id stringlengths 16 145 | text stringlengths 1 179k | title stringclasses 1
value |
|---|---|---|
R_base_tools/R_micropan_30_0.txt | [ RDocumentation ](/)
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# translate: From nucleotides to proteins
## Description
Translates nucleotide strings (... | |
R_base_tools/R_micropan_12_0.txt | [ RDocumentation ](/)
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# negTruncLogLike: Negative truncated log-likelihood function
## Description
The negativ... | |
R_base_tools/R_base_all_188_0.txt | [ RDocumentation ](/)
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# system2: Invoke a System Command
## Description
` system2 ` invokes the OS command specifi... | |
R_base_tools/R_base_all_250_0.txt | [ RDocumentation ](/)
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# NA: ‘Not Available’ / Missing Values
## Description
` NA ` is a logical constant of length... | |
R_base_tools/R_base_all_161_1.txt | itespace character is a . are taken as blank lines (allowing for multi-paragraph field values).
5. Records are separated by one or more empty (i.e., whitespace only) lines.
6. Individual lines may not be arbitrarily long; prior to R 3.0.2 the length limit was approximately 8191 bytes per line.
Note that `... | |
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# date: System Date and Time
## Description
Returns a character string of the current system... | |
R_base_tools/R_base_all_224_1.txt | ple_in_workspace)
# NOT RUN {
eval(2 ^ 2 ^ 3)
mEx <- expression(2^2^3); mEx; 1 + eval(mEx)
eval({ xx <- pi; xx^2}) ; xx
a <- 3 ; aa <- 4 ; evalq(evalq(a+b+aa, list(a = 1)), list(b = 5)) # == 10
a <- 3 ; aa <- 4 ; evalq(evalq(a+b+aa, -1), list(b = 5)) # == 12
ev <-... | |
R_base_tools/R_base_all_180_1.txt | (https://app.datacamp.com/workspace/preview?_tag=rdocs&rdocsPath=packages%2Fbase%2Fversions%2F3.6.2%2Ftopics%2Fdump&utm_source=r-docs&utm_medium=docs&utm_term=dump&utm_content=run_example_in_workspace)
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# files: File Manipulation
## Description
These functions provide a low-level interface to t... | |
R_base_tools/R_base_all_114_2.txt | cribed in the system's man page. As PCRE has been feature-frozen
for some time (essentially 2012), the man pages at [
http://www.pcre.org/original/doc/html/
](http://www.pcre.org/original/doc/html/) should be a good match.)
Perl regular expressions can be computed byte-by-byte or (UTF-8) character-by-
character: the l... | |
R_base_tools/R_base_all_416_1.txt | ompute the positions of the split matches (note that we cannot call
## strsplit() on x with match data from s).
m <- gregexpr(", *", s)
## And finally extract the non-matched parts.
regmatches(x, m, invert = TRUE)
# }
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# dput: Write an Object to a File or Recreate it
## Description
Writes an ASCII text represe... | |
R_base_tools/R_base_all_90_2.txt | orry about escaping embedded quotes.)
` command ` must be an executable (extensions ` .exe ` , ` .com ` ) or a batch
file (extensions ` .cmd ` and ` .bat ` ): these extensions are tried in turn
if none is supplied. This means that redirection, pipes, DOS internal
commands, … cannot be used: see ` [ shell
](/link/shell... | |
R_base_tools/R_base_all_39_1.txt | erval(tt, X)
tt[it < 1 | it >= N] # only first and last are outside range(X)
## 'left.open = TRUE' means "mirroring" :
N <- length(v)
stopifnot(identical(
findInterval( x, v, left.open=TRUE) ,
N - findInterval(-x, -v[N:1])))
# }
Run the code abo... | |
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# xzcompress: xz (un)compress a file
## Description
xz (un)compress a file
## Usage
... | |
R_base_tools/stringr.html4_9_0.txt | ## Coercion
We discussed coercian briefly in the second lab, but it is worth reviewing
briefly here as this is a very common problem in data analysis. | |
R_base_tools/R_base_all_145_1.txt | ors encountered) and the result is an
ordered factor if and only if all the components were ordered factors. (The
last point differs from S-PLUS.) Old-style categories (integer vectors with
levels) are promoted to factors.
