Mon, 04 Feb 2019

Package diffractometry (with last version 0.1-10) was removed from CRAN

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

2018-03-16 0.1-10
2013-12-11 0.1-8
2013-06-17 0.1-7
2011-03-11 0.1-03
2010-03-07 0.1-02
2008-06-13 0.1-00

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Package isni updated to version 0.4 with previous version 0.3 dated 2018-06-16

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>

Diff between isni versions 0.3 dated 2018-06-16 and 0.4 dated 2019-02-04

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Package zTree updated to version 1.0.6 with previous version 1.0.5 dated 2019-01-02

Title: Functions to Import Data from 'z-Tree' into R
Description: Read '.xls' and '.sbj' files which are written by the Microsoft Windows program 'z-Tree'. The latter is a software for developing and carrying out economic experiments (see <http://www.ztree.uzh.ch/> for more information).
Author: Oliver Kirchkamp
Maintainer: Oliver Kirchkamp <oliver@kirchkamp.de>

Diff between zTree versions 1.0.5 dated 2019-01-02 and 1.0.6 dated 2019-02-04

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Package rlas updated to version 1.3.0 with previous version 1.2.9 dated 2018-10-25

Title: Read and Write 'las' and 'laz' Binary File Formats Used for Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://www.asprs.org/committee-general/laser-las-file-format-exchange-activities.html>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.3 <https://www.laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph], Florian De Boissieu [aut, ctb] (Enable the support of .lax file and extra byte attributes), Martin Isenburg [cph] (Is the author of the LASlib and LASzip libraries), David Auty [ctb] (Reviewed the documentation), Pierrick Marie [ctb] (Helped to compile LASlib code in R), Tiago de Conto [ctb] (Implemented the -thin_with_voxel filter method)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>

Diff between rlas versions 1.2.9 dated 2018-10-25 and 1.3.0 dated 2019-02-04

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Package matchingMarkets updated to version 1.0-1 with previous version 1.0-0 dated 2018-12-04

Title: Analysis of Stable Matchings
Description: Implements structural estimators to correct for the sample selection bias from observed outcomes in matching markets. This includes one-sided matching of agents into groups as well as two-sided matching of students to schools. The package also contains algorithms to find stable matchings in the three most common matching problems: the stable roommates problem, the college admissions problem, and the house allocation problem.
Author: Thilo Klein [aut, cre], Robert Aue [ctb], Sven Giegerich [ctb], Alexander Sauer [ctb]
Maintainer: Thilo Klein <thilo@klein.uk>

Diff between matchingMarkets versions 1.0-0 dated 2018-12-04 and 1.0-1 dated 2019-02-04

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Package FactorsR updated to version 1.4 with previous version 1.3 dated 2018-12-06

Title: Identification of the Factors Affecting Species Richness
Description: It identifies the factors significantly related to species richness, and their relative contribution, using multiple regressions and support vector machine models. It uses an output file of 'ModestR' (<http://www.ipez.es/ModestR>) with data of richness of the species and environmental variables in a cell size defined by the user. The residuals of the support vector machine model are shown on a map. Negative residuals may be potential areas with undiscovered and/or unregistered species, or areas with decreased species richness due to the negative effect of anthropogenic factors.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>

Diff between FactorsR versions 1.3 dated 2018-12-06 and 1.4 dated 2019-02-04

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More information about FactorsR at CRAN
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Package rsinaica updated to version 0.6.1 with previous version 0.6.0 dated 2018-10-24

Title: Download Data from Mexico's Air Quality Information System
Description: Easy-to-use functions for downloading air quality data from the Mexican National Air Quality Information System (SINAICA). Allows you to query pollution and meteorological parameters from more than a hundred monitoring stations located throughout Mexico. See <https://sinaica.inecc.gob.mx> for more information.
Author: Diego Valle-Jones [aut, cre]
Maintainer: Diego Valle-Jones <diego@diegovalle.net>

Diff between rsinaica versions 0.6.0 dated 2018-10-24 and 0.6.1 dated 2019-02-04

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Package MHCtools updated to version 1.1.1 with previous version 1.1.0 dated 2017-10-23

Title: Analysis of MHC Data in Non-Model Species
Description: Ten tools for analysis of major histocompatibility complex (MHC) data in non- model species. The functions are tailored for amplicon data sets that have been filtered using the 'dada2' method (for more information visit <https://benjjneb.github.io/dada2>), but even other data sets can be analysed, if the data tables are formatted according to the description in each function. The ReplMatch() function matches replicates in data sets in order to evaluate genotyping success. The GetReplTable() and GetReplStats() functions perform such an evaluation. The HpltFind() function infers putative haplotypes from families in the data set. The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of the haplotype inference. The PapaDiv() function compares parent pairs in the data set and calculate their joint MHC diversity, taking into account sequence variants that occur in both parents. The MeanPdist() function calculates the mean p-distance from pairwise comparisons sequences in each sample in a data set. The function includes the option to specify which codons to compare. The CreateFas() function creates a fasta file with all the sequences in the data set. The CreateSamplesFas() function creates a fasta file for each sample in the data set.
Author: Jacob Roved [aut, cre]
Maintainer: Jacob Roved <jacob.roved@biol.lu.se>

