Tue, 25 Jun 2019

New package wpp2019 with initial version 1.0-0
Package: wpp2019
Version: 1.0-0
Date: 2019-06-17
Title: World Population Prospects 2019
Author: United Nations Population Division
Maintainer: Hana Sevcikova <hanas@uw.edu>
Depends: R (>= 2.14.2)
Suggests: data.table
Description: Provides data from the United Nation's World Population Prospects 2019.
License: file LICENSE
URL: http://population.un.org/wpp
NeedsCompilation: no
Packaged: 2019-06-17 18:00:49 UTC; hana
Repository: CRAN
Date/Publication: 2019-06-25 16:10:03 UTC

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Package pgraph updated to version 1.5 with previous version 0.8 dated 2016-10-13

Title: Build Dependency Graphs using Projection
Description: Implements a general framework for creating dependency graphs using projection as introduced in Fan, Feng and Xia (2019)<arXiv:1501.01617>. Both lasso and sparse additive model projections are implemented. Both Pearson correlation and distance covariance options are available to generate the graph.
Author: Jianqing Fan, Yang Feng and Lucy Xia
Maintainer: Yang Feng <yang.feng@columbia.edu>

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New package PakPMICS2018 with initial version 0.1.0
Package: PakPMICS2018
Type: Package
Title: Multiple Indicator Cluster Survey (MICS) 2017-18 Data for Punjab, Pakistan
Version: 0.1.0
Authors@R: c(person(c("Muhammad", "Yaseen"), email = "myaseen208@gmail.com", role = c("aut", "cre")))
Author: Muhammad Yaseen [aut, cre]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Description: Provides data set and function for exploration of Multiple Indicator Cluster Survey (MICS) 2017-18 data for Punjab, Pakistan. The results of the present survey are critically important for the purposes of SDG monitoring, as the survey produces information on 32 global SDG indicators. The data was collected from 53,840 households selected at the second stage with systematic random sampling out of a sample of 2,692 clusters selected using Probability Proportional to size sampling. Six questionnaires were used in the survey: (1) a household questionnaire to collect basic demographic information on all de jure household members (usual residents), the household, and the dwelling; (2) a water quality testing questionnaire administered in three households in each cluster of the sample; (3) a questionnaire for individual women administered in each household to all women age 15-49 years; (4) a questionnaire for individual men administered in every second household to all men age 15-49 years; (5) an under-5 questionnaire, administered to mothers (or caretakers) of all children under 5 living in the household; and (6) a questionnaire for children age 5-17 years, administered to the mother (or caretaker) of one randomly selected child age 5-17 years living in the household (<http://www.mics.unicef.org/surveys>).
Depends: R (>= 3.5.0)
Imports: tibble
License: GPL-2
URL: https://github.com/myaseen208/PakPMICS2018, https://myaseen208.github.io/PakPMICS2018/
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Note: Department of Mathematics and Statistics, University of Agriculture Faisalabad, Faisalabad-Pakistan.
Suggests: testthat, R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2019-06-20 01:39:43 UTC; myaseen
Repository: CRAN
Date/Publication: 2019-06-25 15:40:06 UTC

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Package GLMMadaptive updated to version 0.6-0 with previous version 0.5-1 dated 2019-01-29

Title: Generalized Linear Mixed Models using Adaptive Gaussian Quadrature
Description: Fits generalized linear mixed models for a single grouping factor under maximum likelihood approximating the integrals over the random effects with an adaptive Gaussian quadrature rule; Jose C. Pinheiro and Douglas M. Bates (1995) <doi:10.1080/10618600.1995.10474663>.
Author: Dimitris Rizopoulos [aut, cre] (<https://orcid.org/0000-0001-9397-0900>)
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>

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Package SimilaR updated to version 1.0.4 with previous version 1.0.3 dated 2019-02-25

Title: R Source Code Similarity Evaluation
Description: An implementation of a novel method to quantify the similarity the code-base of R functions by means of program dependence graphs. Possible use cases include detection of code clones for improving software quality and of plagiarism among students' homework assignments.
Author: Maciej Bartoszuk [aut, cre] (<https://orcid.org/0000-0001-6088-8273>), Marek Gagolewski [aut] (<https://orcid.org/0000-0003-0637-6028>)
Maintainer: Maciej Bartoszuk <bartoszuk@rexamine.com>

