Man pages for qPharmetra/PMDatR
Pharmacometric Data Management in R
| adjust_dose_time | adjust the dose time |
| append.CovT | Append time-varying covariates to an event data frame |
| append.events | Append event data frames |
| as.data.frame.domain.metadata | Format a metadata object as a dataframe |
| as_numeric | safely coerce to numeric |
| bind_rows | bind rows for dataframes with units |
| blank_to_missing | Convert whitespace to a missing value |
| boxcox | Applies Box-Cox transformation with known lambda |
| calc_addl | calc_addl is a vectorized function which provides the number... |
| cfb_abs | absolute change from baseline |
| cfb_percent | percent change from baseline |
| cfb_ratio | ratio change from baseline |
| combine_rows_by_tol | Combine data frame rows by tolerance on a value |
| compare_mappings | compare_mappings |
| conc_to_molar | conc_to_molar converts a concentration to molar |
| conditional_values | Create a character column based on named conditions |
| contains_one_of | Check if a value matches multiple regular expressions |
| contains_one_of_ | Check if a value matches multiple regular expressions |
| convert | convert units to a chosen value |
| convert_units_from_list | convert_units_from_list converts units for all output columns... |
| count_if | Increments a counter when the criteria is met |
| covariate_plots | Summary plot of dataset |
| crcl | Compute creatinine clearance |
| createDDD | Generate Data Definition Table |
| create.domain | Create a domain object from file and mappings information |
| DataManagement | Create a Data Management Object |
| date_in_range | Test where a date falls relative to a date range |
| datetimeformat | Date and Time formatting for text output |
| default_missing_column | Create a default value in a dataframe column if the column... |
| diagnostics.domain | ## Diagnostics ## diagnostic functions should return a list... |
| diagnostics_premerge | Pre-merge diagnostic checks |
| domain | Create a domain object from a list of settings. |
| domains.save.metadata | Save meta data for a list of domains |
| dot- | Generate a character vector from unquoted names |
| dot-getDependencyList | Title |
| elapsed.time | Compute elapsed time from beginning of POSIX vector |
| enumerate | Give numeric identifiers to a vector of values |
| exclusion_codes | Create an exclusion column |
| expand_addl | expand rows that correspond to addl records |
| fill | Fill NA values in columns |
| fill_occasion | Fills occasion in a dataframe |
| find_mismatched_TRT | Find mismatched Treatment codes across domains |
| find_subjects_no_dosing | Find subjects with no dosing records |
| find_subjects_no_obs | Find subjects with no observation records |
| find_subjects_placebo_obs | Find placebo subjects with positive DV |
| formatDDD | Format a DDD object as a dataframe |
| get_addl_dosing | derive necessary information about addl and append to given... |
| get_baseline | Find a baseline value |
| getCov | Processes domain data for merged covariates |
| getCovT | Processes domain data for time-varying covariates |
| getDomain | Processes source data |
| getDV | Processes domain data for specified dependent variables (DV) |
| get_from_domain | Get a column from a domain |
| getIndividualDoses | Processes domain data for individual doses |
| get_metadata | Gather metadata from a data frame |
| get_nm_attributes | Get column attributes for nonmem formatted output |
| guess_dosing_sequence | guess dosing sequence based on time of day |
| impute_fn | impute a value to all missing |
| impute_value | impute by a calculated value for any NA's in a column impute... |
| increment_to_nominal_time | increment a time record to some nominal time |
| is_file_writable | Check if a file is writable |
| is.integral | Determine if a value can be coerced to an integer type |
| is.number | Determine if a value can be coerced to a numeric type |
| iso_duration | Convert ISO duration to numeric |
| is_one_of | Test if value in x is one of several values |
| iso_to_posix | Convert an ISO8601 date/time to POSIXct |
| load.domain | Load a domain from a domain object or from settings |
| load.domain.mappings | Load mappings list from mappings file |
| load_excel | Load an Excel sheet from a workbook |
| load_sas7bdat | Load a sas7bdat file into a domain object |
| load_table | Load a delimited text file |
| load_xpt | Load a sas xport file into a domain object |
| locf | Fill NA values in a vector using previous non-NA value |
| lookup_in_domain | Lookup a value in domain data |
| lookup_intervals | lookup intervals is a vectorized function that returns the... |
| merge.Cov | Merge events with covariates |
| numerize | Combine several numbers together into a string |
| occasion | Enumerate on condition 1 when followed by condition 2 |
| OutputDataset | Format a dataframe for output to nonmem |
| overlay_dosing | overlay dosing records onto an existing ggplot |
| parse_usubjid | Recombine pieces of a delimited string |
| partial_join | Join two dataframes with partial matching of keys |
| plot_individual | Plot individual subject profiles in NONMEM dataset |
| plot_outlier_byCuts | Plot outliers by cutpoints |
| plot_spaghetti | Plot NONMEM data as spaghetti plot |
| posix_to_date | convert posixct to date |
| post.merge.refactoring | Perform routine generic checks on NONMEM data and apply... |
| post_process_dosing | Apply ADDL and Missing doses to a dosing data frame |
| post_transform_message | Send a message during a piped operation |
| power | Applies a power transform y=a*x^b |
| pre.merge | Pre-merge one domain with another |
| Query | Create a Query object |
| recode_values | Recode/Replace values in a data frame column |
| relative_time | relative time such that first record is at time 0 |
| replace_values | Replace values in a vector with supplied values |
| resolve_units | resolve unit requirements across data frames |
| R.installation.qualification | Run installation qualification for PMDatR in current R... |
| separate_rows | Split rows based on a delimited string column |
| set_units | set_units sets the units for a given vector |
| set_units_from_list | set_units_from_list sets units for all columns that match a... |
| spread_ | spread that understands units |
| statfuns | Summary functions overridden by PMDatR |
| strip_units | strip attributes from a vector if they exist |
| strip_units_df | strip all unit columns from a dataframe |
| summary_table | Summary table of dataset |
| table_dv | Summarise observations by EVID in NONMEM dataset |
| table_outlier_byCuts | Summarise DV by strata or cutpoint to look for outliers |
| table_time | Summarise time variables in NONMEM dataset |
| time_after_criteria | time_after_criteria calculates the time after some filter... |
| time_after_dose | time after dose |
| time_after_first_dose | time after the first dose |
| time_diff | Time difference |
| time_of_first_dose | Time of the first dose |
| time_varying_codes | Convert a dataframe of codes with start/stop time to a flat,... |
| transform.tbl_df | Add new variables to a data_frame |
| unit_cols | get the units columns present in a dataframe and what the... |
| units.pmunits | retrieve measurement units from 'pmunits' object |
| visualize_dosing | visualize dosing history |
| WriteCode.DataManagement | Write R functions corresponding to a DataManagement objet |
