Title: Dynamic Panel Models with Orthogonal Reparameterization of Fixed
Effects
Description: Implements the orthogonal reparameterization
approach recommended by Lancaster (2002) to estimate dynamic panel
models with fixed effects (and optionally: panel specific
intercepts). The approach uses a likelihood-based estimator and
produces estimates that are asymptotically unbiased as N goes to
infinity, with a T as low as 2.
Author: Davor Cubranic [aut],
Mark Pickup [aut, cre],
Paul Gustafson [aut],
Geoffrey Evans [aut],
Jonoska Stojkova Biljana [ctb]
Maintainer: Mark Pickup <mark.pickup@sfu.ca>
Diff between OrthoPanels versions 1.1-2 dated 2019-04-05 and 1.1-3 dated 2019-05-09
DESCRIPTION | 8 MD5 | 10 build/vignette.rds |binary inst/doc/intro-opm.R | 60 +-- inst/doc/intro-opm.html | 813 +++++++++++++++++++++++----------------------- tests/testthat/test-opm.R | 6 6 files changed, 456 insertions(+), 441 deletions(-)
Title: Clustering Genetic Sequence Data Using the HierBAPS Algorithm
Description: Implements the hierarchical Bayesian analysis of populations structure (hierBAPS)
algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences
from multiple sequence alignments in FASTA format.
The implementation includes improved defaults and plotting capabilities
and unlike the original 'MATLAB' version removes singleton SNPs by default.
Author: Gerry Tonkin-Hill [cre, aut]
Maintainer: Gerry Tonkin-Hill <g.tonkinhill@gmail.com>
Diff between rhierbaps versions 1.1.0 dated 2018-10-10 and 1.1.2 dated 2019-05-09
rhierbaps-1.1.0/rhierbaps/R/log_stirling2.R |only rhierbaps-1.1.0/rhierbaps/man/log_stirling2.Rd |only rhierbaps-1.1.2/rhierbaps/DESCRIPTION | 12 rhierbaps-1.1.2/rhierbaps/MD5 | 20 - rhierbaps-1.1.2/rhierbaps/NEWS.md | 6 rhierbaps-1.1.2/rhierbaps/R/calc_log_ml.R | 5 rhierbaps-1.1.2/rhierbaps/R/join_units_2.R | 10 rhierbaps-1.1.2/rhierbaps/README.md | 8 rhierbaps-1.1.2/rhierbaps/inst/doc/introduction.html | 155 ++++++---- rhierbaps-1.1.2/rhierbaps/inst/vignette-supp/unnamed-chunk-15-1.png |binary rhierbaps-1.1.2/rhierbaps/inst/vignette-supp/unnamed-chunk-16-1.png |binary rhierbaps-1.1.2/rhierbaps/inst/vignette-supp/unnamed-chunk-17-1.png |binary 12 files changed, 141 insertions(+), 75 deletions(-)
Title: Quasi Variances for Factor Effects in Statistical Models
Description: Functions to compute quasi variances and associated measures of approximation error.
Author: David Firth
Maintainer: David Firth <d.firth@warwick.ac.uk>
Diff between qvcalc versions 0.9-1 dated 2017-09-19 and 1.0.0 dated 2019-05-09
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NEWS.md | 26 +++++++++++++------------- R/qvcalc.R | 2 +- man/plot.qv.Rd | 11 ++++++++--- 5 files changed, 33 insertions(+), 28 deletions(-)
Title: PC Algorithm with the Principle of Mendelian Randomization
Description: A PC Algorithm with the Principle of Mendelian Randomization. This package implements the MRPC
(PC with the principle of Mendelian randomization) algorithm to infer causal graphs. It also
contains functions to simulate data under a certain topology, to visualize a graph in different
ways, and to compare graphs and quantify the differences.
See Badsha and Fu (2018) <doi:10.1101/171348>,Badsha, Martin and Fu (2018) <arXiv:1806.01899>.
Author: Md Bahadur Badsha [aut,cre],Evan A Martin [ctb] and Audrey Qiuyan Fu [aut]
Maintainer: Md Bahadur Badsha <mdbadsha@uidaho.edu>
Diff between MRPC versions 2.0.0 dated 2018-10-13 and 2.1.0 dated 2019-05-09
MRPC-2.0.0/MRPC/R/Case_1P.R |only MRPC-2.0.0/MRPC/R/Case_2P.R |only MRPC-2.0.0/MRPC/R/Case_3P.R |only MRPC-2.0.0/MRPC/R/Case_NP.R |only MRPC-2.0.0/MRPC/R/Cut_Modules.R |only MRPC-2.0.0/MRPC/R/DendroModuleGraph.R |only MRPC-2.0.0/MRPC/R/InferenceAccuracyExample.R |only MRPC-2.0.0/MRPC/R/Recall_Precision.R |only MRPC-2.0.0/MRPC/R/SimulatedData.R |only MRPC-2.0.0/MRPC/R/SimulationDemo.R |only MRPC-2.0.0/MRPC/data/Data_GEUVADIS.rda |only MRPC-2.0.0/MRPC/data/Data_withoutlier.rda |only MRPC-2.0.0/MRPC/data/Data_withoutoutlier.rda |only MRPC-2.0.0/MRPC/data/ExampleMRPC.rda |only MRPC-2.0.0/MRPC/data/simu.data_M0.rda |only MRPC-2.0.0/MRPC/data/simu.data_M1.rda |only MRPC-2.0.0/MRPC/data/simu.data_M2.rda |only MRPC-2.0.0/MRPC/data/simu.data_M3.rda |only MRPC-2.0.0/MRPC/data/simu.data_M4.rda |only MRPC-2.0.0/MRPC/data/simu.data_layered.rda |only MRPC-2.0.0/MRPC/data/simu.data_multiparent.rda |only MRPC-2.0.0/MRPC/data/simu.data_starshaped.rda |only MRPC-2.0.0/MRPC/man/Case_1P.Rd |only MRPC-2.0.0/MRPC/man/Case_2P.Rd |only MRPC-2.0.0/MRPC/man/Case_3P.Rd |only MRPC-2.0.0/MRPC/man/Case_NP.Rd |only MRPC-2.0.0/MRPC/man/Cut_Modules.Rd |only MRPC-2.0.0/MRPC/man/Data_GEUVADIS.Rd |only MRPC-2.0.0/MRPC/man/Data_withoutlier.Rd |only MRPC-2.0.0/MRPC/man/Data_withoutoutlier.Rd |only MRPC-2.0.0/MRPC/man/DendroModuleGraph.Rd |only MRPC-2.0.0/MRPC/man/ExampleMRPC.Rd |only MRPC-2.0.0/MRPC/man/Example_Outlier.Rd |only MRPC-2.0.0/MRPC/man/InferenceAccuracyExample.Rd |only MRPC-2.0.0/MRPC/man/Recall_Precision.Rd |only MRPC-2.0.0/MRPC/man/SimulatedData.Rd |only MRPC-2.0.0/MRPC/man/SimulationDemo.Rd |only MRPC-2.0.0/MRPC/man/simudata_Layered.Rd |only MRPC-2.0.0/MRPC/man/simudata_M0.Rd |only MRPC-2.0.0/MRPC/man/simudata_M1.Rd |only MRPC-2.0.0/MRPC/man/simudata_M2.Rd |only MRPC-2.0.0/MRPC/man/simudata_M3.Rd |only MRPC-2.0.0/MRPC/man/simudata_M4.Rd |only MRPC-2.0.0/MRPC/man/simudata_multiparent.Rd |only MRPC-2.0.0/MRPC/man/simudata_starshaped.Rd |only MRPC-2.1.0/MRPC/DESCRIPTION | 17 ++- MRPC-2.1.0/MRPC/MD5 | 119 +++++++++++----------- MRPC-2.1.0/MRPC/NAMESPACE | 21 ++- MRPC-2.1.0/MRPC/R/CompareMethodsNodeOrdering.R |only MRPC-2.1.0/MRPC/R/CompareMethodsVStructure.R |only MRPC-2.1.0/MRPC/R/CutModules.R |only MRPC-2.1.0/MRPC/R/EdgeOrientation.R | 10 - MRPC-2.1.0/MRPC/R/ModiSkeleton.R | 24 +++- MRPC-2.1.0/MRPC/R/PlotDendrogram.R |only MRPC-2.1.0/MRPC/R/PlotGraphWithModules.R |only MRPC-2.1.0/MRPC/R/RecallPrecision.R |only MRPC-2.1.0/MRPC/R/SimulateData.R |only MRPC-2.1.0/MRPC/R/SimulateData1P.R |only MRPC-2.1.0/MRPC/R/SimulateData2P.R |only MRPC-2.1.0/MRPC/R/SimulateData3P.R |only MRPC-2.1.0/MRPC/R/SimulateDataNP.R |only MRPC-2.1.0/MRPC/README.md | 38 ++++--- MRPC-2.1.0/MRPC/data/data_GEUVADIS.rda |only MRPC-2.1.0/MRPC/data/data_examples.rda |only MRPC-2.1.0/MRPC/data/data_with_outliers.rda |only MRPC-2.1.0/MRPC/data/data_without_outliers.rda |only MRPC-2.1.0/MRPC/data/simu_data_M0.rda |only MRPC-2.1.0/MRPC/data/simu_data_M1.rda |only MRPC-2.1.0/MRPC/data/simu_data_M2.rda |only MRPC-2.1.0/MRPC/data/simu_data_M3.rda |only MRPC-2.1.0/MRPC/data/simu_data_M4.rda |only MRPC-2.1.0/MRPC/data/simu_data_layered.rda |only MRPC-2.1.0/MRPC/data/simu_data_multiparent.rda |only MRPC-2.1.0/MRPC/data/simu_data_starshaped.rda |only MRPC-2.1.0/MRPC/man/CompareMethodsNodeOrdering.Rd |only MRPC-2.1.0/MRPC/man/CompareMethodsVStructure.Rd |only MRPC-2.1.0/MRPC/man/CutModules.Rd |only MRPC-2.1.0/MRPC/man/EdgeOrientation.Rd | 30 +++-- MRPC-2.1.0/MRPC/man/MRPC.Rd | 104 ++++++++++--------- MRPC-2.1.0/MRPC/man/MRPCclass.Rd | 6 - MRPC-2.1.0/MRPC/man/MRPCtruth.Rd | 9 + MRPC-2.1.0/MRPC/man/ModiSkeleton.Rd | 65 ++++-------- MRPC-2.1.0/MRPC/man/PlotDendrogram.Rd |only MRPC-2.1.0/MRPC/man/PlotGraphWithModules.Rd |only MRPC-2.1.0/MRPC/man/RecallPrecision.Rd |only MRPC-2.1.0/MRPC/man/RobustCor.Rd | 4 MRPC-2.1.0/MRPC/man/SimulateData.Rd |only MRPC-2.1.0/MRPC/man/SimulateData1P.Rd |only MRPC-2.1.0/MRPC/man/SimulateData2P.Rd |only MRPC-2.1.0/MRPC/man/SimulateData3P.Rd |only MRPC-2.1.0/MRPC/man/SimulateDataNP.Rd |only MRPC-2.1.0/MRPC/man/aSHD.Rd | 2 MRPC-2.1.0/MRPC/man/data_GEUVADIS.Rd |only MRPC-2.1.0/MRPC/man/data_examples.Rd |only MRPC-2.1.0/MRPC/man/data_with_outliers.Rd |only MRPC-2.1.0/MRPC/man/data_without_outliers.Rd |only MRPC-2.1.0/MRPC/man/mpinv.Rd | 6 - MRPC-2.1.0/MRPC/man/seqDiff.Rd | 4 MRPC-2.1.0/MRPC/man/simu_data_M0.Rd |only MRPC-2.1.0/MRPC/man/simu_data_M1.Rd |only MRPC-2.1.0/MRPC/man/simu_data_M2.Rd |only MRPC-2.1.0/MRPC/man/simu_data_M3.Rd |only MRPC-2.1.0/MRPC/man/simu_data_M4.Rd |only MRPC-2.1.0/MRPC/man/simu_data_layered.Rd |only MRPC-2.1.0/MRPC/man/simu_data_multiparent.Rd |only MRPC-2.1.0/MRPC/man/simu_data_starshaped.Rd |only 106 files changed, 249 insertions(+), 210 deletions(-)
Title: Analysis of Symbolic Data
Description: Symbolic data analysis methods: importing/exporting data from ASSO XML Files, distance calculation for symbolic data (Ichino-Yaguchi, de Carvalho measure), zoom star plot, 3d interval plot, multidimensional scaling for symbolic interval data, dynamic clustering based on distance matrix, HINoV method for symbolic data, Ichino's feature selection method, principal component analysis for symbolic interval data, decision trees for symbolic data based on optimal split with bagging, boosting and random forest approach (+visualization), kernel discriminant analysis for symbolic data, Kohonen's self-organizing maps for symbolic data, replication and profiling, artificial symbolic data generation.
