Sun, 10 Nov 2024

Package ProbBreed updated to version 1.0.4.4 with previous version 1.0.4.3 dated 2024-11-06

Title: Probability Theory for Selecting Candidates in Plant Breeding
Description: Use probability theory under the Bayesian framework for calculating the risk of selecting candidates in a multi-environment context. Contained are functions used to fit a Bayesian multi-environment model (based on the available presets), extract posterior values and maximum posterior values, compute the variance components, check the model’s convergence, and calculate the probabilities. For both across and within-environments scopes, the package computes the probability of superior performance and the pairwise probability of superior performance. Furthermore, the probability of superior stability and the pairwise probability of superior stability across environments is estimated. A joint probability of superior performance and stability is also provided.
Author: Saulo Chaves [aut, cre] , Kaio Dias [aut, cph] , Matheus Krause [aut]
Maintainer: Saulo Chaves <saulo.chaves@ufv.br>

Diff between ProbBreed versions 1.0.4.3 dated 2024-11-06 and 1.0.4.4 dated 2024-11-10

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Package bootES updated to version 1.3.1 with previous version 1.3.0 dated 2023-04-10

Title: Bootstrap Confidence Intervals on Effect Sizes
Description: Calculate robust measures of effect sizes using the bootstrap.
Author: Daniel Gerlanc [aut, cre], Kris Kirby [aut]
Maintainer: Daniel Gerlanc <dan@gerlanc.com>

Diff between bootES versions 1.3.0 dated 2023-04-10 and 1.3.1 dated 2024-11-10

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Package viewscape updated to version 2.0.1 with previous version 2.0.0 dated 2024-11-09

Title: Viewscape Analysis
Description: A collection of functions to make R a more effective viewscape analysis tool for calculating viewscape metrics based on computing the viewable area for given a point/multiple viewpoints and a digital elevation model.The method of calculating viewscape metrics implemented in this package are based on the work of Tabrizian et al. (2020) <doi:10.1016/j.landurbplan.2019.103704>. The algorithm of computing viewshed is based on the work of Franklin & Ray. (1994) <https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=555780f6f5d7e537eb1edb28862c86d1519af2be>.
Author: Xiaohao Yang [aut, cre, cph], Nathan Fox [aut], Derek Van Berkel [aut], Mark Lindquist [aut]
Maintainer: Xiaohao Yang <xiaohaoy@umich.edu>

Diff between viewscape versions 2.0.0 dated 2024-11-09 and 2.0.1 dated 2024-11-10

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Package maditr updated to version 0.8.5 with previous version 0.8.4 dated 2024-01-11

Title: Fast Data Aggregation, Modification, and Filtering with Pipes and 'data.table'
Description: Provides pipe-style interface for 'data.table'. Package preserves all 'data.table' features without significant impact on performance. 'let' and 'take' functions are simplified interfaces for most common data manipulation tasks. For example, you can write 'take(mtcars, mean(mpg), by = am)' for aggregation or 'let(mtcars, hp_wt = hp/wt, hp_wt_mpg = hp_wt/mpg)' for modification. Use 'take_if/let_if' for conditional aggregation/modification. Additionally there are some conveniences such as automatic 'data.frame' conversion to 'data.table'.
Author: Gregory Demin [aut, cre]
Maintainer: Gregory Demin <gdemin@gmail.com>

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Package CohortSurvival updated to version 0.6.0 with previous version 0.5.2 dated 2024-06-29

Title: Estimate Survival from Common Data Model Cohorts
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
Author: Edward Burn [aut, cre] , Kim Lopez-Gueell [aut] , Marti Catala [aut] , Xintong Li [aut] , Danielle Newby [aut] , Nuria Mercade-Besora [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>

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Package CodelistGenerator updated to version 3.3.0 with previous version 3.2.1 dated 2024-10-17

Title: Identify Relevant Clinical Codes and Evaluate Their Use
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] , Marti Catala [ctb] , Xihang Chen [aut] , Nuria Mercade-Besora [aut] , Mike Du [ctb] , Danielle Newby [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>

Diff between CodelistGenerator versions 3.2.1 dated 2024-10-17 and 3.3.0 dated 2024-11-10

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Package isopam updated to version 3.0 with previous version 2.0 dated 2024-01-09

Title: Clustering of Sites with Species Data
Description: Clustering algorithm developed for use with plot inventories of species. It groups plots by subsets of diagnostic species rather than overall species composition. There is an unsupervised and a supervised mode, the latter accepting suggestions for species with greater weight and cluster medoids.
Author: Sebastian Schmidtlein [aut, cre] , Jason Collison [aut], Robin Pfannendoerfer [aut], Lubomir Tichy [ctb]
Maintainer: Sebastian Schmidtlein <schmidtlein@kit.edu>

