.2.7/igraph/src/clustertool.cpp | 981 igraph-1.2.7/igraph/src/cocitation.c | 587 igraph-1.2.7/igraph/src/cohesive_blocks.c | 1019 igraph-1.2.7/igraph/src/coloring.c | 49 igraph-1.2.7/igraph/src/community.c | 5617 ++--- igraph-1.2.7/igraph/src/community_leiden.c |only igraph-1.2.7/igraph/src/complex.c | 572 igraph-1.2.7/igraph/src/components.c | 1686 - igraph-1.2.7/igraph/src/config.h.in | 17 igraph-1.2.7/igraph/src/conversion.c | 1389 - igraph-1.2.7/igraph/src/cores.c | 220 igraph-1.2.7/igraph/src/decomposition.c | 756 igraph-1.2.7/igraph/src/degree_sequence.cpp |only igraph-1.2.7/igraph/src/distances.c | 265 igraph-1.2.7/igraph/src/dotproduct.c | 326 igraph-1.2.7/igraph/src/dqueue.c | 10 igraph-1.2.7/igraph/src/dqueue.pmt | 385 igraph-1.2.7/igraph/src/drl_Node.h | 64 igraph-1.2.7/igraph/src/drl_Node_3d.h | 64 igraph-1.2.7/igraph/src/drl_graph.cpp | 2024 - igraph-1.2.7/igraph/src/drl_graph.h | 178 igraph-1.2.7/igraph/src/drl_graph_3d.cpp | 1461 - igraph-1.2.7/igraph/src/drl_graph_3d.h | 162 igraph-1.2.7/igraph/src/drl_layout.cpp | 562 igraph-1.2.7/igraph/src/drl_layout.h | 62 igraph-1.2.7/igraph/src/drl_layout_3d.cpp | 86 igraph-1.2.7/igraph/src/drl_layout_3d.h | 62 igraph-1.2.7/igraph/src/drl_parse.cpp | 240 igraph-1.2.7/igraph/src/drl_parse.h | 74 igraph-1.2.7/igraph/src/eigen.c | 2669 +- igraph-1.2.7/igraph/src/embedding.c | 1703 - igraph-1.2.7/igraph/src/fast_community.c | 1666 - igraph-1.2.7/igraph/src/feedback_arc_set.c | 1046 - igraph-1.2.7/igraph/src/flow.c | 3469 +-- igraph-1.2.7/igraph/src/foreign-dl-header.h | 37 igraph-1.2.7/igraph/src/foreign-dl-lexer.c | 95 igraph-1.2.7/igraph/src/foreign-dl-lexer.l | 7 igraph-1.2.7/igraph/src/foreign-gml-header.h | 18 igraph-1.2.7/igraph/src/foreign-gml-lexer.c | 48 igraph-1.2.7/igraph/src/foreign-gml-lexer.l | 8 igraph-1.2.7/igraph/src/foreign-graphml.c | 3179 +-- igraph-1.2.7/igraph/src/foreign-lgl-header.h | 26 igraph-1.2.7/igraph/src/foreign-lgl-lexer.c | 48 igraph-1.2.7/igraph/src/foreign-lgl-lexer.l | 8 igraph-1.2.7/igraph/src/foreign-ncol-header.h | 24 igraph-1.2.7/igraph/src/foreign-ncol-lexer.c | 48 igraph-1.2.7/igraph/src/foreign-ncol-lexer.l | 8 igraph-1.2.7/igraph/src/foreign-pajek-header.h | 42 igraph-1.2.7/igraph/src/foreign-pajek-lexer.c | 48 igraph-1.2.7/igraph/src/foreign-pajek-lexer.l | 8 igraph-1.2.7/igraph/src/foreign-pajek-parser.c | 4 igraph-1.2.7/igraph/src/foreign-pajek-parser.y | 4 igraph-1.2.7/igraph/src/foreign.c | 5304 ++--- igraph-1.2.7/igraph/src/forestfire.c | 343 igraph-1.2.7/igraph/src/fortran_intrinsics.c | 38 igraph-1.2.7/igraph/src/games.c | 6785 +++--- igraph-1.2.7/igraph/src/gengraph_box_list.cpp | 119 igraph-1.2.7/igraph/src/gengraph_box_list.h | 82 igraph-1.2.7/igraph/src/gengraph_definitions.h | 119 igraph-1.2.7/igraph/src/gengraph_degree_sequence.cpp | 451 igraph-1.2.7/igraph/src/gengraph_degree_sequence.h | 111 igraph-1.2.7/igraph/src/gengraph_graph_molloy_hash.cpp | 1080 - igraph-1.2.7/igraph/src/gengraph_graph_molloy_hash.h | 311 igraph-1.2.7/igraph/src/gengraph_graph_molloy_optimized.cpp | 2775 +- igraph-1.2.7/igraph/src/gengraph_graph_molloy_optimized.h | 447 igraph-1.2.7/igraph/src/gengraph_hash.h | 342 igraph-1.2.7/igraph/src/gengraph_header.h | 85 igraph-1.2.7/igraph/src/gengraph_mr-connected.cpp | 196 igraph-1.2.7/igraph/src/gengraph_powerlaw.cpp | 356 igraph-1.2.7/igraph/src/gengraph_powerlaw.h | 86 igraph-1.2.7/igraph/src/gengraph_qsort.h | 718 igraph-1.2.7/igraph/src/gengraph_random.cpp | 60 igraph-1.2.7/igraph/src/gengraph_random.h | 54 igraph-1.2.7/igraph/src/gengraph_vertex_cover.h | 68 igraph-1.2.7/igraph/src/glet.c | 1404 - igraph-1.2.7/igraph/src/glpk_support.c | 87 igraph-1.2.7/igraph/src/gml_tree.c | 370 igraph-1.2.7/igraph/src/hacks.c | 13 igraph-1.2.7/igraph/src/heap.c | 1273 - igraph-1.2.7/igraph/src/heap.pmt | 326 igraph-1.2.7/igraph/src/hrg_dendro.h | 351 igraph-1.2.7/igraph/src/hrg_graph.h | 158 igraph-1.2.7/igraph/src/hrg_graph_simp.h | 134 igraph-1.2.7/igraph/src/hrg_rbtree.h | 148 igraph-1.2.7/igraph/src/hrg_splittree_eq.h | 180 igraph-1.2.7/igraph/src/igraph_arpack_internal.h | 310 igraph-1.2.7/igraph/src/igraph_blas_internal.h | 69 igraph-1.2.7/igraph/src/igraph_buckets.c | 210 igraph-1.2.7/igraph/src/igraph_cliquer.c | 124 igraph-1.2.7/igraph/src/igraph_cliquer.h | 16 igraph-1.2.7/igraph/src/igraph_error.c | 219 igraph-1.2.7/igraph/src/igraph_estack.c | 54 igraph-1.2.7/igraph/src/igraph_estack.h | 22 igraph-1.2.7/igraph/src/igraph_f2c.h | 286 igraph-1.2.7/igraph/src/igraph_fixed_vectorlist.c | 98 igraph-1.2.7/igraph/src/igraph_flow_internal.h | 25 igraph-1.2.7/igraph/src/igraph_glpk_support.h | 20 igraph-1.2.7/igraph/src/igraph_gml_tree.h | 74 igraph-1.2.7/igraph/src/igraph_grid.c | 832 igraph-1.2.7/igraph/src/igraph_hacks_internal.h | 32 igraph-1.2.7/igraph/src/igraph_handle_exceptions.h |only