id stringlengths 16 145 | text stringlengths 1 179k | title stringclasses 1
value |
|---|---|---|
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# panPrep: Preparing FASTA files for pan-genomics
## Description
Preparing a FASTA file ... | |
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# all: Are All Values True?
## Description
Given a set of logical vectors, are all of the va... | |
R_base_tools/strings.html7_118_0.txt | * ` dotall = TRUE ` allows ` . ` to match everything, including ` \n ` .
There are three other functions you can use instead of ` regex() ` : | |
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# comment: Query or Set a ` "comment" ` Attribute
## Description
These functions set and que... | |
R_base_tools/stringr.html4_60_0.txt |
s <- c("a1", "b2", "c3", "d4")
# Anything BUT 1 or 3
str_subset(s, pattern = "[^13]")
## [1] "a1" "b2" "c3" "d4"
str_view(s, pattern = "[^13]")
## [1] │ <a>1
## [2] │ <b><2>
## [3] │ <c>3
## [4] │ <d><4>
By playing around a bit, we can mo... | |
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# readFasta and writeFasta: Read and write biological sequence files.
## Description
Rea... | |
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# conditions: Condition Handling and Recovery
## Description
These functions provide a mecha... | |
R_base_tools/strings.html7_78_0.txt | Typically, however, your strings will be one column of a data frame, and
you’ll want to use filter instead:
df <- tibble(
word = words,
i = seq_along(word)
)
df %>%
filter(str_detect(word, "x$"))
#> # A tibble: 4 × 2
#> word i
#> <chr> <int>
#> 1 box ... | |
R_base_tools/stringr.html3_4_0.txt |
str_length("abc")
#> [1] 3
This is now equivalent to the base R function ` nchar() ` . Previously it was
needed to work around issues with ` nchar() ` such as the fact that it
returned 2 for ` nchar(NA) ` . This has been fixed as of R 3.3.0, so it is no
longer so important. | |
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# R.Version: Version Information
## Description
` R.Version() ` provides detailed informatio... | |
R_base_tools/stringr.html3_27_0.txt |
str_detect(a1, fixed(a2))
#> [1] FALSE
str_detect(a1, coll(a2))
#> [1] TRUE
#### Collation search | |
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# force: Force Evaluation of an Argument
## Description
Forces the evaluation of a function ... | |
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# ns-load: Loading and Unloading Name Spaces
## Description
Functions to load and unload nam... | |
R_base_tools/R_base_all_90_3.txt | ed by [ DataCamp ](https://www.datacamp.com/)
| |
R_base_tools/R_base_all_360_3.txt | cepted.
` %z `
Signed offset in hours and minutes from UTC, so ` -0800 ` is 8 hours behind
UTC. Values up to ` +1400 ` are accepted. (Standard only for output. For input
R currently supports it on all platforms.)
` %Z `
(Output only.) Time zone abbreviation as a character string (empty if not
available... | |
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# Mpneumoniae: Data sets for the _Mycoplasma pneumoniae_ casestudy
## Description
This d... | |
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# integer: Integer Vectors
## Description
Creates or tests for objects of type ` "integer" `... | |
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# norm: Compute the Norm of a Matrix
## Description
Computes a matrix norm of ` x ` using LA... | |
R_base_tools/strings.html7_108_0.txt |
"a|b|c|d" %>%
str_split("\\|") %>%
.[[1]]
#> [1] "a" "b" "c" "d"
Otherwise, like the other stringr functions that return a list, you can use `
simplify = TRUE ` to return a matrix: | |
R_base_tools/R_base_all_294_1.txt | stopifnot(all(rx[,1] == rx))
# }
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R_base_tools/R_base_all_93_1.txt | S and R < 2.5.0. For
compatibility with S, integer values of double vectors are deparsed with a
trailing decimal point. Backticks are not used.
