Title: Manipulate, Validate and Resolve 'IP' Addresses
Description: A toolkit for manipulating, validating and testing 'IP' addresses and
ranges, along with datasets relating to 'IP' addresses. Tools are also provided
to map 'IPv4' blocks to country codes. While it primarily has support for the 'IPv4'
address space, more extensive 'IPv6' support is intended.
Author: Bob Rudis <bob@rud.is> [aut, cre],
Oliver Keyes <ironholds@gmail.com> [aut],
Tim Smith [ctb]
Maintainer: Bob Rudis <bob@rud.is>
Diff between iptools versions 0.4.0 dated 2016-04-04 and 0.6.0 dated 2018-09-24
iptools-0.4.0/iptools/R/iptools.R |only iptools-0.4.0/iptools/inst/js |only iptools-0.6.0/iptools/DESCRIPTION | 20 iptools-0.6.0/iptools/MD5 | 92 +- iptools-0.6.0/iptools/NAMESPACE | 14 iptools-0.6.0/iptools/R/RcppExports.R | 129 +++ iptools-0.6.0/iptools/R/aaa.r |only iptools-0.6.0/iptools/R/cidr.r |only iptools-0.6.0/iptools/R/country_ranges.R | 38 - iptools-0.6.0/iptools/R/iptools-package.R |only iptools-0.6.0/iptools/R/zzz.R | 1 iptools-0.6.0/iptools/build/vignette.rds |binary iptools-0.6.0/iptools/inst/doc/introduction_to_iptools.html | 362 ++++++++--- iptools-0.6.0/iptools/inst/doc/iptools_datasets.html | 340 ++++++++-- iptools-0.6.0/iptools/man/asn_table_to_trie.Rd |only iptools-0.6.0/iptools/man/cached_country_cidrs.Rd | 1 iptools-0.6.0/iptools/man/country_ranges.Rd | 1 iptools-0.6.0/iptools/man/expand_ipv6.Rd |only iptools-0.6.0/iptools/man/flush_country_cidrs.Rd | 1 iptools-0.6.0/iptools/man/get_all_country_ranges.Rd | 3 iptools-0.6.0/iptools/man/hilbert_encode.Rd |only iptools-0.6.0/iptools/man/host_count.Rd |only iptools-0.6.0/iptools/man/hostname_to_ip.Rd | 1 iptools-0.6.0/iptools/man/iana_assignments.Rd | 1 iptools-0.6.0/iptools/man/iana_ports.Rd | 1 iptools-0.6.0/iptools/man/iana_special_assignments.Rd | 1 iptools-0.6.0/iptools/man/ip_classify.Rd | 5 iptools-0.6.0/iptools/man/ip_in_any.Rd |only iptools-0.6.0/iptools/man/ip_in_range.Rd | 1 iptools-0.6.0/iptools/man/ip_numeric.Rd | 1 iptools-0.6.0/iptools/man/ip_numeric_to_binary_string.Rd |only iptools-0.6.0/iptools/man/ip_random.Rd | 1 iptools-0.6.0/iptools/man/ip_to_asn.Rd |only iptools-0.6.0/iptools/man/ip_to_binary_string.Rd |only iptools-0.6.0/iptools/man/ip_to_hostname.Rd | 1 iptools-0.6.0/iptools/man/ips_in_cidrs.Rd |only iptools-0.6.0/iptools/man/iptools.Rd | 3 iptools-0.6.0/iptools/man/iptools_refresh.Rd | 3 iptools-0.6.0/iptools/man/is_checks.Rd | 8 iptools-0.6.0/iptools/man/range_boundaries.Rd | 1 iptools-0.6.0/iptools/man/range_boundaries_to_cidr.Rd |only iptools-0.6.0/iptools/man/range_generate.Rd | 1 iptools-0.6.0/iptools/man/v6_scope.Rd |only iptools-0.6.0/iptools/man/validate_range.Rd | 1 iptools-0.6.0/iptools/man/xff_extract.Rd | 1 iptools-0.6.0/iptools/src/Makevars | 2 iptools-0.6.0/iptools/src/Makevars.win | 2 iptools-0.6.0/iptools/src/RcppExports.cpp | 216 ++++-- iptools-0.6.0/iptools/src/asio_bindings.cpp | 172 ++++- iptools-0.6.0/iptools/src/asio_bindings.h | 37 - iptools-0.6.0/iptools/src/hilbert.cpp |only iptools-0.6.0/iptools/src/iptools.cpp | 186 +++++ iptools-0.6.0/iptools/tests/testthat/test_ip_in_range.R | 4 iptools-0.6.0/iptools/tests/testthat/test_is.R | 11 iptools-0.6.0/iptools/tests/testthat/test_range_validation.R | 4 55 files changed, 1312 insertions(+), 355 deletions(-)
More information about behaviorchange at CRAN
Permanent link
Title: Flexible Cluster Algorithms
Description: The main function kcca implements a general framework for
k-centroids cluster analysis supporting arbitrary distance measures
and centroid computation. Further cluster methods include hard
competitive learning, neural gas, and QT clustering. There are
numerous visualization methods for cluster results (neighborhood
graphs, convex cluster hulls, barcharts of centroids, ...), and
bootstrap methods for the analysis of cluster stability.
Author: Friedrich Leisch [aut, cre] (<https://orcid.org/0000-0001-7278-1983>),
Evgenia Dimitriadou [ctb],
Bettina Gruen [aut] (<https://orcid.org/0000-0001-7265-4773>)
Maintainer: Friedrich Leisch <Friedrich.Leisch@R-project.org>
Diff between flexclust versions 1.3-5 dated 2018-02-14 and 1.4-0 dated 2018-09-24
flexclust-1.3-5/flexclust/tests/grouping.R |only flexclust-1.4-0/flexclust/DESCRIPTION | 47 ++-- flexclust-1.4-0/flexclust/MD5 | 129 +++++++------ flexclust-1.4-0/flexclust/NAMESPACE | 31 ++- flexclust-1.4-0/flexclust/NEWS | 29 +++ flexclust-1.4-0/flexclust/R/AAA-classes.R | 27 ++ flexclust-1.4-0/flexclust/R/barplot.R | 153 ++++++++++++---- flexclust-1.4-0/flexclust/R/bclust.R |only flexclust-1.4-0/flexclust/R/bootstrap.R | 71 ++++++- flexclust-1.4-0/flexclust/R/boxplot.R | 64 ++++-- flexclust-1.4-0/flexclust/R/bundestag.R | 2 flexclust-1.4-0/flexclust/R/cclust.R | 16 - flexclust-1.4-0/flexclust/R/conversion.R | 28 ++ flexclust-1.4-0/flexclust/R/distances.R | 6 flexclust-1.4-0/flexclust/R/family.R | 2 flexclust-1.4-0/flexclust/R/grouping.R | 3 flexclust-1.4-0/flexclust/R/histogram.R |only flexclust-1.4-0/flexclust/R/info.R | 2 flexclust-1.4-0/flexclust/R/kcca.R | 2 flexclust-1.4-0/flexclust/R/plot.R | 7 flexclust-1.4-0/flexclust/R/predict.R | 2 flexclust-1.4-0/flexclust/R/pricefeat.R | 7 flexclust-1.4-0/flexclust/R/qtclust.R | 2 flexclust-1.4-0/flexclust/R/randIndex.R | 2 flexclust-1.4-0/flexclust/R/relabel.R |only flexclust-1.4-0/flexclust/R/resample.R |only flexclust-1.4-0/flexclust/R/shadow.R | 10 - flexclust-1.4-0/flexclust/R/stepflexclust.R | 14 - flexclust-1.4-0/flexclust/R/stripes.R | 3 flexclust-1.4-0/flexclust/R/tour.R | 2 flexclust-1.4-0/flexclust/R/utils.R | 4 flexclust-1.4-0/flexclust/data/vacmot.RData |only flexclust-1.4-0/flexclust/inst/CITATION | 22 ++ flexclust-1.4-0/flexclust/man/achieve.Rd | 10 - flexclust-1.4-0/flexclust/man/auto.Rd | 102 +++++----- flexclust-1.4-0/flexclust/man/barplot-methods.Rd | 24 +- flexclust-1.4-0/flexclust/man/bclust.Rd |only flexclust-1.4-0/flexclust/man/birth.Rd | 6 flexclust-1.4-0/flexclust/man/bootFlexclust.Rd | 5 flexclust-1.4-0/flexclust/man/bundestag.Rd | 32 +-- flexclust-1.4-0/flexclust/man/bwplot-methods.Rd | 12 + flexclust-1.4-0/flexclust/man/cclust.Rd | 20 +- flexclust-1.4-0/flexclust/man/clusterSim.Rd | 6 flexclust-1.4-0/flexclust/man/conversion.Rd | 36 ++- flexclust-1.4-0/flexclust/man/dentitio.Rd | 18 - flexclust-1.4-0/flexclust/man/dist2.Rd | 8 flexclust-1.4-0/flexclust/man/flexclustControl-class.Rd | 18 - flexclust-1.4-0/flexclust/man/flxColors.Rd | 10 - flexclust-1.4-0/flexclust/man/histogram-methods.Rd |only flexclust-1.4-0/flexclust/man/info.Rd | 20 +- flexclust-1.4-0/flexclust/man/kcca.Rd | 12 - flexclust-1.4-0/flexclust/man/milk.Rd | 12 - flexclust-1.4-0/flexclust/man/nutrient.Rd | 12 - flexclust-1.4-0/flexclust/man/pairs.Rd | 4 flexclust-1.4-0/flexclust/man/parameters.Rd | 6 flexclust-1.4-0/flexclust/man/plot-methods.Rd | 6 flexclust-1.4-0/flexclust/man/priceFeature.Rd | 9 flexclust-1.4-0/flexclust/man/propBarchart.Rd | 15 + flexclust-1.4-0/flexclust/man/qtclust.Rd | 6 flexclust-1.4-0/flexclust/man/relabel.Rd |only flexclust-1.4-0/flexclust/man/shadow.Rd | 10 - flexclust-1.4-0/flexclust/man/shadowStars.Rd | 24 +- flexclust-1.4-0/flexclust/man/slsaplot.Rd |only flexclust-1.4-0/flexclust/man/slswFlexclust.Rd |only flexclust-1.4-0/flexclust/man/stepFlexclust.Rd | 13 - flexclust-1.4-0/flexclust/man/stripes.Rd | 27 +- flexclust-1.4-0/flexclust/man/vacmot.Rd |only flexclust-1.4-0/flexclust/man/volunteers.Rd | 18 + flexclust-1.4-0/flexclust/src/cclust.c | 2 flexclust-1.4-0/flexclust/src/flexclust.h |only flexclust-1.4-0/flexclust/src/index.c | 1 flexclust-1.4-0/flexclust/src/init.c | 32 +-- 72 files changed, 775 insertions(+), 448 deletions(-)
Title: Spectral Decomposition of Connectedness Measures
Description: Accompanies a paper (Barunik, Krehlik (2018) <doi:10.1093/jjfinec/nby001>) dedicated to spectral decomposition of connectedness measures and their interpretation. We implement all the developed estimators as well as the historical counterparts. For more information, see the help or GitHub page (<https://github.com/tomaskrehlik/frequencyConnectedness>) for relevant information.
Author: Tomas Krehlik [aut, cre]
Maintainer: Tomas Krehlik <tomas.krehlik@gmail.com>
Diff between frequencyConnectedness versions 0.2.0 dated 2018-01-03 and 0.2.1 dated 2018-09-24
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NEWS | 4 +++- 3 files changed, 10 insertions(+), 8 deletions(-)
More information about frequencyConnectedness at CRAN
Permanent link
Title: Acquisition and Processing of NASA Soil Moisture Active-Passive
(SMAP) Data
Description: Facilitates programmatic access to NASA Soil Moisture Active
Passive (SMAP) data with R. It includes functions to search for, acquire,
and extract SMAP data.
