Sat, 16 Jun 2018

Package ahnr updated to version 0.3.0 with previous version 0.2.0 dated 2017-08-18

Title: An Implementation of the Artificial Hydrocarbon Networks
Description: Implementation of the Artificial Hydrocarbon Networks for data modeling.
Author: Jose Roberto Ayala Solares [aut, cre]
Maintainer: Jose Roberto Ayala Solares <ichbinjras@gmail.com>

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Package sads updated to version 0.4.2 with previous version 0.4.1 dated 2017-10-24

Title: Maximum Likelihood Models for Species Abundance Distributions
Description: Maximum likelihood tools to fit and compare models of species abundance distributions and of species rank-abundance distributions.
Author: Paulo I. Prado, Murilo Dantas Miranda and Andre Chalom
Maintainer: Paulo I. Prado <prado@ib.usp.br>

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Package supernova updated to version 1.1 with previous version 1.0 dated 2018-02-23

Title: Judd & McClelland Formatting for ANOVA Output
Description: Produces ANOVA tables in the format used by Judd, McClelland, and Ryan (2017, ISBN:978-1138819832) in their introductory textbook, Data Analysis. This includes proportional reduction in error and formatting to improve ease the transition between the book and R.
Author: Jim Stigler [cre, aut], Jeff Chrabaszcz [aut]
Maintainer: Jim Stigler <jstigler@gmail.com>

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New package RxODE with initial version 0.7.2-4
Package: RxODE
Version: 0.7.2-4
Title: Facilities for Simulating from ODE-Based Models
Authors@R: c( person("Matthew L.","Fidler", role = "aut", email = "matthew.fidler@gmail.com"), person("Melissa", "Hallow", role = "aut", email = "hallowkm@uga.edu"), person("Wenping", "Wang", role = c("aut", "cre"), email = "wwang8198@gmail.com"), person("Zufar", "Mulyukov", role="ctb", email="zufar.mulyukov@novartis.com"), person("Justin", "Wilkins", role = "ctb", email = "justin.wilkins@occams.com"), person("Simon", "Frost", role="ctb"), person("Heng", "Li", role="ctb"), person("Yu", "Feng", role="ctb"), person("Alan", "Hindmarsh",role="ctb"), person("Linda", "Petzold", role="ctb"), person("Ernst", "Hairer", role="ctb"), person("Gerhard", "Wanner", role="ctb"), person("J", "Colinge", role="ctb"), person("Hadley", "Wickham", role="ctb"), person("G", "Grothendieck", role="ctb"), person("Robert", "Gentleman",role="ctb"), person("Ross", "Ihaka",role="ctb"), person("R core team", role="cph"), person("odepack authors", role="cph") )
Maintainer: Wenping Wang <wwang8198@gmail.com>
Depends: R (>= 3.3.0)
Suggests: knitr, nlme, shiny, tcltk, testthat, devtools, covr, rmarkdown, SnakeCharmR, rSymPy, dplyr, tidyr, tibble, curl, ggplot2, gridExtra, microbenchmark, scales, stringi, htmltools
Imports: utils, methods, digest, rex, dparser (>= 0.1.8), brew, memoise, magrittr, Rcpp (>= 0.12.3), inline, Matrix, R.utils, PreciseSums (>= 0.3), mvnfast, cli, crayon
Description: Facilities for running simulations from ordinary differential equation (ODE) models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The VODE and LSODA are in the public domain. The information is available in the inst/COPYRIGHTS.
BugReports: https://github.com/nlmixrdevelopment/RxODE/issues
NeedsCompilation: yes
VignetteBuilder: knitr
License: GPL (>= 2)
URL: https://www.r-project.org, https://github.com/nlmixrdevelopment/RxODE
RoxygenNote: 6.0.1
LinkingTo: dparser(>= 0.1.8), Rcpp (>= 0.12.3), RcppArmadillo(>= 0.5.600.2.0), PreciseSums (>= 0.3)
Packaged: 2018-06-16 17:01:38 UTC; WANGWEZ
Author: Matthew L. Fidler [aut], Melissa Hallow [aut], Wenping Wang [aut, cre], Zufar Mulyukov [ctb], Justin Wilkins [ctb], Simon Frost [ctb], Heng Li [ctb], Yu Feng [ctb], Alan Hindmarsh [ctb], Linda Petzold [ctb], Ernst Hairer [ctb], Gerhard Wanner [ctb], J Colinge [ctb], Hadley Wickham [ctb], G Grothendieck [ctb], Robert Gentleman [ctb], Ross Ihaka [ctb], R core team [cph], odepack authors [cph]
Repository: CRAN
Date/Publication: 2018-06-16 19:32:24 UTC