` "hexNumeric" ` :
Real and finite complex numbers are output in "%a" format as binary
fractions (coded as hexadecimal: see ` [ sprintf
](/link/sprintf?package=base... | |
R_base_tools/R_base_all_334_1.txt | o zero: First,
the mean absolute difference of the two numerical vectors is computed. If this
is smaller than ` tolerance ` or not finite, absolute differences are used,
otherwise relative differences scaled by the mean absolute ` target ` value.
Note that these comparisons are computed only for those vector elements w... | |
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# rep: Replicate Elements of Vectors and Lists
## Description
` rep ` replicates the values ... | |
R_base_tools/R_base_all_52_3.txt | ant to see more:
trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15g)\n", ncp))),
print = FALSE) # <- not showing typical extra
power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:
untrace(pt)
# }
# NOT RUN {
<!-- %% methods is loaded when neede... | |
R_base_tools/strings.html7_79_0.txt | A variation on ` str_detect() ` is ` str_count() ` : rather than a simple
yes or no, it tells you how many matches there are in a string:
x <- c("apple", "banana", "pear")
str_count(x, "a")
#> [1] 1 3 1
# On average, how many vowels per word?
mean(str_count(words, "[aeiou]"))
#... | |
R_base_tools/strings.html7_56_0.txt | ### 14.3.4 Repetition
The next step up in power involves controlling how many times a pattern
matches: | |
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# cut.POSIXt: Convert a Date or Date-Time Object to a Factor
## Description
Method for ` [ c... | |
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# matrix: Matrices
## Description
` matrix ` creates a matrix from the given set of values.
... | |
R_base_tools/R_base_all_52_1.txt | he
other of those values sets the state. If the tracing state is ` FALSE ` , none
of the trace actions will actually occur (used, for example, by debugging
functions to shut off tracing during debugging).
expr, msg
arguments to the support function ` .doTrace ` , calls to which are inserted
into the modified function... | |
R_base_tools/strings.html7_68_0.txt | 3. Contain one letter repeated in at least three places (e.g. “eleven” contains three “e”s.)
## 14.4 Tools | |
R_base_tools/stringr.html4_31_0.txt |
val <- 1:10
str_c("The mean value of val is: ", mean(val))
## [1] "The mean value of val is: 5.5"
` str_c ` can also be used to turn a character vector into a single string by
using the ` collapse ` argument | |
R_base_tools/R_base_all_239_1.txt | assign("Global.res", x^2, envir = .GlobalEnv)
innerf(x+1)
}
myf(3)
Global.res # 16
a <- 1:4
assign("a[1]", 2)
a[1] == 2 # FALSE
get("a[1]") == 2 # TRUE
# }
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# nlevels: The Number of Levels of a Factor
## Description
Return the number of levels which... | |
R_base_tools/R_micropan_25_1.txt | ndividually. In ` [ plotScores
](/link/plotScores?package=micropan&version=1.0) ` you can again supply a
vector of colors, and name every element with a GID-tag to make certain they
are used correctly. In ` [ plotLoadings
](/link/plotLoadings?package=micropan&version=1.0) ` you can supply a vector
of colors, but you mu... | |
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# find.package: Find Packages
## Description
Find the paths to one or more packages.
## Us... | |
R_base_tools/strings.html7_63_0.txt | 1. Start with three consonants.
2. Have three or more vowels in a row.
3. Have two or more vowel-consonant pairs in a row.
4. Solve the beginner regexp crosswords at https://regexcrossword.com/challenges/beginner .
### 14.3.5 Grouping and backreferences | |
R_base_tools/stringr.html3_23_0.txt | * Regular expressions, the default, as shown above, and described in ` vignette("regular-expressions") ` .