(Milligan, G.W., Cooper, M.C. (1985) <doi:10.1007/BF02294245>,
Breiman, L. (1996), <doi:10.1007/BF00058655>,
Hubert, L., Arabie, P. (1985), <doi:10.1007%2FBF01908075>,
Ichino, M., & Yaguchi, H. (1994), <doi:10.1109/21.286391>,
Rand, W.M. (1971) <doi:10.1080/01621459.1971.10482356>,
Calinski, T., Harabasz, J. (1974) <doi:10.1080/03610927408827101>,
Breckenridge, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>,
Groenen, P.J.F, Winsberg, S., Rodriguez, O., Diday, E. (2006) <doi:10.1016/j.csda.2006.04.003>,
Walesiak, M., Dudek, A. (2008) <doi:10.1007/978-3-540-78246-9_11>,
Dudek, A. (2007), <doi:10.1007/978-3-540-70981-7_4>).
Author: Andrzej Dudek, Marcin Pelka <marcin.pelka@ue.wroc.pl>, Justyna Wilk<justyna.wilk@ue.wroc.pl> (to 2017-09-20), Marek Walesiak <Marek.Walesiak@ue.wroc.pl> (from 2018-02-01)
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between symbolicDA versions 0.5-3 dated 2018-03-25 and 0.6-1 dated 2019-05-09
symbolicDA-0.5-3/symbolicDA/man/dist.SDA.rd |only symbolicDA-0.6-1/symbolicDA/DESCRIPTION | 13 symbolicDA-0.6-1/symbolicDA/INDEX | 126 ++-- symbolicDA-0.6-1/symbolicDA/MD5 | 116 +-- symbolicDA-0.6-1/symbolicDA/NAMESPACE | 2 symbolicDA-0.6-1/symbolicDA/R/DClust.r | 8 symbolicDA-0.6-1/symbolicDA/R/HINoV.SDA.r | 4 symbolicDA-0.6-1/symbolicDA/R/SO2Simple.R | 2 symbolicDA-0.6-1/symbolicDA/R/dist.SDA.r | 2 symbolicDA-0.6-1/symbolicDA/R/kernel.SDA.r | 4 symbolicDA-0.6-1/symbolicDA/R/parse.SO.r | 2 symbolicDA-0.6-1/symbolicDA/R/plot3dInterval.r | 30 - symbolicDA-0.6-1/symbolicDA/R/replication.SDA.r | 2 symbolicDA-0.6-1/symbolicDA/R/symbolicDA2RSDA.r | 209 ------- symbolicDA-0.6-1/symbolicDA/man/DClust.rd | 4 symbolicDA-0.6-1/symbolicDA/man/HINoV.SDA.rd | 8 symbolicDA-0.6-1/symbolicDA/man/PCA.centers.SDA.rd | 78 +- symbolicDA-0.6-1/symbolicDA/man/PCA.mrpca.SDA.rd | 80 +- symbolicDA-0.6-1/symbolicDA/man/PCA.spaghetti.SDA.rd | 80 +- symbolicDA-0.6-1/symbolicDA/man/PCA.spca.SDA.rd | 80 +- symbolicDA-0.6-1/symbolicDA/man/PCA.vertices.SDA.rd | 80 +- symbolicDA-0.6-1/symbolicDA/man/RSDA2SymbolicDA.Rd | 204 +++--- symbolicDA-0.6-1/symbolicDA/man/SO2Simple.rd | 2 symbolicDA-0.6-1/symbolicDA/man/bagging.SDA.rd | 98 +-- symbolicDA-0.6-1/symbolicDA/man/boosting.SDA.rd | 90 +-- symbolicDA-0.6-1/symbolicDA/man/data_symbolic.rd | 2 symbolicDA-0.6-1/symbolicDA/man/decisionTree.SDA.rd | 124 ++-- symbolicDA-0.6-1/symbolicDA/man/dist_SDA.rd |only symbolicDA-0.6-1/symbolicDA/man/draw.decisionTree.SDA.rd | 100 +-- symbolicDA-0.6-1/symbolicDA/man/generate.SO.rd | 2 symbolicDA-0.6-1/symbolicDA/man/index.G1d.rd | 6 symbolicDA-0.6-1/symbolicDA/man/interscal.sda.rd | 94 +-- symbolicDA-0.6-1/symbolicDA/man/iscal.sda.rd | 90 +-- symbolicDA-0.6-1/symbolicDA/man/kernel.SDA.rd | 96 +-- symbolicDA-0.6-1/symbolicDA/man/parse.SO.rd | 2 symbolicDA-0.6-1/symbolicDA/man/plot3dInterval.rd | 88 +- symbolicDA-0.6-1/symbolicDA/man/random.forest.SDA.rd | 80 +- symbolicDA-0.6-1/symbolicDA/man/replication.SDA.rd | 4 symbolicDA-0.6-1/symbolicDA/man/save.SO.rd | 2 symbolicDA-0.6-1/symbolicDA/man/simple2SO.rd | 2 symbolicDA-0.6-1/symbolicDA/man/subsdt.SDA.rd | 2 symbolicDA-0.6-1/symbolicDA/man/symbolic.object.rd | 294 +++++----- symbolicDA-0.6-1/symbolicDA/man/symscal.sda.rd | 86 +- symbolicDA-0.6-1/symbolicDA/man/zoomStar.rd | 2 symbolicDA-0.6-1/symbolicDA/tests/DClust.R | 2 symbolicDA-0.6-1/symbolicDA/tests/DClust.Rout.save | 13 symbolicDA-0.6-1/symbolicDA/tests/HINoV.SDA.Rout.save | 11 symbolicDA-0.6-1/symbolicDA/tests/SClust.Rout.save | 11 symbolicDA-0.6-1/symbolicDA/tests/cars.Rout.save | 11 symbolicDA-0.6-1/symbolicDA/tests/cluster.Description.SDA.Rout.save | 11 symbolicDA-0.6-1/symbolicDA/tests/dist.SDA.R | 2 symbolicDA-0.6-1/symbolicDA/tests/dist.SDA.Rout.save | 13 symbolicDA-0.6-1/symbolicDA/tests/index.G1d.R | 4 symbolicDA-0.6-1/symbolicDA/tests/index.G1d.Rout.save | 15 symbolicDA-0.6-1/symbolicDA/tests/plot3dInterval.R | 36 - symbolicDA-0.6-1/symbolicDA/tests/plot3dInterval.Rout.save | 11 symbolicDA-0.6-1/symbolicDA/tests/replication.SDA.Rout.save | 221 +++---- symbolicDA-0.6-1/symbolicDA/tests/save.SO.Rout.save | 11 symbolicDA-0.6-1/symbolicDA/tests/zoomStar.R | 4 symbolicDA-0.6-1/symbolicDA/tests/zoomStar.Rout.save | 13 60 files changed, 1258 insertions(+), 1531 deletions(-)
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>
Diff between rr2 versions 1.0.1 dated 2019-02-04 and 1.0.2 dated 2019-05-09
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 2 +- R/r2.R | 26 +++++++++++++++++++++++++- R/r2_resid.R | 44 ++++++++++++++++++++++++++++++++++++++++---- man/R2.Rd | 23 +++++++++++++++++++++++ man/R2.resid.Rd | 24 ++++++++++++++++++++++++ 7 files changed, 122 insertions(+), 15 deletions(-)
Title: Semiparametric Competing Risks Regression under Interval
Censoring
Description: Semiparametric regression models on the cumulative incidence function with interval-censored competing risks data as described in Bakoyannis, Yu, & Yiannoutsos (2017) <doi:10.1002/sim.7350>. The main function fits the proportional subdistribution hazards model (Fine-Gray model), the proportional odds model, and other models that belong to the class of semiparametric generalized odds rate transformation models.
Author: Giorgos Bakoyannis <gbakogia@iu.edu>, Jun Park <jp84@iu.edu>
Maintainer: Jun Park <jp84@iu.edu>
Diff between intccr versions 1.1.3 dated 2019-05-06 and 1.1.4 dated 2019-05-09
intccr-1.1.3/intccr/vignettes/park2019intccr.pdf |only intccr-1.1.4/intccr/DESCRIPTION | 8 ++++---- intccr-1.1.4/intccr/MD5 | 8 ++++---- intccr-1.1.4/intccr/R/bssmle_se.R | 2 +- intccr-1.1.4/intccr/inst/doc/intccr.pdf |binary intccr-1.1.4/intccr/vignettes/Park2019intccr.pdf |only 6 files changed, 9 insertions(+), 9 deletions(-)
Title: Gaussian Processes for Pareto Front Estimation and Optimization
Description: Gaussian process regression models, a.k.a. Kriging models, are
applied to global multi-objective optimization of black-box functions.
Multi-objective Expected Improvement and Step-wise Uncertainty Reduction
sequential infill criteria are available. A quantification of uncertainty
on Pareto fronts is provided using conditional simulations.
Author: Mickael Binois, Victor Picheny
Maintainer: Mickael Binois <mbinois@mcs.anl.gov>
Diff between GPareto versions 1.1.2 dated 2018-12-10 and 1.1.3 dated 2019-05-09
DESCRIPTION | 8 +-- MD5 | 29 ++++++------ NEWS | 5 +- R/GPareto-package.R | 4 + R/RcppExports.R | 7 +-- R/easyGParetoptim.R | 8 ++- build/vignette.rds |binary inst/CITATION |only inst/doc/GPareto_vignette.R | 3 - inst/doc/GPareto_vignette.Rnw | 93 ++++++++++++++++++++--------------------- inst/doc/GPareto_vignette.pdf |binary man/GPareto-package.Rd | 4 + man/easyGParetoptim.Rd | 4 + man/nonDomSet.Rd | 6 +- src/domination.cpp | 34 +++++++------- vignettes/GPareto_vignette.Rnw | 93 ++++++++++++++++++++--------------------- 16 files changed, 155 insertions(+), 143 deletions(-)
Title: Encrypts and Decrypts Strings
Description: Encrypts and decrypts strings using either the Caesar cipher or a
pseudorandom number generation (using set.seed()) method.
Author: Jacob Kaplan [aut, cre] (<https://orcid.org/0000-0002-0601-0387>)
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between caesar versions 0.1.0 dated 2017-01-18 and 1.0.0 dated 2019-05-09
DESCRIPTION | 21 +++-- LICENSE |only MD5 | 22 +++++- NEWS.md |only R/caesar.R | 189 +++++++++++++++++++++-------------------------------- R/utils.R |only README.md |only build |only inst |only man/caesar.Rd | 28 +++---- man/seed_cipher.Rd | 37 +++++----- tests |only vignettes |only 13 files changed, 139 insertions(+), 158 deletions(-)
Title: Bayesian A/B Testing
Description: Provides functions for Bayesian A/B testing including prior elicitation
options based on Kass and Vaidyanathan (1992) <doi:10.1111/j.2517-6161.1992.tb01868.x>.
