diff --git a/NAMESPACE b/NAMESPACE index 6a743c3..bb5b46c 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,149 +1,3 @@ # Generated by roxygen2: do not edit by hand -export(hello_admiral) -importFrom(admiral,derive_vars_dy) -importFrom(admiraldev,assert_character_scalar) -importFrom(admiraldev,assert_character_vector) -importFrom(admiraldev,assert_data_frame) -importFrom(admiraldev,assert_filter_cond) -importFrom(admiraldev,assert_logical_scalar) -importFrom(admiraldev,assert_numeric_vector) -importFrom(admiraldev,assert_order_vars) -importFrom(admiraldev,assert_symbol) -importFrom(admiraldev,assert_vars) -importFrom(dplyr,arrange) -importFrom(dplyr,bind_cols) -importFrom(dplyr,bind_rows) -importFrom(dplyr,case_when) -importFrom(dplyr,coalesce) -importFrom(dplyr,desc) -importFrom(dplyr,distinct) -importFrom(dplyr,ends_with) -importFrom(dplyr,filter) -importFrom(dplyr,full_join) -importFrom(dplyr,group_by) -importFrom(dplyr,if_else) -importFrom(dplyr,mutate) -importFrom(dplyr,mutate_at) -importFrom(dplyr,mutate_if) -importFrom(dplyr,n) -importFrom(dplyr,n_distinct) -importFrom(dplyr,na_if) -importFrom(dplyr,pull) -importFrom(dplyr,rename) -importFrom(dplyr,rename_at) -importFrom(dplyr,row_number) -importFrom(dplyr,select) -importFrom(dplyr,slice) -importFrom(dplyr,starts_with) -importFrom(dplyr,summarise) -importFrom(dplyr,summarise_at) -importFrom(dplyr,tibble) -importFrom(dplyr,transmute) -importFrom(dplyr,ungroup) -importFrom(dplyr,union) -importFrom(dplyr,vars) -importFrom(hms,as_hms) -importFrom(lifecycle,deprecate_stop) -importFrom(lifecycle,deprecate_warn) -importFrom(lifecycle,deprecated) -importFrom(lubridate,"%--%") -importFrom(lubridate,as_datetime) -importFrom(lubridate,ceiling_date) -importFrom(lubridate,date) -importFrom(lubridate,days) -importFrom(lubridate,duration) -importFrom(lubridate,floor_date) -importFrom(lubridate,hours) -importFrom(lubridate,is.Date) -importFrom(lubridate,is.instant) -importFrom(lubridate,minutes) -importFrom(lubridate,time_length) -importFrom(lubridate,weeks) -importFrom(lubridate,years) -importFrom(lubridate,ymd) -importFrom(lubridate,ymd_hms) -importFrom(magrittr,"%>%") -importFrom(purrr,compose) -importFrom(purrr,every) -importFrom(purrr,flatten) -importFrom(purrr,keep) -importFrom(purrr,map) -importFrom(purrr,map2) -importFrom(purrr,map_chr) -importFrom(purrr,map_if) -importFrom(purrr,map_lgl) -importFrom(purrr,modify_at) -importFrom(purrr,modify_if) -importFrom(purrr,reduce) -importFrom(purrr,transpose) -importFrom(purrr,walk) -importFrom(rlang,":=") -importFrom(rlang,.data) -importFrom(rlang,abort) -importFrom(rlang,arg_match) -importFrom(rlang,as_function) -importFrom(rlang,as_string) -importFrom(rlang,call2) -importFrom(rlang,call_name) -importFrom(rlang,caller_env) -importFrom(rlang,current_env) -importFrom(rlang,enexpr) -importFrom(rlang,enquo) -importFrom(rlang,eval_bare) -importFrom(rlang,eval_tidy) -importFrom(rlang,expr) -importFrom(rlang,expr_interp) -importFrom(rlang,expr_label) -importFrom(rlang,f_lhs) -importFrom(rlang,f_rhs) -importFrom(rlang,inform) -importFrom(rlang,is_bare_formula) -importFrom(rlang,is_call) -importFrom(rlang,is_character) -importFrom(rlang,is_formula) -importFrom(rlang,is_integerish) -importFrom(rlang,is_logical) -importFrom(rlang,is_quosure) -importFrom(rlang,is_quosures) -importFrom(rlang,is_symbol) -importFrom(rlang,new_formula) -importFrom(rlang,parse_expr) -importFrom(rlang,parse_exprs) -importFrom(rlang,quo) -importFrom(rlang,quo_get_env) -importFrom(rlang,quo_get_expr) -importFrom(rlang,quo_is_call) -importFrom(rlang,quo_is_missing) -importFrom(rlang,quo_is_null) -importFrom(rlang,quo_is_symbol) -importFrom(rlang,quo_set_env) -importFrom(rlang,quo_squash) -importFrom(rlang,quo_text) -importFrom(rlang,quos) -importFrom(rlang,set_names) -importFrom(rlang,sym) -importFrom(rlang,syms) -importFrom(rlang,type_of) -importFrom(rlang,warn) -importFrom(stringr,str_c) -importFrom(stringr,str_detect) -importFrom(stringr,str_extract) -importFrom(stringr,str_glue) -importFrom(stringr,str_remove) -importFrom(stringr,str_remove_all) -importFrom(stringr,str_replace) -importFrom(stringr,str_to_lower) -importFrom(stringr,str_to_title) -importFrom(stringr,str_to_upper) -importFrom(stringr,str_trim) -importFrom(tidyr,drop_na) -importFrom(tidyr,nest) -importFrom(tidyr,pivot_longer) -importFrom(tidyr,pivot_wider) -importFrom(tidyr,unnest) -importFrom(tidyselect,all_of) -importFrom(tidyselect,contains) -importFrom(tidyselect,vars_select) -importFrom(utils,capture.output) -importFrom(utils,str) +importFrom(utils,data) diff --git a/man/admiral_ae.Rd b/man/admiral_ae.Rd new file mode 100644 index 0000000..94322e2 --- /dev/null +++ b/man/admiral_ae.