Diff between MHCtools versions 1.1.0 dated 2017-10-23 and 1.1.1 dated 2019-02-04

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New package safetyGraphics with initial version 0.7.3
Package: safetyGraphics
Title: Create Interactive Graphics Related to Clinical Trial Safety
Version: 0.7.3
Authors@R: c( person("Jeremy", "Wildfire", email = "jeremy_wildfire@rhoworld.com", role = c("cre","aut")), person("Becca", "Krouse", role="aut"), person("Preston","Burns", role="aut"), person("Xiao","Ni", role = "aut"), person("James","Buchanan", role="aut"), person("Susan","Duke", role="aut"), person("Rho Inc.", role = "cph"))
Maintainer: Jeremy Wildfire <jeremy_wildfire@rhoworld.com>
Description: A framework for evaluation of clinical trial safety. Users can interactively explore their data using the 'Shiny' application or create standalone 'htmlwidget' charts. Interactive charts are built using 'd3.js' and 'webcharts.js' 'JavaScript' libraries.
Depends: R (>= 3.5)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: testthat, shinytest, knitr
Imports: dplyr, htmlwidgets, purrr, stringr, jsonlite, shiny, magrittr, DT, shinyjs, rmarkdown, rlang
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-01-31 05:57:42 UTC; jeremy
Author: Jeremy Wildfire [cre, aut], Becca Krouse [aut], Preston Burns [aut], Xiao Ni [aut], James Buchanan [aut], Susan Duke [aut], Rho Inc. [cph]
Repository: CRAN
Date/Publication: 2019-02-04 20:40:03 UTC

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Package RMark updated to version 2.2.6 with previous version 2.2.5 dated 2018-07-13

Title: R Code for Mark Analysis
Description: An interface to the software package MARK that constructs input files for MARK and extracts the output. MARK was developed by Gary White and is freely available at <http://www.phidot.org/software/mark/downloads/> but is not open source.
Author: Jeff Laake <jefflaake@gmail.com> with code contributions from Eldar Rakhimberdiev, Ben Augustine, Daniel Turek and Brett McClintock and example data and analysis from Bret Collier, Jay Rotella, David Pavlacky, Andrew Paul, Luke Eberhart- Phillips, and Jake Ivan.
Maintainer: Jeff Laake <jefflaake@gmail.com>

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Package httk updated to version 1.9 with previous version 1.8 dated 2018-01-23

Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") as in Pearce et al. (2017) <doi:10.18637/jss.v079.i04>. Chemical-specific in vitro data have been obtained from relatively high throughput experiments. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability (Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>) and measurement limitations. Calibrated methods are included for predicting tissue:plasma partition coefficients and volume of distribution (Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>). These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., Tox21, ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK") (Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).
Author: John Wambaugh [aut, cre], Robert Pearce [aut], Caroline Ring [aut], Greg Honda [aut], Jimena Davis [ctb], Nisha Sipes [ctb], Barbara Wetmore [ctb], Woodrow Setzer [ctb]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>