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Package superb updated to version 0.95.19 with previous version 0.95.15 dated 2024-08-17

Title: Summary Plots with Adjusted Error Bars
Description: Computes standard error and confidence interval of various descriptive statistics under various designs and sampling schemes. The main function, superbPlot(), return a plot. superbData() returns a dataframe with the statistic and its precision interval so that other plotting package can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109> or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005) <doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012) <doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>, Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding <doi:10.20982/tqmp.15.1.p001> for specific references.
Author: Denis Cousineau [aut, cre], Bradley Harding [ctb], Marc-Andre Goulet [ctb], Jesika Walker [art, pre]
Maintainer: Denis Cousineau <denis.cousineau@uottawa.ca>

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Package lemon updated to version 0.5.0 with previous version 0.4.9 dated 2024-02-08

Title: Freshing Up your 'ggplot2' Plots
Description: Functions for working with legends and axis lines of 'ggplot2', facets that repeat axis lines on all panels, and some 'knitr' extensions.
Author: Stefan McKinnon Edwards [aut, ctb, cre] , Baptiste Auguie [ctb] , Shaun Jackman [ctb] , Hadley Wickham [ctb] , Winston Chang [ctb]
Maintainer: Stefan McKinnon Edwards <sme@iysik.com>

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Package GeoModels updated to version 2.0.8 with previous version 2.0.7 dated 2024-10-25

Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large) Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. Se [...truncated...]
Author: Moreno Bevilacqua [aut, cre] , Victor Morales-Onate [aut] , Christian Caamano-Carrillo [aut]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>

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Package sampcompR updated to version 0.2.4 with previous version 0.2.3 dated 2024-08-19

Title: Comparing and Visualizing Differences Between Surveys
Description: Easily analyze and visualize differences between samples (e.g., benchmark comparisons, nonresponse comparisons in surveys) on three levels. The comparisons can be univariate, bivariate or multivariate. On univariate level the variables of interest of a survey and a comparison survey (i.e. benchmark) are compared, by calculating one of several difference measures (e.g., relative difference in mean), and an average difference between the surveys. On bivariate level a function can calculate significant differences in correlations for the surveys. And on multivariate levels a function can calculate significant differences in model coefficients between the surveys of comparison. All of those differences can be easily plotted and outputted as a table. For more detailed information on the methods and example use see Rohr, B., Silber, H., & Felderer, B. (2024). „Comparing the Accuracy of Univariate, Bivariate, and Multivariate Estimates across Probability and Non-Probability Surveys with [...truncated...]
Author: Bjoern Rohr [aut, cre, cph], Barbara Felderer [aut]
Maintainer: Bjoern Rohr <bjoern.rohr@gesis.org>

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Package Rcssplot updated to version 1.1.0 with previous version 1.0.0 dated 2019-12-13

Title: Styling of Graphics using Cascading Style Sheets
Description: Provides a means to style plots through cascading style sheets. This separates the aesthetics from the data crunching in plots and charts.
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>

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Package r2pmml updated to version 0.29.0 with previous version 0.28.0 dated 2024-07-25

Title: Convert R Models to PMML
Description: R wrapper for the JPMML-R library <https://github.com/jpmml/jpmml-r>, which converts R models to Predictive Model Markup Language (PMML).
Author: Villu Ruusmann [aut, cre]
Maintainer: Villu Ruusmann <villu.ruusmann@gmail.com>

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Package PakPMICS2018 updated to version 1.2.0 with previous version 1.1.0 dated 2024-09-13

Title: Multiple Indicator Cluster Survey (MICS) 2017-18 Data for Punjab, Pakistan
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 [...truncated...]
Author: Muhammad Yaseen [aut, cre]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>

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Package nodbi updated to version 0.11.0 with previous version 0.10.7 dated 2024-09-29

Title: 'NoSQL' Database Connector
Description: Simplified JSON document database access and manipulation, providing a common API across supported 'NoSQL' databases 'Elasticsearch', 'CouchDB', 'MongoDB' as well as 'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Author: Ralf Herold [aut, cre] , Scott Chamberlain [aut] , Rich FitzJohn [aut], Jeroen Ooms [aut]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>

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Package inline updated to version 0.3.20 with previous version 0.3.19 dated 2021-05-31

Title: Functions to Inline C, C++, Fortran Function Calls from R
Description: Functionality to dynamically define R functions and S4 methods with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling conventions.
Author: Oleg Sklyar [aut], Dirk Eddelbuettel [aut, cre] , Romain Francois [aut] , Mike Smith [ctb], Duncan Murdoch [ctb], Karline Soetaert [ctb] , Johannes Ranke [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package ggreveal updated to version 0.1.4 with previous version 0.1.3 dated 2024-08-30

