summarise -> summarize

R/change_params_small.R

@@ -15,7 +15,7 @@
 #' @param ms_pol The polarity used. Must be either "pos" or "neg". STRING
 #' @param org_tax If your experiment contains a single taxon, its scientific name. "Homo sapiens". STRING
 #' @param hig_con Filter high confidence candidates only. BOOLEAN
-#' @param summarise Summarize all candidates per feature to a single row. BOOLEAN
+#' @param summarize Summarize all candidates per feature to a single row. BOOLEAN
 #'
 #' @export
 #'
@@ -33,7 +33,7 @@
 #'   ms_pol = "pos",
 #'   org_tax = "Gentiana lutea",
 #'   hig_con = TRUE,
-#'   summarise = FALSE
+#'   summarize = FALSE
 #' )
 #' }
 change_params_small <- function(fil_pat = NULL,
@@ -44,7 +44,7 @@ change_params_small <- function(fil_pat = NULL,
                                 ms_pol = NULL,
                                 org_tax = NULL,
                                 hig_con = NULL,
-                                summarise = NULL) {
+                                summarize = NULL) {
   tima:::go_to_cache()
   paths_data_source <- tima:::get_default_paths()$data$source$path
   paths_data_interim_annotations <-
@@ -113,8 +113,8 @@ change_params_small <- function(fil_pat = NULL,
   if (!is.null(hig_con)) {
     yaml_small$options$high_confidence <- hig_con
   }
-  if (!is.null(summarise)) {
-    yaml_small$options$summarise <- summarise
+  if (!is.null(summarize)) {
+    yaml_small$options$summarize <- summarize
   }
 
   yaml::write_yaml(

R/clean_chemo.R

@@ -20,7 +20,7 @@
 #' @param minimal_ms1_condition Condition to be used. Must be "OR" or "AND".
 #' @param high_confidence Report high confidence candidates only. BOOLEAN
 #' @param remove_ties Remove ties. BOOLEAN
-#' @param summarise Boolean. summarise results (1 row per feature)
+#' @param summarize Boolean. summarize results (1 row per feature)
 #'
 #' @return A table containing the chemically weighted annotation
 #'    where only a given number of initial candidates are kept
@@ -39,7 +39,7 @@ clean_chemo <-
            minimal_ms1_condition = get("minimal_ms1_condition", envir = parent.frame()),
            high_confidence = get("high_confidence", envir = parent.frame()),
            remove_ties = get("remove_ties", envir = parent.frame()),
-           summarise = get("summarise", envir = parent.frame())) {
+           summarize = get("summarize", envir = parent.frame())) {
     model <- tima:::columns_model()
 
     log_debug(
@@ -186,7 +186,7 @@ clean_chemo <-
         tidytable::distinct(c(feature_id, rank_final), .keep_all = TRUE)
     }
 
-    if (summarise == TRUE) {
+    if (summarize == TRUE) {
       log_debug("Collecting garbage ...")
       gc()
       log_debug("summarizing results \n")

R/parse_cli_params.R

@@ -443,8 +443,8 @@ parse_cli_params <- function(arguments, parameters) {
     if (!is.null(arguments$remove_ties)) {
       parameters$options$remove_ties <- as.logical(arguments$remove_ties)
     }
-    if (!is.null(arguments$summarise)) {
-      parameters$options$summarise <- as.logical(arguments$summarise)
+    if (!is.null(arguments$summarize)) {
+      parameters$options$summarize <- as.logical(arguments$summarize)
     }
   }
   return(parameters)

R/prepare_params.R

@@ -170,7 +170,7 @@ prepare_params <- function(params_small = get_params(step = "prepare_params"),
   opt_hig_con <- params_advanced$options$high_confidence
   opt_for <- params_advanced$options$force
   opt_rem_tie <- params_advanced$options$remove_ties
-  opt_sum <- params_advanced$options$summarise
+  opt_sum <- params_advanced$options$summarize
 
   log_debug(x = "Small params")
   fil_pat <- params_small$files$pattern
@@ -181,7 +181,7 @@ prepare_params <- function(params_small = get_params(step = "prepare_params"),
   ms_pol <- params_small$ms$polarity
   org_tax <- params_small$organisms$taxon
   opt_hig_con <- params_small$options$high_confidence
-  opt_sum <- params_small$options$summarise
+  opt_sum <- params_small$options$summarize
 
   if (!is.null(org_tax)) {
     if (org_tax == "") {
@@ -616,7 +616,7 @@ prepare_params <- function(params_small = get_params(step = "prepare_params"),
         opt_hig_con
       yamls_params$weight_annotations$options$remove_ties <-
         opt_rem_tie
-      yamls_params$weight_annotations$options$summarise <-
+      yamls_params$weight_annotations$options$summarize <-
         opt_sum
     }
   )