* Fixed bytewise matching, with ` fixed() ` . | |
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# sample: Random Samples and Permutations
## Description
` sample ` takes a sample of the sp... | |
R_base_tools/R_base_all_347_3.txt | 4
txt[i]
## Double all 'a' or 'b's; "\" must be escaped, i.e., 'doubled'
gsub("([ab])", "\\1_\\1_", "abc and ABC")
txt <- c("The", "licenses", "for", "most", "software", "are",
"designed", "to", "take", "away", "your", "freedom",
"to", "share", "and", "change", "it.",
"", "... | |
R_base_tools/strings.html6_16_0.txt | * ` str_c(..., sep = "", collapse = NULL) ` : Join multiple strings into a single string.
str_c(letters, LETTERS)
* ` str_flatten(string, collapse = "") ` : Combines into a single string, separated by collapse.
str_flatten(fruit, ", ") | |
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# Extract.factor: Extract or Replace Parts of a Factor
## Description
Extract or replace sub... | |
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# strptime: Date-time Conversion Functions to and from Character
## Description
Functions to... | |
R_base_tools/stringr.html3_28_0.txt | ` coll(x) ` looks for a match to ` x ` using human-language coll ation
rules, and is particularly important if you want to do case insensitive
matching. Collation rules differ around the world, so youâll also need to
supply a ` locale ` parameter.
i <- c("I", "İ", "i", "ı")
i
#> [1] "I" "Ä°... | |
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# stopifnot: Ensure the Truth of R Expressions
## Description
If any of the expressions (in ... | |
R_base_tools/R_base_all_246_1.txt | A?package=base&version=3.6.2) ` and ` [ NaN
](/link/NaN?package=base&version=3.6.2) ` in numeric or complex vectors, or
for strings with different encodings, see also above.
## Examples
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R_base_tools/strings.html7_122_0.txt | Both ` fixed() ` and ` regex() ` have ` ignore_case ` arguments, but they do
not allow you to pick the locale: they always use the default locale. You can
see what that is with the following code; more on stringi later.
stringi::stri_locale_info()
#> $Language
#> [1] "c"
#>
#> $Country
... | |
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# rev: Reverse Elements
## Description
` rev ` provides a reversed version of its argument. ... | |
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# getLoadedDLLs: Get DLLs Loaded in Current Session
## Description
This function provides a ... | |
R_base_tools/R_base_all_199_3.txt | al" ` , which uses a pager similar to the GUI console.
Another possibility is ` "console" ` to use the console itself.
Can be a character string or an R function, in which case it needs to accept
the arguments ` (files, header, title, delete.file) ` corresponding to the
first four arguments of ` [ file.show
](/link/... | |
R_base_tools/R_base_all_367_1.txt | in the base package,
with ‘mangled’ names.
## See Also
` [ library ](/link/library?package=base&version=3.6.2) ` , ` [ detach
](/link/detach?package=base&version=3.6.2) ` , ` [ loadNamespace
](/link/loadNamespace?package=base&version=3.6.2) ` .
See ` [ :: ](/link/%3A%3A?package=base&version=3.6.2) ` for a discussio... | |
R_base_tools/R_micropan_9_1.txt | Mpneumoniae.table$GID.tag
cols <- Mpneumoniae.table$Color
names(cols) <- Mpneumoniae.table$GID.tag
plot(my.tree, leaf.lab=labels, col=cols,
cex=0.8, xlab="Shell-weighted Manhattan distances")
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# Rhome: Return the R Home Directory
## Description
Return the R home directory, or the fu... | |
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# Startup: Initialization at Start of an R Session
## Description
In R , the startup mecha... | |
R_base_tools/R_base_all_247_1.txt | or(...)
lst <- unclass(attenu$station) > 20 # logical with NAs
## summary.default() for logicals -- different from *.factor:
summary(lst)
summary(as.factor(lst))
# }
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R_base_tools/R_micropan_3_1.txt | l models, and the input K.range specifies which values of K to try
out. There no real point using K less than 3, and the default is
K.range=3:5 . In general, the more genomes you have the larger you can choose
K without overfitting. Computations will be slower for larger values of K .
