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Changelog

Source: NEWS.md

james 1.7.3 (August 2025)

This is a maintenance release that includes various infrastructure updates, enhancements to the OpenAPI specification, and minor bug fixes.

New features

  • Adds the template inst/spec/openapi.in.yaml and the function james:::update_openapi_spec(), which updates the OpenAPI template to the current JAMES version and saves it as inst/spec/openapi.yaml. This enables:

    1. Easy maintenance of the OpenAPI specification.
    2. Serving API documentation directly from the JAMES server at https://<host>/docs, removing the dependency on SwaggerHub.

  • Includes versioned JSON schemas (bds_vx.y.json) for data exchange, now bundled with the package and downloadable from https://<host>/schemas.

  • Updates all R and JavaScript code to default to localhost:8080 as the OpenCPU server URL (previously localhost:80). Port 8080 is used to prevent confusion with Docker or system-level port 80.

  • Adds qmd/JAMES_version_maintaince.qmd, a Quarto file to be run after each version change. This script updates version numbers across the package, including the OpenAPI spec, index.html, and the getting_started.Rmd vignette.

Infrastructure and development changes

  • Updates the package to use R 4.5.0.

  • Cleans renv.lock by removing all development-only packages (e.g., "roxygen2", "devtools", "desc", "evaluate", "jamesdemodata", "pkgload") and their dependencies. This reduces the package’s footprint in production environments.

    After running renv::restore() to install production dependencies, call james:::install_dev_packages() once to install development tools. Do not include development packages in renv.lock. Only snapshot production dependencies defined in the DESCRIPTION file using renv::snapshot().

  • Adds a test to test-request_site() that demonstrates:

    • How request_site() fails on nested data uploads when using localhost.
    • A working alternative solution.

    This change ensures that the jamesdemo Shiny app can now also demonstrate a fully functioning localhost server.

  • Adapts links to reflect the change of BDS-maintenance from NCJ TO NICTIZ

  • Updates getting_started.Rmd to work with localhost:8080 and show two-step data upload

james 1.7.2 (Feb 2025)

  • Evades a problem in vignettes/articles/getting_started.Rmd that occasionally occurs when the validate = TRUE flag is active

james 1.7.1 (Feb 2025)

james 1.7.0 (Nov 2024)

  • Adds a target height indicator to height charts for ages 1–21 years and 0–21 years. The target height is calculated using the mid-parental height method described by Hermanussen and Cole (2004). This indicator is plotted at the age of 20.5 years and includes the 95% target height range. The calculation requires the heights of both biological parents (preferred) but can also be performed using only the mother’s height. The target height is adjusted based on the child’s sex and the population standard used for comparison. In the JAMES interface, the target height is automatically recalculated when the user selects a different population.

james 1.6.5 (Oct 2024)

  • Solves an issue for same-sex couples with two mothers or two fathers in BDS 63 field . The bdsreader 0.27.0 package returns the correct data for these cases. See https://github.com/growthcharts/bdsreader/issues/10.
  • Adds a inst/CITATION file for suggestion a citation to JAMES
  • Changes the return value of version to conform to swagger documentation

james 1.6.4 (May 2024)

  • Solves an issue where the week sliders for pre-terms were not properly initialized in the case that the child has no data for the first four years (#6)

james 1.6.3 (May 2024)

Automatic donordata selection

  • Simplifies individual prediction by means of curve matching. The user needs to specify “now” and “future” age and the number of desired matches, and JAMES automatically select appropriate donor data based on the “future” age. This update resolves two issues related to choice and updating of the donordata menu. (#5, #31)

james 1.6.2 (May 2024)

Better chart initialisation

  • When the data contain only developmental data, JAMES initialises to the D-score chart (#33)

james 1.6.1 (May 2024)

Administrative updates and workflow improvements

  • Updates to R 4.4.0 and associated libraries
  • Adds helper james:::update_version_files() to automate references to current version (#32)
  • Adds a description of package update actions: qmd/deploy_JAMES.rmd
  • Updates the GH workflow for package checking

james 1.6.0 (Apr 2024)

Visible changes

  • Changes the version number so that the JAMES package has the same version as the JAMES docker
  • Updates to growthscreener 1.21.0, which changes weight for height criteria into weight-for-age
  • Changes the definition and processing of BDS 71 (parental birth land) to provide a string with 4 digits (was numeric and integer previously) to conform to alphanumeric typology in BDS (updates to bdsreader 0.25.0)
  • Introduces throttling of 3 sec for checkbox, sliders and radio buttons
  • Resolves the WFH sequence problem when later height is shorter (#24)
  • Added JAMES, version and copyright note to “Meldingen”
  • Removed the superfluous header “GROEIDIAGRAMMEN” from the left panel
  • Adds a check and warning if the stored OpenCPU session does not contain data created by read_bds()

