updates to version 1.0.7

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.0.6
-Date: 2023-11-25 12:56:02 UTC
+Version: 1.0.7
+Date: 2024-03-11 22:12:54 UTC
 SHA: 11f89935f939a7a7430eceaba1fda06445134587

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: OpenSpecy
 Type: Package
 Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
-Version: 1.0.6
-Date: 2023-11-25
+Version: 1.0.7
+Date: 2024-03-11
 Authors@R: c(person("Win", "Cowger", role = c("cre", "aut", "dtc"),
       email = "[email protected]",
       comment = c(ORCID = "0000-0001-9226-3104")),
@@ -13,6 +13,8 @@ Authors@R: c(person("Win", "Cowger", role = c("cre", "aut", "dtc"),
       comment = c(ORCID = "0009-0008-3313-4132")),
     person("Andrea", "Faltynkova", role = c("aut", "dtc"),
       comment = c(ORCID = "0000-0003-2523-3137")),
+    person("Hannah", "Sherrod", role = c("aut"),
+      comment = c(ORCID = "0009-0001-0497-8693")),
     person("Andrew B", "Gray", role = c("ctb"),
       comment = c(ORCID = "0000-0003-2252-7367")), 
     person("Hannah", "Hapich", role = c("ctb"),

NAMESPACE

@@ -173,6 +173,7 @@ importFrom(signal,sgolay)
 importFrom(stats,approx)
 importFrom(stats,cor)
 importFrom(stats,dist)
+importFrom(stats, IQR, quantile)
 importFrom(stats,lm)
 importFrom(stats,median)
 importFrom(stats,model.frame)

NEWS.md

@@ -1,3 +1,10 @@
+# OpenSpecy 1.0.7
+
+## Minor Improvements
+
+- Modified `manage_na.R`
+- Added to NAMESPACE
+
 # OpenSpecy 1.0.6
 
 ## Minor Improvements

R/manage_na.R

@@ -18,11 +18,11 @@
 #'
 #' @examples
 #' manage_na(c(NA, -1, NA, 1, 10))
-#' manage_na(c(NA, -1, NA, 1, 10), lead_tail_only = F)
-#' manage_na(c(NA, 0, NA, 1, 10), lead_tail_only = F, ig_zero = T)
+#' manage_na(c(NA, -1, NA, 1, 10), lead_tail_only = FALSE)
+#' manage_na(c(NA, 0, NA, 1, 10), lead_tail_only = FALSE, ig_zero = TRUE)
 #' data(raman_hdpe)
 #' raman_hdpe$spectra[[1]][1:10] <- NA
-#' manage_na(raman_hdpe, fun = make_rel) #would normally return all NA without na.rm = T but doesn't here. 
+#' manage_na(raman_hdpe, fun = make_rel) #would normally return all NA without na.rm = TRUE but doesn't here. 
 #' manage_na(raman_hdpe, type = "remove") #will remove the first 10 values we set to NA
 #' 
 #' @author
@@ -40,26 +40,26 @@ manage_na <- function(x, ...) {
 
 #' @rdname manage_na
 #' @export
-manage_na.default <- function(x, lead_tail_only = T, ig_zero = F, ...) {
+manage_na.default <- function(x, lead_tail_only = TRUE, ig_zero = FALSE, ...) {
 
     if(all(is.na(x))) stop("All intensity values are NA, cannot remove or ignore with manage na.")
 
     if(lead_tail_only){
         na_positions <- logical(length(x))
         if(is.na(x[1])){
-            criteria = T
+            criteria = TRUE
             y = 1
             while(criteria){
-                if(is.na(x[y])|(ig_zero & x[y] == 0)) na_positions[y] <- T 
+                if(is.na(x[y])|(ig_zero & x[y] == 0)) na_positions[y] <- TRUE 
                 y = y + 1
                 criteria = is.na(x[y])|(ig_zero & x[y] == 0) 
             }
         }
         if(is.na(x[length(x)])){
-            criteria = T
+            criteria = TRUE
             y = length(x)
             while(criteria){
-                if(is.na(x[y])|(ig_zero & x[y] == 0)) na_positions[y] <- T 
+                if(is.na(x[y])|(ig_zero & x[y] == 0)) na_positions[y] <- TRUE 
                 y = y - 1
                 criteria = is.na(x[y])|(ig_zero & x[y] == 0) 
             }
@@ -74,7 +74,7 @@ manage_na.default <- function(x, lead_tail_only = T, ig_zero = F, ...) {
 
 #' @rdname manage_na
 #' @export
-manage_na.OpenSpecy <- function(x, lead_tail_only = T, ig_zero = F, fun, type = "ignore", ...) {
+manage_na.OpenSpecy <- function(x, lead_tail_only = TRUE, ig_zero = FALSE, fun, type = "ignore", ...) {
 
     consistent <- x$spectra[, lapply(.SD, manage_na, 
                                lead_tail_only = lead_tail_only, 

tests/testthat/test-manage_na.R

@@ -3,9 +3,9 @@
 test_that("manage_na works as expected", {
     manage_na(c(NA, -1, NA, 1, 10)) |> 
         expect_identical(c(TRUE, FALSE, FALSE, FALSE, FALSE))
-    manage_na(c(NA, -1, NA, 1, 10), lead_tail_only = F) |> 
+    manage_na(c(NA, -1, NA, 1, 10), lead_tail_only = FALSE) |> 
         expect_identical(c(TRUE, FALSE, TRUE, FALSE, FALSE))
-    manage_na(c(NA, 0, NA, 1, 10), lead_tail_only = F, ig_zero = T) |>
+    manage_na(c(NA, 0, NA, 1, 10), lead_tail_only = FALSE, ig_zero = TRUE) |>
         expect_identical(c(TRUE, TRUE, TRUE, FALSE, FALSE))
 
     data(raman_hdpe)