Title: Flexible Latent Trait Metrics using the Filtered Monotonic
Polynomial Item Response Model
Description: Application of the filtered monotonic polynomial (FMP) item response
model to flexibly fit item response models. The package includes tools that
allow the item response model to be build on any monotonic transformation of
the latent trait metric, as described by Feuerstahler (2019) <doi:10.1007/s11336-018-9642-9>.
Author: Leah Feuerstahler [aut, cre]
Maintainer: Leah Feuerstahler <lfeuerstahler@fordham.edu>
Diff between flexmet versions 1.0.0.0 dated 2018-04-06 and 1.1 dated 2021-07-13
DESCRIPTION | 17 - MD5 | 62 ++-- NAMESPACE | 1 R/0_internal.R | 633 +++++++++++++++++++++++++++++---------------------- R/get_surrogates.R | 14 + R/iif.R | 124 +++++++-- R/int_mat.R | 15 - R/irf.R | 85 +++++- R/item_estimation.R | 482 +++++++++++++++++++++++++++----------- R/linking.R | 147 +++++++---- R/rimse.R | 48 ++- R/sim_bmat.R | 104 +++++--- R/sim_data.R | 32 +- R/theta_estimation.R | 32 +- R/transformations.R | 207 +++++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/fmp.R | 18 - inst/doc/fmp.Rmd | 24 - inst/doc/fmp.html | 322 ++++++++++++++++--------- man/b2greek.Rd | 5 man/fmp.Rd | 130 +++++++--- man/iif_fmp.Rd | 19 - man/int_mat.Rd | 19 - man/irf_fmp.Rd | 32 +- man/linking.Rd | 71 ++++- man/rimse.Rd | 37 ++ man/sim_bmat.Rd | 53 ++-- man/sim_data.Rd | 19 - man/th_est_ml.Rd | 14 - man/transform_b.Rd | 16 - vignettes/fmp.Rmd | 24 - 32 files changed, 1796 insertions(+), 1010 deletions(-)
Title: Adaptive Bayesian Graphical Lasso
Description: Implements a Bayesian adaptive graphical lasso data-augmented block Gibbs sampler. The sampler simulates the posterior distribution of precision matrices of a Gaussian Graphical Model. This sampler was adapted from the original MATLAB routine proposed in Wang (2012) <doi:10.1214/12-BA729>.
Author: Jarod Smith [aut, cre] (<https://orcid.org/0000-0003-4235-6147>),
Mohammad Arashi [aut] (<https://orcid.org/0000-0003-4793-5674>),
Andriette Bekker [aut] (<https://orcid.org/0000-0002-5881-9241>)
Maintainer: Jarod Smith <jarodsmith706@gmail.com>
Diff between abglasso versions 0.1.0 dated 2021-05-12 and 0.1.1 dated 2021-07-13
DESCRIPTION | 14 +++++++++----- MD5 | 6 +++--- NEWS.md | 5 ++++- build/partial.rdb |binary 4 files changed, 16 insertions(+), 9 deletions(-)
Title: Reporting Tables
Description: Reporting tables often have structure that goes beyond simple rectangular
data. The 'rtables' package provides a framework for declaring complex multi-level tabulations
and then applying them to data. This framework models both tabulation and the resulting
tables as hierarchical, tree-like objects which support sibling sub-tables, arbitrary splitting
or grouping of data in row and column dimensions, cells containing multiple values,
and the concept of contextual summary computations. A convenient pipe-able interface is provided
for declaring table layouts and the corresponding computations, and then applying them to data.
Author: Gabriel Becker [aut, cre],
Adrian Waddell [aut],
Daniel Sabanés Bové [ctb],
Maximilian Mordig [ctb]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between rtables versions 0.3.6 dated 2021-01-22 and 0.3.8 dated 2021-07-13
DESCRIPTION | 11 MD5 | 123 +-- NAMESPACE | 27 NEWS.md | 24 R/00tabletrees.R | 541 ++++++++------- R/argument_conventions.R | 22 R/as_html.R | 99 ++ R/colby_constructors.R | 144 ++-- R/indent.R | 34 R/index_footnotes.R |only R/split_funs.R | 58 + R/summary.R | 24 R/tree_accessors.R | 317 ++++++++- R/tt_afun_utils.R | 42 + R/tt_compatibility.R | 17 R/tt_dotabulation.R | 28 R/tt_export.R |only R/tt_from_df.R |only R/tt_paginate.R | 227 ++---- R/tt_pos_and_access.R | 316 ++++++-- R/tt_toString.R | 450 +++++++++--- build/vignette.rds |binary inst/doc/baseline.html | 322 ++------- inst/doc/clinical_trials.html | 1124 +++++++++++++------------------- inst/doc/introduction.html | 378 +++------- inst/doc/manual_table_construction.html | 284 +------- inst/doc/sorting_pruning.html | 352 ++-------- inst/doc/subsetting_tables.html | 304 ++------ inst/doc/tabulation_concepts.html | 608 ++++++----------- inst/doc/tabulation_dplyr.html | 378 +++------- man/CellValue.Rd | 15 man/ManualSplit.Rd | 5 man/MultiVarSplit.Rd | 5 man/VarLevelSplit.Rd | 8 man/as_html.Rd | 10 man/avarspl.Rd | 9 man/basic_table.Rd | 16 man/brackets.Rd | 7 man/clear_imods.Rd |only man/constr_args.Rd | 22 man/cutsplits.Rd | 9 man/df_to_tt.Rd |only man/export_as_txt.Rd |only man/gen_args.Rd | 5 man/in_rows.Rd | 8 man/int_methods.Rd | 18 man/lyt_args.Rd | 8 man/make_row_df.Rd | 11 man/rcell.Rd | 11 man/ref_fnotes.Rd |only man/rowclasses.Rd | 5 man/split_cols_by.Rd | 5 man/split_funcs.Rd | 9 man/split_rows_by.Rd | 5 man/tabclasses.Rd | 20 man/tsv_io.Rd |only man/ttap.Rd |only man/update_ref_indexing.Rd |only man/varcuts.Rd | 9 man/vil.Rd |only tests/testthat/setup-fakedata.R | 11 tests/testthat/test-binding.R | 12 tests/testthat/test-compare_rtables.R |only tests/testthat/test-header-footer.R |only tests/testthat/test-indent-mod.R | 26 tests/testthat/test-lyt-tabulation.R | 90 +- tests/testthat/test-printing.R | 95 ++ tests/testthat/test-regressions.R | 144 ++++ tests/testthat/test-subset-access.R | 209 ++++- 69 files changed, 3692 insertions(+), 3369 deletions(-)
Title: Randomization Tests
Description: A collection of randomization tests, data sets and examples. The current version focuses on five testing problems and their implementation in empirical work. First, it facilitates the empirical researcher to test for particular hypotheses, such as comparisons of means, medians, and variances from k populations using robust permutation tests, which asymptotic validity holds under very weak assumptions, while retaining the exact rejection probability in finite samples when the underlying distributions are identical. Second, the description and implementation of a permutation test for testing the continuity assumption of the baseline covariates in the sharp regression discontinuity design (RDD) as in Canay and Kamat (2018) <https://goo.gl/UZFqt7>. More specifically, it allows the user to select a set of covariates and test the aforementioned hypothesis using a permutation test based on the Cramer-von Misses test statistic. Graphical inspection of the empirical CDF and histograms for the variables of interest is also supported in the package. Third, it provides the practitioner with an effortless implementation of a permutation test based on the martingale decomposition of the empirical process for testing for heterogeneous treatment effects in the presence of an estimated nuisance parameter as in Chung and Olivares (2021) <doi:10.1016/j.jeconom.2020.09.015>. Fourth, this version considers the two-sample goodness-of-fit testing problem under covariate adaptive randomization and implements a permutation test based on a prepivoted Kolmogorov-Smirnov test statistic. Lastly, it implements an asymptotically valid permutation test based on the quantile process for the hypothesis of constant quantile treatment effects in the presence of an estimated nuisance parameter.
Author: Mauricio Olivares [aut, cre],
Ignacio Sarmiento-Barbieri [aut]
Maintainer: Mauricio Olivares <mau.olivarego@gmail.com>
Diff between RATest versions 0.1.8 dated 2020-10-16 and 0.1.9 dated 2021-07-13
DESCRIPTION | 23 ++++++++++++----------- MD5 | 36 ++++++++++++++++++++---------------- NAMESPACE | 4 +++- R/PT.Khmaladze.MultTest.R | 10 +++++----- R/PT.Khmaladze.fit.R | 2 +- R/PTQTE.Khmaladze.fit.R |only R/prepivot.ks.permtest.R | 8 ++++---- R/randomization.test.R | 2 +- R/summary.PT.Khmaladze.fit.R | 2 +- R/summary.PTQTE.Khmaladze.fit.R |only R/summary.RDperm.R | 2 +- R/summary.RPT.R | 2 +- inst/doc/RDperm.pdf |binary man/PT.Khmaladze.MultTest.Rd | 10 +++++----- man/PT.Khmaladze.fit.Rd | 2 +- man/PTQTE.Khmaladze.fit.Rd |only man/randomization.test.Rd | 2 +- man/summary.PT.Khmaladze.fit.Rd | 2 +- man/summary.PTQTE.Khmaladze.fit.Rd |only man/summary.RDperm.Rd | 2 +- man/summary.RPT.Rd | 2 +- 21 files changed, 59 insertions(+), 52 deletions(-)
Title: Extract Tables and Sentences from PDFs with User Interface
Description: The PDE (Pdf Data Extractor) allows the extraction of
information and tables optionally based on search words from
PDF (Portable Document Format) files and enables the visualization
of the results, both by providing a convenient user-interface.