Author: Quentin F. Gronau [aut, cre],
Akash Raj [ctb],
Eric-Jan Wagenmakers [ths]
Maintainer: Quentin F. Gronau <Quentin.F.Gronau@gmail.com>
Diff between abtest versions 0.1.2 dated 2019-05-03 and 0.1.3 dated 2019-05-09
DESCRIPTION | 8 +++---- MD5 | 5 ++-- NEWS |only R/ab_test_internals.R | 54 +++++++++----------------------------------------- 4 files changed, 17 insertions(+), 50 deletions(-)
Title: Performs Quality Control, Data Normalization, and Batch Effect
Correction for 'NanoString nCounter' Data
Description: Provides quality control (QC), normalization, and
batch effect correction operations for 'NanoString nCounter' data,
Talhouk et al. (2016) <doi:10.1371/journal.pone.0153844>. Various
metrics are used to determine which samples passed or failed QC. Gene
expression should first be normalized to housekeeping genes, before a
reference-based approach is used to adjust for batch effects. Raw
NanoString data can be imported in the form of Reporter Code Count
(RCC) files.
Author: Derek Chiu [aut, cre],
Aline Talhouk [aut],
Samuel Leung [aut]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between nanostringr versions 0.1.3 dated 2019-04-24 and 0.1.4 dated 2019-05-09
DESCRIPTION | 12 +++---- MD5 | 28 +++++++++--------- NAMESPACE | 2 - NEWS.md | 10 ++++++ R/HKnorm.R | 26 +++++++---------- R/NanoStringQC.R | 18 ++++++----- R/nanostringr-package.R | 3 - R/read_rcc.R | 11 +++---- R/refMethod.R | 4 +- inst/doc/Overview.R | 37 ++++++++++++------------ inst/doc/Overview.Rmd | 73 ++++++++++++++++++++++++------------------------ inst/doc/Overview.html | 36 ++++++++++++----------- man/HKnorm.Rd | 18 +++++------ man/NanoStringQC.Rd | 10 +++--- vignettes/Overview.Rmd | 73 ++++++++++++++++++++++++------------------------ 15 files changed, 187 insertions(+), 174 deletions(-)
Title: Reproducible Retrieval of Pew Research Center Datasets
Description: Reproducible, programmatic retrieval of survey datasets from the
Pew Research Center.
Author: Frederick Solt [aut, cre],
Yue Hu [aut],
Eric Persson [ctb]
Maintainer: Frederick Solt <frederick-solt@uiowa.edu>
Diff between pewdata versions 0.2.0 dated 2016-09-24 and 0.3.0 dated 2019-05-09
DESCRIPTION | 18 - LICENSE | 2 MD5 | 26 - NAMESPACE | 22 - NEWS.md | 36 +- R/pew_download.R | 348 ++++++++++++++----------- README.md | 39 +- build/vignette.rds |binary inst/doc/pewdata-vignette.R | 28 -- inst/doc/pewdata-vignette.Rmd | 152 +++++------ inst/doc/pewdata-vignette.html | 550 ++++++++++++++++++++++++++++------------ man/pew_download.Rd | 154 +++++------ vignettes/gender-leadership.png |binary vignettes/pewdata-vignette.Rmd | 152 +++++------ 14 files changed, 912 insertions(+), 615 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] (Reviews the documentation),
Florian De Boissieu [ctb] (Fixed bugs and improved catalog features),
Andrew Sánchez Meador [ctb] (Implemented lassnags)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 2.0.2 dated 2019-03-03 and 2.0.3 dated 2019-05-09
DESCRIPTION | 19 +-- MD5 | 63 +++++----- NEWS.md | 10 + R/Class-LAS.r | 5 R/algo_digital_surface_model.r | 8 + R/algo_ground_segmentation.r | 14 ++ R/algo_points_decimation.r | 12 ++ R/algo_tree_detection.R | 8 - R/algo_tree_segmentation.r | 49 +++++--- R/grid_canopy.r | 3 R/io_readLAS.r | 2 R/lasfilter.r | 6 - R/lasmergespatial.r | 38 +----- R/lidR-package.r |only R/tree_hulls.r | 3 README.md | 3 build/vignette.rds |binary inst/doc/lidR-LAS-class.html | 3 inst/doc/lidR-LAScatalog-class.html | 5 inst/doc/lidR-catalog-apply-examples.html | 3 inst/doc/lidR-computation-speed-LAScatalog.html | 5 man/figures |only man/grid_canopy.Rd | 3 man/lasfilter.Rd | 6 - man/lidR-package.Rd |only man/tree_hulls.Rd | 3 src/BoundingBox.cpp | 11 + src/BoundingBox.h | 1 src/C_li2012.cpp | 2 src/C_points_in_polygons_wkt.cpp | 21 ++- src/Shapes.cpp | 11 + tests/testthat/Rplots.pdf |binary tests/testthat/test-catalog_apply.R | 138 ++++++++++++++++-------- tests/testthat/test-grid_terrain.R | 10 - 34 files changed, 303 insertions(+), 162 deletions(-)
Title: Capital Budgeting Analysis, Annuity Loan Calculations and
Amortization Schedules
Description: Provides Capital Budgeting Analysis functionality and the essential Annuity loan functions.
Also computes Loan Amortization Schedules including schedules with irregular payments.
Author: John T. Buynak
Maintainer: John T. Buynak <jbuynak94@gmail.com>
Diff between capitalR versions 1.1.0 dated 2019-04-10 and 1.2.0 dated 2019-05-09
DESCRIPTION | 6 +-- MD5 | 12 +++---- R/capitalR.R | 84 +++++++++++++++++++++++++++++++++++++++++++------ inst/doc/capitalr.Rmd | 3 + inst/doc/capitalr.html | 7 ++-- man/irregular.Rd | 9 +++-- vignettes/capitalr.Rmd | 3 + 7 files changed, 97 insertions(+), 27 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
such as getting database specific taxonomic identifiers, verifying
species names, getting taxonomic hierarchies, fetching downstream and
upstream taxonomic names, getting taxonomic synonyms, converting
scientific to common names and vice versa, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Eduard Szoecs [aut],
Zachary Foster [aut],
Zebulun Arendsee [aut],
Carl Boettiger [ctb],
Karthik Ram [ctb],
Ignasi Bartomeus [ctb],
John Baumgartner [ctb],
James O'Donnell [ctb],
Jari Oksanen [ctb],
Bastian Greshake Tzovaras [ctb],
Philippe Marchand [ctb],
Vinh Tran [ctb],
Maëlle Salmon [ctb],
Gaopeng Li [ctb],
Matthias Grenié [ctb],
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.9.6 dated 2019-02-24 and 0.9.7 dated 2019-05-09
DESCRIPTION | 18 MD5 | 532 +- NEWS.md | 9 R/apg.R | 4 R/apg_lookup.R | 10 R/bold_search.R | 62 R/children.R | 17 R/class2tree.R | 38 R/classification.R | 57 R/col_children.R | 22 R/col_downstream.R | 35 R/col_search.R | 25 R/comm2sci.R | 24 R/downstream.R | 26 R/eol_dataobjects.R | 19 R/eol_pages.R | 32 R/eol_search.R | 29 R/eubon.R | 26 R/eubon_capabilities.R | 4 R/eubon_children.R | 12 R/eubon_hierarchy.R | 12 R/fungorum.R | 12 R/gbif_downstream.R | 12 R/gbif_name_usage.R | 6 R/gbif_parse.R | 10 R/genbank2uid.R | 6 R/get-id-details.R | 109 R/get_boldid.R | 36 R/get_colid.R | 55 R/get_eolid.R | 52 R/get_gbifid.R | 32 R/get_ids.R | 32 R/get_iucn.R | 25 R/get_natservid.R | 28 R/get_nbnid.R | 14 R/get_pow.R | 22 R/get_tolid.R | 15 R/get_tpsid.R | 22 R/get_tsn.R | 12 R/get_ubioid.R | 20 R/get_uid.R | 42 R/get_wiki.R | 18 R/get_wormsid.R | 16 R/getkey.R | 2 R/gni_details.R | 6 R/gni_parse.R | 18 R/gni_search.R | 51 R/gnr_datasources.R | 6 R/gnr_resolve.R | 109 R/id2name.R | 43 R/ion.R | 4 R/iplant_resolve.R | 6 R/ipni_search.R | 83 R/itis_acceptname.R | 17 R/itis_downstream.R | 8 R/itis_getrecord.R | 2 R/itis_hierarchy.R | 8 R/itis_lsid.R | 4 R/itis_native.R | 6 R/itis_taxrank.R | 6 R/itis_terms.R | 2 R/iucn_getname.R | 4 R/iucn_id.R | 6 R/iucn_summary.R | 58 R/key_helpers.R | 6 R/limited_print.R | 2 R/lowest_common.R | 25 R/nbn_classification.R | 2 R/nbn_search.R | 4 R/nbn_synonyms.R | 2 R/ncbi_children.R | 41 R/ncbi_downstream.R | 12 R/ncbi_get_taxon_summary.R | 17 R/ping.R | 11 R/plantminer.R | 7 R/pow_search.R | 10 R/resolve.R | 6 R/sci2comm.R | 22 R/scrapenames.r | 22 R/status_codes.R | 2 R/synonyms.R | 41 R/tax_agg.R | 22 R/tax_name.R | 18 R/tax_rank.R | 25 R/taxize-authentication.R | 32 R/taxize-package.R | 160 R/tnrs.R | 17 R/tnrs_sources.r | 2 R/tol_resolve.R | 21 R/tp_accnames.R | 4 R/tp_dist.R | 6 R/tp_refs.R | 4 R/tp_search.R | 12 R/tp_summary.R | 4 R/tp_synonyms.R | 4 R/tpl_families.r | 8 R/tpl_get.r | 8 R/upstream.R | 15 R/vascan_search.r | 4 R/worms_downstream.R | 10 README.md | 17 build/vignette.rds |binary inst/CITATION | 7 inst/doc/name_cleaning.Rmd | 25 inst/doc/name_cleaning.html | 25 inst/doc/taxize_vignette.Rmd | 16 inst/doc/taxize_vignette.html | 16 inst/ignore/aou_notes.R | 6 inst/vign/name_cleaning.md | 25 inst/vign/taxize_vignette.md | 16 man/apg.Rd | 4 man/apg_families.Rd | 10 man/apg_lookup.Rd | 6 man/apg_orders.Rd | 8 man/bold_search.Rd | 58 man/children.Rd | 11 man/class2tree.Rd | 17 man/classification.Rd | 55 man/col_children.Rd | 18 man/col_downstream.Rd | 20 man/col_search.Rd | 24 man/col_search_paginate.Rd | 6 man/comm2sci.Rd | 16 man/downstream.Rd | 24 man/eol_dataobjects.Rd | 15 man/eol_pages.Rd | 6 man/eol_search.Rd | 23 man/eubon.Rd | 18 man/eubon_capabilities.Rd | 2 man/eubon_children.Rd | 8 man/eubon_hierarchy.Rd | 8 man/fungorum.Rd | 2 man/gbif_downstream.Rd | 10 man/gbif_name_usage.Rd | 4 man/gbif_parse.Rd | 6 man/genbank2uid.Rd | 4 man/get_boldid.Rd | 24 man/get_colid.Rd | 41 man/get_eolid.Rd | 32 man/get_gbifid.Rd | 16 man/get_id_details.Rd | 102 man/get_ids.Rd | 28 man/get_iucn.Rd | 28 man/get_natservid.Rd | 17 man/get_nbnid.Rd | 10 man/get_pow.Rd | 28 man/get_tolid.Rd | 7 man/get_tpsid.Rd | 18 man/get_tsn.Rd | 6 man/get_ubioid-defunct.Rd | 20 man/get_uid.Rd | 52 man/get_wiki.Rd | 14 man/get_wormsid.Rd | 10 man/gni_details.Rd | 4 man/gni_parse.Rd | 6 man/gni_search.Rd | 46 man/gnr_datasources.Rd | 6 man/gnr_resolve.Rd | 69 man/id2name.Rd | 13 man/ion.Rd | 4 man/iplant_resolve.Rd | 6 man/ipni_search.Rd | 57 man/itis_acceptname.Rd | 16 man/itis_downstream.Rd | 8 man/itis_getrecord.Rd | 2 man/itis_hierarchy.Rd | 8 man/itis_lsid.Rd | 4 