v 0.2.2

DESCRIPTION

@@ -25,7 +25,7 @@ BugReports: https://github.com/ropensci/spiro/issues
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports: 
     ggplot2,
     xml2,

NEWS.md

@@ -1,11 +1,21 @@
-spiro (development version)
+spiro 0.2.2 (2025-02-17)
 ===========================
 
-* Fix bug in ZAN import when several dead space parameters are given
-* Fix bug in ZAN import when meta data contained special characters
+### NEW FEATURES
+
+* Add support for Vyntus files in English (thanks to Michael Beaven)
+
+### MINOR IMPROVEMENTS
+
 * Improve import for German Cosmed files
 * Update spiro_plot() to recent changes in ggplot2 version 3.5
 
+### BUG FIXES
+
+* Fix bug in ZAN import when several dead space parameters are given
+* Fix bug in ZAN import when meta data contained special characters
+
+
 
 spiro 0.2.1 (2023-08-14)
 ===========================

R/spiro.R

@@ -24,8 +24,8 @@
 #'   English or German language)
 #'   \item \strong{COSMED} (\code{.xlsx} or \code{.xls} files, in English or
 #'   German language)
-#'   \item \strong{Vyntus} (\code{.txt} files in French, German or Norwegian
-#'   language)
+#'   \item \strong{Vyntus} (\code{.txt} files in English, French, German or
+#'   Norwegian language)
 #'   \item \strong{ZAN} (\code{.dat} files in German language, usually with
 #'   names in the form of \code{"EXEDxxx"})
 #' }

R/spiro_get.R

@@ -58,7 +58,7 @@ spiro_get <- function(file, device = NULL, anonymize = TRUE) {
 #' @noRd
 guess_device <- function(file) {
   if (grepl("\\.xls$", file, ignore.case = TRUE) ||
-      grepl("\\.xlsx$", file, ignore.case = TRUE)) { # Excel file
+    grepl("\\.xlsx$", file, ignore.case = TRUE)) { # Excel file
     # Read head of the Excel file
     head <- readxl::read_excel(file, range = "A1:B8", col_names = c("V1", "V2"))
 
@@ -96,7 +96,7 @@ guess_device <- function(file) {
     # files from ZAN devices usually start with a line "[person]"
     if (any(head == "[person]")) {
       device <- "zan"
-    } else if (any(head == "Tid" | head == "Temps" | head == "Zeit")) {
+    } else if (any(head == "Tid" | head == "Temps" | head == "Zeit" | head == "Time" | head == "t-ph" | head == "t")) {
       device <- "vyntus"
     } else {
       device <- "none"
@@ -423,7 +423,7 @@ spiro_get_vyntus <- function(file) {
   head_rm <- as.data.frame(apply(head, 2, trimws))
 
   colstart <- which(
-    head_rm == "Tid" | head_rm == "Temps" | head_rm == "Zeit",
+    head_rm == "Tid" | head_rm == "Temps" | head_rm == "Zeit" | head_rm == "Time" | head_rm == "t-ph" | head_rm == "t",
     arr.ind = TRUE
   )
 
@@ -439,15 +439,15 @@ spiro_get_vyntus <- function(file) {
 
   df <- data.frame(
     time = to_seconds(
-      get_data(data_mod, c("Tid", "Temps", "Zeit"), as_numeric = FALSE)
+      get_data(data_mod, c("Tid", "Time", "Temps", "Zeit", "t.ph", "t"), as_numeric = FALSE)
     ),
     VO2 = get_data(data_mod, "V.O2"),
     VCO2 = get_data(data_mod, "V.CO2"),
     RR = get_data(data_mod, c("BF", "FR")),
     VT = get_data(data_mod, "VTex"),
     VE = get_data(data_mod, c("V.E", "VeSTPD")),
-    HR = get_data(data_mod, c("HF", "FC")),
-    load = get_data(data_mod, c("Last", "Vitesse", "Watt")),
+    HR = get_data(data_mod, c("HR", "HF", "FC")),
+    load = get_data(data_mod, c("Load", "Last", "Vitesse", "Watt")),
     PetO2 = get_data(data_mod, "PETO2") * 7.50062, # convert from kPa to mmHg
     PetCO2 = get_data(data_mod, "PETCO2") * 7.50062 # convert from kPa to mmHg
   )