igraph-1.2.7/igraph/src/igraph_hashtable.c | 148 igraph-1.2.7/igraph/src/igraph_heap.c | 10 igraph-1.2.7/igraph/src/igraph_hrg.cc | 1549 - igraph-1.2.7/igraph/src/igraph_hrg_types.cc | 5912 ++--- igraph-1.2.7/igraph/src/igraph_interrupt_internal.h | 38 igraph-1.2.7/igraph/src/igraph_isoclasses.h |only igraph-1.2.7/igraph/src/igraph_lapack_internal.h | 280 igraph-1.2.7/igraph/src/igraph_marked_queue.c | 112 igraph-1.2.7/igraph/src/igraph_marked_queue.h | 28 igraph-1.2.7/igraph/src/igraph_math.h | 40 igraph-1.2.7/igraph/src/igraph_psumtree.c | 102 igraph-1.2.7/igraph/src/igraph_set.c | 250 igraph-1.2.7/igraph/src/igraph_stack.c | 32 igraph-1.2.7/igraph/src/igraph_strvector.c | 651 igraph-1.2.7/igraph/src/igraph_threading.h | 16 igraph-1.2.7/igraph/src/igraph_trie.c | 504 igraph-1.2.7/igraph/src/igraph_types_internal.h | 246 igraph-1.2.7/igraph/src/igraph_version.h | 20 igraph-1.2.7/igraph/src/include/igraph.h | 12 igraph-1.2.7/igraph/src/include/igraph_adjlist.h | 145 igraph-1.2.7/igraph/src/include/igraph_arpack.h | 114 igraph-1.2.7/igraph/src/include/igraph_array.h | 10 igraph-1.2.7/igraph/src/include/igraph_array_pmt.h | 46 igraph-1.2.7/igraph/src/include/igraph_attributes.h | 545 igraph-1.2.7/igraph/src/include/igraph_bipartite.h | 88 igraph-1.2.7/igraph/src/include/igraph_blas.h | 27 igraph-1.2.7/igraph/src/include/igraph_centrality.h | 242 igraph-1.2.7/igraph/src/include/igraph_cliques.h | 78 igraph-1.2.7/igraph/src/include/igraph_cocitation.h | 38 igraph-1.2.7/igraph/src/include/igraph_cohesive_blocks.h | 24 igraph-1.2.7/igraph/src/include/igraph_coloring.h | 24 igraph-1.2.7/igraph/src/include/igraph_community.h | 271 igraph-1.2.7/igraph/src/include/igraph_complex.h | 78 igraph-1.2.7/igraph/src/include/igraph_components.h | 39 igraph-1.2.7/igraph/src/include/igraph_constants.h | 211 igraph-1.2.7/igraph/src/include/igraph_constructors.h | 58 igraph-1.2.7/igraph/src/include/igraph_conversion.h | 37 igraph-1.2.7/igraph/src/include/igraph_datatype.h | 49 igraph-1.2.7/igraph/src/include/igraph_decls.h | 29 igraph-1.2.7/igraph/src/include/igraph_dqueue.h | 14 igraph-1.2.7/igraph/src/include/igraph_dqueue_pmt.h | 46 igraph-1.2.7/igraph/src/include/igraph_eigen.h | 132 igraph-1.2.7/igraph/src/include/igraph_embedding.h | 57 igraph-1.2.7/igraph/src/include/igraph_epidemics.h | 24 igraph-1.2.7/igraph/src/include/igraph_error.h | 373 igraph-1.2.7/igraph/src/include/igraph_flow.h | 156 igraph-1.2.7/igraph/src/include/igraph_foreign.h | 64 igraph-1.2.7/igraph/src/include/igraph_games.h | 287 igraph-1.2.7/igraph/src/include/igraph_graphlets.h | 30 igraph-1.2.7/igraph/src/include/igraph_heap.h | 10 igraph-1.2.7/igraph/src/include/igraph_heap_pmt.h | 42 igraph-1.2.7/igraph/src/include/igraph_hrg.h | 67 igraph-1.2.7/igraph/src/include/igraph_interface.h | 109 igraph-1.2.7/igraph/src/include/igraph_interrupt.h | 16 igraph-1.2.7/igraph/src/include/igraph_iterators.h | 208 igraph-1.2.7/igraph/src/include/igraph_lapack.h | 100 igraph-1.2.7/igraph/src/include/igraph_layout.h | 263 igraph-1.2.7/igraph/src/include/igraph_lsap.h | 10 igraph-1.2.7/igraph/src/include/igraph_matching.h | 28 igraph-1.2.7/igraph/src/include/igraph_matrix.h | 12 igraph-1.2.7/igraph/src/include/igraph_matrix_pmt.h | 286 igraph-1.2.7/igraph/src/include/igraph_memory.h | 14 igraph-1.2.7/igraph/src/include/igraph_microscopic_update.h | 38 igraph-1.2.7/igraph/src/include/igraph_mixing.h | 30 igraph-1.2.7/igraph/src/include/igraph_motifs.h | 48 igraph-1.2.7/igraph/src/include/igraph_neighborhood.h | 27 igraph-1.2.7/igraph/src/include/igraph_nongraph.h | 49 igraph-1.2.7/igraph/src/include/igraph_operators.h | 44 igraph-1.2.7/igraph/src/include/igraph_paths.h | 181 igraph-1.2.7/igraph/src/include/igraph_pmt.h | 186 igraph-1.2.7/igraph/src/include/igraph_pmt_off.h | 78 igraph-1.2.7/igraph/src/include/igraph_progress.h | 114 igraph-1.2.7/igraph/src/include/igraph_psumtree.h | 30 igraph-1.2.7/igraph/src/include/igraph_qsort.h | 16 igraph-1.2.7/igraph/src/include/igraph_random.h | 77 igraph-1.2.7/igraph/src/include/igraph_scan.h | 50 igraph-1.2.7/igraph/src/include/igraph_scg.h | 219 igraph-1.2.7/igraph/src/include/igraph_separators.h | 26 igraph-1.2.7/igraph/src/include/igraph_sparsemat.h | 464 igraph-1.2.7/igraph/src/include/igraph_spmatrix.h | 42 igraph-1.2.7/igraph/src/include/igraph_stack.h | 10 igraph-1.2.7/igraph/src/include/igraph_stack_pmt.h | 38 igraph-1.2.7/igraph/src/include/igraph_statusbar.h | 86 igraph-1.2.7/igraph/src/include/igraph_structural.h | 128 igraph-1.2.7/igraph/src/include/igraph_strvector.h | 68 igraph-1.2.7/igraph/src/include/igraph_threading.h.in | 16 igraph-1.2.7/igraph/src/include/igraph_topology.h | 293 igraph-1.2.7/igraph/src/include/igraph_transitivity.h | 60 igraph-1.2.7/igraph/src/include/igraph_types.h | 34 igraph-1.2.7/igraph/src/include/igraph_vector.h | 55 