Note that for result column ` j ` , ` [ factor
](/link/factor?package=base&version=3.6.2) (., ex... | |
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# heaps: Heaps law estimate
## Description
Estimating if a pan-genome is open or closed ... | |
R_base_tools/strings.html6_12_0.txt | * ` str_to_upper(string, locale = "en") ` 1 : Convert strings to upper case.
str_to_upper(sentences)
* ` str_to_title(string, locale = "en") ` 1 : Convert strings to title case. Also ` str_to_setence() ` .
str_to_title(sentences) | |
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# isSymmetric: Test if a Matrix or other Object is Symmetric (Hermitian)
## Description
Gene... | |
R_base_tools/stringr.html4_12_0.txt | Often, it’s the presence of a single character that can cause issues,
contaminating a dataset. Consider this data.frame, for example, in which both
of our intended numeric columns are corrupted:
dat <- read.csv("https://remiller1450.github.io/data/char_dom.csv")
dat
## ID messy_x mes... | |
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# stop: Stop Function Execution
## Description
` stop ` stops execution of the current expre... | |
R_base_tools/strings.html7_17_0.txt | Use the ` sep ` argument to control how they’re separated:
str_c("x", "y", sep = ", ")
#> [1] "x, y" | |
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# funprog: Common Higher-Order Functions in Functional Programming Languages
## Description
... | |
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# Memory: Memory Available for Data Storage
## Description
How R manages its workspace.
#... | |
R_base_tools/strings.html6_29_0.txt | Some characters cannot be directly represented in an R string. These must be
represented as special characters , sequences of characters that have a
specific meaning, e.g. ` \\ ` represents ` \ ` , ` \" ` represents ` " ` , and
` \n ` represents a new line. Run ` ?"'" ` to see a complete list.
Because of this, whene... | |
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# svd: Singular Value Decomposition of a Matrix
## Description
Compute the singular-value de... | |
R_base_tools/R_base_all_330_2.txt | elper functions to
enable standard output and standard error units in ` gfortran ` when executing
external code via ` system ` and ` system2 ` . By default, these units are
disabled by the Windows profile when running inside RGui.
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R_base_tools/R_base_all_360_4.txt | content=run_example_in_workspace)
# NOT RUN {
## locale-specific version of date()
format(Sys.time(), "%a %b %d %X %Y %Z")
## time to sub-second accuracy (if supported by the OS)
format(Sys.time(), "%H:%M:%OS3")
## read in date info in format 'ddmmmyyyy'
## This will giv... | |
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# by: Apply a Function to a Data Frame Split by Factors
## Description
Function ` by ` is an... | |
R_base_tools/R_base_all_158_1.txt | rdcoded to ` "showAttributes" ` , which
is the default currently; ` deparseCtrl = "all" ` may be preferable, when
strict back compatibility is not of importance.
chdir
logical; if ` TRUE ` and ` file ` is a pathname, the R working directory is
temporarily changed to the directory containing ` file ` for evaluating.... | |
R_base_tools/R_base_all_199_2.txt | on and it causes performance overhead when loading packages.
` keep.source ` :
When ` TRUE ` , the source code for functions (newly defined or loaded) is
stored internally allowing comments to be kept in the right places. Retrieve
the source by printing or using ` deparse(fn, control = "useSource") ` .