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Package recipes updated to version 0.1.3 with previous version 0.1.2 dated 2018-01-11

Title: Preprocessing Tools to Create Design Matrices
Description: An extensible framework to create and preprocess design matrices. Recipes consist of one or more data manipulation and analysis "steps". Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting design matrices can then be used as inputs into statistical or machine learning models.
Author: Max Kuhn [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>

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New package graphicalVAR with initial version 0.2.2
Package: graphicalVAR
Type: Package
Title: Graphical VAR for Experience Sampling Data
Version: 0.2.2
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Description: Estimates within and between time point interactions in experience sampling data, using the Graphical vector autoregression model in combination with regularization. See also Epskamp, Waldorp, Mottus & Borsboom (2018) <doi:10.1080/00273171.2018.1454823>.
License: GPL (>= 2)
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp (>= 0.11.3), Matrix, glasso, glmnet, mvtnorm, qgraph (>= 1.3.1), dplyr, methods, igraph
Depends: R (>= 3.1.0)
NeedsCompilation: yes
Packaged: 2018-06-16 13:50:55 UTC; sachaepskamp
Repository: CRAN
Date/Publication: 2018-06-16 19:28:45 UTC

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Package languageserver updated to version 0.2.3 with previous version 0.2.2 dated 2018-05-09

Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol> for details.
Author: Randy Lai
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

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Package cdata updated to version 0.7.1 with previous version 0.7.0 dated 2018-04-09

Title: Fluid Data Transformations
Description: Supplies higher-order fluid data transform operators that include pivot and anti-pivot as special cases. The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <http://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , doi:10.5281/zenodo.1173299 . Based on the 'DBI' database interface.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package isni updated to version 0.3 with previous version 0.2 dated 2018-04-09

Title: Index of Local Sensitivity to Nonignorability
Description: The current version provides functions to compute, print and summarize the Index of Sensitivity to Nonignorability (ISNI) in the generalized linear model for independent data, and in the marginal multivariate Gaussian model and the linear mixed model for longitudinal/clustered data. It allows for arbitrary patterns of missingness in the regression outcomes caused by dropout and/or intermittent missingness. One can compute the sensitivity index without estimating any nonignorable models or positing specific magnitude of nonignorability. Thus ISNI provides a simple quantitative assessment of how robust the standard estimates assuming missing at random is with respect to the assumption of ignorability. For a tutorial, download at <http://huixie.people.uic.edu/Research/ISNI_R_tutorial.pdf>. For more details, see Troxel Ma and Heitjan (2004) and Xie and Heitjan (2004) <doi:10.1191/1740774504cn005oa> and Ma Troxel and Heitjan (2005) <doi:10.1002/sim.2107> and Xie (2008) <doi:10.1002/sim.3117> and Xie (2012) <doi:10.1016/j.csda.2010.11.021> and Xie and Qian (2012) <doi:10.1002/jae.1157>.
Author: Hui Xie <huixie@uic.edu>, Weihua Gao, Baodong Xing, Daniel Heitjan, Donald Hedeker, Chengbo Yuan
Maintainer: Hui Xie <huixie@uic.edu>

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Package data.tree updated to version 0.7.6 with previous version 0.7.5 dated 2018-03-06

Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and traverse the tree in various orders. Aggregate, cumulate, print, plot, convert to and from data.frame and more. Useful for decision trees, machine learning, finance, conversion from and to JSON, and many other applications.
Author: Facundo Munoz [ctb] (improve list conversion), Markus Wamser [ctb] (fixed some typos), Pierre Formont [ctb] (additional features), Kent Russel [ctb] (documentation), Noam Ross [ctb] (fixes), Duncan Garmonsway [ctb] (fixes), Christoph Glur [aut, cre] (R interface)
Maintainer: Christoph Glur <christoph.glur@ipub.com>

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Package DisImpact updated to version 0.0.2 with previous version 0.0.1 dated 2018-05-27

Title: Calculates Disproportionate Impact When Binary Success Data are Disaggregated by Subgroups
Description: Implements methods for calculating disproportionate impact: the percentage point gap, proportionality index, and the 80% index. California Community Colleges Chancellor's Office (2017). Percentage Point Gap Method. <http://extranet.cccco.edu/Portals/1/TRIS/Research/Analysis/PercentagePointGapMethod2017.pdf>. California Community Colleges Chancellor's Office (2014). Guidelines for Measuring Disproportionate Impact in Equity Plans. <http://extranet.cccco.edu/Portals/1/TRIS/Research/Accountability/GUIDELINES%20FOR%20MEASURING%20DISPROPORTIONATE%20IMPACT%20IN%20EQUITY%20PLANS.pdf>.
Author: Vinh Nguyen [aut, cre]
Maintainer: Vinh Nguyen <nguyenvq714@gmail.com>

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Package GSODR updated to version 1.2.1 with previous version 1.2.0 dated 2018-03-29

Title: Global Surface Summary of the Day (GSOD) Weather Data from R
Description: Provides automated downloading, parsing, cleaning, unit conversion and formatting of Global Surface Summary of the Day (GSOD) weather data from the from the USA National Centers for Environmental Information (NCEI) for use in R. Units are converted from from United States Customary System (USCS) units to International System of Units (SI). Stations may be individually checked for number of missing days defined by the user, where stations with too many missing observations are omitted. Only stations with valid reported latitude and longitude values are permitted in the final data. Additional useful elements, saturation vapour pressure (es), actual vapour pressure (ea) and relative humidity are calculated from the original data and included in the final data set. The resulting data include station identification information, state, country, latitude, longitude, elevation, weather observations and associated flags. Data may be automatically saved to disk. File output may be returned as a comma-separated values (CSV) or GeoPackage (GPKG) file. Additional data are included with this R package: a list of elevation values for stations between -60 and 60 degrees latitude derived from the Shuttle Radar Topography Measuring Mission (SRTM). For information on the GSOD data from NCEI, please see the GSOD readme.txt file available from, <http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Tomislav Hengl [aut] (<https://orcid.org/0000-0002-9921-5129>), Andrew Nelson [aut] (<https://orcid.org/0000-0002-7249-3778>), Hugh Parsonage [cph, ctb] (<https://orcid.org/0000-0003-4055-0835>), Bob Rudis [cph, ctb] (<https://orcid.org/0000-0001-5670-2640>), Gwenael Giboire [ctb] (Several bug reports in early versions and testing feedback), Łukasz Pawlik [ctb] (Reported bug in windspeed conversion calculation), Ross Darnell [ctb] (Reported bug in Windows OS versions causing GSOD data untarring to fail)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

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Package dmm updated to version 2.1-4 with previous version 2.1-3 dated 2018-01-19

Title: Dyadic Mixed Model for Pedigree Data
Description: Dyadic mixed model analysis with multi-trait responses and pedigree-based partitioning of individual variation into a range of environmental and genetic variance components for individual and maternal effects.
Author: Neville Jackson
Maintainer: Neville Jackson <nanddjackson@bigpond.com>

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Package QTL.gCIMapping updated to version 3.0 with previous version 2.0 dated 2018-04-30

Title: QTL Genome-Wide Composite Interval Mapping
Description: Conduct multiple quantitative trait loci (QTL) mapping under the framework of random-QTL-effect mixed linear model. First, each position on the genome is detected in order to construct a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve are viewed as potential QTL, all the effects of the potential QTL are included in a multi-QTL model, their effects are estimated by empirical Bayes in doubled haploid or by adaptive lasso in F2, and true QTL are identified by likelihood radio test. Wang S-B, Wen Y-J, Ren W-L, Ni Y-L, Zhang J, Feng J-Y, Zhang Y-M (2016) <doi:10.1038/srep29951>.
Author: Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

