Title: Optimal Test Design Approach to Fixed and Adaptive Test
Construction
Description: Use the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and
van der Linden (2018) <doi:10.1201/9781315117430> in constructing fixed and adaptive tests. Supports the following
mixed-integer programming (MIP) solver packages: 'lpsymphony', 'Rsymphony', 'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package
is not available from CRAN; see <https://www.gurobi.com/downloads/>. See vignette for installing 'Rsymphony' package
on Mac systems.
Author: Seung W. Choi [aut, cre] (<https://orcid.org/0000-0003-4777-5420>),
Sangdon Lim [aut] (<https://orcid.org/0000-0002-2988-014X>)
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between TestDesign versions 1.1.3 dated 2020-10-01 and 1.2.0 dated 2021-01-22
TestDesign-1.1.3/TestDesign/man/plotCAT-methods.Rd |only TestDesign-1.1.3/TestDesign/man/plotShadow-methods.Rd |only TestDesign-1.1.3/TestDesign/man/showConstraints.Rd |only TestDesign-1.1.3/TestDesign/man/updateConstraints.Rd |only TestDesign-1.1.3/TestDesign/tests/testthat/test_item_exclusion.R |only TestDesign-1.2.0/TestDesign/DESCRIPTION | 11 TestDesign-1.2.0/TestDesign/MD5 | 155 +- TestDesign-1.2.0/TestDesign/NAMESPACE | 6 TestDesign-1.2.0/TestDesign/NEWS.md | 25 TestDesign-1.2.0/TestDesign/R/constraint_functions.R | 38 TestDesign-1.2.0/TestDesign/R/extensions.R | 6 TestDesign-1.2.0/TestDesign/R/helper_functions.R | 13 TestDesign-1.2.0/TestDesign/R/import.R | 40 TestDesign-1.2.0/TestDesign/R/item_class.R | 15 TestDesign-1.2.0/TestDesign/R/item_pool_operators.R | 25 TestDesign-1.2.0/TestDesign/R/loading_functions.R | 110 - TestDesign-1.2.0/TestDesign/R/other_functions.R | 4 TestDesign-1.2.0/TestDesign/R/plot_functions.R | 33 TestDesign-1.2.0/TestDesign/R/print_functions.R | 19 TestDesign-1.2.0/TestDesign/R/shadow_class.R | 29 TestDesign-1.2.0/TestDesign/R/shadow_functions.R | 403 ++---- TestDesign-1.2.0/TestDesign/R/solver_functions.R | 75 - TestDesign-1.2.0/TestDesign/R/static_class.R | 2 TestDesign-1.2.0/TestDesign/R/summary_functions.R | 19 TestDesign-1.2.0/TestDesign/R/theta_functions.R | 81 + TestDesign-1.2.0/TestDesign/R/xdata_functions.R | 28 TestDesign-1.2.0/TestDesign/build/vignette.rds |binary TestDesign-1.2.0/TestDesign/data/constraints_bayes.rda |binary TestDesign-1.2.0/TestDesign/data/constraints_bayes_data.rda |binary TestDesign-1.2.0/TestDesign/data/constraints_fatigue.rda |binary TestDesign-1.2.0/TestDesign/data/constraints_fatigue_data.rda |binary TestDesign-1.2.0/TestDesign/data/constraints_reading.rda |binary TestDesign-1.2.0/TestDesign/data/constraints_reading_data.rda |binary TestDesign-1.2.0/TestDesign/data/constraints_science.rda |binary TestDesign-1.2.0/TestDesign/data/constraints_science_data.rda |binary TestDesign-1.2.0/TestDesign/data/itemattrib_bayes.rda |binary TestDesign-1.2.0/TestDesign/data/itemattrib_bayes_data.rda |binary TestDesign-1.2.0/TestDesign/data/itemattrib_fatigue.rda |binary TestDesign-1.2.0/TestDesign/data/itemattrib_fatigue_data.rda |binary TestDesign-1.2.0/TestDesign/data/itemattrib_reading.rda |binary TestDesign-1.2.0/TestDesign/data/itemattrib_reading_data.rda |binary TestDesign-1.2.0/TestDesign/data/itemattrib_science.rda |binary TestDesign-1.2.0/TestDesign/data/itemattrib_science_data.rda |binary TestDesign-1.2.0/TestDesign/data/itemcontent_fatigue_data.rda |binary TestDesign-1.2.0/TestDesign/data/itempool_bayes.rda |binary TestDesign-1.2.0/TestDesign/data/itempool_bayes_data.rda |binary TestDesign-1.2.0/TestDesign/data/itempool_fatigue.rda |binary TestDesign-1.2.0/TestDesign/data/itempool_fatigue_data.rda |binary TestDesign-1.2.0/TestDesign/data/itempool_reading.rda |binary TestDesign-1.2.0/TestDesign/data/itempool_reading_data.rda |binary TestDesign-1.2.0/TestDesign/data/itempool_science.rda |binary TestDesign-1.2.0/TestDesign/data/itempool_science_data.rda |binary TestDesign-1.2.0/TestDesign/data/itempool_se_bayes_data.rda |binary TestDesign-1.2.0/TestDesign/data/resp_fatigue_data.rda |binary TestDesign-1.2.0/TestDesign/data/stimattrib_reading.rda |binary TestDesign-1.2.0/TestDesign/data/stimattrib_reading_data.rda |binary TestDesign-1.2.0/TestDesign/inst/doc/constraints.Rmd | 6 TestDesign-1.2.0/TestDesign/inst/doc/constraints.html | 140 +- TestDesign-1.2.0/TestDesign/inst/doc/rsymphony.Rmd | 12 TestDesign-1.2.0/TestDesign/inst/doc/rsymphony.html | 45 TestDesign-1.2.0/TestDesign/inst/extdata/constraints_bayes_320.csv | 34 TestDesign-1.2.0/TestDesign/inst/extdata/constraints_fatigue_95.csv | 224 +-- TestDesign-1.2.0/TestDesign/inst/extdata/constraints_reading_303.csv | 38 TestDesign-1.2.0/TestDesign/inst/extdata/constraints_science_1000.csv | 74 - TestDesign-1.2.0/TestDesign/inst/extdata/example_datasets.R | 6 TestDesign-1.2.0/TestDesign/inst/extdata/itemattrib_reading_303.csv | 606 +++++----- TestDesign-1.2.0/TestDesign/inst/extdata/stimattrib_reading_303.csv | 70 - TestDesign-1.2.0/TestDesign/man/Shadow-methods.Rd | 14 TestDesign-1.2.0/TestDesign/man/constraint-class.Rd | 4 TestDesign-1.2.0/TestDesign/man/createShadowTestConfig.Rd | 8 TestDesign-1.2.0/TestDesign/man/createStaticTestConfig.Rd | 2 TestDesign-1.2.0/TestDesign/man/item_pool-class.Rd | 2 TestDesign-1.2.0/TestDesign/man/item_pool-operators.Rd | 6 TestDesign-1.2.0/TestDesign/man/loadItemPool.Rd | 4 TestDesign-1.2.0/TestDesign/man/mle-methods.Rd | 10 TestDesign-1.2.0/TestDesign/man/mlef-methods.Rd | 10 TestDesign-1.2.0/TestDesign/man/plot-methods.Rd | 11 TestDesign-1.2.0/TestDesign/man/summary-methods.Rd | 8 TestDesign-1.2.0/TestDesign/tests/testthat/test-gfi.R |only TestDesign-1.2.0/TestDesign/tests/testthat/test_excluding.R |only TestDesign-1.2.0/TestDesign/vignettes/constraints.Rmd | 6 TestDesign-1.2.0/TestDesign/vignettes/rsymphony.Rmd | 12 82 files changed, 1378 insertions(+), 1111 deletions(-)
Title: End-to-End Marine Food Web Model
Description: A dynamic model of
the big-picture, whole ecosystem effects of hydrodynamics,
temperature, nutrients, and fishing on continental shelf marine
food webs. The package is described in: Heath, M.R.,
Speirs, D.C., Thurlbeck, I. and Wilson, R.J. (2020)
<doi:10.1111/2041-210X.13510> StrathE2E2: An R package
for modelling the dynamics of marine food webs and
fisheries. 8pp.
