| Title: | 'systemPipeShiny' Utility Functions |
|---|---|
| Description: | The systemPipeShiny (SPS) framework comes with many useful utility functions. However, installing the whole framework is heavy and takes some time. If you like only a few useful utility functions from SPS, install this package is enough. |
| Authors: | Le Zhang [aut, cre] |
| Maintainer: | Le Zhang <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 0.2.2 |
| Built: | 2024-11-03 02:48:43 UTC |
| Source: | https://github.com/lz100/spsutil |
Help you to check if you have certain packages and return missing package names
checkNameSpace( packages, quietly = FALSE, from = "CRAN", time_out = 1, on_timeout = { FALSE } )checkNameSpace( packages, quietly = FALSE, from = "CRAN", time_out = 1, on_timeout = { FALSE } )
packages |
vector of strings |
quietly |
bool, give you warning on fail? |
from |
string, where this package is from like, "CRAN", "GitHub", only for output message display purpose |
time_out |
numeric, how long to wait before reaching the time limit. Sometimes there are too many pkgs installed and takes too long to scan the whole list. Set this timeout in seconds to prevent the long waiting. |
on_timeout |
expressions, call back experssions to run when reaches timeout time.
Default is return |
vector of strings, of missing package names, character(0) if no missing
checkNameSpace("ggplot2") checkNameSpace("random_pkg") checkNameSpace("random_pkg", quietly = TRUE)checkNameSpace("ggplot2") checkNameSpace("random_pkg") checkNameSpace("random_pkg", quietly = TRUE)
check if a URL can be reached, return TRUE if yes and FALSE if cannot or with other status code
checkUrl(url, timeout = 5)checkUrl(url, timeout = 5)
url |
string, the URL to request |
timeout |
seconds to wait before return FALSE |
TRUE if url is reachable, FALSE if not
checkUrl("https://google.com") try(checkUrl("https://randomwebsite123.com", 1))checkUrl("https://google.com") try(checkUrl("https://randomwebsite123.com", 1))
Some methods for a history stack data structure. It can store history of certain repeating actions. For example, building the back-end of a file/image editor, allow undo/redo actions.
If the stack reaches the limit and you are trying to add more history, the first history step will be removed , all history will be shift to the left by one step and finally add the new step to the end.
When history returning methods are called, like the get(), forward(), backward()
methods, it will not directly return the item saved, but a list, contains 4
components: 1. item, the actual item stored; 2. pos, current posistion value;
3. first, boolean value, if this history is stored on the first position of stack;
4. last, boolean value, if this history is stored on the last position of stack;
If you forward beyond last step, or backward to prior the first
step, it will be stopped with errors.
Starting history stack with no initial history will return a special
stack, where the pos = 0, len = 0, first = TRUE, and last = TRUE.
This means you cannot move forward or backward. When you get(), it will be
an empty list list(). After adding any new history, pos will never be
0 again, it will always be a larger than 0 value.
an R6 class object
new()
create the history object
historyStack$new(items = NULL, limit = 25, verbose = TRUE)
itemslist, initial history step items to store on start
limitint, how many history steps can be stored in the stack, default 25 steps
verbosebool, print some verbose message?
clear()
clear all history steps in the stack
historyStack$clear()
get()
retrieve the history from a certain position in the stack
historyStack$get(pos = private$pos)
posint, which position to get the history from, default is current step.
getPos()
get current step position in the history stack
historyStack$getPos()
status()
print out some status of the stack
historyStack$status()
returns a list of pos: current position (int); len: current
length of the history stack (int); limit: history stack storing limit (int);
first: is current step position the first of the stack (bool);
last: is current step position the last of the stack (bool)
forward()
move one step forward in the history stack and return item in that position
historyStack$forward()
backward()
move one step backward in the history stack and return item in that position
historyStack$backward()
add()
Add an item to the history and move one step forward
historyStack$add(item)
itemany object you want to add to the stack. Everything store in the item will be moved into a list, so even if item may be something length > 1, it will still be treated as a single item and single history step.
