Title: Estimating Finite State Machine Models from Data
Description: Automatic generation of finite state machine models of dynamic
decision-making that both have strong predictive power and are
interpretable in human terms. We use an efficient model representation and
a genetic algorithm-based estimation process to generate simple
deterministic approximations that explain most of the structure of complex
stochastic processes. We have applied the software to empirical data, and
demonstrated it's ability to recover known data-generating processes by
simulating data with agent-based models and correctly deriving the
underlying decision models for multiple agent models and degrees of
stochasticity.
Author: Nay John J. [aut],
Gilligan Jonathan M. [cre, aut]
Maintainer: Gilligan Jonathan M. <jonathan.gilligan@vanderbilt.edu>
Diff between datafsm versions 0.2.1 dated 2017-10-20 and 0.2.2 dated 2018-08-08
datafsm-0.2.1/datafsm/inst/doc/datafsmVignette.R |only datafsm-0.2.1/datafsm/inst/doc/datafsmVignette.Rmd |only datafsm-0.2.1/datafsm/inst/doc/datafsmVignette.html |only datafsm-0.2.1/datafsm/vignettes/datafsmVignette.Rmd |only datafsm-0.2.2/datafsm/DESCRIPTION | 30 datafsm-0.2.2/datafsm/LICENSE | 2 datafsm-0.2.2/datafsm/MD5 | 52 - datafsm-0.2.2/datafsm/NEWS.md | 10 datafsm-0.2.2/datafsm/R/RcppExports.R | 18 datafsm-0.2.2/datafsm/R/class_def.R | 4 datafsm-0.2.2/datafsm/R/data.R |only datafsm-0.2.2/datafsm/R/evolve_model.R | 344 +++++----- datafsm-0.2.2/datafsm/R/evolve_model_cv.R | 67 - datafsm-0.2.2/datafsm/R/evolve_model_ntimes.R | 52 - datafsm-0.2.2/datafsm/build/vignette.rds |binary datafsm-0.2.2/datafsm/data |only datafsm-0.2.2/datafsm/inst/doc/FRD_vignette.Rmd |only datafsm-0.2.2/datafsm/inst/doc/FRD_vignette.html |only datafsm-0.2.2/datafsm/inst/doc/datafsm_introduction.R |only datafsm-0.2.2/datafsm/inst/doc/datafsm_introduction.Rmd |only datafsm-0.2.2/datafsm/inst/doc/datafsm_introduction.html |only datafsm-0.2.2/datafsm/man/NV_games.Rd |only datafsm-0.2.2/datafsm/man/datafsm.Rd | 1 datafsm-0.2.2/datafsm/man/evolve_model.Rd | 173 ++--- datafsm-0.2.2/datafsm/man/evolve_model_cv.Rd | 75 +- datafsm-0.2.2/datafsm/man/evolve_model_ntimes.Rd | 132 +-- datafsm-0.2.2/datafsm/man/figures/README/plot.evolution-1.png |binary datafsm-0.2.2/datafsm/man/figures/README/plot.fsm-1.png |binary datafsm-0.2.2/datafsm/man/fitnessCPP.Rd | 12 datafsm-0.2.2/datafsm/man/ga_fsm-class.Rd | 22 datafsm-0.2.2/datafsm/src/RcppExports.cpp | 14 datafsm-0.2.2/datafsm/src/fitnessCPP.cpp | 125 ++- datafsm-0.2.2/datafsm/vignettes/FRD_vignette.Rmd |only datafsm-0.2.2/datafsm/vignettes/datafsm_introduction.Rmd |only 34 files changed, 607 insertions(+), 526 deletions(-)
Title: Taxonomic Classes
Description: Provides taxonomic classes for
groupings of taxonomic names without data, and those
with data. Methods provided are "taxonomically aware", in
that they know about ordering of ranks, and methods that
filter based on taxonomy also filter associated data.
Author: Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Zachary Foster [aut, cre] (<https://orcid.org/0000-0002-5075-0948>)
Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>
Diff between taxa versions 0.2.1 dated 2018-05-03 and 0.3.1 dated 2018-08-08
DESCRIPTION | 6 MD5 | 76 ++--- NAMESPACE | 9 NEWS.md | 40 ++ R/taxmap--class.R | 470 ++++++++++++++++++++++--------- R/taxmap--docs.R | 130 ++++++-- R/taxmap--internal.R | 64 +++- R/taxmap--option_parsers.R |only R/taxmap--parsers.R | 40 +- R/taxmap--printers.R | 64 ++++ R/taxmap--s3.R | 113 ++++--- R/taxonomy--class.R | 133 ++++++++ R/taxonomy--docs.R | 61 ++++ R/taxonomy--internal.R | 65 +++- R/taxonomy--s3.R | 38 ++ data/ex_taxmap.rda |binary data/ex_taxonomy.rda |binary inst/doc/taxa-introduction.html | 4 man/arrange_obs.Rd | 13 man/can_be_used_in_taxmap.Rd |only man/extract_tax_data.Rd | 2 man/filter_obs.Rd | 21 - man/get_dataset.Rd |only man/highlight_taxon_ids.Rd |only man/lookup_tax_data.Rd | 4 man/mutate_obs.Rd | 9 man/n_obs.Rd | 9 man/n_obs_1.Rd | 9 man/obs.Rd | 4 man/parse_dataset.Rd |only man/parse_raw_heirarchies_to_taxonomy.Rd |only man/parse_tax_data.Rd | 18 - man/print_tree.Rd |only man/sample_frac_obs.Rd | 13 man/sample_n_obs.Rd | 13 man/select_obs.Rd | 16 - man/taxmap.Rd | 13 man/taxonomy.Rd | 8 man/taxonomy_table.Rd |only man/transmute_obs.Rd | 9 tests/testthat/test--taxmap.R | 84 ++++- tests/testthat/test--taxmap_parsers.R | 39 +- tests/testthat/test--taxonomy.R | 19 + 43 files changed, 1234 insertions(+), 382 deletions(-)
Title: Plot Flow Charts According to the "PRISMA" Statement
Description: Plot a PRISMA <http://prisma-statement.org/> flow
chart describing the identification, screening, eligibility and
inclusion or studies in systematic reviews. PRISMA is an
evidence-based minimum set of items for reporting in systematic
reviews and meta-analyses. PRISMA focuses on the reporting of reviews
evaluating randomized trials, but can also be used as a basis for
reporting systematic reviews of other types of research, particularly
evaluations of interventions.