Author: Michael Heath [aut],
Ian Thurlbeck [ctb]
Maintainer: Michael Heath <m.heath@strath.ac.uk>
Diff between StrathE2E2 versions 3.2.0 dated 2020-09-02 and 3.3.0 dated 2021-01-22
StrathE2E2-3.2.0/StrathE2E2/inst/extdata/Models/North_Sea/1970-1999/Param/fishing_power_NORTH_SEA.csv |only StrathE2E2-3.2.0/StrathE2E2/inst/extdata/Models/North_Sea/2003-2013/Param/fishing_power_NORTH_SEA.csv |only StrathE2E2-3.3.0/StrathE2E2/DESCRIPTION | 20 StrathE2E2-3.3.0/StrathE2E2/MD5 | 98 - StrathE2E2-3.3.0/StrathE2E2/NAMESPACE | 1 StrathE2E2-3.3.0/StrathE2E2/NEWS.md | 21 StrathE2E2-3.3.0/StrathE2E2/R/StrathE2E2.R | 21 StrathE2E2-3.3.0/StrathE2E2/R/derive_annual_results_inshore.R | 2 StrathE2E2-3.3.0/StrathE2E2/R/derive_annual_results_offshore.R | 2 StrathE2E2-3.3.0/StrathE2E2/R/derive_annual_results_wholedomain.R | 2 StrathE2E2-3.3.0/StrathE2E2/R/derive_model_target_results.R | 6 StrathE2E2-3.3.0/StrathE2E2/R/e2e_get_senscrit.R |only StrathE2E2-3.3.0/StrathE2E2/R/e2e_plot_opt_diagnostics.R | 2 StrathE2E2-3.3.0/StrathE2E2/R/e2e_run_sens.R | 280 +++- StrathE2E2-3.3.0/StrathE2E2/R/e2e_run_ycurve.R | 2 StrathE2E2-3.3.0/StrathE2E2/R/generate_df_yield_curve_data.R | 2 StrathE2E2-3.3.0/StrathE2E2/R/generate_pf_yield_curve_data.R | 2 StrathE2E2-3.3.0/StrathE2E2/R/internal.R | 2 StrathE2E2-3.3.0/StrathE2E2/R/perturb_parameters.R | 2 StrathE2E2-3.3.0/StrathE2E2/R/perturb_parameters_all.R | 6 StrathE2E2-3.3.0/StrathE2E2/R/plot_act_hr_optimization_diagnostics.R | 2 StrathE2E2-3.3.0/StrathE2E2/R/plot_eco_hr_act_eco_optimization_diagnostics.R | 2 StrathE2E2-3.3.0/StrathE2E2/R/plot_inshore_vs_offshore_anavmass.R | 6 StrathE2E2-3.3.0/StrathE2E2/R/plot_sensitivity_results.R | 23 StrathE2E2-3.3.0/StrathE2E2/R/process_sensitivity_analysis_results.R | 20 StrathE2E2-3.3.0/StrathE2E2/README.md | 8 StrathE2E2-3.3.0/StrathE2E2/inst/CITATION | 8 StrathE2E2-3.3.0/StrathE2E2/inst/doc/StrathE2E2_CheatSheet.pdf |binary StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Internal.data/StrathE2E_parameter_list.csv | 9 StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/1970-1999/MODEL_SETUP.csv | 2 StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/1970-1999/Param/fishing_activity_NORTH_SEA_1970-1999.csv | 24 StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/1970-1999/Param/fishing_fleet_NORTH_SEA_1970-1999.csv | 2 StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/1970-1999/Param/fishing_power_NORTH_SEA_1970-1999.csv |only StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/1970-1999/Param/fitted_preference_matrix_NORTH_SEA.csv | 16 StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/1970-1999/Param/fitted_uptake_mort_rates_NORTH_SEA.csv | 34 StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/1970-1999/Param/initial_values_NORTH_SEA_1970-1999.csv | 142 +- StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/2003-2013/MODEL_SETUP.csv | 2 StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/2003-2013/Param/fishing_activity_NORTH_SEA_2003-2013.csv | 24 StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/2003-2013/Param/fishing_fleet_NORTH_SEA_2003-2013.csv | 2 StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/2003-2013/Param/fishing_power_NORTH_SEA_2003-2013.csv |only StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/2003-2013/Param/fitted_preference_matrix_NORTH_SEA.csv | 16 StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/2003-2013/Param/fitted_uptake_mort_rates_NORTH_SEA.csv | 34 StrathE2E2-3.3.0/StrathE2E2/inst/extdata/Models/North_Sea/2003-2013/Param/initial_values_NORTH_SEA_2003-2013.csv | 142 +- StrathE2E2-3.3.0/StrathE2E2/man/StrathE2E2-package.Rd | 21 StrathE2E2-3.3.0/StrathE2E2/man/e2e_get_senscrit.Rd |only StrathE2E2-3.3.0/StrathE2E2/man/e2e_plot_opt_diagnostics.Rd | 2 StrathE2E2-3.3.0/StrathE2E2/man/e2e_run_sens.Rd | 66 - StrathE2E2-3.3.0/StrathE2E2/man/e2e_run_ycurve.Rd | 2 StrathE2E2-3.3.0/StrathE2E2/src/StrathE2E2_ecology_model_function.c | 566 +++++++--- StrathE2E2-3.3.0/StrathE2E2/tests/testdata/models/Testbed/Const/Param/initial_values_Testbed.csv | 136 +- StrathE2E2-3.3.0/StrathE2E2/tests/testthat/test-for-steady-state-in-testbed-model.R | 2 StrathE2E2-3.3.0/StrathE2E2/tests/testthat/test-top-predator-fluxes.R | 120 +- StrathE2E2-3.3.0/StrathE2E2/vignettes/CheatSheet.pdf |binary 53 files changed, 1177 insertions(+), 727 deletions(-)
Title: Partitioning of Individual Autozygosity into Multiple
Homozygous-by-Descent Classes
Description: Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to
estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes
with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct
for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the
segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the
parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity
probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017)
<doi:10.1111/mec.14324>.
Author: Tom Druet, Naveen Kumar Kadri, Amandine Bertrand and Mathieu Gautier
Maintainer: Tom Druet <tom.druet@uliege.be>
Diff between RZooRoH versions 0.2.4 dated 2021-01-20 and 0.3.0 dated 2021-01-22
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/zooroh-vignette.pdf |binary src/zooSIM.f90 | 5 ++--- 4 files changed, 8 insertions(+), 9 deletions(-)
Title: Process Accelerometer Data for Physical Activity Measurement
Description: It provides a function "wearingMarking" for classification of monitor
wear and nonwear time intervals in accelerometer data collected to assess
physical activity. The package also contains functions for making plot for
accelerometer data and obtaining the summary of various information including
daily monitor wear time and the mean monitor wear time during valid days.
"deliveryPred" and "markDelivery" can classify days for ActiGraph delivery by mail;
"deliveryPreprocess" can process accelerometry data for analysis by zeropadding incomplete
days and removing low activity days; "markPAI" can categorize physical activity
intensity level based on user-defined cut-points of accelerometer counts. It also
supports importing ActiGraph AGD files with "readActigraph" and "queryActigraph" functions.
Author: Leena Choi [aut, cre] (<https://orcid.org/0000-0002-2544-7090>),
Cole Beck [aut] (<https://orcid.org/0000-0002-6849-6255>),
Zhouwen Liu [aut],
Ryan Moore [aut],
Charles E. Matthews [aut],
Maciej S. Buchowski [aut]
Maintainer: Leena Choi <leena.choi@Vanderbilt.Edu>
Diff between PhysicalActivity versions 0.2-2 dated 2018-05-18 and 0.2-4 dated 2021-01-22
DESCRIPTION | 60 ++++++++++++++++++++++++++-------------- MD5 | 48 ++++++++++++++++++++------------ NAMESPACE | 7 ++++ R/PhysicalActivity-package.R | 8 +++-- R/dataSec.R | 2 + R/deliveryData.R | 2 + R/deliveryFeatures.R |only R/deliveryPred.R |only R/deliveryPrediction.R |only R/deliveryPreprocess.R |only R/summaryData.R | 25 +++++++++++++--- R/utils.R |only inst |only man/PhysicalActivity-package.Rd | 14 ++------- man/dataSec.Rd | 8 +++-- man/deliveryData.Rd | 8 +++-- man/deliveryFeatures.Rd |only man/deliveryPred.Rd |only man/deliveryPrediction.Rd |only man/deliveryPreprocess.Rd |only man/deliveryThreshold.Rd | 9 ++++-- man/markDelivery.Rd | 14 ++++++--- man/markPAI.Rd | 10 ++++-- man/marking.Rd | 10 +++++- man/pa-internal.Rd |only man/plotData.Rd | 12 ++++++-- man/sumVct.Rd | 10 +++++- man/summaryData.Rd | 20 ++++++++++--- man/wearingMarking.Rd | 18 +++++++++--- 29 files changed, 198 insertions(+), 87 deletions(-)
More information about PhysicalActivity at CRAN
Permanent link
Title: Tools for HTML
Description: Tools for HTML generation and output.
Author: Joe Cheng [aut],
Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>),
Winston Chang [aut],
Yihui Xie [aut],
Jeff Allen [aut],
RStudio [cph]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between htmltools versions 0.5.1 dated 2021-01-12 and 0.5.1.1 dated 2021-01-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NEWS.md | 6 ++++++ 3 files changed, 12 insertions(+), 6 deletions(-)
Title: Modular Hydrological Model
Description: The HBV hydrological model (Bergström, S. and Lindström, G., (2015) <doi:10.1002/hyp.10510>) has been split in modules to allow the user to build his/her own model. This version was developed by the author in IANIGLA-CONICET (Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales - Consejo Nacional de Investigaciones Cientificas y Tecnicas) for hydroclimatic studies in the Andes. HBV.IANIGLA incorporates routines for clean and debris covered glacier melt simulations.
Author: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>
Maintainer: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>
Diff between HBV.IANIGLA versions 0.2.0 dated 2021-01-21 and 0.2.1 dated 2021-01-22
DESCRIPTION | 6 +-- MD5 | 18 +++++----- inst/doc/alerce_mass_balance.html | 4 +- inst/doc/glacio-hydrological_model.html | 4 +- inst/doc/lumped_basin.html | 4 +- inst/doc/model_overview.html | 4 +- inst/doc/semi-distributed_basin.html | 4 +- inst/doc/tupungato_river_basin.html | 4 +- src/Routing_HBV.cpp | 36 ++++++++++----------- src/SnowGlacier_HBV.cpp | 54 ++++++++++++++++---------------- 10 files changed, 69 insertions(+), 69 deletions(-)
Title: List Comprehension and Tools
Description: Create list comprehensions (and other types of comprehension) similar to those in
'python', 'haskell', and other languages. List comprehension in 'R' converts a
regular for() loop into a vectorized lapply() function. Support for looping
with multiple variables, parallelization, and across non-standard objects included. Package
also contains a variety of functions to help with list comprehension.
Author: Chris Mann <cmann3@unl.edu>
Maintainer: Chris Mann <cmann3@unl.edu>
Diff between eList versions 0.0.1.0 dated 2021-01-11 and 0.2.0 dated 2021-01-22
eList-0.0.1.0/eList/R/fun_helpers.R |only eList-0.0.1.0/eList/R/funprog.R |only eList-0.0.1.0/eList/R/lambda.R |only eList-0.0.1.0/eList/man/funprog.Rd |only eList-0.0.1.0/eList/man/helpersFun.Rd |only eList-0.0.1.0/eList/man/lambda.Rd |only eList-0.2.0/eList/DESCRIPTION | 12 - eList-0.2.0/eList/MD5 | 36 ++-- eList-0.2.0/eList/NAMESPACE | 26 --- eList-0.2.0/eList/NEWS.md |only eList-0.2.0/eList/R/comprehension.R | 94 ++++++++---- eList-0.2.0/eList/R/flatten.R | 8 - eList-0.2.0/eList/R/internal.R | 31 +++- eList-0.2.0/eList/R/iter_helpers.R | 2 eList-0.2.0/eList/R/list_tools.R | 5 eList-0.2.0/eList/README.md |only eList-0.2.0/eList/build/vignette.rds |binary eList-0.2.0/eList/inst/doc/VectorComprehension.R | 5 eList-0.2.0/eList/inst/doc/VectorComprehension.Rmd | 8 + eList-0.2.0/eList/inst/doc/VectorComprehension.html | 149 +++++++++++--------- eList-0.2.0/eList/man/comprehension.Rd | 4 eList-0.2.0/eList/man/null.omit.Rd | 2 eList-0.2.0/eList/vignettes/VectorComprehension.Rmd | 8 + 23 files changed, 229 insertions(+), 161 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxonomic, phylogenetic and functional). It allows
performing a number of analyses based on species identities/abundances, phylogenetic/functional trees, convex-hulls or kernel density n-dimensional hypervolumes
depicting species relationships.
Author: Pedro Cardoso, Stefano Mammola, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 2.4.1 dated 2020-12-17 and 2.4.2 dated 2021-01-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/BAT.R | 33 ++++++++++++++++++--------------- man/cwd.Rd | 4 +++- man/cwe.Rd | 4 +++- man/cwm.Rd | 4 +++- 7 files changed, 38 insertions(+), 29 deletions(-)
Title: Microbiome Regression-Based Analysis Tests
Description: Test for overall association between microbiome composition data and phenotypes via phylogenetic kernels.