If current position is not the last position, and when a new step item is added to the stack, all history records (items) after current position will be removed before adding the new history item.
clone()
The objects of this class are cloneable with this method.
historyStack$clone(deep = FALSE)
deepWhether to make a deep clone.
his <- historyStack$new() # add some history his$add(1) his$add(2) his$add(3) his$add(4) his$add(5) # check status his$status() # get item at current history position his$get() # go back to previous step his$backward() # going back to step 2 his$backward() his$backward() # going forward 1 step tp step 3 his$forward() # check current status his$status() # adding a new step at position 3 will remove the old step 4,5 before adding his$add("new 4") # only 3 steps + 1 new step = 4 steps left his$status()his <- historyStack$new() # add some history his$add(1) his$add(2) his$add(3) his$add(4) his$add(5) # check status his$status() # get item at current history position his$get() # go back to previous step his$backward() # going back to step 2 his$backward() his$backward() # going forward 1 step tp step 3 his$forward() # check current status his$status() # adding a new step at position 3 will remove the old step 4,5 before adding his$add("new 4") # only 3 steps + 1 new step = 4 steps left his$status()
In-place operations like i += 1, i -= 1 is not support in
R. These functions implement these operations in R.
inc(e1, e2 = 1) mult(e1, e2 = 2) divi(e1, e2 = 2)inc(e1, e2 = 1) mult(e1, e2 = 2) divi(e1, e2 = 2)
e1 |
object, most likely a numeric object |
e2 |
the operation value, the value to add, subtract, multiply, divide of. |
inc(i) is the same as i <- i + 1.
inc(i, -1) is the same as i <- i - 1.
mult(i) is the same as i <- i * 2.
divi(i) is the same as i <- i / 2.
No return, directly assign the value back to e1
If you want shiny::reactiveVal version of these operators, check spsComps. shiny::reactiveValues operation will be the same as normal values.
i <- 0 inc(i) # add 1 i inc(i) # add 1 i inc(i, -1) # minus 1 i inc(i, -1) # minus 1 i x <- 1 mult(x) # times 2 x mult(x) # times 2 x divi(x) # divide 2 x divi(x) # divide 2 xi <- 0 inc(i) # add 1 i inc(i) # add 1 i inc(i, -1) # minus 1 i inc(i, -1) # minus 1 i x <- 1 mult(x) # times 2 x mult(x) # times 2 x divi(x) # divide 2 x divi(x) # divide 2 x
If
use_color = TRUE or
under SPS main package use_crayonoption is TRUE
In a console that supports colors
Then the message will be colorful, other wise no color.
"INFO" level spawns message, "WARNING" is warning, "ERROR" spawns stop,
other levels use cat.
spsinfo, spswarn, spserror are higher level wrappers of msg. The
only difference is they have SPS- prefix.
spsinfo has an additional
arg verbose. This arg works similarly to all other verbose args in
SPS:
if not specified, it follows the project option. If SPS option verbose is
set to TRUE, message will be displayed; if FALSE, mute the message.
It can be be forced to TRUE and FALSE. TRUE will forcibly generate the msg, and FALSE
will mute the message.
msg( msg, level = "INFO", .other_color = NULL, info_text = "INFO", warning_text = "WARNING", error_text = "ERROR", use_color = TRUE ) spsinfo(msg, verbose = NULL) spswarn(msg) spserror(msg)msg( msg, level = "INFO", .other_color = NULL, info_text = "INFO", warning_text = "WARNING", error_text = "ERROR", use_color = TRUE ) spsinfo(msg, verbose = NULL) spswarn(msg) spserror(msg)
msg |
a character string of message or a vector of character strings, each item in the vector presents one line of words |
level |
typically, one of "INFO", "WARNING", "ERROR", not case sensitive. Other custom levels will work too. |
.other_color |
hex color code or named colors, when levels are not in "INFO", "WARNING", "ERROR", this value will be used |
info_text |
info level text prefix, use with "INFO" level |
warning_text |
warning level text prefix, use with "WARNING" level |
error_text |
error level text prefix, use with "ERROR" level |
use_color |
bool, default |
verbose |
bool, default get from sps project options, can be overwritten |
If use_color is TRUE, output message will forcibly use color if the console has color
support, ignore SPS use_crayon option.
If use_color is FALSE, but you are using within SPS framework, the use_crayon option
is set to TRUE, color will be used.
