Chapter 5 Basic R

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Save & Load R objects

save(..., f_name) and saveRDS()

save() When loaded the named object is restored to the current environment (in general use this is the global environment — the workspace) with the same name it had when saved.

save writes an external representation of R objects to the specified file. The objects can be read back from the file at a later date by using the function load or attach (or data in some cases).

save(..., list = character(), file = stop("'file' must be specified"), ascii = FALSE, version = NULL, envir = parent.frame(), compress = isTRUE(!ascii), compression_level, eval.promises = TRUE, precheck = TRUE)

  • ... The names of the objects to be saved (as symbols or character strings).
  • list A character vector containing the names of objects to be saved.
    • The names of the objects specified either as symbols (or character strings) in ... or as a character vector in list are used to look up the objects from environment envir.
  • file the name of the file where the data will be saved.

saveRDS() doesn’t save the both the object and its name it just saves a representation of the object. As a result, the saved object can be loaded into a named object within R that is different from the name it had when originally serialized.

Serialization is the process of converting a data structure or object state into a format that can be stored (for example, in a file or memory buffer, or transmitted across a network connection link) and “resurrected” later in the same or another computer environment.

saveRDS works only for saving a single R object, save() can save multiple R objects in one file. A workaround for saveRDS is to save all target objects in a single R object (e.g., in a list), and then use saveRDS() to save it at once.

datalist = list(mtcars = mtcars, pressure=pressure)
saveRDS(datalist, "twodatasets.RDS")
rm(list=ls())

datalist = readRDS("twodatasets.RDS")
datalist

Load R objects

load(f_name) to load .rda file.

readRDS(f_name) to load .rds file.

Naming conventions:

  • rda and rds for selected objects
  • .RData for all objectes in your workspace
  • The file extensions are up to you; you can use whatever file extensions you want.

An example

> require(mgcv)
Loading required package: mgcv
This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
> mod <- gam(Ozone ~ s(Wind), data = airquality, method = "REML")
> mod

Family: gaussian
Link function: identity

Formula:
Ozone ~ s(Wind)

Estimated degrees of freedom:
3.529  total = 4.529002

REML score: 529.4881
> save(mod, file = "mymodel.rda")
> ls()
[1] "mod"
> load(file = "mymodel.rda")
> ls()
[1] "mod"


> ls()
[1] "mod"
> saveRDS(mod, "mymodel.rds")
> mod2 <- readRDS("mymodel.rds")
> ls()
[1] "mod"  "mod2"
> identical(mod, mod2, ignore.environment = TRUE)
[1] TRUE

Save figures in a list

p_list <- list(p_ano=p_ano, p_tr=p_tr)
# p_list[[name]] <- p_obj
p_list[[1]]

f_name <- paste0(fig_dir, sprintf("trend_analysis/image_list_%s.rds", con_name))
# saveRDS(p_list, f_name)

# plot in a panel grid
p_allCON <- plot_grid(plotlist=p_list, align="vh", labels=sprintf("(%s)", letters[1:length(p_list)]), hjust=-1, nrow=3, label_size=12)
p_allCON