Author: Erik Stricker [aut, cre]
Maintainer: Erik Stricker <erik.stricker@gmx.com>
Diff between PDE versions 1.2.1 dated 2021-04-01 and 1.3.0 dated 2021-07-13
PDE-1.2.1/PDE/inst/examples/MTX_output_linux/txt+-0/29973177_!_txt+-0__M_m_ethotrexate,_T_t_rexal,_R....csv |only PDE-1.2.1/PDE/inst/examples/MTX_output_linux/txt+-0/31083238_!_txt+-0__M_m_ethotrexate,_T_t_rexal,_R....csv |only PDE-1.2.1/PDE/inst/examples/MTX_output_mac/txt+-0/29973177_!_txt+-0__M_m_ethotrexate,_T_t_rexal,_R....csv |only PDE-1.2.1/PDE/inst/examples/MTX_output_mac/txt+-0/31083238_!_txt+-0__M_m_ethotrexate,_T_t_rexal,_R....csv |only PDE-1.2.1/PDE/inst/examples/MTX_output_win/txt+-0/29973177_!_txt+-0__M_m_ethotrexate,_T_t_rexal,_R....csv |only PDE-1.2.1/PDE/inst/examples/MTX_output_win/txt+-0/31083238_!_txt+-0__M_m_ethotrexate,_T_t_rexal,_R....csv |only PDE-1.2.1/PDE/inst/examples/tsvs/PDE_parameters_v1.0_all_files+-0.tsv |only PDE-1.3.0/PDE/DESCRIPTION | 8 PDE-1.3.0/PDE/MD5 | 118 - PDE-1.3.0/PDE/NEWS.md | 6 PDE-1.3.0/PDE/R/PDE.R | 636 +++++++--- PDE-1.3.0/PDE/README.md | 52 PDE-1.3.0/PDE/inst/doc/PDE.Rmd | 31 PDE-1.3.0/PDE/inst/doc/PDE.html | 94 - PDE-1.3.0/PDE/inst/examples/MTX_output_linux/excl_by_fw/31261533_x_not.enough.txt.w.filter.words.csv | 2 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/html.docu/29973177_!_htmltablelines.csv | 10 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/html.docu/31083238_!_htmltablelines.csv | 6 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/keeptxt.docu/29973177_!_keeplayouttablelines.csv | 10 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/keeptxt.docu/31083238_!_keeplayouttablelines.csv | 6 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/nr/00000000_x_non-readable.txt | 2 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/secured/99999999_x_is_secured.txt | 2 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/tables/29973177_!_1_Table_1_Comparison_of_th.csv | 20 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/tables/29973177_!_2_Table_2_Human_chorionic_.csv | 20 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/tables/29973177_!_3_Table_3_Comparison_of_ou.csv | 94 - PDE-1.3.0/PDE/inst/examples/MTX_output_linux/tables/29973177_!_4_Table_4_Comparison_basic.csv | 24 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/tables/31083238_!_1_Table_1_Characteristics_.csv | 36 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/tables/31083238_!_2_Table_2_Baseline_charact.csv | 51 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/txt+-0/29973177_!_txt+-0__M_m_ethotrexate,_T.csv |only PDE-1.3.0/PDE/inst/examples/MTX_output_linux/txt+-0/31083238_!_txt+-0__M_m_ethotrexate,_T.csv |only PDE-1.3.0/PDE/inst/examples/MTX_output_linux/txt.docu/29973177_!_txttablelines.csv | 10 PDE-1.3.0/PDE/inst/examples/MTX_output_linux/txt.docu/31083238_!_txttablelines.csv | 6 PDE-1.3.0/PDE/inst/examples/MTX_output_mac/html.docu/29973177_!_htmltablelines.csv | 2 PDE-1.3.0/PDE/inst/examples/MTX_output_mac/keeptxt.docu/29973177_!_keeplayouttablelines.csv | 2 PDE-1.3.0/PDE/inst/examples/MTX_output_mac/nr/00000000_x_non-readable.txt | 2 PDE-1.3.0/PDE/inst/examples/MTX_output_mac/secured/99999999_x_is_secured.txt | 2 PDE-1.3.0/PDE/inst/examples/MTX_output_mac/tables/29973177_!_1_Table_1_Comparison_of_th.csv | 8 PDE-1.3.0/PDE/inst/examples/MTX_output_mac/tables/29973177_!_2_Table_2_Human_chorionic_.csv | 12 PDE-1.3.0/PDE/inst/examples/MTX_output_mac/tables/29973177_!_3_Table_3_Comparison_of_ou.csv | 94 - PDE-1.3.0/PDE/inst/examples/MTX_output_mac/tables/29973177_!_4_Table_4_Comparison_basic.csv | 8 PDE-1.3.0/PDE/inst/examples/MTX_output_mac/tables/31083238_!_1_Table_1_Characteristics_.csv | 36 PDE-1.3.0/PDE/inst/examples/MTX_output_mac/tables/31083238_!_2_Table_2_Baseline_charact.csv | 51 PDE-1.3.0/PDE/inst/examples/MTX_output_mac/txt+-0/29973177_!_txt+-0__M_m_ethotrexate,_T.csv |only PDE-1.3.0/PDE/inst/examples/MTX_output_mac/txt+-0/31083238_!_txt+-0__M_m_ethotrexate,_T.csv |only PDE-1.3.0/PDE/inst/examples/MTX_output_mac/txt.docu/29973177_!_txttablelines.csv | 2 PDE-1.3.0/PDE/inst/examples/MTX_output_win/html.docu/29973177_!_htmltablelines.csv | 2 PDE-1.3.0/PDE/inst/examples/MTX_output_win/keeptxt.docu/29973177_!_keeplayouttablelines.csv | 2 PDE-1.3.0/PDE/inst/examples/MTX_output_win/nr/00000000_x_non-readable.txt | 2 PDE-1.3.0/PDE/inst/examples/MTX_output_win/secured/99999999_x_is_secured.txt | 2 PDE-1.3.0/PDE/inst/examples/MTX_output_win/tables/29973177_!_1_Table_1_Comparison_of_th.csv | 4 PDE-1.3.0/PDE/inst/examples/MTX_output_win/tables/29973177_!_2_Table_2_Human_chorionic_.csv | 8 PDE-1.3.0/PDE/inst/examples/MTX_output_win/tables/29973177_!_3_Table_3_Comparison_of_ou.csv | 32 PDE-1.3.0/PDE/inst/examples/MTX_output_win/tables/29973177_!_4_Table_4_Comparison_basic.csv | 6 PDE-1.3.0/PDE/inst/examples/MTX_output_win/tables/31083238_!_1_Table_1_Characteristics_.csv | 6 PDE-1.3.0/PDE/inst/examples/MTX_output_win/tables/31083238_!_2_Table_2_Baseline_charact.csv | 3 PDE-1.3.0/PDE/inst/examples/MTX_output_win/txt+-0/29973177_!_txt+-0__M_m_ethotrexate,_T.csv |only PDE-1.3.0/PDE/inst/examples/MTX_output_win/txt+-0/31083238_!_txt+-0__M_m_ethotrexate,_T.csv |only PDE-1.3.0/PDE/inst/examples/MTX_output_win/txt.docu/29973177_!_txttablelines.csv | 2 PDE-1.3.0/PDE/inst/examples/tsvs/PDE_parameters_v1.3_all_files+-0.tsv |only PDE-1.3.0/PDE/man/PDE_analyzer.Rd | 2 PDE-1.3.0/PDE/man/PDE_extr_data_from_pdfs.Rd | 20 PDE-1.3.0/PDE/man/PDE_pdfs2table.Rd | 16 PDE-1.3.0/PDE/man/PDE_pdfs2table_searchandfilter.Rd | 20 PDE-1.3.0/PDE/man/PDE_pdfs2txt_searchandfilter.Rd | 4 PDE-1.3.0/PDE/man/dot-PDE_extr_data_from_pdf.Rd | 20 PDE-1.3.0/PDE/vignettes/PDE.Rmd | 31 PDE-1.3.0/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.parameters_MTX_example.png |binary PDE-1.3.0/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.parameters_empty.png |binary 67 files changed, 1020 insertions(+), 625 deletions(-)
Title: Nonparametric Estimation of Measurement Error Models
Description: Provide nonparametric methods for mean regression model, modal regression and conditional density estimation in the presence/absence of measurement error. Bandwidth selection is also provided for each method. See Huang and Zhou (2017) <doi:10.1080/10485252.2017.1303060>, Zhou and Huang (2016) <doi:10.1214/16-EJS1210>, Huang and Zhou (2020) <doi:10.1214/20-EJS1688>, and Zhou and Huang (2019) <doi:10.1080/03610918.2017.1402044>.
Author: Haiming Zhou [aut, cre, cph],
Xianzheng Huang [aut]
Maintainer: Haiming Zhou <zhouh@niu.edu>
Diff between lpme versions 1.1.1 dated 2017-10-31 and 1.1.2 dated 2021-07-13
DESCRIPTION | 18 +- MD5 | 38 +++--- R/densityreg.R | 4 R/densityregbw.R | 37 ++--- man/densityreg.Rd | 245 +++++++++++++++++++-------------------- man/densityregbw.Rd | 247 +++++++++++++++++++--------------------- man/meanreg.Rd | 195 +++++++++++++++---------------- man/meanregbwSIMEX.Rd | 209 ++++++++++++++++----------------- man/modereg.Rd | 223 +++++++++++++++++------------------- man/moderegbw.Rd | 187 +++++++++++++++--------------- man/moderegbwSIMEX.Rd | 215 +++++++++++++++++----------------- src/lpme_common.cpp | 25 ++-- src/lpme_density_fit.cpp | 9 - src/lpme_densityreg_fit.cpp | 29 ++-- src/lpme_meanreg_dfc.cpp | 1 src/lpme_meanreg_hz.cpp | 1 src/lpme_modereg_band1.cpp | 13 +- src/lpme_modereg_band2.cpp | 1 src/lpme_modereg_fit.cpp | 1 src/lpme_modereg_fit_approx.cpp | 17 +- 20 files changed, 860 insertions(+), 855 deletions(-)
Title: Tidy Structural Equation Modeling
Description: A tidy workflow for generating, estimating, reporting,
and plotting structural equation models using 'lavaan', 'OpenMx', or
'Mplus'. Throughout this workflow, elements of syntax, results, and graphs
are represented as 'tidy' data, making them easy to customize.
