wincowgerDEV · zsteinmetz · Sep 4, 2023 · Sep 1, 2023 · Sep 1, 2023 · Sep 1, 2023
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.0.0
-Date: 2023-09-01 14:53:15 UTC
-SHA: 1924ab057e7bd36723eccdd4649204fef0b2366c
+Version: 1.0.1
+Date: 2023-09-04 13:32:12 UTC
+SHA: 0ae4952382c771ea3f729f1303fd6431182d7d95
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: OpenSpecy
 Type: Package
 Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
 Version: 1.0.1
-Date: 2023-09-01
+Date: 2023-09-04
 Authors@R: c(person("Win", "Cowger", role = c("cre", "aut", "dtc"),
       email = "[email protected]",
       comment = c(ORCID = "0000-0001-9226-3104")),

diff --git a/NEWS.md b/NEWS.md
@@ -3,7 +3,7 @@
 ## Bug Fixes
 
 - Fixed spelling mistakes
-- Reduced example run time for CRAN
+- Reduced example and test run times for CRAN
 
 
 # OpenSpecy 1.0.0

diff --git a/R/OpenSpecy-package.R b/R/OpenSpecy-package.R
@@ -6,11 +6,11 @@
 #' Infrared Spectroscopy.” \emph{Applied Spectroscopy}, \strong{74}(9),
 #' 1167–1183. \doi{10.1177/0003702820923993}.
 #'
-#' Cowger W, Gray A, Christiansen SH, Christiansen SH, Christiansen SH,
-#' De Frond H, Deshpande AD, Hemabessiere L, Lee E, Mill L, et al. (2020).
-#' “Critical Review of Processing and Classification Techniques for Images and
-#' Spectra in Microplastic Research.” \emph{Applied Spectroscopy},
-#' \strong{74}(9), 989–1010. \doi{10.1177/0003702820929064}.
+#' Cowger W, Gray A, Christiansen SH, De Frond H, Deshpande AD, Hemabessiere L,
+#' Lee E, Mill L, et al. (2020). “Critical Review of Processing and
+#' Classification Techniques for Images and Spectra in Microplastic Research.”
+#' \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}.
 #'

diff --git a/R/interactive_plots.R b/R/interactive_plots.R
@@ -76,35 +76,41 @@ plotly_spec.OpenSpecy <- function(x, x2 = NULL,
                                   line2 = list(dash = "dot",
                                                color = "rgb(255,0,0)"),
                                   font = list(color = '#FFFFFF'),
-                                  plot_bgcolor = 'rgb(17, 0, 73)',
+                                  plot_bgcolor = 'rgba(17, 0, 73, 0)',
                                   paper_bgcolor = 'rgb(0, 0, 0)',
                                   ...) {
+  x <- make_rel(x, na.rm = T)
   dt <- cbind(wavenumber = x$wavenumber, x$spectra) |>
     melt(id.vars = "wavenumber", variable.name = "id", value.name = "intensity")
 
-  p <- plot_ly(dt, type = "scatter", mode = "lines", ...) |>
-    add_trace(x = ~wavenumber, y = ~make_rel(intensity, na.rm = T),
-              color = ~id, line = line,
-              name = "x1", showlegend = F) |>
+  p <- plot_ly(dt, type = "scatter", mode = "lines") |>
+    add_trace(x = ~wavenumber,
+              y = ~intensity,
+              split = ~id,
+              line = line,
+              name = "x1",
+              showlegend = F) |>
     layout(xaxis = list(title = "wavenumber [cm<sup>-1</sup>]",
                         autorange = "reversed"),
            yaxis = list(title = "intensity [-]"),
            plot_bgcolor = plot_bgcolor,
            paper_bgcolor = paper_bgcolor,
-           legend = list(orientation = 'h', y = 1.1), font = font)
+           legend = list(orientation = 'h', y = 1.1),
+           font = font)
 