R/weight_annotations.R

@@ -80,7 +80,7 @@
 #' @param compounds_names Report compounds names. Can be very large. BOOLEAN
 #' @param high_confidence Report high confidence candidates only. BOOLEAN
 #' @param remove_ties Remove ties. BOOLEAN
-#' @param summarise Summarize results (1 row per feature). BOOLEAN
+#' @param summarize Summarize results (1 row per feature). BOOLEAN
 #' @param pattern Pattern to identify your job. STRING
 #'
 #' @return The path to the weighted annotations
@@ -216,7 +216,7 @@ weight_annotations <- function(library = get_params(step = "weight_annotations")
                                compounds_names = get_params(step = "weight_annotations")$options$compounds_names,
                                high_confidence = get_params(step = "weight_annotations")$options$high_confidence,
                                remove_ties = get_params(step = "weight_annotations")$options$remove_ties,
-                               summarise = get_params(step = "weight_annotations")$options$summarise,
+                               summarize = get_params(step = "weight_annotations")$options$summarize,
                                pattern = get_params(step = "weight_annotations")$files$pattern,
                                force = get_params(step = "weight_annotations")$options$force) {
   stopifnot("Annotations file(s) do(es) not exist" = all(purrr::map(.x = annotations, .f = file.exists) |> unlist()))

codemeta.json

@@ -671,7 +671,6 @@
       }
     }
   ],
-  "releaseNotes": "https://github.com/taxonomicallyinformedannotation/tima/blob/master/NEWS.md",
   "readme": "https://github.com/taxonomicallyinformedannotation/tima/blob/main/README.md",
   "contIntegration": ["https://github.com/taxonomicallyinformedannotation/tima/actions/workflows/R-CMD-check.yaml", "https://app.codecov.io/gh/taxonomicallyinformedannotation/tima"],
   "developmentStatus": "https://lifecycle.r-lib.org/articles/stages.html#experimental"

inst/_targets.R

@@ -1813,7 +1813,7 @@ list(
         compounds_names = par_wei_ann$options$compounds_names,
         high_confidence = par_wei_ann$options$high_confidence,
         remove_ties = par_wei_ann$options$remove_ties,
-        summarise = par_wei_ann$options$summarise,
+        summarize = par_wei_ann$options$summarize,
         pattern = par_wei_ann$files$pattern,
         force = par_wei_ann$options$force
       )
@@ -2662,7 +2662,7 @@ list(
           compounds_names = benchmark_def_wei_ann$options$compounds_names,
           high_confidence = FALSE,
           remove_ties = benchmark_def_wei_ann$options$remove_ties,
-          summarise = benchmark_def_wei_ann$options$summarise,
+          summarize = benchmark_def_wei_ann$options$summarize,
           pattern = benchmark_def_wei_ann$files$pattern,
           force = benchmark_def_wei_ann$options$force
         )

inst/app.R

@@ -1538,8 +1538,8 @@ ui <- shiny::fluidPage(
             )
           ),
         shiny::checkboxInput(
-          inputId = "summarise",
-          label = "Summarise results to one row per feature",
+          inputId = "summarize",
+          label = "summarize results to one row per feature",
           value = FALSE
         ) |>
           shinyhelper::helper(
@@ -1828,7 +1828,7 @@ ui <- shiny::fluidPage(
   }
   hig_con <- shiny::isolate(input$high_confidence)
   ms_pol <- shiny::isolate(input$ms_pol)
-  summarise <- shiny::isolate(input$summarise)
+  summarize <- shiny::isolate(input$summarize)
 
   message(x = "Changing parameters ...")
   message(x = "... Small")
@@ -1841,7 +1841,7 @@ ui <- shiny::fluidPage(
   yaml_small$ms$polarity <- ms_pol
   yaml_small$organisms$taxon <- org_tax
   yaml_small$options$high_confidence <- hig_con
-  yaml_small$options$summarise <- summarise
+  yaml_small$options$summarize <- summarize
   tima:::create_dir("params")
   yaml::write_yaml(x = yaml_small, file = tima:::get_default_paths()$params$prepare_params)
 