Author: Maxwell Joseph [aut, cre],
Matthew Oakley [aut],
Zachary Schira [aut]
Maintainer: Maxwell Joseph <maxwell.b.joseph@colorado.edu>
Diff between smapr versions 0.1.2 dated 2018-06-19 and 0.2.0 dated 2018-09-24
smapr-0.1.2/smapr/inst/img |only smapr-0.2.0/smapr/DESCRIPTION | 13 smapr-0.2.0/smapr/MD5 | 43 smapr-0.2.0/smapr/NAMESPACE | 1 smapr-0.2.0/smapr/NEWS.md | 7 smapr-0.2.0/smapr/R/download_smap.R | 22 smapr-0.2.0/smapr/R/extract_smap.R | 12 smapr-0.2.0/smapr/R/find_smap.R | 8 smapr-0.2.0/smapr/R/set_smap_credentials.R |only smapr-0.2.0/smapr/R/zzz.R | 78 - smapr-0.2.0/smapr/README.md | 61 smapr-0.2.0/smapr/build/vignette.rds |binary smapr-0.2.0/smapr/inst/doc/smapr-intro.R | 52 smapr-0.2.0/smapr/inst/doc/smapr-intro.Rmd | 159 +- smapr-0.2.0/smapr/inst/doc/smapr-intro.html | 815 ++++++++--- smapr-0.2.0/smapr/man/download_smap.Rd | 11 smapr-0.2.0/smapr/man/figures |only smapr-0.2.0/smapr/man/find_smap.Rd | 8 smapr-0.2.0/smapr/man/set_smap_credentials.Rd |only smapr-0.2.0/smapr/tests/testthat/test-download_smap.R | 14 smapr-0.2.0/smapr/tests/testthat/test-extract_smap.R | 44 smapr-0.2.0/smapr/tests/testthat/test-find_smap.R | 8 smapr-0.2.0/smapr/tests/testthat/test-set_smap_credentials.R |only smapr-0.2.0/smapr/tests/testthat/test-zzz.R | 40 smapr-0.2.0/smapr/vignettes/smapr-intro.Rmd | 159 +- 25 files changed, 1180 insertions(+), 375 deletions(-)
Title: Utilities for Working with Air Quality Monitoring Data
Description: Utilities for working with air quality monitoring data
with a focus on small particulates (PM2.5) generated by wildfire
smoke. Functions are provided for downloading available data from
the United States 'EPA' <https://www.epa.gov/outdoor-air-quality-data> and
it's 'AirNow' air quality site <https://www.airnow.gov>.
Additional sources of PM2.5 data made accessible by the package include:
'AIRSIS' (password protected) <https://www.oceaneering.com/data-management/>
and 'WRCC' <https://wrcc.dri.edu/cgi-bin/smoke.pl>.
Data compilations are provided by 'PWFSL'
<https://www.fs.fed.us/pnw/pwfsl/>.
Author: Jonathan Callahan [aut, cre],
Rohan Aras [aut],
Zach Dingels [aut],
Jon Hagg [aut],
Jimin Kim [aut],
Helen Miller [aut],
Spencer Pease [aut],
Rex Thompson [aut],
Alice Yang [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between PWFSLSmoke versions 1.0.20 dated 2018-05-08 and 1.0.33 dated 2018-09-24
PWFSLSmoke-1.0.20/PWFSLSmoke/R/addGoogleMetadata.R |only PWFSLSmoke-1.0.20/PWFSLSmoke/man/addGoogleMetadata.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/DESCRIPTION | 14 PWFSLSmoke-1.0.33/PWFSLSmoke/MD5 | 176 +++++----- PWFSLSmoke-1.0.33/PWFSLSmoke/NAMESPACE | 15 PWFSLSmoke-1.0.33/PWFSLSmoke/R/PWFSLSmoke.R | 85 ++++ PWFSLSmoke-1.0.33/PWFSLSmoke/R/addEsriAddress.R |only PWFSLSmoke-1.0.33/PWFSLSmoke/R/addGoogleAddress.R | 44 +- PWFSLSmoke-1.0.33/PWFSLSmoke/R/addGoogleElevation.R | 17 PWFSLSmoke-1.0.33/PWFSLSmoke/R/airsis_EBAMQualityControl.R | 2 PWFSLSmoke-1.0.33/PWFSLSmoke/R/airsis_createMetaDataframe.R | 29 + PWFSLSmoke-1.0.33/PWFSLSmoke/R/airsis_createMonitorObject.R | 11 PWFSLSmoke-1.0.33/PWFSLSmoke/R/airsis_identifyMonitorType.R | 25 + PWFSLSmoke-1.0.33/PWFSLSmoke/R/airsis_parseData.R | 35 + PWFSLSmoke-1.0.33/PWFSLSmoke/R/aqiColors.R |only PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitorEsriMap.R | 5 PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitorGoogleMap.R | 7 PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitorMap.R | 5 PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitorMap_performance.R | 1 PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitorPlot_dailyBarplot.R | 3 PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitorPlot_hourlyBarplot.R | 5 PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitor_currentData.R |only PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitor_dailyStatistic.R | 2 PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitor_dailyStatisticList.R |only PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitor_isTidy.R |only PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitor_join.R | 39 +- PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitor_nowcast.R | 25 + PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitor_print.R |only PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitor_subsetBy.R | 7 PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitor_subsetByDistance.R | 8 PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitor_toTidy.R |only PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitor_writeCSV.R |only PWFSLSmoke-1.0.33/PWFSLSmoke/R/monitor_writeCurrentGeoJSON.R |only PWFSLSmoke-1.0.33/PWFSLSmoke/R/wrcc_createMetaDataframe.R | 33 + PWFSLSmoke-1.0.33/PWFSLSmoke/R/wrcc_createMonitorObject.R | 11 PWFSLSmoke-1.0.33/PWFSLSmoke/README.md | 2 PWFSLSmoke-1.0.33/PWFSLSmoke/build/vignette.rds |binary PWFSLSmoke-1.0.33/PWFSLSmoke/data/Carmel_Valley.RData |binary PWFSLSmoke-1.0.33/PWFSLSmoke/data/Northwest_Megafires.RData |binary PWFSLSmoke-1.0.33/PWFSLSmoke/data/WRCC.RData |binary PWFSLSmoke-1.0.33/PWFSLSmoke/inst/doc/Maps_and_Timeseries_Plots.R | 4 PWFSLSmoke-1.0.33/PWFSLSmoke/inst/doc/Maps_and_Timeseries_Plots.Rmd | 6 PWFSLSmoke-1.0.33/PWFSLSmoke/inst/doc/Maps_and_Timeseries_Plots.html | 8 PWFSLSmoke-1.0.33/PWFSLSmoke/inst/doc/NowCast.Rmd | 23 - PWFSLSmoke-1.0.33/PWFSLSmoke/inst/doc/NowCast.html | 50 +- PWFSLSmoke-1.0.33/PWFSLSmoke/man/addAQILegend.Rd | 3 PWFSLSmoke-1.0.33/PWFSLSmoke/man/addEsriAddress.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/addGoogleAddress.Rd | 2 PWFSLSmoke-1.0.33/PWFSLSmoke/man/addIcon.Rd | 3 PWFSLSmoke-1.0.33/PWFSLSmoke/man/addMarker.Rd | 4 PWFSLSmoke-1.0.33/PWFSLSmoke/man/addShadedBackground.Rd | 4 PWFSLSmoke-1.0.33/PWFSLSmoke/man/airnow_createDataDataframes.Rd | 3 PWFSLSmoke-1.0.33/PWFSLSmoke/man/airnow_downloadHourlyData.Rd | 3 PWFSLSmoke-1.0.33/PWFSLSmoke/man/airnow_downloadSites.Rd | 3 PWFSLSmoke-1.0.33/PWFSLSmoke/man/airsis_BAM1020QualityControl.Rd | 4 PWFSLSmoke-1.0.33/PWFSLSmoke/man/airsis_EBAMQualityControl.Rd | 4 PWFSLSmoke-1.0.33/PWFSLSmoke/man/airsis_ESAMQualityControl.Rd | 6 PWFSLSmoke-1.0.33/PWFSLSmoke/man/airsis_availableUnits.Rd | 6 PWFSLSmoke-1.0.33/PWFSLSmoke/man/airsis_createMetaDataframe.Rd | 6 PWFSLSmoke-1.0.33/PWFSLSmoke/man/airsis_createMonitorObject.Rd | 17 PWFSLSmoke-1.0.33/PWFSLSmoke/man/airsis_createRawDataframe.Rd | 7 PWFSLSmoke-1.0.33/PWFSLSmoke/man/airsis_downloadData.Rd | 6 PWFSLSmoke-1.0.33/PWFSLSmoke/man/aqiColors.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/epa_downloadData.Rd | 3 PWFSLSmoke-1.0.33/PWFSLSmoke/man/esriMap_getMap.Rd | 5 PWFSLSmoke-1.0.33/PWFSLSmoke/man/esriToken.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/getEsriToken.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/getGoogleApiKey.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/googleApiKey.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitorDygraph.Rd | 5 PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitorEsriMap.Rd | 4 PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitorGoogleMap.Rd | 8 PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitorLeaflet.Rd | 7 PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitorMap.Rd | 3 PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitorPlot_hourlyBarplot.Rd | 9 PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitorPlot_timeOfDaySpaghetti.Rd | 5 PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitor_currentData.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitor_dailyStatistic.Rd | 4 PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitor_dailyStatisticList.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitor_isTidy.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitor_join.Rd | 3 PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitor_nowcast.Rd | 8 PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitor_performance.Rd | 4 PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitor_print.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitor_toTidy.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitor_writeCSV.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/monitor_writeCurrentGeoJSON.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/rawPlot_timeseries.Rd | 9 PWFSLSmoke-1.0.33/PWFSLSmoke/man/raw_getHighlightDates.Rd | 4 PWFSLSmoke-1.0.33/PWFSLSmoke/man/setEsriToken.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/setGoogleApiKey.Rd |only PWFSLSmoke-1.0.33/PWFSLSmoke/man/skill_ROCPlot.Rd | 4 PWFSLSmoke-1.0.33/PWFSLSmoke/man/wrcc_EBAMQualityControl.Rd | 4 PWFSLSmoke-1.0.33/PWFSLSmoke/man/wrcc_ESAMQualityControl.Rd | 6 PWFSLSmoke-1.0.33/PWFSLSmoke/man/wrcc_createMetaDataframe.Rd | 9 PWFSLSmoke-1.0.33/PWFSLSmoke/man/wrcc_createMonitorObject.Rd | 18 - PWFSLSmoke-1.0.33/PWFSLSmoke/man/wrcc_createRawDataframe.Rd | 10 PWFSLSmoke-1.0.33/PWFSLSmoke/man/wrcc_downloadData.Rd | 7 PWFSLSmoke-1.0.33/PWFSLSmoke/man/wrcc_loadDaily.Rd | 3 PWFSLSmoke-1.0.33/PWFSLSmoke/man/wrcc_loadLatest.Rd | 3 PWFSLSmoke-1.0.33/PWFSLSmoke/vignettes/Maps_and_Timeseries_Plots.Rmd | 6 PWFSLSmoke-1.0.33/PWFSLSmoke/vignettes/NowCast.Rmd | 23 - 102 files changed, 642 insertions(+), 310 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps/>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
Author: Dylan Beaudette [aut, cre],
Pierre Roudier [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@ca.usda.gov>
Diff between aqp versions 1.16 dated 2018-04-12 and 1.16-3 dated 2018-09-24
DESCRIPTION | 11 +++++----- MD5 | 33 ++++++++++++++++++------------ NEWS | 6 +++-- R/accuracy_uncertainty.R | 1 R/aggregateSoilDepth.R | 8 +++++-- R/estimateSoilDepth.R | 9 ++++++++ R/munsell2rgb.R | 3 +- R/panel.depth_function.R | 47 +++++++++++++++++++++++++++----------------- R/prepanel.depth_function.R | 46 ++++++++++++++++++++++++++----------------- R/profile_plot.R | 11 +++++++--- man/SPC-plotting.Rd | 2 + man/SPC-slab-methods.Rd | 28 ++++++++++++++++++++++++++ man/aggregateSoilDepth.Rd | 2 - man/munsell2rgb.Rd | 2 - tests |only 15 files changed, 145 insertions(+), 64 deletions(-)
Title: Display and Analyze ROC Curves
Description: Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.
