NEWS.md

In metrumresearchgroup/yspec: Data Specification for Pharmacometrics

yspec 0.6.2

Breaking changes

• nm_input() was significantly refactored to produce output more typically seen in practice as well as adding some convenience features (#150).
  • the default output is now wide format
  • data set labels can get renamed with <new name> = <old name> syntax, passed under ...
  • columns with type <character> are dropped by default
  • the cat argument was renamed .cat
  • the .drop argument was added to indicate a group of data items to drop from the problem
  • the previous long output can be recreated using .long = TRUE
  • the .decodes argument was added to control appearance of categorical data decode information in the long output

yspec 0.6.1

• Use all_of() when tidy selecting; this will suppress warnings in ys_extend() and ys_add_factors() (#145).

yspec 0.6.0

• Adds ys_factors() to replace data set columns with their factor version, optionally retaining the original values in new columns (#141).

yspec 0.5.3

• Fix bug where character type was inferred whenever values were character, overriding what the user specified; now, only infer when user doesn't specify type (#129).

• Add ys_col_note() to generate a string of column names and definitions based on short or label; use this when column names appear in a table and require explanation in a a footnote (#119, #120).

• Put stories in yaml format; add script to build validation docs from the yaml file (#123, #124).

yspec 0.5.2

• Adds ys_extend() to extend a spec object with additional columns with any external yaml file; adds extend_file field in SETUP__: to identify a single file which can be automatically called upon for extension #112, #113.

• ys_add_factors() refactored to only add factors for available columns #88, #91.

• ys_add_factors() restores tidyselect semantics when specifying a subset of columns for adding factors #109, #110.

• Add ys_table() to render the spec in TeX table code to be included in a report appendix #98, #104.

• ys_select() returns an empty spec object when nothing is selected #100, #101.

• Add ys_prune() to select any data columns that appear in the spec as well as other optional columns #87, #97. #99.

• Add ys_recode() to convert a vector of data set column names to short version, optionally adding unit #86, #114.

• ys_load() will now detect if values / decode are mis-coded as a list of lists; all items in values and decode must be atomic #106, #108.

• ys_load() will issue more informative error message when short contains too many characters #102, 105.

• ys_document() now accepts sponsor and projectnumber arguments which get passed through to the rendered define document #90, #92.

yspec 0.5.1

• Fix bug where dots in lookup file were not properly inherited by spec columns that didn't already have a dots list (#69)

• Fix bug in namespace creation when multiple fields include namespace info (#81)

• Fix bug where specification document didn't properly render when using R 4.1 (#73)

• ys_add_factors() now substitutes missing values (NA) with a character string supplied by the user prior to making the factor; the decode list is also updated so that the "missing" data is the last level; the string is supplied by the new argument .missing argument (#79)

yspec 0.5.0

• ys_select() will now rename columns if new names are provided (#62)
• ys_filter() will subset a yspec object based on logical criteria (#65)
• ys_rename() will rename columns in a yspec object (#63)
• ys_join() will combine two or more yspec objects together (#64)
• New SETUP__ field called flags that can be used to flag sets of columns (#62)
• ys_fill_dots() will supplement the dots list with default values (#62)
• Add vignettes back to the package

yspec 0.4.2

• Add ys_select() to select a subset of columns from a yspec object #24
• Refactor axis_col_labs to add vars argument; if missing, all col / labs will be created; otherwise, the user can select a subset to be created
• Deprecate mrgtemplate(); added definetemplate() that is used as default for a more styled define document #37
• Add ability to include alternate representations of field information through namespacing #38
• Fix bug in ys_check where the return value was not correct when error_on_fail was set to FALSE #31
• Add nm_input function to print nonmem input data text to the console #8
• Fix bug where some meta data (data_stem, name, spec_file) was not updated when importing from another spec #5
• Fix bug where ys_get_short_unit was not returning a list #2
• Fix bug where axis_col_labs doesn't do title case or short max #26
• Better reporting of bad values in discrete data column #27

