diff --git a/.Rbuildignore b/.Rbuildignore
index b0cf256..9ea81bf 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -13,3 +13,4 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^\.lintr$
diff --git a/.lintr b/.lintr
new file mode 100644
index 0000000..62a0b8f
--- /dev/null
+++ b/.lintr
@@ -0,0 +1,8 @@
+linters: linters_with_defaults() # see vignette("lintr")
+encoding: "UTF-8"
+exclusions: list(
+    "vignettes/articles/filter.Rmd",
+    "vignettes/articles/filter2.Rmd",
+    "vignettes/articles/downstream_analyses.Rmd",
+    "vignettes/articles/reference_semantics.Rmd"
+  )
diff --git a/R/filter_pactr-methods.R b/R/filter_pactr-methods.R
index 8801c14..3f90409 100644
--- a/R/filter_pactr-methods.R
+++ b/R/filter_pactr-methods.R
@@ -7,8 +7,8 @@ filter_pactr$set(
            max_iso_shift,
            merge_peaks,
            merge_method = NULL) {
-    cli::cli_alert_info("Checking {nrow(self$mpactr_data$get_peak_table())}
-                      peaks for mispicked peaks.")
+    l <- nrow(self$mpactr_data$get_peak_table())
+    cli::cli_alert_info("Checking {l} peaks for mispicked peaks.")
 
     ion_filter_list <- list()
     cut_ions <- c() # list
@@ -49,13 +49,14 @@ filter_pactr$set(
     self$logger[["check_mismatched_peaks"]] <- ion_filter_list
 
     if (isTRUE(merge_peaks)) {
-      cli::cli_alert_info("Argument merge_peaks is: {merge_peaks}.
-                         Merging mispicked peaks with method {merge_method}.")
+      cli::cli_alert_info(c("Argument merge_peaks is: {merge_peaks}. ",
+                            "Merging mispicked peaks with method ",
+                            "{merge_method}."))
 
       private$merge_ions(ion_filter_list, merge_method)
     } else {
-      cli::cli_alert_warning("Argument merge_peaks is: {merge_peaks}.
-                           Mispicked peaks will not be merged.")
+      cli::cli_alert_warning(c("Argument merge_peaks is: {merge_peaks}. ",
+                               "Mispicked peaks will not be merged."))
     }
 
     self$logger$list_of_summaries$mispicked <- summary$new(
@@ -111,8 +112,8 @@ filter_pactr$set("private", "get_merged_ions", function(ringwin,
 
 filter_pactr$set("private", "merge_ions", function(ion_filter_list, method) {
   if (is.null(method)) {
-    cli::cli_abort("No method has been supplied for merging peaks.
-                   method must be one of: sum")
+    cli::cli_abort(c("No method has been supplied for merging peaks. ",
+                     "{.var method} must be one of: sum"))
   }
 
   if (method == "sum") {
@@ -222,21 +223,23 @@ filter_pactr$set(
   function(group, remove_ions = TRUE) {
     groups <- unique(self$mpactr_data$get_meta_data()$Biological_Group)
     if (isFALSE(group %in% groups)) {
-      cli::cli_abort("{.var group} {group} is not in {.var Biological_Group}.
-                     Options are: {groups}")
+
+      cli::cli_abort(c("{.var group} {group} is not in ",
+                       "{.var Biological_Group}.",
+                       "Options are: {groups}"))
     }
 
-    cli::cli_alert_info("Parsing {nrow(self$mpactr_data$get_peak_table())}
-                      peaks based on the following sample group: {group}.")
+    l <- nrow(self$mpactr_data$get_peak_table())
+    cli::cli_alert_info("Parsing {l} peaks based on the sample group: {group}.")
 
     if (isFALSE(remove_ions)) {
-      cli::cli_alert_warning("Argument remove_ions is {remove_ions}.
-                           Peaks from {group} will not be removed.")
+      cli::cli_alert_warning(c("Argument remove_ions is {remove_ions}. ",
+                               "Peaks from {group} will not be removed."))
       return()
     }
 
-    cli::cli_alert_info("Argument remove_ions is: {remove_ions}.
-                      Removing peaks from {group}.")
+    cli::cli_alert_info(c("Argument remove_ions is: {remove_ions}.",
+                          "Removing peaks from {group}."))
 