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Package gggenes updated to version 0.3.1 with previous version 0.3.0 dated 2018-05-26

Title: Draw Gene Arrow Maps in 'ggplot2'
Description: Provides a 'ggplot2' geom and helper functions for drawing gene arrow maps.
Author: David Wilkins [aut, cre]
Maintainer: David Wilkins <david@wilkox.org>

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Package FunChisq updated to version 2.4.5-1 with previous version 2.4.5 dated 2018-02-20

Title: Chi-Square and Exact Tests for Model-Free Functional Dependency
Description: Statistical hypothesis testing methods for model-free functional dependency using asymptotic chi-square or exact distributions. Functional chi-squares are asymmetric and functionally optimal, unique from other related statistics. Tests in this package reveal evidence for causality based on the causality-by-functionality principle. They include asymptotic functional chi-square tests, an exact functional test, a comparative functional chi-square test, and also a comparative chi-square test. The normalized non-constant functional chi-square test was used by Best Performer NMSUSongLab in HPN-DREAM (DREAM8) Breast Cancer Network Inference Challenges. For continuous data, these tests offer an advantage over regression analysis when a parametric functional form cannot be assumed; for categorical data, they provide a novel means to assess directional dependency not possible with symmetrical Pearson's chi-square or Fisher's exact tests.
Author: Yang Zhang [aut], Hua Zhong [aut], Ruby Sharma [aut], Sajal Kumar [aut], Joe Song [aut, cre]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>

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Package bomrang updated to version 0.2.1 with previous version 0.2.0 dated 2018-05-19

Title: Australian Government Bureau of Meteorology Data from R
Description: Provides functions to interface with Australian Government Bureau of Meteorology (BOM) data, fetching data and returning a tidy data frame of précis forecasts, historical and current weather data from stations, agriculture bulletin data, BOM 0900 or 1500 weather bulletins or a raster stack object of satellite imagery from GeoTIFF files. Data (c) Australian Government Bureau of Meteorology Creative Commons (CC) Attribution 3.0 licence or Public Access Licence (PAL) as appropriate. See <http://www.bom.gov.au/other/copyright.shtml> for further details.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Jonathan Carroll [aut] (<https://orcid.org/0000-0002-1404-5264>), Mark Padgham [aut, rev] (<https://orcid.org/0000-0003-2172-5265>), Hugh Parsonage [aut] (<https://orcid.org/0000-0003-4055-0835>), Keith Pembleton [aut] (<https://orcid.org/0000-0002-1896-4516>), James Balamuta [ctb] (<https://orcid.org/0000-0003-2826-8458>), Brooke Anderson [rev] (<https://orcid.org/0000-0002-5012-9035>)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

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Package tranSurv (with last version 1.1-5) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-04-18 1.1-5
2017-02-08 1.1-4
2016-07-18 1.0-0

Permanent link
Package xfun updated to version 0.2 with previous version 0.1 dated 2018-01-22

Title: Miscellaneous Functions by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>)
Maintainer: Yihui Xie <xie@yihui.name>

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Package getCRUCLdata updated to version 0.2.4 with previous version 0.2.3 dated 2018-05-17

Title: Use and Explore CRU CL v. 2.0 Climatology Elements in R
Description: Provides functions that automate downloading and importing University of East Anglia Climate Research Unit (CRU) CL v. 2.0 climatology data into R, facilitates the calculation of minimum temperature and maximum temperature and formats the data into a tidy data frame as a tibble or a list of raster stack objects for use in an R session. CRU CL v. 2.0 data are a gridded climatology of 1961-1990 monthly means released in 2002 and cover all land areas (excluding Antarctica) at 10 arcminutes (0.1666667 degree) resolution. For more information see the description of the data provided by the University of East Anglia Climate Research Unit, <https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

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