From b0b72a1443f87c5e4c483f3ec5cc60fdebea049c Mon Sep 17 00:00:00 2001
From: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Date: Thu, 30 Jan 2025 09:58:53 -0800
Subject: [PATCH 1/4] require base pipe

---
 .lintr | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.lintr b/.lintr
index 26740641d..b53fffaf4 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"
 

From 539f8ea372bede152eb459646d0a74a188a2ee67 Mon Sep 17 00:00:00 2001
From: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Date: Thu, 30 Jan 2025 10:01:18 -0800
Subject: [PATCH 2/4] Increment version number to 1.3.0.9007

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9838a83b9..90f825260 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 4190e1111..8f716fafc 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 ()
 * Removed `ldpar()` from API (#345)
 * Added test for `sim.cs()` (#344)
 * Added test for internal function `ab()` (#342)

From a2b48d5e77974c6439ecb940c6d881fd9ab89f68 Mon Sep 17 00:00:00 2001
From: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Date: Thu, 30 Jan 2025 10:01:54 -0800
Subject: [PATCH 3/4] finish news

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 8f716fafc..698be48ee 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -9,7 +9,7 @@
 ## Internal changes
 
 * Started checking for use of base pipe instead of magrittr pipe
-by linter ()
+by linter (#347)
 * Removed `ldpar()` from API (#345)
 * Added test for `sim.cs()` (#344)
 * Added test for internal function `ab()` (#342)

From be04786dc40d4db0a8e31d51e33f37e7bb8f4b8d Mon Sep 17 00:00:00 2001
From: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Date: Thu, 30 Jan 2025 10:17:37 -0800
Subject: [PATCH 4/4] clean up word list after moving references to bibtex file

---
 inst/WORDLIST | 75 +++------------------------------------------------
 1 file changed, 3 insertions(+), 72 deletions(-)

diff --git a/inst/WORDLIST b/inst/WORDLIST
index 265e41445..df59e5a1a 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