@@ -2144,7 +2144,7 @@ ui <- shiny::fluidPage(
     shiny::isolate(input$force)
   yaml_advanced$options$remove_ties <-
     shiny::isolate(input$remove_ties)
-  yaml_advanced$options$summarise <- summarise
+  yaml_advanced$options$summarize <- summarize
 
   if (!is.null(prefil_met_raw)) {
     yamls_params$prepare_taxa$files$metadata$raw <- fil_met_raw

inst/params/default/weight_annotations.yaml

@@ -190,5 +190,5 @@ options:
   #' Remove ties. BOOLEAN
   remove_ties: no
 
-  #' Summarise results to one row per feature. BOOLEAN
-  summarise: no
+  #' summarize results to one row per feature. BOOLEAN
+  summarize: no

inst/params/prepare_params.yaml

@@ -33,4 +33,4 @@ options:
   #' Filter high confidence candidates only. BOOLEAN
   high_confidence: yes
   #' Summarize all candidates per feature to a single row. BOOLEAN
-  summarise: no
+  summarize: no

inst/params/prepare_params_advanced.yaml

@@ -716,4 +716,4 @@ options:
   remove_ties: no
 
   #' Summarize all candidates per feature to a single row. BOOLEAN
-  summarise: no
+  summarize: no

inst/scripts/docopt/weight_annotations.txt

@@ -2,7 +2,7 @@ You can use this script with the following example:
   Rscript inst/scripts/weight_annotations.R
 
 Usage:
-  weight_annotations.R [--ann-can-fin=<ann-can-fin>] [--ann-ms1only=<ann-ms1only>] [--ann-thr-ms1-bio=<ann-thr-ms1-bio>] [--ann-thr-ms1-che=<ann-thr-ms1-che>] [--ann-thr-ms1-con=<ann-thr-ms1-con>] [--ann-thr-con=<ann-thr-con>] [--fil-ann-fil=<fil-ann-fil>] [--fil-ann-pre-can=<fil-ann-pre-can>] [--fil-ann-pre-for=<fil-ann-pre-for>] [--fil-ann-pro=<fil-ann-pro>] [--fil-lib-sop-mer=<fil-lib-sop-mer>] [--fil-net-spe-edg-pre=<fil-net-spe-edg-pre>] [--fil-met-pre=<fil-met-pre>] [--wei-glo-bio=<wei-glo-bio>] [--wei-glo-che=<wei-glo-che>] [--wei-glo-spe=<wei-glo-spe>] [--wei-bio-01=<wei-bio-01>] [--wei-bio-02=<wei-bio-02>] [--wei-bio-03=<wei-bio-03>] [--wei-bio-04=<wei-bio-04>] [--wei-bio-05=<wei-bio-05>] [--wei-bio-06=<wei-bio-06>] [--wei-bio-07=<wei-bio-07>] [--wei-bio-08=<wei-bio-08>] [--wei-bio-09=<wei-bio-09>] [--wei-bio-10=<wei-bio-10>] [--wei-bio-11=<wei-bio-11>] [--wei-bio-12=<wei-bio-12>] [--wei-bio-13=<wei-bio-13>] [--wei-bio-14=<wei-bio-14>] [--wei-bio-15=<wei-bio-15>] [--wei-che-11=<wei-che-11>] [--wei-che-12=<wei-che-12>] [--wei-che-13=<wei-che-13>]  [--wei-che-14=<wei-che-14>] [--wei-che-21=<wei-che-21>] [--wei-che-22=<wei-che-22>] [--wei-che-23=<wei-che-23>] [--compounds-names=<compounds-names>] [--high-confidence=<high-confidence>] [--remove-ties=<remove-ties>] [--summarise=<summarise>] [--force=<force>]
+  weight_annotations.R [--ann-can-fin=<ann-can-fin>] [--ann-ms1only=<ann-ms1only>] [--ann-thr-ms1-bio=<ann-thr-ms1-bio>] [--ann-thr-ms1-che=<ann-thr-ms1-che>] [--ann-thr-ms1-con=<ann-thr-ms1-con>] [--ann-thr-con=<ann-thr-con>] [--fil-ann-fil=<fil-ann-fil>] [--fil-ann-pre-can=<fil-ann-pre-can>] [--fil-ann-pre-for=<fil-ann-pre-for>] [--fil-ann-pro=<fil-ann-pro>] [--fil-lib-sop-mer=<fil-lib-sop-mer>] [--fil-net-spe-edg-pre=<fil-net-spe-edg-pre>] [--fil-met-pre=<fil-met-pre>] [--wei-glo-bio=<wei-glo-bio>] [--wei-glo-che=<wei-glo-che>] [--wei-glo-spe=<wei-glo-spe>] [--wei-bio-01=<wei-bio-01>] [--wei-bio-02=<wei-bio-02>] [--wei-bio-03=<wei-bio-03>] [--wei-bio-04=<wei-bio-04>] [--wei-bio-05=<wei-bio-05>] [--wei-bio-06=<wei-bio-06>] [--wei-bio-07=<wei-bio-07>] [--wei-bio-08=<wei-bio-08>] [--wei-bio-09=<wei-bio-09>] [--wei-bio-10=<wei-bio-10>] [--wei-bio-11=<wei-bio-11>] [--wei-bio-12=<wei-bio-12>] [--wei-bio-13=<wei-bio-13>] [--wei-bio-14=<wei-bio-14>] [--wei-bio-15=<wei-bio-15>] [--wei-che-11=<wei-che-11>] [--wei-che-12=<wei-che-12>] [--wei-che-13=<wei-che-13>]  [--wei-che-14=<wei-che-14>] [--wei-che-21=<wei-che-21>] [--wei-che-22=<wei-che-22>] [--wei-che-23=<wei-che-23>] [--compounds-names=<compounds-names>] [--high-confidence=<high-confidence>] [--remove-ties=<remove-ties>] [--summarize=<summarize>] [--force=<force>]
 