More informative Meldingen panel

JAMES now writes on Meldingen for rq1 (james::convert_tgt_chartadvice()) and rq2 (james::draw_chart()):

  1. The session ID
  2. The ocpu.call from javascript to the R function
  3. A summary of the response from R
  4. If present: warnings from R
  5. If present: messages from R

Note: The update of “Meldingen” when the call failed does always work, so it may be that “Meldingen” displays the results from the last functional call instead of the failed call. If the request failed, there will be a pop-up window with a stack trace from R.

Internal changes

  • Updates javascript, HTML and CSS for clarity and efficiency
  • Moves styling from index.html to main.css
  • Removes allegro blend (#20)
  • Returns txt, session and site in blend response as strings (#21)
  • Transfers all event binding functionality from index.html into start.js
  • Refactors JS code https://github.com/growthcharts/james/pull/26/#issue-2197694510
  • Updates all packages and renv to CRAN version March 2024

Bug fixes

  • Fixes a bug during initialization of children > 4y (#29)
  • Resolves Error in eval(predvars, data, env) : object 'hgt_z_0' not found (#23)
  • Solves issue #19 which appears when JAMES cannot find the child data.

Simplified update logic

  • The JS call to update() (which draws the chart) is now removed from the call-back function of rq1. Thus, initialization of controls and drawing of charts are now done independently and in parallel. This removes a nested ocpu.call() call, thereby improveing performance.
  • This change was undone in 1.5.6 because controls were not properly updated.

james 0.68.0

  • Updates all packages, includes growthscreener 1.20.0, which include language development guideline
  • Version meant to test and solve various implementation issues reported by K Nienhuis, okt 2023

james 0.67.0

  • Adds support for the validate and intermediate flags to upload_data()
  • Updates to faster and cleaner bdsreader 0.23.0 package

james 0.66.0

Solves problems with the javascript interface

  1. The interface did not select the correct chart for lollypop children. The problem was related to an incorrect gestational age field in the demodata. The bdsreader::write_bds() was refactored. All demodata were updated with the correct values.

  2. Made a change in the data schema: Reference –> reference to adhere to camelCase in BDS schema

  3. Added a new possibility to run the javascript interface in the local environment. See ../notes/debug-javascript.qmd for details.

  4. Repaired the chartcode field in the interface

james 0.65.0

  • Repairs some error in the JSON schema V2.0 and V3.0 by an update to bdsreader 0.19.0

james 0.64.0

Two major enhancements

  • Adds support for JSON schema V3.0 by updating to bdsreader 0.18.0
  • Replaces Dutch D-score charts by GSED Phase 1 references and charts

james 0.63.0

  • Resolves a problem with the weight-for-age references for 0-15 months
  • Updates JAMES to latest R packages

james 0.62.0

  • Add pathname in URL construction to make JAMES browsers requests reachable when URL is something like htpps://site/path/request.

james 0.61.0

A few changes intended to support external hosting of JS functionality:

  • Make the href locations of index.html, css and js relative to /var/www/html. The directory james/www should be copied into /var/www/html/app to make JAMES work.
  • Support CORS with hostname in ocpu.seturl()

james 0.60.0

  • Refreshes renv.lock by starting from fresh library
  • Tweak test to pass windows conf

james 0.59.2

  • Version used to build james docker 1.3.0
  • Update packages
  • Make library snapshot, update renv.lock

james 0.59.1

  • Update all packages
  • Make new library snapshot

james 0.59.0

  • Update all packages
  • Make new library snapshot

james 0.58.2

james 0.58.1

  • Update README and documentation to JAMES API 1.2.0

james 0.58.0

  • Changes to make an isolated http API
  • Allows for host names such as http://myhost/module with a partial path
  • Reads OpenCPU session from the local file system
  • Removes host arguments to functions
  • Removes host parameter from javascript calls
  • Introduces sitehost argument for request_site()
  • Update to jamesclient 0.30.0

james 0.57.0

  • Makes host definitions consistent everywhere as http://myhost
  • Uses txt, host, session, format argument sequence in all functions
  • Obtains current host and protocol from javascript URL
  • Replaces uloc session indicator by uses (user session)
  • Adds arguments scheme, host and session to convert_tgt_chartadvice()
  • Renames $key to $session in JS

james 0.56.0

Breaking changes

  • Uses generalised httr response object as defined in jamesclient 0.26.1
  • Replaces loc parameter by session parameter
  • Adds deprecated notes about the loc parameter
  • Replaces all calls to jamesclient::upload_txt() by jamesclient::james_post()
  • Update renv.lock with jamesclient and other R package updates
  • Adds processing steps for new session query argument