In order to choose the o... | |
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# mapply: Apply a Function to Multiple List or Vector Arguments
## Description
` mapply ` is... | |
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# library: Loading/Attaching and Listing of Packages
## Description
` library ` and ` requir... | |
R_base_tools/strings.html7_64_0.txt | Earlier, you learned about parentheses as a way to disambiguate complex
expressions. Parentheses also create a numbered capturing group (number 1, 2
etc.). A capturing group stores the part of the string matched by the part
of the regular expression inside the parentheses. You can refer to the same
text as previous... | |
R_base_tools/R_base_all_47_1.txt | m a1
print(c(a0, a2), digits = 16)
# }
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# margin.table: Compute table margin
## Description
For a contingency table in array form, c... | |
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# tilde: Tilde Operator
## Description
Tilde is used to separate the left- and right-hand si... | |
R_base_tools/stringr.html4_63_0.txt | ### Quantifiers
Quantifiers are special characters in regular expressions that allow us to
quantify patterns in particular ways. In all cases, quantifiers modify the
pattern that immediately precedes them. The first of these we will look at is
` "*" ` , which indicates “zero or more” matches. Here, we use it to find
... | |
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# NOT RUN {
require(splines) # package
detach(package:splines)
## or also
library(splines)
pkg <- "package:splines"
# }
... | |
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# print.default: Default Printing
## Description
` print.default ` is the _default_ method o... | |
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R_base_tools/stringr.html4_39_0.txt |
s <- c("dog", "cat", "parrot", "hamster")
str_detect(s, pattern = "o")
## [1] TRUE FALSE TRUE FALSE
This can be used similarly to ` str_subset ` above wher the logical vector
indicates which we would keep | |
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# expand.grid: Create a Data Frame from All Combinations of Factor Variables
## Description
... | |
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# copyright: Copyrights of Files Used to Build R
## Description
R is released under the ‘GN... | |
R_base_tools/strings.html7_67_0.txt | 1. Start and end with the same character.
2. Contain a repeated pair of letters (e.g. “church” contains “ch” repeated twice.) | |
R_base_tools/R_base_all_327_1.txt | ckManager()
# add a callback
h$add(function(expr, value, ok, visible) {
cat("In handler\n")
return(TRUE)
}, name = "simpleHandler")
# look at the internal callbacks.
getTaskCallbackNames()
# look at the R-l... | |
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# withVisible: Return both a Value and its Visibility
## Description
This function evaluates... | |
R_base_tools/R_micropan_7_0.txt | [ RDocumentation ](/)
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# panpca: Principal component analysis of a pan-matrix
## Description
Computes a princip... | |
R_base_tools/R_base_all_76_1.txt | ariables are converted to factor columns unless protected by ` [ I
](/link/I?package=base&version=3.6.2) ` .
If a data frame is supplied, all classes preceding ` "data.frame" ` are
stripped, and the row names are changed if that argument is supplied.
If ` row.names = NULL ` , row names are constructed from the names ... | |
R_base_tools/R_base_all_348_1.txt |
assumed to match. Lines (elements 1, 3) and parsed lines (elements 7, 8) may
differ if a ` #line ` directive is used in code: the former will respect the
directive, the latter will just count lines. If only 4 or 6 elements are
given, the parsed lines will be assumed to match the lines.
Methods are defined for ` print... | |
R_base_tools/stringr.html4_35_0.txt | The next collection of functions deals with subsetting and extraction. We
already saw ` str_sub ` in a few contexts, so we will not repeat that here.
The two primary functions here are ` str_extract ` and ` str_subset ` . The
first of these, ` str_extract ` , simply extracts from the string any pattern
that matches ` p... | |
R_base_tools/R_base_all_30_0.txt | [ RDocumentation ](/)
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# eigen: Spectral Decomposition of a Matrix
## Description
Computes eigenvalues and eigenvec... | |
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# grepRaw: Pattern Matching for Raw Vectors
## Description
` grepRaw ` searches for substrin... | |
R_base_tools/stringr.html4_37_0.txt | These two functions seem a bit silly here, but we will return to them after we
introduce regular expressions.
