Title: Automated Schema on Read
Description: Provides schema-on-read tools including a single function call (e.g., schemaOnRead("filename")) that reads text ('TXT'), comma separated value ('CSV'), raster image ('BMP', 'PNG', 'GIF', 'TIFF', and 'JPG'), R data ('RDS'), HDF5, NetCDF, spreadsheet ('XLS', 'XLSX', 'ODS', and 'DIF'), Weka Attribute-Relation File Format ('ARFF'), Epi Info ('REC'), SPSS ('SAV'), Systat ('SYS'), and Stata ('DTA') files. It also recursively reads folders (e.g., schemaOnRead("folder")), returning a nested list of the contained elements.
Author: Michael North [aut, cre]
Maintainer: Michael North <north@anl.gov>
Diff between SchemaOnRead versions 1.0.0 dated 2015-10-24 and 1.0.1 dated 2015-11-03
DESCRIPTION | 17 MD5 | 20 - NAMESPACE | 6 NEWS.md |only R/SchemaOnRead.R | 813 ++++++++++++++++++++++++----------------------- README.md |only tests/testthat/test.08.R | 1 tests/testthat/test.12.R | 1 tests/testthat/test.13.R | 1 tests/testthat/test.14.R | 1 tests/testthat/test.15.R | 1 tests/testthat/test.19.R | 1 12 files changed, 439 insertions(+), 423 deletions(-)
Title: Tools for Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such
as calculating spectral indices, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [cre, aut],
Ned Horning [aut]
Maintainer: Benjamin Leutner <benjamin.leutner@uni-wuerzburg.de>
Diff between RStoolbox versions 0.1.1 dated 2015-09-08 and 0.1.2 dated 2015-11-03
DESCRIPTION | 17 ++--- MD5 | 78 +++++++++++++------------ NAMESPACE | 2 NEWS | 9 ++ R/RStoolbox.R | 6 + R/RcppExports.R | 8 +- R/coregisterImages.R | 10 +-- R/ggR.R | 29 ++++++--- R/ggRGB.R | 2 R/internalFunctions.R | 25 +++++++- R/mlc.R |only R/panSharpen.R | 14 ++-- R/radCor.R | 14 +++- R/rasterCVA.R | 12 +-- R/readMeta.R | 4 - R/readSLI.R | 38 +++++------- R/sam.R | 2 R/spectralIndices.R | 104 ++++++++++++++++++++-------------- R/superClass.R | 47 +++++++++++---- R/tasseledCap.R | 9 +- man/coregisterImages.Rd | 10 +-- man/ggR.Rd | 10 +++ man/panSharpen.Rd | 13 +--- man/radCor.Rd | 4 - man/rasterCVA.Rd | 10 --- man/rlogo.Rd | 1 man/spectralIndices.Rd | 28 +++++---- man/srtm.Rd | 1 man/superClass.Rd | 14 ++-- man/tasseledCap.Rd | 9 +- src/Makevars |only src/Makevars.win |only src/RcppExports.cpp | 39 ++++++++---- src/classQA.cpp | 4 - src/gainOffsetRescale.cpp | 4 - src/predictMlc.cpp |only src/spectralIndices.cpp | 39 ++++++++---- tests/testthat.R | 1 tests/testthat/test-entropy.R | 4 - tests/testthat/test-ggplot.R | 2 tests/testthat/test-multicore.R | 2 tests/testthat/test-spectralIndices.R | 7 +- 42 files changed, 390 insertions(+), 242 deletions(-)
Title: An Algorithm to Infer Relatedness
Description: Inference of relatedness coefficients from a bi-allelic genotype matrix using a Maximum Likelihood estimation.
Author: Fabien Laporte
Maintainer: Fabien Laporte <fabien.laporte@moulon.inra.fr>
Diff between Relatedness versions 1.1 dated 2015-09-16 and 1.2 dated 2015-11-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/RelCoef.R | 2 +- src/BoucleEMacc.c | 1 - 4 files changed, 7 insertions(+), 8 deletions(-)
Title: Spatial Interpolation of Genetic Data
Description: The spatial interpolation of genetic distances between
samples is based on a modified kriging method that
accepts a genetic distance matrix and generates a map of
probability of lineage presence. This package also offers
tools to generate a map of potential contact zones
between groups with user-defined thresholds in the tree
to account for old and recent divergence. Additionally,
it has functions for IDW interpolation using genetic data
and midpoints.