The phenotype can be univariate continuous or binary (Zhao et al. (2015) <doi:10.1016/j.ajhg.2015.04.003>),
survival outcomes (Plantinga et al. (2017) <doi:10.1186/s40168-017-0239-9>),
multivariate (Zhan et al. (2017) <doi:10.1002/gepi.22030>) and
structured phenotypes (Zhan et al. (2017) <doi:10.1111/biom.12684>).
The package can also use robust and quantile regression (Fu et al. (2020+), in preparation).
In each case, the microbiome community effect is modeled nonparametrically through a kernel function,
which can incorporate phylogenetic tree information.
Author: Anna Plantinga [aut, cre],
Nehemiah Wilson [aut, ctb],
Haotian Zheng [aut, ctb],
Xiang Zhan [aut, ctb],
Michael Wu [aut],
Ni Zhao [aut, ctb],
Jun Chen [aut]
Maintainer: Anna Plantinga <amp9@williams.edu>
Diff between MiRKAT versions 1.1.1 dated 2020-08-27 and 1.1.2 dated 2021-01-22
DESCRIPTION | 6 MD5 | 36 +- NAMESPACE | 1 R/CSKAT.R | 80 ------ R/CSKAT_helper.R | 23 - R/GLMMMiRKAT.R | 43 ++- R/MiRKAT.R | 9 R/MiRKAT_Binary.R | 50 ++-- R/MiRKAT_Continuous.R | 9 build/vignette.rds |binary inst/doc/MiRKAT_Vignette.R | 23 - inst/doc/MiRKAT_Vignette.Rmd | 43 --- inst/doc/MiRKAT_Vignette.html | 510 ++++++++++++------------------------------ man/CSKAT.Rd | 24 - man/GLMMMiRKAT.Rd | 10 man/MiRKAT.Rd | 2 man/MiRKAT_continuous.Rd | 4 man/inner.CSKAT.Rd | 7 vignettes/MiRKAT_Vignette.Rmd | 43 --- 19 files changed, 304 insertions(+), 619 deletions(-)
Title: Companion Software for the Coursera Statistics with R
Specialization
Description: Data and functions to support Bayesian and frequentist inference and decision making
for the Coursera Specialization "Statistics with R".
See <https://github.com/StatsWithR/statsr> for more information.
Author: Colin Rundel [aut],
Mine Cetinkaya-Rundel [aut],
Merlise Clyde [aut, cre],
David Banks [aut]
Maintainer: Merlise Clyde <clyde@duke.edu>
Diff between statsr versions 0.2.0 dated 2020-05-05 and 0.3.0 dated 2021-01-22
statsr-0.2.0/statsr/R/bayes_single_mean.R |only statsr-0.3.0/statsr/DESCRIPTION | 16 - statsr-0.3.0/statsr/LICENSE | 1 statsr-0.3.0/statsr/MD5 | 81 ++++--- statsr-0.3.0/statsr/NAMESPACE | 2 statsr-0.3.0/statsr/NEWS.md | 11 - statsr-0.3.0/statsr/R/BF_app.R |only statsr-0.3.0/statsr/R/ames_sampling_dist.R | 14 + statsr-0.3.0/statsr/R/bandit_posterior.R | 9 statsr-0.3.0/statsr/R/bandit_sim.R | 35 +++ statsr-0.3.0/statsr/R/bayes_inference.R | 248 ++++++++++++++++++++--- statsr-0.3.0/statsr/R/bayes_single_mean_JZS.R |only statsr-0.3.0/statsr/R/bayes_single_mean_sim.R |only statsr-0.3.0/statsr/R/bayes_single_mean_theo.R |only statsr-0.3.0/statsr/R/bayes_two_mean.R | 112 ++++------ statsr-0.3.0/statsr/R/calc_streak.R | 2 statsr-0.3.0/statsr/R/credible_interval.R | 15 + statsr-0.3.0/statsr/R/inference.R | 27 ++ statsr-0.3.0/statsr/R/mlb11.R | 2 statsr-0.3.0/statsr/R/plot_ss.R | 26 +- statsr-0.3.0/statsr/R/rep_sample_n.R | 5 statsr-0.3.0/statsr/R/rstudio.R | 3 statsr-0.3.0/statsr/R/statsr.R | 18 + statsr-0.3.0/statsr/R/tapwater.R |only statsr-0.3.0/statsr/R/zinc.R |only statsr-0.3.0/statsr/README.md | 27 +- statsr-0.3.0/statsr/data/tapwater.rda |only statsr-0.3.0/statsr/data/zinc.rda |only statsr-0.3.0/statsr/inst/WORDLIST |only statsr-0.3.0/statsr/inst/lab.css | 121 +++++------ statsr-0.3.0/statsr/man/BF_app.Rd |only statsr-0.3.0/statsr/man/allow_shiny.Rd | 5 statsr-0.3.0/statsr/man/ames_sampling_dist.Rd | 11 - statsr-0.3.0/statsr/man/bandit_posterior.Rd | 7 statsr-0.3.0/statsr/man/bandit_sim.Rd | 36 +++ statsr-0.3.0/statsr/man/bayes_inference.Rd | 95 ++++++++ statsr-0.3.0/statsr/man/calc_streak.Rd | 4 statsr-0.3.0/statsr/man/credible_interval_app.Rd | 14 + statsr-0.3.0/statsr/man/figures |only statsr-0.3.0/statsr/man/inference.Rd | 28 ++ statsr-0.3.0/statsr/man/mlb11.Rd | 2 statsr-0.3.0/statsr/man/plot_bandit_posterior.Rd | 4 statsr-0.3.0/statsr/man/plot_ss.Rd | 11 - statsr-0.3.0/statsr/man/rep_sample_n.Rd | 8 statsr-0.3.0/statsr/man/statsr.Rd | 18 + statsr-0.3.0/statsr/man/tapwater.Rd |only statsr-0.3.0/statsr/man/zinc.Rd |only statsr-0.3.0/statsr/tests |only 48 files changed, 773 insertions(+), 245 deletions(-)
Title: Exploratory Data Analysis System
Description: Performs an exploratory data analysis through a 'shiny' interface. It includes basic methods such as the mean, median, mode, normality test, among others. It also includes clustering techniques such as Principal Components Analysis, Hierarchical Clustering and the K-Means Method.
Author: Oldemar Rodriguez [aut, cre],
Diego Jiménez [ctb]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between discoveR versions 1.2.9 dated 2020-08-03 and 2.1.6 dated 2021-01-22
discoveR-1.2.9/discoveR/R/init_discover.R |only discoveR-1.2.9/discoveR/inst/application |only discoveR-1.2.9/discoveR/man/init_discover.Rd |only discoveR-2.1.6/discoveR/DESCRIPTION | 31 ++- discoveR-2.1.6/discoveR/MD5 | 102 ++++++++++-- discoveR-2.1.6/discoveR/NAMESPACE | 118 +++++++++++++-- discoveR-2.1.6/discoveR/R/app_config.R |only discoveR-2.1.6/discoveR/R/app_server.R |only discoveR-2.1.6/discoveR/R/app_ui.R |only discoveR-2.1.6/discoveR/R/discoveR.R |only discoveR-2.1.6/discoveR/R/golem_utils_server.R |only discoveR-2.1.6/discoveR/R/golem_utils_ui.R |only discoveR-2.1.6/discoveR/R/mod_acercade.R |only discoveR-2.1.6/discoveR/R/mod_acp.R |only discoveR-2.1.6/discoveR/R/mod_acp_fct.R |only discoveR-2.1.6/discoveR/R/mod_acp_utils.R |only discoveR-2.1.6/discoveR/R/mod_carga_datos.R |only discoveR-2.1.6/discoveR/R/mod_carga_datos_utils.R |only discoveR-2.1.6/discoveR/R/mod_cj.R |only discoveR-2.1.6/discoveR/R/mod_cj_utils.R |only discoveR-2.1.6/discoveR/R/mod_cluster_utils.R |only discoveR-2.1.6/discoveR/R/mod_correlacion.R |only discoveR-2.1.6/discoveR/R/mod_correlacion_utils.R |only discoveR-2.1.6/discoveR/R/mod_dispersion.R |only discoveR-2.1.6/discoveR/R/mod_dispersion_utils.R |only discoveR-2.1.6/discoveR/R/mod_distribuciones.R |only discoveR-2.1.6/discoveR/R/mod_distribuciones_fct.R |only discoveR-2.1.6/discoveR/R/mod_distribuciones_utils.R |only discoveR-2.1.6/discoveR/R/mod_kmedias.R |only discoveR-2.1.6/discoveR/R/mod_kmedias_utils.R |only discoveR-2.1.6/discoveR/R/mod_normal.R |only discoveR-2.1.6/discoveR/R/mod_normal_fct.R |only discoveR-2.1.6/discoveR/R/mod_normal_utils.R |only discoveR-2.1.6/discoveR/R/mod_r_numerico.R |only discoveR-2.1.6/discoveR/R/mod_r_numerico_utils.R |only discoveR-2.1.6/discoveR/R/run_app.R |only discoveR-2.1.6/discoveR/R/utils_inputs.R |only discoveR-2.1.6/discoveR/inst/app |only discoveR-2.1.6/discoveR/inst/golem-config.yml |only discoveR-2.1.6/discoveR/inst/rstudio/addins.dcf | 2 discoveR-2.1.6/discoveR/man/BP.Rd |only discoveR-2.1.6/discoveR/man/WP.Rd |only discoveR-2.1.6/discoveR/man/app_server.Rd |only discoveR-2.1.6/discoveR/man/calc.centros.Rd |only discoveR-2.1.6/discoveR/man/datos.disyuntivos.Rd |only discoveR-2.1.6/discoveR/man/dfnormal.Rd |only discoveR-2.1.6/discoveR/man/discoveR.Rd |only discoveR-2.1.6/discoveR/man/get_hist_data.Rd |only discoveR-2.1.6/discoveR/man/gg_dendrograma.Rd |only discoveR-2.1.6/discoveR/man/hc_cat.Rd |only discoveR-2.1.6/discoveR/man/hc_horiz.Rd |only discoveR-2.1.6/discoveR/man/hc_inercia.Rd |only discoveR-2.1.6/discoveR/man/hc_jambu.Rd |only discoveR-2.1.6/discoveR/man/hc_mapa.Rd |only discoveR-2.1.6/discoveR/man/hc_radar.Rd |only discoveR-2.1.6/discoveR/man/hc_silhouette.Rd |only discoveR-2.1.6/discoveR/man/hc_vert.Rd |only discoveR-2.1.6/discoveR/man/hchistboxplot.Rd |only discoveR-2.1.6/discoveR/man/hchistnormal.Rd |only discoveR-2.1.6/discoveR/man/hcpcabi.Rd |only discoveR-2.1.6/discoveR/man/hcpcaind.Rd |only discoveR-2.1.6/discoveR/man/hcpcavar.Rd |only discoveR-2.1.6/discoveR/man/hcqq.Rd |only discoveR-2.1.6/discoveR/man/inercia.total.Rd |only discoveR-2.1.6/discoveR/man/mod_acp_server.Rd |only discoveR-2.1.6/discoveR/man/mod_carga_datos_server.Rd |only discoveR-2.1.6/discoveR/man/mod_cj_server.Rd |only discoveR-2.1.6/discoveR/man/mod_correlacion_server.Rd |only discoveR-2.1.6/discoveR/man/mod_dispersion_server.Rd |only discoveR-2.1.6/discoveR/man/mod_distribuciones_server.Rd |only discoveR-2.1.6/discoveR/man/mod_kmedias_server.Rd |only discoveR-2.1.6/discoveR/man/mod_normal_server.Rd |only discoveR-2.1.6/discoveR/man/mod_r_numerico_server.Rd |only discoveR-2.1.6/discoveR/man/plotly_mapa.Rd |only discoveR-2.1.6/discoveR/man/plotly_pcabi.Rd |only discoveR-2.1.6/discoveR/man/plotly_pcaind.Rd |only discoveR-2.1.6/discoveR/man/plotly_pcavar.Rd |only discoveR-2.1.6/discoveR/man/run_app.Rd |only discoveR-2.1.6/discoveR/man/var.categoricas.Rd |only discoveR-2.1.6/discoveR/man/var.numericas.Rd |only 80 files changed, 210 insertions(+), 43 deletions(-)
Title: In-Silico Knockout Experiments from Single-Cell Gene Regulatory
Networks
Description: A workflow based on 'scTenifoldNet' to perform in-silico knockout experiments using single-cell RNA sequencing (scRNA-seq) data from wild-type (WT) control samples as input. First, the package constructs a single-cell gene regulatory network (scGRN) and knocks out a target gene from the adjacency matrix of the WT scGRN by setting the gene’s outdegree edges to zero. Then, it compares the knocked out scGRN with the WT scGRN to identify differentially regulated genes, called virtual-knockout perturbed genes, which are used to assess the impact of the gene knockout and reveal the gene’s function in the analyzed cells.