R/spiro_plot.R

@@ -816,14 +816,14 @@ vert_lines <- function(data, plot = TRUE) {
       if (any(ptcl$type == "load")) {
         t1i <- min(which(ptcl$type == "load"))
         if (t1i >= 2) { # requires measurements prior to first load
-          t1 <- cs[t1i-1]
+          t1 <- cs[t1i - 1]
         }
       }
       # time point 2: first warm-up load
       if (any(ptcl$type == "warm up")) {
         t2i <- min(which(ptcl$type == "warm up"))
         if (t2i >= 2) { # requires measurements prior to first load
-          t2 <- cs[t2i-1]
+          t2 <- cs[t2i - 1]
         }
       }
       # time point 3: last load

R/spiro_raw.R

@@ -61,8 +61,10 @@ spiro_raw.spiro <- function(data, device = NULL, anonymize = TRUE) {
   }
   if (!is.null(device)) {
     warning(
-      paste0("'device' argument in spiro_raw() is ignored when called for an ",
-             " spiro object")
+      paste0(
+        "'device' argument in spiro_raw() is ignored when called for an ",
+        " spiro object"
+      )
     )
   }
   # rewrite meta data attribute

README.Rmd

@@ -101,7 +101,7 @@ spiro_plot(gxt_data)
 
 ## Citation
 
-```{r citation}
+```{r citation, collapse=FALSE, comment=""}
 citation("spiro")
 ```
 
@@ -114,7 +114,7 @@ additionally offers functions for analyzing VO2 kinetics.
 ## Acknowledgment
 
 The following persons contributed to this package by providing raw data files, reviewing code and/or suggesting features:
-Daniel Appelhans, James Hunter, Virgile Lecoultre, Sebastian Mühlenhoff, Manuel Ramon, Anton Schiffer, Yannick Schwarz, Adrian Swoboda, Andreas Wagner.
+Daniel Appelhans, Michael Beaven, James Hunter, Virgile Lecoultre, Sebastian Mühlenhoff, Manuel Ramon, Anton Schiffer, Yannick Schwarz, Adrian Swoboda, Andreas Wagner.
 
 ## Contributing
 

README.md

@@ -135,28 +135,28 @@ spiro_plot(gxt_data)
 
 ``` r
 citation("spiro")
-#> 
-#> To cite spiro in publications use:
-#> 
-#>   Simon Nolte (2023). spiro: An R package for analyzing data from
-#>   cardiopulmonary exercise testing. Journal of Open Source Software,
-#>   8(81), 5089, https://doi.org/10.21105/joss.05089
-#> 
-#> A BibTeX entry for LaTeX users is
-#> 
-#>   @Article{,
-#>     title = {spiro: An R package for analyzing data from cardiopulmonary exercise testing},
-#>     author = {Simon Nolte},
-#>     year = {2023},
-#>     volume = {8},
-#>     number = {81},
-#>     pages = {5089},
-#>     journal = {Journal of Open Source Software},
-#>     url = {https://joss.theoj.org/papers/10.21105/joss.05089},
-#>     doi = {10.21105/joss.05089},
-#>   }
 ```
 
+    To cite spiro in publications use:
+
+      Simon Nolte (2023). spiro: An R package for analyzing data from
+      cardiopulmonary exercise testing. Journal of Open Source Software,
+      8(81), 5089, https://doi.org/10.21105/joss.05089
+
+    A BibTeX entry for LaTeX users is
+
+      @Article{,
+        title = {spiro: An R package for analyzing data from cardiopulmonary exercise testing},
+        author = {Simon Nolte},
+        year = {2023},
+        volume = {8},
+        number = {81},
+        pages = {5089},
+        journal = {Journal of Open Source Software},
+        url = {https://joss.theoj.org/papers/10.21105/joss.05089},
+        doi = {10.21105/joss.05089},
+      }
+
 ## Related Work
 
 The [whippr](https://github.com/fmmattioni/whippr) package offers a
@@ -167,8 +167,9 @@ testing. It additionally offers functions for analyzing VO2 kinetics.
 
 The following persons contributed to this package by providing raw data
 files, reviewing code and/or suggesting features: Daniel Appelhans,
-James Hunter, Virgile Lecoultre, Sebastian Mühlenhoff, Manuel Ramon,
-Anton Schiffer, Yannick Schwarz, Adrian Swoboda, Andreas Wagner.
+Michael Beaven, James Hunter, Virgile Lecoultre, Sebastian Mühlenhoff,
+Manuel Ramon, Anton Schiffer, Yannick Schwarz, Adrian Swoboda, Andreas
+Wagner.
 
 ## Contributing
 

spiro.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 3872f95e-6eeb-4ae0-a43f-272208c7e164
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

tests/testthat/test-spiro_raw.R

@@ -19,4 +19,3 @@ test_that("overriding of anonymization works", {
 test_that("device argument is ignored for spiro class method", {
   expect_warning(spiro_raw(spiro(file), device = "cortex"))
 })
-

tests/testthat/test_spiro_plot.R

@@ -13,7 +13,8 @@ p_color <- spiro_plot(
   style_args = list(
     color_VO2 = "black", color_VCO2 = "purple", color_RER = "pink",
     color_VE = "royalblue", color_VT = "orange", color_HR = "lightblue",
-    color_pulse = "grey")
+    color_pulse = "grey"
+  )
 )
 p_theme <- spiro_plot(
   data,

vignettes/import_processing.Rmd

@@ -41,7 +41,6 @@ library(spiro)
 file <- spiro_example("zan_gxt")
 
 spiro(file)
-
 ```
 