man/itis_native.Rd | 6 man/itis_taxrank.Rd | 4 man/itis_terms.Rd | 2 man/iucn_getname.Rd | 4 man/iucn_id.Rd | 4 man/iucn_status.Rd | 4 man/iucn_summary.Rd | 28 man/key_helpers.Rd | 12 man/limited_print.Rd | 12 man/lowest_common.Rd | 21 man/nbn_classification.Rd | 4 man/nbn_search.Rd | 10 man/nbn_synonyms.Rd | 4 man/ncbi_children.Rd | 55 man/ncbi_downstream.Rd | 8 man/ncbi_get_taxon_summary.Rd | 25 man/phylomatic_format-defunct.Rd | 2 man/ping.Rd | 11 man/plantminer.Rd | 5 man/pow_lookup.Rd | 4 man/pow_search.Rd | 10 man/rank_ref.Rd | 6 man/resolve.Rd | 20 man/sci2comm.Rd | 22 man/scrapenames.Rd | 4 man/species_plantarum_binomials.Rd | 38 man/status_codes.Rd | 2 man/synonyms.Rd | 29 man/tax_agg.Rd | 18 man/tax_name.Rd | 18 man/tax_rank.Rd | 27 man/taxize-authentication.Rd | 24 man/taxize-defunct.Rd | 67 man/taxize-package.Rd | 2 man/theplantlist.Rd | 12 man/tnrs.Rd | 13 man/tnrs_sources.Rd | 4 man/tol_resolve.Rd | 15 man/tp_accnames.Rd | 4 man/tp_dist.Rd | 4 man/tp_refs.Rd | 4 man/tp_search.Rd | 4 man/tp_summary.Rd | 4 man/tp_synonyms.Rd | 4 man/tpl_families.Rd | 10 man/tpl_get.Rd | 8 man/upstream.Rd | 13 man/vascan_search.Rd | 4 man/worms_downstream.Rd | 12 tests/fixtures/classification_pow_cbind_rbind.yml | 149 tests/fixtures/classification_pow_more_name_egs.yml | 126 tests/fixtures/col_children.yml | 1862 -------- tests/fixtures/col_downstream.yml | 1360 ----- tests/fixtures/downstream.yml | 687 -- tests/fixtures/downstream_id_input.yml | 555 -- tests/fixtures/downstream_multiple_data_sources.yml | 594 -- tests/fixtures/fg_author_search.yml | 41 tests/fixtures/fg_name_search.yml | 219 tests/fixtures/gbif_downstream.yml | 339 - tests/fixtures/gbif_downstream_intermediate.yml | 286 - tests/fixtures/gbif_parse.yml | 20 tests/fixtures/get_gbifid.yml | 128 tests/fixtures/get_tpsid_warnings_dots.yml | 31 tests/fixtures/iucn_id.yml | 52 tests/fixtures/iucn_summary.yml | 133 tests/fixtures/iucn_summary_other_egs.yml | 457 - tests/fixtures/pow_lookup.yml | 60 tests/fixtures/pow_lookup_include_param.yml | 146 tests/fixtures/pow_search.yml | 233 - tests/fixtures/tp_accnames.yml | 48 tests/fixtures/tp_dist.yml | 4593 -------------------- tests/fixtures/tp_search.yml | 211 tests/fixtures/tp_summary.yml | 25 tests/fixtures/tp_synonyms.yml | 495 -- tests/fixtures/trpicos_ping.yml | 78 tests/fixtures/vascan_ping.yml | 95 tests/fixtures/vascan_search.yml | 206 tests/testthat/Rplots.pdf |binary tests/testthat/test-class2tree.R | 2 tests/testthat/test-classification-pow.R | 4 tests/testthat/test-col_children.R | 2 tests/testthat/test-col_downstream.R | 2 tests/testthat/test-downstream.R | 6 tests/testthat/test-fungorum.R | 4 tests/testthat/test-gbif_downstream.R | 4 tests/testthat/test-gbif_parse.R | 2 tests/testthat/test-get_gbifid.R | 2 tests/testthat/test-get_tpsid.R | 2 tests/testthat/test-iucn_id.R | 2 tests/testthat/test-iucn_summary.R | 4 tests/testthat/test-ping.R | 4 tests/testthat/test-pow_search.R | 6 tests/testthat/test-tp_accnames.R | 2 tests/testthat/test-tp_dist.R | 2 tests/testthat/test-tp_search.R | 2 tests/testthat/test-tp_summary.R | 2 tests/testthat/test-tp_synonyms.R | 2 tests/testthat/test-vascan_search.r | 2 vignettes/name_cleaning.Rmd | 25 vignettes/taxize_vignette.Rmd | 16 267 files changed, 3334 insertions(+), 14525 deletions(-)
Title: R Front End for 'Apache Spark'
Description: Provides an R Front end for 'Apache Spark' <https://spark.apache.org>.
Author: Shivaram Venkataraman [aut, cre],
Xiangrui Meng [aut],
Felix Cheung [aut],
The Apache Software Foundation [aut, cph]
Maintainer: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Diff between SparkR versions 2.4.2 dated 2019-04-25 and 2.4.3 dated 2019-05-09
DESCRIPTION | 8 - MD5 | 6 build/vignette.rds |binary inst/doc/sparkr-vignettes.html | 303 ++++++++++++++++++----------------------- 4 files changed, 146 insertions(+), 171 deletions(-)
Title: Epistemic Network Analysis
Description: ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016) <doi:10.18608/jla.2016.33.3>.
Author: Cody L Marquart [aut, cre],
Zachari Swiecki [aut],
Wesley Collier [aut],
Brendan Eagan [aut],
Roman Woodward [aut],
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Diff between rENA versions 0.1.6 dated 2019-02-07 and 0.1.6.1 dated 2019-05-09
rENA-0.1.6.1/rENA/DESCRIPTION | 14 ++-- rENA-0.1.6.1/rENA/MD5 | 30 +++++++--- rENA-0.1.6.1/rENA/NAMESPACE | 2 rENA-0.1.6.1/rENA/R/accumulate.data.R | 2 rENA-0.1.6.1/rENA/R/ena.R |only rENA-0.1.6.1/rENA/R/rENA.R | 2 rENA-0.1.6.1/rENA/R/zzz.R | 2 rENA-0.1.6.1/rENA/build |only rENA-0.1.6.1/rENA/data/RS.data.rda |binary rENA-0.1.6.1/rENA/demo/fullExample.R | 17 ++--- rENA-0.1.6.1/rENA/inst/CITATION |only rENA-0.1.6.1/rENA/inst/doc |only rENA-0.1.6.1/rENA/inst/rmd/methods.rmd | 4 - rENA-0.1.6.1/rENA/man/ena.Rd |only rENA-0.1.6.1/rENA/tests/testthat/test.weighted.single.window.R |only rENA-0.1.6.1/rENA/vignettes |only rENA-0.1.6/rENA/R/roll.sum.pad.R |only 17 files changed, 42 insertions(+), 31 deletions(-)
Title: A Universal Non-Uniform Random Number Generator
Description: A universal non-uniform random number generator
for quite arbitrary distributions with piecewise twice
differentiable densities.
Author: Josef Leydold, Carsten Botts and Wolfgang H\"ormann
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between Tinflex versions 1.2 dated 2017-06-08 and 1.4 dated 2019-05-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 15 +++++++++++++++ R/plot.R | 7 ++++--- R/print.R | 7 ++----- R/setup.R | 31 ++++++++++++++++++++++++------- man/Tinflex-package.Rd | 4 ++-- man/plot.Tinflex.Rd | 5 +++-- src/Tinflex_source.h | 11 ++++++----- 9 files changed, 68 insertions(+), 36 deletions(-)
More information about photosynthesis at CRAN
Permanent link
More information about paws.machine.learning at CRAN
Permanent link
More information about paws.analytics at CRAN
Permanent link
Title: Create Japanese Administration Area and Office Maps
Description: Utilizing the data that Japanese administration area provided
by the National Land Numerical Information download service (<http://nlftp.mlit.go.jp/ksj/index.html>).
This package provide map data is based on the Digital Map 25000 (Map Image) published
by Geospatial Information Authority of Japan (Approval No.603FY2017 information usage <http://www.gsi.go.jp>).
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>),
Geospatial Information Authority of Japan [dtc] (This package data
sets, National Land numerical information by the Geographical
Survey Institute with the approval of Geographical Survey Institute
Head (Approval No.603FY2017 information usage))
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between jpndistrict versions 0.3.2 dated 2018-06-14 and 0.3.3 dated 2019-05-09
jpndistrict-0.3.2/jpndistrict/man/admins_code_validate.Rd |only jpndistrict-0.3.3/jpndistrict/DESCRIPTION | 14 jpndistrict-0.3.3/jpndistrict/MD5 | 43 +-- jpndistrict-0.3.3/jpndistrict/NAMESPACE | 17 - jpndistrict-0.3.3/jpndistrict/NEWS.md | 15 + jpndistrict-0.3.3/jpndistrict/R/city_name_table.R |only jpndistrict-0.3.3/jpndistrict/R/code_validate.R |only jpndistrict-0.3.3/jpndistrict/R/data.R | 16 - jpndistrict-0.3.3/jpndistrict/R/district_viewer.R | 21 + jpndistrict-0.3.3/jpndistrict/R/export_mesh.R | 13 jpndistrict-0.3.3/jpndistrict/R/find_city.R | 82 +++-- jpndistrict-0.3.3/jpndistrict/R/spdf_jpn.R | 26 + jpndistrict-0.3.3/jpndistrict/R/util.R | 82 ++--- jpndistrict-0.3.3/jpndistrict/data/jpnprefs.rda |binary jpndistrict-0.3.3/jpndistrict/data/prefecture_mesh.rda |binary jpndistrict-0.3.3/jpndistrict/inst/extdata/citycode_sets.rds |only jpndistrict-0.3.3/jpndistrict/man/code_reform.Rd |only jpndistrict-0.3.3/jpndistrict/man/code_validate.Rd |only jpndistrict-0.3.3/jpndistrict/man/figures/logo.png |binary jpndistrict-0.3.3/jpndistrict/man/find_jis_code.Rd |only jpndistrict-0.3.3/jpndistrict/man/jpn_pref.Rd | 2 jpndistrict-0.3.3/jpndistrict/man/jpnprefs.Rd | 6 jpndistrict-0.3.3/jpndistrict/man/prefecture_mesh.Rd | 10 jpndistrict-0.3.3/jpndistrict/tests/testthat/test-find_city.R | 64 ++-- jpndistrict-0.3.3/jpndistrict/tests/testthat/test-spdf_jpn.R | 10 jpndistrict-0.3.3/jpndistrict/tests/testthat/test-util.R | 143 +++++++++- 26 files changed, 386 insertions(+), 178 deletions(-)
Title: Tidy RSS for R
Description: With the objective of including data from RSS feeds into your analysis, 'tidyRSS' parses RSS, Atom XML, JSON and geoRSS feeds and returns a tidy data frame.
Author: Robert Myles McDonnell
Maintainer: Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>
Diff between tidyRSS versions 1.2.8 dated 2019-03-05 and 1.2.9 dated 2019-05-09
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/geo_parse.R | 16 ++++++++++++++-- R/rss_parse.R | 23 +++++++++++++---------- build/vignette.rds |binary inst/doc/tidyrss.html | 9 ++++++--- 7 files changed, 47 insertions(+), 24 deletions(-)
Title: Copy Number Estimation from Tumor Genome Sequencing Data
Description: Tools to analyze genomic sequencing data from
paired normal-tumor samples, including cellularity and ploidy estimation; mutation
and copy number (allele-specific and total copy number) detection, quantification
and visualization.