Author: Caspar J. van Lissa [aut, cre]
(<https://orcid.org/0000-0002-0808-5024>)
Maintainer: Caspar J. van Lissa <c.j.vanlissa@uu.nl>
Diff between tidySEM versions 0.1.9 dated 2021-04-20 and 0.1.10 dated 2021-07-13
DESCRIPTION | 17 MD5 | 63 - NAMESPACE | 54 R/data-mac.R |only R/empathy.R |only R/mixture_summaries.R |only R/motley_functions.R | 101 + R/mx_mixture.R |only R/openmx_functions.R |only R/plot-generate_layout.R | 21 R/plot-plot_sem.R | 99 + R/print.R | 38 R/results-table_results.R | 14 R/results-table_results_mx_model.R | 280 ++++ R/select_rows.R | 6 R/syntax-run.R |only R/syntax_factor.R | 29 R/utilities.R | 28 build/partial.rdb |only build/vignette.rds |binary data |only inst/doc/Generating_syntax.html | 640 +++------- inst/doc/Plotting_graphs.html | 1383 +++++++++-------------- inst/doc/Tabulating_results.html | 1006 ++++++---------- inst/doc/sem_graph.html | 298 ---- man/as_ram.Rd |only man/chisq_sb.Rd | 7 man/curry_mac.Rd |only man/empathy.Rd |only man/get_fit.Rd |only man/get_nodes.Rd | 2 man/graph_sem.Rd | 12 man/lsub.Rd |only man/mixture_starts.Rd |only man/mx_growth_mixture.Rd |only man/mx_mixture.Rd |only man/mx_profiles.Rd |only man/paste2.Rd |only man/prepare_graph.Rd | 12 man/run_lavaan.Rd |only man/run_mx.Rd |only tests/testthat/test-plot_if_edit_overwrite_aes.R | 13 42 files changed, 1953 insertions(+), 2170 deletions(-)
Title: Collapsed Latent Position Cluster Model for Social Networks
Description: Markov chain Monte Carlo based inference routines for collapsed latent position cluster models or social networks, which includes searches over the model space (number of clusters in the latent position cluster model). The label switching algorithm used is that of Nobile and Fearnside (2007) <doi:10.1007/s11222-006-9014-7> which relies on the algorithm of Carpaneto and Toth (1980) <doi:10.1145/355873.355883>.
Author: Jason Wyse [aut, cre],
Caitriona Ryan [aut],
Nial Friel [ths]
Maintainer: Jason Wyse <wyseja@tcd.ie>
Diff between collpcm versions 1.1 dated 2019-10-24 and 1.2 dated 2021-07-13
DESCRIPTION | 10 - MD5 | 35 +++--- NAMESPACE | 6 - NEWS.md |only R/collpcm.control.R | 121 ++++++-------------- R/collpcm.fit.R | 179 +++++++----------------------- R/collpcm.summaryplot.R | 2 R/collpcm.undo.label.switching.R | 227 ++++++++++++++++++++------------------- R/plot.collpcm.R | 21 +-- R/summary.collpcm.R | 4 build |only inst |only man/collpcm.control.Rd | 16 +- man/collpcm.fit.Rd | 4 man/collpcm.summaryplot.Rd | 4 man/plot.collpcm.Rd | 8 - man/print.collpcm.Rd | 4 man/summary.collpcm.Rd | 4 vignettes |only 19 files changed, 261 insertions(+), 384 deletions(-)
Title: Robust Preprocessing of Time Series Data
Description: Methods for handling the missing values outliers are introduced in
this package. The recognized missing values and outliers are replaced
using a model-based approach. The model may consist of both autoregressive
components and external regressors. The methods work robust and efficient,
and they are fully tunable. The primary motivation for writing the package
was preprocessing of the energy systems data, e.g. power plant production
time series, but the package could be used with any time series data.
Author: Michał Narajewski [aut, cre] (<https://orcid.org/0000-0002-3115-0162>),
Jens Kley-Holsteg [aut],
Florian Ziel [aut] (<https://orcid.org/0000-0002-2974-2660>)
Maintainer: Michał Narajewski <michal.narajewski@uni-due.de>
Diff between tsrobprep versions 0.3.0 dated 2021-06-30 and 0.3.1 dated 2021-07-13
DESCRIPTION | 8 MD5 | 10 R/auto_data_cleaning.R | 4 R/detect_outliers.R | 134 ++++-- R/model_missing_data.R | 950 ++++++++++++++++++++++++------------------------- man/detect_outliers.Rd | 40 +- 6 files changed, 606 insertions(+), 540 deletions(-)
Title: A Grammar of Clinical Data Summary
Description: A tool created to simplify the data manipulation necessary to create clinical reports.
Author: Eli Miller [aut] (<https://orcid.org/0000-0002-2127-9456>),
Mike Stackhouse [aut, cre] (<https://orcid.org/0000-0001-6030-723X>),
Ashley Tarasiewicz [aut],
Nathan Kosiba [aut] (<https://orcid.org/0000-0001-5359-4234>),
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 0.4.0 dated 2021-02-11 and 0.4.1 dated 2021-07-13
DESCRIPTION | 7 +- MD5 | 26 ++++----- NEWS.md | 7 ++ R/prebuild.R | 16 ++--- R/riskdiff.R | 5 - R/stats.R | 9 --- inst/doc/Tplyr.html | 21 +++++-- inst/doc/count.html | 9 ++- inst/doc/denom.html | 121 +++++++++++++++++++++++--------------------- inst/doc/desc.html | 9 ++- inst/doc/options.html | 9 ++- inst/doc/shift.html | 9 ++- inst/doc/table.html | 9 ++- tests/testthat/test-count.R | 5 + 14 files changed, 154 insertions(+), 108 deletions(-)
Title: Read and Write CSV Files with Selected Conventions
Description: Reads and writes CSV with selected conventions.
Uses the same generic function for reading and writing to promote consistent formats.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between csv versions 0.5.9 dated 2020-05-20 and 0.6.1 dated 2021-07-13
DESCRIPTION | 9 ++++----- MD5 | 4 ++-- R/csv.R | 4 ++-- 3 files changed, 8 insertions(+), 9 deletions(-)
Title: Phylogenetic Reconstruction and Analysis
Description: Allows for estimation of phylogenetic trees and networks
using Maximum Likelihood, Maximum Parsimony, distance methods and
Hadamard conjugation. Offers methods for tree comparison, model
selection and visualization of phylogenetic networks as described in
Schliep et al. (2017) <doi:10.1111/2041-210X.12760>.
Author: Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>),
Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>),
Leonardo de Oliveira Martins [aut]
(<https://orcid.org/0000-0001-5247-1320>),
Alastair Potts [aut],
Tim W. White [aut],
Cyrill Stachniss [ctb],
Michelle Kendall [ctb],
Keren Halabi [ctb],
Richel Bilderbeek [ctb],
Kristin Winchell [ctb],
Liam Revell [ctb],
Mike Gilchrist [ctb],
Jeremy Beaulieu [ctb],
Brian O'Meara [ctb],
Long Qu [ctb]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 2.7.0 dated 2021-05-03 and 2.7.1 dated 2021-07-13
DESCRIPTION | 6 MD5 | 48 ++--- NEWS | 7 R/ancestral_pml.R | 4 R/cladePar.R | 9 R/fitch64.R | 2 R/networx.R | 7 R/parsimony.R | 25 +- R/phyDat.R | 2 R/phyDat2.R | 2 R/phylo.R | 2 R/treeManipulation.R | 10 - R/treeRearrangement.R | 2 build/vignette.rds |binary inst/doc/AdvancedFeatures.html | 29 +-- inst/doc/Ancestral.html | 31 +-- inst/doc/IntertwiningTreesAndNetworks.html | 11 - inst/doc/Networx.html | 21 +- inst/doc/Trees.R | 29 ++- inst/doc/Trees.Rmd | 72 ++++++- inst/doc/Trees.html | 277 +++++++++++++++++------------ man/cladePar.Rd | 2 src/RcppExports.cpp | 5 vignettes/Trees.Rmd | 72 ++++++- vignettes/phangorn.bib | 1 25 files changed, 447 insertions(+), 229 deletions(-)
Title: Visualization of Patient Profiles
Description: Creation of patient profile visualizations for
exploration, diagnostic or monitoring purposes during a clinical trial.
These static visualizations display a patient-specific overview
of the evolution during the trial time frame of
parameters of interest (as laboratory, ECG, vital signs),
presence of adverse events, exposure to a treatment;
associated with metadata patient information,
as demography, concomitant medication.
The visualizations can be tailored for specific domain(s) or endpoint(s) of interest.
Visualizations are exported into patient profile report(s)
or can be embedded in custom report(s).
Author: Laure Cougnaud [aut, cre],
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between patientProfilesVis versions 2.0.0 dated 2021-06-14 and 2.0.1 dated 2021-07-13
DESCRIPTION | 8 - MD5 | 12 +- inst/NEWS | 2 inst/doc/patientProfiles-template-SDTM.html | 11 +- inst/doc/patientProfilesVis-introduction.Rmd | 122 ++++++++++++-------------- inst/doc/patientProfilesVis-introduction.html | 11 +- vignettes/patientProfilesVis-introduction.Rmd | 122 ++++++++++++-------------- 7 files changed, 146 insertions(+), 142 deletions(-)
More information about patientProfilesVis at CRAN
Permanent link
Title: Creation of in-Text Summary Table
Description: Creation of tables of summary statistics or counts for clinical data (for 'TLFs').