 `spiro()` will return interpolated data for the following parameters:
@@ -98,7 +97,7 @@ The `spiro` package supports different metabolic carts. The metabolic cart a dat
 
 * **CORTEX** (`"cortex"`): .xlsx, .xls or .xml files in English or German language
 * **COSMED** (`"cosmed"`): .xlsx or .xls files in English or German language
-* **VYNTUS** (`"vyntus"`): .txt files (tab-separated) in French, German or Norwegian language
+* **VYNTUS** (`"vyntus"`): .txt files (tab-separated) in English, French, German or Norwegian language
 * **ZAN** (`"zan"`): .dat files, usually with the name "EXED*" in German language
 
 To only import the raw data without further processing (such as interpolation, exercise protocol guessing,...) use the function `spiro_raw()`:
@@ -127,7 +126,7 @@ protocol guess after a `spiro()` call, access the `"protocol"` attribute.
 
 ```{r protocol}
 s <- spiro(file)
-attr(s,"protocol")
+attr(s, "protocol")
 ```
 
 ### Protocol setting {#protocol-set}
@@ -144,8 +143,8 @@ frame with `add_protocol()`.
 ```{r set_protocol_manual}
 # manually setting a test protocol
 pt <- set_protocol_manual(
-  duration = c(60,300,30,300,30,300,30,300,30,300,30,300,30,300,30,300,30,300),
-  load = c(0,3,0,3.2,0,3.4,0,3.6,0,3.8,0,4,0,4.2,0,4.4,0,4.6)
+  duration = c(60, 300, 30, 300, 30, 300, 30, 300, 30, 300, 30, 300, 30, 300, 30, 300, 30, 300),
+  load = c(0, 3, 0, 3.2, 0, 3.4, 0, 3.6, 0, 3.8, 0, 4, 0, 4.2, 0, 4.4, 0, 4.6)
 )
 
 # attach protocol within spiro call
@@ -161,78 +160,82 @@ With `set_protocol()` a protocol can be defined without specifying every single
 ```{r set_protocol-variables, echo=FALSE}
 ar2 <- arrow(length = unit(0.1, "inches"), type = "closed", ends = "both")
 path <- data.frame(
-  x = c(0,0.1,0.1,0.3,0.3,0.32,0.32,0.42,0.42,0.44,0.44,0.54,0.54,0.56,0.56,
-        0.66,0.66,0.68,0.68,0.78,0.78,0.8,0.8,0.9,0.9,0.95),
-  y = c(0,0,0.2,0.2,0,0,0.4,0.4,0,0,0.5,0.5,0,0,0.6,0.6,0,0,
-        0.7,0.7,0,0,0.8,0.8,0,0),
+  x = c(
+    0, 0.1, 0.1, 0.3, 0.3, 0.32, 0.32, 0.42, 0.42, 0.44, 0.44, 0.54, 0.54, 0.56, 0.56,
+    0.66, 0.66, 0.68, 0.68, 0.78, 0.78, 0.8, 0.8, 0.9, 0.9, 0.95
+  ),
+  y = c(
+    0, 0, 0.2, 0.2, 0, 0, 0.4, 0.4, 0, 0, 0.5, 0.5, 0, 0, 0.6, 0.6, 0, 0,
+    0.7, 0.7, 0, 0, 0.8, 0.8, 0, 0
+  ),
   type = factor(
-    c("pre","wu","wu","wu","wu",rep("load",21)),
-    levels = c("pre","wu","load")
+    c("pre", "wu", "wu", "wu", "wu", rep("load", 21)),
+    levels = c("pre", "wu", "load")
   )
 )
 ggplot() +