Author: Pedro Tarroso, Guillermo Velo-Anton, Silvia Carvalho
Maintainer: Pedro Tarroso <ptarroso@cibio.up.pt>
Diff between phylin versions 1.0 dated 2014-07-25 and 1.1.1 dated 2015-11-03
DESCRIPTION | 31 ++++++++++++----------- MD5 | 23 ++++++++++++----- NAMESPACE | 10 ++++++- R/gen.variogram.R | 56 ++++++++++++++++++++---------------------- R/gen.variogram.multi.R |only R/gen.variogram.single.R |only R/krig.R | 5 +++ R/plot.gv_WITHMULTI.R |only build |only inst |only man/gen.variogram.Rd | 62 ++++++++++++++++++++++++++++++----------------- man/phylin-package.Rd | 4 +-- man/plot.gv.Rd | 6 +++- vignettes |only 14 files changed, 119 insertions(+), 78 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.6.4 dated 2015-10-23 and 1.6.5 dated 2015-11-03
DESCRIPTION | 7 +- MD5 | 132 ++++++++++++++++++++++----------------------- NAMESPACE | 2 R/TaylorDiagram.R | 58 ++++++++++--------- R/TheilSen.R | 2 R/corPlot.R | 2 R/getMeta.R | 2 R/import.R | 21 +------ R/importAURN.R | 6 +- R/importKCL.R | 6 +- R/polarCluster.R | 4 - R/scatterPlot.R | 65 ++++++++++++---------- R/utilities.R | 6 +- README.md | 2 man/GoogleMapsPlot.Rd | 13 ++-- man/TaylorDiagram.Rd | 9 ++- man/TheilSen.Rd | 10 ++- man/airbaseFindCode.Rd | 3 - man/airbaseInfo.Rd | 2 man/airbaseSplice.Rd | 2 man/airbaseStats.Rd | 2 man/aqStats.Rd | 5 + man/calcFno2.Rd | 4 + man/calcPercentile.Rd | 5 + man/calendarPlot.Rd | 5 + man/conditionalEval.Rd | 5 + man/conditionalQuantile.Rd | 7 ++ man/corPlot.Rd | 5 + man/cutData.Rd | 7 +- man/drawOpenKey.Rd | 6 +- man/import.Rd | 23 +------ man/importADMS.Rd | 6 +- man/importAURN.Rd | 12 ++-- man/importAURNCsv.Rd | 6 +- man/importAirbase.Rd | 2 man/importKCL.Rd | 14 +++- man/importMeta.Rd | 4 - man/importSAQN.Rd | 6 +- man/importTraj.Rd | 8 +- man/kernelExceed.Rd | 6 +- man/linearRelation.Rd | 6 +- man/modStats.Rd | 5 + man/mydata.Rd | 6 +- man/openColours.Rd | 5 + man/openair.Rd | 5 + man/percentileRose.Rd | 5 + man/polarAnnulus.Rd | 6 +- man/polarCluster.Rd | 8 +- man/polarFreq.Rd | 7 +- man/polarPlot.Rd | 6 +- man/quickText.Rd | 6 +- man/rollingMean.Rd | 5 + man/scatterPlot.Rd | 40 +++++++------ man/selectByDate.Rd | 4 + man/selectRunning.Rd | 4 + man/smoothTrend.Rd | 4 + man/splitByDate.Rd | 5 + man/summaryPlot.Rd | 6 +- man/timeAverage.Rd | 23 ++++--- man/timePlot.Rd | 5 + man/timeProp.Rd | 4 + man/timeVariation.Rd | 9 ++- man/trajCluster.Rd | 2 man/trajLevel.Rd | 3 - man/trajPlot.Rd | 4 + man/trendLevel.Rd | 8 ++ man/windRose.Rd | 5 + 67 files changed, 409 insertions(+), 279 deletions(-)
Title: Methods for Multivariate Quadrature
Description: Provides methods to construct multivariate grids,
which can be used for multivariate quadrature. This grids can be based on
different quadrature rules like Newton-Cotes formulas (trapezoidal-, Simpson's-
rule, ...) or Gauss quadrature (Gauss-Hermite, Gauss-Legendre, ...). For the
construction of the multidimensional grid the product-rule or the combination-
technique can be applied.
Author: Constantin Weiser (HHU of Duesseldorf / Germany)
Maintainer: Constantin Weiser <weiserc@hhu.de>
Diff between mvQuad versions 1.0-2 dated 2015-11-01 and 1.0-3 dated 2015-11-03
mvQuad-1.0-2/mvQuad/vignettes/library.bib |only mvQuad-1.0-3/mvQuad/DESCRIPTION | 8 +- mvQuad-1.0-3/mvQuad/MD5 | 15 ++-- mvQuad-1.0-3/mvQuad/R/mvQuad.R | 7 +- mvQuad-1.0-3/mvQuad/inst/CITATION |only mvQuad-1.0-3/mvQuad/inst/NEWS |only mvQuad-1.0-3/mvQuad/inst/doc/mvQuad_intro.Rmd | 84 ++++++++++++++++++++++++- mvQuad-1.0-3/mvQuad/inst/doc/mvQuad_intro.html | 6 - mvQuad-1.0-3/mvQuad/man/mvQuad-package.Rd | 4 - mvQuad-1.0-3/mvQuad/vignettes/mvQuad_intro.Rmd | 84 ++++++++++++++++++++++++- 10 files changed, 185 insertions(+), 23 deletions(-)
Title: Generalized Hermite Distribution
Description: Probability functions and other utilities for the generalized Hermite distribution.
Author: David Moriña, Manuel Higueras, Pedro Puig and MarÃa Oliveira
Maintainer: David Moriña Soler <david.morina@uab.cat>
Diff between hermite versions 1.1.0 dated 2015-04-27 and 1.1.1 dated 2015-11-03
DESCRIPTION | 8 ++++---- MD5 | 6 ++++-- NAMESPACE | 5 +++++ data/hot100.rda |only man/hot100.Rd |only 5 files changed, 13 insertions(+), 6 deletions(-)
Title: The Bayesian Causal Effect Estimation Algorithm
Description: Implementation of the Bayesian Causal Effect Estimation algorithm,
a data-driven method for the estimation of the causal effect of an exposure
on a continuous outcome. For more details, see Talbot et al. (2015) DOI:10.1515/jci-2014-0035.
Author: Denis Talbot, Geneviève Lefebvre, Juli Atherton.