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Package matrixTests updated to version 0.1.4 with previous version 0.1.3 dated 2019-06-10

Title: Fast Statistical Hypothesis Tests on Rows and Columns of Matrices
Description: Functions to perform fast statistical hypothesis tests on rows/columns of matrices. The main goals are: 1) speed via vectorization, 2) output that is detailed and easy to use, 3) compatibility with tests implemented in R (like those available in the 'stats' package).
Author: Karolis Koncevičius [aut, cre]
Maintainer: Karolis Koncevičius <karolis.koncevicius@gmail.com>

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Package gsrsb updated to version 1.1.1 with previous version 1.0.3 dated 2017-04-28

Title: Group Sequential Refined Secondary Boundary
Description: A gate-keeping procedure to test a primary and a secondary endpoint in a group sequential design with multiple interim looks. Computations related to group sequential primary and secondary boundaries. Refined secondary boundaries are calculated for a gate-keeping test on a primary and a secondary endpoint in a group sequential design with multiple interim looks. The choices include both the standard boundaries and the boundaries using error spending functions. Version 1.0.0 was released on April 12, 2017. See Tamhane et al. (2018), "A gatekeeping procedure to test a primary and a secondary endpoint in a group sequential design with multiple interim looks", Biometrics, 74(1), 40-48.
Author: Jiangtao Gou and Fengqing (Zoe) Zhang
Maintainer: Jiangtao Gou <gouRpackage@gmail.com>

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Package DAMisc updated to version 1.5 with previous version 1.4-3 dated 2016-07-04

Title: Dave Armstrong's Miscellaneous Functions
Description: Miscellaneous set of functions I use in my teaching either at the University of Western Ontario or the Inter-university Consortium for Political and Social Research (ICPSR) Summer Program in Quantitative Methods. Broadly, the functions help with presentation and interpretation of LMs and GLMs, but also implement some new tools like Alternating Least Squares Optimal Scaling for dependent variables, a Bayesian analog to the ALSOS algorithm. There are also tools to help understand interactions in both LMs and binary GLMs.
Author: Dave Armstrong [aut, cre]
Maintainer: Dave Armstrong <dave@quantoid.net>

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Package RcppTOML updated to version 0.1.6 with previous version 0.1.5 dated 2018-10-31

Title: 'Rcpp' Bindings to Parser for Tom's Obvious Markup Language
Description: The configuration format defined by 'TOML' (which expands to "Tom's Obvious Markup Language") specifies an excellent format (described at <https://github.com/toml-lang/toml>) suitable for both human editing as well as the common uses of a machine-readable format. This package uses 'Rcpp' to connect the 'cpptoml' parser written by Chase Geigle (in modern C++11) to R.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package trialr updated to version 0.1.2 with previous version 0.1.1 dated 2019-05-24

Title: Clinical Trial Designs in 'rstan'
Description: A collection of clinical trial designs and methods, implemented in 'rstan' and R, including: the Continual Reassessment Method by O'Quigley et al. (1990) <doi:10.2307/2531628>; EffTox by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; and the Augmented Binary method by Wason & Seaman (2013) <doi:10.1002/sim.5867>; and more. We provide functions to aid model-fitting and analysis. The 'rstan' implementations may also serve as a cookbook to anyone looking to extend or embellish these models. We hope that this package encourages the use of Bayesian methods in clinical trials. There is a preponderance of early phase trial designs because this is where Bayesian methods are used most. If there is a method you would like implemented, please get in touch.
Author: Kristian Brock [aut, cre] (<https://orcid.org/0000-0002-3921-0166>), Trustees of Columbia University [cph]
Maintainer: Kristian Brock <kristian.brock@gmail.com>