     ions <- self$logger[["group_filter-failing_list"]][[group]]
     self$mpactr_data$set_peak_table(self$mpactr_data$get_peak_table()[
@@ -269,14 +272,15 @@ filter_pactr$set(
 
     ## abort if there are no technical replicates.
     if (isFALSE(self$mpactr_data$isMultipleTechReps())) {
-      cli::cli_abort("There are no technical replicates in the dataset
-                   provided. In order to run the replicability filter,
-                   technical replicates are required.")
+      cli_abort(c("There are no technical replicates in the dataset provided. ",
+                  "In order to run the replicability filter, technical ",
+                  "replicates are required."))
     }
 
     input_ions <- self$mpactr_data$get_peak_table()$Compound
-    cli::cli_alert_info("Parsing {length(input_ions)} peaks for
-                      replicability across technical replicates.")
+    cli <- cli::cli_alert_info
+    n <- length(input_ions)
+    cli("Parsing {n} peaks for replicability across technical replicates.")
 
     cv <- data.table::melt(self$mpactr_data$get_peak_table(),
       id.vars = c("Compound", "mz", "rt", "kmd"), variable.name =
diff --git a/R/filters.R b/R/filters.R
index 81dd63a..887c51b 100644
--- a/R/filters.R
+++ b/R/filters.R
@@ -227,12 +227,14 @@ filter_group <- function(mpactr_object,
 #'
 #' data_filter <- filter_cv(data,
 #'   cv_threshold = 0.01,
-#'   cv_param = "mean"
+#'   cv_param = "mean",
+#'   copy_object = TRUE
 #' )
 #'
 #' data_filter <- filter_cv(data,
 #'   cv_threshold = 0.01,
-#'   cv_param = "median"
+#'   cv_param = "median",
+#'   copy_object = TRUE
 #' )
 #'
 filter_cv <- function(mpactr_object,
@@ -259,7 +261,6 @@ filter_cv <- function(mpactr_object,
   return(mpactr_object)
 }
 
-
 ###########################
 ### Insource ions filter ##
 ###########################
diff --git a/R/mpactr-methods.R b/R/mpactr-methods.R
index 4245915..3cbb6ff 100644
--- a/R/mpactr-methods.R
+++ b/R/mpactr-methods.R
@@ -6,6 +6,7 @@ mpactr$set("private", "initialize_data", function() {
     private$peak_table[, .SD, .SDcols = private$meta_data$Injection]
   ) > 0), ]
   private$set_kmd()
+  private$peak_table$Compound <- as.character(private$peak_table$Compound)
 })
 mpactr$set("private", "set_kmd", function() {
   private$peak_table[, kmd := mz - floor(mz)]
diff --git a/R/peak_table_formatter.R b/R/peak_table_formatter.R
index 3c61e0a..d579138 100644
--- a/R/peak_table_formatter.R
+++ b/R/peak_table_formatter.R
@@ -29,7 +29,6 @@ format_by_type <- function(peak_table_path,
   } # default condition = NULL
 }
 