Maintainer: Denis Talbot <denis.talbot@fmed.ulaval.ca>
Diff between BCEE versions 1.0 dated 2015-06-24 and 1.1 dated 2015-11-03
ChangeLog |only DESCRIPTION | 12 ++++++------ MD5 | 15 ++++++++------- NAMESPACE | 4 +++- R/ABCEE.R | 4 ++-- R/NBCEE.R | 15 ++++++++------- man/ABCEE.Rd | 10 +++++++--- man/BCEE-package.Rd | 6 +++--- man/NBCEE.Rd | 10 ++++++---- 9 files changed, 43 insertions(+), 33 deletions(-)
More information about surveyplanning at CRAN
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Title: R to Symbolic Data Analysis
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Author: Oldemar Rodriguez R. with contributions from Olger Calderon, Roberto Zuniga and Jorge Arce
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between RSDA versions 1.2 dated 2014-03-18 and 1.3 dated 2015-11-03
RSDA-1.2/RSDA/inst |only RSDA-1.3/RSDA/DESCRIPTION | 17 +-- RSDA-1.3/RSDA/MD5 | 85 +++++++++++------- RSDA-1.3/RSDA/NAMESPACE | 11 +- RSDA-1.3/RSDA/R/SDS.to.RSDA.R |only RSDA-1.3/RSDA/R/centers.interval.R |only RSDA-1.3/RSDA/R/classic.to.sym.R | 103 +++++++++++----------- RSDA-1.3/RSDA/R/dist.vect.R |only RSDA-1.3/RSDA/R/dist.vect.matrix.R |only RSDA-1.3/RSDA/R/neighbors.vertex.R |only RSDA-1.3/RSDA/R/norm.vect.R |only RSDA-1.3/RSDA/R/process.continuum.variable.R | 2 RSDA-1.3/RSDA/R/process.histogram.variable.R | 62 ++++++------- RSDA-1.3/RSDA/R/process.interval.variable.R | 8 - RSDA-1.3/RSDA/R/process.set.variable.R | 46 +++++----- RSDA-1.3/RSDA/R/sym.interval.pc.R |only RSDA-1.3/RSDA/R/sym.interval.pc.limits.R |only RSDA-1.3/RSDA/R/variance.princ.curve.R |only RSDA-1.3/RSDA/R/vertex.interval.R |only RSDA-1.3/RSDA/data/Cardiological.rda |binary RSDA-1.3/RSDA/data/StudentsGrades.rda |binary RSDA-1.3/RSDA/data/USCrime.rda |binary RSDA-1.3/RSDA/data/VeterinaryData.rda |binary RSDA-1.3/RSDA/data/abalone.rda |binary RSDA-1.3/RSDA/data/ex1_db2so.rda |binary RSDA-1.3/RSDA/data/ex_cfa1.rda |binary RSDA-1.3/RSDA/data/ex_cfa2.rda |binary RSDA-1.3/RSDA/data/example1.rda |binary RSDA-1.3/RSDA/data/example2.rda |binary RSDA-1.3/RSDA/data/example3.rda |binary RSDA-1.3/RSDA/data/example4.rda |binary RSDA-1.3/RSDA/data/example5.rda |binary RSDA-1.3/RSDA/data/example6.rda |binary RSDA-1.3/RSDA/data/example7.rda |binary RSDA-1.3/RSDA/data/facedata.rda |only RSDA-1.3/RSDA/data/int_prost_test.rda |binary RSDA-1.3/RSDA/data/int_prost_train.rda |binary RSDA-1.3/RSDA/data/lynne1.rda |binary RSDA-1.3/RSDA/data/lynne2.rda |binary RSDA-1.3/RSDA/data/oils.rda |binary RSDA-1.3/RSDA/data/uscrime_int.rda |binary RSDA-1.3/RSDA/man/RSDA-package.Rd | 8 - RSDA-1.3/RSDA/man/SDS.to.RSDA.Rd |only RSDA-1.3/RSDA/man/SODAS.to.RSDA.Rd | 6 - RSDA-1.3/RSDA/man/centers.interval.Rd |only RSDA-1.3/RSDA/man/dist.vect.Rd |only RSDA-1.3/RSDA/man/dist.vect.matrix.Rd |only RSDA-1.3/RSDA/man/facedata.Rd |only RSDA-1.3/RSDA/man/neighbors.vertex.Rd |only RSDA-1.3/RSDA/man/norm.vect.Rd |only RSDA-1.3/RSDA/man/sym.interval.pc.Rd |only RSDA-1.3/RSDA/man/sym.interval.pc.limits.Rd |only RSDA-1.3/RSDA/man/sym.interval.pca.Rd | 122 +++++++++++++-------------- RSDA-1.3/RSDA/man/variance.princ.curve.Rd |only RSDA-1.3/RSDA/man/vertex.interval.Rd |only 55 files changed, 248 insertions(+), 222 deletions(-)
Title: Randomized Response Techniques for Complex Surveys
Description: Point and interval estimation of linear parameters with data
obtained from complex surveys (including stratified and clustered samples)
when randomization techniques are used. The randomized response technique
was developed to obtain estimates that are more valid when studying
sensitive topics. Estimators and variances for 14 randomized response
methods for qualitative variables and 7 randomized response methods for
quantitative variables are also implemented. In addition, some data sets
from surveys with these randomization methods are included in the package.