Title: Reveal a 'ggplot' Incrementally
Description: Provides functions that make it easy to reveal 'ggplot2' graphs incrementally. The functions take a plot produced with 'ggplot2' and return a list of plots showing data incrementally by panels, layers, groups, the values in an axis or any arbitrary aesthetic.
Author: Weverthon Machado [aut, cre, cph]
Maintainer: Weverthon Machado <weverthonmachado@gmail.com>

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Package ctrdata updated to version 1.19.5 with previous version 1.19.4 dated 2024-09-29

Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: A system for querying, retrieving and analyzing protocol- and results-related information on clinical trials from four public registers, the 'European Union Clinical Trials Register' ('EUCTR', <https://www.clinicaltrialsregister.eu/>), 'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also translating queries the retired classic interface), the 'ISRCTN' (<http://www.isrctn.com/>) and the 'European Union Clinical Trials Information System' ('CTIS', <https://euclinicaltrials.eu/>). Trial information is downloaded, converted and stored in a database ('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi'). Documents in registers associated with trials can also be downloaded. Other functions identify deduplicated records, easily find and extract variables (fields) of interest even from complex nested data as used by the registers, merge variables and update queries. The package can be used for meta-analysis and trend-analysis of the design and cond [...truncated...]
Author: Ralf Herold [aut, cre]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>

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Permanent link

Package UPG updated to version 0.3.5 with previous version 0.3.4 dated 2023-11-04

Title: Efficient Bayesian Algorithms for Binary and Categorical Data Regression Models
Description: Efficient Bayesian implementations of probit, logit, multinomial logit and binomial logit models. Functions for plotting and tabulating the estimation output are available as well. Estimation is based on Gibbs sampling where the Markov chain Monte Carlo algorithms are based on the latent variable representations and marginal data augmentation algorithms described in "Gregor Zens, Sylvia Frühwirth-Schnatter & Helga Wagner (2023). Ultimate Pólya Gamma Samplers – Efficient MCMC for possibly imbalanced binary and categorical data, Journal of the American Statistical Association <doi:10.1080/01621459.2023.2259030>".
Author: Gregor Zens [aut, cre], Sylvia Fruehwirth-Schnatter [aut], Helga Wagner [aut]
Maintainer: Gregor Zens <zens@iiasa.ac.at>

Diff between UPG versions 0.3.4 dated 2023-11-04 and 0.3.5 dated 2024-11-10

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Package singleRcapture updated to version 0.2.1.3 with previous version 0.2.1.2 dated 2024-07-18

Title: Single-Source Capture-Recapture Models
Description: Implementation of single-source capture-recapture methods for population size estimation using zero-truncated, zero-one truncated and zero-truncated one-inflated Poisson, Geometric and Negative Binomial regression as well as Zelterman's and Chao's regression. Package includes point and interval estimators for the population size with variances estimated using analytical or bootstrap method. Details can be found in: van der Heijden et all. (2003) <doi:10.1191/1471082X03st057oa>, Böhning and van der Heijden (2019) <doi:10.1214/18-AOAS1232>, Böhning et al. (2020) Capture-Recapture Methods for the Social and Medical Sciences or Böhning and Friedl (2021) <doi:10.1007/s10260-021-00556-8>.
Author: Piotr Chlebicki [aut, cre], Maciej Beresewicz [aut, ctb]
Maintainer: Piotr Chlebicki <piotrek.pecet@gmail.com>

Diff between singleRcapture versions 0.2.1.2 dated 2024-07-18 and 0.2.1.3 dated 2024-11-10

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Package scoringfunctions updated to version 0.0.7 with previous version 0.0.6 dated 2023-06-12

Title: A Collection of Scoring Functions for Assessing Point Forecasts
Description: Implements multiple consistent scoring functions (Gneiting T (2011) <doi:10.1198/jasa.2011.r10138>) for assessing point forecasts and point predictions. Detailed documentation of scoring functions' properties is included for facilitating interpretation of results.
Author: Hristos Tyralis [aut, cre] , Georgia Papacharalampous [aut]
Maintainer: Hristos Tyralis <montchrister@gmail.com>

Diff between scoringfunctions versions 0.0.6 dated 2023-06-12 and 0.0.7 dated 2024-11-10

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Package ottr updated to version 1.5.1 with previous version 1.5.0 dated 2024-02-01

Title: An R Autograding Extension for Otter-Grader
Description: An R autograding extension for Otter-Grader (<https://otter-grader.readthedocs.io>). It supports grading R scripts, R Markdown documents, and R Jupyter Notebooks.
Author: Christopher Pyles [aut, cre] , UC Berkeley Data Science Education Program [cph]
Maintainer: Christopher Pyles <cpyles@berkeley.edu>

Diff between ottr versions 1.5.0 dated 2024-02-01 and 1.5.1 dated 2024-11-10

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 ottr-1.5.1/ottr/NAMESPACE                                                             |   18 
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Package leafletZH updated to version 0.1.1 with previous version 0.1.0 dated 2024-10-25