igraph-1.2.7/igraph/src/include/igraph_vector_pmt.h | 302 igraph-1.2.7/igraph/src/include/igraph_vector_ptr.h | 38 igraph-1.2.7/igraph/src/include/igraph_vector_type.h | 18 igraph-1.2.7/igraph/src/include/igraph_version.h.in | 18 igraph-1.2.7/igraph/src/include/igraph_visitor.h | 80 igraph-1.2.7/igraph/src/infomap.cc | 462 igraph-1.2.7/igraph/src/infomap_FlowGraph.cc | 637 igraph-1.2.7/igraph/src/infomap_FlowGraph.h | 68 igraph-1.2.7/igraph/src/infomap_Greedy.cc | 1077 - igraph-1.2.7/igraph/src/infomap_Greedy.h | 98 igraph-1.2.7/igraph/src/infomap_Node.cc | 87 igraph-1.2.7/igraph/src/infomap_Node.h | 43 igraph-1.2.7/igraph/src/init.c | 22 igraph-1.2.7/igraph/src/interrupt.c | 35 igraph-1.2.7/igraph/src/iterators.c | 2119 +- igraph-1.2.7/igraph/src/lad.c | 2940 +- igraph-1.2.7/igraph/src/lapack.c | 1311 - igraph-1.2.7/igraph/src/layout.c | 3804 +-- igraph-1.2.7/igraph/src/layout_dh.c | 673 igraph-1.2.7/igraph/src/layout_fr.c | 1143 - igraph-1.2.7/igraph/src/layout_gem.c | 375 igraph-1.2.7/igraph/src/layout_kk.c | 1098 - igraph-1.2.7/igraph/src/lsap.c | 753 igraph-1.2.7/igraph/src/matching.c | 1534 - igraph-1.2.7/igraph/src/math.c | 320 igraph-1.2.7/igraph/src/matrix.c | 120 igraph-1.2.7/igraph/src/matrix.pmt | 1366 - igraph-1.2.7/igraph/src/maximal_cliques.c | 607 igraph-1.2.7/igraph/src/maximal_cliques_template.h | 551 igraph-1.2.7/igraph/src/memory.c | 30 igraph-1.2.7/igraph/src/microscopic_update.c | 1100 - igraph-1.2.7/igraph/src/mixing.c | 372 igraph-1.2.7/igraph/src/motifs.c | 1651 - igraph-1.2.7/igraph/src/operators.c | 1891 - igraph-1.2.7/igraph/src/optimal_modularity.c | 345 igraph-1.2.7/igraph/src/other.c | 480 igraph-1.2.7/igraph/src/paths.c | 210 igraph-1.2.7/igraph/src/plfit/error.c | 11 igraph-1.2.7/igraph/src/plfit/error.h | 6 igraph-1.2.7/igraph/src/plfit/gss.c | 7 igraph-1.2.7/igraph/src/plfit/gss.h | 8 igraph-1.2.7/igraph/src/plfit/hzeta.c |only igraph-1.2.7/igraph/src/plfit/hzeta.h |only igraph-1.2.7/igraph/src/plfit/kolmogorov.c | 6 igraph-1.2.7/igraph/src/plfit/kolmogorov.h | 10 igraph-1.2.7/igraph/src/plfit/mt.c |only igraph-1.2.7/igraph/src/plfit/mt.h |only igraph-1.2.7/igraph/src/plfit/options.c | 31 igraph-1.2.7/igraph/src/plfit/platform.c |only igraph-1.2.7/igraph/src/plfit/platform.h | 25 igraph-1.2.7/igraph/src/plfit/plfit.c | 1037 igraph-1.2.7/igraph/src/plfit/plfit.h | 104 igraph-1.2.7/igraph/src/plfit/plfit.inc | 5 igraph-1.2.7/igraph/src/plfit/rbinom.c |only igraph-1.2.7/igraph/src/plfit/sampling.c |only igraph-1.2.7/igraph/src/plfit/sampling.h |only igraph-1.2.7/igraph/src/pottsmodel_2.cpp | 3914 +-- igraph-1.2.7/igraph/src/pottsmodel_2.h | 130 igraph-1.2.7/igraph/src/progress.c | 131 igraph-1.2.7/igraph/src/prpack.cpp | 24 igraph-1.2.7/igraph/src/prpack.h | 26 igraph-1.2.7/igraph/src/prpack/prpack_base_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_csc.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_csr.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_edge_list.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_igraph_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_ge_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_gs_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_scc_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_schur_graph.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_result.h | 6 igraph-1.2.7/igraph/src/prpack/prpack_solver.cpp | 2 igraph-1.2.7/igraph/src/prpack/prpack_solver.h | 2 igraph-1.2.7/igraph/src/prpack/prpack_utils.cpp | 2 igraph-1.2.7/igraph/src/prpack/prpack_utils.h | 2 igraph-1.2.7/igraph/src/pstdint.h | 1170 - igraph-1.2.7/igraph/src/qsort.c | 262 igraph-1.2.7/igraph/src/random.c | 2529 +- igraph-1.2.7/igraph/src/random_walk.c | 163 igraph-1.2.7/igraph/src/rinterface.c | 173 igraph-1.2.7/igraph/src/sbm.c | 974 igraph-1.2.7/igraph/src/scan.c | 1351 - igraph-1.2.7/igraph/src/scg.c | 3176 +-- igraph-1.2.7/igraph/src/scg_approximate_methods.c | 239 igraph-1.2.7/igraph/src/scg_exact_scg.c | 78 igraph-1.2.7/igraph/src/scg_headers.h | 86 igraph-1.2.7/igraph/src/scg_kmeans.c | 134 igraph-1.2.7/igraph/src/scg_optimal_method.c | 391 igraph-1.2.7/igraph/src/scg_utils.c | 115 igraph-1.2.7/igraph/src/separators.c | 1365 - igraph-1.2.7/igraph/src/sir.c | 362 igraph-1.2.7/igraph/src/spanning_trees.c | 566 igraph-1.2.7/igraph/src/sparsemat.c | 3936 +-- igraph-1.2.7/igraph/src/spectral_properties.c | 727 igraph-1.2.7/igraph/src/spmatrix.c | 996 igraph-1.2.7/igraph/src/st-cuts.c | 2575 +- igraph-1.2.7/igraph/src/stack.pmt | 276 igraph-1.2.7/igraph/src/statusbar.c | 88 igraph-1.2.7/igraph/src/structural_properties.c |10394 +++++----- igraph-1.2.7/igraph/src/structural_properties_internal.h | 31 igraph-1.2.7/igraph/src/structure_generators.c | 3288 +-- igraph-1.2.7/igraph/src/sugiyama.c | 1898 - igraph-1.2.7/igraph/src/topology.c | 4767 ++-- igraph-1.2.7/igraph/src/triangles.c | 1352 - igraph-1.2.7/igraph/src/triangles_template.h | 161 igraph-1.2.7/igraph/src/triangles_template1.h | 111 igraph-1.2.7/igraph/src/type_indexededgelist.c | 2204 +- igraph-1.2.7/igraph/src/types.c | 192 igraph-1.2.7/igraph/src/uuid/gen_uuid.c | 2 igraph-1.2.7/igraph/src/vector.c | 598 igraph-1.2.7/igraph/src/vector.pmt | 2575 +- igraph-1.2.7/igraph/src/vector_ptr.c | 453 igraph-1.2.7/igraph/src/version.c | 54 igraph-1.2.7/igraph/src/visitors.c | 811 igraph-1.2.7/igraph/src/walktrap.cpp | 155 igraph-1.2.7/igraph/src/walktrap_communities.cpp | 1479 - igraph-1.2.7/igraph/src/walktrap_communities.h | 202 igraph-1.2.7/igraph/src/walktrap_graph.cpp | 304 igraph-1.2.7/igraph/src/walktrap_graph.h | 66 igraph-1.2.7/igraph/src/walktrap_heap.cpp | 238 igraph-1.2.7/igraph/src/walktrap_heap.h | 117 igraph-1.2.7/igraph/src/zeroin.c | 277 igraph-1.2.7/igraph/tests/testthat.R | 2 igraph-1.2.7/igraph/tests/testthat/test-make_graph.R | 22 igraph-1.2.7/igraph/tests/testthat/test-make_lattice.R |only igraph-1.2.7/igraph/tests/testthat/test_add.edges.R | 2 igraph-1.2.7/igraph/tests/testthat/test_all.st.cuts.R | 6 igraph-1.2.7/igraph/tests/testthat/test_are.connected.R | 18 igraph-1.2.7/igraph/tests/testthat/test_arpack.R | 4 igraph-1.2.7/igraph/tests/testthat/test_as.directed.R | 4 igraph-1.2.7/igraph/tests/testthat/test_ba.game.R | 18 igraph-1.2.7/igraph/tests/testthat/test_bipartite.projection.R | 36 igraph-1.2.7/igraph/tests/testthat/test_bipartite.random.game.R | 20 igraph-1.2.7/igraph/tests/testthat/test_bug-1073705-indexing.R | 4 igraph-1.2.7/igraph/tests/testthat/test_cliques.R | 3 igraph-1.2.7/igraph/tests/testthat/test_communities.R | 5 igraph-1.2.7/igraph/tests/testthat/test_correlated.R | 8 igraph-1.2.7/igraph/tests/testthat/test_count.multiple.R | 2 igraph-1.2.7/igraph/tests/testthat/test_degree.sequence.game.R | 4 igraph-1.2.7/igraph/tests/testthat/test_delete.vertices.R | 2 igraph-1.2.7/igraph/tests/testthat/test_evcent.R | 3 igraph-1.2.7/igraph/tests/testthat/test_get.adjacency.R | 8 igraph-1.2.7/igraph/tests/testthat/test_get.adjlist.R | 7 igraph-1.2.7/igraph/tests/testthat/test_get.edge.R | 2 igraph-1.2.7/igraph/tests/testthat/test_get.edgelist.R | 2 igraph-1.2.7/igraph/tests/testthat/test_get.shortest.paths.R | 4 igraph-1.2.7/igraph/tests/testthat/test_graph.adjacency.R | 6 igraph-1.2.7/igraph/tests/testthat/test_graph.adjlist.R | 4 igraph-1.2.7/igraph/tests/testthat/test_graph.atlas.R | 8 igraph-1.2.7/igraph/tests/testthat/test_graph.complementer.R | 2 igraph-1.2.7/igraph/tests/testthat/test_graph.compose.R | 4 igraph-1.2.7/igraph/tests/testthat/test_graph.de.bruijn.R | 6 igraph-1.2.7/igraph/tests/testthat/test_graph.edgelist.R | 6 igraph-1.2.7/igraph/tests/testthat/test_graph.knn.R | 8 igraph-1.2.7/igraph/tests/testthat/test_graph.subisomorphic.lad.R | 10 igraph-1.2.7/igraph/tests/testthat/test_graph.subisomorphic.vf2.R | 4 igraph-1.2.7/igraph/tests/testthat/test_graphNEL.R | 4 igraph-1.2.7/igraph/tests/testthat/test_graphlets.R | 4 igraph-1.2.7/igraph/tests/testthat/test_hsbm.R | 12 igraph-1.2.7/igraph/tests/testthat/test_igraph.options.R | 4 igraph-1.2.7/igraph/tests/testthat/test_is.bipartite.R | 2 igraph-1.2.7/igraph/tests/testthat/test_layout.kk.R | 3 igraph-1.2.7/igraph/tests/testthat/test_layout.merge.R | 2 igraph-1.2.7/igraph/tests/testthat/test_leiden.R |only igraph-1.2.7/igraph/tests/testthat/test_minimum.size.separators.R | 2 igraph-1.2.7/igraph/tests/testthat/test_modularity_matrix.R | 15 igraph-1.2.7/igraph/tests/testthat/test_multilevel.community.R | 8 igraph-1.2.7/igraph/tests/testthat/test_neighborhood.R | 2 igraph-1.2.7/igraph/tests/testthat/test_operators.R | 10 igraph-1.2.7/igraph/tests/testthat/test_operators3.R | 22 igraph-1.2.7/igraph/tests/testthat/test_pajek.R | 4 igraph-1.2.7/igraph/tests/testthat/test_sbm.game.R | 3 igraph-1.2.7/igraph/tests/testthat/test_sphere.R | 10 igraph-1.2.7/igraph/tests/testthat/test_unfold.tree.R | 4 igraph-1.2.7/igraph/tests/testthat/test_watts.strogatz.game.R | 2 553 files changed, 103568 insertions(+), 95314 deletions(-)
Title: Genetic Algorithms
Description: Flexible general-purpose toolbox implementing genetic algorithms (GAs) for stochastic optimisation. Binary, real-valued, and permutation representations are available to optimize a fitness function, i.e. a function provided by users depending on their objective function. Several genetic operators are available and can be combined to explore the best settings for the current task. Furthermore, users can define new genetic operators and easily evaluate their performances. Local search using general-purpose optimisation algorithms can be applied stochastically to exploit interesting regions. GAs can be run sequentially or in parallel, using an explicit master-slave parallelisation or a coarse-grain islands approach.
