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HVTI Recipes 3.1.7

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@ehrlinger ehrlinger released this 13 Oct 01:06
v3.1.7
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Learn about vigilant mode.

A patch edition with one correction you should know about, a new recipe on journal colour palettes, and a re-render against the family's current releases.

Read it: https://ehrlinger.github.io/hvtiGraphics/

A correction first

The JTCVS summary table in Manuscript tables had no p-values in 3.1.5 and 3.1.6 (#93). The table built with hv_tbl_summary(compare = "pvalue") printed an empty p-value column, and hv_test_footnotes_jtcvs() returned no footnotes, so the letters naming each test were missing too. The cause was the build, not the packages: the CI render that drew the chapter lacked broom, which gtsummary's comparison tests call through cardx, and the warning saying so was suppressed in the book. Both are restored (Wilcoxon rank sum for the continuous rows, chi-square for diabetes). If you copied that table's layout, the p-value column belongs in it. broom is now in the book's install line, because a fresh machine hits the same silent blank.

3.1.7

  • A new recipe, "Journal palettes" (#91), in the colour chapter. ggsci packages the palettes of NEJM, The Lancet, JAMA, BMJ, JCO, Science, Nature and Frontiers as ggplot2 scales; the recipe shows them side by side and says what each is for. It also reports a check under simulated red-green colour blindness: Lancet pairs red with green, BMJ's blue and purple nearly merge, and AAAS and Frontiers are weak, while JAMA, JCO and Nature hold up about as well as the house palette. None of the cardiothoracic journals (JTCVS, The Annals of Thoracic Surgery, EJCTS) has a palette, so the house palette stays the default there.
  • The box-plot jitter recipe sets its own seed (#93). hvtiPlotR 2.8.6 stopped the sample_*() data generators from leaving set.seed() behind in your session, which is the right behaviour, and which showed that the recipe's geom_jitter() had been leaning on it. It now uses position_jitter(seed = ), and the text says why.
  • proc_means() prints the group's report statistics (#93). Under hvtiRutilities 1.5.2 its default adds the 15th percentile, median and 85th percentile; the data tables chapter describes the new default and the SAS-parity caveat.
  • The CONSORT diagram is redrawn under consort 1.2.4, which changed its layout. The counts are unchanged.
  • The version check now watches ggsci and consort alongside randomForestSRC, varPro and mlbench.

Everything else is unchanged: 160 of 168 HTML figures are pixel-identical to 3.1.6.

Built against

hvtiR 1.2.7, hvtiPlotR 2.8.6, hvtiRutilities 1.5.2, hvtiRtables 1.0.3, TemporalHazard 1.2.15 and ggRandomForests 4.0.0 (3753051, v4.0.0-rc8), with randomForestSRC 3.9.0, varPro 3.3.0, mlbench 2.1-11, consort 1.2.4 and ggsci 5.2.0. sibling-versions.json records them. The HTML cache comes from a CI build against those versions; the PDF was rebuilt locally against the same commits.

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