Author: Jack O. Wasey [aut, cre, cph]
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Diff between PRISMAstatement versions 1.0.3 dated 2018-08-04 and 1.0.4 dated 2018-08-08
DESCRIPTION | 8 MD5 | 21 - NAMESPACE | 1 NEWS.md | 5 R/prisma.r | 49 +- inst/doc/PRISMA.R | 17 inst/doc/PRISMA.Rmd | 40 +- inst/doc/PRISMA.html | 734 ++++++++++++++++++++++++------------------- man/prisma.Rd | 2 man/prisma_pdf.Rd |only tests/testthat/test-prisma.r | 13 vignettes/PRISMA.Rmd | 40 +- 12 files changed, 556 insertions(+), 374 deletions(-)
More information about PRISMAstatement at CRAN
Permanent link
Title: Efficient Iterator for Permutations and Combinations
Description: Iterator for generating permutations and combinations. They
can be either drawn with or without replacement, or with distinct/ non-distinct
items (multiset). The generated sequences are in lexicographical order
(dictionary order). The algorithms to generate permutations and combinations are
memory efficient. These iterative algorithms enable users to process all sequences
without putting all results in the memory at the same time.
The algorithms are written in C/C++ for faster performance. Note: 'iterpc' is no longer
being maintained. Users are recommended to switch to 'arrangements'.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between iterpc versions 0.4.0 dated 2018-04-24 and 0.4.1 dated 2018-08-08
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/iterpc.R | 18 +++++++++++++++--- build/vignette.rds |binary inst/doc/combinations.html | 32 +++++++++++++------------------- inst/doc/permutations.html | 33 ++++++++++++--------------------- man/iterpc.Rd | 6 ++++-- 7 files changed, 55 insertions(+), 56 deletions(-)
Title: Clinical Trial Designs in 'RStan'
Description: A showcase of Bayesian clinical trial designs, implemented in
'RStan' and R. Some designs are implemented in R for the first
time (e.g. 'EffTox' by Thall and Cook, 2004,
<https://biostatistics.mdanderson.org/softwaredownload/SingleSoftware.aspx?Software_Id=2>).
Given the emphasis on flexibility in Bayesian analysis,
the implementations in a common language and style may serve as a cookbook
to encourage the use of Bayesian methods in trials. Compiled 'RStan' models
are provided in addition to helper classes and functions to perform
simulations and inference on observed trial outcomes.
There is a preponderance of early phase trial designs because this is where
Bayesian methods are used most. If there is a published Bayesian design you
want implemented in 'Stan', get in touch.
Author: Kristian Brock [aut, cre],
Trustees of Columbia University [cph]
Maintainer: Kristian Brock <kristian.brock@gmail.com>
Diff between trialr versions 0.0.1 dated 2017-11-21 and 0.0.2 dated 2018-08-08
trialr-0.0.1/trialr/R/efftox.R |only trialr-0.0.1/trialr/exec/ThallHierachicalBinary.stan |only trialr-0.0.1/trialr/man/Rcpp_model_ThallHierachicalBinary-class.Rd |only trialr-0.0.1/trialr/man/efftox_params.Rd |only trialr-0.0.1/trialr/man/model_ThallHierachicalBinary.Rd |only trialr-0.0.2/trialr/DESCRIPTION | 23 trialr-0.0.2/trialr/MD5 | 160 trialr-0.0.2/trialr/NAMESPACE | 87 trialr-0.0.2/trialr/NEWS.md | 28 trialr-0.0.2/trialr/R/CRM.R |only trialr-0.0.2/trialr/R/EffTox.R |only trialr-0.0.2/trialr/R/dosefinding.R |only trialr-0.0.2/trialr/R/peps2.R | 562 trialr-0.0.2/trialr/R/ranBin2.R | 160 trialr-0.0.2/trialr/R/zzz.R | 10 trialr-0.0.2/trialr/README.md | 506 trialr-0.0.2/trialr/build/partial.rdb |binary trialr-0.0.2/trialr/build/vignette.rds |binary trialr-0.0.2/trialr/exec/BebopInPeps2.stan | 168 trialr-0.0.2/trialr/exec/CrmEmpiricNormalPrior.stan |only trialr-0.0.2/trialr/exec/CrmOneParamLogisticGammaPrior.stan |only trialr-0.0.2/trialr/exec/CrmOneParamLogisticNormalPrior.stan |only trialr-0.0.2/trialr/exec/CrmTwoParamLogisticNormalPrior.stan |only trialr-0.0.2/trialr/exec/EffTox.stan | 234 trialr-0.0.2/trialr/exec/ThallHierarchicalBinary.stan | 100 trialr-0.0.2/trialr/inst/doc/BEBOP.R | 98 trialr-0.0.2/trialr/inst/doc/BEBOP.Rmd | 322 trialr-0.0.2/trialr/inst/doc/BEBOP.html | 948 trialr-0.0.2/trialr/inst/doc/CRM-visualisation.R |only trialr-0.0.2/trialr/inst/doc/CRM-visualisation.Rmd |only