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>),
Yan Zhong [aut, ctb],
Guanxun Li [aut, ctb],
Qian Xu [aut, ctb],
Andrew Hillhouse [aut, ctb],
Jingshu Chen [aut, ctb],
Laurie Davidson [aut, ctb],
Yanan Tian [aut, ctb],
Robert Chapkin [aut, ctb],
Jianhua Huang [aut, ctb],
James Cai [aut, ctb, ths] (<https://orcid.org/0000-0002-8081-6725>)
Maintainer: Daniel Osorio <dcosorioh@tamu.edu>
Diff between scTenifoldKnk versions 1.0.0 dated 2020-11-23 and 1.0.1 dated 2021-01-22
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- R/qFilter.R |only R/scTenifoldKnk.R | 25 +++++++++++++++++++------ R/strictDirection.R |only man/scTenifoldKnk.Rd | 6 ++++++ 6 files changed, 33 insertions(+), 12 deletions(-)
Title: Whole-Genome Sequencing Data Analysis via Knockoff Statistics
Description: Functions for identification of putative causal loci in whole-genome sequencing data. The functions allow genome-wide association scan. It also includes an efficient knockoff generator for genetic data.
Author: Zihuai He <zihuai@stanford.edu>
Maintainer: Zihuai He <zihuai@stanford.edu>
Diff between KnockoffScreen versions 0.1.0 dated 2020-08-11 and 0.2.0 dated 2021-01-22
DESCRIPTION | 8 +-- MD5 | 10 ++-- NAMESPACE | 2 R/KnockoffScreen.R | 130 ++++++++++++++++++++++++++++++++++++----------------- man/KS.VCF.chr.Rd | 4 - man/create.MK.Rd | 8 ++- 6 files changed, 108 insertions(+), 54 deletions(-)
More information about KnockoffScreen at CRAN
Permanent link
Title: Visualizing Generalized Canonical Discriminant and Canonical
Correlation Analysis
Description: Functions for computing and visualizing
generalized canonical discriminant analyses and canonical correlation analysis
for a multivariate linear model.
Traditional canonical discriminant analysis is restricted to a one-way 'MANOVA'
design and is equivalent to canonical correlation analysis between a set of quantitative
response variables and a set of dummy variables coded from the factor variable.
The 'candisc' package generalizes this to higher-way 'MANOVA' designs
for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The graphic functions provide low-rank (1D, 2D, 3D)
visualizations of terms in an 'mlm' via the 'plot.candisc' and 'heplot.candisc' methods. Related plots are
now provided for canonical correlation analysis when all predictors are quantitative.
Author: Michael Friendly [aut, cre],
John Fox [aut]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between candisc versions 0.8-3 dated 2020-04-22 and 0.8-5 dated 2021-01-22
DESCRIPTION | 8 MD5 | 23 + NEWS | 8 R/plot.candisc.R | 17 + build/partial.rdb |only demo/painters.R | 4 inst/doc/diabetes.html | 530 ++++++++++++++++++++++++++++++++-------------- man/can_lm.Rd | 8 man/candisc-package.Rd | 10 man/candisc.Rd | 4 man/heplot.candisc.Rd | 6 man/heplot.candiscList.Rd | 2 man/varOrder.Rd | 2 13 files changed, 428 insertions(+), 194 deletions(-)
Title: Multidimensional Scaling of Asymmetric Data
Description: Multidimensional scaling models and methods for the visualization for asymmetric data <doi:10.1111/j.2044-8317.1996.tb01078.x>. An asymmetric matrix has the same number of rows and columns, and these rows and columns refer to the same set of objects. At least some elements in the upper-triangle are different from the corresponding elements in the lower triangle. An example is a student migration table, where the rows correspond to the countries of origin of the students and the columns to the destination countries. This package provides the slide-vector model <doi:10.1007/BF02294474>, a scaling model with unique dimensions and the asymscal model for asymmetric multidimensional scaling. Furthermore, a heat map for skew-symmetric data, and the decomposition of asymmetry are provided for the analysis of asymmetric tables.
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>
Diff between asymmetry versions 2.0.2 dated 2019-07-10 and 2.0.3 dated 2021-01-22
DESCRIPTION | 8 +++--- MD5 | 34 +++++++++++++------------- R/asymscal.R | 6 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/asymmetry.R | 26 ++++++++++---------- inst/doc/asymmetry.html | 56 +++++++++++++++++++++++++++++++++----------- man/asymscal.Rd | 3 -- man/hmap.Rd | 4 --- man/mdsunique.Rd | 3 -- man/plot.mdsunique.Rd | 1 man/plot.slidevector.Rd | 1 man/print.slidevector.Rd | 1 man/skewsymmetry.Rd | 3 -- man/slidevector.Rd | 3 -- man/summary.mdsunique.Rd | 2 - man/summary.skewsymmetry.Rd | 4 --- man/summary.slidevector.Rd | 1 18 files changed, 85 insertions(+), 71 deletions(-)
Title: Sankey or Ribbon Plots
Description: Sankey plots are a type of diagram that is convenient to
illustrate how flow of information, resources etc. separates and joins,
much like observing how rivers split and merge. For example, they can be
used to compare different clusterings.
Author: January Weiner <january.weiner@gmail.com>
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between riverplot versions 0.6 dated 2017-02-17 and 0.10 dated 2021-01-22
DESCRIPTION | 17 MD5 | 47 +- NAMESPACE | 7 R/curveseg.R | 92 ++++ R/draw.R |only R/importexport.R | 135 +++++- R/minard.R | 54 +- R/riverplot-class.R | 6 R/riverplot-styles.R | 3 R/riverplot.R | 848 ++++++++++++++++++++++++++++--------------- R/riverplot.example.R | 56 ++ R/styles.R | 20 - build |only data/minard.rda |binary inst |only man/bglabel.Rd |only man/colorRampPaletteAlpha.Rd | 1 man/curveseg.Rd | 15 man/makeRiver.Rd | 27 - man/minard.Rd | 53 +- man/riverplot-package.Rd | 2 man/riverplot-styles.Rd | 5 man/riverplot.Rd | 83 +++- man/riverplot.example.Rd | 10 vignettes |only 25 files changed, 1044 insertions(+), 437 deletions(-)
Title: Eigenvalues and Singular Values and Vectors from Large Matrices
Description: R interface to 'PRIMME' <http://www.cs.wm.edu/~andreas/software/>, a C library for computing a few
eigenvalues and their corresponding eigenvectors of a real symmetric or complex
Hermitian matrix, or generalized Hermitian eigenproblem. It can also compute
singular values and vectors of a square or rectangular matrix. 'PRIMME' finds
largest, smallest, or interior singular/eigenvalues and can use preconditioning
to accelerate convergence. General description of the methods are provided in the papers
Stathopoulos (2010, <doi:10.1145/1731022.1731031>) and Wu (2017, <doi:10.1137/16M1082214>).
See 'citation("PRIMME")' for details.
