Title: Calculating Proportionality Between Vectors of Compositional
Data
Description: The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, this approach lacks statistical validity
when applied to relative data. This includes, for example, biological count data
generated by high-throughput RNA-sequencing, chromatin immunoprecipitation (ChIP),
ChIP-sequencing, Methyl-Capture sequencing, and other techniques. This package
implements several metrics for proportionality, including
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and
rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. This package also
implements several metrics for differential proportionality. Unlike correlation,
these measures give the same result for both relative and absolute data.
Author: Thomas Quinn [aut, cre],
David Lovell [aut],
Ionas Erb [aut],
Anders Bilgrau [ctb],
Greg Gloor [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between propr versions 3.0.6 dated 2017-08-01 and 3.0.7 dated 2017-09-06
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/propr.R | 11 +++++++++++ build/vignette.rds |binary inst/doc/a_introduction.html | 4 ++-- inst/doc/b_visualization.html | 4 ++-- inst/doc/c_indexing.html | 4 ++-- inst/doc/d_advanced.html | 4 ++-- inst/doc/e_differential.Rmd | 2 +- inst/doc/e_differential.html | 4 ++-- inst/doc/f_questions.html | 4 ++-- man/proportionality.Rd | 5 +++++ vignettes/e_differential.Rmd | 2 +- 15 files changed, 53 insertions(+), 31 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers.
Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures
can either be created and verified manually or via x509 certificates. AES can be
used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public
key) encryption or EC for Diffie Hellman. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure
random number generator, and 'bignum' math methods for manually performing
crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut],
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between openssl versions 0.9.6 dated 2016-12-30 and 0.9.7 dated 2017-09-06
DESCRIPTION | 16 ++--- LICENSE | 2 MD5 | 116 ++++++++++++++++++++++--------------------- NAMESPACE | 6 +- NEWS | 14 +++++ R/aes.R | 2 R/bignum.R | 17 +++++- R/cert.R | 6 +- R/diffie.R | 2 R/envelope.R | 2 R/read.R | 31 ++++++++++- R/stopifnot.R |only build/vignette.rds |binary configure | 37 +++++++++---- inst/doc/bignum.Rmd | 2 inst/doc/bignum.html | 36 ++++++------- inst/doc/crypto_hashing.Rmd | 2 inst/doc/crypto_hashing.html | 16 ++--- inst/doc/keys.html | 48 ++++++++--------- inst/doc/secure_rng.html | 24 ++++---- man/aes_cbc.Rd | 3 - man/askpass.Rd | 1 man/base64_encode.Rd | 1 man/bignum.Rd | 5 - man/certificates.Rd | 5 - man/ec_dh.Rd | 3 - man/encrypt_envelope.Rd | 3 - man/fingerprint.Rd | 1 man/hash.Rd | 1 man/keygen.Rd | 1 man/my_key.Rd | 1 man/openssl.Rd | 1 man/openssl_config.Rd | 1 man/pkcs12.Rd | 1 man/rand_bytes.Rd | 1 man/read_key.Rd | 3 - man/rsa_encrypt.Rd | 1 man/signatures.Rd | 1 man/write_pem.Rd | 1 src/Makevars.win | 7 +- src/aes.c | 4 + src/base64.c | 1 src/bignum.c | 7 ++ src/cert.c | 1 src/keygen.c | 28 ++++------ src/keys.c | 11 ++-- src/onload.c | 4 + src/openssh.c | 11 ++-- src/pem.c | 26 +++++++-- src/pkcs12.c | 9 +-- src/pkcs7.c | 9 +-- src/rsa.c | 1 src/signing.c | 15 ++++- src/ssl.c | 9 ++- src/tests |only tests/testthat/test_bignum.R | 7 ++ tests/testthat/test_google.R |only tools/winlibs.R | 8 +- vignettes/bignum.Rmd | 2 vignettes/crypto_hashing.Rmd | 2 60 files changed, 343 insertions(+), 233 deletions(-)
Title: May All Data be Reproducible and Transparent (MADRaT) *
Description: Provides a framework which should improve reproducibility and transparency in data processing. It provides functionality such as automatic meta data creation and management, rudimentary quality management, data caching, work-flow management and data aggregation.
* The title is a wish not a promise. By no means we expect this package to deliver everything what is needed to achieve full reproducibility and transparency, but we believe that it supports efforts in this direction.
Author: Jan Philipp Dietrich [aut, cre],
Lavinia Baumstark [aut],
Anastasis Giannousakis [aut],
Benjamin Leon Bodirsky [ctb],
Ulrich Kreidenweis [ctb]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between madrat versions 1.8.0 dated 2017-05-29 and 1.22.1 dated 2017-09-06
madrat-1.22.1/madrat/DESCRIPTION | 19 madrat-1.22.1/madrat/MD5 | 65 +- madrat-1.22.1/madrat/NAMESPACE | 14 madrat-1.22.1/madrat/R/calcOutput.R | 27 - madrat-1.22.1/madrat/R/convertTau.R | 2 madrat-1.22.1/madrat/R/downloadSource.R | 8 madrat-1.22.1/madrat/R/getDependentCalls.R |only madrat-1.22.1/madrat/R/getMainfolder.R | 8 madrat-1.22.1/madrat/R/initializeConfig.R | 4 madrat-1.22.1/madrat/R/madlapply.R |only madrat-1.22.1/madrat/R/prepFunctionName.R | 30 - madrat-1.22.1/madrat/R/readSource.R | 8 madrat-1.22.1/madrat/R/readTau.R | 68 +- madrat-1.22.1/madrat/R/retrieveData.R | 14 madrat-1.22.1/madrat/R/setConfig.R | 13 madrat-1.22.1/madrat/R/spatial_header.R | 3 madrat-1.22.1/madrat/R/sysdata.rda |only madrat-1.22.1/madrat/R/toolAggregate.R | 413 ++++++----------- madrat-1.22.1/madrat/R/toolISOhistorical.R | 4 madrat-1.22.1/madrat/R/toolMappingFile.R | 83 +-- madrat-1.22.1/madrat/R/toolNAreplace.R | 69 +- madrat-1.22.1/madrat/R/toolendmessage.R | 4 madrat-1.22.1/madrat/R/toolstartmessage.R | 2 madrat-1.22.1/madrat/README.md |only madrat-1.22.1/madrat/build |only madrat-1.22.1/madrat/inst/doc |only madrat-1.22.1/madrat/inst/extdata/country2iso.csv | 4 madrat-1.22.1/madrat/inst/extdata/regionmappingH12.csv |only madrat-1.22.1/madrat/man/calcOutput.Rd | 6 madrat-1.22.1/madrat/man/getDependentCalls.Rd |only madrat-1.22.1/madrat/man/madlapply.Rd |only madrat-1.22.1/madrat/man/prepFunctionName.Rd | 4 madrat-1.22.1/madrat/man/readTau.Rd | 2 madrat-1.22.1/madrat/man/setConfig.Rd | 8 madrat-1.22.1/madrat/man/toolAggregate.Rd | 14 madrat-1.22.1/madrat/man/toolNAreplace.Rd | 12 madrat-1.22.1/madrat/vignettes |only madrat-1.8.0/madrat/inst/extdata/iso_cell.csv |only 38 files changed, 454 insertions(+), 454 deletions(-)
Title: Export Data Frames to 'xlsx' Format
Description: Portable, light-weight data frame to 'xlsx' exporter based on 'libxlsxwriter'.