Author: Xavier Robin [cre, aut] (<https://orcid.org/0000-0002-6813-3200>),
Natacha Turck [aut],
Alexandre Hainard [aut],
Natalia Tiberti [aut],
Frédérique Lisacek [aut],
Jean-Charles Sanchez [aut],
Markus Müller [aut],
Stefan Siegert [ctb] (Fast DeLong code)
Maintainer: Xavier Robin <pROC-cran@xavier.robin.name>
Diff between pROC versions 1.12.1 dated 2018-05-06 and 1.13.0 dated 2018-09-24
DESCRIPTION | 8 ++-- MD5 | 34 ++++++++++---------- NEWS | 8 ++++ R/ci.auc.R | 6 +-- R/cov.R | 16 +++------ R/ggroc.R | 2 - R/roc.R | 26 +++++++-------- R/roc.test.R | 13 ++----- R/roc.utils.R | 4 +- R/var.R | 12 ++----- inst/extra/sos_clashes.R |only man/ci.auc.Rd | 6 +-- man/cov.Rd | 3 - man/ggroc.Rd | 31 +++++++++++++----- man/roc.Rd | 6 +++ man/roc.test.Rd | 20 +---------- man/var.Rd | 3 - tests/testthat/test-numeric-Inf.R |only tests/testthat/test-numeric-accuracy.R | 56 +++++++++++++++++++++++++++++++++ 19 files changed, 156 insertions(+), 98 deletions(-)
Title: Parallel Distance Matrix Computation using Multiple Threads
Description: A fast parallelized alternative to R's native 'dist' function to
calculate distance matrices for continuous, binary, and multi-dimensional
input matrices, which supports a broad variety of 39 predefined distance
functions from the 'stats', 'proxy' and 'dtw' R packages, as well as user-
defined functions written in C++. For ease of use, the 'parDist' function
extends the signature of the 'dist' function and uses the same parameter
naming conventions as distance methods of existing R packages. The package
is mainly implemented in C++ and leverages the 'RcppParallel' package to
parallelize the distance computations with the help of the 'TinyThread'
library. Furthermore, the 'Armadillo' linear algebra library is used for
optimized matrix operations during distance calculations. The curiously
recurring template pattern (CRTP) technique is applied to avoid virtual
functions, which improves the Dynamic Time Warping calculations while
the implementation stays flexible enough to support different DTW step
patterns and normalization methods.
Author: Alexander Eckert [aut, cre]
Maintainer: Alexander Eckert <info@alexandereckert.com>
Diff between parallelDist versions 0.2.1 dated 2017-12-04 and 0.2.2 dated 2018-09-24
DESCRIPTION | 6 MD5 | 41 - NAMESPACE | 8 R/RcppExports.R | 22 R/parDist.R | 288 +++++----- README.md | 138 ++-- build/vignette.rds |binary inst/NEWS.Rd | 48 - inst/doc/parallelDist.R | 560 +++++++++---------- inst/doc/parallelDist.Rnw | 800 ++++++++++++++-------------- inst/doc/parallelDist.pdf |binary man/parDist.Rd | 676 +++++++++++------------ src/DistanceDTWGeneric.h | 37 - src/StepPattern.h | 95 +-- tests/testthat.R | 53 + tests/testthat/testMatrixCustomDistances.R | 139 ++-- tests/testthat/testMatrixDTWDistances.R | 222 ++++--- tests/testthat/testMatrixDistances.R | 452 +++++++-------- tests/testthat/testMatrixListDTWDistances.R |only tests/testthat/testMatrixListDistances.R | 431 +++++++-------- vignettes/parallelDist.Rnw | 800 ++++++++++++++-------------- vignettes/parallelDist.bib | 104 +-- 22 files changed, 2468 insertions(+), 2452 deletions(-)
Title: Foreach Parallel Adaptor for the 'parallel' Package
Description: Provides a parallel backend for the %dopar% function using
the parallel package.
Author: Rich Calaway [cre],
Microsoft Corporation [aut, cph],
Steve Weston [aut],
Dan Tenenbaum [ctb]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between doParallel versions 1.0.11 dated 2017-09-28 and 1.0.14 dated 2018-09-24
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- NEWS | 11 +++++++++++ R/doParallel.R | 15 ++++++++++++--- build/vignette.rds |binary inst/doc/gettingstartedParallel.pdf |binary inst/unitTests/options.R | 1 - tests/doRUnit.R | 2 +- 8 files changed, 38 insertions(+), 19 deletions(-)
Title: R Interface to C API of COIN-OR Clp
Description: R Interface to C API of COIN-OR Clp, depends on COIN-OR Clp Version >= 1.12.0.
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut],
C. Jonathan Fritzemeier [ctb]
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
Diff between clpAPI versions 1.2.7 dated 2016-04-19 and 1.2.9 dated 2018-09-24
DESCRIPTION | 19 ++-- MD5 | 144 ++++++++++++++++++----------------- NAMESPACE | 6 + R/clpAPI.R | 63 +++++++++++++++ build/vignette.rds |binary inst/INSTALL | 10 +- inst/NEWS.Rd | 20 ++++ inst/doc/clpAPI.pdf |binary man/addColsCLP.Rd | 4 man/addRowsCLP.Rd | 4 man/chgColLowerCLP.Rd | 4 man/chgColUpperCLP.Rd | 4 man/chgObjCoefsCLP.Rd | 4 man/chgRowLowerCLP.Rd | 4 man/chgRowUpperCLP.Rd | 4 man/clpAPI-package.Rd | 4 man/clpPtr-class.Rd | 4 man/copyNamesCLP.Rd | 4 man/delColsCLP.Rd | 4 man/delProbCLP.Rd | 4 man/delRowsCLP.Rd | 4 man/dropNamesCLP.Rd | 4 man/dualCLP.Rd | 4 man/getColDualCLP.Rd | 4 man/getColLowerCLP.Rd | 4 man/getColPrimCLP.Rd | 4 man/getColUpperCLP.Rd | 4 man/getHitMaximumIterationsCLP.Rd |only man/getIndCLP.Rd | 4 man/getLogLevelCLP.Rd | 4 man/getMaximumIterationsCLP.Rd |only man/getMaximumSecondsCLP.Rd |only man/getNnzCLP.Rd | 4 man/getNumColsCLP.Rd | 4 man/getNumNnzCLP.Rd | 4 man/getNumRowsCLP.Rd | 4 man/getObjCoefsCLP.Rd | 4 man/getObjDirCLP.Rd | 4 man/getObjValCLP.Rd | 4 man/getRowDualCLP.Rd | 4 man/getRowLowerCLP.Rd | 4 man/getRowPrimCLP.Rd | 4 man/getRowUpperCLP.Rd | 4 man/getScaleFlagCLP.Rd | 4 man/getSolStatusCLP.Rd | 4 man/getVecLenCLP.Rd | 4 man/getVecStartCLP.Rd | 4 man/idiotCLP.Rd | 4 man/initProbCLP.Rd | 4 man/lengthNamesCLP.Rd | 4 man/loadMatrixCLP.Rd | 4 man/loadProblemCLP.Rd | 4 man/primalCLP.Rd | 4 man/printModelCLP.Rd | 4 man/probNameCLP.Rd | 4 man/readMPSCLP.Rd | 4 man/resizeCLP.Rd | 4 man/restoreModelCLP.Rd | 4 man/return_codeCLP.Rd | 4 man/saveModelCLP.Rd | 4 man/scaleModelCLP.Rd | 4 man/setLogLevelCLP.Rd | 4 man/setMaximumIterationsCLP.Rd |only man/setMaximumSecondsCLP.Rd |only man/setNumberIterationsCLP.Rd |only man/setObjDirCLP.Rd | 4 man/solveInitialBarrierCLP.Rd | 4 man/solveInitialBarrierNoCrossCLP.Rd | 4 man/solveInitialCLP.Rd | 4 man/solveInitialDualCLP.Rd | 4 man/solveInitialPrimalCLP.Rd | 4 man/status_codeCLP.Rd | 4 man/versionCLP.Rd | 4 src/clpAPI.c | 82 +++++++++++++++++++ src/clpAPI.h | 18 ++++ src/init.c | 6 + 76 files changed, 404 insertions(+), 200 deletions(-)
More information about userfriendlyscience at CRAN
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Title: Reverse Engineering Summarized Data
Description: Decoupled (e.g. separate averages) and censored (e.g. > 100 species) variables are continually reported by many well-established organizations (e.g. World Health Organization (WHO), Centers for Disease Control and Prevention (CDC), World Bank, and various national censuses). The challenge therefore is to infer what the original data could have been given summarized information. We present an R package that reverse engineers decoupled and/or censored count data with two main functions. The cnbinom.pars() function estimates the average and dispersion parameter of a censored univariate frequency table. The rec() function reverse engineers summarized data into an uncensored bivariate table of probabilities.
Author: Samantha Duchscherer [aut, cre],
UT-Battelle, LLC [cph]
Maintainer: Samantha Duchscherer <sam.duchscherer@gmail.com>
Diff between revengc versions 1.0.2 dated 2018-07-18 and 1.0.3 dated 2018-09-24
revengc-1.0.2/revengc/R/estimated_lambda_function.R |only revengc-1.0.2/revengc/R/poisson_trunc_functions.R |only revengc-1.0.2/revengc/man/column_marginal.Rd |only revengc-1.0.2/revengc/man/dqpois_trunc.Rd |only revengc-1.0.2/revengc/man/estimated_lambda.Rd |only revengc-1.0.2/revengc/man/row_marginal.Rd |only revengc-1.0.3/revengc/DESCRIPTION | 12 revengc-1.0.3/revengc/MD5 | 43 revengc-1.0.3/revengc/NAMESPACE | 3 revengc-1.0.3/revengc/R/cnbinom.pars_function.R |only revengc-1.0.3/revengc/R/format_data_for_functions.R | 194 -- revengc-1.0.3/revengc/R/rec_function.R | 702 +++------- revengc-1.0.3/revengc/R/reweight.contingencytable.R |only revengc-1.0.3/revengc/R/reweight.univariatetable.R |only revengc-1.0.3/revengc/R/seedmatrix_function.R | 108 - revengc-1.0.3/revengc/README.md | 176 +- revengc-1.0.3/revengc/build/vignette.rds |binary revengc-1.0.3/revengc/inst/doc/duchscherer-stewart-urban.ltx | 320 ++-- revengc-1.0.3/revengc/inst/doc/duchscherer-stewart-urban.pdf |binary revengc-1.0.3/revengc/man/cnbinom.pars.Rd |only revengc-1.0.3/revengc/man/column.marginal.Rd |only revengc-1.0.3/revengc/man/rec.Rd | 140 - revengc-1.0.3/revengc/man/reweight.contingencytable.Rd |only revengc-1.0.3/revengc/man/reweight.univariatetable.Rd |only revengc-1.0.3/revengc/man/row.marginal.Rd |only revengc-1.0.3/revengc/man/seedmatrix.Rd | 54 revengc-1.0.3/revengc/vignettes/Thumbs.db |only revengc-1.0.3/revengc/vignettes/duchscherer-stewart-urban.bib | 114 - revengc-1.0.3/revengc/vignettes/duchscherer-stewart-urban.ltx | 320 ++-- revengc-1.0.3/revengc/vignettes/workflow_overview.png |binary 30 files changed, 809 insertions(+), 1377 deletions(-)
Title: Local Interpretable (Model-Agnostic) Visual Explanations
Description: Interpretability of complex machine learning models is a growing concern.
This package helps to understand key factors that drive the
decision made by complicated predictive model (so called black box model).
This is achieved through local approximations that are either based on
additive regression like model or CART like model that allows for
higher interactions. The methodology is based on Tulio Ribeiro, Singh, Guestrin (2016) <doi:10.1145/2939672.2939778>.
More details can be found in Staniak, Biecek (2018) <arXiv:1804.01955>.
