Update documentation

Author: smnnlt

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,

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_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

man/spiro.Rd

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

spiro.Rproj

@@ -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_raw.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,

tests/testthat/test_spiro_plot.R

@@ -32,7 +32,6 @@ library(spiro)
 file <- spiro_example("zan_gxt")
 gxt_data <- spiro(file)
 gxt_data
-
 ```
 
 ## Stepwise summary with `spiro_summary()`
@@ -69,7 +68,7 @@ You can individually select and combine panels of the 9-Panel Plot by setting th
 
 ```{r spiro_plot-select, fig.width = 7, fig.height = 4}
 # Plot only V-Slope (Panel 5) and VO2/VCO2 over time (Panel 3)
-spiro_plot(data, which = c(5,3))
+spiro_plot(data, which = c(5, 3))
 ```
 
 Data over time (Panel 1,2,3,6,8,9) will be displayed smoothed, as determined via the `smooth` argument. The other panels (4,5,7) use the raw breath-by-breath data for visualization. 
@@ -79,7 +78,7 @@ You can control the appearance of the plots in `spiro_plot()`. Use the `style_ar
 ```{r spiro_plot-style-1, fig.width = 10, fig.height = 8, message = FALSE}
 # Change size of points, width of lines and color of VO2 points/lines
 spiro_plot(
-  data, 
+  data,
   style_args = list(
     size = 1,
     linewidth = 2,
@@ -93,8 +92,8 @@ Use the `base_size` argument to change the plot base size. You can pass other st
 ```{r spiro_plot-style-2, fig.width = 10, fig.height = 8, message = FALSE}
 # Change base size and axis label font
 spiro_plot(
-  data, 
-  base_size = 9, 
+  data,
+  base_size = 9,
   style_args = list(
     axis.title = ggplot2::element_text(face = "italic", colour = "blue")
   )