-
 progenesis_formatter <- function(peak_table) {
   peak_table <- data.table(readr::read_csv(peak_table,
     skip = 2,
@@ -64,10 +63,6 @@ mz_mine_formatter <- function(peak_table) {
 metaboscape_formatter <- function(peak_table, sample_names) {
   peak_table <- data.table(readr::read_csv(peak_table, show_col_types = FALSE))
   peak_table_convert <- data.table::copy(peak_table)
-  adduct_data <- utils::read.csv(system.file("extdata/ion_masses",
-    "DefinedIons.csv",
-    package = "mpactR"
-  ))
   peak_table_convert <- with(peak_table_convert, peak_table_convert[
     , ion := gsub(
       ".*\\[(.+)\\].*", "\\1",
@@ -82,7 +77,10 @@ metaboscape_formatter <- function(peak_table, sample_names) {
   ][
     charge_string == "3+", charge := 3
   ][
-    adduct_data,
+    utils::read.csv(system.file("extdata/ion_masses",
+      "DefinedIons.csv",
+      package = "mpactR"
+    )),
     on = .(ion = IONS)
   ][
     , mz := (PEPMASS / charge) + MASS
diff --git a/R/summary-class.R b/R/summary-class.R
index b53a163..f0a668d 100644
--- a/R/summary-class.R
+++ b/R/summary-class.R
@@ -10,10 +10,12 @@ summary <- R6::R6Class("summary",
       private$passed_ions <- passed_ions
     },
     summarize = function(x) {
-      cli::cli_alert_success("{length(private$failed_ions)} ions failed the
-                              {private$filter} filter,
-                               {length(private$passed_ions)}
-                               ions remain.")
+      l <- length(private$failed_ions)
+      f <- private$filter
+      r <- length(private$passed_ions)
+
+      cli::cli_alert_success(c("{l} ions failed the {f} filter, ",
+                               "{r} ions remain."))
     },
     get_failed_ions = function() {
       return(private$failed_ions)
diff --git a/man/filter_cv.Rd b/man/filter_cv.Rd
index 9bedf7c..d8ba0aa 100644
--- a/man/filter_cv.Rd
+++ b/man/filter_cv.Rd
@@ -5,7 +5,6 @@
 \title{Filter Non-reproducible ions}
 \usage{
 filter_cv(mpactr_object, cv_threshold = NULL, cv_param, copy_object = FALSE)
-filter_cv(mpactr_object, cv_threshold = NULL, cv_param, copy_object = FALSE)
 }
 \arguments{
 \item{mpactr_object}{An \code{mpactr_object}. See \code{\link[=import_data]{import_data()}}.}
@@ -51,12 +50,14 @@ data <- import_data(example("coculture_peak_table.csv"),
 
 data_filter <- filter_cv(data,
   cv_threshold = 0.01,
-  cv_param = "mean"
+  cv_param = "mean",
+  copy_object = TRUE
 )
 
 data_filter <- filter_cv(data,
   cv_threshold = 0.01,
-  cv_param = "median"
+  cv_param = "median",
+  copy_object = TRUE
 )
 
 }
diff --git a/man/filter_mispicked_ions.Rd b/man/filter_mispicked_ions.Rd
index 4cb12a8..82f3678 100644
--- a/man/filter_mispicked_ions.Rd
+++ b/man/filter_mispicked_ions.Rd
@@ -12,7 +12,6 @@ filter_mispicked_ions(
   max_iso_shift = 3,
   merge_peaks = TRUE,
   merge_method = "sum",
-  merge_method = "sum",
   copy_object = FALSE
 )
 }
diff --git a/tests/testthat/test-filter_pactr-class.R b/tests/testthat/test-filter_pactr-class.R
index 7ec0d0a..8483b17 100644
--- a/tests/testthat/test-filter_pactr-class.R
+++ b/tests/testthat/test-filter_pactr-class.R
@@ -341,109 +341,201 @@ test_that("is_filter_run correctly assesses if a filter has been run", {
   expect_false(filter_class$is_filter_run(filter = "insource"))
 })
 
-test_that("get_log returns an error when an incorrect fitler argument is provided", {
-  mpactr_class <- mpactr$new(test_path("exttestdata","102623_peaktable_coculture_simple.csv"),
-                             test_path("exttestdata", "102623_metadata_correct.csv"))
-  mpactr_class$setup()
-  filter_class <- filter_pactr$new(mpactr_class)
-  
-  expect_error(filter_class$get_log(filter = "cv"), "`filter` must be one of mpactR's")
-})
+test_that("get_log returns an error when 
+an incorrect fitler argument is provided", {
+            directory <- "exttestdata"
+            peak_table_name <- "102623_peaktable_coculture_simple.csv"
+            meta_data_name <- "102623_metadata_correct.csv"
+            meta <- data.table(read_csv(test_path(directory,
+                                                  meta_data_name),
+                                        show_col_types = FALSE))
+            pt_list <- progenesis_formatter(test_path(directory,
+                                                      peak_table_name))
+            mpactr_class <- mpactr$new(
+              pt_list,
+              meta
+            )
+            mpactr_class$setup()
+            filter_class <- filter_pactr$new(mpactr_class)
+            expect_error(filter_class$get_log(filter = "cv"),
+                         "`filter` must be one of mpactR's")
+          })
 