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New package secsse with initial version 2.0.0
Package: secsse
Type: Package
Title: Several Examined and Concealed States-Dependent Speciation and Extinction
Version: 2.0.0
Date: 2019-06-22
License: GPL-3
Authors@R: c( person("Leonel", "Herrera Alsina", email = "leonelhalsina@gmail.com", role = "cre"), person("Paul", "van Els", email = "paulvanels@gmail.com", role = "aut"), person("Rampal", "Etienne", email = "r.s.etienne@rug.nl", role = "aut"))
Description: Simultaneously infers state-dependent diversification across two or more states of a single or multiple traits while accounting for the role of a possible concealed trait. See Herrera-Alsina et al. 2019 Systematic Biology 68: 317-328 <DOI:10.1093/sysbio/syy057>.
Depends: R (>= 3.5.0)
Imports: utils, DDD (>= 4.0), ape, foreach, doParallel, apTreeshape, phylobase, geiger, deSolve
Suggests: diversitree, phytools, testthat, testit, knitr, rmarkdown
Enhances: doMC
NeedsCompilation: yes
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.1.1
Packaged: 2019-06-23 15:46:35 UTC; rampa
Author: Leonel Herrera Alsina [cre], Paul van Els [aut], Rampal Etienne [aut]
Maintainer: Leonel Herrera Alsina <leonelhalsina@gmail.com>
Repository: CRAN
Date/Publication: 2019-06-25 11:30:03 UTC

More information about secsse at CRAN
Permanent link

Package RDML updated to version 1.0 with previous version 0.9-9 dated 2017-09-25

Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR Data Markup Language (RDML) and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization for the structure of RDML object and GUI for RDML editing.
Author: Konstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut] (<https://orcid.org/0000-0001-8926-582X>), Andrej-Nikolai Spiess [aut]
Maintainer: Konstantin A. Blagodatskikh <k.blag@yandex.ru>

Diff between RDML versions 0.9-9 dated 2017-09-25 and 1.0 dated 2019-06-25

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Package nparcomp updated to version 3.0 with previous version 2.6 dated 2015-03-12

Title: Multiple Comparisons and Simultaneous Confidence Intervals
Description: With this package, it is possible to compute nonparametric simultaneous confidence intervals for relative contrast effects in the unbalanced one way layout. Moreover, it computes simultaneous p-values. The simultaneous confidence intervals can be computed using multivariate normal distribution, multivariate t-distribution with a Satterthwaite Approximation of the degree of freedom or using multivariate range preserving transformations with Logit or Probit as transformation function. 2 sample comparisons can be performed with the same methods described above. There is no assumption on the underlying distribution function, only that the data have to be at least ordinal numbers. See Konietschke et al. (2015) <doi:10.18637/jss.v064.i09> for details.
Author: Frank Konietschke [aut, cre], Kimihiro Noguchi [ctr], Kerstin Rubarth
Maintainer: Kerstin Rubarth <kerstin.rubarth@charite.de>

Diff between nparcomp versions 2.6 dated 2015-03-12 and 3.0 dated 2019-06-25

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Package islasso updated to version 1.1.0 with previous version 1.0.0 dated 2019-04-29

Title: The Induced Smoothed Lasso
Description: An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper: Cilluffo, G., Sottile, G., La Grutta, S. and Muggeo, V. (2019) The Induced Smoothed lasso: A practical framework for hypothesis testing in high dimensional regression. <doi:10.1177/0962280219842890>, and discussed in a tutorial: Sottile, G., Cilluffo, G., and Muggeo, V. (2019) The R package islasso: estimation and hypothesis testing in lasso regression. <doi:10.13140/RG.2.2.16360.11521>.
Author: Gianluca Sottile [aut, cre], Giovanna Cilluffo [aut, ctb], Vito MR Muggeo [aut, cre]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>

Diff between islasso versions 1.0.0 dated 2019-04-29 and 1.1.0 dated 2019-06-25

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Package Gifi updated to version 0.3-9 with previous version 0.3-8 dated 2018-10-03

Title: Multivariate Analysis with Optimal Scaling
Description: Implements categorical principal component analysis ('PRINCALS'), multiple correspondence analysis ('HOMALS'), monotone regression analysis ('MORALS'). It replaces the 'homals' package.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut], Patrick J. F. Groenen [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>

Diff between Gifi versions 0.3-8 dated 2018-10-03 and 0.3-9 dated 2019-06-25

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Package augmentedRCBD (with last version 0.1.0) was removed from CRAN

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

2018-07-10 0.1.0

Permanent link
Package rvg updated to version 0.2.1 with previous version 0.2.0 dated 2019-04-06