trialr-0.0.2/trialr/inst/doc/CRM-visualisation.html |only trialr-0.0.2/trialr/inst/doc/CRM.R |only trialr-0.0.2/trialr/inst/doc/CRM.Rmd |only trialr-0.0.2/trialr/inst/doc/CRM.html |only trialr-0.0.2/trialr/inst/doc/EffTox.R | 185 trialr-0.0.2/trialr/inst/doc/EffTox.Rmd | 607 trialr-0.0.2/trialr/inst/doc/EffTox.html | 976 trialr-0.0.2/trialr/inst/doc/HierarchicalBayesianResponse.R | 58 trialr-0.0.2/trialr/inst/doc/HierarchicalBayesianResponse.Rmd | 222 trialr-0.0.2/trialr/inst/doc/HierarchicalBayesianResponse.html | 884 trialr-0.0.2/trialr/inst/doc/trialr-overview.R |only trialr-0.0.2/trialr/inst/doc/trialr-overview.Rmd |only trialr-0.0.2/trialr/inst/doc/trialr-overview.html |only trialr-0.0.2/trialr/man/Rcpp_model_ThallHierarchicalBinary-class.Rd | 17 trialr-0.0.2/trialr/man/as.data.frame.crm_fit.Rd |only trialr-0.0.2/trialr/man/as.data.frame.efftox_fit.Rd |only trialr-0.0.2/trialr/man/crm_fit-class.Rd |only trialr-0.0.2/trialr/man/crm_params-class.Rd |only trialr-0.0.2/trialr/man/crm_process.Rd |only trialr-0.0.2/trialr/man/df_parse_outcomes.Rd |only trialr-0.0.2/trialr/man/efftox_analysis.Rd | 1 trialr-0.0.2/trialr/man/efftox_analysis_to_df.Rd | 60 trialr-0.0.2/trialr/man/efftox_contour_plot.Rd | 136 trialr-0.0.2/trialr/man/efftox_dtps.Rd | 104 trialr-0.0.2/trialr/man/efftox_fit-class.Rd |only trialr-0.0.2/trialr/man/efftox_get_tox.Rd | 102 trialr-0.0.2/trialr/man/efftox_parameters_demo.Rd | 56 trialr-0.0.2/trialr/man/efftox_params-class.Rd |only trialr-0.0.2/trialr/man/efftox_parse_outcomes.Rd | 97 trialr-0.0.2/trialr/man/efftox_process.Rd | 76 trialr-0.0.2/trialr/man/efftox_simulate.Rd | 123 trialr-0.0.2/trialr/man/efftox_solve_p.Rd | 72 trialr-0.0.2/trialr/man/efftox_superiority.Rd | 64 trialr-0.0.2/trialr/man/efftox_utility.Rd | 81 trialr-0.0.2/trialr/man/efftox_utility_density_plot.Rd | 78 trialr-0.0.2/trialr/man/figures |only trialr-0.0.2/trialr/man/gather_samples.crm_fit.Rd |only trialr-0.0.2/trialr/man/gather_samples.efftox_fit.Rd |only trialr-0.0.2/trialr/man/model_BebopInPeps2.Rd | 78 trialr-0.0.2/trialr/man/model_EffTox.Rd | 90 trialr-0.0.2/trialr/man/model_ThallHierarchicalBinary.Rd | 66 trialr-0.0.2/trialr/man/peps2_get_data.Rd | 216 trialr-0.0.2/trialr/man/peps2_process.Rd | 156 trialr-0.0.2/trialr/man/peps2_run_sims.Rd | 128 trialr-0.0.2/trialr/man/plot.crm_fit.Rd |only trialr-0.0.2/trialr/man/plot.efftox_fit.Rd |only trialr-0.0.2/trialr/man/print.crm_fit.Rd |only trialr-0.0.2/trialr/man/print.efftox_fit.Rd |only trialr-0.0.2/trialr/man/ranBin2.Rd | 72 trialr-0.0.2/trialr/man/stan_crm.Rd |only trialr-0.0.2/trialr/man/stan_efftox.Rd |only trialr-0.0.2/trialr/man/stan_efftox_demo.Rd |only trialr-0.0.2/trialr/man/summary.crm_fit.Rd |only trialr-0.0.2/trialr/man/summary.efftox_fit.Rd |only trialr-0.0.2/trialr/man/thallhierarchicalbinary_parameters_demo.Rd | 56 trialr-0.0.2/trialr/man/trialr-package.Rd | 200 trialr-0.0.2/trialr/src/Modules.cpp | 145 trialr-0.0.2/trialr/src/include/models.hpp | 4363 ++- trialr-0.0.2/trialr/tests |only trialr-0.0.2/trialr/vignettes/BEBOP.Rmd | 322 trialr-0.0.2/trialr/vignettes/CRM-visualisation.Rmd |only trialr-0.0.2/trialr/vignettes/CRM.Rmd |only trialr-0.0.2/trialr/vignettes/EffTox.Rmd | 607 trialr-0.0.2/trialr/vignettes/EffTox_cache/html/__packages | 22 trialr-0.0.2/trialr/vignettes/EffTox_cache/html/run_sims_f82b60090eba4ebe42c302621d520c5f.RData |binary trialr-0.0.2/trialr/vignettes/EffTox_cache/html/run_sims_f82b60090eba4ebe42c302621d520c5f.rdx |binary trialr-0.0.2/trialr/vignettes/EffTox_files |only trialr-0.0.2/trialr/vignettes/HierarchicalBayesianResponse.Rmd | 222 trialr-0.0.2/trialr/vignettes/library.bib |11388 ++++++---- trialr-0.0.2/trialr/vignettes/trialr-overview.Rmd |only 100 files changed, 15218 insertions(+), 10318 deletions(-)
Title: Weighted Cumulative Exposure Models
Description: A flexible method for modeling cumulative effects of time-varying exposures, weighted according to their relative proximity in time, and represented by time-dependent covariates. The current implementation estimates the weight function in the Cox proportional hazards model. The function that assigns weights to doses taken in the past is estimated using cubic regression splines.