Diff between httk versions 1.8 dated 2018-01-23 and 1.9 dated 2019-02-04

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 httk-1.9/httk/NAMESPACE                                                               |    4 
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 httk-1.9/httk/R/Parameterize_PBTK.r                                                   |   25 
 httk-1.9/httk/R/Parameterize_SteadyState.R                                            |   52 
 httk-1.9/httk/R/Predict_partitioning_Schmitt.R                                        |   12 
 httk-1.9/httk/R/add_chemtable.R                                                       |  204 
 httk-1.9/httk/R/age_draw_smooth.R                                                     |    8 
 httk-1.9/httk/R/armitage.R                                                            |only
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 httk-1.9/httk/R/calc_analytic_css.R                                                   |  414 +
 httk-1.9/httk/R/calc_chem_stats.R                                                     |    1 
 httk-1.9/httk/R/calc_css.R                                                            |   96 
 httk-1.9/httk/R/calc_mc_css.R                                                         |  198 
 httk-1.9/httk/R/calc_mc_oral_equiv.R                                                  |   50 
 httk-1.9/httk/R/ckd_epi_eq.R                                                          |    8 
 httk-1.9/httk/R/convert_httk.R                                                        |  213 
 httk-1.9/httk/R/data.R                                                                |  122 
 httk-1.9/httk/R/draw_fup_clint.R                                                      |  193 
 httk-1.9/httk/R/estimate_gfr.R                                                        |    8 
 httk-1.9/httk/R/estimate_gfr_ped.R                                                    |    8 
 httk-1.9/httk/R/estimate_hematocrit.R                                                 |    8 
 httk-1.9/httk/R/gen_age_height_weight.R                                               |    8 
 httk-1.9/httk/R/gen_height_weight.R                                                   |    8 
 httk-1.9/httk/R/get_Wetmore_Css.R                                                     |    8 
 httk-1.9/httk/R/get_Wetmore_Oral_Equiv.R                                              |    6 
 httk-1.9/httk/R/get_Wetmore_cheminfo.R                                                |    2 
 httk-1.9/httk/R/get_chem_id.R                                                         |    2 
 httk-1.9/httk/R/get_cheminfo.R                                                        |    2 
 httk-1.9/httk/R/get_gfr_category.R                                                    |    8 
 httk-1.9/httk/R/get_httk_params.R                                                     |   59 
 httk-1.9/httk/R/get_rblood2plasma.R                                                   |    5 
 httk-1.9/httk/R/get_weight_class.R                                                    |    8 
 httk-1.9/httk/R/hematocrit_infants.R                                                  |    8 
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 httk-1.9/httk/R/httkpop.R                                                             |   10 
 httk-1.9/httk/R/httkpop_bio.R                                                         |    8 
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 httk-1.9/httk/R/httkpop_direct_resample_inner.R                                       |    8 
 httk-1.9/httk/R/httkpop_generate.R                                                    |   10 
 httk-1.9/httk/R/httkpop_virtual_indiv.R                                               |    8 
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 httk-1.9/httk/R/load_sipes2017.R                                                      |   35 
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 httk-1.9/httk/R/modelinfo_3comp.R                                                     |only
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 httk-1.9/httk/R/monte_carlo.R                                                         |    5 
 httk-1.9/httk/R/parameterize_1comp.R                                                  |  131 
 httk-1.9/httk/R/parameterize_schmitt.R                                                |   16 
 httk-1.9/httk/R/r_left_censored_norm.R                                                |    6 
 httk-1.9/httk/R/solve_1comp.R                                                         |   28 
 httk-1.9/httk/R/solve_3comp.R                                                         |   12 
 httk-1.9/httk/R/solve_pbtk.R                                                          |   12 
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 httk-1.9/httk/R/tissue_masses_flows.R                                                 |    7 
 httk-1.9/httk/R/tissue_scale.R                                                        |    8 
 httk-1.9/httk/R/utils.R                                                               |   16 
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 httk-1.9/httk/data/datalist                                                           |    4 
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Package stable updated to version 1.1.4 with previous version 1.1.3 dated 2018-05-26

Title: Probability Functions and Generalized Regression Models for Stable Distributions
Description: Density, distribution, quantile and hazard functions of a stable variate; generalized regression models for the parameters of a stable distribution. See the README for how to make equivalent calls to those of 'stabledist'. See github for Journal article.
Author: Bruce Swihart [cre, aut], Jim Lindsey [aut] (Jim created this package, Bruce is maintaining the CRAN version), Philippe Lambert [aut]
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>

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Package dlnm updated to version 2.3.8 with previous version 2.3.6 dated 2018-09-12

Title: Distributed Lag Non-Linear Models
Description: Collection of functions for distributed lag linear and non-linear models.
Author: Antonio Gasparrini [aut, cre], Ben Armstrong [aut], Fabian Scheipl [ctb]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>

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Package spec updated to version 0.1.6 with previous version 0.1.3 dated 2017-04-13

Title: A Data Specification Format and Interface
Description: Creates a data specification that describes the columns of a table (data.frame). Provides methods to read, write, and update the specification. Checks whether a table matches its specification. See specification.data.frame(),read.spec(), write.spec(), as.csv.spec(), respecify.character(), and %matches%.data.frame().
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

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Package metaplot updated to version 0.8.2 with previous version 0.8.0 dated 2018-09-30

Title: Data-Driven Plot Design
Description: Designs plots in terms of core structure. See 'example(metaplot)'. Primary arguments are (unquoted) column names; order and type (numeric or not) dictate the resulting plot. Specify any y variables, x variable, any groups variable, and any conditioning variables to metaplot() to generate density plots, boxplots, mosaic plots, scatterplots, scatterplot matrices, or conditioned plots. Use multiplot() to arrange plots in grids. Wherever present, scalar column attributes 'label' and 'guide' are honored, producing fully annotated plots with minimal effort. Attribute 'guide' is typically units, but may be encoded() to provide interpretations of categorical values (see '?encode'). Utility unpack() transforms scalar column attributes to row values and pack() does the reverse, supporting tool-neutral storage of metadata along with primary data. The package supports customizable aesthetics such as such as reference lines, unity lines, smooths, log transformation, and linear fits. The user may choose between trellis and ggplot output. Compact syntax and integrated metadata promote workflow scalability.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

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Package growth updated to version 1.1.1 with previous version 1.1.0 dated 2016-12-08

Title: Multivariate Normal and Elliptically-Contoured Repeated Measurements Models
Description: Functions for fitting various normal theory (growth curve) and elliptically-contoured repeated measurements models with ARMA and random effects dependence.
Author: Bruce Swihart [cre, aut], Jim Lindsey [aut] (Jim created this package, Bruce is maintaining the CRAN version)
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>