No 'Java' or 'Excel' required.
Author: Jeroen Ooms [aut, cre],
John McNamara [cph] (Author of libxlsxwriter (see AUTHORS and COPYRIGHT
files for details))
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between writexl versions 0.1 dated 2017-08-30 and 0.2 dated 2017-09-06
DESCRIPTION | 6 - MD5 | 11 +- NAMESPACE | 2 NEWS |only R/write_xlsx.R | 18 ++-- src/write_xlsx.c | 178 +++++++++++++++++++++++--------------------- tests/testthat/test-types.R | 1 7 files changed, 117 insertions(+), 99 deletions(-)
Title: Graph Matching Library for R
Description: This is a wrapper package for the graph matching library 'graphm'. The original 'graphm' C/C++ library can be found in <http://cbio.mines-paristech.fr/graphm/> . Latest version ( 0.52 ) of this library is slightly modified to fit 'Rcpp' usage and included in the source package. The development version of the package is also available at <https://github.com/adalisan/RGraphM> .
Author: Mikhail Zaslavskiy, Sancar Adali
Maintainer: Sancar Adali <sancar.adali@gmail.com>
Diff between RGraphM versions 0.1.10 dated 2017-08-26 and 0.1.11 dated 2017-09-06
DESCRIPTION | 6 +-- MD5 | 40 ++++++++++----------- src/Makevars.in | 3 + src/graphm/algorithm.cpp | 39 +++++++++++++++----- src/graphm/algorithm.h | 4 +- src/graphm/algorithm_ca.cpp | 1 src/graphm/algorithm_ext.cpp | 4 +- src/graphm/algorithm_fsol.cpp | 7 ++- src/graphm/algorithm_iden.cpp | 3 + src/graphm/algorithm_lp.cpp | 15 ++++--- src/graphm/algorithm_path.cpp | 7 ++- src/graphm/algorithm_qcv.cpp | 74 ++++++++++++++++++++------------------- src/graphm/algorithm_rand.cpp | 3 + src/graphm/algorithm_rank.cpp | 55 ++++++++++++++-------------- src/graphm/algorithm_sch.cpp | 13 +++--- src/graphm/algorithm_umeyama.cpp | 25 ++++++------- src/graphm/algorithm_unif.cpp | 1 src/graphm/experiment.cpp | 5 ++ src/graphm/graph.cpp | 13 +++++- src/graphm/rpc.h | 3 + src/graphmatch_rcpp.cpp | 1 21 files changed, 186 insertions(+), 136 deletions(-)
Title: Data Class and Tools for Handling Spatial-Temporal Data
Description: Data class for increased interoperability working with spatial-
temporal data together with corresponding functions and methods (conversions,
basic calculations and basic data manipulation). The class distinguishes
between spatial, temporal and other dimensions to facilitate the development
and interoperability of tools build for it. Additional features are name-based
addressing of data and internal consistency checks (e.g. checking for the right
data order in calculations).
Author: Jan Philipp Dietrich,
Benjamin Bodirsky,
Misko Stevanovic,
Lavinia Baumstark,
Christoph Bertram,
Markus Bonsch,
Anastasis Giannousakis,
Florian Humpenoeder,
David Klein,
Ina Neher,
Michaja Pehl,
Anselm Schultes,
Xiaoxi Wang
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between magclass versions 4.39 dated 2017-05-26 and 4.51.1 dated 2017-09-06
DESCRIPTION | 12 MD5 | 50 ++-- NAMESPACE | 2 R/add_columns.R | 1 R/as.magpie.R | 539 +++++++++++++++++++++++--------------------- R/collapseNames.R | 158 ++++++------ R/convert.report.R | 16 + R/dimOrder.R | 2 R/dimReduce.R |only R/getItems.R |only R/magpie-class.R | 549 ++++++++++++++++++++++----------------------- R/mselect.R | 3 R/sysdata.rda |binary R/write.report.R | 4 R/write.report2.R | 167 +++++++------ R/write.reportProject.R | 156 +++++++++++- README.md |only build |only inst |only man/collapseNames.Rd | 3 man/convert.report.Rd | 2 man/dimReduce.Rd |only man/getItems.Rd |only man/magpie-class.Rd | 5 man/write.report2.Rd | 5 man/write.reportProject.Rd | 21 + vignettes |only 27 files changed, 959 insertions(+), 736 deletions(-)
Title: Graph/Network Visualization
Description: Graph and network visualization using tabular data.
Author: Knut Sveidqvist [aut, cph] (mermaid.js library in htmlwidgets/lib,
http://github.com/knsv/mermaid/),
Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib,
http://github.com/cpettitt/dagre-d3),
Mike Daines [aut, cph] (viz.js library in htmlwidgets/lib,
http://github.com/mdaines/viz.js/),
Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone <riannone@me.com>
Diff between DiagrammeR versions 0.9.1 dated 2017-08-21 and 0.9.2 dated 2017-09-06
DESCRIPTION | 21 +++---- MD5 | 58 +++++++++++-------- NAMESPACE | 5 + NEWS.md | 10 +++ R/add_balanced_tree.R | 41 ++++++++----- R/add_cycle.R | 18 +++--- R/add_full_graph.R | 62 ++++++++++++--------- R/add_grid_2d.R |only R/add_grid_3d.R |only R/add_path.R | 43 +++++++------- R/get_similar_nbrs.R | 4 + R/mutate_edge_attrs.R | 11 +++ R/mutate_edge_attrs_ws.R |only R/mutate_node_attrs.R | 12 +++- R/mutate_node_attrs_ws.R |only R/print.R | 31 ++++++---- R/select_edges.R | 21 ++++++- R/select_nodes.R | 8 -- README.md | 12 +++- man/add_balanced_tree.Rd | 45 +++++++++------ man/add_cycle.Rd | 18 +++--- man/add_full_graph.Rd | 62 ++++++++++++--------- man/add_grid_2d.Rd |only man/add_grid_3d.Rd |only man/add_path.Rd | 43 +++++++------- man/mutate_edge_attrs_ws.Rd |only man/mutate_node_attrs.Rd | 1 man/mutate_node_attrs_ws.Rd |only man/select_edges.Rd | 5 + tests/testthat/test-neighbors.R | 8 +- tests/testthat/test-rescale_node_edge_attrs.R | 28 +++++---- tests/testthat/test-set_get_node_edge_attrs.R | 21 ++----- tests/testthat/test-set_node_attr_to_display.R | 6 +- tests/testthat/test-traversals_copying_attr_vals.R | 26 ++++---- 34 files changed, 373 insertions(+), 247 deletions(-)
Title: Business Process Analytics in R
Description: Functionalities for process analysis in R. This packages implements an S3-class for event log objects, and related handler functions. Imports related packages for subsetting event data, computation of descriptive statistics, handling of Petri Net objects and visualization of process maps. See also packages 'edeaR','processmapR', 'eventdataR' and 'processmonitR'.