Author: Mateusz Staniak [cre, aut],
Przemysław Biecek [aut]
Maintainer: Mateusz Staniak <mateusz.staniak@math.uni.wroc.pl>
Diff between live versions 1.5.7 dated 2018-06-03 and 1.5.8 dated 2018-09-24
DESCRIPTION | 12 +++---- MD5 | 49 +++++++++++++++++------------- NAMESPACE | 9 +++++ NEWS.md | 7 ++++ R/dalex_shortcut.R |only R/explain.R | 3 + R/explore.R | 13 +++++-- R/local_perimp.R |only R/plot.R | 4 +- R/sampling_methods.R | 20 +++++++++--- R/zzz.R |only README.md | 6 +-- build/vignette.rds |binary inst/doc/wine_quality.html | 6 +-- man/generate_neighbourhood2.Rd | 5 ++- man/give_predictions2.Rd | 4 +- man/live_shiny.Rd | 3 + man/local_approximation.Rd |only man/local_permutation_importance.Rd |only man/normal_neighbourhood.Rd | 5 ++- man/permutation_neighbourhood.Rd | 5 ++- man/plot.live_explainer.Rd | 6 +-- man/plot.local_permutation_importance.Rd |only man/plot_explanation.Rd | 3 + man/print.local_permutation_importance.Rd |only man/sample_locally2.Rd | 4 +- tests/testthat.R | 3 + tests/testthat/test_local_varimp.R |only tests/testthat/test_shortcut.R |only tests/testthat/test_simulating.R | 7 ++++ 30 files changed, 118 insertions(+), 56 deletions(-)
Title: Dynamic Modeling in R
Description: Intensive longitudinal data have become increasingly prevalent in
various scientific disciplines. Many such data sets are noisy, multivariate,
and multi-subject in nature. The change functions may also be continuous, or
continuous but interspersed with periods of discontinuities (i.e., showing
regime switches). The package 'dynr' (Dynamic Modeling in R) is an R package
that implements a set of computationally efficient algorithms for handling a
broad class of linear and nonlinear discrete- and continuous-time models with
regime-switching properties under the constraint of linear Gaussian measurement
functions. The discrete-time models can generally take on the form of a state-
space or difference equation model. The continuous-time models are generally
expressed as a set of ordinary or stochastic differential equations. All
estimation and computations are performed in C, but users are provided with the
option to specify the model of interest via a set of simple and easy-to-learn
model specification functions in R. Model fitting can be performed using single-
subject time series data or multiple-subject longitudinal data.
Author: Lu Ou [aut],
Michael D. Hunter [aut, cre],
Sy-Miin Chow [aut]
Maintainer: Michael D. Hunter <mhunter.ou@gmail.com>
Diff between dynr versions 0.1.13-3 dated 2018-09-16 and 0.1.13-4 dated 2018-09-24
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 5 +++-- R/dynrVersion.R | 2 +- build/partial.rdb |binary inst/doc/InstallationForDevelopers.pdf |binary inst/doc/InstallationForUsers.pdf |binary inst/doc/LinearDiscreteTimeModels.pdf |binary inst/doc/NonlinearContinuousTimeModels.pdf |binary src/mainR.c | 8 ++++---- 10 files changed, 21 insertions(+), 20 deletions(-)
Title: Distributional Method for the Dichotomisation of Continuous
Outcomes
Description: Contains a range of functions covering the present
development of the distributional method for the dichotomisation of continuous outcomes.
The method provides estimates with standard error of a comparison of proportions
(difference, odds ratio and risk ratio) derived, with similar precision, from a comparison of means.
See the URL below or <arXiv:1809.03279> for more information.
Author: Odile Sauzet
Maintainer: Odile Sauzet <odile.sauzet@uni-bielefeld.de>
Diff between distdichoR versions 0.1-0 dated 2018-09-19 and 0.1-1 dated 2018-09-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/regdistdicho.R | 34 +++++++++++++++++----------------- 3 files changed, 23 insertions(+), 23 deletions(-)
Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and traverse the
tree in various orders. Aggregate, cumulate, print, plot, convert to and from
data.frame and more. Useful for decision trees, machine learning, finance,
conversion from and to JSON, and many other applications.
Author: Chris Hammil [ctb] (improve getting),
Facundo Munoz [ctb] (improve list conversion),
Markus Wamser [ctb] (fixed some typos),
Pierre Formont [ctb] (additional features),
Kent Russel [ctb] (documentation),
Noam Ross [ctb] (fixes),
Duncan Garmonsway [ctb] (fixes),
Christoph Glur [aut, cre] (R interface)
Maintainer: Christoph Glur <christoph.glur@ipub.com>
Diff between data.tree versions 0.7.7 dated 2018-09-23 and 0.7.8 dated 2018-09-24
DESCRIPTION | 8 +++---- MD5 | 10 ++++----- NAMESPACE | 2 - NEWS | 5 +++- inst/doc/applications.html | 48 ++++++++++++++++++++++----------------------- inst/doc/data.tree.html | 16 +++++++-------- 6 files changed, 46 insertions(+), 43 deletions(-)
Title: Computational Graphs
Description: Allows to create, evaluate, and differentiate computational graphs in R. A computational graph is a graph representation of a multivariate function decomposed by its (elementary) operations. Nodes in the graph represent arrays while edges represent dependencies among the arrays. An advantage of expressing a function as a computational graph is that this enables to differentiate the function by automatic differentiation. The 'cgraph' package supports various functions including basic arithmetic, trigonometry functions, and linear algebra functions. It differentiates computational graphs by reverse automatic differentiation. The flexible architecture of the package makes it applicable to solve a variety of problems including local sensitivity analysis, gradient-based optimization, and machine learning.
Author: Ron Triepels
Maintainer: Ron Triepels <dev@cgraph.org>
Diff between cgraph versions 2.0.2 dated 2018-08-19 and 2.0.3 dated 2018-09-24
DESCRIPTION | 6 +-- MD5 | 53 ++++++++++++++++++------------ NAMESPACE | 69 ++++++++++++++++++++++++++-------------- NEWS.md | 16 +++++++++ R/array.R | 16 ++++----- R/cgraph.R | 8 ++-- R/logical.R |only R/math.R | 10 +++++ R/misc.R | 20 ++++++++++- R/session.R | 4 +- R/transform.R | 6 +++ R/trig.R | 24 +++++++++++++ man/approx.grad.Rd | 2 - man/cg.approx.grad.Rd | 2 - man/cg.constant.grad.Rd |only man/cg.equal.Rd |only man/cg.gradients.Rd | 2 - man/cg.greater.Rd |only man/cg.greater.equal.Rd |only man/cg.less.Rd |only man/cg.less.equal.Rd |only man/cg.not.Rd |only man/cg.not.equal.Rd |only man/cg.sigmoid.Rd | 2 - man/gradients.Rd | 2 - man/sigmoid.Rd |only src/cgraph.c | 14 ++++---- src/init.c | 5 ++ src/internal.c | 15 ++------ src/misc.c |only tests/testthat/test.math.R | 4 +- tests/testthat/test.transform.R | 16 ++++----- tests/testthat/test.trig.R | 8 ++-- 33 files changed, 203 insertions(+), 101 deletions(-)
Title: Generalized Random Forests (Beta)
Description: A pluggable package for forest-based statistical estimation and inference.
GRF currently provides methods for non-parametric least-squares regression,
quantile regression, and treatment effect estimation (optionally using instrumental
variables). This package is currently in beta, and we expect to make continual
improvements to its performance and usability.
Author: Julie Tibshirani [aut, cre],
Susan Athey [aut],
Stefan Wager [aut],
Rina Friedberg [ctb],
Luke Miner [ctb],
Marvin Wright [ctb]
Maintainer: Julie Tibshirani <jtibs@cs.stanford.edu>
Diff between grf versions 0.10.0 dated 2018-05-09 and 0.10.1 dated 2018-09-24
DESCRIPTION | 14 - MD5 | 103 ++++++------ NAMESPACE | 5 R/RcppExports.R | 24 +- R/analysis_tools.R | 15 + R/average_partial_effect.R | 58 +++++-- R/average_treatment_effect.R | 155 +++++++++++-------- R/causal_forest.R | 79 ++++++--- R/causal_tuning.R | 12 + R/custom_forest.R | 19 +- R/forest_summary.R |only R/input_utilities.R | 58 +++++++ R/instrumental_forest.R | 73 ++++++-- R/local_linear_forest.R |only R/local_linear_tuning.R |only R/plot.R |only R/print.R | 4 R/quantile_forest.R | 21 +- R/regression_forest.R | 98 ++++++++---- R/regression_tuning.R | 27 ++- R/tuning_utilities.R | 2 man/average_partial_effect.Rd | 8 man/average_treatment_effect.Rd | 10 + man/causal_forest.Rd | 17 +- man/create_dot_body.Rd |only man/custom_forest.Rd | 14 + man/export_graphviz.Rd |only man/get_tree.Rd | 15 + man/grf.Rd | 53 +++++- man/instrumental_forest.Rd | 19 +- man/local_linear_forest.Rd |only man/plot.grf_tree.Rd |only man/predict.local_linear_forest.Rd |only man/predict.regression_forest.Rd | 14 + man/quantile_forest.Rd | 15 + man/regression_forest.Rd | 21 +- man/test_calibration.Rd |only man/tune_causal_forest.Rd | 13 + man/tune_local_linear_forest.Rd |only man/tune_regression_forest.Rd | 12 - src/AnalysisToolsBindings.cpp | 12 + src/CustomForestBindings.cpp | 5 src/InstrumentalForestBindings.cpp | 5 src/QuantileForestBindings.cpp | 5 src/RcppExports.cpp | 52 +++--- src/RegressionForestBindings.cpp | 13 - src/src/forest/ForestOptions.cpp | 3 src/src/forest/ForestOptions.h | 1 src/src/forest/ForestPredictors.cpp | 4 src/src/forest/ForestPredictors.h | 2 src/src/forest/ForestTrainer.cpp | 10 + src/src/prediction/LocalLinearPredictionStrategy.cpp | 85 +++++----- src/src/prediction/LocalLinearPredictionStrategy.h | 12 + src/src/sampling/RandomSampler.cpp | 62 +++---- src/src/sampling/RandomSampler.h | 10 - src/src/tree/TreeOptions.cpp | 6 src/src/tree/TreeOptions.h | 4 src/src/tree/TreeTrainer.cpp | 2 58 files changed, 849 insertions(+), 422 deletions(-)
Title: Fixed Effects Nonlinear Maximum Likelihood Models
Description: Efficient estimation of multiple fixed-effects maximum likelihood models
with, possibly, non-linear in parameters right hand sides. Standard-errors
can easily be clustered and estimations exported.
Author: Laurent Berge [aut, cre]
Maintainer: Laurent Berge <laurent.berge@uni.lu>
Diff between FENmlm versions 2.2.1 dated 2018-09-15 and 2.2.2 dated 2018-09-24
DESCRIPTION | 17 - MD5 | 40 +- NAMESPACE | 4 R/FENmlm.R | 4 R/MiscFuns.R | 2 R/RcppExports.R | 24 + R/femlm.R | 685 +++++++++++++++++++++++++++++++------------- build/vignette.rds |binary inst/NEWS.Rd | 28 + inst/doc/FENmlm.R | 3 inst/doc/FENmlm.Rmd | 23 - inst/doc/FENmlm.html | 62 ++- man/FENmlm-package.Rd | 4 man/femlm.Rd | 18 - man/predict.femlm.Rd | 3 man/res2table.Rd | 8 man/res2tex.Rd | 11 man/vcov.femlm.Rd | 4 src/RcppExports.cpp | 74 +++- src/Rcpp_get_derivative.cpp | 134 ++++++++ vignettes/FENmlm.Rmd | 23 - 21 files changed, 854 insertions(+), 317 deletions(-)
Title: Checks if a Number is Valid Using the Luhn Algorithm
Description: Confirms if the number is Luhn compliant.
Can check if credit card, IMEI number or any other Luhn based number is correct.
For more info see: <https://en.wikipedia.org/wiki/Luhn_algorithm>.
