Package: BiostatsUHNplus 0.0.10

BiostatsUHNplus: Nested Data Summary, Adverse Events and REDCap

Tools and code snippets for summarizing nested data, adverse events and REDCap study information.

Authors:Lisa Avery [aut], Zeynep Baskurt [aut], Osvaldo Espin-Garcia [aut], Katrina Hueniken [aut], Katherine Lajkosz [aut], Xuan Li [aut], Tyler Pittman [cre, aut], Anna Santiago [aut], Jessica Weiss [aut], Wei Xu [aut]

BiostatsUHNplus_0.0.10.tar.gz
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BiostatsUHNplus_0.0.10.tgz(r-4.4-any)BiostatsUHNplus_0.0.10.tgz(r-4.3-any)
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BiostatsUHNplus.pdf |BiostatsUHNplus.html✨
BiostatsUHNplus/json (API)
NEWS

# Install 'BiostatsUHNplus' in R:

install.packages('BiostatsUHNplus', repos = c('https://tylerpittman.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

ae - Simulated adverse events for patients receiving two study agents.
demography - Simulated demography for patients.
drug1_admin - Simulated study agent 1 for patients.
drug2_admin - Simulated study agent 2 for patients.
enrollment - Enrollment data Simulated enrollment for patients.
ineligibility - Simulated ineligibility for patients.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

8 exports 0.36 score 125 dependencies 4 scripts 219 downloads

Last updated 4 months agofrom:d89656ef51. Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 23 2024
R-4.5-win	NOTE	Aug 23 2024
R-4.5-linux	NOTE	Aug 23 2024
R-4.4-win	OK	Aug 23 2024
R-4.4-mac	OK	Aug 23 2024
R-4.3-win	OK	Aug 23 2024
R-4.3-mac	OK	Aug 23 2024

Exports:ae_timeline_plot as_numeric_parse caterpillar_plot dsmb_ccru nice_mcmcglmm nice_mcmcglmm_icc redcap_data_out rm_covsum_nested

Dependencies:abind afex aod ape backports base64enc boot broom bslib cachem car carData cli clue cluster cmprsk coda colorspace corpcor corrplot cowplot cpp11 cubature Deriv digest doBy dplyr evaluate fansi farver fastmap fBasics fontawesome forcats fs geepack generics ggh4x ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gss gtable highr htmltools isoband jquerylib jsonlite kableExtra knitr labeling lattice lifecycle lme4 lmerTest magrittr MASS Matrix MatrixModels MCMCglmm memoise mgcv microbenchmark mime minqa modeest modelr munsell nlme nloptr nnet numDeriv openxlsx pander pbkrtest pillar pkgconfig plyr polynom purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen reportRmd reshape2 rlang rmarkdown rmutil rpart rstatix rstudioapi sass scales SparseM spatial stable stabledist statip stringi stringr survival svglite systemfonts tensorA tibble tidyr tidyselect timeDate timeSeries tinytex utf8 vctrs viridisLite withr xfun xml2 yaml zip

Citation

Readme and manuals

Help Manual

Help page	Topics
Simulated adverse events for patients receiving two study agents.	ae
Outputs related adverse event timeline plots including just system organ class (AE category), or system organ class and lowest level term (AE detail). This function can fit up to 5 different attributions. Modify width, height and scale parameters in ggsave() to customize fit for large plot.	ae_timeline_plot
Modification of the as.numeric function that prints entries that fail to parse as a message	as_numeric_parse
Caterpillar plot. Useful for plotting random effects from hierarchical models, such as MCMCglmm::MCMCglmm() object, that have binary outcome.	caterpillar_plot
Nested version of reportRmd covsum()	covsum_nested
Simulated demography for patients.	demography
Simulated study agent 1 for patients.	drug1_admin
Simulated study agent 2 for patients.	drug2_admin
Outputs the three DSMB-CCRU AE summary tables in Excel format per UHN template	dsmb_ccru
Enrollment data Simulated enrollment for patients.	enrollment
Simulated ineligibility for patients.	ineligibility
Nice table of model output from MCMCglmm::MCMCglmm()	nice_mcmcglmm
Nice table of intraclass correlation coefficients from MCMCglmm::MCMCglmm() model output	nice_mcmcglmm_icc
Combines exported REDCap raw and label .csv files together with data dictionary. Tranforms the exported data into Excel sheets by survey instrument with one row per participant	redcap_data_out
Outputs a nested version of reportRmd::rm_covsum()	rm_covsum_nested

Package: BiostatsUHNplus 0.0.10

BiostatsUHNplus: Nested Data Summary, Adverse Events and REDCap

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)