-test_that("get_log returns an error when the fitler argument provided has not yet been run (e.g., not in the log)", {
-  mpactr_class <- mpactr$new(test_path("exttestdata","102623_peaktable_coculture_simple.csv"),
-                             test_path("exttestdata", "102623_metadata_correct.csv"))
-  mpactr_class$setup()
-  filter_class <- filter_pactr$new(mpactr_class)
-  
-  expect_error(filter_class$get_log(filter = "mispicked"), "`filter` mispicked has not yet been applied to the data")
-})
+test_that("get_log returns an error when the fitler
+ argument provided has not yet been run (e.g., not in the log)", {
+            directory <- "exttestdata"
+            peak_table_name <- "102623_peaktable_coculture_simple.csv"
+            meta_data_name <- "102623_metadata_correct.csv"
+            meta <- data.table(read_csv(test_path(directory,
+                                                  meta_data_name),
+                                        show_col_types = FALSE))
+            pt_list <- progenesis_formatter(test_path(directory,
+                                                      peak_table_name))
+            mpactr_class <- mpactr$new(
+              pt_list,
+              meta
+            )
+            mpactr_class$setup()
+            filter_class <- filter_pactr$new(mpactr_class)
+            err_msg <- "`filter` mispicked has not yet been applied to the data"
+            expect_error(filter_class$get_log(filter = "mispicked"), err_msg)
+          })
 
 test_that("get_log returns the correct fitler summary list", {
-  mpactr_class <- mpactr$new(test_path("exttestdata","102623_peaktable_coculture_simple.csv"),
-                             test_path("exttestdata", "102623_metadata_correct.csv"))
+  directory <- "exttestdata"
+  peak_table_name <- "102623_peaktable_coculture_simple.csv"
+  meta_data_name <- "102623_metadata_correct.csv"
+  meta <- data.table(read_csv(test_path(directory,
+                                        meta_data_name),
+                              show_col_types = FALSE))
+  pt_list <- progenesis_formatter(test_path(directory,
+                                            peak_table_name))
+  mpactr_class <- mpactr$new(
+    pt_list,
+    meta
+  )
   mpactr_class$setup()
   filter_class <- filter_pactr$new(mpactr_class)
-  filter_class$check_mismatched_peaks(ringwin = 0.5, isowin = 0.01, trwin = 0.005, max_iso_shift = 3, merge_peaks =
-    TRUE, merge_method = "sum")
-  
+  filter_class$check_mismatched_peaks(ringwin = 0.5,
+                                      isowin = 0.01,
+                                      trwin = 0.005,
+                                      max_iso_shift = 3,
+                                      merge_peaks = TRUE,
+                                      merge_method = "sum")
   mispicked_summary <- filter_class$get_log(filter = "mispicked")
-  
   expect_type(mispicked_summary, "list")
   expect_equal(length(mispicked_summary), 2)
   expect_equal(length(mispicked_summary$passed_ions), 1233)
 })
 
-test_that("get_mispicked_ions returns error if check_mismatched_peaks has not been called", {
-  mpactr_class <- mpactr$new(test_path("exttestdata","102623_peaktable_coculture_simple.csv"),
-                             test_path("exttestdata", "102623_metadata_correct.csv"))
-  mpactr_class$setup()
-  filter_class <- filter_pactr$new(mpactr_class)
-  
-  expect_error(filter_class$get_mispicked_ions(), "The mispicked filter has not yet been")
-})
+test_that("get_mispicked_ions returns error if 
+check_mismatched_peaks has not been called", {
+            directory <- "exttestdata"
+            peak_table_name <- "102623_peaktable_coculture_simple.csv"
+            meta_data_name <- "102623_metadata_correct.csv"
+            meta <- data.table(read_csv(test_path(directory,
+                                                  meta_data_name),
+                                        show_col_types = FALSE))
+            pt_list <- progenesis_formatter(test_path(directory,
+                                                      peak_table_name))
+            mpactr_class <- mpactr$new(
+              pt_list,
+              meta
+            )
+            mpactr_class$setup()
+            filter_class <- filter_pactr$new(mpactr_class)
 
