diff --git a/.lintr b/.lintr index 26740641..b53fffaf 100644 --- a/.lintr +++ b/.lintr @@ -1,4 +1,5 @@ linters: linters_with_defaults( - return_linter = NULL) + return_linter = NULL, + pipe_consistency_linter(pipe = "|>")) encoding: "UTF-8" diff --git a/DESCRIPTION b/DESCRIPTION index 9838a83b..90f82526 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: serocalculator Title: Estimating Infection Rates from Serological Data -Version: 1.3.0.9006 +Version: 1.3.0.9007 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), diff --git a/NEWS.md b/NEWS.md index 4190e111..698be48e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -8,6 +8,8 @@ ## Internal changes +* Started checking for use of base pipe instead of magrittr pipe +by linter (#347) * Removed `ldpar()` from API (#345) * Added test for `sim.cs()` (#344) * Added test for internal function `ab()` (#342) diff --git a/inst/WORDLIST b/inst/WORDLIST index 265e4144..df59e5a1 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,119 +1,54 @@ Aga -Ang -Anik -BMC -Bonačić -Bordetella CMD -Campylobacter -Ceper Chiang Codecov -De Dhulikhel -Diekmann -Duynhoven -Eijkeren FIC -Falkenhorst Fogarty -Friesema GHA -Gageldonk -Graaf -Gras Grolemund -Hassen -Heijden Hessians HlyE IgA IgG IgM -Jernberg -Juba -Juma -Kamenskaya -Kretzschmar -Krogfelt -Kuusi LV Lik -Linneberg Lotka -Marinović -Melker -Mertens -Molbak -Monge -Mughini -Muktadir -Munira NIAID NLL Nadu OSF Orientia -PLoS PRs -Pebody -Polina RStudio Rai -Roord Rtools -Rumunu -Sadkowska -Saha -Saiful -Sajib -Sarkar -Schellekens -Seidman -Senjuti -Sero SeroEpidemiology Seroincidence Serological -Simonsen -Sira -Sium -Strid -Syed TW -Todys Unif -Valk Vectorized Vellore -Versteegh Volterra -Wetering -Wiens -Zota al ast behaviour bioassays biomarker +biomarkers boldsymbol callout -campylobacteriosis cdot -codecov csv -de -der devtools displaystyle -doi dt -epidem et expf forall frac -fx geoms ggproto hemolysin @@ -122,17 +57,17 @@ invf isos isotype isotypes -jinf jitter kDa le leq +linter llik logf +magrittr mathbb mathbf mathcal -mc mcmc modelled multicohort @@ -144,7 +79,6 @@ overline param params pipetting -pmed pmf pre predation @@ -154,7 +88,6 @@ qquad recombinant renewcommand rescale -savePath sectionally sera seroconversion @@ -164,14 +97,12 @@ seroepidemiology seroincidence seroincidences serologic -serological seronegative seroresponse seroresponses serosurvey serosurveys smp -smpl subfigures th tibble