Author: Beatriz Cobo RodrÃguez, MarÃa del Mar Rueda GarcÃa, Antonio Arcos
Cebrián
Maintainer: Beatriz Cobo RodrÃguez <beacr@ugr.es>
Diff between RRTCS versions 0.0.2 dated 2015-07-02 and 0.0.3 dated 2015-11-03
DESCRIPTION | 8 +++-- MD5 | 63 +++++++++++++++++++++++++---------------- R/DianaPerri1.R | 14 ++++----- R/DianaPerri2.R | 16 +++++----- R/Estimator.R | 14 ++++----- R/ForcedResponse.R | 9 +++++ R/ForcedResponseData.R | 2 - R/ForcedResponseDataSt.R |only R/Horvitz.R | 12 +++++++ R/HorvitzData.R | 2 - R/HorvitzDataRealSurvey.R |only R/HorvitzDataStCl.R | 2 - R/JackknifeVariance.R | 6 +-- R/Qualitative.R | 39 ++++++++++++++----------- R/Quantitative.R | 6 +-- R/RRTCS-internal.R | 2 - R/ResamplingVariance.R | 20 +++++++------ R/Saha.R | 12 +++---- build |only data/EichhornHayreData.rda |binary data/ForcedResponseDataSt.rda |only data/HorvitzDataRealSurvey.rda |only inst |only man/DianaPerri1.Rd | 2 - man/DianaPerri2.Rd | 2 - man/ForcedResponse.Rd | 10 ++++++ man/ForcedResponseData.Rd | 2 - man/ForcedResponseDataSt.Rd |only man/Horvitz.Rd | 14 +++++++++ man/HorvitzData.Rd | 2 - man/HorvitzDataRealSurvey.Rd |only man/HorvitzDataStCl.Rd | 2 - man/ResamplingVariance.Rd | 6 +++ vignettes |only 34 files changed, 173 insertions(+), 94 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii) Factor manipulation
functions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix functions,
(vi) Projector and canonical efficiency functions, and (vii) Miscellaneous functions.
A document 'daeDesignRandomization.pdf', available in the doc subdirectory of the
installation directory for 'dae', describes the use of the package for generating randomized
layouts for experiments. The ANOVA functions facilitate the extraction of information when
the 'Error' function has been used in the call to 'aov'.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between dae versions 2.7-5 dated 2015-10-29 and 2.7-6 dated 2015-11-03
DESCRIPTION | 8 - MD5 | 16 +- R/proj.canon.v4.r | 4 R/proj.r | 64 +++++---- R/projs.canon.v4.r | 330 ++++++++++++++++++++++++++---------------------- build/partial.rdb |binary inst/NEWS.Rd | 6 inst/doc/dae-manual.pdf |binary man/summary.pcanon.Rd | 3 9 files changed, 240 insertions(+), 191 deletions(-)
Title: Sample Selection Models
Description: Two-step estimation
and maximum likelihood estimation
of Heckman-type sample selection models:
standard sample selection models (Tobit-2)
and endogenous switching regression models (Tobit-5).
Author: Arne Henningsen <arne.henningsen@gmail.com>,
Ott Toomet <otoomet@ut.ee>
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between sampleSelection versions 1.0-2 dated 2014-06-24 and 1.0-4 dated 2015-11-03
DESCRIPTION | 19 MD5 | 74 NAMESPACE | 29 NEWS | 16 R/CB.R |only R/checkIMRCollinearity.R |only R/coef.selection.R | 2 R/detectModelType.R |only R/heckit5fit.R | 7 R/heckitTfit.R |only R/invMillsRatio.R | 2 R/lambda.R |only R/model.frame.selection.R | 56 R/model.matrix.selection.R | 36 R/predict.selection.R | 93 R/selection.R | 94 R/selectionVariableName.R |only R/summary.probit.R | 2 R/summary.selection.R | 35 R/tobit2Bfit.R | 1 R/tobitTfit.R |only R/tobitType.R |only R/vcov.selection.R | 2 build/vignette.rds |binary demo |only inst/doc/selection.R | 7 inst/doc/selection.Rnw | 5 man/Mroz87.Rd | 130 man/RandHIE.Rd | 281 man/heckit2fit.Rd | 7 man/model.matrix.selection.Rd | 13 man/sampleSelection-internal.Rd | 3 man/selection.Rd | 28 tests/Mroz87SelectionTest.Rout.save | 22 tests/binarySelectionOutcome.R | 5 tests/binarySelectionOutcome.Rout.save | 95 tests/fail.Rout.save | 46 tests/invMillsRatioTest.Rout.save | 58 tests/probit.Rout.save | 10 tests/selection.R | 130 tests/selection.Rout.save |22117 ++++++++++++++++++++++++++++++++- vignettes/selection.Rnw | 5 42 files changed, 22309 insertions(+), 1121 deletions(-)
More information about sampleSelection at CRAN
Permanent link
Title: Clustering Mutations using High Throughput Sequencing (HTS) Data
Description: Using HTS data, clusters mutations in order to recreate putative clones from the data provided. It requires genotype at the location of the variant as well as the depth of coverage and number of reads supporting the mutation. Additional information may be provided, such as the contamination in the tumor sample. This package also provides a function QuantumCat() which simulates data obtained from tumor sequencing. Latest version can be found at github/DeveauP/QuantumClone .