Author: Marie-Pierre Sylvestre, Marie-Eve Beauchamp, Ryan Patrick Kyle, Michal Abrahamowicz
Maintainer: Marie-Pierre Sylvestre <marie-pierre.sylvestre@umontreal.ca>
Diff between WCE versions 1.0.1 dated 2018-07-04 and 1.0.2 dated 2018-08-08
WCE-1.0.1/WCE/R/WCE.data.frame.R |only WCE-1.0.2/WCE/DESCRIPTION | 8 +++---- WCE-1.0.2/WCE/MD5 | 15 ++++++-------- WCE-1.0.2/WCE/NAMESPACE | 1 WCE-1.0.2/WCE/NEWS | 5 ++++ WCE-1.0.2/WCE/R/WCE-internal.R | 40 +++++++++++++++++++++++++++++++++++++++ WCE-1.0.2/WCE/R/WCE.R | 5 ---- WCE-1.0.2/WCE/R/WCE.cox.R | 3 +- WCE-1.0.2/WCE/man/wce-package.Rd | 4 +-- 9 files changed, 62 insertions(+), 19 deletions(-)
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 0.53.4 dated 2018-07-13 and 0.54.3 dated 2018-08-08
DESCRIPTION | 10 +- MD5 | 22 +++--- R/effectpowermc.R |only R/eval_design_mc.R | 118 +++++++++++++++++++++++++++++------ R/gen_design.R | 7 +- R/plot_correlations.R | 2 R/skprGUIserver.R | 10 +- man/effectpowermc.Rd |only man/eval_design_mc.Rd | 16 +++- src/genOptimalDesign.cpp | 3 tests/testthat/Rplots.pdf |binary tests/testthat/testDeltaProcessing.R | 66 +++++++++++++++++-- tests/testthat/testExampleCode.R | 43 ++++++++++++ 13 files changed, 240 insertions(+), 57 deletions(-)
Title: Distributed-Lag Linear Structural Equation Models
Description: Inference functionalities for distributed-lag linear structural equation models (DLSEMs). DLSEMs are Markovian structural causal models (Pearl, 2000, Chapter 5) <ISBN:978-0-521-89560-6>, where each factor of the joint probability distribution is a distributed-lag linear regression model (Judge et al., 1985, Chapters 9-10) <ISBN: 978-0-471-89530-5>. DLSEMs account for temporal delays in the dependence relationships among the variables and allow to perform dynamic causal inference by assessing causal effects at different time lags. Endpoint-constrained quadratic, quadratic decreasing and gamma lag shapes are available.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <alessandro.magrini@unifi.it>
Diff between dlsem versions 2.3 dated 2018-06-08 and 2.4 dated 2018-08-08
Changelog |only DESCRIPTION | 12 MD5 | 29 + NAMESPACE | 8 R/dlsem.r | 669 ++++++++++++++++++++++++++++++------------- inst/doc/dlsem_vignette.R | 32 +- inst/doc/dlsem_vignette.Rnw | 94 ++---- inst/doc/dlsem_vignette.pdf |binary man/agres.Rd | 2 man/causalEff.Rd | 13 man/dlsem-package.Rd | 6 man/dlsem.Rd | 79 ++--- man/lagPlot.Rd | 4 man/uncons.lag.Rd |only man/unirootTest.Rd | 13 man/vcovHAC.Rd |only vignettes/dlsem_vignette.Rnw | 94 ++---- 17 files changed, 654 insertions(+), 401 deletions(-)
Title: Functions for Statistics Classes at Carleton College
Description: Includes commands for bootstrapping and permutation tests, a command for created grouped bar plots, and a demo of the quantile-normal plot for data drawn from different distributions.