Author: Eloy Romero [aut, cre],
Andreas Stathopoulos [aut],
Lingfei Wu [aut],
College of William & Mary [cph]
Maintainer: Eloy Romero <eloy@cs.wm.edu>
Diff between PRIMME versions 3.1-3 dated 2020-10-25 and 3.1-4 dated 2021-01-22
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/eigs.R | 3 +-- R/svds.R | 13 +++++++++---- inst/include/primme_eigs.h | 1 + inst/include/primme_svds.h | 1 + src/Makevars | 4 ---- src/primme/eigs/primme_interface.c | 29 ++++++++++++++--------------- src/primme/include/common.h | 6 ++++-- src/primme/svds/primme_svds_interface.c | 29 +++++++++++++---------------- src/primmeR.cpp | 12 +++++++----- 11 files changed, 64 insertions(+), 62 deletions(-)
Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2017) <doi:10.1093/biomet/asx046>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <https://www.jstor.org/stable/2345592>. See Kosmidis et al (2020) <doi:10.1007/s11222-019-09860-6> for more details. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bias estimates are provided. In the special case of generalized linear models for binomial and multinomial responses (both ordinal and nominal), the adjusted score approaches to mean and media bias reduction have been found to return estimates with improved frequentist properties, that are also always finite, even in cases where the maximum likelihood estimates are infinite (e.g. complete and quasi-complete separation; see Kosmidis and Firth, 2020 <doi:10.1093/biomet/asaa052>, for a proof for mean bias reduction in logistic regression). 'brglm2' also provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in binomial response generalized linear models.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>),
Kjell Konis [ctb],
Euloge Clovis Kenne Pagui [ctb],
Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm2 versions 0.7.0 dated 2020-10-19 and 0.7.1 dated 2021-01-22
DESCRIPTION | 8 - MD5 | 54 ++++--- NAMESPACE | 1 NEWS.md | 117 ++++++++++------- R/bracl.R | 8 - R/brglm2-package.R | 17 +- R/brglmControl.R | 160 +++++++++++++---------- R/brglmFit.R | 57 ++++---- R/brmultinom.R | 15 +- R/check_infinite_estimates.R | 4 R/data.R | 6 R/detect_separation.R | 2 README.md | 245 +++++++++++++++++++++++++++++------- build/partial.rdb |only inst/doc/adjacent.html | 10 + inst/doc/iteration.html | 10 + inst/doc/multinomial.html | 14 +- inst/doc/separation.html | 12 + man/bracl.Rd | 12 - man/brglm2.Rd | 16 +- man/brglmControl.Rd | 164 +++++++++++++----------- man/brglmFit.Rd | 18 +- man/brmultinom.Rd | 8 - man/check_infinite_estimates.glm.Rd | 4 man/coalition.Rd | 2 man/detect_separation.Rd | 2 man/endometrial.Rd | 4 man/figures |only vignettes/brglm2.bib | 8 - 29 files changed, 623 insertions(+), 355 deletions(-)
Title: R Interface to Use 'MiniZinc'
Description: Constraint optimization, or constraint programming, is the name given to identifying
feasible solutions out of a very large set of candidates, where the problem can be modeled in terms
of arbitrary constraints. 'MiniZinc' is a free and open-source constraint modeling language.
Constraint satisfaction and discrete optimization problems can be formulated in a high-level
modeling language. Models are compiled into an intermediate representation that is understood by a
wide range of solvers. 'MiniZinc' itself provides several solvers, for instance 'GeCode'. R users
can use the package to solve constraint programming problems without using 'MiniZinc' directly,
modify existing 'MiniZinc' models and also create their own models.
Author: Akshit Achara, Lars Kotthoff, Hans W. Borchers, Guido Tack
Maintainer: Akshit Achara <acharaakshit@gmail.com>
Diff between rminizinc versions 0.0.3 dated 2021-01-05 and 0.0.4 dated 2021-01-22
DESCRIPTION | 6 ++--- MD5 | 22 ++++++++++----------- NEWS.md | 7 ++++++ configure | 35 +++++++++++++++++++--------------- configure.ac | 21 ++++++++++++-------- configure.win | 35 +++++++++++++++++++--------------- data/proot.RData |binary inst/minizinc/solvers/chuffed.msc | 2 - inst/minizinc/solvers/findmus.msc | 2 - inst/minizinc/solvers/gecode-gist.msc | 2 - inst/minizinc/solvers/gecode.msc | 2 - inst/minizinc/solvers/globalizer.msc | 2 - 12 files changed, 79 insertions(+), 57 deletions(-)
Title: Suite of GR Hydrological Models for Precipitation-Runoff
Modelling
Description: Hydrological modelling tools developed at INRAE-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR5H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] (<https://orcid.org/0000-0002-1503-6204>),
Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>),
Guillaume Thirel [aut] (<https://orcid.org/0000-0002-1444-1830>),
David Dorchies [aut] (<https://orcid.org/0000-0002-6595-7984>),
Charles Perrin [aut, ths] (<https://orcid.org/0000-0001-8552-1881>),
Claude Michel [aut, ths],
Vazken Andréassian [ctb, ths] (<https://orcid.org/0000-0001-7124-9303>),
François Bourgin [ctb] (<https://orcid.org/0000-0002-2820-7260>),
Pierre Brigode [ctb] (<https://orcid.org/0000-0001-8257-0741>),
Nicolas Le Moine [ctb],
Thibaut Mathevet [ctb] (<https://orcid.org/0000-0002-4142-4454>),
Safouane Mouelhi [ctb],
Ludovic Oudin [ctb] (<https://orcid.org/0000-0002-3712-0933>),
Raji Pushpalatha [ctb],
Audrey Valéry [ctb]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGR versions 1.4.3.65 dated 2020-02-28 and 1.6.9.27 dated 2021-01-22
DESCRIPTION | 22 MD5 | 270 ++-- NAMESPACE | 148 +- NEWS.md | 1401 +++++++++++----------- R/Calibration.R | 50 R/Calibration_Michel.R | 961 +++++++-------- R/CreateCalibOptions.R | 898 +++++++------- R/CreateIniStates.R | 633 +++++----- R/CreateInputsCrit.R | 718 +++++------ R/CreateInputsModel.R | 647 +++++----- R/CreateRunOptions.R | 1065 ++++++++--------- R/DataAltiExtrapolation_Valery.R | 1102 +++++++++--------- R/ErrorCrit.R | 158 +- R/ErrorCrit_KGE.R | 184 +-- R/ErrorCrit_KGE2.R | 218 +-- R/ErrorCrit_NSE.R | 94 - R/ErrorCrit_RMSE.R | 86 - R/Imax.R | 118 - R/PE_Oudin.R | 322 ++--- R/PEdaily_Oudin.R | 234 +-- R/RunModel.R | 28 R/RunModel_CemaNeige.R | 322 ++--- R/RunModel_CemaNeigeGR4H.R | 410 +++--- R/RunModel_CemaNeigeGR4J.R | 408 +++--- R/RunModel_CemaNeigeGR5H.R | 448 ++++--- R/RunModel_CemaNeigeGR5J.R | 406 +++--- R/RunModel_CemaNeigeGR6J.R | 418 +++--- R/RunModel_GR1A.R | 196 +-- R/RunModel_GR2M.R | 222 ++- R/RunModel_GR4H.R | 232 ++- R/RunModel_GR4J.R | 230 ++- R/RunModel_GR5H.R | 259 ++-- R/RunModel_GR5J.R | 232 ++- R/RunModel_GR6J.R | 243 ++- R/RunModel_Lag.R |only R/SeriesAggreg.InputsModel.R |only R/SeriesAggreg.OutputsModel.R |only R/SeriesAggreg.R | 219 --- R/SeriesAggreg.data.frame.R |only R/SeriesAggreg.list.R |only R/TransfoParam.R | 8 R/TransfoParam_CemaNeige.R | 86 - R/TransfoParam_CemaNeigeHyst.R | 96 - R/TransfoParam_GR1A.R | 78 - R/TransfoParam_GR2M.R | 86 - R/TransfoParam_GR4H.R | 96 - R/TransfoParam_GR4J.R | 98 - R/TransfoParam_GR5H.R | 100 - R/TransfoParam_GR5J.R | 102 - R/TransfoParam_GR6J.R | 104 - R/TransfoParam_Lag.R |only R/Utils.R | 397 ++---- R/UtilsErrorCrit.R |only R/UtilsSeriesAggreg.R |only R/plot.OutputsModel.R | 1893 +++++++++++++++---------------- README.md | 151 +- build/partial.rdb |only build/vignette.rds |binary data/datalist | 12 inst/CITATION | 83 - inst/doc/V01_get_started.R | 108 - inst/doc/V01_get_started.Rmd | 538 ++++---- inst/doc/V01_get_started.html | 1105 ++++++++++-------- inst/doc/V02.1_param_optim.R | 170 +- inst/doc/V02.1_param_optim.Rmd | 350 ++--- inst/doc/V02.1_param_optim.html | 678 +++++++---- inst/doc/V02.2_param_mcmc.R | 154 +- inst/doc/V02.2_param_mcmc.Rmd | 340 ++--- inst/doc/V02.2_param_mcmc.html | 654 +++++++--- inst/doc/V03_param_sets_GR4J.R | 242 +-- inst/doc/V03_param_sets_GR4J.Rmd | 450 +++---- inst/doc/V03_param_sets_GR4J.html | 692 +++++++---- inst/doc/V04_cemaneige_hysteresis.R | 299 ++-- inst/doc/V04_cemaneige_hysteresis.Rmd | 497 ++++---- inst/doc/V04_cemaneige_hysteresis.html | 997 +++++++++------- inst/doc/V05_sd_model.R |only inst/doc/V05_sd_model.Rmd |only inst/doc/V05_sd_model.html |only inst/vignettesData/vignetteParamMCMC.rda |binary man/BasinInfo.Rd | 76 - man/BasinObs.Rd | 121 - man/Calibration.Rd | 222 +-- man/Calibration_Michel.Rd | 294 ++-- man/CreateCalibOptions.Rd | 296 ++-- man/CreateIniStates.Rd | 300 ++-- man/CreateInputsCrit.Rd | 358 ++--- man/CreateInputsModel.Rd | 241 ++- man/CreateRunOptions.Rd | 329 ++--- man/DataAltiExtrapolation_Valery.Rd | 178 +- man/ErrorCrit.Rd | 238 +-- man/ErrorCrit_KGE.Rd | 234 +-- man/ErrorCrit_KGE2.Rd | 242 +-- man/ErrorCrit_NSE.Rd | 217 +-- man/ErrorCrit_RMSE.Rd | 206 +-- man/Imax.Rd | 188 +-- man/PE_Oudin.Rd | 179 +- man/Param_Sets_GR4J.Rd | 214 +-- man/RunModel.Rd | 173 +- man/RunModel_CemaNeige.Rd | 274 ++-- man/RunModel_CemaNeigeGR4H.Rd | 333 ++--- man/RunModel_CemaNeigeGR4J.Rd | 359 ++--- man/RunModel_CemaNeigeGR5H.Rd | 353 ++--- man/RunModel_CemaNeigeGR5J.Rd | 354 ++--- man/RunModel_CemaNeigeGR6J.Rd | 369 +++--- man/RunModel_GR1A.Rd | 220 +-- man/RunModel_GR2M.Rd | 248 ++-- man/RunModel_GR4H.Rd | 251 ++-- man/RunModel_GR4J.Rd | 246 ++-- man/RunModel_GR5H.Rd | 273 ++-- man/RunModel_GR5J.Rd | 258 ++-- man/RunModel_GR6J.Rd | 254 ++-- man/RunModel_Lag.Rd |only man/SeriesAggreg.Rd | 195 ++- man/TransfoParam.Rd | 189 +-- man/airGR.Rd | 155 +- man/figures/diagramGR2M-EN.pdf |binary man/figures/diagramGR2M-EN.png |binary man/figures/diagramGR5H-EN.pdf |only man/figures/diagramGR5H-EN.png |only man/plot.OutputsModel.Rd | 296 ++-- src/airGR.c | 2 src/frun_CEMANEIGE.f90 | 453 +++---- src/frun_GR1A.f90 | 318 ++--- src/frun_GR2M.f90 | 449 +++---- src/frun_GR4H.f90 | 659 +++++----- src/frun_GR4J.f90 | 638 +++++----- src/frun_GR5H.f90 | 735 +++++------- src/frun_GR5J.f90 | 608 ++++----- src/frun_GR6J.f90 | 691 +++++------ src/frun_PE.f90 |only src/utils_D.f90 | 382 +++--- src/utils_H.f90 | 326 ++--- tests |only vignettes/V00_airgr_ref.bib | 360 ++--- vignettes/V01_get_started.Rmd | 538 ++++---- vignettes/V02.1_param_optim.Rmd | 350 ++--- vignettes/V02.2_param_mcmc.Rmd | 340 ++--- vignettes/V03_param_sets_GR4J.Rmd | 450 +++---- vignettes/V04_cemaneige_hysteresis.Rmd | 497 ++++---- vignettes/V05_sd_model.Rmd |only 140 files changed, 21208 insertions(+), 19787 deletions(-)
Title: Multivariate Data Analysis for Chemometrics
Description: Projection based methods for preprocessing,
exploring and analysis of multivariate data used in chemometrics.