The def... | |
R_base_tools/R_base_all_360_1.txt | version=3.6.2) ` ):
positive values are East of the meridian. Although there have been time zones
with offsets like 00:09:21 (Paris in 1900), and 00:44:30 (Liberia until 1972),
offsets are usually treated as whole numbers of minutes, and are most often
seen in RFC 5322 email headers in forms like ` -0800 ` (e.g., used ... | |
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# col: Column Indexes
## Description
Returns a matrix of integers indicating their column nu... | |
R_base_tools/R_base_all_209_1.txt | _source=r-docs&utm_medium=docs&utm_term=Quotes&utm_content=run_example_in_workspace)
# NOT RUN {
<!-- %% NOTE: Quote the \ even "once more" ! -->
# }
# NOT RUN {
'single quotes can be used more-or-less interchangeably'
"with double quotes to create character vectors"
## Sing... | |
R_base_tools/R_base_all_199_7.txt |
a non-empty character string or an R function that sets the default text
editor, e.g., for ` [ edit ](/link/edit?package=base&version=3.6.2) ` and ` [
file.edit ](/link/file.edit?package=base&version=3.6.2) ` . Set from the
environment variable ` EDITOR ` on UNIX, or if unset ` VISUAL ` or ` vi ` . As
a string ... | |
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# basename: Manipulate File Paths
## Description
` basename ` removes all of the path up to ... | |
R_base_tools/strings.html7_127_0.txt | * ` dir() ` lists all the files in a directory. The ` pattern ` argument takes a regular expression and only returns file names that match the pattern. For example, you can find all the R Markdown files in the current directory with:
head(dir(pattern = "\\.Rmd$"))
#> [1] "communicate-plots.Rmd" "co... | |
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# hmmerScan: Scanning a profile Hidden Markov Model database
## Description
Scanning FAS... | |
R_base_tools/R_base_all_268_1.txt | c)
readChar(zz, nchar(x)+3) # need to read the terminator explicitly
close(zz)
unlink(zzfil)
# }
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R_base_tools/R_base_all_333_1.txt | ](/link/dyn.load?package=base&version=3.6.2) ` for comments
about diagnostic messages which may be seen on Windows.
` library.dynam.unload ` is designed for use in ` [ .onUnload
](/link/.onUnload?package=base&version=3.6.2) ` : it unloads the DLL and
updates the value of ` .dynLibs() `
` .dynLibs ` is used for getti... | |
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# binomixEstimate: Binomial mixture model estimates
## Description
Fits binomial mixture... | |
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# char.expand: Expand a String with Respect to a Target Table
## Description
Seeks a unique ... | |
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# strsplit: Split the Elements of a Character Vector
## Description
Split the elements of a ... | |
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# load: Reload Saved Datasets
## Description
Reload datasets written with the function ` sav... | |
R_base_tools/stringr.html4_33_0.txt |
s <- "cat.dog"
str_split(s, "\\.")
## [[1]]
## [1] "cat" "dog"
This one is a bit strange in that it returns a ` list ` object instead of a
character vector. This is because unlike the other functions we have seen so
far, ` str_split ` will split every instance of the pattern. Return... | |
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# readRenviron: Set Environment Variables from a File
## Description
Read as file such as ` ... | |
R_base_tools/strings.html6_9_0.txt | * ` str_count(string, pattern) ` : Count the number of matches in a string.
str_count(fruit, "a")
## Mutate Strings | |
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# detach: Detach Objects from the Search Path
## Description
Detach a database, i.e., remove... | |
R_base_tools/R_base_all_122_2.txt | low
on the Windows version of this help page. What happens on a FAT or SMB-mounted
file system is OS-specific.)