Author: Laura Chihara
Maintainer: Laura Chihara <lchihara@carleton.edu>
Diff between CarletonStats versions 1.3 dated 2016-07-19 and 2.0 dated 2018-08-08
CarletonStats-1.3/CarletonStats/R/CarletonStats-internal.R |only CarletonStats-2.0/CarletonStats/DESCRIPTION | 12 - CarletonStats-2.0/CarletonStats/MD5 | 90 ++++---- CarletonStats-2.0/CarletonStats/NAMESPACE | 79 +++++-- CarletonStats-2.0/CarletonStats/R/Data.R |only CarletonStats-2.0/CarletonStats/R/anovaSummarized.R | 42 +++- CarletonStats-2.0/CarletonStats/R/boot.R | 58 +++++ CarletonStats-2.0/CarletonStats/R/boot.default.R | 66 ++---- CarletonStats-2.0/CarletonStats/R/boot.formula.R | 23 +- CarletonStats-2.0/CarletonStats/R/bootCor.R | 115 ++++------ CarletonStats-2.0/CarletonStats/R/bootCor.default.R |only CarletonStats-2.0/CarletonStats/R/bootCor.formula.R |only CarletonStats-2.0/CarletonStats/R/bootPaired.R | 126 ++++-------- CarletonStats-2.0/CarletonStats/R/bootPaired.default.R |only CarletonStats-2.0/CarletonStats/R/bootPaired.formula.R |only CarletonStats-2.0/CarletonStats/R/confIntDemo.R | 33 ++- CarletonStats-2.0/CarletonStats/R/corDemo.R | 24 ++ CarletonStats-2.0/CarletonStats/R/groupedBar.R | 45 ++++ CarletonStats-2.0/CarletonStats/R/groupedBar.default.R | 129 ++++++------ CarletonStats-2.0/CarletonStats/R/groupedBar.formula.R | 12 - CarletonStats-2.0/CarletonStats/R/missingLevel.R | 19 + CarletonStats-2.0/CarletonStats/R/permTest.R | 51 ++++ CarletonStats-2.0/CarletonStats/R/permTest.default.R | 34 +-- CarletonStats-2.0/CarletonStats/R/permTest.formula.R | 3 CarletonStats-2.0/CarletonStats/R/permTestCor.R | 120 ++++------- CarletonStats-2.0/CarletonStats/R/permTestCor.default.R |only CarletonStats-2.0/CarletonStats/R/permTestCor.formula.R |only CarletonStats-2.0/CarletonStats/R/permTestPaired.R | 124 ++++------- CarletonStats-2.0/CarletonStats/R/permTestPaired.default.R |only CarletonStats-2.0/CarletonStats/R/permTestPaired.formula.R |only CarletonStats-2.0/CarletonStats/R/qqPlotDemo.R | 33 +++ CarletonStats-2.0/CarletonStats/R/stemPlot.R | 36 +++ CarletonStats-2.0/CarletonStats/R/stemPlot.default.R | 3 CarletonStats-2.0/CarletonStats/R/stemPlot.formula.R | 17 + CarletonStats-2.0/CarletonStats/man/Icecream.Rd | 43 +--- CarletonStats-2.0/CarletonStats/man/Milkshakes.Rd | 50 ++-- CarletonStats-2.0/CarletonStats/man/anovaSummarized.Rd | 67 ++---- CarletonStats-2.0/CarletonStats/man/boot.Rd | 127 ++++++------ CarletonStats-2.0/CarletonStats/man/bootCor.Rd | 115 ++++++---- CarletonStats-2.0/CarletonStats/man/bootPaired.Rd | 116 ++++++----- CarletonStats-2.0/CarletonStats/man/confIntDemo.Rd | 53 ++--- CarletonStats-2.0/CarletonStats/man/corDemo.Rd | 37 +-- CarletonStats-2.0/CarletonStats/man/groupedBar.Rd | 131 +++++------- CarletonStats-2.0/CarletonStats/man/missingLevel.Rd | 44 +--- CarletonStats-2.0/CarletonStats/man/permTest.Rd | 136 ++++++------- CarletonStats-2.0/CarletonStats/man/permTestCor.Rd | 122 +++++++---- CarletonStats-2.0/CarletonStats/man/permTestPaired.Rd | 127 +++++++----- CarletonStats-2.0/CarletonStats/man/qqPlotDemo.Rd | 91 ++++---- CarletonStats-2.0/CarletonStats/man/states03.Rd | 83 ++++--- CarletonStats-2.0/CarletonStats/man/stemPlot.Rd | 87 ++++---- CarletonStats-2.0/CarletonStats/tests |only 51 files changed, 1558 insertions(+), 1165 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, with optional sampling techniques and kernel term.
Author: Alencar Xavier, William Muir, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 1.5.3 dated 2018-06-07 and 1.5.4 dated 2018-08-08
bWGR-1.5.3/bWGR/R/emcv.R |only bWGR-1.5.3/bWGR/src/wgr032018.cpp |only bWGR-1.5.4/bWGR/DESCRIPTION | 8 - bWGR-1.5.4/bWGR/MD5 | 20 ++-- bWGR-1.5.4/bWGR/R/RcppExports.R | 150 +++++++++++++++++++++--------------- bWGR-1.5.4/bWGR/R/cv.R |only bWGR-1.5.4/bWGR/R/mix.R | 4 bWGR-1.5.4/bWGR/man/bWGR.Rd | 6 - bWGR-1.5.4/bWGR/man/em.Rd | 10 +- bWGR-1.5.4/bWGR/man/mix.Rd | 4 bWGR-1.5.4/bWGR/man/wgr.Rd | 35 +++++++- bWGR-1.5.4/bWGR/src/RcppExports.cpp | 138 +++++++++++++++++++++++++++++++++ bWGR-1.5.4/bWGR/src/wgr20180808.cpp |only 13 files changed, 290 insertions(+), 85 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-26 0.0.1
Title: High Performance Container Data Types
Description: Provides high performance container data types such as Queue, Stack, Deque, Dict and OrderedDict. Benchmarks <https://randy3k.github.io/collections/articles/benchmark.html> have shown that these containers are asymptotically more efficient than those offered by other packages.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between collections versions 0.1.0 dated 2018-07-30 and 0.1.1 dated 2018-08-08
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/deque.R | 4 ++-- R/queue.R | 4 ++-- R/stack.R | 4 ++-- man/Deque.Rd | 2 +- man/DequeL.Rd | 2 +- man/Queue.Rd | 2 +- man/QueueL.Rd | 2 +- man/Stack.Rd | 2 +- man/StackL.Rd | 2 +- 11 files changed, 26 insertions(+), 26 deletions(-)
Title: Automated C Code Generation for 'deSolve', 'bvpSolve' and
'Sundials'
Description: Generates all necessary C functions allowing the user to work with
the compiled-code interface of ode() and bvptwp(). The implementation supports
"forcings" and "events". Also provides functions to symbolically compute
Jacobians, sensitivity equations and adjoint sensitivities being the basis for
sensitivity analysis. Alternatively to 'deSolve', the Sundials 'CVODES' solver is
implemented for computation of model sensitivities.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@gmail.com>
Diff between cOde versions 0.3 dated 2017-09-07 and 0.4.1 dated 2018-08-08
cOde-0.3/cOde/man/cOde-package.Rd |only cOde-0.4.1/cOde/DESCRIPTION | 8 - cOde-0.4.1/cOde/MD5 | 28 ++--- cOde-0.4.1/cOde/NAMESPACE | 1 cOde-0.4.1/cOde/R/RcppExports.R | 4 cOde-0.4.1/cOde/R/cOde.R | 118 ++++++++++++++++++++---- cOde-0.4.1/cOde/R/derivedEquations.R | 112 +++++++++++++++++++--- cOde-0.4.1/cOde/R/symbolics.R | 41 +++++++- cOde-0.4.1/cOde/R/tools.R | 9 + cOde-0.4.1/cOde/inst/examples/example1.R | 54 ++++++++++ cOde-0.4.1/cOde/inst/include/cOde_RcppExports.h | 8 - cOde-0.4.1/cOde/man/funC.Rd | 10 +- cOde-0.4.1/cOde/man/odeC.Rd | 54 ++++++++++ cOde-0.4.1/cOde/man/replaceNumbers.Rd |only cOde-0.4.1/cOde/man/sensitivitiesSymb.Rd | 9 + cOde-0.4.1/cOde/src/RcppExports.cpp | 18 +-- 16 files changed, 401 insertions(+), 73 deletions(-)
Title: Teaching Hydrological Modelling with the GR Rainfall-Runoff
Models ('Shiny' Interface Included)
Description: Add-on package to the 'airGR' package that simplifies its use and is aimed at being used for teaching hydrology. The package provides 1) three functions that allow to complete very simply a hydrological modelling exercise 2) plotting functions to help students to explore observed data and to interpret the results of calibration and simulation of the GR ('Génie rural') models 3) a 'Shiny' graphical interface that allows for displaying the impact of model parameters on hydrographs and models internal variables.