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_ae} +\alias{admiral_ae} +\title{Adverse Events Dataset-updated} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1191 rows and 36 columns. +} +\source{ +\url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ae.rda} +} +\usage{ +admiral_ae +} +\description{ +An updated SDTM AE dataset that uses the CDISC pilot project +} +\keyword{datasets} diff --git a/man/admiral_cm.Rd b/man/admiral_cm.Rd new file mode 100644 index 0000000..12053da --- /dev/null +++ b/man/admiral_cm.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_cm} +\alias{admiral_cm} +\title{Concomitant Medication Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 7510 rows and 21 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/cm.xpt?raw=true} # nolint +} +\usage{ +admiral_cm +} +\description{ +A SDTM CM dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/admiral_dm.Rd b/man/admiral_dm.Rd new file mode 100644 index 0000000..5ceba3f --- /dev/null +++ b/man/admiral_dm.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_dm} +\alias{admiral_dm} +\title{Demography Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 306 rows and 25 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/dm.xpt?raw=true} # nolint +} +\usage{ +admiral_dm +} +\description{ +A SDTM DM dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/admiral_ds.Rd b/man/admiral_ds.Rd new file mode 100644 index 0000000..5428fc1 --- /dev/null +++ b/man/admiral_ds.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_ds} +\alias{admiral_ds} +\title{Disposition Dataset-updated} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 850 rows and 13 columns. +} +\source{ +\url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ds.rda} +} +\usage{ +admiral_ds +} +\description{ +An updated SDTM DS dataset that uses the CDISC pilot project +} +\author{ +Gopi Vegesna +} +\keyword{datasets} diff --git a/man/admiral_eg.Rd b/man/admiral_eg.Rd new file mode 100644 index 0000000..135293b --- /dev/null +++ b/man/admiral_eg.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_eg} +\alias{admiral_eg} +\title{Electrocardiogram Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 26669 rows and 24 columns. +} +\usage{ +admiral_eg +} +\description{ +An example of standard SDTM EG dataset to be used in deriving ADEG dataset +} +\keyword{datasets} diff --git a/man/admiral_ex.Rd b/man/admiral_ex.Rd new file mode 100644 index 0000000..abc9d94 --- /dev/null +++ b/man/admiral_ex.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_ex} +\alias{admiral_ex} +\title{Exposure Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 591 rows and 17 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ex.xpt?raw=true} # nolint +} +\usage{ +admiral_ex +} +\description{ +A SDTM EX dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/admiral_lb.Rd b/man/admiral_lb.Rd new file mode 100644 index 0000000..1ec689c --- /dev/null +++ b/man/admiral_lb.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_lb} +\alias{admiral_lb} +\title{Laboratory Measurements Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 59580 rows and 23 columns. +} +\source{ +\url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_lb.rda} +} +\usage{ +admiral_lb +} +\description{ +An updated SDTM LB dataset that uses data from the CDISC pilot project +} +\author{ +Annie Yang +} +\keyword{datasets} diff --git a/man/admiral_mh.Rd b/man/admiral_mh.Rd new file mode 100644 index 0000000..e3a9a3d --- /dev/null +++ b/man/admiral_mh.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_mh} +\alias{admiral_mh} +\title{Medical History Dataset-updated} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1818 rows and 28 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/mh.xpt?raw=true} # nolint +} +\usage{ +admiral_mh +} +\description{ +An updated SDTM MH dataset that uses data from the CDISC pilot project +} +\author{ +Annie Yang +} +\keyword{datasets} diff --git a/man/admiral_oe.Rd b/man/admiral_oe.Rd new file mode 100644 index 0000000..65778d3 --- /dev/null +++ b/man/admiral_oe.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_oe} +\alias{admiral_oe} +\title{Ophthalmic Examinations Dataset} +\format{ +An object of class \code{grouped_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 15344 rows and 25 columns. +} +\usage{ +admiral_oe +} +\description{ +A SDTM OE dataset simulated by Ophthalmology team +} +\author{ +Gordon Miller +} +\keyword{datasets} diff --git a/man/admiral_pc.Rd b/man/admiral_pc.Rd new file mode 100644 index 0000000..c8db9e5 --- /dev/null +++ b/man/admiral_pc.