   # Add dummy trace for Your Spectra
   p <- p |>
     add_trace(x = NULL, y = NULL,
               line = line, name = "x1", showlegend = T)
 
   if (!is.null(x2)) {
+    x2 <- make_rel(x2, na.rm = T)
     dt2 <- cbind(wavenumber = x2$wavenumber, x2$spectra) |>
       melt(id.vars = "wavenumber", variable.name = "id", value.name = "intensity")
 
     p <- p |>
-      add_trace(data = dt2, x = ~wavenumber, y = ~make_rel(intensity, na.rm = T),
-                color = ~id, type = "scatter", mode = "lines",
+      add_trace(data = dt2, x = ~wavenumber, y = ~intensity,
+                split = ~id, type = "scatter", mode = "lines",
                 name = "x2",
                 line = line2, showlegend = F)
 
@@ -157,6 +163,9 @@ heatmap_spec.OpenSpecy <- function(x,
   if (!is.null(cor) && !is.null(min_cor))
     plot_z <- ifelse(cor > min_cor, plot_z, NA)
 
+  if(all(is.na(plot_z)))
+      plot_z = rep(-88, length.out = length(plot_z))
+
   p <- plot_ly(...) |>
     add_trace(x = x$metadata$x, y = x$metadata$y, z = if(!is.numeric(plot_z)){as.numeric(as.factor(plot_z))} else{plot_z},
               colorscale = colorscale, type = "heatmap", hoverinfo = 'text',

diff --git a/R/manage_lib.R b/R/manage_lib.R
@@ -56,11 +56,11 @@
 #' Zacharias Steinmetz, Win Cowger
 #'
 #' @references
-#' Cowger W, Gray A, Christiansen SH, Christiansen SH, Christiansen SH,
-#' De Frond H, Deshpande AD, Hemabessiere L, Lee E, Mill L, et al. (2020).
-#' “Critical Review of Processing and Classification Techniques for Images and
-#' Spectra in Microplastic Research.” \emph{Applied Spectroscopy},
-#' \strong{74}(9), 989–1010. \doi{10.1177/0003702820929064}.
+#' Cowger W, Gray A, Christiansen SH, De Frond H, Deshpande AD, Hemabessiere L,
+#' Lee E, Mill L, et al. (2020). “Critical Review of Processing and
+#' Classification Techniques for Images and Spectra in Microplastic Research.”
+#' \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}.
 #'

diff --git a/R/match_spec.R b/R/match_spec.R
@@ -63,13 +63,6 @@
 #'   process_spec()
 #' cor_spec(unknown, test_lib)
 #'
-#' test_lib_extract <- filter_spec(test_lib,
-#'   logic = grepl("polycarbonate", test_lib$metadata$polymer_class,
-#'                 ignore.case = TRUE)
-#' )
-#'
-#' cor_spec(unknown, library = test_lib_extract)
-#'
 #' match_spec(unknown, test_lib, add_library_metadata = "sample_name",
 #'            top_n = 1)
 #'
@@ -154,9 +147,9 @@ match_spec.OpenSpecy <- function(x, library, na.rm = T, top_n = NULL,
   }
 
   if(!is.null(order)) {
-    .r <- NULL
+    .reorder <- NULL
     match <- match(colnames(order$spectra), res$object_id)
-    setorder(res[, .r := order(match)], .r)[, .r := NULL]
+    setorder(res[, .reorder := order(match)], .reorder)[, .reorder := NULL]
   }
 
   return(res)

diff --git a/R/raman_hdpe.R b/R/raman_hdpe.R
@@ -21,11 +21,11 @@
 #' Zacharias Steinmetz, Win Cowger
 #'
 #' @references
-#' Cowger W, Steinmetz Z, Gray A, Christiansen SH, Christiansen SH, Christiansen SH,
-#' De Frond H, Deshpande AD, Hemabessiere L, Lee E, Mill L, et al. (2020).
-#' “Critical Review of Processing and Classification Techniques for Images and
-#' Spectra in Microplastic Research.” \emph{Applied Spectroscopy},
-#' \strong{74}(9), 989–1010. \doi{10.1177/0003702820929064}.
+#' Cowger W, Gray A, Christiansen SH, De Frond H, Deshpande AD, Hemabessiere L,
+#' Lee E, Mill L, et al. (2020). “Critical Review of Processing and
+#' Classification Techniques for Images and Spectra in Microplastic Research.”
+#' \emph{Applied Spectroscopy}, \strong{74}(9), 989–1010.
+#' \doi{10.1177/0003702820929064}.
 #'
 #' @docType data
 #' @keywords data