Author: Adam Deacon [aut, cre],
Karina Marks [ctb],
Owen Jones [ctb]
Maintainer: Adam Deacon <adam@deaconsworld.org.uk>
Diff between checkLuhn versions 1.0.2 dated 2018-09-03 and 1.1.0 dated 2018-09-24
checkLuhn-1.0.2/checkLuhn/tests/testthat/test.checkLuhn.1.R |only checkLuhn-1.1.0/checkLuhn/DESCRIPTION | 20 +++++++--- checkLuhn-1.1.0/checkLuhn/MD5 | 20 +++++++--- checkLuhn-1.1.0/checkLuhn/NAMESPACE | 7 +++ checkLuhn-1.1.0/checkLuhn/NEWS.md |only checkLuhn-1.1.0/checkLuhn/R/checkLuhn.R | 11 +++--- checkLuhn-1.1.0/checkLuhn/R/issuer.R |only checkLuhn-1.1.0/checkLuhn/R/zzz.R |only checkLuhn-1.1.0/checkLuhn/README.md | 22 +++++++++--- checkLuhn-1.1.0/checkLuhn/data |only checkLuhn-1.1.0/checkLuhn/man/bin_ranges.Rd |only checkLuhn-1.1.0/checkLuhn/man/checkLuhn-package.Rd |only checkLuhn-1.1.0/checkLuhn/man/checkLuhn.Rd | 4 +- checkLuhn-1.1.0/checkLuhn/man/issuer.Rd |only checkLuhn-1.1.0/checkLuhn/tests/testthat/test.checkLuhn.R |only checkLuhn-1.1.0/checkLuhn/tests/testthat/test.issuer.R |only 16 files changed, 61 insertions(+), 23 deletions(-)
Title: CRISPR-Based Salmonella Enterica Serotype Analyzer
Description: Salmonella enterica is a major cause of bacterial food-borne disease worldwide. Serotype identification is the most commonly used typing method to characterize Salmonella isolates. However, experimental serotyping needs great cost on manpower and resources. Recently, we found that the newly incorporated spacer in the clustered regularly interspaced short palindromic repeat (CRISPR) could serve as an effective marker for typing of Salmonella. It was further revealed by Li et. al (2014) <doi:10.1128/JCM.00696-14> that recognized types based on the combination of two newly incorporated spacer in both CRISPR loci showed high accordance with serotypes. Here, we developed an R package 'CSESA' to predict the serotype based on this finding. Considering it’s time saving and of high accuracy, we recommend to predict the serotypes of unknown Salmonella isolates using 'CSESA' before doing the traditional serotyping.
Author: Xia Zhang [aut, cre],
Lang Yang [aut]
Maintainer: Xia Zhang <zhangxia9403@gmail.com>
Diff between CSESA versions 1.0.4 dated 2018-06-15 and 1.1.0 dated 2018-09-24
DESCRIPTION | 6 MD5 | 9 R/CSESA.R | 39 ++- inst/packageData/mapping_tbl.txt | 485 +++++++++++++++++++++++++-------------- inst/primerB2DB |only 5 files changed, 366 insertions(+), 173 deletions(-)
Title: Weighted Mixed-Effects Models, using Multilevel Pseudo Maximum
Likelihood Estimation
Description: Run mixed-effects models that include weights at every level. The WeMix package fits a Weighted Mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. The model is fit using adaptive quadrature.
Author: Paul Bailey, Claire Kelley, Trang Nguyen, Huade Huo.
Maintainer: Claire Kelley <ckelley@air.org>
Diff between WeMix versions 2.0.0 dated 2018-08-14 and 2.1.0 dated 2018-09-24
DESCRIPTION | 8 MD5 | 42 NAMESPACE | 56 R/RcppExports.R | 98 - R/adaptiveQuad.R | 2292 +++++++++++++++++++------------------- R/covarianceConstructors.R | 128 +- R/drv.R | 646 +++++----- R/helpers.R | 132 +- R/lnl.R | 608 +++++----- R/weMix-package.R | 46 build/vignette.rds |binary inst/NEWS.Rd | 56 inst/doc/WeightedMixedModels.R | 286 ++-- inst/doc/WeightedMixedModels.Rmd | 1378 +++++++++++----------- inst/doc/WeightedMixedModels.pdf |binary man/WeMix-package.Rd | 52 man/calc_lin_lnl_quad_fast.Rd | 144 +- man/mix.Rd | 214 +-- tests/testthat/Examples.smcl | 280 ++-- tests/testthat/test-0-main.R | 494 ++++---- tests/testthat_tests.R | 8 vignettes/WeightedMixedModels.Rmd | 1378 +++++++++++----------- 22 files changed, 4188 insertions(+), 4158 deletions(-)
Title: Optimal and Fast Univariate Clustering
Description: Fast optimal univariate clustering and segementation
by dynamic programming. Three types of problem including
univariate k-means, k-median, and k-segments are solved with
guaranteed optimality and reproducibility. The core algorithm
minimizes the sum of within-cluster distances using respective
metrics. Its advantage over heuristic clustering algorithms in
efficiency and accuracy is increasingly pronounced as the
number of clusters k increases. Weighted k-means and unweighted
k-segments algorithms can also optimally segment time series
and perform peak calling. An auxiliary function generates
histograms that are adaptive to patterns in data. In contrast to
heuristic methods, this package provides a powerful set of tools
for univariate data analysis with guaranteed optimality.
Use four spaces when indenting paragraphs within the Description.
Author: Joe Song [aut, cre],
Haizhou Wang [aut]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between Ckmeans.1d.dp versions 4.2.1 dated 2017-07-09 and 4.2.2 dated 2018-09-24
DESCRIPTION | 18 + MD5 | 22 +- NAMESPACE | 6 NEWS | 6 R/Ckmeans.1d.dp.R | 92 +++++++--- R/RcppExports.R |only build/vignette.rds |binary inst/doc/Ckmeans.1d.dp.html | 393 +++++++++++++++++++++++++++++-------------- inst/doc/Weights.html | 199 +++++++++++++++++---- inst/doc/ahist.html | 388 +++++++++++++++++++++++++++++------------- man/Ckmeans.1d.dp-package.Rd | 2 src/Ckmeans.1d.dp_main.cpp | 225 +++++++++++++----------- src/RcppExports.cpp |only 13 files changed, 918 insertions(+), 433 deletions(-)
Title: Distances for Machine Learning and Statistics in the Context of
Big Data
Description: Functions to compute distances between probability measures or any other data object than can be posed in this way, entropy measures for samples of curves, distances and depth measures for functional data, and the Generalized Mahalanobis Kernel distance for high dimensional data. For further details about the metrics please refer to Martos et al (2014) <doi:10.3233/IDA-140706>; Martos et al (2018) <doi:10.3390/e20010033>; Hernandez et al (2018, submitted); Martos et al (2018, submitted).
Author: Gabriel Martos [aut, cre],
Nicolas Hernandez [aut]
Maintainer: Gabriel Martos <gmartos@utdt.edu>
Diff between bigdatadist versions 1.0 dated 2018-07-02 and 1.1 dated 2018-09-24
DESCRIPTION | 8 ++-- MD5 | 8 +++- NAMESPACE | 7 ++-- R/gmdepth.fd.R | 89 ++++++++++++++++++++++++++---------------------------- R/kmdepth.fd.R |only man/kmdepth.fd.Rd |only 6 files changed, 57 insertions(+), 55 deletions(-)
Title: Analysis of Basketball Data
Description: Collection of tools to work with basketball data. Functions available are related to friendly
web scraping and visualization. Data were obtained from <http://www.euroleague.net/>,
<http://www.eurocupbasketball.com/> and <http://www.acb.com>, following the instructions of their
respectives robots.txt files. Tools for visualization include a population pyramid, 2D plots of
archetypoids and the rest of players, percentile circular plots, plots to analyze monthly evolution,
heatmaps, shooting barplots, four factor plots and maps of players' nationalities.
Author: Guillermo Vinue
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between BAwiR versions 1.1.2 dated 2018-09-10 and 1.1.3 dated 2018-09-24
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NEWS | 4 +++- R/get_games_rosters.R | 8 ++++---- R/scraping_games_acb.R | 23 +++++++++++++---------- inst/doc/BAwiR.html | 4 ++-- man/BAwiR-package.Rd | 6 +++--- man/get_games_rosters.Rd | 4 ++-- 8 files changed, 40 insertions(+), 34 deletions(-)
Title: A Community Modeling Foundation for Eco-Hydrology
Description: Provides a flexible foundation for scientists,
engineers, and policy makers to base teaching exercises as well as for
more applied use to model complex eco-hydrological interactions.
Author: Fuka DR, Walter MT, Archibald JA, Steenhuis TS, and Easton ZM
Maintainer: Daniel Fuka <drf28@cornell.edu>
Diff between EcoHydRology versions 0.4.12 dated 2014-04-04 and 0.4.12.1 dated 2018-09-24
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 6 ++++++ R/EstCloudiness.R | 2 +- data/GSOD_history.rda |binary data/OwascoInlet.rda |binary data/change_params.rda |binary data/swat_general.rda |binary 8 files changed, 19 insertions(+), 13 deletions(-)
Title: Infrastructure for Running, Cycling and Swimming Data from
GPS-Enabled Tracking Devices
Description: Provides infrastructure for handling running, cycling and swimming data from GPS-enabled tracking devices within R. The package provides methods to extract, clean and organise workout and competition data into session-based and unit-aware data objects of class 'trackeRdata' (S3 class). The information can then be visualised, summarised, and analysed through flexible and extensible methods. Frick and Kosmidis (2017) <doi: 10.18637/jss.v082.i07>, which is updated and maintained as one of the vignettes, provides detailed descriptions of the package and its methods, and real-data demonstrations of the package functionality.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>),