Other changes

  • Moves all deprecated functions into deprecated.R
  • Creates new internal.R to bundle internal helpers
  • Removes superfluous preloads.R
  • Adapts the last_dscore calculation to work with psn and xyz list components

james 0.55.0

  • Updates to renv 0.15.2
  • Update to current R packages

james 0.54.0

  • Upgrades james.groeidiagrammen.nl to https

james 0.53.0

  • Adds host names ijgz.eaglescience.nl and james.groeidiagrammen.nl to get_host()

james 0.52.1

james 0.52.0

  • Breaking change is data structure
  • Change data structure of read_bds() to a simple list to ease standard JSON representation
  • Adapt various JAMES functions to work with change to simple list
  • Update to bdsreader 0.17.0
  • Update renv.lock

james 0.51.2

  • Remove chart element from request_blend() because of problems with the JSON representation

james 0.51.1

james 0.51.0

james 0.49.0

james 0.48.1

james 0.48.0

james 0.47.0

james 0.46.3

james 0.46.2

  • Pass down arguments in all functions using \dots
  • Sync to jamesclient 0.23.0

james 0.46.1

  • Sync to bdsreader 0.14.0 and jamesclient 0.22.0

james 0.46.0

james 0.45.4

  • Send dots in fetch_loc(...) to bdsreader::read_bds(...)

james 0.45.3

james 0.45.2

james 0.45.1

  • Update renv.lock to jamesclient 0.20.0

james 0.45.0

  • Solves a bug in bdsreader that prevented reading data from a URL

james 0.44.1

james 0.44.0

  • Increase dependencies to bdsreader 0.11.0 and jamesclient 0.18.0

james 0.43.3

  • Prevent “the condition has length > 1 and only the first element will be used” in draw_chart()

james 0.43.2

  • Adds forgotten authenticate to draw_chart()
  • Updates renv.lock to chartplotter 0.28.0

james 0.43.1

  • Update renv to donorloader 0.31.1

james 0.43.0

  • Update renv to brokenstick 2.0.0

james 0.41.1

james 0.42.0

  • Refreshes the public key for Eaglescience integration
  • Solves a problem with token validation

james 0.41.0

  • Builds in fall back in case pubkey is not given to authenticate
  • Changes argument jwt to authToken for easy integration

james 0.40.0

  • Repairs a problem with bdsreader that prevented D-score calculation with format = “2.0”

james 0.39.0

  • Adds authentication of externally facing services with a JSON web token

james 0.38.0

  • Adds full stack of Down Syndrome charts to javascript site

james 0.37.0

Major changes

  • Adds support for data formats “1.0” (Allegro Sultum), “1.1” (numeric version) and “2.0” (Eaglescience)
  • Introduces the format argument to bds_read() and bds_write()
  • Introduces auto_format as a way to minimise confusion about the data format

Minor changes

  • Uses longer paths in the javascript header to deal with Apache rewrites

james 0.36.0

  • Update to R 4.1.0
  • Solves a bug that resulted from changes in the internal format of the grid package. The james package now depends on grid 4.1.0 and hence on R >= 4.1.

james 0.35.0

  • Checks spelling and updates word list
  • Adds token to GHA R-CMD-CHECK
  • Removes LICENCE file, which makes CMD-CHECK complain
  • Install V8 lib in linux workflow

james 0.34.0

  • Update dependency versions
  • Removes unneeded nlreferences dependency

james 0.33.0

  • Tranfers repo to growthcharts organisation
  • Adds schema argument to users facing functions, set bds_schema_str.json as default
  • Adds automatic GHA R CMD check
  • Cleans out error so that R CMD check runs without errors

james 0.32.0

  • Breaking changes
  • Replaces jamestest dependency by jamesdemodata package
  • Replaces minihealth dependency by bdsreader package
  • Styles all files
  • Switches to markdown documentation
  • Uses localhost in examples (localhost should be on)

james 0.31.0

  • Removes clopus dependency

james 0.30.0

  • Uses the nlreferences package

james 0.29.1

james 0.29.0

  • Includes svglite dependency as needed by the javascript calls

james 0.28.2

  • Downgrades to chartplotter 0.15.0

james 0.28.1

  • Includes jamesyzy dependency

james 0.28.0

  • Switches to an age-related choice for donordata: 0-2, 2-4 and 4-18.