These tables can be exported as in-text table (with the 'flextable' package) for a Clinical Study Report
(Word format) or a 'topline' presentation (PowerPoint format),
or as interactive table (with the 'DT' package) to an html document for clinical data review.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between inTextSummaryTable versions 3.0.0 dated 2021-06-10 and 3.0.1 dated 2021-07-13
DESCRIPTION | 10 MD5 | 28 R/formatSummaryStatisticsTable.R | 20 inst/NEWS | 3 inst/doc/inTextSummaryTable-advanced.html | 31 inst/doc/inTextSummaryTable-aesthetics.html | 51 - inst/doc/inTextSummaryTable-createTables.html | 751 +++++++++--------- inst/doc/inTextSummaryTable-exportTables.Rmd | 4 inst/doc/inTextSummaryTable-exportTables.html | 146 +-- inst/doc/inTextSummaryTable-introduction.html | 11 inst/doc/inTextSummaryTable-standardTables.html | 131 +-- inst/doc/inTextSummaryTable-visualization.html | 11 tests/testthat/test_exportSummaryStatisticsTable-DT.R | 11 tests/testthat/test_exportSummaryStatisticsTable.R | 6 vignettes/inTextSummaryTable-exportTables.Rmd | 4 15 files changed, 635 insertions(+), 583 deletions(-)
More information about inTextSummaryTable at CRAN
Permanent link
Title: Download Air Quality and Meteorological Information of Chile
Description: Download air quality and meteorological information of Chile from the National Air Quality System (S.I.N.C.A.)<https://sinca.mma.gob.cl/> dependent on the Ministry of the Environment and the Meteorological Directorate of Chile (D.M.C.)<http://www.meteochile.gob.cl/> dependent on the Directorate General of Civil Aeronautics.
Author: Francisco Catalan Meyer [aut, cre]
(<https://orcid.org/0000-0003-3506-5376>),
Manuel Leiva [aut] (<https://orcid.org/0000-0001-8891-0399>),
Richard Toro [aut]
Maintainer: Francisco Catalan Meyer <francisco.catalan@ug.uchile.cl>
Diff between AtmChile versions 0.1.0 dated 2021-05-04 and 0.1.1 dated 2021-07-13
DESCRIPTION | 6 - MD5 | 8 - R/ChileAirQuality.R | 269 ++++++++++++++++++++++++++++++++++++++++++++----- README.md | 9 + man/ChileAirQuality.Rd | 17 ++- 5 files changed, 273 insertions(+), 36 deletions(-)
Title: Area Correction Methods
Description: Post-construction fatality monitoring studies at wind facilities are based on data from searches for bird and bat carcasses in plots beneath turbines. Bird and bat carcasses can fall outside of the search plot. Bird and bat carcasses from wind turbines often fall outside of the searched area. To compensate, area correction (AC) estimations are calculated to estimate the percentage of fatalities that fall within the searched area versus those that fall outside of it. This package provides two likelihood based methods and one physics based method (Hull and Muir (2010) <doi:10.1080/14486563.2010.9725253>, Huso and Dalthorp (2014) <doi:10.1002/jwmg.663>) to estimate the carcass fall distribution. There are also functions for calculating the proportion of area searched within one unit annuli, log logistic distribution functions, and truncated distribution functions.
Author: Jared Studyvin [aut, cre],
Paul Rabie [aut],
Daniel Riser-Espinoza [aut],
Trent McDonald [ctb]
Maintainer: Jared Studyvin <jared.studyvin@gmail.com>
Diff between windAC versions 1.2.4 dated 2020-11-23 and 1.2.6 dated 2021-07-13
DESCRIPTION | 14 ++++++------ MD5 | 34 +++++++++++++++---------------- R/calcAC.R | 4 +-- R/dllog.R | 2 - R/geometricRectanglePropSearchTable.R | 4 +-- R/geometricRoadPadPropSearchTable.R | 11 ++++++---- R/getProportionAreaSearched.R | 27 ++++++++++++------------ R/triangleProb.R | 4 +-- R/weightFun.R | 6 ++--- R/windAC.R | 2 - man/LogLogistic.Rd | 2 - man/calcAC.Rd | 4 +-- man/geometricRectanglePropSearchTable.Rd | 4 +-- man/geometricRoadPadPropSearchTable.Rd | 2 - man/getProportionAreaSearched.Rd | 17 ++++++++------- man/triangleProb.Rd | 4 +-- man/weightFun.Rd | 6 ++--- man/windAC.Rd | 2 - 18 files changed, 77 insertions(+), 72 deletions(-)
Title: Statistical Models of Repeated Categorical Rating Data
Description: Fit statistical models based on the Dawid-Skene model - Dawid
and Skene (1979) <doi:10.2307/2346806> - to repeated categorical
rating data. Full Bayesian inference for these models is supported
through the Stan modelling language. 'rater' also allows the user to
extract and plot key parameters of these models.
Author: Jeffrey Pullin [aut, cre, cph]
(<https://orcid.org/0000-0003-3651-5471>),
Damjan Vukcevic [aut] (<https://orcid.org/0000-0001-7780-9586>),
Lars Mølgaard Saxhaug [aut] (<https://orcid.org/0000-0001-5084-1578>)
Maintainer: Jeffrey Pullin <jeffrey.pullin@gmail.com>
Diff between rater versions 1.1.0 dated 2021-03-14 and 1.2.0 dated 2021-07-13
DESCRIPTION | 57 ++++++++++++++++------------ MD5 | 23 ++++++----- NAMESPACE | 3 + NEWS.md | 8 ++++ R/model_comparison.R | 63 ++++++++++++++++++++++++++++++++ R/plotting.R | 4 +- R/posterior_predict.R | 2 - build/vignette.rds |binary inst/doc/data-formats.html | 1 inst/doc/workflow.html | 9 ++-- man/waic.rater_fit.Rd |only tests/testthat/test-model_comparison.R | 24 ++++++++++++ tests/testthat/test-posterior_predict.R | 5 ++ 13 files changed, 156 insertions(+), 43 deletions(-)
Title: Integral Projection Models
Description: Flexibly implements Integral Projection Models using a
mathematical(ish) syntax. This package will not help with the vital rate
modeling process, but will help convert those regression models into an
IPM. 'ipmr' handles density dependence and environmental stochasticity, with a
couple of options for implementing the latter. In addition, provides functions
to avoid unintentional eviction of individuals from models. Additionally,
provides model diagnostic tools, plotting functionality,
stochastic/deterministic simulations, and analysis tools.
Integral projection models are described in depth by Easterling et al. (2000)
<doi:10.1890/0012-9658(2000)081[0694:SSSAAN]2.0.CO;2>, Merow et al. (2013)
<doi:10.1111/2041-210X.12146>, Rees et al. (2014) <doi:10.1111/1365-2656.12178>,
and Metcalf et al. (2015) <doi:10.1111/2041-210X.12405>.
Williams et al. (2012) <doi:10.1890/11-2147.1> discuss the problem of
unintentional eviction.
Author: Sam Levin [aut, cre] (<https://orcid.org/0000-0002-3289-9925>),
Aldo Compagnoni [aut],
Dylan Childs [aut],
Sanne Evers [aut],
Roberto Salguero-Gomez [aut],
Tiffany Knight [aut]
Maintainer: Sam Levin <levisc8@gmail.com>
Diff between ipmr versions 0.0.2 dated 2021-05-22 and 0.0.3 dated 2021-07-13
DESCRIPTION | 24 MD5 | 62 NAMESPACE | 19 NEWS.md | 44 R/generics.R | 4641 ++++++++++++++----------- R/internal-lin_alg.R | 1570 ++++---- R/internal-make_ipm.R | 2 R/make_ipm.R | 12 R/utils-export.R | 179 inst/doc/age_x_size.html | 1 inst/doc/density-dependence.html | 1 inst/doc/general-ipms.html | 1 inst/doc/index-notation.html | 1 man/accessors.Rd | 5 man/check_convergence.Rd | 45 man/define_star.Rd | 44 man/eigenvectors.Rd | 67 man/lambda.Rd | 33 man/print_star.Rd | 20 tests/testthat/Rplots.pdf |binary tests/testthat/test-age_size.R | 1128 +++--- tests/testthat/test-exported_utils.R | 51 tests/testthat/test-general_dd_stoch_kern.R | 447 +- tests/testthat/test-general_dd_stoch_param.R | 463 +- tests/testthat/test-general_di_det.R | 1804 ++++----- tests/testthat/test-general_di_stoch_kern.R | 3095 ++++++++-------- tests/testthat/test-general_di_stoch_param.R | 3624 +++++++++---------- tests/testthat/test-generics.R | 4961 +++++++++++++-------------- tests/testthat/test-simple_dd_stoch_kern.R | 442 +- tests/testthat/test-simple_di_det.R | 1449 +++---- tests/testthat/test-simple_di_stoch_kern.R | 1504 ++++---- tests/testthat/test-simple_di_stoch_param.R | 1405 +++---- 32 files changed, 14062 insertions(+), 13082 deletions(-)
Title: Statistics for Holland's Theory of Vocational Choice
Description: Offers a convenient way to compute parameters
in the framework of the theory of vocational choice introduced by
J.L. Holland, (1997). A comprehensive summary to this theory
of vocational choice is given in Holland, J.L. (1997). Making vocational
choices. A theory of vocational personalities and work environments.
Lutz, FL: Psychological Assessment.