Hannah Frick [aut] (<https://orcid.org/0000-0002-6049-5258>),
Robin Hornak [aut]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between trackeR versions 1.0.0 dated 2017-11-27 and 1.1 dated 2018-09-24
trackeR-1.0.0/trackeR/NEWS |only trackeR-1.0.0/trackeR/R/distanceCorrection.R |only trackeR-1.0.0/trackeR/R/funcPCA.R |only trackeR-1.0.0/trackeR/R/imputeSpeeds.R |only trackeR-1.0.0/trackeR/R/read.R |only trackeR-1.0.0/trackeR/inst/extdata/2013-06-08-090442.TCX |only trackeR-1.0.0/trackeR/inst/icons/credits.txt |only trackeR-1.0.0/trackeR/man/append.xprofile.Rd |only trackeR-1.0.0/trackeR/man/changeUnits.Rd |only trackeR-1.0.0/trackeR/man/changeUnits.conProfile.Rd |only trackeR-1.0.0/trackeR/man/changeUnits.distrProfile.Rd |only trackeR-1.0.0/trackeR/man/changeUnits.trackeRWprime.Rd |only trackeR-1.0.0/trackeR/man/changeUnits.trackeRdata.Rd |only trackeR-1.0.0/trackeR/man/changeUnits.trackeRdataSummary.Rd |only trackeR-1.0.0/trackeR/man/concentrationProfile.Rd |only trackeR-1.0.0/trackeR/man/decreasingSmoother.Rd |only trackeR-1.0.0/trackeR/man/distributionProfile.Rd |only trackeR-1.0.0/trackeR/man/generateBaseUnits.Rd |only trackeR-1.0.0/trackeR/man/generateVariableNames.Rd |only trackeR-1.0.0/trackeR/man/getOperations.Rd |only trackeR-1.0.0/trackeR/man/getOperations.conProfile.Rd |only trackeR-1.0.0/trackeR/man/getOperations.distrProfile.Rd |only trackeR-1.0.0/trackeR/man/getOperations.trackeRdata.Rd |only trackeR-1.0.0/trackeR/man/getUnits.Rd |only trackeR-1.0.0/trackeR/man/getUnits.conProfile.Rd |only trackeR-1.0.0/trackeR/man/getUnits.distrProfile.Rd |only trackeR-1.0.0/trackeR/man/getUnits.trackeRWprime.Rd |only trackeR-1.0.0/trackeR/man/getUnits.trackeRdata.Rd |only trackeR-1.0.0/trackeR/man/getUnits.trackeRdataSummary.Rd |only trackeR-1.0.0/trackeR/man/imputeSpeeds.Rd |only trackeR-1.0.0/trackeR/man/leafletRoute.Rd |only trackeR-1.0.0/trackeR/man/plotRoute.Rd |only trackeR-1.0.0/trackeR/man/readContainer.Rd |only trackeR-1.0.0/trackeR/man/readDirectory.Rd |only trackeR-1.0.0/trackeR/man/restingPeriods.Rd |only trackeR-1.0.0/trackeR/man/sanityChecks.Rd |only trackeR-1.0.0/trackeR/man/smootherControl.distrProfile.Rd |only trackeR-1.0.0/trackeR/man/smootherControl.trackeRdata.Rd |only trackeR-1.0.0/trackeR/man/threshold.Rd |only trackeR-1.0.0/trackeR/tests |only trackeR-1.0.0/trackeR/vignettes/plotRoute.pdf |only trackeR-1.1/trackeR/DESCRIPTION | 57 trackeR-1.1/trackeR/MD5 | 235 trackeR-1.1/trackeR/NAMESPACE | 115 trackeR-1.1/trackeR/NEWS.md |only trackeR-1.1/trackeR/R/Wprime.R | 458 trackeR-1.1/trackeR/R/cleaning.R |only trackeR-1.1/trackeR/R/concentrationProfile.R | 614 - trackeR-1.1/trackeR/R/constants.R |only trackeR-1.1/trackeR/R/data.R | 3 trackeR-1.1/trackeR/R/distributionProfile.R | 1010 + trackeR-1.1/trackeR/R/fda.R |only trackeR-1.1/trackeR/R/helpers.R |only trackeR-1.1/trackeR/R/parallelization.R |only trackeR-1.1/trackeR/R/reading.R |only trackeR-1.1/trackeR/R/thresholds.R | 224 trackeR-1.1/trackeR/R/trackeR.R | 207 trackeR-1.1/trackeR/R/trackeRdata.R | 738 - trackeR-1.1/trackeR/R/trackeRdata_plot.R | 429 trackeR-1.1/trackeR/R/trackeRdata_smoother.R | 108 trackeR-1.1/trackeR/R/trackeRdata_summary.R | 747 - trackeR-1.1/trackeR/R/trackeRdata_zones.R | 326 trackeR-1.1/trackeR/R/units.R | 716 - trackeR-1.1/trackeR/R/zzz_aliases.R |only trackeR-1.1/trackeR/build/vignette.rds |binary trackeR-1.1/trackeR/data/run.rda |binary trackeR-1.1/trackeR/data/runs.rda |binary trackeR-1.1/trackeR/inst/classifier.R |only trackeR-1.1/trackeR/inst/doc/TourDetrackeR.R |only trackeR-1.1/trackeR/inst/doc/TourDetrackeR.Rmd | 101 trackeR-1.1/trackeR/inst/doc/TourDetrackeR.html | 5132 +++++++++- trackeR-1.1/trackeR/inst/doc/trackeR.R | 159 trackeR-1.1/trackeR/inst/doc/trackeR.Rnw | 741 - trackeR-1.1/trackeR/inst/doc/trackeR.pdf |binary trackeR-1.1/trackeR/inst/extdata/gpx |only trackeR-1.1/trackeR/inst/extdata/tcx |only trackeR-1.1/trackeR/inst/notes.org |only trackeR-1.1/trackeR/man/GC2trackeRdata.Rd | 26 trackeR-1.1/trackeR/man/Wexp.Rd | 66 trackeR-1.1/trackeR/man/Wprime.Rd | 165 trackeR-1.1/trackeR/man/append.Rd | 4 trackeR-1.1/trackeR/man/append.trackeRdata.Rd | 4 trackeR-1.1/trackeR/man/change_units.Rd |only trackeR-1.1/trackeR/man/change_units.conProfile.Rd |only trackeR-1.1/trackeR/man/change_units.distrProfile.Rd |only trackeR-1.1/trackeR/man/change_units.trackeRWprime.Rd |only trackeR-1.1/trackeR/man/change_units.trackeRdata.Rd |only trackeR-1.1/trackeR/man/change_units.trackeRdataSummary.Rd |only trackeR-1.1/trackeR/man/change_units.trackeRdataZones.Rd |only trackeR-1.1/trackeR/man/collect_units.Rd |only trackeR-1.1/trackeR/man/compute_breaks.Rd |only trackeR-1.1/trackeR/man/compute_limits.Rd |only trackeR-1.1/trackeR/man/concentration_profile.Rd |only trackeR-1.1/trackeR/man/concentration_profile.distrProfile.Rd |only trackeR-1.1/trackeR/man/conversions.Rd | 53 trackeR-1.1/trackeR/man/decreasing_smoother.Rd |only trackeR-1.1/trackeR/man/distance2speed.Rd | 2 trackeR-1.1/trackeR/man/distribution_profile.Rd |only trackeR-1.1/trackeR/man/find_unit_reference_sport.Rd |only trackeR-1.1/trackeR/man/fortify.conProfile.Rd | 11 trackeR-1.1/trackeR/man/fortify.distrProfile.Rd | 5 trackeR-1.1/trackeR/man/fortify.trackeRWprime.Rd | 5 trackeR-1.1/trackeR/man/fortify.trackeRdata.Rd | 9 trackeR-1.1/trackeR/man/fortify.trackeRdataSummary.Rd | 5 trackeR-1.1/trackeR/man/funPCA.Rd | 15 trackeR-1.1/trackeR/man/generate_thresholds.Rd |only trackeR-1.1/trackeR/man/generate_units.Rd |only trackeR-1.1/trackeR/man/get_operations.Rd |only trackeR-1.1/trackeR/man/get_operations.conProfile.Rd |only trackeR-1.1/trackeR/man/get_operations.distrProfile.Rd |only trackeR-1.1/trackeR/man/get_operations.trackeRdata.Rd |only trackeR-1.1/trackeR/man/get_profile.Rd |only trackeR-1.1/trackeR/man/get_resting_periods.Rd |only trackeR-1.1/trackeR/man/get_sport.Rd |only trackeR-1.1/trackeR/man/get_units.Rd |only trackeR-1.1/trackeR/man/get_units.conProfile.Rd |only trackeR-1.1/trackeR/man/get_units.distrProfile.Rd |only trackeR-1.1/trackeR/man/get_units.trackeRWprime.Rd |only trackeR-1.1/trackeR/man/get_units.trackeRdata.Rd |only trackeR-1.1/trackeR/man/get_units.trackeRdataSummary.Rd |only trackeR-1.1/trackeR/man/get_units.trackeRdataZones.Rd |only trackeR-1.1/trackeR/man/impute_speeds.Rd |only trackeR-1.1/trackeR/man/leaflet_route.Rd |only trackeR-1.1/trackeR/man/nsessions.Rd | 21 trackeR-1.1/trackeR/man/plot.conProfile.Rd | 32 trackeR-1.1/trackeR/man/plot.distrProfile.Rd | 28 trackeR-1.1/trackeR/man/plot.trackeRWprime.Rd | 8 trackeR-1.1/trackeR/man/plot.trackeRdata.Rd | 38 trackeR-1.1/trackeR/man/plot.trackeRdataSummary.Rd | 16 trackeR-1.1/trackeR/man/plot.trackeRdataZones.Rd | 6 trackeR-1.1/trackeR/man/plot.trackeRfpca.Rd | 10 trackeR-1.1/trackeR/man/plot_route.Rd |only trackeR-1.1/trackeR/man/prepare_route.Rd |only trackeR-1.1/trackeR/man/prettifyUnit.Rd |only trackeR-1.1/trackeR/man/print.trackeRdata.Rd |only trackeR-1.1/trackeR/man/profile2fd.Rd | 14 trackeR-1.1/trackeR/man/readX.Rd | 77 trackeR-1.1/trackeR/man/read_container.Rd |only trackeR-1.1/trackeR/man/read_directory.Rd |only trackeR-1.1/trackeR/man/ridges.Rd |only trackeR-1.1/trackeR/man/ridges.conProfile.Rd |only trackeR-1.1/trackeR/man/ridges.distrProfile.Rd |only trackeR-1.1/trackeR/man/ridges.trackeRdata.Rd |only trackeR-1.1/trackeR/man/runs.Rd | 2 trackeR-1.1/trackeR/man/sanity_checks.Rd |only trackeR-1.1/trackeR/man/scaled.Rd | 4 trackeR-1.1/trackeR/man/scaled.distrProfile.Rd | 17 trackeR-1.1/trackeR/man/session_duration.Rd |only trackeR-1.1/trackeR/man/session_times.Rd |only trackeR-1.1/trackeR/man/smoother.Rd | 4 trackeR-1.1/trackeR/man/smoother.conProfile.Rd | 31 trackeR-1.1/trackeR/man/smoother.distrProfile.Rd | 44 trackeR-1.1/trackeR/man/smoother.trackeRdata.Rd | 12 trackeR-1.1/trackeR/man/smoother_control.distrProfile.Rd |only trackeR-1.1/trackeR/man/smoother_control.trackeRdata.Rd |only trackeR-1.1/trackeR/man/sort.trackeRdata.Rd |only trackeR-1.1/trackeR/man/speed2distance.Rd | 2 trackeR-1.1/trackeR/man/summary.trackeRdata.Rd | 47 trackeR-1.1/trackeR/man/threshold.trackeRdata.Rd |only trackeR-1.1/trackeR/man/timeAboveThreshold.Rd | 8 trackeR-1.1/trackeR/man/timeline.Rd | 35 trackeR-1.1/trackeR/man/trackeR.Rd | 27 trackeR-1.1/trackeR/man/trackeRdata.Rd | 104 trackeR-1.1/trackeR/man/unique.trackeRdata.Rd |only trackeR-1.1/trackeR/man/zones.Rd | 32 trackeR-1.1/trackeR/vignettes/TourDetrackeR.Rmd | 101 trackeR-1.1/trackeR/vignettes/plotRouteGoogle.pdf |binary trackeR-1.1/trackeR/vignettes/trackeR.Rnw | 741 - trackeR-1.1/trackeR/vignettes/trackeR.bib | 12 169 files changed, 10077 insertions(+), 3886 deletions(-)
Title: Useful Tools for Structural Equation Modeling
Description: Provides useful tools for structural equation modeling.
