Various bug fixes (#147)

* Add `showlegend` option
* Add dots option for `plotly_spec()`
* Fix bug with `match_spec()`
* Improve syntax
* Fix NA as top by removing NA, also faster logic.
* Force col_id to equal names of the spectra
* Add contributors
* Prepare CRAN submission

---------

Co-authored-by: Zacharias Steinmetz <git@zsteinmetz.de>

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.0.3
-Date: 2023-09-13 15:19:30 UTC
-SHA: 2ff9c1a9be7e2e3c99747f8f65302223b7951830
+Version: 1.0.4
+Date: 2023-10-01 19:33:04 UTC
+SHA: 54ff4c6288617c5b1af0705bcba2278f911a4b0d

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: OpenSpecy
 Type: Package
 Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
-Version: 1.0.3
-Date: 2023-09-13
+Version: 1.0.4
+Date: 2023-10-01
 Authors@R: c(person("Win", "Cowger", role = c("cre", "aut", "dtc"),
       email = "wincowger@gmail.com",
       comment = c(ORCID = "0000-0001-9226-3104")),
@@ -11,13 +11,13 @@ Authors@R: c(person("Win", "Cowger", role = c("cre", "aut", "dtc"),
       comment = c(ORCID = "0000-0001-6675-5033")),
     person("Nick", "Leong", role = c("aut"),
       comment = c(ORCID = "0009-0008-3313-4132")),
-    person("Andrea","Faltynkova", role = c("aut", "dtc"),
+    person("Andrea", "Faltynkova", role = c("aut", "dtc"),
       comment = c(ORCID = "0000-0003-2523-3137")),
     person("Andrew B", "Gray", role = c("ctb"),
       comment = c(ORCID = "0000-0003-2252-7367")), 
     person("Hannah", "Hapich", role = c("ctb"),
       comment = c(ORCID = "0000-0003-0000-6632")),
-    person("Jennifer", "Lynch", role = c("ctb","dtc"),
+    person("Jennifer", "Lynch", role = c("ctb", "dtc"),
       comment = c(ORCID = "0000-0003-3572-8782")),
     person("Hannah", "De Frond", role = c("ctb", "dtc"),
       comment = c(ORCID = "0000-0003-1199-0727")),
@@ -42,6 +42,14 @@ Authors@R: c(person("Win", "Cowger", role = c("cre", "aut", "dtc"),
       comment = c(ORCID = "0000-0003-1211-9351")),
     person("Samiksha", "Singh", role = c("ctb")),
     person("Katherine", "Lasdin", role = c("ctb")),
+    person("Cristiane", "Vidal", role = c("ctb"), 
+      comment = c(ORCID = "0000-0001-6363-9475")),
+    person("Clare", "Murphy-Hagan", role = c("ctb"), 
+      comment = c(ORCID = "0009-0009-9629-2856")),
+    person("Philipp", "Baumann", role = c("ctb"),
+      email = "info@spectral-cockpit.space",
+      comment = c(ORCID = "0000-0002-3194-8975")),
+    person("Pierre", "Roudier", role = c("ctb")),
     person("National Renewable Energy Laboratory", role = c("fnd")), 
     person("Possibility Lab", role = c("fnd")))
 Description: Raman and (FT)IR spectral analysis tool for plastic particles and

NEWS.md

@@ -1,3 +1,16 @@
+# OpenSpecy 1.0.4
+
+## Minor Improvements
+
+- More contributors
+- `showlegend` argument for interactive plots
+
+## Bug Fixes
+
+- Fixes a fatal error in `match_spec()` probably causing incorrect
+  identifications
+
+
 # OpenSpecy 1.0.3
 
 ## Minor Improvements

R/OpenSpecy-package.R

@@ -12,7 +12,7 @@
 #' \emph{Applied Spectroscopy}, \strong{74}(9), 989–1010.
 #' \doi{10.1177/0003702820929064}.
 #'
-#' Cowger, W (2021). “Library data.” \emph{OSF}. \doi{10.17605/OSF.IO/X7DPZ}.
+#' Cowger, W (2023). “Library data.” \emph{OSF}. \doi{10.17605/OSF.IO/X7DPZ}.
 #'
 #' Cowger W, Steinmetz Z, Gray A, Munno K, Lynch J, Hapich H, Primpke S,
 #' De Frond H, Rochman C, Herodotou O (2021). “Microplastic Spectral

R/as_OpenSpecy.R

@@ -182,13 +182,13 @@ as_OpenSpecy.data.frame <- function(x, colnames = list(wavenumber = NULL,
   if (is.null(colnames$wavenumber)) {
     if (any(grepl("wav", ignore.case = T, names(x)))) {
       if (length(grep("wav", ignore.case = T, names(x))) > 1L)
-        warning("Ambiguous column names: taking 'wavenumber' data from the",
+        message("Ambiguous column names: taking 'wavenumber' data from the",
                 " first column; use 'colnames' to supply user-defined columns",
                 call. = F)
       wavenumber <- x[[grep("wav", ignore.case = T, names(x))[1L]]]
       wn <- names(x)[grep("wav", ignore.case = T, names(x))]
     } else {
-      warning("Ambiguous column names: taking 'wavenumber' data from the",
+      message("Ambiguous column names: taking 'wavenumber' data from the",
               " first column; use 'colnames' to supply user-defined columns",
               call. = F)
       wavenumber <- x[[1L]]
@@ -205,7 +205,7 @@ as_OpenSpecy.data.frame <- function(x, colnames = list(wavenumber = NULL,
       spectra <- x[, grepl("(transmit.*)|(reflect.*)|(abs.*)|(intens.*)",
                            ignore.case = T, names(x)), with = F]
     } else {
-      warning("Ambiguous column names: taking 'spectra' data from all but the",
+      message("Ambiguous column names: taking 'spectra' data from all but the",
               " 'wavenumber' column; use 'colnames' to supply user-defined",
               " columns", call. = F)
       spectra <- x[, -wn, with = F]
@@ -274,7 +274,7 @@ as_OpenSpecy.default <- function(x, spectra,
 
   if (inherits(coords, "character")) {
     obj$metadata <- do.call(coords, list(ncol(obj$spectra)))
-  } else if (inherits(coords, c("data.frame", "list")) &&
+  } else if(inherits(coords, c("data.frame", "list")) &&
              all(is.element(c("x", "y"), names(coords)))) {
     obj$metadata <- as.data.table(coords)
   } else if(is.null(coords)){
@@ -286,14 +286,13 @@ as_OpenSpecy.default <- function(x, spectra,
   if (!is.null(metadata)) {
     if (inherits(metadata, c("data.frame", "list"))) {
       obj$metadata <- cbind(obj$metadata, as.data.table(metadata))
+      obj$metadata$col_id <- names(obj$spectra)
       if(session_id)
         obj$metadata$session_id <- paste(digest(Sys.info()),
                                          digest(sessionInfo()),
                                          sep = "/")
       if(!c("file_id") %in% names(obj$metadata))
-        obj$metadata$file_id = digest(obj[c("wavenumber", "spectra")])
-      if(!c("col_id") %in% names(obj$metadata))
-          obj$metadata$col_id = names(obj$spectra)
+        obj$metadata$file_id <- digest(obj[c("wavenumber", "spectra")])
     } else {
       stop("inconsistent input for 'metadata'", call. = F)
     }