Merge pull request #347 from UCD-SERG/lint-pipe-type

require base pipe

.lintr

@@ -1,4 +1,5 @@
 linters: linters_with_defaults(
-   return_linter = NULL)
+   return_linter = NULL,
+   pipe_consistency_linter(pipe = "|>"))
 encoding: "UTF-8"
 

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", , "[email protected]", role = c("aut", "cph"),
            comment = "Author of the method and original code."),

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)

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