File arguments with a marked encoding (see ` [ Encoding
](/link/Encoding?package=base&version=3.6.2) ` are if possible translated to
the native encoding, except on Windows where Unicode file operations are u... | |
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# libcurlVersion: Report Version of libcurl
## Description
Report version of ` libcurl ` in ... | |
R_base_tools/R_base_all_347_4.txt | ply(regmatches(s, gregexpr(pattern, s)),
function(e) regmatches(e, regexec(pattern, e)))
# }
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# abbreviate: Abbreviate Strings
## Description
Abbreviate strings to at least ` minlength `... | |
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# parse: Parse R Expressions
## Description
` parse() ` returns the parsed but unevaluated e... | |
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# Sys.time: Get Current Date and Time
## Description
` Sys.time ` and ` Sys.Date ` returns t... | |
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# log: Logarithms and Exponentials
## Description
` log ` computes logarithms, by default na... | |
R_base_tools/R_base_all_107_1.txt | IXct" ` will validate times in the selected time zone. One issue is what
happens at transitions to and from DST, for example in the UK
as.POSIXct(strptime("2011-03-27 01:30:00", "%Y-%m-%d %H:%M:%S"))
as.POSIXct(strptime("2010-10-31 01:30:00", "%Y-%m-%d %H:%M:%S"))
are respectively invalid (the ... | |
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# seq.Date: Generate Regular Sequences of Dates
## Description
The method for ` [ seq ](/lin... | |
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# with: Evaluate an Expression in a Data Environment
## Description
Evaluate an R expressi... | |
R_base_tools/R_base_all_199_9.txt | t
getOption("width") == options()$width # the latter needs more memory
options(digits = 15)
pi
# set the editor, and save previous value
old.o <- options(editor = "nedit")
old.o
options(check.bounds = TRUE, warn = 1)
x <- NULL; x[4] <- "yes" # gives a warning
opti... | |
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# list2env: From A List, Build or Add To an Environment
## Description
From a _named_ ` [ li... | |
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# plotScores: Plotting scores and loadings in a ` Panpca ` object
## Description
Creates... | |
R_base_tools/stringr.html4_44_0.txt |
## Find all the vowels
str_view("apple", "[aeiou]")
## [1] │ <a>ppl<e>
### Meta-characters | |
R_base_tools/strings.html7_80_0.txt | It’s natural to use ` str_count() ` with ` mutate() ` :
df %>%
mutate(
vowels = str_count(word, "[aeiou]"),
consonants = str_count(word, "[^aeiou]")
)
#> # A tibble: 980 × 4
#> word i vowels consonants
#> <chr> <int> <int> <int>
#> 1 a ... | |
R_base_tools/R_base_all_26_1.txt | = c(4:1, 2:5) - 5i)
x[3, ] <- NA; x[4, 2] <- NA
rowSums(x); colSums(x); rowMeans(x); colMeans(x)
rowSums(x, na.rm = TRUE); colSums(x, na.rm = TRUE)
rowMeans(x, na.rm = TRUE); colMeans(x, na.rm = TRUE)
# }
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# fluidity: Computing genomic fluidity for a pan-genome
## Description
Computes the geno... | |
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# solve: Solve a System of Equations
## Description
This generic function solves the equatio... | |
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# t: Matrix Transpose
## Description
Given a matrix or ` [ data.frame
](/link/data.frame?pac... | |
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# Extract.data.frame: Extract or Replace Parts of a Data Frame
## Description
Extract or rep... | |
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R_base_tools/stringr.html4_45_0.txt | Meta-characters are characters that have a particular meaning in regex
language, meaning that they cannot be used to literally express a string
value. We have seen one of these already in ` R ` , with the period ` . `
which has to be escaped . In regex, the period is used to indicate a
“wildcard” character, meaning i... | |
R_base_tools/strings.html6_48_0.txt | * Edit this page
* Report an issue
| |
R_base_tools/R_base_all_383_1.txt | < total)
if (!keep.me)
cat("handler removing itself\n")
# return
keep.me
}
}
# add the callback that will work for
# 4 top-level tasks and then remove itself.
n <- addTaskCallback(times(4))
# now remove it, assuming it is still first in the lis... | |
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# delayedAssign: Delay Evaluation
## Description
` delayedAssign ` creates a _promise_ to ev... | |
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# Extremes: Maxima and Minima
## Description
Returns the (regular or **p** arallel) maxima a... | |
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# pos.to.env: Convert Positions in the Search Path to Environments
## Description
Returns th... | |
R_base_tools/R_base_all_240_1.txt | lers
are checked, starting with the most recently established ones, for one
matching the class of the condition. When several handlers are supplied in a
single ` tryCatch ` then the first one is considered more recent than the
second. If a handler is found then control is transferred to the ` tryCatch `
call that estab... | |
R_base_tools/strings.html7_87_0.txt | Imagine we want to find all sentences that contain a colour. We first create a
vector of colour names, and then turn it into a single regular expression:
colours <- c("red", "orange", "yellow", "green", "blue", "purple")
colour_match <- str_c(colours, collapse = "|")
colour_match
#> [1] "red|... | |
R_base_tools/R_base_all_94_1.txt | References
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) _The New S Language_ .