 Arguments:
   ann-can-fin                Number of final candidates. INTEGER
@@ -52,7 +52,7 @@ Arguments:
   force                      Do not use it. BOOLEAN
   high-confidence            Report high confidence candidates only. BOOLEAN
   remove-ties                Remove ties. BOOLEAN
-  summarise                  Summarize results (1 row per feature). BOOLEAN
+  summarize                  Summarize results (1 row per feature). BOOLEAN
 
 Options:
   -h --help                  Shows this screen.

tests/testthat/_snaps/shinytest2/001.json

@@ -149,7 +149,7 @@
     "org_tax": "",
     "remove_ties": false,
     "save": 1,
-    "summarise": false,
+    "summarize": false,
     "targets-shiny-accordion": "Choose display",
     "targets-shiny-degree_from": 8,
     "targets-shiny-degree_to": 1,

tests/testthat/test-functions.R

@@ -495,7 +495,7 @@ test_that(desc = "Test functions", code = {
   weight_annotations(
     ms1_only = TRUE,
     remove_ties = TRUE,
-    summarise = TRUE,
+    summarize = TRUE,
     candidates_final = 1,
     minimal_ms1_bio = 0.8,
     minimal_ms1_condition = "AND",
@@ -542,7 +542,7 @@ test_that(desc = "Test functions", code = {
     ms_pol = "pos",
     org_tax = "Gentiana lutea",
     hig_con = TRUE,
-    summarise = FALSE
+    summarize = FALSE
   )
 
   ## CLI arguments check
@@ -679,7 +679,7 @@ test_that(desc = "Test functions", code = {
   arguments$force <- TRUE
   arguments$high_confidence <- TRUE
   arguments$remove_ties <- TRUE
-  arguments$summarise <- TRUE
+  arguments$summarize <- TRUE
 
   parse_cli_params(arguments = arguments, parameters = params)
 

vignettes/tima.Rmd

@@ -123,6 +123,6 @@ tima::change_params_small(
   ms_pol = "pos",
   org_tax = "Gentiana lutea",
   hig_con = TRUE,
-  summarise = FALSE
+  summarize = FALSE
 )
 ```