S. Kucheryavskiy (2020) <doi: 10.1016/j.chemolab.2020.103937>.
Author: Sergey Kucheryavskiy (<https://orcid.org/0000-0002-3145-7244>)
Maintainer: Sergey Kucheryavskiy <svkucheryavski@gmail.com>
Diff between mdatools versions 0.11.2 dated 2020-10-22 and 0.11.3 dated 2021-01-22
DESCRIPTION | 10 - MD5 | 31 +++-- NAMESPACE | 3 NEWS.md | 16 ++ R/ldecomp.R | 25 ++-- R/mdaplot.R | 4 R/pcv.R |only R/plotseries.R | 11 + R/plsdares.R | 2 R/prep.R | 246 ++++++++++++++++++++++--------------------- R/regmodel.R | 2 README.md | 12 +- man/eye.Rd |only man/getR.Rd |only man/ldecomp.plotResiduals.Rd | 3 man/mdatools.Rd | 14 +- man/pcv.Rd |only man/prep.generic.Rd |only man/prep.ref2km.Rd |only man/rotationMatrixToX1.Rd |only 20 files changed, 223 insertions(+), 156 deletions(-)
Title: The Induced Smoothed Lasso
Description: An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper: Cilluffo, G., Sottile, G., La Grutta, S. and Muggeo, V. (2019) The Induced Smoothed lasso: A practical framework for hypothesis testing in high dimensional regression. <doi:10.1177/0962280219842890>, and discussed in a tutorial: Sottile, G., Cilluffo, G., and Muggeo, V. (2019) The R package islasso: estimation and hypothesis testing in lasso regression. <doi:10.13140/RG.2.2.16360.11521>.
Author: Gianluca Sottile [aut, cre],
Giovanna Cilluffo [aut, ctb],
Vito MR Muggeo [aut, cre]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between islasso versions 1.2.0 dated 2021-01-21 and 1.2.2 dated 2021-01-22
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 12 +++++++++++- man/islasso-package.Rd | 2 +- src/auxiliary.f90 | 28 ++++++++++++++++++++-------- src/islasso2.f90 | 7 +------ src/islasso_glm.f90 | 6 ------ 7 files changed, 42 insertions(+), 31 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis, especially raster data. Methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. 'terra' is very similar to the 'raster' package; but 'terra' is simpler, better, and faster.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Karl Forner [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>)
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.0-7 dated 2021-01-04 and 1.0-10 dated 2021-01-22
terra-1.0-10/terra/DESCRIPTION | 8 terra-1.0-10/terra/MD5 | 81 ++--- terra-1.0-10/terra/NAMESPACE | 2 terra-1.0-10/terra/R/Agenerics.R | 3 terra-1.0-10/terra/R/coerce.R | 40 ++ terra-1.0-10/terra/R/generics.R | 24 - terra-1.0-10/terra/R/geom.R | 8 terra-1.0-10/terra/R/merge.R | 8 terra-1.0-10/terra/R/options.R | 4 terra-1.0-10/terra/R/plot.R | 24 + terra-1.0-10/terra/R/rast.R | 9 terra-1.0-10/terra/R/rasterize.R | 7 terra-1.0-10/terra/R/sample.R | 4 terra-1.0-10/terra/R/show.R | 2 terra-1.0-10/terra/R/spatvec.R | 2 terra-1.0-10/terra/R/vect.R | 6 terra-1.0-10/terra/inst/tinytest/test_extract.R | 18 - terra-1.0-10/terra/inst/tinytest/test_window.R | 58 ++-- terra-1.0-10/terra/man/click.Rd | 6 terra-1.0-10/terra/man/geometry.Rd | 2 terra-1.0-10/terra/man/merge.Rd | 6 terra-1.0-10/terra/man/mosaic.Rd |only terra-1.0-10/terra/man/rast.Rd | 6 terra-1.0-10/terra/man/terra-package.Rd | 49 +-- terra-1.0-10/terra/man/terrain.Rd |only terra-1.0-10/terra/man/union.Rd | 15 - terra-1.0-10/terra/man/vect.Rd | 3 terra-1.0-10/terra/src/RcppModule.cpp | 7 terra-1.0-10/terra/src/distRaster.cpp | 110 ++++++- terra-1.0-10/terra/src/extract.cpp | 6 terra-1.0-10/terra/src/math_utils.cpp | 26 + terra-1.0-10/terra/src/raster_methods.cpp | 122 +++++++- terra-1.0-10/terra/src/rasterize.cpp | 10 terra-1.0-10/terra/src/read_ogr.cpp | 14 - terra-1.0-10/terra/src/sample.cpp | 35 ++ terra-1.0-10/terra/src/spatBase.h | 3 terra-1.0-10/terra/src/spatOptions.cpp | 3 terra-1.0-10/terra/src/spatRaster.h | 3 terra-1.0-10/terra/src/spatRasterMultiple.h | 29 +- terra-1.0-10/terra/src/terrain.cpp | 332 +++++++++++++++++++++--- terra-1.0-10/terra/src/write.cpp | 40 +- terra-1.0-7/terra/man/slope.Rd |only terra-1.0-7/terra/src/buffer.cpp |only terra-1.0-7/terra/src/mosaic.cpp |only 44 files changed, 868 insertions(+), 267 deletions(-)
Title: Prioritization of Candidate Cancer Subtype Specific Drugs
Description: A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype.
The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially
expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease
reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <doi:10.1126/science.1132939>). Please cite using <doi:10.1093/bioinformatics/btab011>.
Author: Xudong Han,
Junwei Han,
Chonghui Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between SubtypeDrug versions 0.1.3 dated 2020-11-24 and 0.1.4 dated 2021-01-22
DESCRIPTION | 10 MD5 | 12 - R/plotDScoreHeatmap.R | 4 R/plotGlobalGraph.R | 2 build/vignette.rds |binary inst/doc/vignette.html | 484 +++++++++++++++-------------------------------- man/plotDScoreHeatmap.Rd | 2 7 files changed, 177 insertions(+), 337 deletions(-)
Title: Statistical Framework to Define Subgroups in Complex Datasets
Description: High-dimensional datasets that do not exhibit a clear intrinsic clustered structure pose a challenge to conventional clustering algorithms. For this reason, we developed an unsupervised framework that helps scientists to better subgroup their datasets based on visual cues, please see Gao S, Mutter S, Casey A, Makinen V-P (2019) Numero: a statistical framework to define multivariable subgroups in complex population-based datasets, Int J Epidemiology, 48:369-37, <doi:10.1093/ije/dyy113>. The framework includes the necessary functions to construct a self-organizing map of the data, to evaluate the statistical significance of the observed data patterns, and to visualize the results.
Author: Song Gao [aut],
Stefan Mutter [aut],
Aaron E. Casey [aut],
Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>
Diff between Numero versions 1.7.3 dated 2021-01-11 and 1.7.4 dated 2021-01-22
DESCRIPTION | 8 - MD5 | 20 +-- R/nroPostprocess.R | 5 R/nroPreprocess.R | 6 + R/numero.subgroup.R | 2 inst/doc/intro.R | 48 ++++----- inst/doc/intro.html | 251 ++++++++++++++++++++++++++++++------------------ inst/doc/intro.rmd | 48 ++++----- inst/extcode/examples.R | 4 man/nroPreprocess.Rd | 9 + vignettes/intro.rmd | 48 ++++----- 11 files changed, 270 insertions(+), 179 deletions(-)
Title: Downloading Time Series from ALFRED Database for Various
Vintages
Description: Provides direct access to the ALFRED (<https://alfred.stlouisfed.org>) and FRED (<https://fred.stlouisfed.org>) databases.
Its functions return tidy data frames for different releases of the specified time series.
Note that this product uses the FRED© API but is not endorsed or certified by the Federal Reserve Bank of St. Louis.
Author: Onno Kleen [aut, cre] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Onno Kleen <r@onnokleen.de>
Diff between alfred versions 0.1.10 dated 2021-01-07 and 0.1.11 dated 2021-01-22
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NAMESPACE | 1 - NEWS.md | 1 + R/get_alfred_series.R | 1 - build/vignette.rds |binary inst/doc/alfred.Rmd | 2 +- inst/doc/alfred.html | 8 ++++---- tests/testthat/test_download.R | 2 +- vignettes/alfred.Rmd | 2 +- 10 files changed, 20 insertions(+), 21 deletions(-)
Title: Sign-Simplicity-Regression-Solver
Description: Implementation of the SSR-Algorithm. The Sign-Simplicity-Regression model is a nonparametric statistical model which is based on residual signs and simplicity assumptions on the regression function. Goal is to calculate the most parsimonious regression function satisfying the statistical adequacy requirements. Theory and functions are specified in Metzner (2020, ISBN: 9798682394203, "Trendbasierte Prognostik") and Metzner (2021, ISBN: 9798593470270, "Adäquates Maschinelles Lernen").