Author: Luca Scrucca [aut, cre] (<https://orcid.org/0000-0003-3826-0484>)
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between GA versions 3.2.1 dated 2021-04-21 and 3.2.2 dated 2021-10-15
DESCRIPTION | 8 ++-- MD5 | 27 ++++++++-------- NEWS.md | 4 ++ R/gade.R | 13 ++++++- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 10 +++--- inst/doc/GA.R | 4 +- inst/doc/GA.Rmd | 8 ++-- inst/doc/GA.html | 86 ++++++++++++++++++++++++++-------------------------- man/GA-package.Rd | 5 +-- man/de.Rd | 6 ++- man/ga.Rd | 4 +- src/RcppExports.cpp | 5 +++ vignettes/GA.Rmd | 8 ++-- 15 files changed, 104 insertions(+), 84 deletions(-)
Title: Tools to Visualize CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafvis' R-package provides a collection of R-operators for the analysis and
visualization of CM SAF NetCDF data.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafvis versions 1.1.5 dated 2021-09-06 and 1.1.7 dated 2021-10-15
DESCRIPTION | 24 MD5 | 136 - NAMESPACE | 83 NEWS.md | 8 R/absolute_map.R | 14 R/absolute_map_builder.R | 154 - R/anomaly_map.R | 16 R/calculate_climatology.R | 562 +++--- R/calculate_climatology_mean.R | 142 - R/calculate_climatology_outfile.R | 159 - R/check_infile_monitor_climate.R | 38 R/climatology_map.R | 20 R/cmsaf.diff.R | 9 R/cmsaf.hist.R | 202 +- R/cmsaf.hovmoller.R | 191 +- R/cmsaf.scatter.R | 8 R/cmsaf.side.by.side.R | 770 ++++---- R/cmsaf.time.series.R | 410 ++-- R/compare_grid.R | 90 - R/compare_spatial_range.R | 84 R/create_country_mask.R | 327 +-- R/extractFinalOutfile.R | 195 +- R/extractOutfile.R | 97 - R/extractOutfileMean.R | 88 R/extract_climate_files.R | 324 +-- R/fieldmean_and_anomaly_map.R | 10 R/fieldmean_clima.R | 108 - R/fieldmean_current.R | 162 - R/fieldmean_ensemble.R | 304 +-- R/fieldmean_plot.R | 15 R/getUserOptions.R | 83 R/get_basename.R |only R/monitor_climate.R | 5 R/parse_arguments.R | 32 R/plot_abs_map.R | 10 R/plot_abs_map_mean.R | 8 R/plot_time_series.R | 213 +- R/plot_trend.R | 1086 ++++++------ R/plot_warming_stripes.R | 5 R/quicklook.R | 268 ++- R/render_plot.R | 1271 +++++++------- R/render_plot_hovmoller.R | 118 - R/render_plot_side_by_side.R | 2654 +++++++++++++++--------------- R/render_region_plot.R | 507 ++--- R/reset_par.R |only R/time_series_plot.R | 384 ++-- R/trend_plot.R | 392 ++-- R/warming_stripes_plot.R | 10 build/partial.rdb |binary inst/extdata/CMSAF_NoName_Black_s.png |only inst/extdata/CMSAF_NoName_Colour_crop.png |binary inst/extdata/quicklook_config.yml | 869 +++++++++ man/absolute_map.Rd | 6 man/anomaly_map.Rd | 6 man/climatology_map.Rd | 6 man/cmsaf.diff.Rd | 10 man/cmsaf.hist.Rd | 10 man/cmsaf.hovmoller.Rd | 10 man/cmsaf.scatter.Rd | 10 man/cmsaf.side.by.side.Rd | 10 man/cmsaf.time.series.Rd | 10 man/fieldmean_and_anomaly_map.Rd | 6 man/fieldmean_plot.Rd | 6 man/get_basename.Rd |only man/monitor_climate.Rd | 6 man/quicklook.Rd | 9 man/render_plot_hovmoller.Rd | 10 man/render_region_plot.Rd | 6 man/time_series_plot.Rd | 6 man/trend_plot.Rd | 6 man/warming_stripes_plot.Rd | 6 71 files changed, 7033 insertions(+), 5771 deletions(-)
Title: Analysis of the Nigeria National Data Repository (NDR)
Description: The goal is to simplify routine analysis of the Nigeria National Data Repository (NDR) <https://ndr.shieldnigeriaproject.com> using the PEPFAR Monitoring, Evaluation, and Reporting (MER) indicators (see <https://datim.zendesk.com/hc/en-us/articles/360000084446-MER-Indicator-Reference-Guides>). It is designed to import in to R patient-level line-list downloaded as 'csv' file from the front-end of the NDR.
Author: Stephen Balogun [aut, cre] (<https://orcid.org/0000-0002-9928-3703>),
Scholastica Olanrewaju [ctb],
Oluwaseun Okunuga [ctb],
Temitope Kolade [ctb],
Geraldine Abone [ctb]
Maintainer: Stephen Balogun <stephentaiyebalogun@gmail.com>
Diff between tidyndr versions 0.1.0 dated 2021-03-23 and 0.1.1 dated 2021-10-15
DESCRIPTION | 8 MD5 | 16 - NEWS.md | 11 R/disaggregate.R | 421 ++++++++++++++-------------- README.md | 341 +++++++---------------- build/vignette.rds |binary inst/doc/Augmenting-tidyndr.html | 4 inst/doc/tidyndr.html | 570 ++++++++++++--------------------------- man/disaggregate.Rd | 2 9 files changed, 536 insertions(+), 837 deletions(-)
Title: Obtain Unweighted Natural Strata that Balance Many Covariates
Description: Natural strata can be used in observational studies to balance
the distributions of many covariates across any number of treatment
groups and any number of comparisons. These strata have proportional
amounts of units within each stratum across the treatments, allowing
for simple interpretation and aggregation across strata. Within each
stratum, the units are chosen using randomized rounding of a linear
program that balances many covariates.
To solve the linear program, the 'Gurobi' commercial optimization software
is recommended, but not required. The 'gurobi' R package can be installed following the instructions
at <https://www.gurobi.com/documentation/9.1/refman/ins_the_r_package.html>.
Author: Katherine Brumberg [aut, cre]
Maintainer: Katherine Brumberg <kbrum@wharton.upenn.edu>
Diff between natstrat versions 1.0.0 dated 2021-05-26 and 2.0.0 dated 2021-10-15
DESCRIPTION | 20 - MD5 | 73 ++-- NAMESPACE | 4 NEWS.md | 29 + R/balance_LP.R | 81 +++- R/check_balance.R | 89 +++-- R/create_balance_matrices.R |only R/create_dist_matrix.R | 2 R/data.R | 40 ++ R/generate_constraints.R | 37 +- R/generate_qs.R | 132 +++++-- R/optimize_controls.R | 483 ++++++++++++++++++----------- R/randomized_rounding.R | 61 +-- R/randomized_rounding_expectation.R |only R/stand.R | 88 +---- R/verify_optimize_controls_inputs.R |only README.md | 20 - build/vignette.rds |binary data/nh0506_3groups.rda |only inst/doc/natstrat.R | 50 ++- inst/doc/natstrat.Rmd | 88 +++++ inst/doc/natstrat.html | 131 ++++++- man/balance_LP.Rd | 15 man/check_balance.Rd | 16 man/create_balance_matrices.Rd |only man/create_dist_matrix.Rd | 2 man/generate_constraints.Rd | 27 + man/generate_qs.Rd | 24 - man/get_stand_diffs.Rd | 16 man/nh0506_3groups.Rd |only man/optimize_controls.Rd | 125 ++++++- man/process_qs.Rd |only man/randomized_rounding.Rd | 25 - man/randomized_rounding_expectation.Rd |only man/stand.Rd | 33 - man/verify_inputs.Rd | 24 - man/verify_inputs_EMD.Rd | 15 man/verify_multi_comp_inputs.Rd |only tests/testthat/test-generate_constraints.R | 32 - tests/testthat/test-generate_qs.R | 2 tests/testthat/test-optimize_controls.R | 320 ++++++++++++++++--- vignettes/natstrat.Rmd | 88 +++++ 42 files changed, 1567 insertions(+), 625 deletions(-)
Title: Instrumental-Variables Regression by '2SLS', '2SM', or '2SMM',
with Diagnostics
Description: Instrumental variable estimation for linear models by two-stage least-squares (2SLS) regression or by robust-regression via M-estimation (2SM) or MM-estimation (2SMM). The main ivreg() model-fitting function is designed to provide a workflow as similar as possible to standard lm() regression. A wide range of methods is provided for fitted ivreg model objects, including extensive functionality for computing and graphing regression diagnostics in addition to other standard model tools.