### Detecting patterns | |
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# cbind: Combine R Objects by Rows or Columns
## Description
Take a sequence of vector, matr... | |
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# format: Encode in a Common Format
## Description
Format an R object for pretty printing.... | |
R_base_tools/R_base_2_0.txt | [ RDocumentation ](/)
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# Syntax: Operator Syntax and Precedence
## Description
Outlines R syntax and gives the pr... | |
R_base_tools/strings.html6_42_0.txt | Look arounds regexp | matches | example | example output
(highlighted characters are in <>)
---|---|---|---
` a(?=c) ` | followed by | ` look("a(?=c)") ` |
b<a>cad
` a(?!c) ` | not followed by | ` look("a(?!c)") ` |
bac<a>d
` (?<=b)a ` | preceded by | ` loo... | |
R_base_tools/R_base_all_353_1.txt | .com/)
| |
R_base_tools/R_base_all_96_0.txt | [ RDocumentation ](/)
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# data.frame: Data Frames
## Description
The function ` data.frame() ` creates data frames, ... | |
R_base_tools/R_base_all_198_3.txt | ncoding names are recognized on your platform. Additionally, `
"" ` and ` "native.enc" ` both mean the ‘native’ encoding, that is the
internal encoding of the current locale and hence no translation is done.
When writing to a text connection, the connections code always assumes its
input is in native encoding, so e.g.... | |
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# plot.Panmat: Plotting and printing ` Panmat ` objects
## Description
Generic functions... | |
R_base_tools/stringr.html4_54_0.txt |
s <- c("X25YW", "X91YW", "R30WY", "X11YW")
# We want all X, followed by 2 of any character, then YW
str_subset(s, "X..YW")
## [1] "X25YW" "X91YW" "X11YW"
Some other immediately useful ones are ` "\d" ` and ` "\b" ` which refer to
digits and word boundaries, respectively. Regula... | |
R_base_tools/R_base_all_49_0.txt | [ RDocumentation ](/)
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# zapsmall: Rounding of Numbers: Zapping Small Ones to Zero
## Description
` zapsmall ` dete... | |
R_base_tools/R_base_all_273_0.txt | [ RDocumentation ](/)
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# c: Combine Values into a Vector or List
## Description
This is a generic function which co... | |
R_base_tools/stringr.html4_21_0.txt | Using ` str_sub ` is a bit awkward, however, as it requires positional
indices. More commonly, there is the ` str_replace ` function which takes the
two arguments we mentioned above, string and pattern. In this case, ` string `
is the string we are manipulating and ` pattern ` indicates what we wish to
replace. Finally... | |
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# chol2inv: Inverse from Choleski (or QR) Decomposition
## Description
Invert a symmetric, p... | |
R_base_tools/R_base_all_420_0.txt | [ RDocumentation ](/)
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# is.unsorted: Test if an Object is Not Sorted
## Description
Test if an object is not sorte... | |
R_base_tools/stringr.html4_47_0.txt |
dat <- read.csv("https://remiller1450.github.io/data/char_dom.csv")
dat
## ID messy_x messy_y
## 1 1 100 50
## 2 2 90 40
## 3 3 85 55
## 4 4 90 45
## 5 5 110 55*
## 6 6 Missing 60
## 7 7 ... | |
R_base_tools/R_base_all_321_0.txt | [ RDocumentation ](/)
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# data.class: Object Classes
## Description
Determine the class of an arbitrary R object.
... | |
R_base_tools/R_base_all_201_0.txt | [ RDocumentation ](/)
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# ns-reflect.Rd: Namespace Reflection Support
## Description
Internal functions to support r... | |
R_base_tools/R_base_all_233_0.txt | [ RDocumentation ](/)
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# round.POSIXt: Round / Truncate Data-Time Objects
## Description
Round or truncate date-tim... | |
R_base_tools/R_base_all_100_0.txt | [ RDocumentation ](/)
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# match.call: Argument Matching
## Description
` match.call ` returns a call in which all of... | |
R_base_tools/strings.html7_20_0.txt | Objects of length 0 are silently dropped. This is particularly useful in
conjunction with ` if ` :
name <- "Hadley"
time_of_day <- "morning"
birthday <- FALSE
str_c(
"Good ", time_of_day, " ", name,
if (birthday) " and HAPPY BIRTHDAY",
"."
)
#> [1] "Good morning... |
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