Author: Lars Metzner [aut, cre]
Maintainer: Lars Metzner <lars.metzner@ppi.de>
Diff between sisireg versions 0.7.0 dated 2021-01-14 and 0.8.0 dated 2021-01-22
DESCRIPTION | 6 +-- MD5 | 31 ++++++++++--------- R/snarch.R |only R/ssr.R | 64 +++++++++++++++++++++++++++++----------- man/psplot.Rd | 2 - man/psplot3d.Rd | 2 - man/psplotnd.Rd | 2 - man/psvalid.Rd | 2 - man/runvalid.Rd |only man/snarch.Rd |only man/ssr.Rd | 14 +++++--- man/ssr3d.Rd | 2 - man/ssr3d_predict.Rd | 2 - man/ssr_predict.Rd | 2 - man/ssrnd.Rd | 2 - man/ssrnd_predict.Rd | 2 - src/init.c | 6 +-- src/ssr.c | 81 +++++++++++++++++++++++++++++++++++++++------------ 18 files changed, 149 insertions(+), 71 deletions(-)
Title: Tools to Calculate Climate Targets for Financial Portfolios
Description: These tools help you to assess if a financial
portfolio aligns with climate goals. They summarize key metrics
attributed to the portfolio (e.g. production, emission factors), and
calculate targets based on climate scenarios. They implement in R the
last step of the free software 'PACTA' (Paris Agreement Capital
Transition Assessment; <https://2degrees-investing.org/>). Financial
institutions use 'PACTA' to study how their capital allocation impacts
the climate.
Author: Jackson Hoffart [aut, cre] (<https://orcid.org/0000-0002-8600-5042>),
Mauro Lepore [aut, ctr] (<https://orcid.org/0000-0002-1986-7988>),
Klaus Hogedorn [aut],
2 Degrees Investing Initiative [cph, fnd]
Maintainer: Jackson Hoffart <jackson.hoffart@gmail.com>
Diff between r2dii.analysis versions 0.1.4 dated 2021-01-05 and 0.1.5 dated 2021-01-22
DESCRIPTION | 6 - MD5 | 8 - NEWS.md | 8 + R/target_market_share.R | 65 ++++++++++++++ tests/testthat/test-target_market_share.R | 136 +++++++++++++++++++++++++++++- 5 files changed, 215 insertions(+), 8 deletions(-)
More information about r2dii.analysis at CRAN
Permanent link
Title: World Development Indicators and Other World Bank Data
Description: Search and download data from over 40 databases hosted by the World Bank, including the World Development Indicators ('WDI'), International Debt Statistics, Doing Business, Human Capital Index, and Sub-national Poverty indicators.
Author: Vincent Arel-Bundock [aut, cre]
(<https://orcid.org/0000-0003-2042-7063>),
Etienne Bacher [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between WDI versions 2.7.1 dated 2020-07-05 and 2.7.2 dated 2021-01-22
DESCRIPTION | 18 +++- MD5 | 23 +++-- NAMESPACE | 1 NEWS.md | 7 + R/WDI.R | 177 +++++++++++++++++++++++++++++++++++++-------- README.md | 4 - man/WDI-package.Rd | 16 ++-- man/WDI.Rd | 21 ++++- man/WDIbulk.Rd | 5 + man/languages_supported.Rd |only man/wdi.dl.Rd | 2 man/wdi.query.Rd | 4 - tests |only 13 files changed, 215 insertions(+), 63 deletions(-)
Title: USGS ScienceBase Tools
Description: Tools for interacting with U.S. Geological Survey ScienceBase
<https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and
collaborative data management platform. Functions included for querying
ScienceBase, and creating and fetching datasets.
Author: David Blodgett [cre],
Luke Winslow [aut],
Scott Chamberlain [ctb],
Alison Appling [ctb],
Jordan Read [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between sbtools versions 1.1.12 dated 2020-08-30 and 1.1.13 dated 2021-01-22
sbtools-1.1.12/sbtools/LICENSE.note |only sbtools-1.1.12/sbtools/R/file_helpers.R |only sbtools-1.1.12/sbtools/R/item_append_files.R |only sbtools-1.1.12/sbtools/R/item_upload_create.R |only sbtools-1.1.13/sbtools/DESCRIPTION | 25 - sbtools-1.1.13/sbtools/MD5 | 253 +++++++------- sbtools-1.1.13/sbtools/NAMESPACE | 144 ++++---- sbtools-1.1.13/sbtools/NEWS.md | 4 sbtools-1.1.13/sbtools/R/AAA.R | 9 sbtools-1.1.13/sbtools/R/REST_helpers.R | 4 sbtools-1.1.13/sbtools/R/authenticate_sb.R | 132 +++---- sbtools-1.1.13/sbtools/R/current_session.R | 42 +- sbtools-1.1.13/sbtools/R/folder_create.R | 60 +-- sbtools-1.1.13/sbtools/R/identifier_exists.R | 58 +-- sbtools-1.1.13/sbtools/R/is_logged_in.R | 24 - sbtools-1.1.13/sbtools/R/item_create.R | 68 +-- sbtools-1.1.13/sbtools/R/item_exists.R | 60 +-- sbtools-1.1.13/sbtools/R/item_file_download.R | 154 ++++---- sbtools-1.1.13/sbtools/R/item_get.R | 11 sbtools-1.1.13/sbtools/R/item_get_fields.R | 56 +-- sbtools-1.1.13/sbtools/R/item_get_parent.R | 44 +- sbtools-1.1.13/sbtools/R/item_list_children.R | 78 ++-- sbtools-1.1.13/sbtools/R/item_list_files.R | 34 + sbtools-1.1.13/sbtools/R/item_move.R | 58 +-- sbtools-1.1.13/sbtools/R/item_rename_files.R | 82 ++-- sbtools-1.1.13/sbtools/R/item_replace_files.R | 52 +- sbtools-1.1.13/sbtools/R/item_rm.R | 84 ++-- sbtools-1.1.13/sbtools/R/item_rm_files.R | 88 ++-- sbtools-1.1.13/sbtools/R/item_rm_recursive.R | 100 ++--- sbtools-1.1.13/sbtools/R/item_update.R | 70 +-- sbtools-1.1.13/sbtools/R/item_update_identifier.R | 180 +++++----- sbtools-1.1.13/sbtools/R/item_upload_files.R |only sbtools-1.1.13/sbtools/R/item_upsert.R | 86 ++-- sbtools-1.1.13/sbtools/R/items_create.R | 156 ++++---- sbtools-1.1.13/sbtools/R/items_rm.R | 76 ++-- sbtools-1.1.13/sbtools/R/items_update.R | 108 +++--- sbtools-1.1.13/sbtools/R/items_upsert.R | 120 +++--- sbtools-1.1.13/sbtools/R/query_item_identifier.R | 176 ++++----- sbtools-1.1.13/sbtools/R/query_item_in_folder.R | 44 +- sbtools-1.1.13/sbtools/R/query_items.R | 268 +++++++-------- sbtools-1.1.13/sbtools/R/query_sb.R | 6 sbtools-1.1.13/sbtools/R/query_sb_datatype.R | 3 sbtools-1.1.13/sbtools/R/query_sb_date.R | 92 ++--- sbtools-1.1.13/sbtools/R/query_sb_doi.R | 70 +-- sbtools-1.1.13/sbtools/R/query_sb_spatial.R | 9 sbtools-1.1.13/sbtools/R/query_sb_text.R | 4 sbtools-1.1.13/sbtools/R/sb_item.R | 23 - sbtools-1.1.13/sbtools/R/sb_ping.R | 48 +- sbtools-1.1.13/sbtools/R/sbtools-package.R | 76 ++-- sbtools-1.1.13/sbtools/R/session_age.R | 78 ++-- sbtools-1.1.13/sbtools/R/session_age_reset.R | 48 +- sbtools-1.1.13/sbtools/R/session_authorized.R | 8 sbtools-1.1.13/sbtools/R/session_details.R | 40 +- sbtools-1.1.13/sbtools/R/session_logout.R | 40 +- sbtools-1.1.13/sbtools/R/session_renew.R | 116 +++--- sbtools-1.1.13/sbtools/R/session_set.R | 14 sbtools-1.1.13/sbtools/R/session_validate.R | 100 ++--- sbtools-1.1.13/sbtools/R/set_endpoint.R | 96 ++--- sbtools-1.1.13/sbtools/R/user_id.R | 42 +- sbtools-1.1.13/sbtools/README.md | 27 + sbtools-1.1.13/sbtools/demo/00Index | 4 sbtools-1.1.13/sbtools/demo/figure_fault_code.R | 48 +- sbtools-1.1.13/sbtools/demo/figure_map_code.R | 36 +- sbtools-1.1.13/sbtools/inst/CITATION | 28 - sbtools-1.1.13/sbtools/inst/examples/books.json | 102 ++--- sbtools-1.1.13/sbtools/inst/examples/data.csv | 20 - sbtools-1.1.13/sbtools/inst/examples/species.json | 74 ++-- sbtools-1.1.13/sbtools/man/authenticate_sb.Rd | 36 +- sbtools-1.1.13/sbtools/man/current_session.Rd | 40 +- sbtools-1.1.13/sbtools/man/folder_create.Rd | 68 +-- sbtools-1.1.13/sbtools/man/identifier_exists.Rd | 70 +-- sbtools-1.1.13/sbtools/man/is_logged_in.Rd | 48 +- sbtools-1.1.13/sbtools/man/item_append_files.Rd | 64 +-- sbtools-1.1.13/sbtools/man/item_create.Rd | 90 ++--- sbtools-1.1.13/sbtools/man/item_exists.Rd | 62 +-- sbtools-1.1.13/sbtools/man/item_file_download.Rd | 120 +++--- sbtools-1.1.13/sbtools/man/item_get.Rd | 82 ++-- sbtools-1.1.13/sbtools/man/item_get_fields.Rd | 76 ++-- sbtools-1.1.13/sbtools/man/item_get_parent.Rd | 62 +-- sbtools-1.1.13/sbtools/man/item_list_children.Rd | 88 ++-- sbtools-1.1.13/sbtools/man/item_list_files.Rd | 104 ++--- sbtools-1.1.13/sbtools/man/item_move.Rd | 86 ++-- sbtools-1.1.13/sbtools/man/item_rename_files.Rd | 70 +-- sbtools-1.1.13/sbtools/man/item_replace_files.Rd | 60 +-- sbtools-1.1.13/sbtools/man/item_rm.Rd | 88 ++-- sbtools-1.1.13/sbtools/man/item_rm_files.Rd | 76 ++-- sbtools-1.1.13/sbtools/man/item_rm_recursive.Rd | 80 ++-- sbtools-1.1.13/sbtools/man/item_update.Rd | 66 +-- sbtools-1.1.13/sbtools/man/item_update_identifier.Rd | 92 ++--- sbtools-1.1.13/sbtools/man/item_upload_create.Rd | 68 +-- sbtools-1.1.13/sbtools/man/item_upsert.Rd | 98 ++--- sbtools-1.1.13/sbtools/man/items_create.Rd | 142 ++++---- sbtools-1.1.13/sbtools/man/items_rm.Rd | 76 ++-- sbtools-1.1.13/sbtools/man/items_update.Rd | 78 ++-- sbtools-1.1.13/sbtools/man/items_upsert.Rd | 106 ++--- sbtools-1.1.13/sbtools/man/query_item_identifier.Rd | 112 +++--- sbtools-1.1.13/sbtools/man/query_item_in_folder.Rd | 66 +-- sbtools-1.1.13/sbtools/man/query_items.Rd | 284 ++++++++-------- sbtools-1.1.13/sbtools/man/query_sb.Rd | 194 +++++----- sbtools-1.1.13/sbtools/man/query_sb_datatype.Rd | 73 ++-- sbtools-1.1.13/sbtools/man/query_sb_date.Rd | 96 ++--- sbtools-1.1.13/sbtools/man/query_sb_doi.Rd | 68 +-- sbtools-1.1.13/sbtools/man/query_sb_spatial.Rd | 96 ++--- sbtools-1.1.13/sbtools/man/query_sb_text.Rd | 72 ++-- sbtools-1.1.13/sbtools/man/readPassword.Rd | 24 - sbtools-1.1.13/sbtools/man/sb_datatypes.Rd | 50 +- sbtools-1.1.13/sbtools/man/sb_ping.Rd | 46 +- sbtools-1.1.13/sbtools/man/sbitem.Rd | 90 ++--- sbtools-1.1.13/sbtools/man/sbtools-package.Rd | 86 ++-- sbtools-1.1.13/sbtools/man/sbtools_DELETE.Rd | 42 +- sbtools-1.1.13/sbtools/man/sbtools_GET.Rd | 42 +- sbtools-1.1.13/sbtools/man/sbtools_POST.Rd | 46 +- sbtools-1.1.13/sbtools/man/sbtools_PUT.Rd | 46 +- sbtools-1.1.13/sbtools/man/session_age.Rd | 62 +-- sbtools-1.1.13/sbtools/man/session_age_reset.Rd | 30 - sbtools-1.1.13/sbtools/man/session_details.Rd | 48 +- sbtools-1.1.13/sbtools/man/session_expired.Rd | 42 +- sbtools-1.1.13/sbtools/man/session_logout.Rd | 48 +- sbtools-1.1.13/sbtools/man/session_renew.Rd | 80 ++-- sbtools-1.1.13/sbtools/man/session_set.Rd | 30 - sbtools-1.1.13/sbtools/man/session_validate.Rd | 70 +-- sbtools-1.1.13/sbtools/man/set_endpoint.Rd | 68 +-- sbtools-1.1.13/sbtools/man/set_expiration.Rd | 30 - sbtools-1.1.13/sbtools/man/user_id.Rd | 48 +- sbtools-1.1.13/sbtools/tests/testthat.R | 2 sbtools-1.1.13/sbtools/tests/testthat/test-REST.R | 26 + sbtools-1.1.13/sbtools/tests/testthat/test-auth.R | 226 ++++++------ sbtools-1.1.13/sbtools/tests/testthat/test-eg.R | 34 - sbtools-1.1.13/sbtools/tests/testthat/test-expiration.R | 2 sbtools-1.1.13/sbtools/tests/testthat/test-list_files.R |only sbtools-1.1.13/sbtools/tests/testthat/test_examples.R |only 131 files changed, 4431 insertions(+), 4404 deletions(-)
Title: Empirical Small Telescopes Analysis
Description: We provide functions to perform an empirical small telescopes
analysis. This package contains 2 functions, SimulatePower() and
EstimatePower(). Users only need to call SimulatePower() to conduct
the analysis. For more information on small telescopes analysis see
Uri Simonsohn (2015) <doi:10.1177/0956797614567341>.
Author: John Ruscio [aut, cre],
Samantha Costigan [ctb]
Maintainer: John Ruscio <ruscio@tcnj.edu>
Diff between RSmallTelescopes versions 1.0.2 dated 2020-09-23 and 1.0.3 dated 2021-01-22
DESCRIPTION | 6 +- LICENSE | 2 MD5 | 10 +-- R/empiricalsmalltelescopes.R | 110 +++++++++++++++++++++++++++++++------------ man/EstimatePower.Rd | 10 +++ man/SimulatePower.Rd | 10 +++ 6 files changed, 105 insertions(+), 43 deletions(-)
More information about RSmallTelescopes at CRAN
Permanent link
Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also now included.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] (Contributions to Censored QR code),
Pin Tian Ng [ctb] (Contributions to Sparse QR code),
Blaise Melly [ctb] (Contributions to preprocessing code),
Achim Zeileis [ctb] (Contributions to dynrq code essentially identical
to his dynlm code),
Philip Grosjean [ctb] (Contributions to nlrq code),
Cleve Moler [ctb] (author of several linpack routines),
Yousef Saad [ctb] (author of sparskit2),
Victor Chernozhukov [ctb] (contributions to extreme value inference
code),
Ivan Fernandez-Val [ctb] (contributions to extreme value inference
code),
Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my
everlasting shame -- how could I have been so slow to adopt R!) and
for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.82 dated 2021-01-10 and 5.83 dated 2021-01-22
quantreg-5.82/quantreg/src/ratfor/spwy.r |only quantreg-5.82/quantreg/src/spwy.f |only quantreg-5.83/quantreg/DESCRIPTION | 9 ++- quantreg-5.83/quantreg/MD5 | 32 +++++------- quantreg-5.83/quantreg/NAMESPACE | 2 quantreg-5.83/quantreg/R/rqss.R | 74 ++++++++++++++++++++--------- quantreg-5.83/quantreg/inst/ChangeLog | 14 +++++ quantreg-5.83/quantreg/man/plot.rqss.Rd | 5 + quantreg-5.83/quantreg/man/qss.Rd | 12 +++- quantreg-5.83/quantreg/man/rqss.Rd | 9 +++ quantreg-5.83/quantreg/src/boot.f | 2 quantreg-5.83/quantreg/src/linpack.f | 4 - quantreg-5.83/quantreg/src/powell.f | 2 quantreg-5.83/quantreg/src/ratfor/README | 4 + quantreg-5.83/quantreg/src/ratfor/boot.r | 2 quantreg-5.83/quantreg/src/ratfor/powell.r | 2 quantreg-5.83/quantreg/src/ratfor/sakj.r | 6 +- quantreg-5.83/quantreg/src/sparskit2.f | 12 ++-- 18 files changed, 128 insertions(+), 63 deletions(-)
Title: The Scalable Highly Adaptive Lasso
Description: A scalable implementation of the highly adaptive lasso algorithm,
including routines for constructing sparse matrices of basis functions of the
observed data, as well as a custom implementation of Lasso regression tailored
to enhance efficiency when the matrix of predictors is composed exclusively of
indicator functions. For ease of use and increased flexibility, the Lasso
fitting routines invoke code from the 'glmnet' package by default. The highly
adaptive lasso was first formulated and described by MJ van der Laan (2017)
<doi:10.1515/ijb-2015-0097>, with practical demonstrations of its performance
given by Benkeser and van der Laan (2016) <doi:10.1109/DSAA.2016.93>.
Author: Jeremy Coyle [aut, cre] (<https://orcid.org/0000-0002-9874-6649>),
Nima Hejazi [aut] (<https://orcid.org/0000-0002-7127-2789>),
David Benkeser [ctb] (<https://orcid.org/0000-0002-1019-8343>),
Oleg Sofrygin [ctb],
Rachael Phillips [ctb] (<https://orcid.org/0000-0002-8474-591X>),
Weixin Cai [ctb] (<https://orcid.org/0000-0003-2680-3066>),
Mark van der Laan [aut, cph, ths]
(<https://orcid.org/0000-0003-1432-5511>)
Maintainer: Jeremy Coyle <jeremyrcoyle@gmail.com>
Diff between hal9001 versions 0.2.6 dated 2020-06-27 and 0.2.7 dated 2021-01-22
DESCRIPTION | 16 MD5 | 37 NAMESPACE | 8 NEWS.md | 8 R/hal.R | 52 R/predict.R | 11 R/reduce_basis_filter.R | 2 R/summary.R |only README.md | 55 build/vignette.rds |binary inst/CITATION | 13 inst/REFERENCES.bib | 66 inst/doc/intro_hal9001.R | 8 inst/doc/intro_hal9001.Rmd | 18 inst/doc/intro_hal9001.html |34075 ------------------------------ man/make_reduced_basis_map.Rd | 1 man/predict.hal9001.Rd | 2 man/summary.hal9001.Rd |only tests/testthat/test-reduce_basis_filter.R | 4 tests/testthat/test-summary.R |only vignettes/intro_hal9001.Rmd | 18 21 files changed, 577 insertions(+), 33817 deletions(-)
Title: Access the 'Geographic Name Resolution Service'
Description: Provides tools for interacting with the 'geographic name resolution service' ('GNRS') API <https://github.com/ojalaquellueva/gnrs> and associated functionality. The 'GNRS' is a batch application for resolving & standardizing political division names against standard name in the geonames database <http://www.geonames.org/>. The 'GNRS' resolves political division names at three levels: country, state/province and county/parish. Resolution is performed in a series of steps, beginning with direct matching to standard names, followed by direct matching to alternate names in different languages, followed by direct matching to standard codes (such as ISO and FIPS codes). If direct matching fails, the 'GNRS' attempts to match to standard and then alternate names using fuzzy matching, but does not perform fuzzing matching of political division codes. The 'GNRS' works down the political division hierarchy, stopping at the current level if all matches fail. In other words, if a country cannot be matched, the 'GNRS' does not attempt to match state or county.
Author: Brad Boyle [aut],
Brian Maitner [aut, cre]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Diff between GNRS versions 0.1.0 dated 2020-04-28 and 0.1.1 dated 2021-01-22
DESCRIPTION | 8 - MD5 | 24 ++-- NAMESPACE | 3 NEWS | 12 ++ R/gnrs.R | 72 ++++++++---- R/gnrs_super_simple.R | 21 ++- R/gnrs_version.R |only inst/doc/GNRS.Rmd | 2 inst/doc/GNRS.html | 244 ++++++++++++++++++++++------------------- inst/extdata/gnrs_testfile.csv | 44 +++---- man/GNRS.Rd | 9 + man/GNRS_super_simple.Rd | 5 man/GNRS_version.Rd |only vignettes/GNRS.Rmd | 2 14 files changed, 265 insertions(+), 181 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-20 0.3.7
2018-08-22 0.3.6
2018-01-24 0.3.3
2018-01-08 0.3.2.1
2018-01-04 0.3.2
2017-11-26 0.3.1
2017-10-31 0.2.2
2017-09-19 0.2.1
2017-07-25 0.2.0
2017-06-23 0.1.2
2017-05-25 0.1.1
2017-04-25 0.1.0
2017-04-02 0.0.3
2017-04-01 0.0.2
2017-03-16 0.0.1