Author: Paul Deveau [aut, cre]
Maintainer: Paul Deveau <paul.deveau@curie.fr>
Diff between QuantumClone versions 0.9.15 dated 2015-09-15 and 0.15.11 dated 2015-11-03
QuantumClone-0.15.11/QuantumClone/DESCRIPTION | 11 + QuantumClone-0.15.11/QuantumClone/MD5 | 65 ++++++---- QuantumClone-0.15.11/QuantumClone/NAMESPACE | 35 ++++- QuantumClone-0.15.11/QuantumClone/R/EM.R | 25 ++- QuantumClone-0.15.11/QuantumClone/R/QuantumClone.R |only QuantumClone-0.15.11/QuantumClone/R/data.R |only QuantumClone-0.15.11/QuantumClone/R/plots.R |only QuantumClone-0.15.11/QuantumClone/README.md |only QuantumClone-0.15.11/QuantumClone/build |only QuantumClone-0.15.11/QuantumClone/data |only QuantumClone-0.15.11/QuantumClone/inst |only QuantumClone-0.15.11/QuantumClone/man/CellularitiesFromFreq.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/Cluster_plot_from_cell.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/From_freq_to_cell.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/Input_Example.Rd |only QuantumClone-0.15.11/QuantumClone/man/One_D_plot.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/One_step_clustering.Rd | 21 +-- QuantumClone-0.15.11/QuantumClone/man/Patient_schrodinger_cellularities.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/Probability.to.belong.to.clone.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/QC_output.Rd |only QuantumClone-0.15.11/QuantumClone/man/QuantumClone.Rd | 13 -- QuantumClone-0.15.11/QuantumClone/man/ThreeD_plot.Rd | 7 - QuantumClone-0.15.11/QuantumClone/man/Tree.Rd |only QuantumClone-0.15.11/QuantumClone/man/Tree_generation.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/add_leaf_list.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/evolution_plot.Rd |only QuantumClone-0.15.11/QuantumClone/man/find_x_position.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/is_included.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/longueur.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/manual_plot_trees.Rd | 9 + QuantumClone-0.15.11/QuantumClone/man/multiplot_trees.Rd | 7 - QuantumClone-0.15.11/QuantumClone/man/plot_QC_out.Rd |only QuantumClone-0.15.11/QuantumClone/man/plot_cell_from_Return_out.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/plot_with_margins_densities.Rd | 12 - QuantumClone-0.15.11/QuantumClone/man/strcount.Rd | 2 QuantumClone-0.15.11/QuantumClone/vignettes |only QuantumClone-0.9.15/QuantumClone/R/QuantumClone_v3.R |only 37 files changed, 138 insertions(+), 93 deletions(-)
Title: Langevin Analysis in One and Two Dimensions
Description: Estimate drift and diffusion functions from time series and
generate synthetic time series from given drift and diffusion coefficients.
Author: Philip Rinn [aut, cre],
Pedro G. Lind [aut],
David Bastine [ctb]
Maintainer: Philip Rinn <philip.rinn@uni-oldenburg.de>
Diff between Langevin versions 1.0.3 dated 2015-08-26 and 1.1.1 dated 2015-11-03
Langevin-1.0.3/Langevin/R/RcppExports.R |only Langevin-1.1.1/Langevin/ChangeLog | 26 ++ Langevin-1.1.1/Langevin/DESCRIPTION | 19 - Langevin-1.1.1/Langevin/MD5 | 49 ++-- Langevin-1.1.1/Langevin/NAMESPACE | 9 Langevin-1.1.1/Langevin/R/Langevin-package.r | 6 Langevin-1.1.1/Langevin/R/Langevin1D.r |only Langevin-1.1.1/Langevin/R/Langevin2D.r |only Langevin-1.1.1/Langevin/R/plot.Langevin.r |only Langevin-1.1.1/Langevin/R/print.Langevin.r |only Langevin-1.1.1/Langevin/R/summary.Langevin.r |only Langevin-1.1.1/Langevin/R/timeseries1D.r |only Langevin-1.1.1/Langevin/R/timeseries2D.r | 6 Langevin-1.1.1/Langevin/build/vignette.rds |binary Langevin-1.1.1/Langevin/inst/CITATION |only Langevin-1.1.1/Langevin/inst/doc/Langevin.Rnw | 274 +++++++++++++----------- Langevin-1.1.1/Langevin/inst/doc/Langevin.pdf |binary Langevin-1.1.1/Langevin/man/Langevin-package.Rd | 6 Langevin-1.1.1/Langevin/man/Langevin1D.Rd | 10 Langevin-1.1.1/Langevin/man/Langevin2D.Rd | 11 Langevin-1.1.1/Langevin/man/plot.Langevin.Rd |only Langevin-1.1.1/Langevin/man/print.Langevin.Rd |only Langevin-1.1.1/Langevin/man/summary.Langevin.Rd |only Langevin-1.1.1/Langevin/man/timeseries1D.Rd | 8 Langevin-1.1.1/Langevin/man/timeseries2D.Rd | 6 Langevin-1.1.1/Langevin/src/Langevin1D.cpp | 81 ------- Langevin-1.1.1/Langevin/src/Langevin2D.cpp | 84 +------ Langevin-1.1.1/Langevin/src/RcppExports.cpp | 14 - Langevin-1.1.1/Langevin/src/timeseries1D.cpp | 45 --- Langevin-1.1.1/Langevin/src/timeseries2D.cpp | 28 +- Langevin-1.1.1/Langevin/vignettes/Langevin.Rnw | 274 +++++++++++++----------- 31 files changed, 448 insertions(+), 508 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Emily Beylerian [ctb],