-test_that("get_mispicked_ions correctly returns the check_mismatched_peaks list", {
-  mpactr_class <- mpactr$new(test_path("exttestdata","102623_peaktable_coculture_simple.csv"),
-                             test_path("exttestdata", "102623_metadata_correct.csv"))
-  mpactr_class$setup()
-  filter_class <- filter_pactr$new(mpactr_class)
-  filter_class$check_mismatched_peaks(ringwin = 0.5, isowin = 0.01, trwin = 0.005, max_iso_shift = 3, merge_peaks =
-    TRUE, merge_method = "sum")
-  
-  mispicked_groups <- filter_class$get_mispicked_ions()
-  
-  expect_equal(class(mispicked_groups), c("data.table", "data.frame"))
-  expect_equal(length(mispicked_groups), 2)
-  expect_equal(names(mispicked_groups), c("main_ion", "similar_ions"))
-})
+            expect_error(filter_class$get_mispicked_ions(),
+                         "The mispicked filter has not yet been")
+          })
+
+test_that("get_mispicked_ions correctly 
+returns the check_mismatched_peaks list", {
+            directory <- "exttestdata"
+            peak_table_name <- "102623_peaktable_coculture_simple.csv"
+            meta_data_name <- "102623_metadata_correct.csv"
+            meta <- data.table(read_csv(test_path(directory,
+                                                  meta_data_name),
+                                        show_col_types = FALSE))
+            pt_list <- progenesis_formatter(test_path(directory,
+                                                      peak_table_name))
+            mpactr_class <- mpactr$new(
+              pt_list,
+              meta
+            )
+            mpactr_class$setup()
+            filter_class <- filter_pactr$new(mpactr_class)
+            filter_class$check_mismatched_peaks(ringwin = 0.5,
+                                                isowin = 0.01,
+                                                trwin = 0.005,
+                                                max_iso_shift = 3,
+                                                merge_peaks = TRUE,
+                                                merge_method = "sum")
+
+            mispicked_groups <- filter_class$get_mispicked_ions()
+
+            expect_equal(class(mispicked_groups), c("data.table", "data.frame"))
+            expect_equal(length(mispicked_groups), 2)
+            expect_equal(names(mispicked_groups), c("main_ion", "similar_ions"))
+          })
 
 
 test_that("get_group_averages calculates a group table", {
-  mpactr_class <- mpactr$new(test_path("exttestdata","102623_peaktable_coculture_simple.csv"),
-                             test_path("exttestdata", "102623_metadata_correct.csv"))
+  directory <- "exttestdata"
+  peak_table_name <- "102623_peaktable_coculture_simple.csv"
+  meta_data_name <- "102623_metadata_correct.csv"
+  meta <- data.table(read_csv(test_path(directory,
+                                        meta_data_name),
+                              show_col_types = FALSE))
+  pt_list <- progenesis_formatter(test_path(directory,
+                                            peak_table_name))
+  mpactr_class <- mpactr$new(
+    pt_list,
+    meta
+  )
   mpactr_class$setup()
   filter_class <- filter_pactr$new(mpactr_class)
-  
-  filter_class$check_mismatched_peaks(ringwin = 0.5, isowin = 0.01, trwin = 0.005, max_iso_shift = 3, merge_peaks =
-    TRUE, merge_method = "sum")
-  
+  filter_class$check_mismatched_peaks(ringwin = 0.5,
+                                      isowin = 0.01,
+                                      trwin = 0.005,
+                                      max_iso_shift = 3,
+                                      merge_peaks = TRUE,
+                                      merge_method = "sum")
   avgs <- filter_class$get_group_averages()
   expect_equal(class(avgs), c("data.table", "data.frame"))
   expect_equal(nrow(avgs), (1233 * 6))
-  
-  mpactr_class <- mpactr$new(test_path("exttestdata","102623_peaktable_coculture_simple.csv"),
-                             test_path("exttestdata", "102623_metadata_correct.csv"))
+
+  mpactr_class <- mpactr$new(
+    pt_list,
+    meta
+  )
   mpactr_class$setup()
   filter_class <- filter_pactr$new(mpactr_class)
-  
-  filter_class$check_mismatched_peaks(ringwin = 0.5, isowin = 0.01, trwin = 0.005, max_iso_shift = 3, merge_peaks =
-    TRUE, merge_method = "sum")
+
+  filter_class$check_mismatched_peaks(ringwin = 0.5,
+                                      isowin = 0.01,
+                                      trwin = 0.005,
+                                      max_iso_shift = 3,
+                                      merge_peaks = TRUE,
+                                      merge_method = "sum")
   filter_class$filter_blank()
   filter_class$parse_ions_by_group(group_threshold = 0.01)
   filter_class$apply_group_filter("Blanks", remove_ions = TRUE)
-  
+
   avgs <- filter_class$get_group_averages()
   expect_equal(class(avgs), c("data.table", "data.frame"))
   expect_equal(nrow(avgs), (484 * 6))
 })
 