Otherwise message will be no color.
see description and details
msg("this is info") msg("this is warning", "warning") try(msg("this is error", "error")) msg("this is another level", "my level", "green") spsinfo("some msg, verbose false", verbose = FALSE) # will not show up spsinfo("some msg, verbose true", verbose = TRUE) spswarn("sps warning") try(spserror("sps error"))msg("this is info") msg("this is warning", "warning") try(msg("this is error", "error")) msg("this is another level", "my level", "green") spsinfo("some msg, verbose false", verbose = FALSE) # will not show up spsinfo("some msg, verbose true", verbose = TRUE) spswarn("sps warning") try(spserror("sps error"))
judge if an object is or not a falsy value. This includes:
empty value, empty string "", NULL, NA, length of 0 and FALSE itself
notFalsy(x) isFalsy(x) emptyIsFalse(x)notFalsy(x) isFalsy(x) emptyIsFalse(x)
x |
any R object |
R does not have good built-in methods to judge falsy values and these kind
of values often cause errors in if conditions, for example
if(NULL) 1 else 2 will cause error. So this function will be useful to
handle this kind of situations: if(notFalsy(NULL)) 1 else 2.
not working on S4 class objects.
isFalsy is the reverse of notFalsy: isFalsy(x) = !notFalsy(x)
emptyIsFalse is the old name for notFalsy
Useful for if statement. Normal empty object in if will spawn error. Wrap the
expression with emptyIsFalse can avoid this. See examples
NA, "", NULL, length(0), nchar == 0 and FALSE will return
FALSE, otherwise TRUE in notFalsy and the opposite in isFalsy
notFalsy(NULL) notFalsy(NA) notFalsy("") try(`if(NULL) "not empty" else "empty"`) # this will generate error if(notFalsy(NULL)) "not falsy" else "falsy" # but this will work # Similar for `NA`, `""`, `character(0)` and more isFalsy(NULL) isFalsy(NA) isFalsy("")notFalsy(NULL) notFalsy(NA) notFalsy("") try(`if(NULL) "not empty" else "empty"`) # this will generate error if(notFalsy(NULL)) "not falsy" else "falsy" # but this will work # Similar for `NA`, `""`, `character(0)` and more isFalsy(NULL) isFalsy(NA) isFalsy("")
Useful if you want to suppress cat, print, message and warning. You can choose what to mute. Default all four methods are muted.
quiet(x, print_cat = TRUE, message = TRUE, warning = TRUE)quiet(x, print_cat = TRUE, message = TRUE, warning = TRUE)
x |
function or expression or value assignment expression |
print_cat |
bool, mute |
message |
bool, mute |
warning |
bool, mute |
If your original functions has a return, it will return in
invisible(x)
quiet(warning(123)) quiet(message(123)) quiet(print(123)) quiet(cat(123)) quiet(warning(123), warning = FALSE) quiet(message(123), message = FALSE) quiet(print(123), print_cat = FALSE) quiet(cat(123), print_cat = FALSE)quiet(warning(123)) quiet(message(123)) quiet(print(123)) quiet(cat(123)) quiet(warning(123), warning = FALSE) quiet(message(123), message = FALSE) quiet(print(123), print_cat = FALSE) quiet(cat(123), print_cat = FALSE)
Remove ANSI pre-/suffix-fix in a character string.
remove_ANSI(strings)remove_ANSI(strings)
strings |
strings, a character vector |
strings with out ANSI characters
remove_ANSI("\033[34m\033[1ma\033[22m\033[39m") remove_ANSI(c("\033[34m\033[1ma\033[22m\033[39m", "\033[34m\033[1mb\033[22m\033[39m"))remove_ANSI("\033[34m\033[1ma\033[22m\033[39m") remove_ANSI(c("\033[34m\033[1ma\033[22m\033[39m", "\033[34m\033[1mb\033[22m\033[39m"))
A simple stack data structure in R, with supporting of assiocated methods, like push, pop and others.
an R6 class object
new()
initialize a new object
simepleStack$new(items = list(), limit = Inf)
itemslist, list of items to add to the initial stack
limitint, how many items can be pushed to the stack, default is unlimited.
len()
returns current length of the stack
simepleStack$len()
get()
returns the full current stack of all items
simepleStack$get()
clear()
remove all items in current stack
simepleStack$clear()
push()
add item(s) to the stack
simepleStack$push(items, after = self$len())
itemslist, list of items to add to the stack
afterint, which position to push items after, default is after the current last item. 0 will be before the first item.
pop()
remove item(s) from the stack and return as results
simepleStack$pop(len = 1, tail = FALSE)
lenint, how many items to pop from stack, default is 1 item a time.
tailbool, to pop in the reverse order (from the last item)? Default
is FALSE, pop from the top (first item).
clone()
The objects of this class are cloneable with this method.
simepleStack$clone(deep = FALSE)
deepWhether to make a deep clone.