Author: Gert Janssenswillen
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between bupaR versions 0.2.0 dated 2017-06-19 and 0.3.0 dated 2017-09-06
DESCRIPTION | 12 ++++++------ MD5 | 20 +++++++++++++------- NAMESPACE | 9 +++++++++ R/bupar.R | 1 + R/eventlog.R | 7 +++++-- R/group_by.eventlog.R |only R/mutate.eventlog.R |only R/simple_eventlog.R |only R/utils.R | 8 ++++++++ man/eventlog.Rd | 3 ++- man/group_by.eventlog.Rd |only man/mutate.eventlog.Rd |only man/reexports.Rd | 6 +++++- man/simple_eventlog.Rd |only 14 files changed, 49 insertions(+), 17 deletions(-)
Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments',
this package provides a parallel implementation of the Map function for high
performance computing systems managed by schedulers 'IBM Spectrum LSF'
(<http://www-03.ibm.com/systems/spectrum-computing/products/lsf/>),
'OpenLava' (<http://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid
Engine' (<http://www.univa.com/>), 'Slurm' (<http://slurm.schedmd.com/>),
'TORQUE/PBS'
(<http://www.adaptivecomputing.com/products/open-source/torque/>), or
'Docker Swarm' (<https://docs.docker.com/swarm/>).
A multicore and socket mode allow the parallelization on a local machines,
and multiple machines can be hooked up via SSH to create a makeshift
cluster. Moreover, the package provides an abstraction mechanism to define
large-scale computer experiments in a well-organized and reproducible way.
Author: Michel Lang [cre, aut],
Bernd Bischl [aut],
Dirk Surmann [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between batchtools versions 0.9.5 dated 2017-08-18 and 0.9.6 dated 2017-09-06
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/RDSReader.R | 26 ++++++++++++++++++-------- inst/doc/batchtools.Rmd | 4 ++-- inst/doc/batchtools.pdf |binary tests/testthat/test_chunk.R | 14 ++++++++++++++ vignettes/batchtools.Rmd | 4 ++-- 8 files changed, 51 insertions(+), 22 deletions(-)
Title: Import/Export Routines for 'MALDIquant'
Description: Functions for reading (tab, csv, Bruker fid, Ciphergen
XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and
writing (tab, csv, mMass MSD, mzML, imzML) different file
formats of mass spectrometry data into/from 'MALDIquant'
objects.
Author: Sebastian Gibb [aut, cre],
Pietro Franceschi [ctb]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquantForeign versions 0.10 dated 2015-10-31 and 0.11 dated 2017-09-06
DESCRIPTION | 21 ++++----- MD5 | 62 ++++++++++++++-------------- NEWS | 16 +++++++ R/analyze-functions.R | 10 +--- R/export-methods.R | 2 R/exportMsd-methods.R | 2 R/exportMzMl-methods.R | 4 - R/exportTab-methods.R | 8 +-- R/filename-functions.R | 2 R/filename-methods.R | 4 - R/ibd-functions.R | 8 +-- R/import-functions.R | 22 ++++----- R/importImzMl-functions.R | 2 R/importTab-functions.R | 2 R/imzMl-functions.R | 15 +++--- R/package.R | 4 - R/parseMsd.R | 20 ++++----- R/parseMzMl.R | 22 ++++----- R/sanitize-functions.R | 3 - R/testChecksum-functions.R | 2 build/vignette.rds |binary inst/doc/MALDIquantForeign-intro.pdf |binary inst/exampledata/compressed/csv.tar.gz |binary man/MALDIquantForeign-package.Rd | 4 - tests/testthat/test_compression-functions.R | 2 tests/testthat/test_download-functions.R | 1 tests/testthat/test_exportImzMl-methods.R | 25 ++++++++--- tests/testthat/test_exportMsd-methods.R | 24 +++++++--- tests/testthat/test_exportMzMl-methods.R | 17 ++++--- tests/testthat/test_exportTab-methods.R | 17 ++++++- tests/testthat/test_ibd-functions.R | 16 +++---- tests/testthat/test_msg-functions.R | 2 32 files changed, 196 insertions(+), 143 deletions(-)
More information about MALDIquantForeign at CRAN
Permanent link
More information about UdderQuarterInfectionData at CRAN
Permanent link
Title: Fix Data and Create Report Tables from Different Objects
Description: Fixes data errors in numerical, factor and date variables, checks data quality, performs exploratory analysis and creates report tables from models and summaries.