Author: Francesco Favero [aut, cre] (<https://orcid.org/0000-0003-3684-2659>),
Andrea Marion Marquard [rev] (<https://orcid.org/0000-0003-2928-6017>),
Tejal Joshi [rev] (<https://orcid.org/0000-0002-0939-2982>),
Aron Charles Eklund [aut, ths]
(<https://orcid.org/0000-0003-0861-1001>)
Maintainer: Francesco Favero <favero.francesco@gmail.com>
Diff between sequenza versions 2.1.2 dated 2015-10-09 and 3.0.0 dated 2019-05-09
sequenza-2.1.2/sequenza/R/analysis.R |only sequenza-2.1.2/sequenza/R/next.R |only sequenza-2.1.2/sequenza/R/workflows.R |only sequenza-2.1.2/sequenza/data/example.seqz.txt.gz |only sequenza-2.1.2/sequenza/exec |only sequenza-2.1.2/sequenza/inst/doc/sequenza.Rnw |only sequenza-2.1.2/sequenza/inst/doc/sequenza.pdf |only sequenza-2.1.2/sequenza/man/VarScan2seqz.Rd |only sequenza-2.1.2/sequenza/man/baf.bayes.Rd |only sequenza-2.1.2/sequenza/man/find.breaks.Rd |only sequenza-2.1.2/sequenza/man/gc.norm.Rd |only sequenza-2.1.2/sequenza/man/get.ci.Rd |only sequenza-2.1.2/sequenza/man/model.points.Rd |only sequenza-2.1.2/sequenza/man/mutation.table.Rd |only sequenza-2.1.2/sequenza/man/read.seqz.Rd |only sequenza-2.1.2/sequenza/man/theoretical.baf.Rd |only sequenza-2.1.2/sequenza/man/types.matrix.Rd |only sequenza-2.1.2/sequenza/man/workflows.Rd |only sequenza-2.1.2/sequenza/vignettes/sequenza.Rnw |only sequenza-2.1.2/sequenza/vignettes/sequenza.bib |only sequenza-3.0.0/sequenza/DESCRIPTION | 44 - sequenza-3.0.0/sequenza/MD5 | 82 +- sequenza-3.0.0/sequenza/NAMESPACE | 175 ++-- sequenza-3.0.0/sequenza/NEWS | 13 sequenza-3.0.0/sequenza/R/bayes.R | 354 ++++----- sequenza-3.0.0/sequenza/R/extract.R |only sequenza-3.0.0/sequenza/R/fit.R |only sequenza-3.0.0/sequenza/R/gcstats.R |only sequenza-3.0.0/sequenza/R/graphics.R | 834 +++++++++++------------ sequenza-3.0.0/sequenza/R/misc.R | 94 ++ sequenza-3.0.0/sequenza/R/model.R | 195 ++--- sequenza-3.0.0/sequenza/R/mutations.R |only sequenza-3.0.0/sequenza/R/read.R |only sequenza-3.0.0/sequenza/R/results.R |only sequenza-3.0.0/sequenza/R/segments.R |only sequenza-3.0.0/sequenza/R/solutions.R |only sequenza-3.0.0/sequenza/R/windows.R |only sequenza-3.0.0/sequenza/build/vignette.rds |binary sequenza-3.0.0/sequenza/data/CP.example.RData |binary sequenza-3.0.0/sequenza/data/example.seqz.rda |binary sequenza-3.0.0/sequenza/inst/doc/sequenza.R | 331 ++------- sequenza-3.0.0/sequenza/inst/doc/sequenza.Rmd |only sequenza-3.0.0/sequenza/inst/doc/sequenza.html |only sequenza-3.0.0/sequenza/inst/extdata |only sequenza-3.0.0/sequenza/man/CP.data.Rd | 33 sequenza-3.0.0/sequenza/man/baf.model.fit.Rd | 136 ++- sequenza-3.0.0/sequenza/man/bayes.Rd |only sequenza-3.0.0/sequenza/man/breaks.Rd |only sequenza-3.0.0/sequenza/man/chromosome.view.Rd | 234 +++--- sequenza-3.0.0/sequenza/man/cp.plot.Rd | 31 sequenza-3.0.0/sequenza/man/example.seqz.Rd | 61 + sequenza-3.0.0/sequenza/man/gc.Rd |only sequenza-3.0.0/sequenza/man/model_points.Rd |only sequenza-3.0.0/sequenza/man/mutations.Rd |only sequenza-3.0.0/sequenza/man/plotWindows.Rd | 78 +- sequenza-3.0.0/sequenza/man/read_seqz.Rd |only sequenza-3.0.0/sequenza/man/theoretical.Rd |only sequenza-3.0.0/sequenza/man/type_matrix.Rd |only sequenza-3.0.0/sequenza/man/windowValues.Rd | 97 +- sequenza-3.0.0/sequenza/man/workflow.Rd |only sequenza-3.0.0/sequenza/tests |only sequenza-3.0.0/sequenza/vignettes/sequenza.Rmd |only 62 files changed, 1433 insertions(+), 1359 deletions(-)
Title: GUI Tools for Interactive Image Processing with 'magick'
Description: Enables us to use the functions of the package 'magick' interactively.
Author: Shota Ochi [aut, cre]
Maintainer: Shota Ochi <shotaochi1990@gmail.com>
Diff between magickGUI versions 0.1.0 dated 2019-03-13 and 1.0.1 dated 2019-05-09
DESCRIPTION | 7 ++++--- MD5 | 10 +++++----- NAMESPACE | 2 ++ R/interactive_modulate.R | 3 ++- R/misc.R | 15 +++++++++++++++ tests/testthat.R | 14 +++++++++++++- 6 files changed, 41 insertions(+), 10 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Description: Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.
Author: Sacha Epskamp [aut, cre],
Giulio Costantini [aut],
Jonas Haslbeck [aut],
Angelique O. J. Cramer [ctb],
Lourens J. Waldorp [ctb],
Verena D. Schmittmann [ctb],
Denny Borsboom [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between qgraph versions 1.6.1 dated 2019-02-13 and 1.6.2 dated 2019-05-09
COPYRIGHTS | 20 ++++++++++---------- DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 3 +++ R/centralityTable.R | 14 +++++++++++--- R/qgraph.R | 44 ++++++++++++++++++++++++++++---------------- 6 files changed, 60 insertions(+), 37 deletions(-)
Title: Query 'R' Versions, Including 'r-release' and 'r-oldrel'
Description: Query the main 'R' 'SVN' repository to find the
versions 'r-release' and 'r-oldrel' refer to, and also all
previous 'R' versions and their release dates.
Author: Gábor Csárdi [aut, cre],
Jeroen Ooms [ctb],
R Consortium [fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between rversions versions 1.1.0 dated 2019-04-11 and 2.0.0 dated 2019-05-09
DESCRIPTION | 6 - MD5 | 20 +-- R/macos.R | 2 R/nicks.R | 2 R/rversions.R | 4 R/tarball.R | 2 R/urls.R | 26 +++- R/win.R | 2 inst/NEWS.md | 7 + inst/README.md | 237 ++++++++++++++++++++-------------------- tests/testthat/test-rversions.R | 4 11 files changed, 171 insertions(+), 141 deletions(-)
Title: Processing Pipeline for 'SamBada' from Pre- To Post-Processing
Description: Processing pipeline for 'SamBada' from pre- to post-processing.
'SamBada' is a landscape genomic software designed to run univariate or multivariate logistic regression between the presence of a genotype and one or several environmental variables. See Stucki (2017) <doi:10.1111/1755-0998.12629> and <https://github.com/Sylvie/sambada>.
The package provides functions that can be classified into four categories:
1) Install 'SamBada'
2) Preprocessing (prepare genomic file into standards compatible with 'SamBada' and apply quality-control; retrieve environmental conditions at sampling location; prepare environmental file including removal of correlated variables and computation of population structure)
3) Processing (run 'SamBada' on multiple cores using 'Supervision')
4) Post-processing (calculate p-values and q-values, produce interactive Manhattan plots and query 'Ensembl' database, produce maps).
Author: Solange Duruz, Sylvie Stucki, Oliver Selmoni, Elia Vajana
Maintainer: Solange Duruz <solange.duruz@alumni.epfl.ch>
Diff between R.SamBada versions 0.1.0 dated 2019-04-12 and 0.1.1 dated 2019-05-09
R.SamBada-0.1.0/R.SamBada/inst/doc/R.Sambada.R |only R.SamBada-0.1.0/R.SamBada/inst/doc/R.Sambada.Rmd |only R.SamBada-0.1.0/R.SamBada/inst/doc/R.Sambada.html |only R.SamBada-0.1.0/R.SamBada/vignettes/R.Sambada.Rmd |only R.SamBada-0.1.1/R.SamBada/DESCRIPTION | 8 R.SamBada-0.1.1/R.SamBada/MD5 | 27 R.SamBada-0.1.1/R.SamBada/NEWS.md |only R.SamBada-0.1.1/R.SamBada/R/Postprocessing.R | 64 R.SamBada-0.1.1/R.SamBada/R/Preprocessing.R | 6 R.SamBada-0.1.1/R.SamBada/R/Run_sambada.R | 4 R.SamBada-0.1.1/R.SamBada/R/install_sambada.r | 2 R.SamBada-0.1.1/R.SamBada/build/vignette.rds |binary R.SamBada-0.1.1/R.SamBada/inst/doc/R.SamBada.R |only R.SamBada-0.1.1/R.SamBada/inst/doc/R.SamBada.Rmd |only R.SamBada-0.1.1/R.SamBada/inst/doc/R.SamBada.html |only R.SamBada-0.1.1/R.SamBada/inst/extdata/uganda-subset-mol-Out-2.csv | 2774 ---------- R.SamBada-0.1.1/R.SamBada/man/createEnv.Rd | 4 R.SamBada-0.1.1/R.SamBada/man/prepareEnv.Rd | 3 R.SamBada-0.1.1/R.SamBada/vignettes/R.SamBada.Rmd |only 19 files changed, 56 insertions(+), 2836 deletions(-)
Title: Bootstrap Methods for Various Network Estimation Routines
Description: Bootstrap methods to assess accuracy and stability of estimated network structures
and centrality indices. Allows for flexible specification of any undirected network
estimation procedure in R, and offers default sets for 'qgraph', 'IsingFit', 'IsingSampler',
'glasso', 'huge' and 'parcor' packages.
Author: Sacha Epskamp [aut, cre],
Eiko I. Fried [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between bootnet versions 1.2 dated 2019-01-24 and 1.2.2 dated 2019-05-09
DESCRIPTION | 8 +-- MD5 | 16 +++---- NAMESPACE | 1 NEWS | 7 +++ R/Smetric.R | 2 R/bootThreshold.R | 2 R/bootnet.R | 7 +-- R/defaultFunctions.R | 109 +++++++++++++++++++++++++++++++------------------ man/estimateNetwork.Rd | 13 ++++- 9 files changed, 107 insertions(+), 58 deletions(-)
Title: Analysis of Diffusion Weighted Imaging (DWI) Data
Description: Diffusion Weighted Imaging (DWI) is a Magnetic Resonance Imaging
modality, that measures diffusion of water in tissues like the human
brain. The package contains R-functions to process diffusion-weighted
data. The functionality includes diffusion tensor imaging (DTI),
diffusion kurtosis imaging (DKI), modeling for high angular resolution
diffusion weighted imaging (HARDI) using Q-ball-reconstruction and
tensor mixture models, several methods for structural adaptive
smoothing including POAS and msPOAS, and a streamline fiber tracking
for tensor and tensor mixture models.
The package provides functionality to manipulate and visualize results
in 2D and 3D.