Author: Olivier Delaigue [aut, cre],
Laurent Coron [aut],
Pierre Brigode [aut],
Guillaume Thirel [ctb]
Maintainer: Olivier Delaigue <airGR@irstea.fr>
Diff between airGRteaching versions 0.2.2.2 dated 2018-03-21 and 0.2.3.2 dated 2018-08-08
airGRteaching-0.2.2.2/airGRteaching/R/zz_dygraphs_group.R |only airGRteaching-0.2.2.2/airGRteaching/R/zz_dygraphs_plotters.R |only airGRteaching-0.2.2.2/airGRteaching/R/zz_dygraphs_series.R |only airGRteaching-0.2.2.2/airGRteaching/R/zz_dygraphs_utils.R |only airGRteaching-0.2.3.2/airGRteaching/DESCRIPTION | 14 +- airGRteaching-0.2.3.2/airGRteaching/MD5 | 47 ++++++---- airGRteaching-0.2.3.2/airGRteaching/NAMESPACE | 14 -- airGRteaching-0.2.3.2/airGRteaching/NEWS | 10 ++ airGRteaching-0.2.3.2/airGRteaching/R/Utils.R | 8 - airGRteaching-0.2.3.2/airGRteaching/R/dyplot.default.R | 2 airGRteaching-0.2.3.2/airGRteaching/build/vignette.rds |binary airGRteaching-0.2.3.2/airGRteaching/inst/CITATION | 14 +- airGRteaching-0.2.3.2/airGRteaching/inst/ShinyGR/server.R | 14 +- airGRteaching-0.2.3.2/airGRteaching/inst/doc/get_started.html | 8 - airGRteaching-0.2.3.2/airGRteaching/inst/doc/get_started.rmd | 6 - airGRteaching-0.2.3.2/airGRteaching/man/airGRteaching.Rd | 2 airGRteaching-0.2.3.2/airGRteaching/vignettes/fig |only airGRteaching-0.2.3.2/airGRteaching/vignettes/get_started.rmd | 6 - 18 files changed, 74 insertions(+), 71 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-08 0.8.3
2018-07-22 0.8.2
Title: Data-Driven Identification of SVAR Models
Description: Implements data-driven identification methods for structural vector autoregressive (SVAR) models.
Based on an existing VAR model object (provided by e.g. VAR() from the 'vars' package), the structural
impact matrix is obtained via data-driven identification techniques (i.e. changes in volatility (Rigobon, R. (2003) <doi:10.1162/003465303772815727>),
least dependent innovations (Herwartz, H., Ploedt, M., (2016) <doi:10.1016/j.jimonfin.2015.11.001>) or non-Gaussian maximum likelihood (Lanne, M., Meitz, M., Saikkonen, P. (2017) <doi:10.1016/j.jeconom.2016.06.002>).