Author: John Fox [aut, cre] (<https://orcid.org/0000-0002-1196-8012>),
Christian Kleiber [aut] (<https://orcid.org/0000-0002-6781-4733>),
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>),
Nikolas Kuschnig [ctb] (<https://orcid.org/0000-0002-6642-2543>)
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between ivreg versions 0.6-0 dated 2021-05-28 and 0.6-1 dated 2021-10-15
DESCRIPTION | 16 +- MD5 | 36 ++--- NEWS.md | 21 +++ R/ivreg.R | 13 + R/ivreg.fit.R | 6 R/ivregDiagnostics.R | 177 +++++++++++--------------- R/ivregMethods.R | 25 ++- build/vignette.rds |binary inst/doc/Diagnostics-for-2SLS-Regression.html | 27 +-- inst/doc/ivreg.Rmd | 4 inst/doc/ivreg.html | 25 ++- man/figures/README-effects-1.png |binary man/figures/README-influenceplot-1.png |binary man/figures/README-qqplot-1.png |binary man/ivreg.Rd | 9 + man/ivreg.fit.Rd | 2 man/ivregDiagnostics.Rd | 12 - man/ivregMethods.Rd | 2 vignettes/ivreg.Rmd | 4 19 files changed, 200 insertions(+), 179 deletions(-)
Title: Collect and Clean Hockey Stats
Description: Various functions to scrape hockey play-by-play data from the
<https://www.nhl.com/>. It also contains functions to scrape data from <https://www.hockey-reference.com/>,
including standings, player stats, and jersey number history.
Author: Daniel Morse [aut, cre]
Maintainer: Daniel Morse <danmorse8642@gmail.com>
Diff between hockeyR versions 0.1.0 dated 2021-09-20 and 0.1.1 dated 2021-10-15
DESCRIPTION | 12 MD5 | 48 NAMESPACE | 2 NEWS.md | 13 R/fix_player_columns.R | 64 R/get_game_ids.R | 196 +- R/get_game_info.R | 160 +- R/get_game_rosters.R | 62 R/get_game_shifts.R | 190 +- R/get_jersey_players.R | 172 +- R/get_player_stats_hr.R | 56 R/get_rosters.R | 312 +-- R/get_team_records.R | 206 +- R/load_pbp.R | 124 - R/scrape_day.R | 68 R/scrape_game.R | 1672 ++++++++++----------- R/scrape_season.R | 74 R/utils-pipe.R |only README.md | 38 inst/doc/hockey-ref-scrapers.R | 31 inst/doc/hockey-ref-scrapers.Rmd | 31 inst/doc/hockey-ref-scrapers.html | 42 man/pipe.Rd |only vignettes/hockey-ref-scrapers.Rmd | 31 vignettes/man/figures/vignettes-plot-example-1.png |binary vignettes/man/figures/vignettes-rosters-1.png |binary 26 files changed, 1821 insertions(+), 1783 deletions(-)
Title: Generalized Linear Models with Truncated Lasso Penalty
Description: Extremely efficient procedures for fitting regularization path with l0, l1, and truncated lasso penalty for linear regression and logistic regression models. This version is a completely new version compared with our previous version, which was mainly based on R. New core algorithms are developed and are now written in C++ and highly optimized.
Author: Chunlin Li [aut],
Yu Yang [aut, cre],
Chong Wu [aut]
Maintainer: Yu Yang <yang6367@umn.edu>
Diff between glmtlp versions 1.1 dated 2018-02-07 and 2.0.0 dated 2021-10-15
glmtlp-1.1/glmtlp/R/cvglmTLP.R |only glmtlp-1.1/glmtlp/R/glmTLP.R |only glmtlp-1.1/glmtlp/data/QuickStartExample.RData |only glmtlp-1.1/glmtlp/man/QuickStartExample.Rd |only glmtlp-1.1/glmtlp/man/cv.glmTLP.Rd |only glmtlp-1.1/glmtlp/man/glmTLP.Rd |only glmtlp-1.1/glmtlp/man/glmtlp-package.Rd |only glmtlp-1.1/glmtlp/man/x.Rd |only glmtlp-1.1/glmtlp/man/y.Rd |only glmtlp-2.0.0/glmtlp/DESCRIPTION | 36 +++++++++---- glmtlp-2.0.0/glmtlp/MD5 | 68 ++++++++++++++++++++----- glmtlp-2.0.0/glmtlp/NAMESPACE | 28 ++++++++-- glmtlp-2.0.0/glmtlp/NEWS.md |only glmtlp-2.0.0/glmtlp/R/cv.glmtlp.R |only glmtlp-2.0.0/glmtlp/R/data.R |only glmtlp-2.0.0/glmtlp/R/gaussian_l0_reg.R |only glmtlp-2.0.0/glmtlp/R/gaussian_l1_reg.R |only glmtlp-2.0.0/glmtlp/R/gaussian_tlp_reg.R |only glmtlp-2.0.0/glmtlp/R/glmtlp.R |only glmtlp-2.0.0/glmtlp/R/glmtlp_package.R |only glmtlp-2.0.0/glmtlp/R/lambda_names.R |only glmtlp-2.0.0/glmtlp/R/logistic_l0_reg.R |only glmtlp-2.0.0/glmtlp/R/logistic_l1_reg.R |only glmtlp-2.0.0/glmtlp/R/logistic_tlp_reg.R |only glmtlp-2.0.0/glmtlp/R/loss.R |only glmtlp-2.0.0/glmtlp/R/plot_cv_glmtlp.R |only glmtlp-2.0.0/glmtlp/R/plot_glmtlp.R |only glmtlp-2.0.0/glmtlp/R/predict.R |only glmtlp-2.0.0/glmtlp/R/predict_cv.R |only glmtlp-2.0.0/glmtlp/R/setup_lambda.R |only glmtlp-2.0.0/glmtlp/R/standardize.R |only glmtlp-2.0.0/glmtlp/README.md |only glmtlp-2.0.0/glmtlp/build |only glmtlp-2.0.0/glmtlp/data/bin_data.rda |only glmtlp-2.0.0/glmtlp/data/gau_data.rda |only glmtlp-2.0.0/glmtlp/inst |only glmtlp-2.0.0/glmtlp/man/bin_data.Rd |only glmtlp-2.0.0/glmtlp/man/cv.glmtlp.Rd |only glmtlp-2.0.0/glmtlp/man/figures |only glmtlp-2.0.0/glmtlp/man/gau_data.Rd |only glmtlp-2.0.0/glmtlp/man/glmtlp.Rd |only glmtlp-2.0.0/glmtlp/man/plot.cv.glmtlp.Rd |only glmtlp-2.0.0/glmtlp/man/plot.glmtlp.Rd |only glmtlp-2.0.0/glmtlp/man/predict.cv.glmtlp.Rd |only glmtlp-2.0.0/glmtlp/man/predict.glmtlp.Rd |only glmtlp-2.0.0/glmtlp/src |only glmtlp-2.0.0/glmtlp/vignettes |only 47 files changed, 106 insertions(+), 26 deletions(-)
Title: Diewert and Fox's Method of Value Added Growth Decomposition
Description: Decomposing value added growth into explanatory factors.