Author: Terrence D. Jorgensen [aut, cre]
(<https://orcid.org/0000-0001-5111-6773>),
Sunthud Pornprasertmanit [aut],
Alexander Schoemann [aut],
Yves Rosseel [aut],
Patrick Miller [ctb],
Corbin Quick [ctb],
Mauricio Garnier-Villarreal [ctb],
James Selig [ctb],
Aaron Boulton [ctb],
Kristopher Preacher [ctb],
Donna Coffman [ctb],
Mijke Rhemtulla [ctb],
Alexander Robitzsch [ctb],
Craig Enders [ctb],
Ruber Arslan [ctb],
Bell Clinton [ctb],
Pavel Panko [ctb],
Edgar Merkle [ctb],
Steven Chesnut [ctb],
Jarrett Byrnes [ctb],
Jason D. Rights [ctb],
Ylenio Longo [ctb],
Maxwell Mansolf [ctb]
Maintainer: Terrence D. Jorgensen <TJorgensen314@gmail.com>
Diff between semTools versions 0.5-0 dated 2018-06-27 and 0.5-1 dated 2018-09-24
semTools-0.5-0/semTools/R/lisrel2lavaan.R |only semTools-0.5-0/semTools/R/semTools-deprecated.R |only semTools-0.5-0/semTools/man/lisrel2lavaan-deprecated.Rd |only semTools-0.5-0/semTools/man/longInvariance.Rd |only semTools-0.5-0/semTools/man/measurementInvariance.Rd |only semTools-0.5-0/semTools/man/measurementInvarianceCat.Rd |only semTools-0.5-1/semTools/DESCRIPTION | 10 semTools-0.5-1/semTools/MD5 | 124 semTools-0.5-1/semTools/NAMESPACE | 14 semTools-0.5-1/semTools/R/NET.R | 210 - semTools-0.5-1/semTools/R/TSML.R | 530 +-- semTools-0.5-1/semTools/R/aa_semTools-deprecated.R |only semTools-0.5-1/semTools/R/compareFit.R | 572 ++-- semTools-0.5-1/semTools/R/efa.R | 47 semTools-0.5-1/semTools/R/longInvariance.R | 375 +- semTools-0.5-1/semTools/R/measEq.R |only semTools-0.5-1/semTools/R/measurementInvariance.R | 208 - semTools-0.5-1/semTools/R/measurementInvarianceCat.R | 166 - semTools-0.5-1/semTools/R/missingBootstrap.R | 341 +- semTools-0.5-1/semTools/R/monteCarloMed.R | 270 - semTools-0.5-1/semTools/R/partialInvariance.R | 548 ++-- semTools-0.5-1/semTools/R/permuteMeasEq.R | 1209 ++++---- semTools-0.5-1/semTools/R/powerAnalysisSS.R | 272 +- semTools-0.5-1/semTools/R/reliability.R | 2 semTools-0.5-1/semTools/R/runMI-LRT.R |only semTools-0.5-1/semTools/R/runMI-Wald.R |only semTools-0.5-1/semTools/R/runMI-methods.R | 1359 +++------- semTools-0.5-1/semTools/R/runMI-modification.R | 277 +- semTools-0.5-1/semTools/R/runMI-score.R | 332 +- semTools-0.5-1/semTools/R/runMI.R | 479 ++- semTools-0.5-1/semTools/R/semTools.R | 160 - semTools-0.5-1/semTools/R/standardizeMx.R | 193 - semTools-0.5-1/semTools/build/vignette.rds |binary semTools-0.5-1/semTools/inst/doc/partialInvariance.pdf |binary semTools-0.5-1/semTools/man/BootMiss-class.Rd | 3 semTools-0.5-1/semTools/man/EFA-class.Rd | 2 semTools-0.5-1/semTools/man/FitDiff-class.Rd | 30 semTools-0.5-1/semTools/man/Net-class.Rd | 5 semTools-0.5-1/semTools/man/SSpower.Rd | 2 semTools-0.5-1/semTools/man/auxiliary.Rd | 4 semTools-0.5-1/semTools/man/bsBootMiss.Rd | 7 semTools-0.5-1/semTools/man/calculate.D2.Rd |only semTools-0.5-1/semTools/man/clipboard.Rd | 1 semTools-0.5-1/semTools/man/compareFit.Rd | 73 semTools-0.5-1/semTools/man/indProd.Rd | 1 semTools-0.5-1/semTools/man/lavTestLRT.mi.Rd |only semTools-0.5-1/semTools/man/lavTestScore.mi.Rd | 50 semTools-0.5-1/semTools/man/lavTestWald.mi.Rd |only semTools-0.5-1/semTools/man/lavaan.mi-class.Rd | 223 - semTools-0.5-1/semTools/man/longInvariance-deprecated.Rd |only semTools-0.5-1/semTools/man/measEq.syntax-class.Rd |only semTools-0.5-1/semTools/man/measEq.syntax.Rd |only semTools-0.5-1/semTools/man/measurementInvariance-deprecated.Rd |only semTools-0.5-1/semTools/man/measurementInvarianceCat-deprecated.Rd |only semTools-0.5-1/semTools/man/modindices.mi.Rd | 61 semTools-0.5-1/semTools/man/monteCarloMed.Rd | 6 semTools-0.5-1/semTools/man/net.Rd | 16 semTools-0.5-1/semTools/man/parcelAllocation.Rd | 4 semTools-0.5-1/semTools/man/partialInvariance.Rd | 24 semTools-0.5-1/semTools/man/permuteMeasEq-class.Rd | 3 semTools-0.5-1/semTools/man/permuteMeasEq.Rd | 47 semTools-0.5-1/semTools/man/plotProbe.Rd | 3 semTools-0.5-1/semTools/man/plotRMSEApower.Rd | 4 semTools-0.5-1/semTools/man/poolMAlloc.Rd | 9 semTools-0.5-1/semTools/man/reliability.Rd | 2 semTools-0.5-1/semTools/man/rotate.Rd | 2 semTools-0.5-1/semTools/man/runMI.Rd | 73 semTools-0.5-1/semTools/man/semTools-deprecated.Rd | 40 semTools-0.5-1/semTools/man/semTools.Rd | 4 semTools-0.5-1/semTools/man/standardizeMx-deprecated.Rd | 4 semTools-0.5-1/semTools/man/twostage-class.Rd | 22 semTools-0.5-1/semTools/man/twostage.Rd | 11 72 files changed, 4244 insertions(+), 4190 deletions(-)
Title: Analytical Tool for Aquatic Respirometry
Description: Calculates metabolic rate of fish and other aquatic organisms measured using
an intermittent-flow respirometry approach. The tool is used to run a set of graphical
QC tests of raw respirometry data, correct it for background respiration and chamber
effect, filter and extract target values of absolute and mass-specific metabolic rate.
Experimental design should include background respiration tests and measuring of one
or more metabolic rate traits. The package allows a user to import raw respirometry
data obtained from 'AquaResp' (free software), 'AutoResp' ('LoligoSystems'), 'OxyView'
('PreSens'), 'Pyro Oxygen Logger' ('PyroScience') and 'Q-box Aqua' ('QubitSystems').
Author: Sergey Morozov [aut, cre],
R.J. Scott McCairns [aut, ths],
Federico Calboli [ctb],
Juha Merila [ths],
Stephen White [dtc],
Daniel Montgomery [dtc],
Laura Almodovar-Acevedo [dtc],
Niclas Kolm [dtc],
Alexander Kotrschal [dtc]
Maintainer: Sergey Morozov <sergey.morozov@helsinki.fi>
Diff between FishResp versions 0.4.0 dated 2018-08-27 and 1.0.0 dated 2018-09-24
FishResp-0.4.0/FishResp/inst/extdata/qbox-aqua |only FishResp-1.0.0/FishResp/DESCRIPTION | 51 +++--- FishResp-1.0.0/FishResp/MD5 | 122 +++++++-------- FishResp-1.0.0/FishResp/NAMESPACE | 1 FishResp-1.0.0/FishResp/R/AMR.R | 28 +-- FishResp-1.0.0/FishResp/R/AMR.clean.R | 30 +-- FishResp-1.0.0/FishResp/R/AMR.raw.R | 22 +- FishResp-1.0.0/FishResp/R/AMR.slope.R | 20 +- FishResp-1.0.0/FishResp/R/FishResp.R | 10 + FishResp-1.0.0/FishResp/R/QC.activity.R | 9 - FishResp-1.0.0/FishResp/R/QC.meas.R | 12 - FishResp-1.0.0/FishResp/R/QC.slope.R | 157 +++++++++----------- FishResp-1.0.0/FishResp/R/SMR.R | 28 +-- FishResp-1.0.0/FishResp/R/SMR.clean.R | 30 +-- FishResp-1.0.0/FishResp/R/SMR.raw.R | 20 +- FishResp-1.0.0/FishResp/R/SMR.slope.R | 18 +- FishResp-1.0.0/FishResp/R/calculate.MR.R | 30 +-- FishResp-1.0.0/FishResp/R/convert.rMR.R | 22 +- FishResp-1.0.0/FishResp/R/convert.respirometry.R | 22 +- FishResp-1.0.0/FishResp/R/correct.meas.R | 12 - FishResp-1.0.0/FishResp/R/export.MR.R | 13 + FishResp-1.0.0/FishResp/R/extract.slope.R | 19 +- FishResp-1.0.0/FishResp/R/import.meas.R | 127 ++++++++-------- FishResp-1.0.0/FishResp/R/import.test.R | 99 ++++++------ FishResp-1.0.0/FishResp/R/info.R | 8 - FishResp-1.0.0/FishResp/R/input.info.R | 2 FishResp-1.0.0/FishResp/R/post.R | 18 +- FishResp-1.0.0/FishResp/R/pre.R | 16 +- FishResp-1.0.0/FishResp/R/presens.aquaresp.R | 16 +- FishResp-1.0.0/FishResp/R/pyroscience.aquaresp.R | 16 +- FishResp-1.0.0/FishResp/R/results.R | 20 +- FishResp-1.0.0/FishResp/R/rm.data.R |only FishResp-1.0.0/FishResp/data/AMR.RData |binary FishResp-1.0.0/FishResp/data/SMR.RData |binary FishResp-1.0.0/FishResp/data/results.RData |binary FishResp-1.0.0/FishResp/inst/extdata/qboxaqua |only FishResp-1.0.0/FishResp/man/AMR.Rd | 28 +-- FishResp-1.0.0/FishResp/man/AMR.clean.Rd | 30 +-- FishResp-1.0.0/FishResp/man/AMR.raw.Rd | 22 +- FishResp-1.0.0/FishResp/man/AMR.slope.Rd | 20 +- FishResp-1.0.0/FishResp/man/FishResp.Rd | 11 + FishResp-1.0.0/FishResp/man/QC.activity.Rd | 2 FishResp-1.0.0/FishResp/man/QC.meas.Rd | 10 - FishResp-1.0.0/FishResp/man/QC.slope.Rd | 11 - FishResp-1.0.0/FishResp/man/SMR.Rd | 28 +-- FishResp-1.0.0/FishResp/man/SMR.clean.Rd | 30 +-- FishResp-1.0.0/FishResp/man/SMR.raw.Rd | 20 +- FishResp-1.0.0/FishResp/man/SMR.slope.Rd | 18 +- FishResp-1.0.0/FishResp/man/calculate.MR.Rd | 6 FishResp-1.0.0/FishResp/man/convert.rMR.Rd | 18 +- FishResp-1.0.0/FishResp/man/convert.respirometry.Rd | 18 +- FishResp-1.0.0/FishResp/man/correct.meas.Rd | 12 - FishResp-1.0.0/FishResp/man/export.MR.Rd | 6 FishResp-1.0.0/FishResp/man/extract.slope.Rd | 17 +- FishResp-1.0.0/FishResp/man/import.meas.Rd | 33 ++-- FishResp-1.0.0/FishResp/man/import.test.Rd | 17 +- FishResp-1.0.0/FishResp/man/info.Rd | 8 - FishResp-1.0.0/FishResp/man/input.info.Rd | 2 FishResp-1.0.0/FishResp/man/post.Rd | 18 +- FishResp-1.0.0/FishResp/man/pre.Rd | 16 +- FishResp-1.0.0/FishResp/man/presens.aquaresp.Rd | 16 +- FishResp-1.0.0/FishResp/man/pyroscience.aquaresp.Rd | 16 +- FishResp-1.0.0/FishResp/man/results.Rd | 20 +- FishResp-1.0.0/FishResp/man/rm.data.Rd |only 64 files changed, 740 insertions(+), 711 deletions(-)
Title: Basic Statistical Functions for Package 'ff'
Description: Extends the out of memory vectors of 'ff' with
statistical functions and other utilities to ease their usage.
Author: Edwin de Jonge, Jan Wijffels, Jan van der Laan
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between ffbase versions 0.12.3 dated 2016-03-22 and 0.12.5 dated 2018-09-24
DESCRIPTION | 9 +- MD5 | 163 +++++++++++++++++++++++----------------------- NAMESPACE | 5 + NEWS | 4 - R/auxilary.R | 2 R/bigglm.R | 2 R/binned_sum.R | 2 R/binned_sumsq.R | 2 R/binned_tabulate.R | 2 R/byMean.R | 3 R/ffdfdply.R | 2 man/all.ff.Rd | 1 man/any.ff.Rd | 1 man/as.Date.ff_vector.Rd | 1 man/as.character.ff.Rd | 1 man/as.ffdf.ffdf.Rd | 1 man/as.ram.ffdf.Rd | 1 man/bigglm.ffdf.Rd | 1 man/binned_sum.Rd | 1 man/binned_sumsq.Rd | 5 - man/binned_tabulate.Rd | 5 - man/byMean.Rd | 1 man/bySum.Rd | 1 man/c.ff.Rd | 1 man/chunkexpr.Rd | 1 man/chunkify.Rd | 1 man/compact.Rd | 1 man/condMean.Rd | 1 man/condSum.Rd | 1 man/cumsum.ff.Rd | 5 - man/cut.ff.Rd | 1 man/diff.ff.Rd | 1 man/droplevels.ff.Rd | 1 man/droplevels.ffdf.Rd | 1 man/duplicated.ff.Rd | 1 man/expand.ffgrid.Rd | 1 man/ff_arithmetic.Rd | 9 +- man/ff_math.Rd | 35 ++++----- man/ff_ops.Rd | 13 +-- man/ffappend.Rd | 1 man/ffbase-package.Rd | 4 - man/ffdfappend.Rd | 1 man/ffdfdply.Rd | 1 man/ffdfrbind.fill.Rd | 1 man/ffdfwith.Rd | 1 man/ffextract.Rd | 1 man/ffextractffdf.Rd | 1 man/ffifelse.Rd | 1 man/ffmatch.Rd | 5 - man/ffordered.Rd | 1 man/ffrandom.Rd | 1 man/ffrep.int.Rd | 1 man/ffseq.Rd | 1 man/ffseq_len.Rd | 1 man/ffwhich.Rd | 1 man/format.ff_vector.Rd | 1 man/grouprunningcumsum.Rd | 1 man/hist.ff.Rd | 1 man/hist2d.ff.Rd | 1 man/ikey.Rd | 1 man/is.na.ff.Rd | 1 man/laf_to_ffdf.Rd | 1 man/load.ffdf.Rd | 1 man/mean.ff.Rd | 1 man/merge.ffdf.Rd | 8 +- man/min.ff.Rd | 3 man/move.ffdf.Rd | 1 man/pack.ffdf.Rd | 1 man/pkg-deprecated.Rd | 1 man/quantile.ff.Rd | 1 man/rle_ff.Rd | 1 man/save.ffdf.Rd | 1 man/set_ffbase_logging.Rd | 1 man/subset.ff.Rd | 1 man/sum.ff.Rd | 1 man/table.Rd | 1 man/tabulate.ff.Rd | 1 man/transform.ffdf.Rd | 1 man/unique.ff.Rd | 1 man/unpack.ffdf.Rd | 1 man/with.ffdf.Rd | 1 man/within.ffdf.Rd | 1 src/init.c |only 83 files changed, 144 insertions(+), 205 deletions(-)
Title: Inference Using Simulation
Description: Implements functions for simulation-based inference. In particular, implements functions to perform likelihood inference from data summaries whose distributions are simulated (Rousset et al. 2017 <doi:10.1111/1755-0998.12627>).