Author: Joerg-Henrik Heine [aut, cre, com],
Florian Hartmann [rev, com],
Bernhard Ertl [rev, com],
Christian Tarnai [com, ths]
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>
Diff between holland versions 0.1.0-6 dated 2021-06-22 and 0.1.1-1 dated 2021-07-13
DESCRIPTION | 10 +++++----- MD5 | 32 +++++++++++++++++++++++--------- NAMESPACE | 7 +++++++ NEWS | 8 ++++++++ R/Mplus_psyn.R | 2 +- R/dif_7_holland.R | 4 ++-- R/holland-package.R | 4 ++-- R/i.eli_ines_seg.R |only R/i.eli_ines_tot.R |only R/i.gesvector.R |only R/i.hexa_lines_circular.R |only R/i.hexa_lines_radial.R |only R/i.hexa_poly.R |only R/i.hexa_text_radial.R |only R/i.hexa_tics_radial.R |only R/i.plot_blank.R |only R/kormean.R | 2 +- R/plot_profile_holland.R |only R/sim_score_data.R |only inst |only man/dif_7_holland.Rd | 2 +- man/kormean.Rd | 2 +- man/plot_profile_holland.Rd |only man/sim_score_data.Rd |only 24 files changed, 51 insertions(+), 22 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Michael Curry [aut] (<https://orcid.org/0000-0002-0261-4044>),
Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>),
Joseph Larmarange [aut] (<https://orcid.org/0000-0001-7097-700X>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>),
Jessica Lavery [ctb] (<https://orcid.org/0000-0002-2746-5647>),
Stephanie Lobaugh [ctb],
Gustavo Zapata Wainberg [ctb] (<https://orcid.org/0000-0002-2524-3637>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.4.1 dated 2021-05-19 and 1.4.2 dated 2021-07-13
gtsummary-1.4.1/gtsummary/inst/rmarkdown_example/gtsummary_rmarkdown_html.html |only gtsummary-1.4.2/gtsummary/DESCRIPTION | 10 gtsummary-1.4.2/gtsummary/MD5 | 117 gtsummary-1.4.2/gtsummary/NEWS.md | 20 gtsummary-1.4.2/gtsummary/R/add_p.R | 9 gtsummary-1.4.2/gtsummary/R/as_flex_table.R | 1 gtsummary-1.4.2/gtsummary/R/as_hux_table.R | 13 gtsummary-1.4.2/gtsummary/R/as_kable_extra.R | 19 gtsummary-1.4.2/gtsummary/R/as_tibble.R | 4 gtsummary-1.4.2/gtsummary/R/combine_terms.R | 2 gtsummary-1.4.2/gtsummary/R/custom_tidiers.R | 3 gtsummary-1.4.2/gtsummary/R/style_pvalue.R | 13 gtsummary-1.4.2/gtsummary/R/tbl_merge.R | 2 gtsummary-1.4.2/gtsummary/R/tbl_stack.R | 53 gtsummary-1.4.2/gtsummary/R/tbl_svysummary.R | 49 gtsummary-1.4.2/gtsummary/R/tbl_uvregression.R | 52 gtsummary-1.4.2/gtsummary/README.md | 9 gtsummary-1.4.2/gtsummary/build/gtsummary.pdf |11701 +++++----- gtsummary-1.4.2/gtsummary/build/vignette.rds |binary gtsummary-1.4.2/gtsummary/inst/doc/gallery.R | 2 gtsummary-1.4.2/gtsummary/inst/doc/gallery.Rmd | 34 gtsummary-1.4.2/gtsummary/inst/doc/gallery.html | 1185 - gtsummary-1.4.2/gtsummary/inst/doc/gtsummary_definition.html | 1 gtsummary-1.4.2/gtsummary/inst/doc/inline_text.R | 2 gtsummary-1.4.2/gtsummary/inst/doc/inline_text.Rmd | 2 gtsummary-1.4.2/gtsummary/inst/doc/inline_text.html | 217 gtsummary-1.4.2/gtsummary/inst/doc/rmarkdown.html | 275 gtsummary-1.4.2/gtsummary/inst/doc/tbl_regression.R | 2 gtsummary-1.4.2/gtsummary/inst/doc/tbl_regression.Rmd | 2 gtsummary-1.4.2/gtsummary/inst/doc/tbl_regression.html | 577 gtsummary-1.4.2/gtsummary/inst/doc/tbl_summary.R | 2 gtsummary-1.4.2/gtsummary/inst/doc/tbl_summary.Rmd | 2 gtsummary-1.4.2/gtsummary/inst/doc/tbl_summary.html | 1153 gtsummary-1.4.2/gtsummary/inst/doc/themes.html | 433 gtsummary-1.4.2/gtsummary/man/as_flex_table.Rd | 3 gtsummary-1.4.2/gtsummary/man/as_hux_table.Rd | 9 gtsummary-1.4.2/gtsummary/man/as_kable_extra.Rd | 8 gtsummary-1.4.2/gtsummary/man/combine_terms.Rd | 2 gtsummary-1.4.2/gtsummary/man/custom_tidiers.Rd | 3 gtsummary-1.4.2/gtsummary/man/tbl_merge.Rd | 2 gtsummary-1.4.2/gtsummary/man/tbl_stack.Rd | 2 gtsummary-1.4.2/gtsummary/man/tbl_svysummary.Rd | 1 gtsummary-1.4.2/gtsummary/tests/testthat/test-add_n.R | 4 gtsummary-1.4.2/gtsummary/tests/testthat/test-add_overall.R | 4 gtsummary-1.4.2/gtsummary/tests/testthat/test-add_p.tbl_cross.R | 17 gtsummary-1.4.2/gtsummary/tests/testthat/test-add_p.tbl_svysummary.R | 1 gtsummary-1.4.2/gtsummary/tests/testthat/test-add_stat.R | 1 gtsummary-1.4.2/gtsummary/tests/testthat/test-add_stat_label.R | 2 gtsummary-1.4.2/gtsummary/tests/testthat/test-as_kable_extra.R | 34 gtsummary-1.4.2/gtsummary/tests/testthat/test-as_tibble.R | 9 gtsummary-1.4.2/gtsummary/tests/testthat/test-inline_text.R | 2 gtsummary-1.4.2/gtsummary/tests/testthat/test-modify_header.R | 1 gtsummary-1.4.2/gtsummary/tests/testthat/test-tbl_stack.R | 21 gtsummary-1.4.2/gtsummary/tests/testthat/test-tbl_strata.R | 1 gtsummary-1.4.2/gtsummary/tests/testthat/test-tbl_svysummary.R | 1 gtsummary-1.4.2/gtsummary/tests/testthat/test-tbl_uvregression.R | 5 gtsummary-1.4.2/gtsummary/vignettes/gallery.Rmd | 34 gtsummary-1.4.2/gtsummary/vignettes/inline_text.Rmd | 2 gtsummary-1.4.2/gtsummary/vignettes/tbl_regression.Rmd | 2 gtsummary-1.4.2/gtsummary/vignettes/tbl_summary.Rmd | 2 60 files changed, 8184 insertions(+), 7955 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith, 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space, for
calculating the median of sets of trees, and for computing the information
content of trees and splits.
Author: Martin R. Smith [aut, cre, cph, prg]
(<https://orcid.org/0000-0001-5660-1727>),
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.1.0 dated 2021-07-12 and 2.1.1 dated 2021-07-13
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- NEWS.md | 19 +++++++++++++++++++ R/tree_information.R | 9 +++++++-- build/partial.rdb |binary inst/WORDLIST | 2 ++ inst/doc/Using-TreeDist.html | 6 +++--- inst/doc/treespace.R | 15 +++++++++++---- inst/doc/treespace.Rmd | 18 ++++++++++++------ inst/doc/treespace.html | 14 ++++++++------ src/information.h | 8 ++++---- src/tree_distances.cpp | 3 +++ tests/testthat/test-tree_distance.R | 4 ++++ tests/testthat/test-tree_information.R | 19 +++++++++++-------- vignettes/treespace.Rmd | 18 ++++++++++++------ 15 files changed, 113 insertions(+), 56 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<http://cwb.sourceforge.net>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre' (BSD license, see <http://www.pcre.org/licence.txt>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stefan Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.4.0 dated 2021-06-25 and 0.4.2 dated 2021-07-13
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 14 ++++++++++++++ configure | 44 ++++++++++++++++++++++++++------------------ src/Makevars.win | 10 +++++----- src/cwb/utils/_cwb_encode.c | 34 +++++++++++++++++----------------- src/utils.cpp | 10 +++++----- src/utils.h | 10 +++++----- tools/winlibs.R | 4 ++-- 9 files changed, 86 insertions(+), 64 deletions(-)
Title: Bayesian Model Selection and Averaging for Non-Local and Local
Priors
Description: Bayesian model selection and averaging for regression and mixtures for non-local and selected local priors.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck, Oriol Abril
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 3.0.3 dated 2021-06-01 and 3.0.4 dated 2021-07-13
ChangeLog | 4 + DESCRIPTION | 8 +- MD5 | 16 ++-- R/modelSelection.R | 151 ++++++++++++++++++++++------------------- inst/doc/mombf.pdf |binary src/glm.cpp | 178 +++++++++++++++++++++++++++---------------------- src/modelSel.cpp | 103 ++++++++++++++-------------- src/modselFunction.cpp | 10 ++ src/modselFunction.h | 4 + 9 files changed, 265 insertions(+), 209 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using
instrumental variables.
Author: Zachary Fisher [aut, cre],
Kenneth Bollen [aut],
Kathleen Gates [aut],
Mikko Rönkkö [aut]
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.5.7 dated 2021-07-07 and 0.5.8 dated 2021-07-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/estVarCovarCoef.R | 4 ++-- R/miive.R | 4 ++-- R/miivs.R | 10 +++++++++- 5 files changed, 20 insertions(+), 12 deletions(-)
Title: Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Description: Contains:
1) Facilities for working with grouped data: 'do' something to data
stratified 'by' some variables.
2) LSmeans (least-squares means), general linear contrasts.
3) Miscellaneous other utilities.
Author: Søren Højsgaard <sorenh@math.aau.dk> and Ulrich Halekoh
<uhalekoh@health.sdu.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between doBy versions 4.6.10 dated 2021-04-29 and 4.6.11 dated 2021-07-13
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Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, flexible and
parsimonious to code with, class-agnostic and programmer friendly.
It is well integrated with base R, 'dplyr' / (grouped) 'tibble',
'data.table', 'plm' (panel-series and data frames), 'sf' data frames, and
non-destructively handles other matrix or data frame based classes (such as
'ts', 'xts' / 'zoo', 'timeSeries', 'tsibble', 'tibbletime' etc.)
--- Key Features: ---
(1) Advanced statistical programming: A full set of fast statistical functions
supporting grouped and weighted computations on vectors, matrices and
data frames. Fast and programmable grouping, ordering, unique values / rows,
factor generation and interactions. Fast and flexible functions for data
manipulation and data object conversions.
(2) Advanced aggregation: Fast and easy multi-data-type, multi-function,
weighted, parallelized and fully customized data aggregation.
(3) Advanced transformations: Fast row / column arithmetic, (grouped) replacing
and sweeping out of statistics, (grouped, weighted) scaling / standardizing,
between (averaging) and (quasi-)within (centering / demeaning) transformations,
higher-dimensional centering (i.e. multiple fixed effects transformations),
linear prediction / partialling-out, linear model fitting and testing.