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Package estmeansd updated to version 0.1.1 with previous version 0.1.0 dated 2019-01-11

Title: Estimating the Sample Mean and Standard Deviation from Commonly Reported Quantiles in Meta-Analysis
Description: Implements the methods of McGrath et al. (in preparation) for estimating the sample mean and standard deviation from commonly reported quantiles in meta-analysis. These methods can be applied to studies that report the sample median, sample size, and one or both of (i) the sample minimum and maximum values and (ii) the first and third quartiles.
Author: Sean McGrath [aut, cre] (<https://orcid.org/0000-0002-7281-3516>), XiaoFei Zhao [aut], Russell Steele [aut], Andrea Benedetti [aut] (<https://orcid.org/0000-0002-8314-9497>)
Maintainer: Sean McGrath <sean.mcgrath@mail.mcgill.ca>

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Package bender updated to version 0.1.1 with previous version 0.1.0 dated 2019-01-20

Title: Bender Client
Description: R client for Bender Hyperparameters optimizer : <https://bender.dreem.com> The R client allows you to communicate with the Bender API and therefore submit some new trials within your R script itself.
Author: Dylan Heirstraeten
Maintainer: Valentin Thorey <valentin@dreem.com>

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Package colourlovers (with last version 0.2.2) was removed from CRAN

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

2016-10-31 0.2.2

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Package wrangle updated to version 0.5.1 with previous version 0.4 dated 2017-04-13

Title: A Systematic Data Wrangling Idiom
Description: Supports systematic scrutiny, modification, and integration of data. The function status() counts rows that have missing values in grouping columns (returned by na() ), have non-unique combinations of grouping columns (returned by dup() ), and that are not locally sorted (returned by unsorted() ). Functions enumerate() and itemize() give sorted unique combinations of columns, with or without occurrence counts, respectively. Function ignore() drops columns in x that are present in y, and informative() drops columns in x that are entirely NA; constant() returns values that are constant, given a key. Data that have defined unique combinations of grouping values behave more predictably during merge operations.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

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Package nonmemica updated to version 0.8.6 with previous version 0.8.3 dated 2018-09-30

Title: Create and Evaluate NONMEM Models in a Project Context
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests NONMEM output, builds run logs, creates derivative data, generates diagnostics. NONMEM (ICON Development Solutions <http://www.iconplc.com/>) is software for nonlinear mixed effects modeling. See 'package?nonmemica'.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

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Package ggmap updated to version 3.0.0 with previous version 2.6.2 dated 2019-01-23

Title: Spatial Visualization with ggplot2
Description: A collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.
Author: David Kahle [aut, cre] (<https://orcid.org/0000-0002-9999-1558>), Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), Scott Jackson [aut], Mikko Korpela [ctb]
Maintainer: ORPHANED

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New package fedregs with initial version 0.1.1
Package: fedregs
Type: Package
Title: Text Analysis of the US Code of Federal Regulations
Version: 0.1.1
Authors@R: person("Scott", "Large", email = "scott.large@noaa.gov", role = c("cre", "aut"))
Description: The Code of Federal Regulations (CFR) annual edition is the codification of the general and permanent rules published in the Federal Register by the departments and agencies of the Federal Government of the United States of America. Simply, the 'fedregs' package facilitates word processing and sentiment analysis of the CFR using tidy principles. Note: According to the Code of Federal Regulations XML Rendition User Guide Document: "In general, there are no restrictions on re-use of information in Code of Federal Regulations material because U.S. Government works are not subject to copyright. OFR and GPO do not restrict downstream uses of Code of Federal Regulations data, except that independent providers should be aware that only the OFR and GPO are entitled to represent that they are the providers of the official versions of the Code of Federal Regulations and related Federal Register publications."
License: GPL-3
BugReports: https://github.com/slarge/fedregs/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.1.0),
Imports: dplyr (>= 0.7.4), magrittr (>= 1.5), xml2 (>= 1.2.0), purrr(>= 0.2.5), rvest(>= 0.3.2), stringi(>= 1.1.7), httr (>= 1.3.1), tidytext (>= 0.1.9)
Suggests: ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), testthat (>= 2.0.0)
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2019-01-28 20:19:55 UTC; scott.large
Author: Scott Large [cre, aut]
Maintainer: Scott Large <scott.large@noaa.gov>
Repository: CRAN
Date/Publication: 2019-02-04 15:13:30 UTC

More information about fedregs at CRAN
Permanent link

Package auk updated to version 0.3.2 with previous version 0.3.1 dated 2018-12-07

Title: eBird Data Extraction and Processing in R
Description: Extract and process bird sightings records from eBird (<http://ebird.org>), an online tool for recording bird observations. Public access to the full eBird database is via the eBird Basic Dataset (EBD; see <http://ebird.org/ebird/data/download> for access), a downloadable text file. This package is an interface to AWK for extracting data from the EBD based on taxonomic, spatial, or temporal filters, to produce a manageable file size that can be imported into R.
Author: Matthew Strimas-Mackey [aut, cre] (<https://orcid.org/0000-0001-8929-7776>), Eliot Miller [aut], Wesley Hochachka [aut], Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>

