adjust linting requirement

Author: Degoot-AM

.lintr

@@ -6,11 +6,11 @@ linters: all_linters(
     missing_package_linter = NULL,
     library_call_linter = NULL,
     namespace_linter = NULL,
-    one_call_pipe_linter = NULL,
+    #one_call_pipe_linter = NULL,
     unused_import_linter = NULL,
-    consecutive_mutate_linter = NULL,
-    nrow_subset_linter = NULL,
-    return_linter = NULL,
+    #consecutive_mutate_linter = NULL,
+    #nrow_subset_linter = NULL,
+    #return_linter = NULL,
     cyclocomp_linter = NULL,
     undesirable_function_linter(
       modify_defaults(
@@ -19,3 +19,4 @@ linters: all_linters(
       )
     )
   )
+

README.Rmd

@@ -5,7 +5,7 @@ output: github_document
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 ```{r, include = FALSE}
-knitr::opts_chunk$set(
+knitr::opts_chunk[[set]](
   collapse = TRUE,
   comment = "#>"
 )

episodes/clean-data.Rmd

@@ -50,12 +50,12 @@ the advantages of using this.
 
 ```{r, eval=TRUE, message=FALSE, warning=FALSE}
 # Check if a package is already installed and install it if not
-if (!require("pak")) install.packages("pak")
-if (!require("here")) pak::pak("here")
-if (!require("rio")) pak::pak("rio")
-if (!require("dplyr")) pak::pak("dplyr")
-if (!require("magrittr")) pak::pak("magrittr")
-if (!require("cleanepi")) pak::pak("cleanepi")
+if (!requireNamespace("pak", quietly = TRUE)) install.packages("pak")
+if (!requireNamespace("here", quietly = TRUE)) pak::pak("here")
+if (!requireNamespace("rio", quietly = TRUE)) pak::pak("rio")
+if (!requireNamespace("dplyr", quietly = TRUE)) pak::pak("dplyr")
+if (!requireNamespace("magrittr", quietly = TRUE)) pak::pak("magrittr")
+if (!requireNamespace("cleanepi", quietly = TRUE)) pak::pak("cleanepi")
 
 # load the packages
 library(here)
@@ -296,7 +296,8 @@ particular way. These IDs can contain numbers falling within a specific range, a
 
 
 ```{r}
-# check if the subject IDs in the 'case_id' column contains numbers ranging from 0 to 15000
+# check if the subject IDs in the 'case_id' column contains numbers ranging
+# from 0 to 15000
 sim_ebola_data <- cleanepi::check_subject_ids(
   data = sim_ebola_data,
   target_columns = "case_id",

episodes/describe-cases.Rmd

@@ -273,8 +273,8 @@ The example below demonstrates how to configure these three elements for a simpl
 ```{r}
 # Define date breaks for the x-axis
 breaks <- seq.Date(
-  from = min(as.Date(daily_incidence$date_index, na.rm = TRUE)),
-  to = max(as.Date(daily_incidence$date_index, na.rm = TRUE)),
+  from = min(as.Date(daily_incidence[[date_index]], na.rm = TRUE)),
+  to = max(as.Date(daily_incidence[[date_index]], na.rm = TRUE)),
   by = 20 # every 20 days
 )
 

episodes/read-cases.Rmd

@@ -187,7 +187,7 @@ A real-life connection to an external SQLite database would look like this:
 ```{r}
 # in real-life
 db_connection <- DBI::dbConnect(
-  RSQLite::SQLite(), 
+  RSQLite::SQLite(),
   host = "database.epiversetrace.com",
   user = "juanito",
   password = epiversetrace::askForPassword("Database password")
@@ -234,7 +234,7 @@ mytable_db <- dplyr::tbl(src = db_connection, "cases")
 If we apply `{dplyr}` verbs to this table of a SQLite database, these verbs will be translated to an SQL queries.
 
 ```{r}
-# Show the translated SQL queries 
+# Show the translated SQL queries
 mytable_db %>%
   dplyr::filter(confirm > 50) %>%
   dplyr::arrange(desc(confirm)) %>%

episodes/simple-analysis.Rmd

@@ -42,7 +42,7 @@ covid19_eng_case_data <- outbreaks::covid19_england_nhscalls_2020
 # subset the covid19_eng_case_data to include only the first 3 months of data
 df <- base::subset(
   covid19_eng_case_data,
-  covid19_eng_case_data$date <= min(covid19_eng_case_data$date) + 90
+  covid19_eng_case_data[[date]] <= min(covid19_eng_case_data[[date]]) + 90
 )
 
 # uses the incidence() function from the {incidence2} package to compute the