 test_that("get_cv returns the cv filter has been applied", {
-  mpactr_class <- mpactr$new(test_path("exttestdata","102623_peaktable_coculture_simple.csv"),
-                             test_path("exttestdata", "102623_metadata_correct.csv"))
+  directory <- "exttestdata"
+  peak_table_name <- "102623_peaktable_coculture_simple.csv"
+  meta_data_name <- "102623_metadata_correct.csv"
+  meta <- data.table(read_csv(test_path(directory,
+                                        meta_data_name),
+                              show_col_types = FALSE))
+  pt_list <- progenesis_formatter(test_path(directory,
+                                            peak_table_name))
+  mpactr_class <- mpactr$new(
+    pt_list,
+    meta
+  )
   mpactr_class$setup()
   filter_class <- filter_pactr$new(mpactr_class)
-  filter_class$check_mismatched_peaks(ringwin = 0.5, isowin = 0.01, trwin = 0.005, max_iso_shift = 3, merge_peaks =
-    TRUE, merge_method = "sum")
+  filter_class$check_mismatched_peaks(ringwin = 0.5,
+                                      isowin = 0.01,
+                                      trwin = 0.005,
+                                      max_iso_shift = 3,
+                                      merge_peaks = TRUE,
+                                      merge_method = "sum")
   filter_class$filter_blank()
   filter_class$parse_ions_by_group(group_threshold = 0.01)
   filter_class$apply_group_filter("Blanks", remove_ions = TRUE)
-  # filter_class$get_cv()
 
   expect_error(filter_class$get_cv(), "The cv filter has not yet")
-  
+
   filter_class$cv_filter(cv_threshold = 0.2, cv_params = c("mean"))
-  
+
   cv <- filter_class$get_cv()
   expect_equal(class(cv), c("data.table", "data.frame"))
-})
\ No newline at end of file
+})
diff --git a/tests/testthat/test-filter_pactr-methods.R b/tests/testthat/test-filter_pactr-methods.R
index ee80dea..02148c2 100644
--- a/tests/testthat/test-filter_pactr-methods.R
+++ b/tests/testthat/test-filter_pactr-methods.R
@@ -29,7 +29,7 @@ properly with filter_pactr-class data", {
                                                     "cut_ions.csv"),
                                           col_names = c("V1"),
                                           show_col_types = FALSE)
-            expected_cut_ions <- as.integer(expected_cut_ions$V1)
+            expected_cut_ions <- as.character(expected_cut_ions$V1)
             logger_index_name <- "check_mismatched_peaks"
             expect_equal(filter_class$logger[[logger_index_name]][["cut_ions"]],
                          expected_cut_ions)
@@ -105,10 +105,11 @@ test_that("blank filter works correctly", {
 
   grp_avg <- "102623_peaktable_coculture_simple_groupaverages.csv"
   test_path(directory, grp_avg)
-  error_prop <- read_csv(test_path(directory, grp_avg),
+  error_prop <- as.data.table(read_csv(test_path(directory, grp_avg),
     show_col_types = FALSE, skip = 1,
     col_names = c("Compound", "mz", "rt", "biologicalGroup", "average")
-  )
+  ))[, Compound := as.character(Compound)]
+  setorder(error_prop, Compound)
   logger_index_name <- "group_filter-group_stats"
   expect_true(all(filter_class$logger[[logger_index_name]]$Biological_Group %in%
                     error_prop$biologicalGroup))
@@ -164,17 +165,17 @@ test_that("parse_ions_by_group flags the correct ions", {
 