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_pc} +\alias{admiral_pc} +\title{Pharmacokinetics Concentrations Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3556 rows and 20 columns. +} +\source{ +\url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_pc.rda} +} +\usage{ +admiral_pc +} +\description{ +A SDTM PC dataset simulated by Antonio Rodríguez Contestí +} +\author{ +Antonio Rodríguez Contestí +} +\keyword{datasets} diff --git a/man/admiral_pp.Rd b/man/admiral_pp.Rd new file mode 100644 index 0000000..c75d89d --- /dev/null +++ b/man/admiral_pp.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_pp} +\alias{admiral_pp} +\title{Pharmacokinetic Parameters Dataset} +\format{ +An object of class \code{data.frame} with 2346 rows and 14 columns. +} +\source{ +\url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_pp.rda} +} +\usage{ +admiral_pp +} +\description{ +A SDTM PP dataset simulated by Antonio Rodríguez Contestí +} +\author{ +Antonio Rodríguez Contestí +} +\keyword{datasets} diff --git a/man/admiral_qs.Rd b/man/admiral_qs.Rd new file mode 100644 index 0000000..f182c9d --- /dev/null +++ b/man/admiral_qs.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_qs} +\alias{admiral_qs} +\title{Questionnaire Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 202907 rows and 20 columns. +} +\source{ +\url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_qs.rda} # nolint +} +\usage{ +admiral_qs +} +\description{ +A SDTM QS dataset from the CDISC pilot project & Ophthalmology test data +} +\keyword{datasets} diff --git a/man/admiral_rs.Rd b/man/admiral_rs.Rd new file mode 100644 index 0000000..9a8b57f --- /dev/null +++ b/man/admiral_rs.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_rs} +\alias{admiral_rs} +\title{Disease Response Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 5808 rows and 19 columns. +} +\usage{ +admiral_rs +} +\description{ +A SDTM RS dataset simulated by Gopi Vegesna +} +\author{ +Gopi Vegesna +} +\keyword{datasets} diff --git a/man/admiral_sc.Rd b/man/admiral_sc.Rd new file mode 100644 index 0000000..e5cdd32 --- /dev/null +++ b/man/admiral_sc.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_sc} +\alias{admiral_sc} +\title{Subject Characteristic Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 254 rows and 12 columns. +} +\usage{ +admiral_sc +} +\description{ +A SDTM SC dataset simulated by Ophthalmology team +} +\author{ +Gordon Miller +} +\keyword{datasets} diff --git a/man/admiral_sdg_db.Rd b/man/admiral_sdg_db.Rd new file mode 100644 index 0000000..237ebb7 --- /dev/null +++ b/man/admiral_sdg_db.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_sdg_db} +\alias{admiral_sdg_db} +\title{SDG Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 16 rows and 5 columns. +} +\usage{ +admiral_sdg_db +} +\description{ +An example SDG dataset +} +\keyword{datasets} diff --git a/man/admiral_smq_db.Rd b/man/admiral_smq_db.Rd new file mode 100644 index 0000000..d847e2e --- /dev/null +++ b/man/admiral_smq_db.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_smq_db} +\alias{admiral_smq_db} +\title{SMQ Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 44 rows and 6 columns. +} +\usage{ +admiral_smq_db +} +\description{ +An example SMQ dataset +} +\keyword{datasets} diff --git a/man/admiral_suppae.Rd b/man/admiral_suppae.Rd new file mode 100644 index 0000000..425a780 --- /dev/null +++ b/man/admiral_suppae.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_suppae} +\alias{admiral_suppae} +\title{Supplemental Adverse Events Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1191 rows and 10 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppae.xpt?raw=true} # nolint +} +\usage{ +admiral_suppae +} +\description{ +A SDTM SUPPAE dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/admiral_suppdm.Rd b/man/admiral_suppdm.Rd new file mode 100644 index 0000000..9408e02 --- /dev/null +++ b/man/admiral_suppdm.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_suppdm} +\alias{admiral_suppdm} +\title{Supplemental Demography Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1197 rows and 10 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppdm.xpt?raw=true} # nolint +} +\usage{ +admiral_suppdm +} +\description{ +A SDTM SUPPDM dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/admiral_suppds.Rd b/man/admiral_suppds.Rd new file mode 100644 index 0000000..e59b50e --- /dev/null +++ b/man/admiral_suppds.