Author: Karsten Tabelow [aut, cre],
Joerg Polzehl [aut],
Felix Anker [ctb]
Maintainer: Karsten Tabelow <karsten.tabelow@wias-berlin.de>
Diff between dti versions 1.3-0.3 dated 2018-12-20 and 1.4 dated 2019-05-09
DESCRIPTION | 10 ++-- MD5 | 22 +++++---- NAMESPACE | 2 R/dkimisc.r | 11 ++-- R/fibers.r | 60 +++++++++++++++++++++++++ R/io.r | 115 +++++++++++++++++++++++-------------------------- R/misc.r | 24 ++++++++++ R/plot.r | 92 ++++++++++++++++++++++++++++++++++++++- R/show3d.r | 8 +-- R/utilities.r | 6 ++ build/partial.rdb |binary man/AdjacencyMatrix.Rd |only man/dti.options.Rd |only 13 files changed, 265 insertions(+), 85 deletions(-)
Title: Download and Aggregate Data from Public Hire Bicycle Systems
Description: Download and aggregate data from all public hire bicycle systems
which provide open data, currently including 'Santander' Cycles in London,
U.K.; from the U.S.A., 'Ford GoBike' in San Francisco CA, 'citibike' in New
York City NY, 'Divvy' in Chicago IL, 'Capital Bikeshare' in Washington DC,
'Hubway' in Boston MA, 'Metro' in Los Angeles LA, 'Indego' in Philadelphia
PA, and 'Nice Ride' in Minnesota; 'Bixi' from Montreal, Canada; and 'mibici'
from Guadalajara, Mexico.
Author: Mark Padgham [aut, cre] (<https://orcid.org/0000-0003-2172-5265>),
Richard Ellison [aut],
Tom Buckley [aut],
Bea Hernández [rev] (Bea reviewed the package for ropensci, see
https://github.com/ropensci/onboarding/issues/116),
Elaine McVey [rev] (Elaine reviewed the package for ropensci, see
https://github.com/ropensci/onboarding/issues/116),
SQLite Consortium [ctb] (Authors of included SQLite code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between bikedata versions 0.2.2 dated 2018-10-22 and 0.2.3 dated 2019-05-09
DESCRIPTION | 16 ++-- MD5 | 32 ++++----- NEWS.md | 5 + R/bikedata-files.R | 13 ++- R/distmat.R | 2 R/dl-bikedata.R | 2 R/stations.R | 13 +++ R/store-bikedata.R | 2 R/zzz.R | 2 README.md | 7 + build/vignette.rds |binary inst/doc/bikedata.Rmd | 2 inst/doc/bikedata.html | 118 ++++++++++++++++++++++++++------- tests/testthat/test-db-stats.R | 42 +++++++---- tests/testthat/test-download-data.R | 127 +++++++++++++++++++++++------------- tests/testthat/test-stations.R | 16 +++- vignettes/bikedata.Rmd | 2 17 files changed, 275 insertions(+), 126 deletions(-)
Title: Multivariate Analysis
Description: Package for multivariate analysis, having functions that perform simple correspondence analysis (CA) and multiple correspondence analysis (MCA), principal components analysis (PCA), canonical correlation analysis (CCA), factorial analysis (FA), multidimensional scaling (MDS), linear (LDA) and quadratic discriminant analysis (QDA), hierarchical and non-hierarchical cluster analysis, simple and multiple linear regression, multiple factor analysis (MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, projection pursuit (PP), grant tour method and other useful functions for the multivariate analysis.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar versions 2.0.5 dated 2019-03-15 and 2.0.6 dated 2019-05-09
DESCRIPTION | 12 - MD5 | 22 +- NAMESPACE | 16 - R/DA_English.R |only R/GrandTour_English.R | 398 +++++++++++++++++++++++++++++++++-------------- R/MDS_English.R | 144 +++++++++++++---- R/Plot.PP_English.R | 288 +++++++++++++++------------------- man/Cluster_English.Rd | 2 man/DA_English.Rd |only man/GrandTour_English.Rd | 35 ++-- man/MDS_English.Rd | 31 ++- man/MVar-package.Rd | 6 man/Plot.PP_English.Rd | 28 +-- 13 files changed, 623 insertions(+), 359 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication, and GridFS. The online user manual provides an overview
of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
MongoDB, Inc [cph] (Bundled mongo-c-driver, see AUTHORS file)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between mongolite versions 2.0.2 dated 2019-05-02 and 2.1.0 dated 2019-05-09
mongolite-2.0.2/mongolite/src/bson/bson-fnv-private.h |only mongolite-2.0.2/mongolite/src/bson/bson-fnv.c |only mongolite-2.0.2/mongolite/src/bson/bson-thread-private.h |only mongolite-2.0.2/mongolite/src/mongoc/mongoc-cluster-gssapi.c |only mongolite-2.0.2/mongolite/src/mongoc/mongoc-gssapi.c |only mongolite-2.1.0/mongolite/DESCRIPTION | 6 mongolite-2.1.0/mongolite/MD5 | 583 +++++----- mongolite-2.1.0/mongolite/NEWS | 4 mongolite-2.1.0/mongolite/R/gridfs.R | 24 mongolite-2.1.0/mongolite/configure | 9 mongolite-2.1.0/mongolite/man/gridfs.Rd | 24 mongolite-2.1.0/mongolite/src/Makevars.in | 5 mongolite-2.1.0/mongolite/src/Makevars.win | 9 mongolite-2.1.0/mongolite/src/bson/bcon.c | 4 mongolite-2.1.0/mongolite/src/bson/bcon.h | 4 mongolite-2.1.0/mongolite/src/bson/bson-atomic.c | 2 mongolite-2.1.0/mongolite/src/bson/bson-atomic.h | 8 mongolite-2.1.0/mongolite/src/bson/bson-clock.c | 8 mongolite-2.1.0/mongolite/src/bson/bson-clock.h | 13 mongolite-2.1.0/mongolite/src/bson/bson-compat.h | 19 mongolite-2.1.0/mongolite/src/bson/bson-context-private.h | 25 mongolite-2.1.0/mongolite/src/bson/bson-context.c | 352 ++---- mongolite-2.1.0/mongolite/src/bson/bson-context.h | 11 mongolite-2.1.0/mongolite/src/bson/bson-decimal128.c | 10 mongolite-2.1.0/mongolite/src/bson/bson-decimal128.h | 12 mongolite-2.1.0/mongolite/src/bson/bson-endian.h | 13 mongolite-2.1.0/mongolite/src/bson/bson-error.c | 12 mongolite-2.1.0/mongolite/src/bson/bson-error.h | 8 mongolite-2.1.0/mongolite/src/bson/bson-iso8601-private.h | 8 mongolite-2.1.0/mongolite/src/bson/bson-iso8601.c | 30 mongolite-2.1.0/mongolite/src/bson/bson-iter.c | 179 ++- mongolite-2.1.0/mongolite/src/bson/bson-iter.h | 41 mongolite-2.1.0/mongolite/src/bson/bson-json.c | 10 mongolite-2.1.0/mongolite/src/bson/bson-json.h | 9 mongolite-2.1.0/mongolite/src/bson/bson-keys.c | 4 mongolite-2.1.0/mongolite/src/bson/bson-keys.h | 6 mongolite-2.1.0/mongolite/src/bson/bson-macros.h | 9 mongolite-2.1.0/mongolite/src/bson/bson-md5.c | 4 mongolite-2.1.0/mongolite/src/bson/bson-md5.h | 11 mongolite-2.1.0/mongolite/src/bson/bson-memory.c | 10 mongolite-2.1.0/mongolite/src/bson/bson-memory.h | 11 mongolite-2.1.0/mongolite/src/bson/bson-oid.c | 235 ---- mongolite-2.1.0/mongolite/src/bson/bson-oid.h | 26 mongolite-2.1.0/mongolite/src/bson/bson-prelude.h |only mongolite-2.1.0/mongolite/src/bson/bson-private.h | 8 mongolite-2.1.0/mongolite/src/bson/bson-reader.c | 6 mongolite-2.1.0/mongolite/src/bson/bson-reader.h | 13 mongolite-2.1.0/mongolite/src/bson/bson-string.c | 8 mongolite-2.1.0/mongolite/src/bson/bson-string.h | 11 mongolite-2.1.0/mongolite/src/bson/bson-timegm-private.h | 6 mongolite-2.1.0/mongolite/src/bson/bson-timegm.c | 6 mongolite-2.1.0/mongolite/src/bson/bson-types.h | 15 mongolite-2.1.0/mongolite/src/bson/bson-utf8.c | 8 mongolite-2.1.0/mongolite/src/bson/bson-utf8.h | 11 mongolite-2.1.0/mongolite/src/bson/bson-value.c | 8 mongolite-2.1.0/mongolite/src/bson/bson-value.h | 6 mongolite-2.1.0/mongolite/src/bson/bson-version-functions.c | 4 mongolite-2.1.0/mongolite/src/bson/bson-version-functions.h | 6 mongolite-2.1.0/mongolite/src/bson/bson-version.h | 10 mongolite-2.1.0/mongolite/src/bson/bson-writer.c | 6 mongolite-2.1.0/mongolite/src/bson/bson-writer.h | 4 mongolite-2.1.0/mongolite/src/bson/bson.c | 31 mongolite-2.1.0/mongolite/src/bson/bson.h | 65 - mongolite-2.1.0/mongolite/src/common/common-b64-private.h | 13 mongolite-2.1.0/mongolite/src/common/common-b64.c | 6 mongolite-2.1.0/mongolite/src/common/common-md5-private.h | 15 mongolite-2.1.0/mongolite/src/common/common-md5.c | 2 mongolite-2.1.0/mongolite/src/common/common-prelude.h |only mongolite-2.1.0/mongolite/src/common/common-thread-private.h |only mongolite-2.1.0/mongolite/src/jsonsl/jsonsl.c | 4 mongolite-2.1.0/mongolite/src/jsonsl/jsonsl.h | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-apm-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-apm.c | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-apm.h | 21 mongolite-2.1.0/mongolite/src/mongoc/mongoc-array-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-array.c | 2 mongolite-2.1.0/mongolite/src/mongoc/mongoc-async-cmd-private.h | 22 mongolite-2.1.0/mongolite/src/mongoc/mongoc-async-cmd.c | 55 mongolite-2.1.0/mongolite/src/mongoc/mongoc-async-private.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-async.c | 14 mongolite-2.1.0/mongolite/src/mongoc/mongoc-buffer-private.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-buffer.c | 22 mongolite-2.1.0/mongolite/src/mongoc/mongoc-bulk-operation-private.h | 17 mongolite-2.1.0/mongolite/src/mongoc/mongoc-bulk-operation.c | 37 mongolite-2.1.0/mongolite/src/mongoc/mongoc-bulk-operation.h | 14 mongolite-2.1.0/mongolite/src/mongoc/mongoc-change-stream-private.h | 20 mongolite-2.1.0/mongolite/src/mongoc/mongoc-change-stream.c | 130 -- mongolite-2.1.0/mongolite/src/mongoc/mongoc-change-stream.h | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-client-pool-private.h | 16 mongolite-2.1.0/mongolite/src/mongoc/mongoc-client-pool.c | 110 - mongolite-2.1.0/mongolite/src/mongoc/mongoc-client-pool.h | 20 mongolite-2.1.0/mongolite/src/mongoc/mongoc-client-private.h | 40 mongolite-2.1.0/mongolite/src/mongoc/mongoc-client-session-private.h | 13 mongolite-2.1.0/mongolite/src/mongoc/mongoc-client-session.c | 173 ++ mongolite-2.1.0/mongolite/src/mongoc/mongoc-client-session.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-client.c | 105 + mongolite-2.1.0/mongolite/src/mongoc/mongoc-client.h | 40 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cluster-cyrus-private.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cluster-cyrus.c | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cluster-private.h | 43 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cluster-sasl-private.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cluster-sasl.c | 27 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cluster-sspi-private.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cluster-sspi.c | 16 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cluster.c | 119 +- mongolite-2.1.0/mongolite/src/mongoc/mongoc-cmd-private.h | 18 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cmd.c | 28 mongolite-2.1.0/mongolite/src/mongoc/mongoc-collection-private.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-collection.c | 131 +- mongolite-2.1.0/mongolite/src/mongoc/mongoc-collection.h | 32 mongolite-2.1.0/mongolite/src/mongoc/mongoc-compression-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-compression.c | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-config.h | 36 mongolite-2.1.0/mongolite/src/mongoc/mongoc-counters-private.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-counters.c | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-crypto-cng-private.h | 7 mongolite-2.1.0/mongolite/src/mongoc/mongoc-crypto-cng.c | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-crypto-common-crypto-private.h | 7 mongolite-2.1.0/mongolite/src/mongoc/mongoc-crypto-common-crypto.c | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-crypto-openssl-private.h | 11 mongolite-2.1.0/mongolite/src/mongoc/mongoc-crypto-openssl.c | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-crypto-private.h | 9 mongolite-2.1.0/mongolite/src/mongoc/mongoc-crypto.c | 14 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cursor-array.c | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cursor-cmd-deprecated.c | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cursor-cmd.c | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cursor-find-cmd.c | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cursor-find-opquery.c | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cursor-find.c | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cursor-legacy.c | 25 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cursor-private.h | 19 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cursor.c | 108 + mongolite-2.1.0/mongolite/src/mongoc/mongoc-cursor.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cyrus-private.h | 14 mongolite-2.1.0/mongolite/src/mongoc/mongoc-cyrus.c | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-database-private.h | 18 mongolite-2.1.0/mongolite/src/mongoc/mongoc-database.c | 26 mongolite-2.1.0/mongolite/src/mongoc/mongoc-database.h | 22 mongolite-2.1.0/mongolite/src/mongoc/mongoc-errno-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-error.c | 4 mongolite-2.1.0/mongolite/src/mongoc/mongoc-error.h | 13 mongolite-2.1.0/mongolite/src/mongoc/mongoc-find-and-modify-private.