diff --git a/man/OpenSpecy-package.Rd b/man/OpenSpecy-package.Rd
diff --git a/man/interactive_plots.Rd b/man/interactive_plots.Rd
diff --git a/man/manage_lib.Rd b/man/manage_lib.Rd
diff --git a/man/match_spec.Rd b/man/match_spec.Rd
diff --git a/man/raman_hdpe.Rd b/man/raman_hdpe.Rd
diff --git a/tests/testthat/test-def_features.R b/tests/testthat/test-def_features.R
@@ -43,6 +43,8 @@ test_that("check that particles are identified with all TRUE or FALSE logical ve
 })
 
 test_that("the original spectrum remains unmodified and metadata is amended", {
+  skip_on_cran()
+
   map <- read_extdata("CA_tiny_map.zip") |> read_any()
 
   id_map <- def_features(map,ifelse(map$metadata$x == 1,
@@ -60,6 +62,8 @@ test_that("the original spectrum remains unmodified and metadata is amended", {
 })
 
 test_that("collapse particles returns expected values", {
+  skip_on_cran()
+
   particles <- ifelse(map$metadata$y == 1, "particleA", "particleB")
   id_map <- def_features(map, particles)
   expect_true(check_OpenSpecy(id_map))

diff --git a/tests/testthat/test-interactive_plots.R b/tests/testthat/test-interactive_plots.R
@@ -6,7 +6,7 @@ test_that("plotly_spec() handles input errors correctly", {
 })
 
 test_that("plotly_spec() generates 'plotly' object", {
-  plotly_spec(raman_hdpe, select = 1) |>
+  plotly_spec(raman_hdpe) |>
     expect_silent() |>
     expect_s3_class("plotly")
 })
@@ -21,8 +21,13 @@ test_that("heatmap_spec() generates 'plotly' object", {
     expect_s3_class("plotly")
 })
 
+test_that("heatmap_spec() can handle all NA", {
+  heatmap_spec(map, z = map$metadata$y, sn = map$metadata$y, min_sn = 100) |>
+    expect_silent()
+})
+
 test_that("interactive_plot() generates 'plotly' object", {
-  interactive_plot(map, x2 = raman_hdpe, select = 2) |>
-    suppressWarnings() |>
+  interactive_plot(map, x2 = raman_hdpe, select = 2:3) |>
+    expect_silent() |>
     expect_s3_class("plotly")
 })
diff --git a/tests/testthat/test-match_spec.R b/tests/testthat/test-match_spec.R
@@ -9,11 +9,6 @@ preproc <- conform_spec(unknown, range = test_lib$wavenumber,
                         res = spec_res(test_lib)) |>
   process_spec(smooth_intens = T, make_rel = T)
 
-# Create a subset of test_lib for filtering
-test_lib_extract <- filter_spec(
-  test_lib, logic = test_lib$metadata$polymer_class == "polycarbonates"
-  )
-
 test_that("ai_classify() handles input errors correctly", {
   ai_classify(1:1000) |> expect_error()
 })
@@ -43,7 +38,6 @@ test_that("match_spec() handles input errors correctly", {
   match_spec(1:1000) |> expect_error()
 })
 
-# Match_spec function
 test_that("match_spec() returns correct structure", {
   matches <- match_spec(x = preproc, library = test_lib, na.rm = T, top_n = 5,
                         add_library_metadata = "sample_name",
@@ -74,6 +68,8 @@ test_that("cor_spec() handles input errors correctly", {
 
 # Write the tests for cor_spec function
 test_that("cor_spec() returns a data.table with correct columns", {
+  skip_on_cran()
+
   matches <- cor_spec(preproc, library = test_lib) |>
     expect_silent()
 

diff --git a/tests/testthat/test-share_spec.R b/tests/testthat/test-share_spec.R
@@ -7,6 +7,9 @@ data("raman_hdpe")
 wo_meta <- raman_hdpe
 wo_meta$metadata$spectrum_identity <- NULL
 