Title: R Graphics Devices for Vector Graphics Output
Description: Vector Graphics devices for Microsoft PowerPoint and Excel. Functions extending package 'officer' are provided to embed 'DrawingML' graphics into 'Microsoft PowerPoint' presentations and 'Microsoft Excel' workbooks.
Author: David Gohel [aut, cre], Bob Rudis [ctb] (the javascript code used by function set_attr), Francois Brunetti [ctb] (clipping algorithms)
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package flextable updated to version 0.5.5 with previous version 0.5.4 dated 2019-05-14

Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'Microsoft Word' and 'Microsoft PowerPoint' documents. Functions are provided to let users create tables, modify and format their content. It extends package 'officer' that does not contain any feature for customized tabular reporting and can be used within R markdown documents.
Author: David Gohel [aut, cre], Quentin Fazilleau [ctb], Maxim Nazarov [ctb] (rmarkdown for docx output), Titouan Robert [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package jsonvalidate updated to version 1.1.0 with previous version 1.0.0 dated 2016-06-13

Title: Validate 'JSON'
Description: Uses the node library 'is-my-json-valid' or 'ajv' to validate 'JSON' against a 'JSON' schema. Drafts 04, 06 and 07 of 'JSON' schema are supported.
Author: Rich FitzJohn [aut, cre], Ian Lyttle [ctb], Kara Woo [ctb], Mathias Buus [cph], Evgeny Poberezkin [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>

Diff between jsonvalidate versions 1.0.0 dated 2016-06-13 and 1.1.0 dated 2019-06-25

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Permanent link

Package rlang updated to version 0.4.0 with previous version 0.3.4 dated 2019-04-07

Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

Diff between rlang versions 0.3.4 dated 2019-04-07 and 0.4.0 dated 2019-06-25

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Package broomExtra updated to version 0.0.4 with previous version 0.0.3 dated 2019-05-20

Title: Enhancements for 'broom' Package Family
Description: Collection of functions to assist 'broom' and 'broom.mixed' package-related data analysis workflows. In particular, the generic functions tidy(), glance(), and augment() choose appropriate S3 methods from these two packages depending on which package exports the needed method. Additionally, 'grouped_' and 'boot_' variants of the generics provides a convenient way to execute functions across a combination of grouping variable(s) in a dataframe or bootstrap them.
Author: Indrajeet Patil [aut, cre, ctb] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

Diff between broomExtra versions 0.0.3 dated 2019-05-20 and 0.0.4 dated 2019-06-25

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Permanent link

Package xfun updated to version 0.8 with previous version 0.7 dated 2019-05-14

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>), Daijiang Li [ctb], Xianying Tan [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between xfun versions 0.7 dated 2019-05-14 and 0.8 dated 2019-06-25

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More information about xfun at CRAN
Permanent link

Package tinytex updated to version 0.14 with previous version 0.13 dated 2019-05-14

Title: Helper Functions to Install and Maintain 'TeX Live', and Compile 'LaTeX' Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross-platform, portable, and easy-to-maintain version of 'TeX Live'. This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), RStudio, Inc. [cph], Fernando Cagua [ctb], Ethan Heinzen [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between tinytex versions 0.13 dated 2019-05-14 and 0.14 dated 2019-06-25

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Permanent link

Package qs updated to version 0.17.1 with previous version 0.16.1 dated 2019-05-17

Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd and lz4 code), Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled zstd code), Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled code), Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd bundled code), Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled code), Romain Francois [ctb, cph] (Derived example/tutorials for Alt-Rep structures), Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc library)
Maintainer: Travers Ching <traversc@gmail.com>

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Package pavo updated to version 2.2.0 with previous version 2.1.0 dated 2019-03-06

Title: Perceptual Analysis, Visualization and Organization of Spectral Colour Data in R
Description: A cohesive framework for parsing, analyzing and organizing colour from spectral data.
Author: Rafael Maia [aut, cre] (<https://orcid.org/0000-0002-7563-9795>), Thomas White [aut] (<https://orcid.org/0000-0002-3976-1734>), Hugo Gruson [aut] (<https://orcid.org/0000-0002-4094-1476>), John Endler [aut], Chad Eliason [aut], Pierre-Paul Bitton [aut] (<https://orcid.org/0000-0001-5984-2331>)
Maintainer: Rafael Maia <rm72@zips.uakron.edu>