Li Wang [ctb],
Skye Bender-deMoll [ctb]
Maintainer: Samuel Jenness <sjenness@uw.edu>
Diff between EpiModel versions 1.2.1 dated 2015-07-24 and 1.2.2 dated 2015-11-03
EpiModel-1.2.1/EpiModel/man/netsim_parallel.Rd |only EpiModel-1.2.2/EpiModel/DESCRIPTION | 20 EpiModel-1.2.2/EpiModel/MD5 | 221 +++++------ EpiModel-1.2.2/EpiModel/NAMESPACE | 9 EpiModel-1.2.2/EpiModel/NEWS | 38 + EpiModel-1.2.2/EpiModel/R/EpiModel-package.r | 5 EpiModel-1.2.2/EpiModel/R/as.data.frame.R | 29 + EpiModel-1.2.2/EpiModel/R/control.R | 4 EpiModel-1.2.2/EpiModel/R/dendo.R |only EpiModel-1.2.2/EpiModel/R/get.R | 14 EpiModel-1.2.2/EpiModel/R/init.R | 4 EpiModel-1.2.2/EpiModel/R/netdx.R | 2 EpiModel-1.2.2/EpiModel/R/netsim.R | 27 - EpiModel-1.2.2/EpiModel/R/plot.R | 42 +- EpiModel-1.2.2/EpiModel/R/print.r | 15 EpiModel-1.2.2/EpiModel/R/saveout.R | 1 EpiModel-1.2.2/EpiModel/R/shiny.R | 31 - EpiModel-1.2.2/EpiModel/build/vignette.rds |binary EpiModel-1.2.2/EpiModel/inst/doc/Intro.html | 16 EpiModel-1.2.2/EpiModel/inst/shiny/epiicm/server.R | 2 EpiModel-1.2.2/EpiModel/inst/shiny/epinet |only EpiModel-1.2.2/EpiModel/man/EpiModel-package.Rd | 6 EpiModel-1.2.2/EpiModel/man/as.data.frame.dcm.Rd | 3 EpiModel-1.2.2/EpiModel/man/as.data.frame.icm.Rd | 22 - EpiModel-1.2.2/EpiModel/man/as.network.transmat.Rd |only EpiModel-1.2.2/EpiModel/man/as.phylo.transmat.Rd |only EpiModel-1.2.2/EpiModel/man/bipvals.Rd | 3 EpiModel-1.2.2/EpiModel/man/births.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/births.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/brewer_ramp.Rd | 5 EpiModel-1.2.2/EpiModel/man/calc_eql.Rd | 5 EpiModel-1.2.2/EpiModel/man/check_bip_degdist.Rd | 3 EpiModel-1.2.2/EpiModel/man/color_tea.Rd | 2 EpiModel-1.2.2/EpiModel/man/comp_plot.Rd | 3 EpiModel-1.2.2/EpiModel/man/control.dcm.Rd | 2 EpiModel-1.2.2/EpiModel/man/control.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/control.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/copy_toall_attr.Rd | 4 EpiModel-1.2.2/EpiModel/man/crosscheck.dcm.Rd | 2 EpiModel-1.2.2/EpiModel/man/crosscheck.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/crosscheck.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/dcm.Rd | 5 EpiModel-1.2.2/EpiModel/man/dcm.mods.Rd | 4 EpiModel-1.2.2/EpiModel/man/deaths.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/deaths.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/deleteAttr.Rd | 2 EpiModel-1.2.2/EpiModel/man/discord_edgelist.Rd | 2 EpiModel-1.2.2/EpiModel/man/dissolution_coefs.Rd | 6 EpiModel-1.2.2/EpiModel/man/edgelist_censor.Rd | 7 EpiModel-1.2.2/EpiModel/man/edgelist_meanage.Rd | 5 EpiModel-1.2.2/EpiModel/man/edges_correct.Rd | 2 EpiModel-1.2.2/EpiModel/man/epiweb.Rd | 30 - EpiModel-1.2.2/EpiModel/man/get_attr_prop.Rd | 4 EpiModel-1.2.2/EpiModel/man/get_formula_terms.Rd | 2 EpiModel-1.2.2/EpiModel/man/get_network.Rd | 5 EpiModel-1.2.2/EpiModel/man/get_nwparam.Rd | 4 EpiModel-1.2.2/EpiModel/man/get_nwstats.Rd | 5 EpiModel-1.2.2/EpiModel/man/get_prev.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/get_prev.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/get_sims.Rd | 13 EpiModel-1.2.2/EpiModel/man/get_transmat.Rd | 11 EpiModel-1.2.2/EpiModel/man/icm.Rd | 5 EpiModel-1.2.2/EpiModel/man/idmode.Rd | 5 EpiModel-1.2.2/EpiModel/man/infection.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/infection.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/init.dcm.Rd | 2 EpiModel-1.2.2/EpiModel/man/init.icm.Rd | 4 EpiModel-1.2.2/EpiModel/man/init.net.Rd | 4 EpiModel-1.2.2/EpiModel/man/init_pids.Rd | 3 EpiModel-1.2.2/EpiModel/man/init_status.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/init_status.net.Rd | 4 EpiModel-1.2.2/EpiModel/man/initialize.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/initialize.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/mcat.Rd | 2 EpiModel-1.2.2/EpiModel/man/merge.icm.Rd | 3 EpiModel-1.2.2/EpiModel/man/merge.netsim.Rd | 3 EpiModel-1.2.2/EpiModel/man/modeids.Rd | 3 EpiModel-1.2.2/EpiModel/man/modules.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/modules.