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_suppds} +\alias{admiral_suppds} +\title{Supplemental Disposition Dataset-updated} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3 rows and 9 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppds.xpt?raw=true} # nolint +} +\usage{ +admiral_suppds +} +\description{ +A SDTM SUPPDS dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/admiral_supptr.Rd b/man/admiral_supptr.Rd new file mode 100644 index 0000000..97c3751 --- /dev/null +++ b/man/admiral_supptr.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_supptr} +\alias{admiral_supptr} +\title{Supplemental Tumor Results Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 55995 rows and 9 columns. +} +\usage{ +admiral_supptr +} +\description{ +A SDTM SUPPTR dataset simulated by Gopi Vegesna +} +\author{ +Gopi Vegesna +} +\keyword{datasets} diff --git a/man/admiral_sv.Rd b/man/admiral_sv.Rd new file mode 100644 index 0000000..00751ac --- /dev/null +++ b/man/admiral_sv.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_sv} +\alias{admiral_sv} +\title{Subject Visits Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3559 rows and 8 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/sv.xpt?raw=true} # nolint +} +\usage{ +admiral_sv +} +\description{ +A SDTM SV dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/admiral_tr.Rd b/man/admiral_tr.Rd new file mode 100644 index 0000000..7a2e9be --- /dev/null +++ b/man/admiral_tr.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_tr} +\alias{admiral_tr} +\title{Tumor Results Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 55995 rows and 24 columns. +} +\usage{ +admiral_tr +} +\description{ +A SDTM TR dataset simulated by Gopi Vegesna +} +\author{ +Gopi Vegesna +} +\keyword{datasets} diff --git a/man/admiral_ts.Rd b/man/admiral_ts.Rd new file mode 100644 index 0000000..d5d488f --- /dev/null +++ b/man/admiral_ts.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_ts} +\alias{admiral_ts} +\title{Trial Design Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 33 rows and 6 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ts.xpt?raw=true} # nolint +} +\usage{ +admiral_ts +} +\description{ +A SDTM TS dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/admiral_tu.Rd b/man/admiral_tu.Rd new file mode 100644 index 0000000..1edc5f5 --- /dev/null +++ b/man/admiral_tu.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_tu} +\alias{admiral_tu} +\title{Tumor Identification Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 7734 rows and 18 columns. +} +\usage{ +admiral_tu +} +\description{ +A SDTM TU dataset simulated by Gopi Vegesna +} +\author{ +Gopi Vegesna +} +\keyword{datasets} diff --git a/man/admiral_vs.Rd b/man/admiral_vs.Rd new file mode 100644 index 0000000..6b9f277 --- /dev/null +++ b/man/admiral_vs.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{admiral_vs} +\alias{admiral_vs} +\title{Vital Signs Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 29643 rows and 24 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/vs.xpt?raw=true} # nolint +} +\usage{ +admiral_vs +} +\description{ +A SDTM VS dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/admiraldata-package.Rd b/man/admiraldata-package.Rd new file mode 100644 index 0000000..bec62c5 --- /dev/null +++ b/man/admiraldata-package.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/admiraldata-package.R +\docType{package} +\name{admiraldata-package} +\alias{admiraldata} +\alias{admiraldata-package} +\title{admiraldata: Test Data for the 'admiral' Package} +\description{ +\if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} + +A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Interchange Standards Consortium (CDISC) pilot project used for testing and developing Analysis Data Model (ADaM) derivations inside the 'admiral' package. +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://pharmaverse.github.io/admiraldata} + \item \url{https://github.com/pharmaverse/admiraldata} +} + +} +\author{ +\strong{Maintainer}: Edoardo Mancini \email{edoardo.mancini@roche.com} + +} +\keyword{internal} diff --git a/man/admiraltemplate-package.Rd b/man/admiraltemplate-package.Rd deleted file mode 100644 index 6ebcf32..0000000 --- a/man/admiraltemplate-package.Rd +++ /dev/null @@ -1,26 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/admiraltemplate-package.R -\docType{package} -\name{admiraltemplate-package} -\alias{admiraltemplate} -\alias{admiraltemplate-package} -\title{admiraltemplate: ADaM in R Asset Library - Extension} -\description{ -\if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} - -A toolbox for programming Clinical Data Standards Interchange Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, \url{https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package}). -} -\seealso{ -Useful links: -\itemize{ - \item \url{https://pharmaverse.github.io/admiraltemplate} - \item \url{https://github.com/pharmaverse/admiraltemplate} -} - -} -\author{ -\strong{Maintainer}: Edoardo Mancini \email{edoardo.mancini@roche.com} - -} -\concept{internal} -\keyword{internal} diff --git a/man/hello_admiral.Rd b/man/hello_admiral.Rd deleted file mode 100644 index 31d1c3c..0000000 --- a/man/hello_admiral.Rd +++ /dev/null @@ -1,28 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/my_first_fcn.R -\name{hello_admiral} -\alias{hello_admiral} -\title{Derive Extension Example} -\usage{ -hello_admiral(hw = TRUE) -} -\arguments{ -\item{hw}{TRUE or FALSE} -} -\value{ -Happy Message -} -\description{ -Says hello admiral -} -\details{ -In the roxygen documentation you will find tags for family and keywords. -This is to create organized sections for the Reference tab on the pkgdown website. -You can modify the \verb{_pkgdown.yml} as necessary to create appropriate sections as necessary. -Under \code{./man/roxygen/meta.R}, you will find where to store these family/keywords. -} -\examples{ -hello_admiral(hw = FALSE) -} -\concept{der_adxx} -\keyword{der_adxx} diff --git a/man/raw_ae.Rd b/man/raw_ae.Rd new file mode 100644 index 0000000..f27d4dd --- /dev/null +++ b/man/raw_ae.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{raw_ae} +\alias{raw_ae} +\title{Adverse Events Dataset-raw} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1191 rows and 35 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ae.xpt?raw=true} # nolint +} +\usage{ +raw_ae +} +\description{ +A SDTM AE dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/raw_ds.Rd b/man/raw_ds.Rd new file mode 100644 index 0000000..dc077f8 --- /dev/null +++ b/man/raw_ds.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{raw_ds} +\alias{raw_ds} +\title{Disposition Dataset-raw} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 596 rows and 13 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ds.xpt?raw=true} # nolint +} +\usage{ +raw_ds +} +\description{ +A SDTM DS dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/raw_lb.Rd b/man/raw_lb.Rd new file mode 100644 index 0000000..916f441 --- /dev/null +++ b/man/raw_lb.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{raw_lb} +\alias{raw_lb} +\title{Laboratory Measurements Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 59580 rows and 23 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/lb.xpt?raw=true} # nolint +} +\usage{ +raw_lb +} +\description{ +A SDTM LB dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/raw_mh.Rd b/man/raw_mh.Rd new file mode 100644 index 0000000..5f0c55e --- /dev/null +++ b/man/raw_mh.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{raw_mh} +\alias{raw_mh} +\title{Medical History Dataset-raw} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1818 rows and 19 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/mh.xpt?raw=true} # nolint +} +\usage{ +raw_mh +} +\description{ +A SDTM MH dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/raw_qs.Rd b/man/raw_qs.Rd new file mode 100644 index 0000000..50b247c --- /dev/null +++ b/man/raw_qs.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{raw_qs} +\alias{raw_qs} +\title{Questionnaire Dataset} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 121749 rows and 20 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/qs.xpt?raw=true} # nolint +} +\usage{ +raw_qs +} +\description{ +A SDTM QS dataset from the CDISC pilot project +} +\keyword{datasets} diff --git a/man/raw_suppds.Rd b/man/raw_suppds.Rd new file mode 100644 index 0000000..da6608a --- /dev/null +++ b/man/raw_suppds.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{raw_suppds} +\alias{raw_suppds} +\title{Supplemental Disposition Dataset-raw} +\format{ +An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 3 rows and 10 columns. +} +\source{ +\url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppds.xpt?raw=true} # nolint +} +\usage{ +raw_suppds +} +\description{ +A SDTM SUPPDS dataset from the CDISC pilot project +} +\keyword{datasets}