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Permanent link

Package trtf updated to version 0.3-5 with previous version 0.3-4 dated 2019-01-16

Title: Transformation Trees and Forests
Description: Recursive partytioning of transformation models with corresponding random forest for conditional transformation models as described in 'Transformation Forests' (Hothorn and Zeileis, 2017, <arXiv:1701.02110>) and 'Top-Down Transformation Choice' (Hothorn, 2018, <DOI:10.1177/1471082X17748081>).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between trtf versions 0.3-4 dated 2019-01-16 and 0.3-5 dated 2019-02-04

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Package mephas updated to version 1.0.0 with previous version 0.1.0 dated 2019-02-01

Title: Shiny Application of Medical and Pharmaceutical Statistics
Description: The web-based statistical fundamentals, tests, and models, aiming to facilitate researchers to analyze medical, pharmaceutical and genomic data.
Author: Yi Zhou [cre, aut] (<https://orcid.org/0000-0001-9254-324>)
Maintainer: Yi Zhou <zhou-y@phs.osaka-u.ac.jp>

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Package IMIFA updated to version 2.1.0 with previous version 2.0.0 dated 2018-05-01

Title: Infinite Mixtures of Infinite Factor Analysers and Related Models
Description: Provides flexible Bayesian estimation of Infinite Mixtures of Infinite Factor Analysers and related models, for nonparametrically clustering high-dimensional data, introduced by Murphy et al. (2018) <arXiv:1701.07010v4>. The IMIFA model conducts Bayesian nonparametric model-based clustering with factor analytic covariance structures without recourse to model selection criteria to choose the number of clusters or cluster-specific latent factors, mostly via efficient Gibbs updates. Model-specific diagnostic tools are also provided, as well as many options for plotting results, conducting posterior inference on parameters of interest, posterior predictive checking, and quantifying uncertainty.
Author: Keefe Murphy [aut, cre], Cinzia Viroli [ctb], Isobel Claire Gormley [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>

Diff between IMIFA versions 2.0.0 dated 2018-05-01 and 2.1.0 dated 2019-02-04

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Package dynutils updated to version 1.0.1 with previous version 1.0.0 dated 2018-07-18

Title: Common Functionality for the 'dynverse' Packages
Description: Provides common functionality for the 'dynverse' packages. 'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods. For more information, check out <dynverse.org>.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Package bfw updated to version 0.4.0 with previous version 0.3.0 dated 2018-11-04

Title: Bayesian Framework for Computational Modeling
Description: Derived from the work of Kruschke (2015, <ISBN:9780124058880>), the present package aims to provide a framework for conducting Bayesian analysis using Markov chain Monte Carlo (MCMC) sampling utilizing the Just Another Gibbs Sampler ('JAGS', Plummer, 2003, <http://mcmc-jags.sourceforge.net/>). The initial version includes several modules for conducting Bayesian equivalents of chi-squared tests, analysis of variance (ANOVA), multiple (hierarchical) regression, softmax regression, and for fitting data (e.g., structural equation modeling).
Author: Øystein Olav Skaar [aut, cre]
Maintainer: Øystein Olav Skaar <bayesianfw@gmail.com>

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Package transport updated to version 0.11-0 with previous version 0.10-0 dated 2019-01-02

Title: Computation of Optimal Transport Plans and Wasserstein Distances
Description: Solve optimal transport problems. Compute Wasserstein distances (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p distances), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, (weighted) point patterns, and mass vectors.
Author: Dominic Schuhmacher [aut, cre], Björn Bähre [aut] (aha and power diagrams), Carsten Gottschlich [aut] (simplex and shortlist), Valentin Hartmann [aut] (semidiscrete1), Florian Heinemann [aut] (transport_track), Bernhard Schmitzer [aut] (shielding), Jörn Schrieber [aut] (subsampling), Timo Wilm [ctb] (wpp)
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>

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Package eulerr updated to version 5.1.0 with previous version 5.0.0 dated 2018-11-05

Title: Area-Proportional Euler and Venn Diagrams with Ellipses
Description: Generate area-proportional Euler diagrams using numerical optimization. An Euler diagram is a generalization of a Venn diagram, relaxing the criterion that all interactions need to be represented. Diagrams may be fit with ellipses and circles via a wide range of inputs and can be visualized in numerous ways.
Author: Johan Larsson [aut, cre] (<https://orcid.org/0000-0002-4029-5945>), A. Jonathan R. Godfrey [ctb], Peter Gustafsson [ctb], David H. Eberly [ctb] (geometric algorithms), Emanuel Huber [ctb] (root solver code)
Maintainer: Johan Larsson <mail@larssonjohan.com>

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Package rehh updated to version 2.0.3 with previous version 2.0.2 dated 2016-11-18