Author: Victoria Fornes Ferrer, David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>
Diff between clickR versions 0.3.27 dated 2017-09-02 and 0.3.29 dated 2017-09-06
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS | 11 +++++++++++ R/check_quality.R | 4 ++++ R/coefplot.R | 13 +++++++++++++ R/descriptive.R | 4 ++++ R/report_model.R | 24 ++++++++++++++---------- man/GK_assoc.Rd | 5 +++++ man/check_quality.Rd | 5 +++++ man/coefplot.Rd | 9 +++++++++ man/plot.reportmodel.Rd | 6 ++++++ man/report.Rd | 5 +++++ 12 files changed, 91 insertions(+), 25 deletions(-)
Title: Graphical VAR for Experience Sampling Data
Description: Estimates within and between time point interactions in experience sampling data, using the Graphical VAR model in combination with LASSO and EBIC.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between graphicalVAR versions 0.2 dated 2017-03-27 and 0.2.1 dated 2017-09-06
graphicalVAR-0.2.1/graphicalVAR/DESCRIPTION | 6 graphicalVAR-0.2.1/graphicalVAR/MD5 | 22 - graphicalVAR-0.2.1/graphicalVAR/NAMESPACE | 3 graphicalVAR-0.2.1/graphicalVAR/NEWS | 5 graphicalVAR-0.2.1/graphicalVAR/R/RcppExports.R | 8 graphicalVAR-0.2.1/graphicalVAR/R/Rothmana.R | 28 - graphicalVAR-0.2.1/graphicalVAR/R/dataPrep.R | 32 + graphicalVAR-0.2.1/graphicalVAR/R/graphicalVAR.R | 433 ++++++++++---------- graphicalVAR-0.2.1/graphicalVAR/R/methods.R | 4 graphicalVAR-0.2.1/graphicalVAR/man/graphicalVAR.Rd | 11 graphicalVAR-0.2.1/graphicalVAR/src/RcppExports.cpp | 21 graphicalVAR-0.2/graphicalVAR/R/AGV.R |only graphicalVAR-0.2/graphicalVAR/src/registration.c |only 13 files changed, 328 insertions(+), 245 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 and Eiko I. Fried
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between bootnet versions 1.0.0 dated 2017-05-04 and 1.0.1 dated 2017-09-06
DESCRIPTION | 6 +-- MD5 | 24 ++++++------- NAMESPACE | 3 + NEWS | 13 ++++++- R/Smetric.R | 1 R/bootnet.R | 2 - R/bootnetResultsMethods.R | 14 ++++++-- R/defaultFunctions.R | 80 ++++++++++++++++++++++++++++++++++++++-------- R/plotMethod.R | 12 ++++++ R/summaryMethod.R | 1 man/bootnet.Rd | 2 - man/estimateNetwork.Rd | 6 +-- man/plotBootnetResult.Rd | 9 ++++- 13 files changed, 134 insertions(+), 39 deletions(-)
Title: Estimation of the Relative Importance of Factors Affecting
Species Distribution Based on Stability Concept
Description: From output files obtained from the software 'ModestR', the relative contribution of factors to explain species distribution is depicted using several plots. A global geographic raster file for each environmental variable may be also obtained with the mean relative contribution, considering all species present in each raster cell, of the factor to explain species distribution. Finally, for each variable it is also possible to compare the frequencies of any variable obtained in the cells where the species is present with the frequencies of the same variable in the cells of the extent.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>
Diff between SPEDInstabR versions 1.4 dated 2017-06-05 and 1.5 dated 2017-09-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- data/adworld.RData |binary inst/CITATION | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-)
Title: Spatial Position Models
Description: Computes spatial position models: Stewart potentials, Reilly
catchment areas, Huff catchment areas.
Author: Timothée Giraud [cre, aut],
Hadrien Commenges [aut],
Joël Boulier [ctb]
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between SpatialPosition versions 1.1.1 dated 2016-06-13 and 1.2.0 dated 2017-09-06
DESCRIPTION | 16 +-- MD5 | 81 +++++++++-------- NAMESPACE | 2 NEWS | 18 +++ R/gridandmat.R | 92 +++++++++++++++----- R/huff.R | 22 +++- R/mcStewart.R |only R/package.R | 9 + R/quickStewart.R | 17 ++- R/rasterToContourPoly.R | 191 ++++++++++++++++++++---------------------- R/reilly.R | 21 +++- R/smoothy.R |only R/stewart.R | 23 +++-- README.md | 1 build/vignette.rds |binary inst/doc/QGISInterface.Rmd |only inst/doc/QGISInterface.html |only inst/doc/SpatialPosition.Rmd | 3 inst/doc/SpatialPosition.html | 98 ++++++++++++--------- inst/doc/StewartExample.R | 14 ++- inst/doc/StewartExample.Rmd | 14 ++- inst/doc/StewartExample.html | 103 +++++++++++++--------- man/CreateDistMatrix.Rd | 24 +++-- man/CreateGrid.Rd | 4 man/SpatialPosition.Rd | 11 +- man/contourStewart.Rd | 1 man/huff.Rd | 20 ++-- man/mcStewart.Rd |only man/plotHuff.Rd | 1 man/plotReilly.Rd | 1 man/plotStewart.Rd | 1 man/quickStewart.Rd | 12 +- man/rasterHuff.Rd | 1 man/rasterReilly.Rd | 1 man/rasterStewart.Rd | 1 man/rasterToContourPoly.Rd | 1 man/reilly.Rd | 17 ++- man/smoothy.Rd |only man/spatMask.Rd | 1 man/spatPts.Rd | 1 man/spatUnits.Rd | 1 man/stewart.Rd | 17 ++- vignettes/QGISInterface.Rmd |only vignettes/SpatialPosition.Rmd | 3 vignettes/StewartExample.Rmd | 14 ++- 45 files changed, 525 insertions(+), 333 deletions(-)
More information about SpatialPosition at CRAN
Permanent link
Title: Matrix Reconstruction from a Few Entries
Description: Matrix reconstruction, also known as matrix completion, is
the task of inferring missing entries of a partially observed matrix.
This package provides a method called OptSpace,
which was proposed by Keshavan, R.H., Oh, S., and Montanari, A. (2009)
<doi:10.1109/ISIT.2009.5205567> for a case under low-rank assumption.
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kyou@nd.edu>
Diff between ROptSpace versions 0.1.0 dated 2017-09-05 and 0.1.1 dated 2017-09-06
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/OptSpace.R | 6 ++++-- 3 files changed, 9 insertions(+), 7 deletions(-)
Title: A Collection of Graphon Estimation Methods
Description: Provides a not-so-comprehensive list of methods for estimating graphon,
a symmetric measurable function, from a single or multiple of observed networks.
For a detailed introduction on graphon and popular estimation techniques,
see the paper by Orbanz, P. and Roy, D.M.(2014) <doi:10.1109/TPAMI.2014.2334607>.
It also contains several auxiliary functions for generating sample networks
using various network models and graphons.
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kyou@nd.edu>
Diff between graphon versions 0.1.0 dated 2017-09-04 and 0.1.1 dated 2017-09-06
DESCRIPTION | 10 ++++++---- MD5 | 46 ++++++++++++++++++++++++---------------------- NAMESPACE | 2 ++ R/cv.SBA.R | 4 ++-- R/est.LG.R | 8 ++++---- R/est.SBA.R | 10 +++++----- R/est.USVT.R | 4 ++-- R/est.completion.R |only R/est.nbdsmooth.R | 4 ++-- R/gmodel.ER.R | 6 +++--- R/gmodel.P.R | 8 ++++---- R/gmodel.block.R | 10 +++++----- R/gmodel.preset.R | 4 ++-- R/graphon-package.R | 4 +++- man/cv.SBA.Rd | 4 ++-- man/est.LG.Rd | 8 ++++---- man/est.SBA.Rd | 10 +++++----- man/est.USVT.Rd | 4 ++-- man/est.completion.Rd |only man/est.nbdsmooth.Rd | 4 ++-- man/gmodel.ER.Rd | 6 +++--- man/gmodel.P.Rd | 8 ++++---- man/gmodel.block.Rd | 10 +++++----- man/gmodel.preset.Rd | 4 ++-- man/graphon.Rd | 3 ++- 25 files changed, 95 insertions(+), 86 deletions(-)
Title: Graph Kernels
Description: A fast C++ implementation for computing various graph kernels including (1) simple kernels between vertex and/or edge label histograms, (2) graphlet kernels, (3) random walk kernels (popular baselines), and (4) the Weisfeiler-Lehman graph kernel (state-of-the-art).