A cost constrained value added function is defined to specify the
production frontier. Industry estimates can also be aggregated using
a weighted average approach.
Details about the methodology and data can be found in Diewert and Fox (2018)
<doi:10.1093/oxfordhb/9780190226718.013.19>
and Zeng, Parsons, Diewert and Fox (2018)
<https://www.business.unsw.edu.au/research-site/centreforappliedeconomicresearch-site/Documents/emg2018-6_SZeng_EMG-Slides.pdf>.
Author: Shipei Zeng
Maintainer: Shipei Zeng <shipei.zeng@unswalumni.com>
Diff between dfvad versions 0.3.0 dated 2020-03-05 and 0.3.6 dated 2021-10-15
dfvad-0.3.0/dfvad/man/figures/README-unnamed-chunk-5-1.png |only dfvad-0.3.6/dfvad/DESCRIPTION | 14 ++--- dfvad-0.3.6/dfvad/MD5 | 34 ++++++++++--- dfvad-0.3.6/dfvad/NAMESPACE | 3 + dfvad-0.3.6/dfvad/R/dynamics.R |only dfvad-0.3.6/dfvad/R/firms.R |only dfvad-0.3.6/dfvad/R/pb_index.R |only dfvad-0.3.6/dfvad/R/pm_index.R |only dfvad-0.3.6/dfvad/R/prices.R |only dfvad-0.3.6/dfvad/README.md | 19 ++++++- dfvad-0.3.6/dfvad/data/firms.rda |only dfvad-0.3.6/dfvad/data/prices.rda |only dfvad-0.3.6/dfvad/inst/doc/dfvad_vignette.html | 4 - dfvad-0.3.6/dfvad/inst/extdata |only dfvad-0.3.6/dfvad/man/dynamics.Rd |only dfvad-0.3.6/dfvad/man/figures/README-unnamed-chunk-7-1.png |only dfvad-0.3.6/dfvad/man/firms.Rd |only dfvad-0.3.6/dfvad/man/pb_index.Rd |only dfvad-0.3.6/dfvad/man/pm_index.Rd |only dfvad-0.3.6/dfvad/man/prices.Rd |only dfvad-0.3.6/dfvad/tests/testthat/test_dynamics.R |only dfvad-0.3.6/dfvad/tests/testthat/test_pb_index.R |only dfvad-0.3.6/dfvad/tests/testthat/test_pm_index.R |only dfvad-0.3.6/dfvad/tests/testthat/test_t_weight.R | 8 +++ dfvad-0.3.6/dfvad/tests/testthat/test_value_decom.R | 3 + 25 files changed, 68 insertions(+), 17 deletions(-)
Title: Person Fit
Description: Several person-fit statistics
(PFSs; Meijer and Sijtsma, 2001, <doi:10.1177/01466210122031957>)
are offered. These statistics allow assessing whether
individual response patterns to tests or questionnaires are (im)plausible given
the other respondents in the sample or given a specified item response theory model. Some PFSs apply to
dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs
(personal biserial correlation, caution index, (normed) number of Guttman errors,
agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include
extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro
Maintainer: Jorge N. Tendeiro <tendeiro@hiroshima-u.ac.jp>
Diff between PerFit versions 1.4.5 dated 2021-02-21 and 1.4.6 dated 2021-10-15
DESCRIPTION | 10 - MD5 | 8 R/Accessory.R | 446 +++++++++++++++++++++++++------------------------- build/partial.rdb |binary man/PerFit-package.Rd | 1 5 files changed, 233 insertions(+), 232 deletions(-)
Title: Calculate and Predict the Low Density Lipoprotein Values
Description: A wide variety of ways to calculate (through equations) or predict (using 9 Machine learning methods as well as a stack algorithm combination of them all) the Low Density Lipoprotein values of patients based on the values of three other metrics as Total Cholesterol , Triglyceride and High Density Lipoprotein.
Author: Petros Paplomatas [aut, cre],
Kostas Anagnostopoulos [aut]
Maintainer: Petros Paplomatas <P.paplomatas@hotmail.com>
Diff between LDLcalc versions 1.0 dated 2021-09-30 and 1.1 dated 2021-10-15
DESCRIPTION | 17 ++++++++++------- MD5 | 24 ++++++++++++------------ R/9ML_models_functions.R | 6 +++--- R/All9Models.R | 2 +- R/Plot_functions.R | 2 +- R/SampleData.R | 2 +- R/Stacking_Algorith_Model_Functions.R | 3 ++- man/Corr_Plot.Rd | 2 +- man/LDL_ML_Main.Rd | 4 ++-- man/LDL_ML_Main_All_Models.Rd | 2 +- man/LDL_ML_Main_StackingAlgorithm.Rd | 2 +- man/LDL_ML_predict.Rd | 2 +- man/SampleData.Rd | 2 +- 13 files changed, 37 insertions(+), 33 deletions(-)
Title: Interactive Parallel Categories Diagrams for 'easyalluvial'
Description: Complex graphical representations of data are best explored using interactive elements.
'parcats' adds interactive graphing capabilities to the 'easyalluvial' package.
The 'plotly.js' parallel categories diagrams offer a good framework for
creating interactive flow graphs that allow manual drag and drop sorting of dimensions
and categories, highlighting single flows and displaying mouse over information. The
'plotly.js' dependency is quite heavy and therefore is outsourced into a separate package.