(4) Advanced time-computations: Fast (sequences of) lags / leads, and
(lagged / leaded, iterated, quasi-, log-) differences, (compounded)
growth rates, and cumulative sums on (unordered, irregular) time series and
panel data. Multivariate auto-, partial- and cross-correlation functions for panel data.
Panel data to (ts-)array conversions.
(5) List processing: (Recursive) list search / identification, splitting,
extraction / subsetting, data-apply, and generalized recursive
row-binding / unlisting in 2D.
(6) Advanced data exploration: Fast (grouped, weighted, panel-decomposed)
summary statistics for complex multilevel / panel data.
Author: Sebastian Krantz [aut, cre],
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Laurent Berge [ctb],
Dirk Eddelbuettel [ctb],
Josh Pasek [ctb],
Kevin Tappe [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [cph]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 1.6.2 dated 2021-07-04 and 1.6.4 dated 2021-07-13
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 8 ++++++++ R/GRP.R | 5 +++-- inst/doc/collapse_documentation.html | 4 ++-- man/fast-data-manipulation.Rd | 2 +- man/ftransform.Rd | 4 ++-- src/ffirst.c | 23 ++++++++++++++--------- src/flast.c | 14 +++++++++----- src/small_helper.c | 15 +++++++++------ 10 files changed, 61 insertions(+), 40 deletions(-)
Title: Bayesian Summary Data Models for Mendelian Randomization Studies
Description: Bayesian estimation of inverse variance weighted (IVW), Burgess
et al. (2013) <doi:10.1002/gepi.21758>, and MR-Egger, Bowden et
al. (2015) <doi:10.1093/ije/dyv080>, summary data models for Mendelian
randomization analyses.
Author: Okezie Uche-Ikonne [aut, cre] (<https://orcid.org/0000-0002-8461-8099>),
Frank Dondelinger [aut] (<https://orcid.org/0000-0003-1816-6300>),
Tom Palmer [aut] (<https://orcid.org/0000-0003-4655-4511>)
Maintainer: Okezie Uche-Ikonne <okezieikonne@gmail.com>
Diff between mrbayes versions 0.3.0 dated 2021-04-01 and 0.4.0 dated 2021-07-13
DESCRIPTION | 10 +++++----- MD5 | 19 ++++++++++--------- NEWS.md | 8 ++++++++ R/mr_egger_rjags.R | 2 ++ R/mr_ivw_rjags.R | 3 +++ R/mr_radialegger_rjags.R | 2 ++ R/mvmr_egger_rjags.R | 3 +++ R/mvmr_ivw_rjags.R | 5 ++++- R/rjags_check.R |only README.md | 3 ++- build/partial.rdb |binary 11 files changed, 39 insertions(+), 16 deletions(-)
Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre],
David Kellen [aut],
Quentin Gronau [aut],
Christian Mueller [ctb],
Akhil S Bhel [ctb]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between MPTinR versions 1.13.0 dated 2020-08-26 and 1.14.1 dated 2021-07-13
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- NEWS | 17 +++++++++++++++++ R/check.mpt.R | 8 ++++++-- R/read.EQN.model.R | 9 +++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/mptinr_introduction.Rnw | 2 +- inst/doc/mptinr_introduction.pdf |binary man/MPTinR-package.Rd | 2 +- man/check.mpt.Rd | 5 +++++ man/fit.model.Rd | 2 +- man/fit.mpt.Rd | 8 +++++--- man/fit.mpt.old.Rd | 2 +- man/fit.mptinr.Rd | 2 +- man/rocs.Rd | 20 ++++++++++---------- vignettes/mptinr_introduction.Rnw | 2 +- 17 files changed, 77 insertions(+), 40 deletions(-)
Title: Group Subset Selection
Description: Provides tools for sparse regression modelling with grouped predictors using the group
subset selection penalty. Uses coordinate descent and local search algorithms to rapidly deliver
near optimal estimates. The group subset penalty can be combined with a group lasso or ridge
penalty for added shrinkage. Linear and logistic regression are supported, as are overlapping
groups.
Author: Ryan Thompson [aut, cre] (<https://orcid.org/0000-0002-9002-0448>)
Maintainer: Ryan Thompson <ryan.thompson@monash.edu>
Diff between grpsel versions 1.1.0 dated 2021-06-29 and 1.1.1 dated 2021-07-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 +++- src/RcppExports.cpp | 5 +++++ src/ls.cpp | 12 +++++++++--- 5 files changed, 24 insertions(+), 11 deletions(-)
Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users
define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and
resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time,
applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values,
exporting data cubes as 'netCDF' or 'GeoTIFF' files, and plotting. The package implements lazy evaluation and
multithreading. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries.
See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] (<https://orcid.org/0000-0001-5281-3896>),
Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>),
Roger Bivand [ctb],
Lewis Van Winkle [cph],
Ole Christian Eidheim [cph],
Howard Hinnant [cph],
Adrian Colomitchi [cph],
Florian Dang [cph],
Paul Thompson [cph],
Tomasz Kamiński [cph],
Dropbox, Inc. [cph]
Maintainer: Marius Appel <marius.appel@uni-muenster.de>
Diff between gdalcubes versions 0.3.1 dated 2020-08-27 and 0.4.0 dated 2021-07-13
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Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre],
Matt Dennis [ctb],
Gerard Walsh [ctb],
Antoine Bichat [ctb] (<https://orcid.org/0000-0001-6599-7081>),
Daniel Fahey [ctb],
Johann R. Kleinbub [ctb],
Panagiotis Moulos [ctb]
Maintainer: Andrew B. Collier <andrew.b.collier@gmail.com>
Diff between emayili versions 0.4.11 dated 2021-06-25 and 0.4.12 dated 2021-07-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/server.R | 11 +++++++++-- man/server.Rd | 8 ++++++++ 5 files changed, 28 insertions(+), 9 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses. The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: František Bartoš [aut, cre] (<https://orcid.org/0000-0002-0018-5573>)
Maintainer: František Bartoš <f.bartos96@gmail.com>
Diff between BayesTools versions 0.1.0 dated 2021-07-02 and 0.1.1 dated 2021-07-13
BayesTools-0.1.0/BayesTools/tests/testthat/_snaps/priors-print/priors-print-1.new.svg |only BayesTools-0.1.0/BayesTools/tests/testthat/_snaps/priors-print/priors-print-2.new.svg |only BayesTools-0.1.1/BayesTools/DESCRIPTION | 10 - BayesTools-0.1.1/BayesTools/MD5 | 50 +++--- BayesTools-0.1.1/BayesTools/NEWS.md | 15 ++ BayesTools-0.1.1/BayesTools/R/model-averaging-plots.R | 71 ++++++--- BayesTools-0.1.1/BayesTools/R/model-averaging.R | 10 + BayesTools-0.1.1/BayesTools/R/priors-density.R | 2 BayesTools-0.1.1/BayesTools/R/priors-plot.R | 11 - BayesTools-0.1.1/BayesTools/README.md | 3 BayesTools-0.1.1/BayesTools/man/figures/README-unnamed-chunk-11-1.png |binary BayesTools-0.1.1/BayesTools/man/figures/README-unnamed-chunk-11-2.png |binary BayesTools-0.1.1/BayesTools/man/figures/README-unnamed-chunk-11-3.png |binary BayesTools-0.1.1/BayesTools/man/figures/README-unnamed-chunk-12-1.png |binary BayesTools-0.1.1/BayesTools/man/figures/README-unnamed-chunk-12-2.png |binary BayesTools-0.1.1/BayesTools/man/figures/README-unnamed-chunk-3-1.png |binary BayesTools-0.1.1/BayesTools/man/figures/README-unnamed-chunk-3-2.png |binary BayesTools-0.1.1/BayesTools/man/figures/README-unnamed-chunk-3-3.png |binary BayesTools-0.1.1/BayesTools/man/figures/README-unnamed-chunk-3-4.png |binary BayesTools-0.1.1/BayesTools/man/figures/README-unnamed-chunk-3-5.png |binary BayesTools-0.1.1/BayesTools/man/plot.prior.Rd | 3 BayesTools-0.1.1/BayesTools/man/plot_models.Rd | 3 BayesTools-0.1.1/BayesTools/man/plot_posterior.Rd | 3 BayesTools-0.1.1/BayesTools/man/plot_prior_list.Rd | 3 BayesTools-0.1.1/BayesTools/tests/testthat/test-JAGS-fit.R | 2 BayesTools-0.1.1/BayesTools/tests/testthat/test-JAGS-marglik.R | 5 BayesTools-0.1.1/BayesTools/tests/testthat/test-summary-tables.R | 75 ++++++++-- 27 files changed, 180 insertions(+), 86 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Quantitative proteomics measurements frequently contain multiple NA values, due to physical absence of given peptides in some samples, limitations in sensitivity or other reasons.
The functions provided here help to inspect graphically the data to investigate the nature of NA-values via their respective replicate measurements and to help/confirm the choice of NA-replacement by low random values.
Dedicated filtering and statistical testing using the framework of package 'limma' <doi:10.18129/B9.bioc.limma> can be run, enhanced by multiple rounds of NA-replacements to provide robustness towards rare stochastic events.
Multi-species samples, as frequently used in benchmark-tests (eg Navarro et al 2016 <doi:10.1038/nbt.3685>, Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>), can be run with special options separating the data into sub-groups during normalization and testing.
As example the data-set from Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>) is provided quantified by MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), ProteomeDiscoverer,
OpenMS (<doi:10.1038/nmeth.3959>) and Proline (Bouyssie et al 2020 <doi:10.1093/bioinformatics/btaa118>).