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/netdx.Rd | 5 EpiModel-1.2.2/EpiModel/man/netest.Rd | 3 EpiModel-1.2.2/EpiModel/man/netsim.Rd | 5 EpiModel-1.2.2/EpiModel/man/param.dcm.Rd | 2 EpiModel-1.2.2/EpiModel/man/param.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/param.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/plot.dcm.Rd | 5 EpiModel-1.2.2/EpiModel/man/plot.icm.Rd | 3 EpiModel-1.2.2/EpiModel/man/plot.netdx.Rd | 3 EpiModel-1.2.2/EpiModel/man/plot.netsim.Rd | 25 + EpiModel-1.2.2/EpiModel/man/plot.transmat.Rd |only EpiModel-1.2.2/EpiModel/man/recovery.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/recovery.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/resim_nets.Rd | 2 EpiModel-1.2.2/EpiModel/man/saveout.dcm.Rd | 2 EpiModel-1.2.2/EpiModel/man/saveout.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/saveout.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/sim_nets.Rd | 2 EpiModel-1.2.2/EpiModel/man/split_bip.Rd | 2 EpiModel-1.2.2/EpiModel/man/ssample.Rd | 4 EpiModel-1.2.2/EpiModel/man/summary.dcm.Rd | 3 EpiModel-1.2.2/EpiModel/man/summary.icm.Rd | 3 EpiModel-1.2.2/EpiModel/man/summary.netest.Rd | 2 EpiModel-1.2.2/EpiModel/man/summary.netsim.Rd | 3 EpiModel-1.2.2/EpiModel/man/test_icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/test_net.Rd | 2 EpiModel-1.2.2/EpiModel/man/transco.Rd | 3 EpiModel-1.2.2/EpiModel/man/update_nwattr.Rd | 4 EpiModel-1.2.2/EpiModel/man/verbose.dcm.Rd | 2 EpiModel-1.2.2/EpiModel/man/verbose.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/verbose.net.Rd | 2 EpiModel-1.2.2/EpiModel/tests/testthat/test-netdx.R | 18 EpiModel-1.2.2/EpiModel/tests/testthat/test-print.R | 16 EpiModel-1.2.2/EpiModel/tests/testthat/test-transmat-dendo.R |only EpiModel-1.2.2/EpiModel/tests/testthat/test-utils.R | 2 114 files changed, 505 insertions(+), 353 deletions(-)
Title: Sorted L1 Penalized Estimation (SLOPE)
Description: Efficient procedures for Sorted L1 Penalized Estimation (SLOPE).
The sorted L1 norm is useful for statistical estimation and testing,
particularly for variable selection in the linear model.
Author: Malgorzata Bogdan, Ewout van den Berg, Chiara Sabatti, Weijie Su,
Emmanuel Candes, Evan Patterson
Maintainer: Evan Patterson <epatters@stanford.edu>
Diff between SLOPE versions 0.1.1 dated 2015-04-27 and 0.1.3 dated 2015-11-03
DESCRIPTION | 13 - MD5 | 30 +-- NAMESPACE | 6 R/SLOPE.R | 6 R/SLOPE_solver.R | 5 R/util.R | 17 ++ build/vignette.rds |binary inst/doc/intro.html | 96 +++++++---- man/SLOPE.Rd | 4 man/SLOPE_solver.Rd | 4 man/SLOPE_solver_matlab.Rd | 8 man/lambda.Rd | 2 man/prox_sorted_L1.Rd | 4 tests/testthat.R | 9 + tests/testthat/MatlabServer.m | 353 +++++++++++++++++++++++------------------- tests/testthat/test_slope.R | 1 16 files changed, 325 insertions(+), 233 deletions(-)
Title: Maximum Likelihood Models for Species Abundance Distributions
Description: Maximum likelihood tools to fit and compare models of species
abundance distributions and of species rank-abundance distributions.
Author: Paulo I. Prado, Murilo Dantas Miranda and Andre Chalom
Maintainer: Paulo I. Prado <prado@ib.usp.br>
Diff between sads versions 0.2.3 dated 2015-09-25 and 0.2.4 dated 2015-11-03
DESCRIPTION | 8 MD5 | 68 +++--- NAMESPACE | 8 NEWS | 10 R/distr.R |only R/fitbs.R | 2 R/fitgamma.R | 2 R/fitgeom.R | 2 R/fitgs.R | 2 R/fitlnorm.R | 2 R/fitls.R | 2 R/fitmand.R | 2 R/fitmzsm.R | 2 R/fitnbinom.R | 2 R/fitpareto.R | 2 R/fitpoilog.R | 2 R/fitpower.R | 2 R/fitrbs.R | 2 R/fitvolkov.R | 8 R/fitweibull.R | 2 R/fitzipf.R | 2 R/octav.R | 20 + R/sads-classes.R | 13 + R/sads-methods.R | 466 +++++++++++++++++++++++----------------------- inst/doc/sads_intro.Rnw | 2 inst/doc/sads_intro.pdf |binary man/distr.Rd |only man/dvolkov.Rd | 5 man/fitrad-class.Rd | 3 man/fitsad-class.Rd | 3 man/octavpred.Rd | 6 man/qqsad.Rd | 13 - man/radpred.Rd | 15 - man/sads-package.Rd | 4 man/stats.Rd |only man/summary.sads-class.Rd |only vignettes/sads_intro.Rnw | 2 37 files changed, 366 insertions(+), 318 deletions(-)
Title: P-Values for Classification
Description: Computes nonparametric p-values for the potential class
memberships of new observations as well as cross-validated
p-values for the training data. The p-values are based on
permutation tests applied to an estimated Bayesian likelihood
ratio, using a plug-in statistic for the Gaussian model, 'k
nearest neighbors', 'weighted nearest neighbors' or
'penalized logistic regression'.