Author: Bjoern Koneswarakantha [aut, cre]
(<https://orcid.org/0000-0003-4585-7799>)
Maintainer: Bjoern Koneswarakantha <datistics@gmail.com>
Diff between parcats versions 0.0.2 dated 2020-09-09 and 0.0.3 dated 2021-10-15
DESCRIPTION | 19 - MD5 | 30 +- NAMESPACE | 1 NEWS.md | 3 R/parcats.R | 25 + README.md | 50 ++- inst/WORDLIST | 9 inst/htmlwidgets/lib/plotly.js/LICENSE | 2 inst/htmlwidgets/lib/plotly.js/locales/plotly-locale-cs.js | 2 inst/htmlwidgets/lib/plotly.js/plotly.min.js | 33 +- inst/htmlwidgets/parcats.js | 2 inst/htmlwidgets/parcats.yaml | 2 inst/shiny/parcats/rsconnect |only inst/shiny/parcats/server.R | 59 ++++ inst/shiny/parcats/ui.R | 171 ++++++++++++- man/parcats.Rd | 2 man/parcats_demo.Rd |only 17 files changed, 327 insertions(+), 83 deletions(-)
Title: R Interface to 'MiniZinc'
Description: Constraint optimization, or constraint programming, is the name given to identifying
feasible solutions out of a very large set of candidates, where the problem can be modeled in terms
of arbitrary constraints. 'MiniZinc' is a free and open-source constraint modeling language.
Constraint satisfaction and discrete optimization problems can be formulated in a high-level
modeling language. Models are compiled into an intermediate representation that is understood by a
wide range of solvers. 'MiniZinc' itself provides several solvers, for instance 'GeCode'. R users
can use the package to solve constraint programming problems without using 'MiniZinc' directly,
modify existing 'MiniZinc' models and also create their own models.
Author: Akshit Achara, Lars Kotthoff, Hans W. Borchers, Guido Tack
Maintainer: Akshit Achara <acharaakshit@gmail.com>
Diff between rminizinc versions 0.0.7 dated 2021-08-04 and 0.0.8 dated 2021-10-15
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- build/vignette.rds |binary configure | 18 +++++++++--------- configure.ac | 10 +++------- configure.win | 18 +++++++++--------- data/config.RData |binary data/proot.RData |binary data/slvbin.RData |binary src/RcppExports.cpp | 5 +++++ 10 files changed, 39 insertions(+), 38 deletions(-)
Title: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset
Description: Provides a daily summary of the Coronavirus (COVID-19) cases by state/province. Data source: Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus <https://systems.jhu.edu/research/public-health/ncov/>.
Author: Rami Krispin [aut, cre],
Jarrett Byrnes [aut] (<https://orcid.org/0000-0002-9791-9472>)
Maintainer: Rami Krispin <rami.krispin@gmail.com>
Diff between coronavirus versions 0.3.30 dated 2021-09-19 and 0.3.31 dated 2021-10-15
coronavirus-0.3.30/coronavirus/inst/doc/update_dataset_function.R |only coronavirus-0.3.30/coronavirus/inst/doc/update_dataset_function.Rmd |only coronavirus-0.3.30/coronavirus/inst/doc/update_dataset_function.html |only coronavirus-0.3.30/coronavirus/vignettes/update_dataset_function.Rmd |only coronavirus-0.3.31/coronavirus/DESCRIPTION | 6 coronavirus-0.3.31/coronavirus/MD5 | 28 - coronavirus-0.3.31/coronavirus/NEWS.md | 11 coronavirus-0.3.31/coronavirus/R/data.R | 8 coronavirus-0.3.31/coronavirus/R/refresh_coronvirus.R | 5 coronavirus-0.3.31/coronavirus/README.md | 177 +++++----- coronavirus-0.3.31/coronavirus/build/vignette.rds |binary coronavirus-0.3.31/coronavirus/data/coronavirus.rda |binary coronavirus-0.3.31/coronavirus/data/covid19_vaccine.rda |binary coronavirus-0.3.31/coronavirus/man/coronavirus.Rd | 8 coronavirus-0.3.31/coronavirus/man/figures/brazil_cases.svg | 2 coronavirus-0.3.31/coronavirus/man/figures/top20_countries.svg | 2 coronavirus-0.3.31/coronavirus/man/figures/treemap_conf.svg | 2 17 files changed, 141 insertions(+), 108 deletions(-)
Title: Arbitrary-Precision Integer and Floating-Point Mathematics
Description: Classes for storing and manipulating arbitrary-precision
integer vectors and high-precision floating-point vectors. These
extend the range and precision of the 'integer' and 'double' data
types found in R. This package utilizes the 'Boost.Multiprecision' C++
library. It is specifically designed to work well with the 'tidyverse'
collection of R packages.
Author: David Hall [aut, cre, cph] (<https://orcid.org/0000-0002-2193-0480>)
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between bignum versions 0.2.2 dated 2021-09-21 and 0.3.0 dated 2021-10-15
bignum-0.2.2/bignum/inst/doc/operations.R |only bignum-0.2.2/bignum/inst/doc/operations.Rmd |only bignum-0.2.2/bignum/inst/doc/operations.html |only bignum-0.2.2/bignum/vignettes/operations.Rmd |only bignum-0.3.0/bignum/DESCRIPTION | 10 - bignum-0.3.0/bignum/MD5 | 52 ++++----- bignum-0.3.0/bignum/NAMESPACE | 4 bignum-0.3.0/bignum/NEWS.md | 10 + bignum-0.3.0/bignum/R/biginteger.R | 2 bignum-0.3.0/bignum/R/conditions.R | 27 +++- bignum-0.3.0/bignum/R/cpp11.R | 24 ++++ bignum-0.3.0/bignum/R/seq.R |only bignum-0.3.0/bignum/R/vctrs-arith.R | 41 +++++++ bignum-0.3.0/bignum/R/vctrs-compare.R | 21 +++ bignum-0.3.0/bignum/R/vctrs-math.R | 107 +++++++++++++++++++ bignum-0.3.0/bignum/README.md | 2 bignum-0.3.0/bignum/build/vignette.rds |binary bignum-0.3.0/bignum/inst/doc/precision.html | 26 ++-- bignum-0.3.0/bignum/inst/doc/type-hierarchy.html | 57 +++++----- bignum-0.3.0/bignum/man/biginteger.Rd | 2 bignum-0.3.0/bignum/man/bignum-arith.Rd |only bignum-0.3.0/bignum/man/bignum-compare.Rd |only bignum-0.3.0/bignum/man/bignum-math.Rd |only bignum-0.3.0/bignum/man/bignum-package.Rd | 7 - bignum-0.3.0/bignum/man/bignum-special.Rd |only bignum-0.3.0/bignum/man/seq.bignum_vctr.Rd |only bignum-0.3.0/bignum/src/bigfloat_interface.cpp | 81 ++++++++++++++ bignum-0.3.0/bignum/src/biginteger_interface.cpp | 89 +++++++++++++++ bignum-0.3.0/bignum/src/cpp11.cpp | 54 +++++++++ bignum-0.3.0/bignum/tests/testthat/_snaps/seq.md |only bignum-0.3.0/bignum/tests/testthat/test-bigfloat.R | 8 - bignum-0.3.0/bignum/tests/testthat/test-seq.R |only bignum-0.3.0/bignum/tests/testthat/test-vctrs-math.R | 4 33 files changed, 540 insertions(+), 88 deletions(-)