Author: Mahito Sugiyama
Maintainer: Mahito Sugiyama <mahito@nii.ac.jp>
Diff between graphkernels versions 1.2 dated 2017-04-14 and 1.3 dated 2017-09-06
DESCRIPTION | 12 MD5 | 27 - NAMESPACE | 4 R/RcppExports.R | 4 R/graphKernels.R | 45 + data/mutag.RData |binary man/CalculateConnectedGraphletKernel.Rd |only man/CalculateGraphletKernel.Rd |only man/CalculateGraphletKernelCpp.Rd |only man/CalculateKernelCpp.Rd | 2 man/CalculateShortestPathKernel.Rd |only man/GetGraphInfo.Rd | 2 man/graphkernels-package.Rd | 23 man/graphkernels_CalculateGraphletKernelCpp.Rd |only src/RcppExports.cpp | 34 + src/graphKernels.cpp | 615 ++++++++++++++++++++++++- src/graphkernels_init.c | 6 17 files changed, 745 insertions(+), 29 deletions(-)
Title: Identification of the Factors Affecting Species Richness
Description: It identifies the factors significantly related to species richness, and their relative contribution, using multiple regressions and support vector machine models. It uses an output file of 'ModestR' (<http://www.ipez.es/ModestR>) with data of richness of the species and environmental variables in a cell size defined by the user. The residuals of the support vector machine model are shown on a map. Negative residuals may be potential areas with undiscovered and/or unregistered species, or areas with decreased species richness due to the negative effect of anthropogenic factors.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>
Diff between FactorsR versions 1.1 dated 2017-02-17 and 1.2 dated 2017-09-06
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- data/Sharks.RData |binary data/adworld.RData |binary inst/CITATION | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-)
Title: Subnetwork Integration for Multi-Modal Signatures
Description: Algorithms to create prognostic biomarkers using biological networks.
Author: Syed Haider, Michal Grzadkowski, Paul C. Boutros
Maintainer: Syed Haider <Syed.Haider@oicr.on.ca>
Diff between SIMMS versions 1.0.2 dated 2015-09-21 and 1.1.0 dated 2017-09-06
SIMMS-1.0.2/SIMMS/inst/programdata/networkdb/HiC.gm06690 |only SIMMS-1.1.0/SIMMS/DESCRIPTION | 10 SIMMS-1.1.0/SIMMS/MD5 | 15 SIMMS-1.1.0/SIMMS/NEWS | 10 SIMMS-1.1.0/SIMMS/R/create.classifier.multivariate.R | 3 SIMMS-1.1.0/SIMMS/build/vignette.rds |binary SIMMS-1.1.0/SIMMS/inst/doc/Using-SIMMS.html | 647 ++++++++------- SIMMS-1.1.0/SIMMS/man/create.classifier.multivariate.Rd | 7 8 files changed, 411 insertions(+), 281 deletions(-)
Title: Presmoothed Estimation in Survival Analysis
Description: Presmoothed estimators of survival, density, cumulative and non-cumulative hazard functions with right-censored survival data.
Author: Ignacio Lopez de Ullibarri <ilu@udc.es> [aut, cre],
Maria Amalia Jacome <majacome@udc.es> [aut]
Maintainer: Ignacio Lopez de Ullibarri <ilu@udc.es>
Diff between survPresmooth versions 1.1-9 dated 2016-03-11 and 1.1-10 dated 2017-09-06
ChangeLog | 10 ++++++++++ DESCRIPTION | 13 +++++++------ MD5 | 11 ++++++----- NAMESPACE | 2 +- inst/CITATION | 3 +-- man/presmooth.Rd | 2 +- src/init.c |only 7 files changed, 26 insertions(+), 15 deletions(-)
Title: Diagnostic and Prognostic Meta-Analysis
Description: Meta-analysis of diagnostic and prognostic modeling studies. Summarize estimates of diagnostic test accuracy and prediction model performance. Validate, update and combine published prediction models.
Author: Thomas Debray [aut, cre],
Valentijn de Jong [aut]
Maintainer: Thomas Debray <thomas.debray@gmail.com>
Diff between metamisc versions 0.1.5 dated 2017-06-22 and 0.1.6 dated 2017-09-06
DESCRIPTION | 15 ++++++++------- MD5 | 30 +++++++++++++++--------------- R/uvmeta.r | 14 +++++++++----- R/valmeta.r | 15 ++++++++++++--- data/Collins.rda |binary data/DVTipd.rda |binary data/DVTmodels.rda |binary data/Daniels.rda |binary data/EuroSCORE.rda |binary data/Framingham.rda |binary data/Kertai.rda |binary data/Roberts.rda |binary data/Scheidler.rda |binary man/metamisc-package.Rd | 7 ++++--- man/uvmeta.Rd | 5 +++-- man/valmeta.Rd | 2 +- 16 files changed, 52 insertions(+), 36 deletions(-)
Title: Simulation Parameter Analysis R Toolkit ApplicatioN: Spartan
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, first described in our 2013 publication in PLoS Computational Biology, provided code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 added support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions. Version 3.0 offers significant additional functionality that permits the creation of emulations of simulation results, derived using the same sampling techniques in the global sensitivity analysis techniques, and the generation of combinations of these machine learning algorithms to one create one predictive tool, more commonly known as an ensemble model. Version 3.0 also improved the standard of the graphs produced in the original sensitivity analysis techniques, and introduced a polar plot to examine parameter sensitivity.