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-find-and-modify.c | 19 mongolite-2.1.0/mongolite/src/mongoc/mongoc-find-and-modify.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-flags.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-bucket-file-private.h |only mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-bucket-file.c |only mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-bucket-private.h |only mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-bucket.c |only mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-bucket.h |only mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-file-list-private.h | 16 mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-file-list.c | 20 mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-file-list.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-file-page-private.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-file-page.c | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-file-page.h | 16 mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-file-private.h | 18 mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-file.c | 33 mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-file.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs-private.h | 16 mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs.c | 41 mongolite-2.1.0/mongolite/src/mongoc/mongoc-gridfs.h | 20 mongolite-2.1.0/mongolite/src/mongoc/mongoc-handshake-compiler-private.h | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-handshake-os-private.h | 2 mongolite-2.1.0/mongolite/src/mongoc/mongoc-handshake-private.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-handshake.c | 40 mongolite-2.1.0/mongolite/src/mongoc/mongoc-handshake.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-host-list-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-host-list.c | 4 mongolite-2.1.0/mongolite/src/mongoc/mongoc-host-list.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-index.c | 4 mongolite-2.1.0/mongolite/src/mongoc/mongoc-index.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-init.c | 46 mongolite-2.1.0/mongolite/src/mongoc/mongoc-init.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-iovec.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-libressl-private.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-libressl.c | 19 mongolite-2.1.0/mongolite/src/mongoc/mongoc-linux-distro-scanner-private.h | 4 mongolite-2.1.0/mongolite/src/mongoc/mongoc-linux-distro-scanner.c | 16 mongolite-2.1.0/mongolite/src/mongoc/mongoc-list-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-list.c | 2 mongolite-2.1.0/mongolite/src/mongoc/mongoc-log-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-log.c | 36 mongolite-2.1.0/mongolite/src/mongoc/mongoc-log.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-macros.h | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-matcher-op-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-matcher-op.c | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-matcher-private.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-matcher.c | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-matcher.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-memcmp-private.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-memcmp.c | 2 mongolite-2.1.0/mongolite/src/mongoc/mongoc-opcode.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-openssl-private.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-openssl.c | 34 mongolite-2.1.0/mongolite/src/mongoc/mongoc-opts-helpers-private.h | 51 mongolite-2.1.0/mongolite/src/mongoc/mongoc-opts-helpers.c | 114 + mongolite-2.1.0/mongolite/src/mongoc/mongoc-opts-private.h | 69 + mongolite-2.1.0/mongolite/src/mongoc/mongoc-opts.c | 342 ++++- mongolite-2.1.0/mongolite/src/mongoc/mongoc-prelude.h |only mongolite-2.1.0/mongolite/src/mongoc/mongoc-queue-private.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-queue.c | 2 mongolite-2.1.0/mongolite/src/mongoc/mongoc-rand-cng.c | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-rand-common-crypto.c | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-rand-openssl.c | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-rand-private.h | 7 mongolite-2.1.0/mongolite/src/mongoc/mongoc-rand.h | 9 mongolite-2.1.0/mongolite/src/mongoc/mongoc-read-concern-private.h | 15 mongolite-2.1.0/mongolite/src/mongoc/mongoc-read-concern.c | 51 mongolite-2.1.0/mongolite/src/mongoc/mongoc-read-concern.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-read-prefs-private.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-read-prefs.c | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-read-prefs.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-rpc-private.h | 20 mongolite-2.1.0/mongolite/src/mongoc/mongoc-rpc.c | 59 - mongolite-2.1.0/mongolite/src/mongoc/mongoc-sasl-private.h | 16 mongolite-2.1.0/mongolite/src/mongoc/mongoc-sasl.c | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-scram-private.h | 9 mongolite-2.1.0/mongolite/src/mongoc/mongoc-scram.c | 16 mongolite-2.1.0/mongolite/src/mongoc/mongoc-secure-channel-private.h | 14 mongolite-2.1.0/mongolite/src/mongoc/mongoc-secure-channel.c | 34 mongolite-2.1.0/mongolite/src/mongoc/mongoc-secure-transport-private.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-secure-transport.c | 158 +- mongolite-2.1.0/mongolite/src/mongoc/mongoc-server-description-private.h | 4 mongolite-2.1.0/mongolite/src/mongoc/mongoc-server-description.c | 31 mongolite-2.1.0/mongolite/src/mongoc/mongoc-server-description.h | 14 mongolite-2.1.0/mongolite/src/mongoc/mongoc-server-stream-private.h | 16 mongolite-2.1.0/mongolite/src/mongoc/mongoc-server-stream.c | 6 mongolite-2.1.0/mongolite/src/mongoc/mongoc-set-private.h | 16 mongolite-2.1.0/mongolite/src/mongoc/mongoc-set.c | 34 mongolite-2.1.0/mongolite/src/mongoc/mongoc-socket-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-socket.c | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-socket.h | 14 mongolite-2.1.0/mongolite/src/mongoc/mongoc-ssl-private.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-ssl.c | 20 mongolite-2.1.0/mongolite/src/mongoc/mongoc-ssl.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-sspi-private.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-sspi.c | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-buffered.c | 22 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-buffered.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-file.c | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-file.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-gridfs-download-private.h |only mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-gridfs-download.c |only mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-gridfs-upload-private.h |only mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-gridfs-upload.c |only mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-gridfs.c | 14 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-gridfs.h | 16 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-private.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-socket.c | 27 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-socket.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-libressl-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-libressl.c | 41 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-libressl.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-openssl-bio-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-openssl-bio.c | 26 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-openssl-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-openssl.c | 45 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-openssl.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-private.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-secure-channel-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-secure-channel.c | 83 - mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-secure-channel.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-secure-transport-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-secure-transport.c | 59 - mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls-secure-transport.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls.c | 32 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream-tls.h | 16 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream.c | 43 mongolite-2.1.0/mongolite/src/mongoc/mongoc-stream.h | 17 mongolite-2.1.0/mongolite/src/mongoc/mongoc-thread-private.h | 71 - mongolite-2.1.0/mongolite/src/mongoc/mongoc-topology-description-apm-private.h | 9 mongolite-2.1.0/mongolite/src/mongoc/mongoc-topology-description-apm.c | 4 mongolite-2.1.0/mongolite/src/mongoc/mongoc-topology-description-private.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-topology-description.c | 20 mongolite-2.1.0/mongolite/src/mongoc/mongoc-topology-description.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-topology-private.h | 25 mongolite-2.1.0/mongolite/src/mongoc/mongoc-topology-scanner-private.h | 23 mongolite-2.1.0/mongolite/src/mongoc/mongoc-topology-scanner.c | 100 + mongolite-2.1.0/mongolite/src/mongoc/mongoc-topology.c | 221 ++- mongolite-2.1.0/mongolite/src/mongoc/mongoc-trace-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-uri-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-uri.c | 123 +- mongolite-2.1.0/mongolite/src/mongoc/mongoc-uri.h | 22 mongolite-2.1.0/mongolite/src/mongoc/mongoc-util-private.h | 13 mongolite-2.1.0/mongolite/src/mongoc/mongoc-util.c | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-version-functions.c | 4 mongolite-2.1.0/mongolite/src/mongoc/mongoc-version-functions.h | 9 mongolite-2.1.0/mongolite/src/mongoc/mongoc-version.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-write-command-legacy-private.h | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-write-command-legacy.c | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc-write-command-private.h | 29 mongolite-2.1.0/mongolite/src/mongoc/mongoc-write-command.c | 30 mongolite-2.1.0/mongolite/src/mongoc/mongoc-write-concern-private.h | 8 mongolite-2.1.0/mongolite/src/mongoc/mongoc-write-concern.c | 12 mongolite-2.1.0/mongolite/src/mongoc/mongoc-write-concern.h | 10 mongolite-2.1.0/mongolite/src/mongoc/mongoc.h | 77 - mongolite-2.1.0/mongolite/src/mongoc/op-msg.def | 2 mongolite-2.1.0/mongolite/src/mongoc/utlist.h | 2 mongolite-2.1.0/mongolite/src/mongolite.h | 4 mongolite-2.1.0/mongolite/src/osx |only mongolite-2.1.0/mongolite/tools/winlibs.R | 4 302 files changed, 3916 insertions(+), 3430 deletions(-)
Title: A Toolkit for Using Whole Building Simulation Program
'EnergyPlus'
Description: A rich toolkit of using the whole building simulation program
'EnergyPlus'(<https://energyplus.net>), which enables programmatic
navigation, modification of 'EnergyPlus' models and makes it less painful to
do parametric simulations and analysis.
Author: Hongyuan Jia [aut, cre] (<https://orcid.org/0000-0002-0075-8183>)
Maintainer: Hongyuan Jia <hongyuan.jia@bears-berkeley.sg>
Diff between eplusr versions 0.10.0 dated 2019-05-03 and 0.10.1 dated 2019-05-09
DESCRIPTION | 10 ++++----- MD5 | 32 ++++++++++++++--------------- NEWS.md | 17 +++++++++++++++ R/epw.R | 2 - R/idf.R | 7 +++--- R/impl-epw.R | 12 +++++++++-- R/impl-idf.R | 15 +++++++++----- R/parse.R | 6 ++--- inst/doc/eplusr.html | 43 ++++++++++++++-------------------------- man/IddObject.Rd | 7 +++--- man/Idf.Rd | 46 +++++++++++++++++++++++++++++-------------- man/IdfObject.Rd | 3 +- man/idd_object.Rd | 2 + man/idf_object.Rd | 3 +- man/read_idf.Rd | 4 +-- tests/testthat/test_epw.R | 12 +++++++---- tests/testthat/test_format.R | 3 +- 17 files changed, 135 insertions(+), 89 deletions(-)
Title: Complete Stochastic Modelling Solution
Description: A single framework, unifying, extending, and improving a general-purpose modelling strategy, based on the assumption that any process can emerge by transforming a specific 'parent' Gaussian process Papalexiou (2018) <doi:10.1016/j.advwatres.2018.02.013>.