Author: François Rousset [aut, cre, cph]
(<https://orcid.org/0000-0003-4670-0371>)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between Infusion versions 1.2.0 dated 2018-04-04 and 1.3.0 dated 2018-09-24
Infusion-1.2.0/Infusion/R/joint_dens_mclust.R |only Infusion-1.3.0/Infusion/DESCRIPTION | 16 +- Infusion-1.3.0/Infusion/MD5 | 48 +++--- Infusion-1.3.0/Infusion/NAMESPACE | 4 Infusion-1.3.0/Infusion/R/MSL.R | 12 - Infusion-1.3.0/Infusion/R/SLikSQuant.R | 43 ++++- Infusion-1.3.0/Infusion/R/add_simulation.R | 160 +++++++++++++++++++-- Infusion-1.3.0/Infusion/R/calc_all_slices.R | 7 Infusion-1.3.0/Infusion/R/confintLR.SLik.R | 4 Infusion-1.3.0/Infusion/R/coresWrapper.R | 120 +++++++++++---- Infusion-1.3.0/Infusion/R/infer_logLs.R | 27 +-- Infusion-1.3.0/Infusion/R/infer_surface.R | 83 ++++++---- Infusion-1.3.0/Infusion/R/jointDens.R | 10 + Infusion-1.3.0/Infusion/R/plot.SLik.R | 2 Infusion-1.3.0/Infusion/R/plot.SLik_j.R | 2 Infusion-1.3.0/Infusion/R/profile.R | 2 Infusion-1.3.0/Infusion/R/project.R | 31 ++-- Infusion-1.3.0/Infusion/R/quantiles.R | 7 Infusion-1.3.0/Infusion/R/undocumentedFns.R | 7 Infusion-1.3.0/Infusion/inst/NEWS.Rd | 15 + Infusion-1.3.0/Infusion/man/Infusion-internal.Rd | 2 Infusion-1.3.0/Infusion/man/add.simulation.Rd | 57 +++++-- Infusion-1.3.0/Infusion/man/options.Rd | 4 Infusion-1.3.0/Infusion/man/refine.SLik.Rd | 6 Infusion-1.3.0/Infusion/tests/test-all.R | 14 + Infusion-1.3.0/Infusion/tests/testthat/test-3par.R |only 26 files changed, 492 insertions(+), 191 deletions(-)
Title: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
Description: General purpose TIFF file I/O for R users. Currently the only such
package with read and write support for TIFF files with floating point
(real-numbered) pixels, and the only package that can correctly import TIFF
files that were saved from 'ImageJ' and write TIFF files than can be
correctly read by 'ImageJ' <https://imagej.nih.gov/ij/>.
Also supports text image I/O.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>),
Kent Johnson [aut],
Simon Urbanek [ctb],
Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>),
Jeroen Ooms [rev, ctb] (<https://orcid.org/0000-0002-4035-0289>),
Jon Clayden [rev] (<https://orcid.org/0000-0002-6608-0619>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between ijtiff versions 1.4.0 dated 2018-09-10 and 1.4.1 dated 2018-09-24
DESCRIPTION | 13 +++++++------ MD5 | 20 +++++++++++--------- NEWS.md | 9 +++++++++ configure | 15 +++++++++++++-- inst/WORDLIST |only inst/doc/reading-and-writing-images.html | 12 ++++++------ inst/doc/text-images.html | 4 ++-- inst/doc/the-imagej-problem.Rmd | 2 +- inst/doc/the-imagej-problem.html | 6 +++--- tests/spelling.R |only tests/testthat/test_io.R | 2 +- vignettes/the-imagej-problem.Rmd | 2 +- 12 files changed, 54 insertions(+), 31 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-18 0.2.0
2016-11-06 0.1.2
2016-03-08 0.1.1
2016-01-26 0.1.0
2016-01-04 0.0.2
Title: 'Jupyter' Display Machinery
Description: An interface to the rich display capabilities of 'Jupyter' front-ends (e.g. 'Jupyter Notebook') <https://jupyter.org>.
Designed to be used from a running 'IRkernel' session <https://irkernel.github.io>.
Author: Thomas Kluyver [aut, cph],
Philipp Angerer [aut, cph, cre],
Jan Schulz [aut, cph]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between IRdisplay versions 0.5.0 dated 2018-05-17 and 0.6 dated 2018-09-24
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/display.r | 3 ++- R/utils.r | 2 +- man/display.Rd | 5 +++-- 5 files changed, 14 insertions(+), 12 deletions(-)
Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Author: Emmanuel Paradis [aut, cre, cph]
(<https://orcid.org/0000-0003-3092-2199>),
Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>),
Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>),
Joseph Brown [aut, cph],
Julien Claude [aut, cph],
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph],
Benoit Durand [aut, cph],
Julien Dutheil [aut, cph],
RJ Ewing [aut, cph],
Olivier Gascuel [aut, cph],
Thomas Guillerme [aut, cph],
Christoph Heibl [aut, cph],
Anthony Ives [aut, cph],
Bradley Jones [aut, cph],
Franz Krah [aut, cph],
Daniel Lawson [aut, cph],
Vincent Lefort [aut, cph],
Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>),
Jim Lemon [aut, cph],
Eric Marcon [aut, cph],
Rosemary McCloskey [aut, cph],
Johan Nylander [aut, cph],
Rainer Opgen-Rhein [aut, cph],
Andrei-Alin Popescu [aut, cph],
Manuela Royer-Carenzi [aut, cph],
Klaus Schliep [aut, cph],
Korbinian Strimmer [aut, cph],
Damien de Vienne [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between ape versions 5.1 dated 2018-04-04 and 5.2 dated 2018-09-24
DESCRIPTION | 27 ++++++------ MD5 | 68 +++++++++++++++--------------- NAMESPACE | 17 +++++++ R/DNA.R | 37 +++++++++++++++- R/ace.R | 5 +- R/apetools.R | 8 +-- R/as.phylo.formula.R | 83 +++++++++++++++++++----------------- R/checkValidPhylo.R | 4 - R/drop.tip.R | 38 +++++++++++++++- R/makeLabel.R | 55 +++++++++++++++++++++++- R/multi2di.R | 40 ++++++++--------- R/nodelabels.R | 5 +- R/plot.phylo.R | 6 +- R/plot.phyloExtra.R | 12 +++-- R/read.dna.R | 4 - R/read.gff.R | 10 +++- R/read.tree.R | 108 ++---------------------------------------------- R/write.nexus.data.R | 13 +++++ build/vignette.rds |binary inst/CITATION | 12 ++--- inst/doc/MoranI.pdf |binary man/AAbin.Rd | 11 +--- man/ace.Rd | 6 ++ man/apetools.Rd | 2 man/as.phylo.formula.Rd | 41 +++++++++++++----- man/drop.tip.Rd | 7 ++- man/label2table.Rd | 2 man/makeLabel.Rd | 3 - man/mixedFontLabel.Rd | 2 man/plotTreeTime.Rd | 6 ++ man/rDNAbin.Rd |only man/read.caic.Rd | 2 man/read.gff.Rd | 9 +++- man/rlineage.Rd | 3 - man/updateLabel.Rd |only src/me.c | 4 - 36 files changed, 371 insertions(+), 279 deletions(-)
Title: Variable Selection for Optimal Individualized Dynamic Treatment
Regime
Description: Sequential advantage selection (SAS, Fan, Lu and Song, 2016) <arXiv:1405.5239>
and penalized A-learning (PAL, Shi, et al., 2018) methods are implement for selecting
important variables involved in optimal individualized (dynamic) treatment regime in
both single-stage or multi-stage studies.
Author: Chengchun Shi, Ailin Fan, Rui Song and Wenbin Lu
Maintainer: Chengchun Shi <cshi4@ncsu.edu>
Diff between ITRSelect versions 1.0 dated 2018-04-30 and 1.0-1 dated 2018-09-24
DESCRIPTION | 13 +++++++------ MD5 | 13 +++++++------ NEWS |only inst/CITATION | 2 +- man/ITRSelect-package.Rd | 2 +- man/PAL.Rd | 2 +- man/SSTARD.onestage.Rd | 4 ++-- man/SSTARD.twostage.Rd | 4 ++-- 8 files changed, 21 insertions(+), 19 deletions(-)
Title: Analysis of Factorial Experiments
Description: Convenience functions for analyzing factorial experiments using ANOVA or
mixed models. aov_ez(), aov_car(), and aov_4() allow specification of
between, within (i.e., repeated-measures), or mixed (i.e., split-plot)
ANOVAs for data in long format (i.e., one observation per row),
automatically aggregating multiple observations per individual and cell
of the design. mixed() fits mixed models using lme4::lmer() and computes
p-values for all fixed effects using either Kenward-Roger or Satterthwaite
approximation for degrees of freedom (LMM only), parametric bootstrap
(LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs).
afex_plot() provides a high-level interface for interaction or one-way
plots using ggplot2, combining raw data and model estimates. afex uses
type 3 sums of squares as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>),
Ben Bolker [aut],
Jake Westfall [aut],
Frederik Aust [aut] (<https://orcid.org/0000-0003-4900-788X>),
Søren Højsgaard [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb],
Ulf Mertens [ctb],
Jonathon Love [ctb],
Russell Lenth [ctb],
Rune Haubo Bojesen Christensen [ctb]
Maintainer: Henrik Singmann <singmann+afex@gmail.com>
Diff between afex versions 0.21-2 dated 2018-06-24 and 0.22-1 dated 2018-09-24
DESCRIPTION | 67 ++-- MD5 | 66 ++-- NAMESPACE | 15 NEWS | 36 ++ R/afex-package.R | 33 -- R/afex_plot.R |only R/afex_plot_utils.R |only R/aov_car.R | 357 +++++++++++++++++----- R/methods.afex_aov.R | 20 - R/mixed.R | 496 +++++++++++++++++++++++-------- R/nice.R | 134 ++++++-- R/zzz.R | 28 + build/partial.rdb |only build/vignette.rds |binary inst/doc/afex_anova_example.R | 61 ++- inst/doc/afex_anova_example.Rmd | 116 +++++-- inst/doc/afex_anova_example.html | 495 +++++++++++++++---------------- inst/doc/afex_mixed_example.R | 14 inst/doc/afex_mixed_example.Rmd | 16 - inst/doc/afex_mixed_example.html | 121 +++---- inst/doc/afex_plot_introduction.R |only inst/doc/afex_plot_introduction.Rmd |only inst/doc/afex_plot_introduction.html |only inst/doc/introduction-mixed-models.pdf |binary inst/extdata/freeman_reduced_model.rda |only man/afex-package.Rd | 55 ++- man/afex_aov-methods.Rd | 45 +- man/afex_plot.Rd |only man/aov_car.Rd | 376 +++++++++++++++++------- man/fhch2010.Rd | 15 man/mixed.Rd | 501 ++++++++++++++++++++++++-------- man/nice.Rd | 134 ++++++-- man/sk2011.2.Rd | 7 tests/testthat/test-afex_plot-basics.R |only tests/testthat/test-emmeans-interface.R | 80 ++--- tests/testthat/test-mixed-effects.R | 5 vignettes/afex_anova_example.Rmd | 116 +++++-- vignettes/afex_mixed_example.Rmd | 16 - vignettes/afex_plot_introduction.Rmd |only 39 files changed, 2327 insertions(+), 1098 deletions(-)