Author: Kieran Alden [cre, aut],
Mark Read [aut],
Paul Andrews [aut],
Jason Cosgrove [aut],
Mark Coles [aut],
Jon Timmis [aut]
Maintainer: Kieran Alden <kieran.alden@gmail.com>
Diff between spartan versions 2.3 dated 2015-10-19 and 3.0.0 dated 2017-09-06
spartan-2.3/spartan/R/Make_AA_Table_Result.R |only spartan-2.3/spartan/R/aa_getATestResults.R |only spartan-2.3/spartan/R/aa_graphATestsForSampleSize.R |only spartan-2.3/spartan/R/aa_graphSampleSizeSummary.R |only spartan-2.3/spartan/R/aa_sampleSizeSummary.R |only spartan-2.3/spartan/R/aa_summariseReplicateRuns.R |only spartan-2.3/spartan/R/atest.R |only spartan-2.3/spartan/R/efast_cvmethod.R |only spartan-2.3/spartan/R/efast_generate_medians_for_all_parameter_subsets.R |only spartan-2.3/spartan/R/efast_generate_sample.R |only spartan-2.3/spartan/R/efast_generate_sample_netlogo.R |only spartan-2.3/spartan/R/efast_get_overall_medians.R |only spartan-2.3/spartan/R/efast_graph_Results.R |only spartan-2.3/spartan/R/efast_netlogo_get_overall_medians.R |only spartan-2.3/spartan/R/efast_netlogo_run_Analysis.R |only spartan-2.3/spartan/R/efast_parameterdist.R |only spartan-2.3/spartan/R/efast_process_netlogo_result.R |only spartan-2.3/spartan/R/efast_run_Analysis.R |only spartan-2.3/spartan/R/efast_sd.R |only spartan-2.3/spartan/R/efast_setfreq.R |only spartan-2.3/spartan/R/efast_ttest.R |only spartan-2.3/spartan/R/getMediansSubset.R |only spartan-2.3/spartan/R/lhc_calculatePRCCForMultipleTimepoints.R |only spartan-2.3/spartan/R/lhc_constructCoEffDataSet.R |only spartan-2.3/spartan/R/lhc_countSignificantParametersOverTime.R |only spartan-2.3/spartan/R/lhc_generateLHCSummary.R |only spartan-2.3/spartan/R/lhc_generatePRCoEffs.R |only spartan-2.3/spartan/R/lhc_generateTimepointFiles.R |only spartan-2.3/spartan/R/lhc_generate_lhc_sample.R |only spartan-2.3/spartan/R/lhc_generate_lhc_sample_netlogo.R |only spartan-2.3/spartan/R/lhc_generate_netlogo_PRCoEffs.R |only spartan-2.3/spartan/R/lhc_graphMeasuresForParameterChange.R |only spartan-2.3/spartan/R/lhc_graphPRCCForMultipleTimepoints.R |only spartan-2.3/spartan/R/lhc_netlogo_graphMeasuresForParameterChange.R |only spartan-2.3/spartan/R/lhc_plotCoEfficients.R |only spartan-2.3/spartan/R/lhc_process_netlogo_result.R |only spartan-2.3/spartan/R/lhc_process_sample_run_subsets.R |only spartan-2.3/spartan/R/normaliseATest.R |only spartan-2.3/spartan/R/num_decimals.R |only spartan-2.3/spartan/R/oat_countResponsesOfDesiredValue.R |only spartan-2.3/spartan/R/oat_csv_result_file_analysis.R |only spartan-2.3/spartan/R/oat_generate_netlogo_behaviour_space_XML.R |only spartan-2.3/spartan/R/oat_graphATestsForSampleSize.R |only spartan-2.3/spartan/R/oat_graph_Leish_ATestsMultipleTimepoints.R |only spartan-2.3/spartan/R/oat_parameter_sampling.R |only spartan-2.3/spartan/R/oat_plotResultDistribution.R |only spartan-2.3/spartan/R/oat_processParamSubsets.R |only spartan-2.3/spartan/R/oat_process_netlogo_result.R |only spartan-2.3/spartan/R/pcor.mat.R |only spartan-2.3/spartan/R/pcor.rec.R |only spartan-2.3/spartan/R/pcor.test.R |only spartan-2.3/spartan/R/perform_aTest_for_all_sim_measures.R |only spartan-2.3/spartan/R/plotATestsFromTimepointFiles.R |only spartan-2.3/spartan/R/plotPRCCSFromTimepointFiles.R |only spartan-2.3/spartan/R/ploteFASTSiFromTimepointFiles.R |only spartan-2.3/spartan/R/prepare_parameter_value_list.R |only spartan-2.3/spartan/R/subset_results_by_param_value_set.R |only spartan-2.3/spartan/R/table_header_check.R |only spartan-2.3/spartan/data/AA_Example_ATestMaxAndMedians.csv.gz |only spartan-2.3/spartan/data/Curve1_Dummy.csv.gz |only spartan-2.3/spartan/data/Curve1_Results_Summary.csv.gz |only spartan-2.3/spartan/data/Curve1_chemoLowerLinearAdjust.csv.gz |only spartan-2.3/spartan/data/Curve1_chemoThreshold.csv.gz |only spartan-2.3/spartan/data/Curve1_chemoUpperLinearAdjust.csv.gz |only spartan-2.3/spartan/data/Curve1_maxVCAMeffectProbabilityCutoff.csv.gz |only spartan-2.3/spartan/data/Curve1_thresholdBindProbability.csv.gz |only spartan-2.3/spartan/data/Curve1_vcamSlope.csv.gz |only spartan-2.3/spartan/data/EgSet_LHC_corCoeffs.csv.gz |only spartan-2.3/spartan/data/LHC_Parameters_for_Runs.csv.gz |only spartan-2.3/spartan/data/LHC_Summary.csv.gz |only spartan-2.3/spartan/data/OAT_Example_ATests_chemoLowerLinearAdjust.csv.gz |only spartan-2.3/spartan/data/OAT_Medians.csv.gz |only spartan-2.3/spartan/data/OAT_Sampling_chemoThreshold_Values.csv.gz |only spartan-2.3/spartan/data/OAT_Sampling_maxVCAMeffectProbabilityCutoff_Values.csv.gz |only spartan-2.3/spartan/data/eFAST_Analysis.csv.gz |only spartan-2.3/spartan/inst/extdata |only spartan-2.3/spartan/man/Technique1-aleatory_analysis.Rd |only spartan-2.3/spartan/man/Technique2-oat_create_parameter_sample.Rd |only spartan-2.3/spartan/man/Technique2-oat_generate_analysis.Rd |only spartan-2.3/spartan/man/Technique3-lhc_create_parameter_sample.Rd |only spartan-2.3/spartan/man/Technique3-lhc_perform_analysis.Rd |only spartan-2.3/spartan/man/Technique4-efast_create_parameter_sample.Rd |only spartan-2.3/spartan/man/Technique4-efast_generate_analysis_results.Rd |only spartan-2.3/spartan/man/Technique5-spartan_and_netlogo.Rd |only spartan-2.3/spartan/man/Utility-getMediansSubset.Rd |only spartan-2.3/spartan/man/Utility-sampleData.Rd |only spartan-2.3/spartan/man/spartan-internal.Rd |only spartan-3.0.0/spartan/DESCRIPTION | 35 - spartan-3.0.0/spartan/MD5 | 271 ++++++---- spartan-3.0.0/spartan/NAMESPACE | 96 +++ spartan-3.0.0/spartan/R/abc_utilities.R |only spartan-3.0.0/spartan/R/aleatory_analysis.R |only spartan-3.0.0/spartan/R/aleatory_analysis_plotting.R |only spartan-3.0.0/spartan/R/atest_utilities.R |only spartan-3.0.0/spartan/R/datadoc.R |only spartan-3.0.0/spartan/R/efast_analysis.R |only spartan-3.0.0/spartan/R/efast_analysis_netlogo.R |only spartan-3.0.0/spartan/R/efast_plotting.R |only spartan-3.0.0/spartan/R/efast_sampling.R |only spartan-3.0.0/spartan/R/efast_sampling_netlogo.R |only spartan-3.0.0/spartan/R/efast_utilities.R |only spartan-3.0.0/spartan/R/emulation_evolution.R |only spartan-3.0.0/spartan/R/emulation_generation.R |only spartan-3.0.0/spartan/R/emulation_plotting.R |only spartan-3.0.0/spartan/R/emulation_sensitivity_analysis.R |only spartan-3.0.0/spartan/R/emulation_utilities.R |only spartan-3.0.0/spartan/R/ensemble_generation.R |only spartan-3.0.0/spartan/R/ensemble_utilities.R |only spartan-3.0.0/spartan/R/lhc_analysis.R |only spartan-3.0.0/spartan/R/lhc_analysis_netlogo.R |only spartan-3.0.0/spartan/R/lhc_plotting.R |only spartan-3.0.0/spartan/R/lhc_prcc_utilities.R |only spartan-3.0.0/spartan/R/lhc_preprocess.R |only spartan-3.0.0/spartan/R/lhc_sampling.R |only spartan-3.0.0/spartan/R/lhc_sampling_netlogo.R |only spartan-3.0.0/spartan/R/neural_network_utilities.R |only spartan-3.0.0/spartan/R/robustness_analysis.R |only spartan-3.0.0/spartan/R/robustness_analysis_netlogo.R |only spartan-3.0.0/spartan/R/robustness_plotting.R |only spartan-3.0.0/spartan/R/robustness_sampling.R |only spartan-3.0.0/spartan/R/robustness_utilities.R |only spartan-3.0.0/spartan/R/spartan_utilities.R |only spartan-3.0.0/spartan/build |only spartan-3.0.0/spartan/data/emulated_lhc_values.rda |only spartan-3.0.0/spartan/data/sim_data_for_emulation.rda |only spartan-3.0.0/spartan/data/tutorial_consistency_set.rda |only spartan-3.0.0/spartan/inst/doc |only spartan-3.0.0/spartan/man/aa_getATestResults.Rd |only spartan-3.0.0/spartan/man/aa_graphATestsForSampleSize.Rd |only spartan-3.0.0/spartan/man/aa_graphSampleSizeSummary.Rd |only spartan-3.0.0/spartan/man/aa_sampleSizeSummary.Rd |only spartan-3.0.0/spartan/man/aa_summariseReplicateRuns.Rd |only spartan-3.0.0/spartan/man/analysenetwork_structures.Rd |only spartan-3.0.0/spartan/man/atest.Rd |only spartan-3.0.0/spartan/man/build_performance_statistics.Rd |only spartan-3.0.0/spartan/man/calculate_fold_MSE.Rd |only spartan-3.0.0/spartan/man/calculate_weights_for_ensemble_model.Rd |only spartan-3.0.0/spartan/man/check_acceptable_model_type.Rd |only spartan-3.0.0/spartan/man/check_file_extension.Rd |only spartan-3.0.0/spartan/man/createAndEvaluateFolds.Rd |only spartan-3.0.0/spartan/man/createTrainingFold.Rd |only spartan-3.0.0/spartan/man/create_abc_settings_object.Rd |only spartan-3.0.0/spartan/man/create_ensemble.Rd |only spartan-3.0.0/spartan/man/create_neural_network.Rd |only spartan-3.0.0/spartan/man/createtest_fold.Rd |only spartan-3.0.0/spartan/man/denormalise_dataset.Rd |only spartan-3.0.0/spartan/man/determine_optimal_neural_network_structure.Rd |only spartan-3.0.0/spartan/man/efast_cvmethod.Rd |only spartan-3.0.0/spartan/man/efast_generate_medians_for_all_parameter_subsets.Rd |only spartan-3.0.0/spartan/man/efast_generate_sample.Rd |only spartan-3.0.0/spartan/man/efast_generate_sample_netlogo.Rd |only spartan-3.0.0/spartan/man/efast_get_overall_medians.Rd |only spartan-3.0.0/spartan/man/efast_graph_Results.Rd |only spartan-3.0.0/spartan/man/efast_netlogo_get_overall_medians.Rd |only spartan-3.0.0/spartan/man/efast_netlogo_run_Analysis.Rd |only spartan-3.0.0/spartan/man/efast_parameterdist.Rd |only spartan-3.0.0/spartan/man/efast_process_netlogo_result.Rd |only spartan-3.0.0/spartan/man/efast_run_Analysis.Rd |only spartan-3.0.0/spartan/man/efast_sd.Rd |only spartan-3.0.0/spartan/man/efast_setfreq.Rd |only spartan-3.0.0/spartan/man/efast_ttest.Rd |only spartan-3.0.0/spartan/man/emulate_efast_sampled_parameters.Rd |only spartan-3.0.0/spartan/man/emulate_lhc_sampled_parameters.Rd |only spartan-3.0.0/spartan/man/emulated_lhc_values.Rd |only spartan-3.0.0/spartan/man/emulation_algorithm_settings.Rd |only spartan-3.0.0/spartan/man/emulator_parameter_evolution.Rd |only spartan-3.0.0/spartan/man/emulator_predictions.Rd |only spartan-3.0.0/spartan/man/ensemble_abc_wrapper.Rd |only spartan-3.0.0/spartan/man/extract_predictions_from_result_list.Rd |only spartan-3.0.0/spartan/man/generate_emulator_model.Rd |only spartan-3.0.0/spartan/man/generate_emulators_and_ensemble.Rd |only spartan-3.0.0/spartan/man/generate_ensemble_from_existing_emulations.Rd |only spartan-3.0.0/spartan/man/generate_ensemble_training_set.Rd |only spartan-3.0.0/spartan/man/generate_model_formula.Rd |only spartan-3.0.0/spartan/man/generate_predictions_from_emulator.Rd |only spartan-3.0.0/spartan/man/generate_requested_emulations.Rd |only spartan-3.0.0/spartan/man/getMediansSubset.Rd |only spartan-3.0.0/spartan/man/graph_Posteriors_All_Parameters.Rd |only spartan-3.0.0/spartan/man/join_strings.Rd |only spartan-3.0.0/spartan/man/join_strings_nospace.Rd |only spartan-3.0.0/spartan/man/join_strings_space.Rd |only spartan-3.0.0/spartan/man/kfoldCrossValidation.Rd |only spartan-3.0.0/spartan/man/lhc_calculatePRCCForMultipleTimepoints.Rd |only spartan-3.0.0/spartan/man/lhc_constructcoeff_dataset.Rd |only spartan-3.0.0/spartan/man/lhc_countSignificantParametersOverTime.Rd |only spartan-3.0.0/spartan/man/lhc_generateLHCSummary.Rd |only spartan-3.0.0/spartan/man/lhc_generatePRCoEffs.Rd |only spartan-3.0.0/spartan/man/lhc_generateTimepointFiles.Rd |only spartan-3.0.0/spartan/man/lhc_generate_lhc_sample.Rd |only spartan-3.0.0/spartan/man/lhc_generate_lhc_sample_netlogo.Rd |only spartan-3.0.0/spartan/man/lhc_generate_netlogo_PRCoEffs.Rd |only spartan-3.0.0/spartan/man/lhc_graphMeasuresForParameterChange.Rd |only spartan-3.0.0/spartan/man/lhc_graphPRCCForMultipleTimepoints.Rd |only spartan-3.0.0/spartan/man/lhc_netlogo_graphMeasuresForParameterChange.Rd |only spartan-3.0.0/spartan/man/lhc_plotCoEfficients.Rd |only spartan-3.0.0/spartan/man/lhc_polarplot.Rd |only spartan-3.0.0/spartan/man/lhc_process_netlogo_result.Rd |only spartan-3.0.0/spartan/man/lhc_process_sample_run_subsets.Rd |only spartan-3.0.0/spartan/man/make_extension.Rd |only spartan-3.0.0/spartan/man/make_filename.Rd |only spartan-3.0.0/spartan/man/make_path.Rd |only spartan-3.0.0/spartan/man/meanSquaredError.Rd |only spartan-3.0.0/spartan/man/normaliseATest.Rd |only spartan-3.0.0/spartan/man/normalise_dataset.Rd |only spartan-3.0.0/spartan/man/nsga2_set_user_params.Rd |only spartan-3.0.0/spartan/man/num.decimals.Rd |only spartan-3.0.0/spartan/man/oat_countResponsesOfDesiredValue.Rd |only spartan-3.0.0/spartan/man/oat_csv_result_file_analysis.Rd |only spartan-3.0.0/spartan/man/oat_generate_netlogo_behaviour_space_XML.Rd |only spartan-3.0.0/spartan/man/oat_graphATestsForSampleSize.Rd |only spartan-3.0.0/spartan/man/oat_parameter_sampling.Rd |only spartan-3.0.0/spartan/man/oat_plotResultDistribution.Rd |only spartan-3.0.0/spartan/man/oat_processParamSubsets.Rd |only spartan-3.0.0/spartan/man/oat_process_netlogo_result.Rd |only spartan-3.0.0/spartan/man/partition_dataset.Rd |only spartan-3.0.0/spartan/man/pcor.mat.Rd |only spartan-3.0.0/spartan/man/pcor.rec.Rd |only spartan-3.0.0/spartan/man/pcor.test.Rd |only spartan-3.0.0/spartan/man/perform_aTest_for_all_sim_measures.Rd |only spartan-3.0.0/spartan/man/plotATestsFromTimepointFiles.Rd |only spartan-3.0.0/spartan/man/plotPRCCSFromTimepointFiles.Rd |only spartan-3.0.0/spartan/man/plot_compare_sim_observed_to_model_prediction.Rd |only spartan-3.0.0/spartan/man/ploteFASTSiFromTimepointFiles.Rd |only spartan-3.0.0/spartan/man/prepare_parameter_value_list.Rd |only spartan-3.0.0/spartan/man/produce_accuracy_plots_all_measures.Rd |only spartan-3.0.0/spartan/man/produce_accuracy_plots_single_measure.Rd |only spartan-3.0.0/spartan/man/rSquared.Rd |only spartan-3.0.0/spartan/man/screen_nsga2_parameters.Rd |only spartan-3.0.0/spartan/man/selectSuitableStructure.Rd |only spartan-3.0.0/spartan/man/set.nsga_sensitivity_params.Rd |only spartan-3.0.0/spartan/man/sim_data_for_emulation.Rd |only spartan-3.0.0/spartan/man/tutorial_consistency_set.Rd |only spartan-3.0.0/spartan/man/updateErrorForStructure.Rd |only spartan-3.0.0/spartan/man/use_ensemble_to_generate_predictions.Rd |only spartan-3.0.0/spartan/man/visualise_data_distribution.Rd |only spartan-3.0.0/spartan/man/weight_emulator_predictions_by_ensemble.Rd |only spartan-3.0.0/spartan/vignettes |only 237 files changed, 281 insertions(+), 121 deletions(-)
Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill
Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>
Diff between BIGDAWG versions 1.14.2 dated 2017-07-19 and 1.16 dated 2017-09-06
BIGDAWG-1.14.2/BIGDAWG/man/CheckLociName.Rd |only BIGDAWG-1.16/BIGDAWG/DESCRIPTION | 8 BIGDAWG-1.16/BIGDAWG/MD5 | 42 ++-- BIGDAWG-1.16/BIGDAWG/NEWS | 22 ++ BIGDAWG-1.16/BIGDAWG/R/BIGDAWG.R | 239 ++++++++++++++-------------- BIGDAWG-1.16/BIGDAWG/R/DRB_Parser.R |only BIGDAWG-1.16/BIGDAWG/R/ErrLog.R |only BIGDAWG-1.16/BIGDAWG/R/check_functions.R | 79 +++++++-- BIGDAWG-1.16/BIGDAWG/R/general_functions.R | 214 ------------------------- BIGDAWG-1.16/BIGDAWG/R/sysdata.rda |binary BIGDAWG-1.16/BIGDAWG/inst/doc/BIGDAWG.Rmd | 20 +- BIGDAWG-1.16/BIGDAWG/inst/doc/BIGDAWG.html | 21 +- BIGDAWG-1.16/BIGDAWG/man/BIGDAWG.Rd | 2 BIGDAWG-1.16/BIGDAWG/man/Check.Cores.Rd |only BIGDAWG-1.16/BIGDAWG/man/Check.Params.Rd |only BIGDAWG-1.16/BIGDAWG/man/CheckAlleles.Rd | 2 BIGDAWG-1.16/BIGDAWG/man/CheckHLA.Rd | 2 BIGDAWG-1.16/BIGDAWG/man/CheckLoci.Rd | 4 BIGDAWG-1.16/BIGDAWG/man/DRB345.flag.Rd | 2 BIGDAWG-1.16/BIGDAWG/man/DRB345.parser.Rd | 2 BIGDAWG-1.16/BIGDAWG/man/DRB345.zygosity.Rd | 2 BIGDAWG-1.16/BIGDAWG/man/Err.Log.Rd | 2 BIGDAWG-1.16/BIGDAWG/man/FixAlleleName.Rd |only BIGDAWG-1.16/BIGDAWG/man/PreCheck.Rd | 2 BIGDAWG-1.16/BIGDAWG/vignettes/BIGDAWG.Rmd | 20 +- 25 files changed, 287 insertions(+), 398 deletions(-)