Title: Searching for Footprints of Selection using "Extended Haplotype Homozygosity" Based Tests
Description: Population genetic data in form of "Single Nucleotide Polymorphisms" (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. The concept of an "Extended Haplotype Homozygosity" (EHH), introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several derived statistics designed for whole genome scans. The package provides functions to compute three of these, namely: "iHS" (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting selection within a single population as well as "Rsb" (Tang 2007) <doi:10.1371/journal.pbio.0050171> and "XP-EHH" (Sabeti 2007) <doi:10.1038/nature06250> to detect (differential) selection between two populations. Various plotting functions are also included to facilitate visualization and interpretation of these statistics.
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Maintainer: Mathieu Gautier <mathieu.gautier@inra.fr>

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New package PopGenReport with initial version 3.0.4
Package: PopGenReport
Type: Package
Title: A Simple Framework to Analyse Population and Landscape Genetic Data
Version: 3.0.4
Date: 2019-02-04
Authors@R: c( person("Bernd", "Gruber", email="bernd.gruber@canberra.edu.au", role=c("aut","cre")), person("Aaron", "Adamack", email="aaron.adamack@canberra.edu.au", role="aut"))
Description: Provides beginner friendly framework to analyse population genetic data. Based on 'adegenet' objects it uses 'knitr' to create comprehensive reports on spatial genetic data. For detailed information how to use the package refer to the comprehensive tutorials or visit <http://www.popgenreport.org/>.
License: GPL
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0.0), knitr, adegenet (>= 2.0.0)
Imports: lattice, RgoogleMaps, gap, calibrate, xtable, plyr, dismo, reshape, ggplot2, R.utils, ade4, pegas, genetics, rgdal, gdistance, vegan, sp, mmod, GGally, data.table, graphics, grDevices, methods, stats, utils, raster
VignetteBuilder: knitr
URL: https://github.com/green-striped-gecko/PopGenReport
Suggests:
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-04 03:40:39 UTC; s425824
Author: Bernd Gruber [aut, cre], Aaron Adamack [aut]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Repository: CRAN
Date/Publication: 2019-02-04 12:13:23 UTC

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Package exuber updated to version 0.2.0 with previous version 0.1.0 dated 2018-06-17

Title: Econometric Analysis of Explosive Time Series
Description: Testing for and dating periods of explosive dynamics (exuberance) in time series using recursive unit root tests as proposed by Phillips, P. C., Shi, S. and Yu, J. (2015a) <doi:10.1111/iere.12132>. Simulation of a variety of periodically-collapsing bubble processes. The estimation code utilizes the matrix inversion lemma of the recursive least squares algorithm which results in significant speed improvements.
Author: Kostas Vasilopoulos [cre, aut], Eftymios Pavlidis [aut], Simon Spavound [aut], Enríqeu Matrínez-García [aut]
Maintainer: Kostas Vasilopoulos <k.vasilopoulo@gmail.com>

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Package vegan updated to version 2.5-4 with previous version 2.5-3 dated 2018-10-25

Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs, Helene Wagner
Maintainer: Jari Oksanen <jhoksane@gmail.com>

Diff between vegan versions 2.5-3 dated 2018-10-25 and 2.5-4 dated 2019-02-04

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New package MCMC.qpcr with initial version 1.2.3
Package: MCMC.qpcr
Type: Package
Title: Bayesian Analysis of qRT-PCR Data
Version: 1.2.3
Date: 2016-11-07
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Description: Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: <http://bit.ly/1Nwo4CB>.
License: GPL-3
Depends: MCMCglmm,ggplot2,coda
NeedsCompilation: no
Packaged: 2016-11-09 18:51:30 UTC; c-monstr
Repository: CRAN
Date/Publication: 2016-11-09 23:56:55

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New package MCMC.OTU with initial version 1.0.10
Package: MCMC.OTU
Type: Package
Title: Bayesian Analysis of Multivariate Counts Data in DNA Metabarcoding and Ecology
Version: 1.0.10
Date: 2016-02-10
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Description: Poisson-lognormal generalized linear mixed model analysis of multivariate counts data using MCMC, aiming to infer the changes in relative proportions of individual variables. The package was originally designed for sequence-based analysis of microbial communities ("metabarcoding", variables = operational taxonomic units, OTUs), but can be used for other types of multivariate counts, such as in ecological applications (variables = species). The results are summarized and plotted using 'ggplot2' functions. Includes functions to remove sample and variable outliers and reformat counts into normalized log-transformed values for correlation and principal component/coordinate analysis. Walkthrough and examples: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/walkthroughExample_mcmcOTU_R.txt.
License: GPL-3
Depends: MCMCglmm,ggplot2,coda
NeedsCompilation: no
Packaged: 2016-02-11 19:23:29 UTC; c-monstr
Repository: CRAN
Date/Publication: 2016-02-12 00:53:04