Additionally, it provides graphical displays and quantitative
analyses of the p-values.
Author: Niki Zumbrunnen <niki.zumbrunnen@gmail.com>,
Lutz Duembgen <lutz.duembgen@stat.unibe.ch>.
Maintainer: Niki Zumbrunnen <niki.zumbrunnen@gmail.com>
Diff between pvclass versions 1.2 dated 2014-11-24 and 1.3 dated 2015-11-03
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 3 +++ R/cvpvs.gaussian.R | 11 ++++++++--- R/cvpvs.knn.R | 9 +++++++-- R/cvpvs.logreg.R | 10 ++++++++-- R/cvpvs.wnn.R | 10 ++++++++-- R/pvs.gaussian.R | 30 ++++++++++++++++-------------- R/pvs.knn.R | 39 ++++++++++++++++++++++----------------- R/pvs.logreg.R | 34 +++++++++++++++++++++++++++------- R/pvs.wnn.R | 29 ++++++++++++++++------------- R/sigmaSym.R | 23 ++++++++++++----------- 12 files changed, 143 insertions(+), 87 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between packrat versions 0.4.5 dated 2015-10-22 and 0.4.6 dated 2015-11-03
DESCRIPTION | 11 +++-- MD5 | 70 +++++++++++++++++++++++++++++++------ R/dependencies.R | 8 ++-- R/options.R | 59 +++++++++++++++++++++++-------- R/recursive-package-dependencies.R | 10 ++++- R/restore.R | 53 ++++++++++++++++++++-------- R/utils.R | 18 +++++++++ inst/resources/init-rprofile.R | 2 - inst/resources/init.R | 2 - man/appDependencies.Rd | 6 +-- man/packrat-options.Rd | 6 +++ tests |only 12 files changed, 192 insertions(+), 53 deletions(-)
Title: Functions to Analyze and Visualize Likert Type Items
Description: Functions to analyze and visualize likert type items.
Author: Jason Bryer <jason@bryer.org>, Kimberly Speerschneider
<kimkspeer@gmail.com>
Maintainer: Jason Bryer <jason@bryer.org>
Diff between likert versions 1.3.0 dated 2015-10-23 and 1.3.1 dated 2015-11-03
DESCRIPTION | 9 ++--- MD5 | 72 +++++++++++++++++++++--------------------- NAMESPACE | 2 - NEWS | 7 +++- R/xtable.likert.r | 6 ++- build/vignette.rds |binary inst/doc/likert-xtable.pdf |binary man/MathAnxiety.Rd | 6 +-- man/MathAnxietyGender.Rd | 8 ++-- man/abs_formatter.Rd | 2 - man/align.plots.Rd | 2 - man/gap.Rd | 2 - man/label_wrap_mod.Rd | 2 - man/likert-package.Rd | 2 - man/likert.Rd | 6 +-- man/likert.bar.plot.Rd | 6 +-- man/likert.density.plot.Rd | 2 - man/likert.heat.plot.Rd | 2 - man/likert.histogram.plot.Rd | 2 - man/likert.matrix.plot.Rd | 2 - man/mass.Rd | 6 +-- man/pisaitems.Rd | 2 - man/plot.likert.Rd | 4 +- man/plot.likert.gap.Rd | 4 +- man/print.likert.Rd | 2 - man/print.likert.bar.plot.Rd | 6 +-- man/print.likert.gap.Rd | 2 - man/print.likert.heat.plot.Rd | 2 - man/print.xlikert.Rd | 2 - man/recode.Rd | 4 +- man/reverse.levels.Rd | 2 - man/sasr.Rd | 6 +-- man/shinyLikert.Rd | 2 - man/summary.likert.Rd | 6 +-- man/summary.likert.gap.Rd | 4 +- man/xtable.likert.Rd | 18 ++++++---- man/zeroGrob.Rd | 2 - 37 files changed, 114 insertions(+), 100 deletions(-)
Title: Forest Growth Model Utilities
Description: Growth models and forest production require existing data manipulation and the creation of new data, structured from basic forest inventory data. The purpose of this package is provide functions to support these activities.
Author: Clayton Vieira Fraga,
Ana Paula Simiqueli,
Wagner Amorim da Silva Altoe
Maintainer: Clayton Vieira Fraga <altoe.wagner@gmail.com>
Diff between Fgmutils versions 0.2 dated 2015-10-22 and 0.3 dated 2015-11-03
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++++++---- NAMESPACE | 5 +++++ NEWS | 3 +++ R/classificaClasseDAP.R |only R/criaDadosPareados.R | 20 ++++++++++++++++++++ R/defineClasses2.R |only R/ifrm.R |only R/whichmedian.R |only man/classificaClasseDAP.Rd |only man/defineClasses2.Rd |only man/ifrm.Rd |only man/whichmedian.Rd |only 13 files changed, 45 insertions(+), 9 deletions(-)