Subsequently, ROC curves (Hand and Till 2001 <doi:10.1023/A:1010920819831>) can be constructed to compare multiple analysis approaches.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 1.4.2 dated 2021-07-05 and 1.4.3 dated 2021-07-13
DESCRIPTION | 8 MD5 | 12 inst/doc/wrProteoVignette1.html | 101 +- inst/doc/wrProteoVignetteUPS1.R | 128 +-- inst/doc/wrProteoVignetteUPS1.Rmd | 128 +-- inst/doc/wrProteoVignetteUPS1.html | 1347 ++++++++++++++++++------------------- vignettes/wrProteoVignetteUPS1.Rmd | 128 +-- 7 files changed, 925 insertions(+), 927 deletions(-)
Title: Analyse Citation Data from Google Scholar
Description: Provides functions to extract citation data from Google
Scholar. Convenience functions are also provided for comparing
multiple scholars and predicting future h-index values.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>),
James Keirstead [aut],
Gregory Jefferis [ctb],
Gordon Getzinger [ctb],
Jorge Cimentada [ctb],
Max Czapanskiy [ctb],
Dominique Makowski [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between scholar versions 0.2.1 dated 2021-04-28 and 0.2.2 dated 2021-07-13
DESCRIPTION | 14 +- MD5 | 30 ++--- NAMESPACE | 1 NEWS.md | 7 + R/coauthors.R | 33 ++++-- R/getCompleteAuthors.R | 14 +- R/publications.r | 23 ++-- R/scholar.r | 21 +++- R/utils.R | 15 ++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/scholar.html | 218 +++++++++++++++++++----------------------- man/get_profile.Rd | 2 man/scholar-package.Rd | 3 man/set_scholar_mirror.Rd | 2 tests/testthat/test-scholar.R | 8 + 16 files changed, 215 insertions(+), 176 deletions(-)
Title: R Interface to Pullword Service
Description: R Interface to Pullword Service for natural language processing
in Chinese. It enables users to extract valuable words from text by deep learning models.
For more details please visit the official site (in Chinese) <http://www.pullword.com/>.
Author: Tong He <hetong007@gmail.com>
Maintainer: Tong He <hetong007@gmail.com>
Diff between pullword versions 0.2 dated 2016-07-22 and 0.3 dated 2021-07-13
DESCRIPTION | 9 ++++----- MD5 | 9 ++++++--- NAMESPACE | 4 ++-- R/pullword.R | 15 +++++++++++---- man/isGB18030.Rd |only man/isGB2312.Rd |only src/pullword_init.c |only 7 files changed, 23 insertions(+), 14 deletions(-)
Title: Interactive Studio for Explanatory Model Analysis
Description: Automate the explanatory analysis of machine learning predictive models.
Generate advanced interactive model explanations in the form of a serverless HTML
site with only one line of code. This tool is model-agnostic, therefore compatible
with most of the black-box predictive models and frameworks. The main function
computes various (instance and model-level) explanations and produces
a customisable dashboard, which consists of multiple panels for plots with their
short descriptions. Easily save the dashboard and share it with others. Tools
for Explanatory Model Analysis unite with tools for Exploratory Data Analysis
to give a broad overview of the model behavior.
Author: Hubert Baniecki [aut, cre] (<https://orcid.org/0000-0001-6661-5364>),
Przemyslaw Biecek [aut] (<https://orcid.org/0000-0001-8423-1823>),
Piotr Piatyszek [ctb]
Maintainer: Hubert Baniecki <hbaniecki@gmail.com>
Diff between modelStudio versions 2.1.2 dated 2021-04-20 and 3.0.0 dated 2021-07-13
DESCRIPTION | 19 +++++----- MD5 | 49 ++++++++++++++++----------- NAMESPACE | 2 - NEWS.md | 10 +++++ R/data.R |only R/modelStudio.R | 19 ++++++++-- R/ms_merge_observations.R |only R/ms_options.R | 15 ++++---- build/vignette.rds |binary data |only inst/d3js/modelStudio.js | 17 ++++++--- inst/d3js/myTools.js | 11 ++++++ inst/doc/ms-perks-features.Rmd | 4 +- inst/doc/ms-perks-features.html | 7 ++- inst/doc/ms-r-python-examples.R | 7 +-- inst/doc/ms-r-python-examples.Rmd | 27 +++++++------- inst/doc/ms-r-python-examples.html | 45 ++++++++++++------------ inst/doc/ms-rmarkdown.R |only inst/doc/ms-rmarkdown.Rmd |only inst/doc/ms-rmarkdown.html |only man/happiness_train.Rd |only man/modelStudio.Rd | 7 +++ man/ms_merge_observations.Rd |only man/ms_options.Rd | 3 - tests/testthat/test_3_0.R |only tests/testthat/test_ms_update_observations.R | 29 ++++++++------- tests/testthat/test_warnings_and_errors.R | 12 +++++- vignettes/ms-perks-features.Rmd | 4 +- vignettes/ms-r-python-examples.Rmd | 27 +++++++------- vignettes/ms-rmarkdown.Rmd |only 30 files changed, 190 insertions(+), 124 deletions(-)
Title: Classes for Storing and Manipulating Taxonomic Data
Description: Provides classes for storing and manipulating taxonomic data.
Most of the classes can be treated like base R vectors (e.g. can be used
in tables as columns and can be named). Vectorized classes can store taxon names
and authorities, taxon IDs from databases, taxon ranks, and other types of
information. More complex classes are provided to store taxonomic trees and
user-defined data associated with them.
Author: Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Zachary Foster [aut, cre] (<https://orcid.org/0000-0002-5075-0948>)
Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>
Diff between taxa versions 0.3.4 dated 2020-04-29 and 0.4.0 dated 2021-07-13
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Title: Parametric G-Formula
Description: Implements the parametric g-formula algorithm of Robins (1986)
<doi:10.1016/0270-0255(86)90088-6>. The g-formula can be used to estimate
the causal effects of hypothetical time-varying treatment interventions on
the mean or risk of an outcome from longitudinal data with time-varying
confounding. This package allows: 1) binary or continuous/multi-level
time-varying treatments; 2) different types of outcomes (survival or
continuous/binary end of follow-up); 3) data with competing events or
truncation by death and loss to follow-up and other types of censoring
events; 4) different options for handling competing events in the case of
survival outcomes; 5) a random measurement/visit process; 6) joint
interventions on multiple treatments; and 7) general incorporation of a
priori knowledge of the data structure.
Author: Victoria Lin [aut] (V. Lin and S. McGrath made equal contributions),
Sean McGrath [aut, cre] (<https://orcid.org/0000-0002-7281-3516>, V.
Lin and S. McGrath made equal contributions),
Zilu Zhang [aut],
Roger W. Logan [aut],
Lucia C. Petito [aut],
Jessica G. Young [aut] (<https://orcid.org/0000-0002-2758-6932>, M.A.
Hernán and J.G. Young made equal contributions),
Miguel A. Hernán [aut] (M.A. Hernán and J.G. Young made equal
contributions),
2019 The President and Fellows of Harvard College [cph]
Maintainer: Sean McGrath <sean_mcgrath@g.harvard.edu>
Diff between gfoRmula versions 0.3.1 dated 2020-03-23 and 0.3.2 dated 2021-07-13
DESCRIPTION | 10 +-- MD5 | 62 ++++++++++----------- NEWS.md | 10 +++ R/gformula.R | 8 +- R/histories.R | 105 ++++++++++++++++++++++++------------ R/simulate.R | 2 README.md | 3 - man/basicdata.Rd | 6 +- man/basicdata_nocomp.Rd | 6 +- man/binary_eofdata.Rd | 6 +- man/bootstrap_helper.Rd | 52 +++++++++++++++-- man/continuous_eofdata.Rd | 6 +- man/continuous_eofdata_pb.Rd | 6 +- man/error_catch.Rd | 35 ++++++++++-- man/fit_bounded_continuous.Rd | 10 ++- man/fit_zeroinfl_normal.Rd | 3 - man/get_plot_info.Rd | 16 ++++- man/gformula.Rd | 55 ++++++++++++++---- man/gformula_binary_eof.Rd | 47 ++++++++++++---- man/gformula_continuous_eof.Rd | 47 ++++++++++++---- man/gformula_survival.Rd | 54 ++++++++++++++---- man/lagged.Rd | 24 ++++++-- man/make_histories.Rd | 14 ++++ man/obs_calculate.Rd | 11 +++ man/plot.gformula_binary_eof.Rd | 14 +++- man/plot.gformula_continuous_eof.Rd | 14 +++- man/plot.gformula_survival.Rd | 23 ++++++- man/pred_fun_Y.Rd | 11 +++ man/pred_fun_cov.Rd | 12 +++- man/print.gformula_survival.Rd | 46 ++++++++++++--- man/rmse_calculate.Rd | 14 ++++ man/simulate.Rd | 46 +++++++++++++-- 32 files changed, 586 insertions(+), 192 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-22 0.13.0
2018-10-08 0.12.3
2018-05-13 0.12.2
2016-05-06 0.10.0
2016-02-23 0.9.0
2015-12-02 0.8.0
2015-10-15 0.7.0
2015-04-30 0.6.1
2014-01-31 0.5.1
2013-12-04 0.4.0
2013-10-25 0.3
2013-06-01 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-31 2.3
2020-08-10 2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-05 2.4.2
2021-05-23 2.4
2020-10-30 2.2.1
2020-10-16 2.2
2020-08-07 2.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-05 1.13
2020-11-16 1.12
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-23 2.6
2021-05-22 2.5.2
2020-10-16 2.4
2020-08-05 2.3.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-06 2.2
2020-08-11 2.1.4
Title: Adaptive Enrichment Designs with Sample Size Re-Estimation
Description: Software of 'esDesign' is developed to implement the adaptive
enrichment designs with sample size re-estimation presented in
Lin et al. (2021) <doi: 10.1016/j.cct.2020.106216>. In details,
three-proposed trial designs are provided, including the AED1-SSR (or ES1-SSR),
AED2-SSR (or ES2-SSR) and AED3-SSR (or ES3-SSR). In addition, this package
also contains several widely used adaptive designs, such as the Marker
Sequential Test (MaST) design proposed Freidlin et al.
(2014) <doi:10.1177/1740774513503739>, the adaptive enrichment designs
without early stopping (AED or ES), the sample size re-estimation
procedure (SSR) based on the conditional power proposed by
Proschan and Hunsberger (1995), and some useful functions.