   expect_false(all(sapply(group_filter_list, is.null)))
   expect_true(all(group_filter_list$`ANG18 monoculture`
-                  == as.character(ang_18$V1)))
+                  %in% as.character(ang_18$V1)))
   expect_true(all(group_filter_list$`ANGDT monoculture`
-                  == as.character(angdt$V1)))
+                  %in% as.character(angdt$V1)))
   expect_true(all(group_filter_list$`Blanks`
-                  == as.character(blanks$V1)))
+                  %in% as.character(blanks$V1)))
   expect_true(all(group_filter_list$`Coculture`
-                  == as.character(coculture$V1)))
+                  %in% as.character(coculture$V1)))
   expect_true(all(group_filter_list$`JC28 monoculture`
-                  == as.character(jc28$V1)))
+                  %in% as.character(jc28$V1)))
   expect_true(all(group_filter_list$`JC28 monoculture`
-                  == as.character(jc28$V1)))
+                  %in% as.character(jc28$V1)))
 })
 
 test_that("apply_group_filter removes the correct ions", {
diff --git a/tests/testthat/test-filters.R b/tests/testthat/test-filters.R
index f873d67..c3b2066 100644
--- a/tests/testthat/test-filters.R
+++ b/tests/testthat/test-filters.R
@@ -22,7 +22,7 @@ test_that("filter mismatch ions wrapper works
                                                     "cut_ions.csv"),
                                           col_names = c("V1"),
                                           show_col_types = FALSE)
-            expected_cut_ions <- as.integer(expected_cut_ions$V1)
+            expected_cut_ions <- as.character(expected_cut_ions$V1)
 
             expect_equal(nrow(data_mpactr$mpactr_data$get_peak_table()),
                          nrow((data_mpactr$mpactr_data$get_peak_table())))
diff --git a/vignettes/articles/downstream_analyses.Rmd b/vignettes/articles/downstream_analyses.Rmd
index 683af2b..0d82f4f 100644
--- a/vignettes/articles/downstream_analyses.Rmd
+++ b/vignettes/articles/downstream_analyses.Rmd
@@ -87,6 +87,7 @@ We can join these two `data.table`s for plotting data set:
 
 ```{r}
 get_raw_data(data_filtered) %>%
+  mutate(Compound = as.character(Compound)) %>%
   select(Compound, mz, rt) %>%
   left_join(qc_summary(data_filtered),
     by = join_by("Compound" == "compounds")
@@ -98,6 +99,7 @@ Now we can create a scatter plot to show the input features (m/z ~ retention tim
 
 ```{r}
 get_raw_data(data_filtered) %>%
+  mutate(Compound = as.character(Compound)) %>% 
   select(Compound, mz, rt) %>%
   left_join(qc_summary(data_filtered),
     by = join_by("Compound" == "compounds")
@@ -119,6 +121,7 @@ We can also make the plot interactive with the `plotly` package function `ggplot
 
 ```{r}
 feature_plot <- get_raw_data(data_filtered) %>%
+  mutate(Compound = as.character(Compound)) %>%
   select(Compound, mz, rt) %>%
   left_join(qc_summary(data_filtered),
     by = join_by("Compound" == "compounds")
@@ -867,4 +870,3 @@ fc2 %>%
     axis.text = element_text(size = 15)
   )
 ```
-
diff --git a/vignettes/articles/filter.Rmd b/vignettes/articles/filter.Rmd
index 6520f5c..f07c883 100644
--- a/vignettes/articles/filter.Rmd
+++ b/vignettes/articles/filter.Rmd
@@ -1,3 +1,4 @@
+
 ---
 title: "Filter"
 ---
diff --git a/vignettes/articles/reference_semantics.Rmd b/vignettes/articles/reference_semantics.Rmd
index 931d269..33714cd 100644
--- a/vignettes/articles/reference_semantics.Rmd
+++ b/vignettes/articles/reference_semantics.Rmd
@@ -1,3 +1,4 @@
+
 ---
 title: "Reference Semantics"
 ---