+wo_sid <- raman_hdpe
+wo_sid$metadata$session_id <- NULL
+
 test_that("share_text() works locally", {
   share_spec(raman_hdpe, file = read_extdata("raman_hdpe.csv"), share = tmp) |>
     expect_message()
@@ -22,6 +25,9 @@ test_that("share_text() works locally", {
   share_spec(wo_meta, share = tmp) |>
     expect_message() |>
     expect_warning()
+
+  share_spec(wo_sid, share = tmp) |>
+    expect_error()
 })
 
 test_that("share_text() uploads to the cloud", {
@@ -36,6 +42,14 @@ test_that("share_text() uploads to the cloud", {
                s3_secret = Sys.getenv("AWS_SECRET_ACCESS_KEY"),
                s3_region = "us-east-2", s3_bucket = "openspecy")) |>
     expect_message()
+
+  share_spec(raman_hdpe, file = read_extdata("raman_hdpe.csv"), share = "cloud",
+             credentials = list(
+               s3_region = "us-east-2", s3_bucket = "openspecy")) |>
+    expect_error()
+
+  share_spec(raman_hdpe, file = read_extdata("raman_hdpe.csv"), share = "cloud") |>
+    expect_error()
 })
 
 # Tidy up

diff --git a/vignettes/advanced.Rmd b/vignettes/advanced.Rmd
@@ -160,10 +160,10 @@ Process for Identification of Microplastics Based on Fourier Transform Infrared
 Spectroscopy.” *Applied Spectroscopy*, **74**(9), 1167–1183. doi:
 [10.1177/0003702820923993](https://doi.org/10.1177/0003702820923993).
 
-Cowger W, Gray A, Christiansen SH, Christiansen SH, Christiansen SH, De Frond H,
-Deshpande AD, Hemabessiere L, Lee E, Mill L, et al. (2020). “Critical Review of
-Processing and Classification Techniques for Images and Spectra in Microplastic
-Research.” *Applied Spectroscopy*, **74**(9), 989–1010. doi:
+Cowger W, Gray A, Christiansen SH, De Frond H, Deshpande AD, Hemabessiere L, Lee
+E, Mill L, et al. (2020). “Critical Review of Processing and Classification
+Techniques for Images and Spectra in Microplastic Research.” *Applied
+Spectroscopy*, **74**(9), 989–1010. doi:
 [10.1177/0003702820929064](https://doi.org/10.1177/0003702820929064).
 
 Cowger W, Steinmetz Z, Gray A, Munno K, Lynch J, Hapich H, Primpke S,

diff --git a/vignettes/app.Rmd b/vignettes/app.Rmd
@@ -406,10 +406,10 @@ Process for Identification of Microplastics Based on Fourier Transform Infrared
 Spectroscopy.” *Applied Spectroscopy*, **74**(9), 1167–1183. doi:
 [10.1177/0003702820923993](https://doi.org/10.1177/0003702820923993).
 
-Cowger W, Gray A, Christiansen SH, Christiansen SH, Christiansen SH, De Frond H,
-Deshpande AD, Hemabessiere L, Lee E, Mill L, et al. (2020). “Critical Review of
-Processing and Classification Techniques for Images and Spectra in Microplastic
-Research.” *Applied Spectroscopy*, **74**(9), 989–1010. doi:
+Cowger W, Gray A, Christiansen SH, De Frond H, Deshpande AD, Hemabessiere L, Lee
+E, Mill L, et al. (2020). “Critical Review of Processing and Classification
+Techniques for Images and Spectra in Microplastic Research.” *Applied
+Spectroscopy*, **74**(9), 989–1010. doi:
 [10.1177/0003702820929064](https://doi.org/10.1177/0003702820929064).
 
 Cowger W, Steinmetz Z, Gray A, Munno K, Lynch J, Hapich H, Primpke S,