Author: Filip Strnad [aut, cre],
Simon Michael Papalexiou [aut],
Yannis Markonis [ctb]
Maintainer: Filip Strnad <strnadf@fzp.czu.cz>
Diff between CoSMoS versions 0.4.1 dated 2019-04-11 and 1.0.1 dated 2019-05-09
CoSMoS-0.4.1/CoSMoS/R/check.R |only CoSMoS-0.4.1/CoSMoS/man/checkmodel.Rd |only CoSMoS-0.4.1/CoSMoS/man/checkplot.Rd |only CoSMoS-0.4.1/CoSMoS/man/checksimulation.Rd |only CoSMoS-1.0.1/CoSMoS/DESCRIPTION | 9 CoSMoS-1.0.1/CoSMoS/MD5 | 92 +- CoSMoS-1.0.1/CoSMoS/NAMESPACE | 29 CoSMoS-1.0.1/CoSMoS/NEWS.md |only CoSMoS-1.0.1/CoSMoS/R/AR1.R | 1 CoSMoS-1.0.1/CoSMoS/R/ARp.R | 1 CoSMoS-1.0.1/CoSMoS/R/CoSMoS.R | 4 CoSMoS-1.0.1/CoSMoS/R/acs.R | 4 CoSMoS-1.0.1/CoSMoS/R/analyzeTS.R |only CoSMoS-1.0.1/CoSMoS/R/burrIII.R | 2 CoSMoS-1.0.1/CoSMoS/R/checkTS.R |only CoSMoS-1.0.1/CoSMoS/R/ecdf.R |only CoSMoS-1.0.1/CoSMoS/R/errors.R |only CoSMoS-1.0.1/CoSMoS/R/fitACS.R |only CoSMoS-1.0.1/CoSMoS/R/fitDist.R |only CoSMoS-1.0.1/CoSMoS/R/generateTS.R | 55 - CoSMoS-1.0.1/CoSMoS/R/getArg.R |only CoSMoS-1.0.1/CoSMoS/R/ggamma.R | 1 CoSMoS-1.0.1/CoSMoS/R/lmom.R |only CoSMoS-1.0.1/CoSMoS/R/moments.R | 70 + CoSMoS-1.0.1/CoSMoS/R/norm.R |only CoSMoS-1.0.1/CoSMoS/R/plotacti.R | 69 - CoSMoS-1.0.1/CoSMoS/R/plotcosmosts.R | 7 CoSMoS-1.0.1/CoSMoS/R/precip.R |only CoSMoS-1.0.1/CoSMoS/R/seasonalACF.R |only CoSMoS-1.0.1/CoSMoS/R/seasonalAR.R |only CoSMoS-1.0.1/CoSMoS/R/stratifyData.R |only CoSMoS-1.0.1/CoSMoS/README.md | 15 CoSMoS-1.0.1/CoSMoS/build/vignette.rds |binary CoSMoS-1.0.1/CoSMoS/data |only CoSMoS-1.0.1/CoSMoS/inst/CITATION |only CoSMoS-1.0.1/CoSMoS/inst/doc/vignette.R | 217 ++++- CoSMoS-1.0.1/CoSMoS/inst/doc/vignette.Rmd | 330 ++++++-- CoSMoS-1.0.1/CoSMoS/inst/doc/vignette.html | 529 ++++++------- CoSMoS-1.0.1/CoSMoS/man/AR1.Rd | 1 CoSMoS-1.0.1/CoSMoS/man/ARp.Rd | 1 CoSMoS-1.0.1/CoSMoS/man/CoSMoS-package.Rd | 4 CoSMoS-1.0.1/CoSMoS/man/ECDF.Rd |only CoSMoS-1.0.1/CoSMoS/man/N.Rd |only CoSMoS-1.0.1/CoSMoS/man/YW.Rd |only CoSMoS-1.0.1/CoSMoS/man/acs.Rd | 2 CoSMoS-1.0.1/CoSMoS/man/analyzeTS.Rd |only CoSMoS-1.0.1/CoSMoS/man/checkTS.Rd |only CoSMoS-1.0.1/CoSMoS/man/error.Rd |only CoSMoS-1.0.1/CoSMoS/man/fitACS.Rd |only CoSMoS-1.0.1/CoSMoS/man/fitDist.Rd |only CoSMoS-1.0.1/CoSMoS/man/generateTS.Rd | 51 - CoSMoS-1.0.1/CoSMoS/man/getACSArg.Rd |only CoSMoS-1.0.1/CoSMoS/man/getDistArg.Rd |only CoSMoS-1.0.1/CoSMoS/man/lmom.Rd |only CoSMoS-1.0.1/CoSMoS/man/plot.acti.Rd | 4 CoSMoS-1.0.1/CoSMoS/man/plot.checkTS.Rd |only CoSMoS-1.0.1/CoSMoS/man/plot.fitACS.Rd |only CoSMoS-1.0.1/CoSMoS/man/plot.fitDist.Rd |only CoSMoS-1.0.1/CoSMoS/man/precip.Rd |only CoSMoS-1.0.1/CoSMoS/man/sample.moments.Rd |only CoSMoS-1.0.1/CoSMoS/man/seasonalACF.Rd |only CoSMoS-1.0.1/CoSMoS/man/seasonalAR.Rd |only CoSMoS-1.0.1/CoSMoS/man/stratifySeasonData.Rd |only CoSMoS-1.0.1/CoSMoS/tests/testthat/test_distribution_fit.R |only CoSMoS-1.0.1/CoSMoS/tests/testthat/test_get_args.R |only CoSMoS-1.0.1/CoSMoS/tests/testthat/test_l_moments.R |only CoSMoS-1.0.1/CoSMoS/tests/testthat/test_moments.R | 46 - CoSMoS-1.0.1/CoSMoS/vignettes/vignette.Rmd | 330 ++++++-- 68 files changed, 1281 insertions(+), 593 deletions(-)
Title: Bound Constrained Optimal Sample Allocation
Description: Implements bound constrained optimization of sample sizes in power analysis of multilevel regression discontinuity designs (MRDDs) and multilevel randomized trials (MRTs) with continuous outcomes. Bulus, M. & Dong, N. (2019). Bound Constrained Optimization of Sample Sizes Subject to Monetary Restrictions in Planning MRTs and MRDDs (Revise & Resubmit).
Author: Metin Bulus [aut, cre],
Nianbo Dong [aut]
Maintainer: Metin Bulus <bulusmetin@gmail.com>
Diff between cosa versions 1.2.1 dated 2018-12-16 and 1.2.2 dated 2019-05-09
cosa-1.2.1/cosa/R/zzz.R |only cosa-1.2.2/cosa/DESCRIPTION | 16 +++--- cosa-1.2.2/cosa/MD5 | 69 ++++++++++++++-------------- cosa-1.2.2/cosa/NAMESPACE | 1 cosa-1.2.2/cosa/NEWS.md | 24 +++++---- cosa-1.2.2/cosa/R/bcrd3f2.R | 2 cosa-1.2.2/cosa/R/bcrd3r2.R | 2 cosa-1.2.2/cosa/R/bcrd4f3.R | 2 cosa-1.2.2/cosa/R/bcrd4r2.R | 2 cosa-1.2.2/cosa/R/bcrd4r3.R | 2 cosa-1.2.2/cosa/R/bird2f1.R | 2 cosa-1.2.2/cosa/R/bird2r1.R | 2 cosa-1.2.2/cosa/R/bird3r1.R | 2 cosa-1.2.2/cosa/R/bird4r1.R | 2 cosa-1.2.2/cosa/R/crd2r2.R | 2 cosa-1.2.2/cosa/R/crd3r3.R | 2 cosa-1.2.2/cosa/R/crd4r4.R | 2 cosa-1.2.2/cosa/R/ird1r1.R | 1 cosa-1.2.2/cosa/R/utils.R | 16 ++++-- cosa-1.2.2/cosa/R/vectorize.R |only cosa-1.2.2/cosa/README.md | 16 ++---- cosa-1.2.2/cosa/inst/CITATION | 8 +-- cosa-1.2.2/cosa/inst/doc/cosa_tutorial.Rmd | 9 +-- cosa-1.2.2/cosa/inst/doc/cosa_tutorial.html | 16 +++--- cosa-1.2.2/cosa/man/bcrd3r2.Rd | 4 - cosa-1.2.2/cosa/man/bcrd4r2.Rd | 4 - cosa-1.2.2/cosa/man/bcrd4r3.Rd | 4 - cosa-1.2.2/cosa/man/bird2r1.Rd | 4 - cosa-1.2.2/cosa/man/bird3r1.Rd | 4 - cosa-1.2.2/cosa/man/bird4r1.Rd | 4 - cosa-1.2.2/cosa/man/cosa-package.Rd | 8 --- cosa-1.2.2/cosa/man/crd2r2.Rd | 6 +- cosa-1.2.2/cosa/man/crd3r3.Rd | 6 +- cosa-1.2.2/cosa/man/crd4r4.Rd | 4 - cosa-1.2.2/cosa/man/ird1r1.Rd | 4 - cosa-1.2.2/cosa/man/vectorize.Rd |only cosa-1.2.2/cosa/vignettes/cosa_tutorial.Rmd | 9 +-- 37 files changed, 130 insertions(+), 131 deletions(-)
Title: Utilities for Japanese Mesh Code
Description: Helpful functions for using mesh code (80km to 125m) data in Japan. Visualize mesh code using 'ggplot2' and 'leaflet', etc.
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>)
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between jpmesh versions 1.1.2 dated 2019-03-20 and 1.1.3 dated 2019-05-09
DESCRIPTION | 6 MD5 | 12 - NEWS.md | 4 inst/doc/usage.html | 360 ++++++++++++++++++++++++------- tests/testthat/test-fine_separate.R | 16 - tests/testthat/test-meshcode_to_latlon.R | 2 tests/testthat/test-rmesh.R | 10 7 files changed, 308 insertions(+), 102 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-11 2.7.8
2018-05-08 2.6.7
2017-11-29 2.5.2
2017-11-01 2.5
2017-07-17 2.4
2016-11-18 2.2
2016-08-15 2.0
2016-07-30 1.0.3
2016-07-27 1.0.2
2016-07-26 1.0
Title: A Wrapper of the JavaScript Library 'DataTables'
Description: Data objects in R can be rendered as HTML tables using the
JavaScript library 'DataTables' (typically via R Markdown or Shiny). The
'DataTables' library has been included in this R package. The package name
'DT' is an abbreviation of 'DataTables'.
Author: Yihui Xie [aut, cre],
Joe Cheng [aut],
Xianying Tan [aut],
JJ Allaire [ctb],
Maximilian Girlich [ctb],
Greg Freedman Ellis [ctb],
Johannes Rauh [ctb],
jQuery contributors [ctb, cph] (jQuery in htmlwidgets/lib),
SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib),
Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib),
Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib),
Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib),
RStudio Inc [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between DT versions 0.5 dated 2018-11-05 and 0.6 dated 2019-05-09
DT-0.5/DT/NEWS.md |only DT-0.6/DT/DESCRIPTION | 10 DT-0.6/DT/MD5 | 33 +- DT-0.6/DT/NAMESPACE | 1 DT-0.6/DT/R/datatables.R | 18 - DT-0.6/DT/R/shiny.R | 49 ++- DT-0.6/DT/R/utils.R | 46 ++ DT-0.6/DT/README.md | 2 DT-0.6/DT/build/vignette.rds |binary DT-0.6/DT/inst/NEWS.Rd |only DT-0.6/DT/inst/doc/DT.html | 156 +++++++--- DT-0.6/DT/inst/examples/DT-edit/Readme.md | 6 DT-0.6/DT/inst/examples/DT-edit/app.R | 110 +++++-- DT-0.6/DT/inst/examples/DT-edit/rsconnect/shinyapps.io/yihui/DT-edit.dcf | 4 DT-0.6/DT/inst/htmlwidgets/datatables.js | 119 +++++-- DT-0.6/DT/man/dataTableOutput.Rd | 9 DT-0.6/DT/man/datatable.Rd | 14 DT-0.6/DT/man/editData.Rd |only DT-0.6/DT/man/proxy.Rd | 2 19 files changed, 436 insertions(+), 143 deletions(-)