Title: Chinese Leaflet Map Relate Operation
Description: Provides 'sf' data for Chinese provinces and cities, methods for plotting shape maps of Chinese provinces and cities, Convert Coordinates Between Different Systems, and a layer for 'leaflet' with Gaode tiles. It is designed to facilitate geographical data visualization in China.
Author: Damonsoul [aut, cre]
Maintainer: Damonsoul <chenmaowei96@gmail.com>

Diff between leafletZH versions 0.1.0 dated 2024-10-25 and 0.1.1 dated 2024-11-10

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Package data.table.threads updated to version 1.0.1 with previous version 1.0.0 dated 2024-10-11

Title: Analyze Multi-Threading Performance for 'data.table' Functions
Description: Assists in finding the most suitable thread count for the various 'data.table' routines that support parallel processing.
Author: Anirban Chetia [aut, cre]
Maintainer: Anirban Chetia <ac4743@nau.edu>

Diff between data.table.threads versions 1.0.0 dated 2024-10-11 and 1.0.1 dated 2024-11-10

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New package SegEnvIneq with initial version 1.2
Package: SegEnvIneq
Title: Environmental Inequality Indices Based on Segregation Measures
Version: 1.2
Date: 2024-11-07
Description: A set of segregation-based indices and randomization methods to make robust environmental inequality assessments, as described in Schaeffer and Tivadar (2019) "Measuring Environmental Inequalities: Insights from the Residential Segregation Literature" <doi:10.1016/j.ecolecon.2019.05.009>.
Depends: R (>= 4.4.0)
Imports: sf (>= 1.0-16), spdep (>= 1.3-6), OasisR (>= 3.1.1), outliers (>= 0.15)
License: GPL-2 | GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-07 11:05:44 UTC; mtivadar
Author: Mihai Tivadar [aut, cre], Yves Schaeffer [aut]
Maintainer: Mihai Tivadar <mihai.tivadar@inrae.fr>
Repository: CRAN
Date/Publication: 2024-11-10 15:50:06 UTC

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New package maicplus with initial version 0.1.0
Title: Matching Adjusted Indirect Comparison
Package: maicplus
Version: 0.1.0
Date: 2024-10-29
Description: Facilitates performing matching adjusted indirect comparison (MAIC) analysis where the endpoint of interest is either time-to-event (e.g. overall survival) or binary (e.g. objective tumor response). The method is described by Signorovitch et al (2012) <doi:10.1016/j.jval.2012.05.004>.
License: Apache License 2.0
URL: https://github.com/hta-pharma/maicplus/, https://hta-pharma.github.io/maicplus/
BugReports: https://github.com/hta-pharma/maicplus/issues
Depends: R (>= 3.6)
Imports: graphics, grDevices, stats, survival, lubridate, DescTools, MASS, boot, stringr, lmtest, sandwich
Suggests: knitr, testthat (>= 2.0), ggplot2, rmarkdown, dplyr, survminer, flexsurv, tibble, vdiffr, checkmate
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-07 11:31:16 UTC; gravesti
Author: Gregory Chen [aut], Michael Seo [aut], Isaac Gravestock [aut, cre], Miranta Antoniou [ctb], Chrysostomos Kalyvas [ctb], MSD, Inc. [cph, fnd], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Repository: CRAN
Date/Publication: 2024-11-10 15:50:02 UTC

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New package laminr with initial version 0.1.0
Package: laminr
Title: Interface for 'LaminDB'
Version: 0.1.0
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data framework for biology. This package allows you to query and download data from 'LaminDB' instances.
License: Apache License (>= 2)
URL: https://laminr.lamin.ai, https://github.com/laminlabs/laminr
BugReports: https://github.com/laminlabs/laminr/issues
Depends: R (>= 4.0.0)
Imports: cli, httr, jsonlite, purrr, R6, rlang
Suggests: anndata, quarto, s3 (>= 1.1.0), testthat (>= 3.0.0), withr
VignetteBuilder: quarto
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-07 14:07:57 UTC; root
Author: Robrecht Cannoodt [aut, cre], Luke Zappia [aut], Data Intuitive [aut], Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@data-intuitive.com>
Repository: CRAN
Date/Publication: 2024-11-10 16:00:02 UTC

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Package maps updated to version 3.4.2.1 with previous version 3.4.2 dated 2023-12-15

Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').
Author: Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg. Enhancements by Thomas P Minka and Alex Deckmyn.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>

Diff between maps versions 3.4.2 dated 2023-12-15 and 3.4.2.1 dated 2024-11-10

 DESCRIPTION  |    6 +++---
 MD5          |    4 ++--
 src/mapget.c |   18 +++++++++---------
 3 files changed, 14 insertions(+), 14 deletions(-)

More information about maps at CRAN
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