Author: Alexander Lange [aut, cre],
Bernhard Dalheimer [aut],
Helmut Herwartz [aut],
Simone Maxand [aut],
Hannes Riebl [ctb]
Maintainer: Alexander Lange <alexander.lange@uni-goettingen.de>
Diff between svars versions 1.2.0 dated 2018-06-07 and 1.2.1 dated 2018-08-08
svars-1.2.0/svars/R/fev.R |only svars-1.2.0/svars/R/imrf.R |only svars-1.2.0/svars/R/ld.dc.R |only svars-1.2.0/svars/R/plot.irf.R |only svars-1.2.0/svars/R/plot_fevd.R |only svars-1.2.0/svars/man/fev.Rd |only svars-1.2.0/svars/man/imrf.Rd |only svars-1.2.1/svars/DESCRIPTION | 16 svars-1.2.1/svars/MD5 | 110 +++-- svars-1.2.1/svars/NAMESPACE | 20 - svars-1.2.1/svars/R/Wald.test.R | 10 svars-1.2.1/svars/R/bootstrap_mb.R | 67 +-- svars-1.2.1/svars/R/bootstrap_wild.R | 53 +- svars-1.2.1/svars/R/chow.test.R | 292 +++++++++------ svars-1.2.1/svars/R/fevd.svars.R |only svars-1.2.1/svars/R/get_var_objects.R |only svars-1.2.1/svars/R/hd.R | 22 - svars-1.2.1/svars/R/id.cv.R | 68 +-- svars-1.2.1/svars/R/id.cvm.R | 97 ----- svars-1.2.1/svars/R/id.dc.R |only svars-1.2.1/svars/R/id.ngml.R | 307 +--------------- svars-1.2.1/svars/R/id.st.R | 88 +--- svars-1.2.1/svars/R/id_cv_boot.R | 43 -- svars-1.2.1/svars/R/id_ngml_boot.R | 128 +----- svars-1.2.1/svars/R/id_st_boot.R | 41 -- svars-1.2.1/svars/R/identifyNGML.R |only svars-1.2.1/svars/R/identifyVolatility.R | 32 - svars-1.2.1/svars/R/identifyVolatility_boot.R | 16 svars-1.2.1/svars/R/irf.svars.R |only svars-1.2.1/svars/R/iterative_smooth_transition.R | 14 svars-1.2.1/svars/R/js_test.R | 9 svars-1.2.1/svars/R/likelihood_ngml.R | 45 +- svars-1.2.1/svars/R/likelihood_st.R | 4 svars-1.2.1/svars/R/plot.chowpretest.R |only svars-1.2.1/svars/R/plot.sboot.R | 6 svars-1.2.1/svars/R/plot.svarfevd.R |only svars-1.2.1/svars/R/plot.svarirf.R |only svars-1.2.1/svars/R/print.chow.R |only svars-1.2.1/svars/R/print.chowpretest.R |only svars-1.2.1/svars/R/print.hd.R |only svars-1.2.1/svars/R/print.jstest.R |only svars-1.2.1/svars/R/print.sboot.R |only svars-1.2.1/svars/R/print.svarfevd.R |only svars-1.2.1/svars/R/print.svarirf.R |only svars-1.2.1/svars/R/print.svars.R |only svars-1.2.1/svars/R/stability.R |only svars-1.2.1/svars/R/summary.chow.R | 28 - svars-1.2.1/svars/R/summary.jstest.R | 11 svars-1.2.1/svars/R/summary.svars.R | 29 - svars-1.2.1/svars/README.md | 8 svars-1.2.1/svars/man/chow.test.Rd | 45 +- svars-1.2.1/svars/man/fevd.Rd |only svars-1.2.1/svars/man/hd.Rd | 8 svars-1.2.1/svars/man/id.cv.Rd | 13 svars-1.2.1/svars/man/id.cvm.Rd | 14 svars-1.2.1/svars/man/id.dc.Rd | 8 svars-1.2.1/svars/man/id.ngml.Rd | 14 svars-1.2.1/svars/man/id.st.Rd | 18 svars-1.2.1/svars/man/irf.Rd |only svars-1.2.1/svars/man/js.test.Rd | 9 svars-1.2.1/svars/man/mb.boot.Rd | 42 +- svars-1.2.1/svars/man/stability.Rd |only svars-1.2.1/svars/man/svars-package.Rd | 2 svars-1.2.1/svars/man/wild.boot.Rd | 37 + svars-1.2.1/svars/tests/testthat/test-id.st.R |only svars-1.2.1/svars/tests/testthat/test-id_ngml.R | 98 ++++- svars-1.2.1/svars/tests/testthat/test-likelihood_ngml.R | 122 ++++-- svars-1.2.1/svars/tests/testthat/test-likelihood_st.R | 12 svars-1.2.1/svars/tests/testthat/test-mb_boot.R | 51 +- svars-1.2.1/svars/tests/testthat/test-wild_boot.R | 44 +- 70 files changed, 982 insertions(+), 1119 deletions(-)
Title: Designing Population PDX Studies
Description: Run simulations to assess the impact of various designs features
and the underlying biological behaviour on the outcome of a Patient Derived
Xenograft (PDX) population study. This project can either be deployed to a
server as a 'shiny' app or installed locally as a package and run the app
using the command 'populationPDXdesignApp()'.
Author: Maria Luisa Guerriero [aut, cre],
Natasha Karp [aut]
Maintainer: Maria Luisa Guerriero <maria.guerriero@astrazeneca.com>
Diff between populationPDXdesign versions 1.0.2 dated 2018-06-15 and 1.0.3 dated 2018-08-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plotFalsepositive.R | 2 +- R/plotSensitivity.R | 6 +++--- 4 files changed, 11 insertions(+), 11 deletions(-)
More information about populationPDXdesign at CRAN
Permanent link
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available. The methods are described in
Hothorn et al. (2006) <doi:10.1198/106186006X133933>,
Zeileis et al. (2008) <doi:10.1198/106186008X319331> and
Strobl et al. (2007) <doi:10.1186/1471-2105-8-25>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>),
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.3-0 dated 2018-04-20 and 1.3-1 dated 2018-08-08
DESCRIPTION | 11 +++--- MD5 | 14 ++++---- R/varimp.R | 86 +---------------------------------------------------- build/vignette.rds |binary inst/NEWS | 5 +++ inst/doc/MOB.pdf |binary inst/doc/party.pdf |binary man/varimp.Rd | 9 +++-- 8 files changed, 25 insertions(+), 100 deletions(-)
Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression
models with missing values in covariates or the dependent
variable using maximum likelihood or Bayesian estimation
(Ibrahim et al., 2005; <doi:10.1198/016214504000001844>).
The regression model can be nonlinear (e.g., interaction
effects, quadratic effects or B-spline functions).