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New package glmmsr with initial version 0.2.3
Package: glmmsr
Title: Fit a Generalized Linear Mixed Model
Version: 0.2.3
Authors@R: person("Helen", "Ogden", , "heogden12@gmail.com", role = c("aut", "cre"))
Description: Conduct inference about generalized linear mixed models, with a choice about which method to use to approximate the likelihood. In addition to the Laplace and adaptive Gaussian quadrature approximations, which are borrowed from 'lme4', the likelihood may be approximated by the sequential reduction approximation, or an importance sampling approximation. These methods provide an accurate approximation to the likelihood in some situations where it is not possible to use adaptive Gaussian quadrature.
Depends: R (>= 3.2.0)
LinkingTo: Rcpp, RcppEigen, BH
Imports: lme4 (>= 1.1-8), Matrix, R6, Rcpp, methods, stats, utils, numDeriv
URL: http://github.com/heogden/glmmsr
BugReports: http://github.com/heogden/glmmsr/issues
License: GPL (>= 2)
LazyData: true
Suggests: BradleyTerry2, knitr, mdhglm, rmarkdown, testthat
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-01-29 16:16:52 UTC; helen
Author: Helen Ogden [aut, cre]
Maintainer: Helen Ogden <heogden12@gmail.com>
Repository: CRAN
Date/Publication: 2019-02-04 11:09:22 UTC

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Package vortexRdata updated to version 1.0.5 with previous version 1.0.3 dated 2017-03-25

Title: Example Data for R Package 'vortexR'
Description: Contains selected data from two publications, Campbell 'et' 'al'. (2016) <DOI:10.1080/14486563.2015.1028486> and 'Pacioni' 'et' 'al'. (2017) <DOI:10.1071/PC17002>. The data is provided both as raw outputs from the population viability analysis software 'Vortex' and packaged as R objects. The R package 'vortexR' uses the raw data provided here to illustrate its functionality of parsing raw 'Vortex' output into R objects.
Author: Carlo Pacioni [aut, cre], Florian W. Mayer [aut]
Maintainer: Carlo Pacioni <C.Pacioni@Murdoch.edu.au>

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Package tidytransit updated to version 0.3.6 with previous version 0.3.5 dated 2018-10-28

Title: Read, Validate, Analyze, and Map Files in the General Transit Feed Specification
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
Author: Tom Buckley [aut, cre], Danton Noriega-Goodwin [aut], Flavio Poletti [aut], Angela Li [aut], Mark Padgham [aut], Elaine McVey [ctb], Charles Hans Thompson [ctb], Michael Sumner [ctb], Patrick Hausmann [ctb], Bob Rudis [ctb], Kearey Smith [ctb], Dave Vautin [ctb], Kyle Walker [ctb]
Maintainer: Tom Buckley <tom@tbuckl.com>

Diff between tidytransit versions 0.3.5 dated 2018-10-28 and 0.3.6 dated 2019-02-04

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More information about tidytransit at CRAN
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Package paletteer updated to version 0.2.0 with previous version 0.1.0 dated 2018-07-10

Title: Comprehensive Collection of Color Palettes
Description: The choices of color palettes in R can be quite overwhelming with palettes spread over many packages with many different API's. This packages aims to collect all color palettes across the R ecosystem under the same package with a streamlined API.
Author: See AUTHORS file.
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>

Diff between paletteer versions 0.1.0 dated 2018-07-10 and 0.2.0 dated 2019-02-04

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Package lme4 updated to version 1.1-20 with previous version 1.1-19 dated 2018-11-10

Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] (<https://orcid.org/0000-0001-8316-9503>), Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>), Ben Bolker [aut, cre] (<https://orcid.org/0000-0002-2127-0443>), Steven Walker [aut] (<https://orcid.org/0000-0002-4394-9078>), Rune Haubo Bojesen Christensen [ctb] (<https://orcid.org/0000-0002-4494-3399>), Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>), Bin Dai [ctb], Fabian Scheipl [ctb] (<https://orcid.org/0000-0001-8172-3603>), Gabor Grothendieck [ctb], Peter Green [ctb] (<https://orcid.org/0000-0002-0238-9852>), John Fox [ctb]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>

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Package spdplyr updated to version 0.2.0 with previous version 0.1.3 dated 2017-06-02

Title: Data Manipulation Verbs for the Spatial Classes
Description: Methods for 'dplyr' verbs for 'sp' 'Spatial' classes. The basic verbs that modify data attributes, remove or re-arrange rows are supported and provide complete 'Spatial' analogues of the input data. The group by and summarize work flow returns a non-topological spatial union. There is limited support for joins, with left and inner to copy attributes from another table.
Author: Michael D. Sumner [aut, cre], Joscha Legewie [ctb], Jussi Jousimo [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>

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Package rr2 updated to version 1.0.1 with previous version 1.0.0 dated 2018-11-04

Title: R2s for Regression Models
Description: Three methods to calculate R2 for models with correlated errors, including Phylogenetic GLS, Phylogenetic Logistic Regression, Linear Mixed Models (LMMs), and Generalized Linear Mixed Models (GLMMs). See details in Ives 2018 <doi:10.1093/sysbio/syy060>.
Author: Anthony Ives [aut, cre], Daijiang Li [ctb]
Maintainer: Anthony Ives <arives@wisc.edu>