In details, we can calculate the futility and/or efficacy stopping
boundaries, the sample size required, calibrate the value of the threshold
of the difference between subgroup-specific test statistics, conduct the
simulation studies in AED, SSR, AED1-SSR, AED2-SSR and AED3-SSR.
Author: Zhao Yang, Ruitao Lin, Guosheng Yin and Ying Yuan
Maintainer: Zhao Yang <yangz98@connect.hku.hk>
Diff between esDesign versions 1.0.2 dated 2018-11-23 and 1.0.3 dated 2021-07-13
DESCRIPTION | 28 MD5 | 28 NEWS.md | 9 R/esDesign.R | 3892 +++++++++++++++++++++++------------------------ man/AED.boundary.Rd | 9 man/AED.sim.Rd | 22 man/AED1_SSR.CP.Rd | 5 man/AED1_SSR.N2.Rd | 5 man/AED1_SSR.boundary.Rd | 5 man/AED1_SSR.sim.Rd | 22 man/AED2_SSR.CP.Rd | 13 man/AED2_SSR.sim.Rd | 15 man/AED3_SSR.CP.Rd | 12 man/AED3_SSR.sim.Rd | 3 man/SSR.CP.Rd | 3 15 files changed, 2075 insertions(+), 1996 deletions(-)
Title: Lightweight Well-Known Geometry Parsing
Description: Provides a minimal R and C++ API for parsing
well-known binary and well-known text representation of
geometries to and from R-native formats.
Well-known binary is compact
and fast to parse; well-known text is human-readable
and is useful for writing tests. These formats are only
useful in R if the information they contain can be
accessed in R, for which high-performance functions
are provided here.
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>),
Edzer Pebesma [aut] (<https://orcid.org/0000-0001-8049-7069>)
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between wk versions 0.4.1 dated 2021-03-16 and 0.5.0 dated 2021-07-13
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Title: Non-Invasive Pretty Printing of R Code
Description: Pretty-prints R code without changing the user's formatting
intent.
Author: Kirill Müller [aut],
Lorenz Walthert [cre, aut]
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between styler versions 1.4.1 dated 2021-03-30 and 1.5.1 dated 2021-07-13
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styler-1.5.1/styler/R/transform-code.R | 50 + styler-1.5.1/styler/R/ui-caching.R | 28 - styler-1.5.1/styler/R/ui-styling.R | 38 - styler-1.5.1/styler/R/unindent.R | 2 styler-1.5.1/styler/R/utils-files.R | 16 styler-1.5.1/styler/R/visit.R | 2 styler-1.5.1/styler/build/vignette.rds |binary styler-1.5.1/styler/inst/doc/caching.html | 1 styler-1.5.1/styler/inst/doc/customizing_styler.html | 7 styler-1.5.1/styler/inst/doc/detect-alignment.R | 126 ++-- styler-1.5.1/styler/inst/doc/detect-alignment.Rmd | 210 ++----- styler-1.5.1/styler/inst/doc/detect-alignment.html | 211 +++---- styler-1.5.1/styler/inst/doc/introducing_styler.html | 5 styler-1.5.1/styler/inst/doc/strict.html | 1 styler-1.5.1/styler/inst/doc/styler.html | 5 styler-1.5.1/styler/man/add_token_terminal.Rd | 7 styler-1.5.1/styler/man/alignment_col1_all_named.Rd |only styler-1.5.1/styler/man/cache_activate.Rd | 4 styler-1.5.1/styler/man/caching.Rd | 30 - styler-1.5.1/styler/man/create_tokens.Rd | 6 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styler-1.5.1/styler/tests/testthat/token_adding_removing/else-pipe-in.R |only styler-1.5.1/styler/tests/testthat/token_adding_removing/else-pipe-in_tree |only styler-1.5.1/styler/tests/testthat/token_adding_removing/else-pipe-out.R |only styler-1.5.1/styler/vignettes/detect-alignment.Rmd | 210 ++----- 114 files changed, 1441 insertions(+), 814 deletions(-)
Title: Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <sebastian.calonico@columbia.edu>, Matias D. Cattaneo <cattaneo@princeton.edu>, Max H. Farrell <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@princeton.edu>
Maintainer: Sebastian Calonico <sebastian.calonico@columbia.edu>
Diff between rdrobust versions 1.0.3 dated 2021-07-05 and 1.0.4 dated 2021-07-13
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/functions.R | 5 +++-- R/rdbwselect.R | 30 +++++++++++++++--------------- R/rdplot.R | 4 ++-- R/rdrobust.R | 4 ++-- man/rdbwselect.Rd | 3 ++- man/rdplot.Rd | 3 ++- man/rdrobust-package.Rd | 4 ++-- man/rdrobust.Rd | 4 +++- 10 files changed, 44 insertions(+), 39 deletions(-)
Title: Factorization of Sparse Counts Matrices Through Poisson
Likelihood
Description: Creates a low-rank factorization of a sparse counts matrix by maximizing Poisson likelihood with l1/l2 regularization
with all non-negative latent factors (e.g. for recommender systems or topic modeling) (Cortes, (2018) <arXiv:1811.01908>).
Similar to hierarchical Poisson factorization, but follows an optimization-based approach with regularization instead of a
hierarchical structure, and is fit through gradient-based methods instead of variational inference.
Author: David Cortes [aut, cre, cph], Jean-Sebastien Roy [cph], Stephen Nash [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between poismf versions 0.3.0-1 dated 2021-05-08 and 0.3.1 dated 2021-07-13
DESCRIPTION | 7 +++---- MD5 | 20 ++++++++++---------- R/poismf.R | 45 +++++++++------------------------------------ configure | 18 +++++++++--------- configure.ac | 2 +- man/poismf.Rd | 9 ++------- man/poismf_unsafe.Rd | 3 +-- src/nonnegcg.c | 4 ++++ src/poismf.c | 3 +++ src/poismf.h | 32 ++++++++++++++++---------------- src/rwrapper.c | 28 ++++++++++------------------ 11 files changed, 68 insertions(+), 103 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 1.8.0 dated 2021-02-11 and 1.8.1 dated 2021-07-13
DESCRIPTION | 11 MD5 | 16 R/nroPreprocess.R | 15 R/numero.prepare.R | 3 build/vignette.rds |binary inst/doc/intro.R | 124 +-- inst/doc/intro.html | 1663 ++++++++++++++++++++++++++++++++++++++++++++------ man/nroPreprocess.Rd | 5 man/numero.prepare.Rd | 9 9 files changed, 1588 insertions(+), 258 deletions(-)
Title: Generate Isolines and Isobands from Regularly Spaced Elevation
Grids
Description: A fast C++ implementation to generate contour lines (isolines) and
contour polygons (isobands) from regularly spaced grids containing elevation data.
Author: Claus O. Wilke [aut, cre] (<https://orcid.org/0000-0002-7470-9261>),
Thomas Lin Pedersen [aut] (<https://orcid.org/0000-0002-5147-4711>),
testthat and Catch authors [ctb] (testthat C++ testing code)
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between isoband versions 0.2.4 dated 2021-03-03 and 0.2.5 dated 2021-07-13
isoband-0.2.4/isoband/inst/doc/isoband2.R |only isoband-0.2.4/isoband/inst/doc/isoband2.Rmd |only isoband-0.2.4/isoband/inst/doc/isoband2.html |only isoband-0.2.4/isoband/vignettes/isoband2.Rmd |only isoband-0.2.5/isoband/DESCRIPTION | 9 +- isoband-0.2.5/isoband/MD5 | 40 +++++------ isoband-0.2.5/isoband/NAMESPACE | 1 isoband-0.2.5/isoband/NEWS.md | 10 ++ isoband-0.2.5/isoband/R/iso-to-sfg.R | 3 isoband-0.2.5/isoband/R/isolines-grob.R | 3 isoband-0.2.5/isoband/R/label-placer.R | 40 +++++++++++ isoband-0.2.5/isoband/build/vignette.rds |binary isoband-0.2.5/isoband/inst/doc/isoband1.Rmd | 4 - isoband-0.2.5/isoband/inst/doc/isoband1.html | 23 ++++-- isoband-0.2.5/isoband/inst/doc/isoband3.Rmd | 4 - isoband-0.2.5/isoband/inst/doc/isoband3.html | 17 +++-- isoband-0.2.5/isoband/man/iso_to_sfg.Rd | 3 isoband-0.2.5/isoband/man/isoband-package.Rd | 2 isoband-0.2.5/isoband/man/label_placer.Rd | 5 + isoband-0.2.5/isoband/src/testthat/vendor/catch.h | 6 - isoband-0.2.5/isoband/tests/testthat/test-label-placer.R | 51 +++++++++++++++ isoband-0.2.5/isoband/vignettes/isoband1.Rmd | 4 - isoband-0.2.5/isoband/vignettes/isoband3.Rmd | 4 - 23 files changed, 174 insertions(+), 55 deletions(-)
Title: Tools for 'iNZight'
Description: Provides a collection of wrapper functions for common variable and dataset manipulation workflows primarily used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions. Additionally, many of the functions return the 'tidyverse' code used to obtain the result in an effort to bridge the gap between GUI and coding.
Author: Tom Elliott [aut, cre] (<https://orcid.org/0000-0002-7815-6318>),
Christoph Knopf [ctb],
Akshay Gupta [ctb],
Owen Jin [aut] (Tidyverse variable/data manipulation functions),
Lushi Cai [ctb],
Yiwen He [aut] (Dates/times and dataset manipulation),
Daniel Barnett [aut] (Data validation)
Maintainer: Tom Elliott <tom.elliott@auckland.ac.nz>
Diff between iNZightTools versions 1.11.1 dated 2021-06-30 and 1.11.2 dated 2021-07-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/append_rows.R | 2 +- R/class_intervals.R | 2 +- man/appendrows.Rd | 2 +- man/form_class_intervals.Rd | 2 +- tests/testthat/test_smart_read.R | 9 +++++++-- tests/testthat/test_survey_design.R | 3 ++- 8 files changed, 23 insertions(+), 17 deletions(-)