   (if (utils::packageVersion("ggplot2") >= "3.4") {
     list(
       geom_segment(
         aes(x = 0, xend = 0.95, y = 0, yend = 0),
-        colour = "grey", 
+        colour = "grey",
         linewidth = 1
       ),
       geom_path(
-        aes(x = x, y = y, colour = type), 
-        data = path, 
-        linewidth = 1, 
-        group = TRUE, 
+        aes(x = x, y = y, colour = type),
+        data = path,
+        linewidth = 1,
+        group = TRUE,
         show.legend = FALSE
       )
     )
   } else {
     list(
       geom_segment(
         aes(x = 0, xend = 0.95, y = 0, yend = 0),
-        colour = "grey", 
+        colour = "grey",
         size = 1
       ),
       geom_path(
-        aes(x = x, y = y, colour = type), 
-        data = path, 
-        size = 1, 
-        group = TRUE, 
+        aes(x = x, y = y, colour = type),
+        data = path,
+        size = 1,
+        group = TRUE,
         show.legend = FALSE
       )
     )
   }) +
   annotate(
-    "text", 
-    x = c(0.03,0.05,0.05,0.05,0.03), y = c(0.98,0.91,0.84,0.77,0.70), 
+    "text",
+    x = c(0.03, 0.05, 0.05, 0.05, 0.03), y = c(0.98, 0.91, 0.84, 0.77, 0.70),
     label = c(
       "set_protocol(",
       "pt_pre(duration),",
       "pt_wu(duration, load, rest),",
       "pt_steps(duration, load, increment, count, rest)",
       ")"
-    ), 
+    ),
     hjust = "left", vjust = "top",
     colour = c("black", "#d55e00", "#009e73", dsblue, "black"),
     size = 4.5
   ) +
   scale_x_continuous(
-    limits = c(-0.02,1), 
-    expand = expansion(0,0), 
+    limits = c(-0.02, 1),
+    expand = expansion(0, 0),
     breaks = NULL
   ) +
   scale_y_continuous(
-    limits = c(-0.15,1), 
-    expand = expansion(0,0), 
+    limits = c(-0.15, 1),
+    expand = expansion(0, 0),
     breaks = NULL
   ) +
-  scale_colour_manual(values = c("#d55e00","#009e73",dsblue)) +
+  scale_colour_manual(values = c("#d55e00", "#009e73", dsblue)) +
   labs(x = "time", y = "load") +
   theme_minimal()
 ```
 
 ```{r set_protocol}
-set_protocol(pt_pre(60), pt_wu(300,80), pt_steps(180,100,25,6,30))
+set_protocol(pt_pre(60), pt_wu(300, 80), pt_steps(180, 100, 25, 6, 30))
 ```
 
 ## Modify body mass {#bodymass}
@@ -244,9 +247,8 @@ The `spiro` package calculates parameters relative to body mass. Per default `sp
 s <- spiro(file, bodymass = 68.3)
 
 # set body mass using `add_weight()`
-t <- spiro(file) 
+t <- spiro(file)
 u <- add_bodymass(t, 68.3)
-
 ```
 
 ## Work with external heart rate data {#heart-rate}