james 0.27.1

  • Repairs a problem in the slider_list initialisation

james 0.27.0

  • Combines lollypop.term and lollypop.preterm into lollypop
  • Simplifies donordata menu
  • Renames “anthropometric” to “automatic”

james 0.26.0

  • Solves a bug that prevented proper initialisation for 1-21y charts

james 0.25.0

Major changes:

Minor changes

  • Add deprecated warnings to convert_bds_ind(), draw_chart_bds, draw_chart_ind and screen_curves
  • Update tests to account for deprecated functions and arguments
  • Solve problem in screen_curves(). The function now always returns a JSON result

james 0.24.0

  • Re-introduce legacy functions draw_chart_bds, draw_chart_ind
  • Change screen_curves to old behavior, thus producing a list instead of a table
  • Re-introduce arguments bds_data, location, ind_loc and ?ind=

james 0.23.0

  • Major update incorporating the following breaking changes since james 0.16.0
  1. JAMES now consistently uses the txt parameter for JSON child data input, both in the R package and in the javascript. This replaces arguments like bds_data and bds.
  2. JAMES now consistently uses the loc parameters as the URL with uploaded child data. This replaces arguments named location, ind_loc and ind. The query parameter ?ind= in URL’s is outdated, and superseeded by ?loc=.
  3. All analysis functions now accept txt and loc input. When both are specified, txt takes precedence.
  4. For consistency, function upload_txt replaces update_bds.
  5. Function screen_curves no longer returns a list, but only the screening results, consistent with its naming. A new function custom_list takes over this task from screen_curves.
  6. Removed functions: draw_chart_bds, draw_chart_ind, draw_plot (replaced by draw_chart).
  • Enhancements:
  1. The site accept now the ?txt= query parameter, which bypasses the need to upload data.
  2. The new function request_site constructs URL’s for personalised sites.
  3. The new function custom_list creates a custom list of return values (formerly implemented by screen_curves), and adds a new element containing the D-score from the last observation.
  4. A new function update_txt() to upload data to JAMES
  5. The JAMES server location is now independent of the data location, so uploaded data can be stored on an external URL that is under control of the client.
  6. The javascript reduces the number of calls via OpenCPU, resulting in speedier site updates.
  7. Function draw_chart gets a new parameter draw_grob argument, which allows the user to defer drawing and to tweak the gTree object directly.

james 0.22.1

  • Make JAMES server default in get_host()
  • Tweaks behavior of draw_chart() for more intuitive API.
  • Change default in request_site() to upload
  • Solves bug in get_loc()

james 0.22.0

  • Uses better defaults ("" instead of NULL) for outward facing functions.

james 0.21.0

  • The communication between javascript and R is now based on empty strings instead of null and NULL. * The site is functional again!

james 0.20.0

  • Major change: Systematic use of txt and loc arguments in both R and javascript
  • Codes null values in javascript by {} before making request to R
  • Replaces is.null(x) by !length(x)
  • Removes stop() within tryCatch
  • Provides extra argument txt, so making get_tgt() more intelligent
  • Undoes behavior change in draw_chart() in 0.19.0 because that killed interactivity
  • Undoes dots in draw_chart() because that didn’t play well with requests

james 0.19.0

james 0.18.0

  • Simplifies screen_curves()
  • Moves functionality for Allegro Sultum to custom_list()
  • Adds various getters
  • Makes server and data location independent

james 0.17.0

james 0.16.0

  • This version marges the dscore branch, so james now provide a dscore menu

james 0.15.1

james 0.15.0

  • Updated certificates in James and June and ensured that tests produced no errors

james 0.14.4

  • Uses fewer brokenstick knots for Terneuzen donordata

james 0.14.0

  • Uses the svglite shortcut in the javascript calls. This requires opencpu 2.1.5.1001 and the Arial font to be installed on the server.

james 0.10.0

  • Set the max.print option to 100.000 entries in order to allow for printing the full chart list

james 0.8.0

  • Adds function screen_curves() for screening on JGZ guidelines. The function also returns the site URL, so it acts as a one-stop-shop
  • Adds dependencies to growthscreener, jamesclient and jsonlite

james 0.7.0

  • Added: Support for https

james 0.6.0

  • Relocates plotting to new chartplotter package
  • Removes dependency on groeidiagrammen package

james 0.5.1

  • Removes flickering between chart transitions
  • De-emphasizes the chartcode field

james 0.1.0

  • Added a NEWS.md file to track changes to the package.