Wadsworth & Brooks/Cole.
## See Also
` [ double ](/link/double?package=base&version=3.6.2) ` , ` [ integer
](/link/integer?package=base&version=3.6.2) ` , ` [ storage.mode
](/link/storage.mode?package=base&version=3.6.2) ` .
#... | |
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# NULL: The Null Object
## Description
` NULL ` represents the null object in R : it is a ... | |
R_base_tools/R_base_all_91_1.txt | _The New S Language_ .
Wadsworth & Brooks/Cole.
## See Also
` [ aperm ](/link/aperm?package=base&version=3.6.2) ` , ` [ matrix
](/link/matrix?package=base&version=3.6.2) ` , ` [ dim
](/link/dim?package=base&version=3.6.2) ` , ` [ dimnames
](/link/dimnames?package=base&version=3.6.2) ` .
## Examples
[ Run this co... | |
R_base_tools/stringr.html3_24_0.txt | * Locale-sensitive character matching, with ` coll() `
* Text boundary analysis with ` boundary() ` . | |
R_base_tools/R_base_all_127_1.txt | I'm brave") && `I'm brave` &&
identical(.Platform$OS.type, "unix") && grepl("^/tmp/", tempdir())) {
cat("Current tempdir(): ", tempdir(), "\n")
cat("Removing it :", file.remove(tempdir()),
"; dir.exists(tempdir()):", dir.exists(tempdir()), "\n")
cat("and now tempdir(check = TRUE) :",... | |
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# list.files: List the Files in a Directory/Folder
## Description
These functions produce a ... | |
R_base_tools/strings.html6_45_0.txt | More groups string
(type this) | regexp
(to mean this) | matches
(which matches this) | example
(the result is the same as ` ref("abba") ` ) | example output
(highlighted characters are in <>)
---|---|---|---|---
` \\1 ` | ` \1 ` (etc.) | first () group, etc. | ` ref("(a)(b)\\2\\1") ` | ... | |
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# path.expand: Expand File Paths
## Description
Expand a path name, for example by replacing... | |
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# is.single: Is an Object of Single Precision Type?
## Description
` is.single ` reports an ... | |
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# difftime: Time Intervals / Differences
## Description
Time intervals creation, printing, a... | |
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# array: Multi-way Arrays
## Description
Creates or tests for arrays.
## Usage
... | |
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# Sys.glob: Wildcard Expansion on File Paths
## Description
Function to do wildcard expansio... | |
R_base_tools/R_base_all_34_1.txt | l. = FALSE)
testit() ## no call
suppressWarnings(warning("testit"))
# }
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# taskCallbackNames: Query the Names of the Current Internal Top-Level Task
Callbacks
## Desc... | |
R_base_tools/R_base_all_138_1.txt | ormat.POSIXct?package=base&version=3.6.2) ` ) and for
other classes such as ` format.octmode ` and ` format.dist ` .
` format.data.frame ` formats the data frame column by column, applying the
appropriate method of ` format ` for each column. Methods for columns are
often similar to ` as.character ` but offer more con... | |
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# all.equal: Test if Two Objects are (Nearly) Equal
## Description
` all.equal(x, y) ` is a ... | |
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# interactive: Is R Running Interactively?
## Description
Return ` TRUE ` when R is being ... | |
R_base_tools/strings.html7_72_0.txt | This is a somewhat pathological example (because email addresses are actually
surprisingly complex), but is used in real code. See the stackoverflow
discussion at http://stackoverflow.com/a/201378 for more details.
Don’t forget that you’re in a programming language and you have other tools at
your disposal. Instead ... | |
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# Deprecated: Marking Objects as Deprecated
## Description
When an object is about to be rem... | |
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# print: Print Values
## Description
` print ` prints its argument and returns it _invisibly... | |
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# plot.Binomix: Plotting and printing ` Binomix ` objects
## Description
Generic functio... |
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