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Package mvp updated to version 1.0-5 with previous version 1.0-2 dated 2019-01-14

Title: Fast Symbolic Multivariate Polynomials
Description: Fast manipulation of symbolic multivariate polynomials using the 'Map' class of the Standard Template Library. The package uses print and coercion methods from the 'mpoly' package (Kahle 2013, "Multivariate polynomials in R". The R Journal, 5(1):162), but offers speed improvements. It is comparable in speed to the 'spray' package for sparse arrays, but retains the symbolic benefits of 'mpoly'.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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Package asciiSetupReader updated to version 2.0.0 with previous version 1.4.0 dated 2018-06-18

Title: Reads Fixed-Width ASCII Data Files (.txt or .dat) that Have Accompanying Setup Files (.sps or .sas)
Description: Lets you open a fixed-width ASCII file (.txt or .dat) that has an accompanying setup file (.sps or .sas). These file combinations are sometimes referred to as .txt+.sps, .txt+.sas, .dat+.sps, or .dat+.sas. This will only run in a txt-sps or txt-sas pair in which the setup file contains instructions to open that text file. It will NOT open other text files, .sav, .sas, or .por data files. Fixed-width ASCII files with setup files are common in older (pre-2000) government data.
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>

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Package urltools updated to version 1.7.2 with previous version 1.7.1 dated 2018-08-03

Title: Vectorised Tools for URL Handling and Parsing
Description: A toolkit for all URL-handling needs, including encoding and decoding, parsing, parameter extraction and modification. All functions are designed to be both fast and entirely vectorised. It is intended to be useful for people dealing with web-related datasets, such as server-side logs, although may be useful for other situations involving large sets of URLs.
Author: Os Keyes [aut, cre], Jay Jacobs [aut, cre], Drew Schmidt [aut], Mark Greenaway [ctb], Bob Rudis [ctb], Alex Pinto [ctb], Maryam Khezrzadeh [ctb], Peter Meilstrup [ctb], Adam M. Costello [cph], Jeff Bezanson [cph], Peter Meilstrup [ctb], Xueyuan Jiang [ctb]
Maintainer: Os Keyes <ironholds@gmail.com>

Diff between urltools versions 1.7.1 dated 2018-08-03 and 1.7.2 dated 2019-02-04

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Package trread updated to version 0.2.7 with previous version 0.2.5 dated 2018-07-28

Title: Read, Validate, and Analyze Files in the General Transit Feed Specification
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
Author: Tom Buckley [aut, cre], Danton Noriega-Goodwin [aut], Flavio Poletti [aut], Angela Li [aut], Mark Padgham [aut], Elaine McVey [ctb], Charles Hans Thompson [ctb], Michael Sumner [ctb], Patrick Hausmann [ctb], Bob Rudis [ctb], Kearey Smith [ctb], Dave Vautin [ctb], Kyle Walker [ctb]
Maintainer: Tom Buckley <tom@tbuckl.com>

Diff between trread versions 0.2.5 dated 2018-07-28 and 0.2.7 dated 2019-02-04

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Package secrdesign updated to version 2.5.7 with previous version 2.5.6 dated 2019-01-26

Title: Sampling Design for Spatially Explicit Capture-Recapture
Description: Tools for designing spatially explicit capture-recapture studies of animal populations. This is primarily a simulation manager for package 'secr'. Extensions in version 2.5.0 include costing and evaluation of detector spacing.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

Diff between secrdesign versions 2.5.6 dated 2019-01-26 and 2.5.7 dated 2019-02-04

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Package multistateutils updated to version 1.2.2 with previous version 1.2.0 dated 2018-07-21

Title: Utility Functions for Parametric Multi-State Models
Description: Provides functions for working with multi-state modelling, such as efficient simulation routines for estimating transition probabilities and length of stay. It is designed as an extension to multi-state modelling capabilities provided with the 'flexsurv' package (see Jackson (2016) <doi:10.18637/jss.v070.i08>).
Author: Stuart Lacy
Maintainer: Stuart Lacy <stuart.lacy@gmail.com>

Diff between multistateutils versions 1.2.0 dated 2018-07-21 and 1.2.2 dated 2019-02-04

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Package onewaytests updated to version 2.0 with previous version 1.9 dated 2018-10-18

Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests in independent groups designs, pairwise comparisons, graphical approaches, assesses variance homogeneity and normality of data in each group via tests and plots (Dag et al., 2018, <https://journal.r-project.org/archive/2018/RJ-2018-022/RJ-2018-022.pdf>).
Author: Osman Dag [aut, cre], Anil Dolgun [aut], N. Meric Konar [aut]
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>

Diff between onewaytests versions 1.9 dated 2018-10-18 and 2.0 dated 2019-02-04

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Package HIBPwned (with last version 0.1.7) was removed from CRAN

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

2018-04-17 0.1.7
2017-05-30 0.1.6
2017-05-04 0.1.4
2016-09-14 0.1.3
2016-06-01 0.1.0.0

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