yspec 0.4.1

• Add minimum version numbers for dependency packages
• Add long argument to pander_table to create longer tables
• Fix bug where data_stem meta field was not getting propagated into data set name in the define document #35
• Add ability to update project number and sponsor information in a yspec object or a yproj object #36
• Fix bug where unit input was not properly validated #45
• Fix bug where ys_check didn't issue error when data set columns were not in the right order #54
• New field for data set columns: label; this will be used when labeling data sets for xpt export #60
• The label field can be made optional with ys.require.label option #99
• Add function (ys_add_labels) to label data set columns #63
• Add function (update_short) to change the value in the short field #82
• Add meta field (import) to enable import of contents of another spec #84
• Add meta field option (character_last) to push all character columns to the back of the spec object #86
• Add meta field option (comment_col) to identify the column that is for comments; character comment columns will not be pushed to back #86
• Add argument to ys_check so that an error is not generated when checking the data, but rather FALSE is returned #88
• Add functionality to add all possible factors to data set with yspec_add_factors #91
• Add new data column field make_factor that will tell yspec_add_factors to make that column into a factor #91
• The following fields will be collapsed into a single value when they are entered as array: source, comment, long #93
• Add alias ys_add_factors to yspec_add_factors #97
• Add functions to form label, unit, and short; methods for yspec and ycol #100

yspec 0.3.0

• Released into production

yspec 0.2.0.9000

• Fixed bug where column check error were assigned to the wrong column name #7
• Added as_proj_spec function that allows creation of a project spec file from individual data set spec objects
• Added more flexibility for specifying project and data set spec files in different locations #5
• Function ys_load preferred alias for load_spec
• Function ys_load_file preferred alias for load_spec_file
• Function ys_project preferred alias for as_proj_spec
• Function ys_document is a wrapper around both render_define and render_fda_define. Use the type argument to request a "working" document or a "regulatory" document
• Added internal lookup source (ysdb_internal.yml)
• It is no longer an error to put no data in a column specification; the lookup attribute will be added and yspec will attempt to look up the column in formation in one of the lookup tables
• ys_get_lookup will recreate the lookup list for a yspec object
• ys_lookup_source will report on the source of each column in an yspec object
• In general, we no longer write out a project file; use ys_project with a vector of files or yspec objects instead
• The table of contents for the regulatory document (fda_content_table) now links to the corresponding .xpt file; to facilitate testing, arguments loc and ext have been added so that the linking can be better tested (e.g. create a document that links to a .csv file, which should be easier to open on computers that don't have SAS installed). #20
• Arguments data_path and data_stem have been added to ys_load
• Handler !look has been added to indicate that column data should be searched for in the lookup resources
• Handler !value:decode has been added so that maps can be created with the values on the left hand side (- 0 : male)
• Handler !decode:value has been added that recreates the default map handling, but also allows several values to be mapped to the same decode
• An error is generated if the number of characters in a column name is greater than 8. Set the ys.col.len option to control the max allowable characters.
• Added verbose argument to print information to the console while processing a yaml file
• Added ys_help object that includes example / demo materials, including a function that will export a folder of assets that will work out of the box
• Revised package vignettes
• Expanded the ?yspec help topic to outline the suggested workflow and point to other locations for help
• Added custom sanitizer ys_sanitize that can be changed through the ys.sanitize option
• Added a glue field for SETUP__, where a yaml map can be used to connect value with a name; when the name is inserted in to yaml code as <<name>>, the value will be substituted in with glue; this is the proper way to evade the sanitizer when including TeX code in the document
• Only "numeric" or "character" will be accepted in the type field; and error is generated if anything else appears there
• Added c method to combine two yspec objects together

yspec 0.1.0.9001

• render_define changed to generic function, with methods for yproj and `character
• Removed projectnumber and sponsor arguments to render_define; that information will be pulled from the SETUP__ block as in render_fda_define
• The column widths for x_table were made smaller so that they fit on our standard page (8.5 x 11 with 7 cm margins on the left and the right)

yspec 0.1.0

• Initial validated version

metrumresearchgroup/yspec documentation built on May 24, 2024, 12:48 a.m.