Multilevel models with missing data in predictors are
available for Bayesian estimation. Substantive-model compatible
multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between mdmb versions 0.8-47 dated 2018-07-09 and 0.9-43 dated 2018-08-08
DESCRIPTION | 18 ++--- MD5 | 93 +++++++++++++++--------------- NAMESPACE | 1 R/RcppExports.R | 14 ++++ R/bc_trafo_derivative.R |only R/dbct_scaled.R | 26 ++------ R/dbct_scaled_mdmb_regression_wrapper.R |only R/dyjt_scaled.R | 18 +++-- R/dyjt_scaled_log_multiplication.R | 4 - R/fit_mdmb_distribution.R | 27 ++++---- R/fit_yjt_scaled.R | 6 - R/frm_define_model_R_function.R | 5 + R/frm_em.R | 8 +- R/frm_em_calc_likelihood.R | 4 - R/frm_em_calc_likelihood_estimate_model.R | 3 R/frm_fb.R | 3 R/frm_fb_init_imputations.R | 7 +- R/frm_fb_initial_parameters.R | 2 R/frm_fb_partable.R | 5 - R/frm_fb_sample_imputed_values.R | 10 +-- R/frm_fb_sample_imputed_values_proposal.R | 15 ++++ R/frm_fb_sample_parameters.R | 4 - R/frm_mdmb_regression_density.R | 6 - R/frm_prepare_data_em.R | 2 R/frm_prepare_model_nodes_weights.R | 53 ++++++++++++----- R/frm_prepare_models.R | 3 R/frm_prepare_models_descriptives.R |only R/mdmb_dnorm.R | 21 +++++- R/mdmb_regression.R | 38 +++++++----- R/mdmb_regression_R2.R | 6 - R/mdmb_regression_extract_parameters.R | 3 R/mdmb_squeeze.R |only R/ryjt_scaled.R | 6 - R/yj_antitrafo.R | 7 +- R/yj_trafo.R | 8 +- R/yjt_regression.R | 6 - data/data.mb05.rda |only data/datalist | 1 inst/NEWS | 13 ++++ man/data.mb.Rd | 21 ++++++ man/frm.Rd | 69 +++++++++++++++++++--- man/mdmb-package.Rd | 12 +-- man/mdmb_regression.Rd | 9 ++ man/yjt_dist.Rd | 47 ++++++++++++--- src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 44 +++++++++++++- src/mdmb_rcpp_linreg.cpp | 50 +++++++++++++++- src/mdmb_rcpp_linreg.h | 8 ++ src/mdmb_rcpp_yjtreg.cpp | 63 ++++++++++++++++++++ 50 files changed, 567 insertions(+), 206 deletions(-)
Title: Intrinsic Dimension for Data Mining
Description: Contains techniques for mining large and high-dimensional data
sets by using the concept of Intrinsic Dimension (ID). Here the ID is
not necessarily an integer. It is extended to fractal dimensions. And
the Morisita estimator is used for the ID estimation, but other
tools are included as well.
Author: Jean Golay [aut, cre],
Mohamed Laib [aut]
Maintainer: Jean Golay <Jean.Golay@unil.ch>
Diff between IDmining versions 1.0.4 dated 2018-03-21 and 1.0.5 dated 2018-08-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/MINDID_FMC.R | 2 +- R/RenDim.R | 2 +- man/IDmining-package.Rd | 2 +- man/RenDim.Rd | 2 +- 6 files changed, 13 insertions(+), 13 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-19 1.1.6
Title: A Toolkit for Using Whole Building Simulation Program
'EnergyPlus'
Description: A rich toolkit of using the whole building simulation program
'EnergyPlus', which enables programmatic navigation, modification of
'EnergyPlus' models and makes it less painful to do parametric simulations
and analysis.
Author: Hongyuan Jia [aut, cre] (<https://orcid.org/0000-0002-0075-8183>)
Maintainer: Hongyuan Jia <hongyuanjia@cqu.edu.cn>
Diff between eplusr versions 0.8.2 dated 2018-07-22 and 0.8.3 dated 2018-08-08
DESCRIPTION | 8 MD5 | 90 - NAMESPACE | 216 +- NEWS.md | 41 R/assertions.R | 376 ++-- R/constants.R | 118 - R/eplusr.R | 3 R/epw.R | 2142 +++++++++++++-------------- R/format.R | 69 R/idd.R | 947 ++++++------ R/idd_object.R | 82 - R/idf.R | 88 - R/idf_object.R | 888 +++++------ R/impl.R | 102 + R/install.R | 590 +++---- R/job.R | 1269 ++++++++-------- R/param.R | 32 R/parse.R | 2 R/run.R | 974 ++++++------ R/units.R | 1966 ++++++++++++------------- R/validate.R | 816 +++++----- R/zzz.R | 9 README.md | 3028 +++++++++++++++++++-------------------- man/clean_wd.Rd | 30 man/eplus_job.Rd | 48 man/eplusr-package.Rd | 88 - man/eplusr_option.Rd | 90 - man/epw.Rd | 326 ++-- man/idd.Rd | 289 +-- man/idd_object.Rd | 360 ++-- man/idf.Rd | 810 +++++----- man/idf_object.Rd | 485 +++--- man/install_eplus.Rd | 75 man/job.Rd | 261 +-- man/param.Rd | 200 +- man/param_job.Rd | 46 man/read_epw.Rd | 44 man/read_idf.Rd | 56 man/run_model.Rd | 117 - man/use_eplus.Rd | 107 - man/use_idd.Rd | 160 +- tests/testthat.R | 8 tests/testthat/helper-copy.R |only tests/testthat/helper-install.R |only tests/testthat/test_idf.R | 3 tests/testthat/test_idf_object.R | 14 tests/testthat/test_job.R |only tests/testthat/test_param.R |only 48 files changed, 8848 insertions(+), 8625 deletions(-)