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Package commonsMath updated to version 1.2.2 with previous version 1.2 dated 2018-10-26

Title: JAR Files of the Apache Commons Mathematics Library
Description: Java JAR files for the Apache Commons Mathematics Library for use by users and other packages.
Author: David B. Dahl [cre], The Apache Software Foundation [aut, cph]
Maintainer: David B. Dahl <dahl@stat.byu.edu>

Diff between commonsMath versions 1.2 dated 2018-10-26 and 1.2.2 dated 2019-06-25

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Package aws.alexa updated to version 0.1.7 with previous version 0.1.6 dated 2018-03-27

Title: Client for the Amazon Alexa Web Information Services API
Description: Use the Amazon Alexa Web Information Services API to find information about domains, including the kind of content that they carry, how popular are they---rank and traffic history, sites linking to them, among other things. See <https://aws.amazon.com/awis/> for more information.
Author: Gaurav Sood [aut, cre], Thomas Leeper [ctb]
Maintainer: Gaurav Sood <gsood07@gmail.com>

Diff between aws.alexa versions 0.1.6 dated 2018-03-27 and 0.1.7 dated 2019-06-25

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Permanent link

Package RSocrata updated to version 1.7.9-5 with previous version 1.7.8-4 dated 2019-05-15

Title: Download or Upload 'Socrata' Data Sets
Description: Provides easier interaction with 'Socrata' open data portals <http://dev.socrata.com>. Users can provide a 'Socrata' data set resource URL, or a 'Socrata' Open Data API (SoDA) web query, or a 'Socrata' "human-friendly" URL, returns an R data frame. Converts dates to 'POSIX' format and manages throttling by 'Socrata'. Users can upload data to 'Socrata' portals directly from R.
Author: Hugh Devlin, Ph. D., Tom Schenk, Jr., Gene Leynes, Nick Lucius, John Malc, Mark Silverberg, and Peter Schmeideskamp
Maintainer: "Tom Schenk Jr." <developers@cityofchicago.org>

Diff between RSocrata versions 1.7.8-4 dated 2019-05-15 and 1.7.9-5 dated 2019-06-25

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 README.md                 |    3 +--
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Package abbyyR updated to version 0.5.5 with previous version 0.5.4 dated 2018-05-30

Title: Access to Abbyy Optical Character Recognition (OCR) API
Description: Get text from images of text using Abbyy Cloud Optical Character Recognition (OCR) API. Easily OCR images, barcodes, forms, documents with machine readable zones, e.g. passports. Get the results in a variety of formats including plain text and XML. To learn more about the Abbyy OCR API, see <http://ocrsdk.com/>.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>

Diff between abbyyR versions 0.5.4 dated 2018-05-30 and 0.5.5 dated 2019-06-25

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 R/processBarcodeField.R      |    4 +-
 R/processBusinessCard.R      |    4 +-
 R/processCheckmarkField.R    |    4 +-
 R/processDocument.R          |    4 +-
 R/processFields.R            |    4 +-
 R/processImage.R             |    8 +---
 R/processMRZ.R               |    4 +-
 R/processPhotoId.R           |    4 +-
 R/processRemoteImage.R       |    4 +-
 R/processTextField.R         |    4 +-
 R/submitImage.R              |    4 +-
 build/vignette.rds           |binary
 inst/doc/example.html        |   85 +++++++++++++++++++++++++++++++++++++++----
 inst/doc/overview.html       |   85 +++++++++++++++++++++++++++++++++++++++----
 inst/doc/wiscads.html        |   85 +++++++++++++++++++++++++++++++++++++++----
 man/abbyyR-package.Rd        |    4 +-
 man/processBarcodeField.Rd   |    4 +-
 man/processBusinessCard.Rd   |    5 +-
 man/processCheckmarkField.Rd |    4 +-
 man/processDocument.Rd       |   12 +++---
 man/processImage.Rd          |   20 ++++------
 man/processPhotoId.Rd        |    4 +-
 man/processRemoteImage.Rd    |   12 +++---
 man/processTextField.Rd      |    4 +-
 33 files changed, 357 insertions(+), 115 deletions(-)

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Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.