Merge pull request #95 from orichters/smallfix

allow as.quitte + read.quitte + read.snapshot to read rds files

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '623091040'
+ValidationKey: '623603320'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'quitte: Bits and pieces of code to use with quitte-style data frames'
-version: 0.3133.0
-date-released: '2024-06-14'
+version: 0.3134.0
+date-released: '2024-06-24'
 abstract: A collection of functions for easily dealing with quitte-style data frames,
   doing multi-model comparisons and plots.
 authors:

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: quitte
 Title: Bits and pieces of code to use with quitte-style data frames
-Version: 0.3133.0
-Date: 2024-06-14
+Version: 0.3134.0
+Date: 2024-06-24
 Authors@R: c(
     person("Michaja", "Pehl", , "[email protected]", role = c("aut", "cre")),
     person("Nico", "Bauer", , "[email protected]", role = "aut"),

R/as.quitte.R

@@ -32,7 +32,7 @@ as.quitte <- function(x, periodClass = "integer", addNA = FALSE, na.rm = FALSE)
 
 #' @export
 as.quitte.character <- function(x, periodClass = "integer", addNA = FALSE, na.rm = FALSE) { # nolint
-    if (all(file.exists(x) & grepl("\\.(mif|csv|xlsx?)$", x)))
+    if (all(file.exists(x) & grepl("\\.(mif|csv|rds|xlsx?)$", x)))
         return(as.quitte(read.quitte(x, sep = NULL),
                          periodClass = periodClass, addNA = addNA, na.rm = na.rm))
     stop(

R/read.quitte.R

@@ -1,9 +1,9 @@
-#' Read IAMC-style .csv or .xlsx files
+#' Read IAMC-style .csv or .xlsx files, or object from rds file.
 #'
-#' Reads IAMC-style .csv or .xlsx files into a quitte data frame.
+#' Reads IAMC-style .csv or .xlsx files or object from rds file into a quitte data frame.
 #'
 #' @md
-#' @param file Path of IAMC-style .csv or xlsx. file or vector of paths to read.
+#' @param file Path of IAMC-style .csv, .xlsx, or rds file or vector of paths to read.
 #' @param sep Column separator, defaults to ";" in read_mif_header().
 #' @param quote Quote characters, empty by default.
 #' @param na.strings Entries to interpret as NA; defaults to
@@ -113,6 +113,10 @@ read.quitte <- function(file,
             }
             return(filter.function(as.quitte(data)))
         }
+        if (grepl("\\.rds$", f)) {
+            return(filter.function(as.quitte(readRDS(f))))
+        }
+
         # Check the header for correct names, periods all in one block and no
         # additional columns after the periods
 

R/read.snapshot.R

@@ -1,12 +1,12 @@
 #' Reads IAMC-style .csv or .xlsx files obtained as a IIASA snapshot into a quitte data frame,
-#' allowing to filter the loaded data. If head, tail and grep are on your system, a pre-filtering
-#' improves performance.
+#' or data from rds file, allowing to filter the loaded data.
+#' If head, tail and grep are on your system, a pre-filtering improves performance for csv files.
 #'
 #' @md
 #' @param file Path of single IAMC-style .csv/.mif file
 #' @param keep list with quitte columns as names and data points that should be kept.
-#' If head, tail and grep are available, this list is used to extract the data before reading it
-#' into R. The more you restrict the data here, the faster the data is read.
+#' If head, tail and grep are available and a csv/mif file is read, this list is used to extract the
+#' data before reading it into R. The more you restrict the data here, the faster the data is read.
 #' @param filter.function A function used to filter data during read, see read.quitte description.
 #' This allows for more complex filtering, but no performance-enhancing pre-filtering using grep is used.
 #' The 'keep' list and the 'filter.function' can be combined.
@@ -38,7 +38,7 @@ read.snapshot <- function(file, keep = list(), filter.function = identity) {
 
   # temporary file
   tmpfile <- tempfile(pattern = "data", fileext = gsub("^.*\\.", ".", basename(file)))
-  if (length(setdiff(names(keep), "period")) > 0 && !grepl("\\.xlsx?$", file)) {
+  if (length(setdiff(names(keep), "period")) > 0 && !grepl("\\.(rds|xlsx?)$", file)) {
     # check whether system commands are supported
     testcommand <- c("grep", "head", "tail")
     notavailable <- Sys.which(testcommand) == ""

README.md

@@ -1,6 +1,6 @@
 # Bits and pieces of code to use with quitte-style data frames
 
-R package **quitte**, version **0.3133.0**
+R package **quitte**, version **0.3134.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/quitte)](https://cran.r-project.org/package=quitte)  [![R build status](https://github.com/pik-piam/quitte/workflows/check/badge.svg)](https://github.com/pik-piam/quitte/actions) [![codecov](https://codecov.io/gh/pik-piam/quitte/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/quitte) [![r-universe](https://pik-piam.r-universe.dev/badges/quitte)](https://pik-piam.r-universe.dev/builds)
 
@@ -47,7 +47,7 @@ In case of questions / problems please contact Michaja Pehl <michaja.pehl@pik-po
 
 To cite package **quitte** in publications use:
 
-Pehl M, Bauer N, Hilaire J, Levesque A, Luderer G, Schultes A, Dietrich J, Richters O (2024). _quitte: Bits and pieces of code to use with quitte-style data frames_. R package version 0.3133.0, <https://github.com/pik-piam/quitte>.
+Pehl M, Bauer N, Hilaire J, Levesque A, Luderer G, Schultes A, Dietrich J, Richters O (2024). _quitte: Bits and pieces of code to use with quitte-style data frames_. R package version 0.3134.0, <URL: https://github.com/pik-piam/quitte>.
 
 A BibTeX entry for LaTeX users is
 
@@ -56,7 +56,7 @@ A BibTeX entry for LaTeX users is
   title = {quitte: Bits and pieces of code to use with quitte-style data frames},
   author = {Michaja Pehl and Nico Bauer and Jérôme Hilaire and Antoine Levesque and Gunnar Luderer and Anselm Schultes and Jan Philipp Dietrich and Oliver Richters},
   year = {2024},
-  note = {R package version 0.3133.0},
+  note = {R package version 0.3134.0},
   url = {https://github.com/pik-piam/quitte},
 }
 ```

tests/testthat/test-as.quitte.R

@@ -94,3 +94,12 @@ test_that(
     expect_equal(nrow(as.quitte(NULL)), 0)
   }
 )
+
+test_that(
+  'as.quitte works on rds files',
+  {
+    rdsfile <- tempfile(pattern = "report", fileext = ".rds")
+    saveRDS(quitte_example_data, rdsfile)
+    expect_identical(as.quitte(rdsfile), quitte_example_data)
+  }
+)