Package index • stcsanalysis

Read/write STCS dataset

Read or write the STCS dataset

stcs_read() stcs_read1(): Read STCS datastcs

stcs_write_csv(): Write a list of STCS dataset into CSV file

Tailored tables

Create pre-defined tables

tailored_organsurvival(): Tailored analysis tables with main dates related to organs.

tailored_patientbl(): Tailored analysis tables with baseline patient data.

tailored_patientsurvival(): Tailored analysis tables with main dates related to patients

tailored_psq(): Tailored wide PSQ table

tailored_tables(): Return a list of tailored tables

tailored_transplantationbl(): Tailored analysis tables with with baseline transplantation data.

tailored_transplantationsurvival(): Tailored analysis tables with main dates related to transplantation

Manipulation of the full cohort

Modifiy all SCTCS tables with VariableMetaData

stcs_filter_patientkey(): Filter the row of all tables given the patientkey

stcs_anonymize() stcs_remove_emptytab() stcs_select_organrelevance() stcs_select_table(): Select variable of the STCS dataset

validate_metadata(): Validate the VariableMetadata

Functions to create custom dataset

Set of function to help merging variables

data_patientkey() data_organkey() data_soaskey(): Get STCS key

add_var() expand_var_from() new_var_from(): Generic function to add columns

var_available(): Print variables which are available given your current dataset

detect_from() detect_by(): Detect if the tables/key can be automatically retrieve

Utilitary function

Other functions

age_int() age_months(): Calculate the age in years between 2 dates

which.pmin() which.pmin_chr(): Indicate the index of the row-wise minimal value

egfr_2021(): eGFR

pediatric_egfr_2009(): Swchartz bedside pediatric eGFR formula

is_truemissing() truemissing_to_na(): Confirmed missing values

serology_combination(): Serology combination

impute_lastday(): Impute to the last day of the month/year

paste_valuecomment(): Merge value and their associated comment

vec_names(): Assigned names to a vector

noinf_min(): Return minimum without infinity