my_stack <- simepleStack$new() # check length my_stack$len() # add some thing my_stack$push(list(1, 2, 3)) # print current stack str(my_stack$get()) # check length my_stack$len() # add before the current first my_stack$push(list(0), after = 0) # print current stack str(my_stack$get()) # pop one item my_stack$pop() # print current stack str(my_stack$get()) # pop one item from the tail my_stack$pop(tail = TRUE) # print current stack str(my_stack$get()) # pop more than one items my_stack$pop(2) # print current stack str(my_stack$get()) # nothing leftmy_stack <- simepleStack$new() # check length my_stack$len() # add some thing my_stack$push(list(1, 2, 3)) # print current stack str(my_stack$get()) # check length my_stack$len() # add before the current first my_stack$push(list(0), after = 0) # print current stack str(my_stack$get()) # pop one item my_stack$pop() # print current stack str(my_stack$get()) # pop one item from the tail my_stack$pop(tail = TRUE) # print current stack str(my_stack$get()) # pop more than one items my_stack$pop(2) # print current stack str(my_stack$get()) # nothing left
Some functions in spsUtil, spsComps and systempPipeShiny will behave differently if some SPS options are changed, but it is optional. All functions have a default value. If SPS options are not changed, they will just use the default setting. Read help files of individual functions for detail.
spsOption(opt, value = NULL, .list = NULL, empty_is_false = TRUE)spsOption(opt, value = NULL, .list = NULL, empty_is_false = TRUE)
opt |
string, length 1, what option you want to get or set |
value |
if this is not |
.list |
list, set many SPS options together at once by passing a list to this function. |
empty_is_false |
bool, when trying to get an option value, if the
option is |
return the option value if value exists; return FALSE if the value
is empty, like NULL, NA, ""; return NULL if empty_is_false = FALSE;
see notFalsy
If value != NULL will set the option to this new value, no returns.
spsOption("test1") # get a not existing option spsOption("test1", 1) # set the value spsOption("test1") # get the value again spsOption("test2") spsOption("test2", empty_is_false = FALSE) spsOption(.list = list( test1 = 123, test2 = 456 )) spsOption("test1") spsOption("test2")spsOption("test1") # get a not existing option spsOption("test1", 1) # set the value spsOption("test1") # get the value again spsOption("test2") spsOption("test2", empty_is_false = FALSE) spsOption(.list = list( test1 = 123, test2 = 456 )) spsOption("test1") spsOption("test2")
Fix duplicated values in a character vector, useful in column names and some ID structures that requires unique identifiers. If any duplicated string is found in the vector, a numeric index will be added after the these strings.
strUniquefy(x, sep_b = "_", sep_a = "", mark_first = TRUE)strUniquefy(x, sep_b = "_", sep_a = "", mark_first = TRUE)
x |
character vector |
sep_b |
string, separator before the number index |
sep_a |
string, separator after the number index |
mark_first |
bool, if duplicated values are found, do you want to add the
numeric index starting from the first copy? |
The input can also be a numeric vector, but the return will always be character.
returns a character vector
strUniquefy(c(1,1,1,2,3)) strUniquefy(c(1,1,1,2,3), mark_first = FALSE) strUniquefy(c(1,1,1,2,3), sep_b = "(", sep_a = ")") strUniquefy(c("a","b","c","a","d","b"))strUniquefy(c(1,1,1,2,3)) strUniquefy(c(1,1,1,2,3), mark_first = FALSE) strUniquefy(c(1,1,1,2,3), sep_b = "(", sep_a = ")") strUniquefy(c("a","b","c","a","d","b"))
Add a time limit for R expressions
timeout( expr, time_out = 1, on_timeout = { stop("Timout reached", call. = FALSE) }, on_final = { }, env = parent.frame() )timeout( expr, time_out = 1, on_timeout = { stop("Timout reached", call. = FALSE) }, on_final = { }, env = parent.frame() )
expr |
expressions, wrap them inside |
time_out |
numeric, timeout time, in seconds |
on_timeout |
expressions, callback expressions to run it the time out limit is reached but expression is still running. Default is to return an error. |
on_final |
expressions, callback expressions to run in the end regardless the state and results |
env |
environment, which environment to evaluate the expressions. Default is
the same environment as where the |
Expressions will be evaluated in the parent environment by default, for example
if this function is called at global level, all returns, assignments inside
expr will directly go to global environment as well.
default return, all depends on what return the expr will have
# The `try` command in following examples are here to make sure the # R CMD check will pass on package check. In a real case, you do not # need it. # default try(timeout({Sys.sleep(0.1)}, time_out = 0.01)) # timeout is evaluating expressions the same level as you call it timeout({abc <- 123}) # so you should get `abc` even outside the function call abc # custom timeout callback timeout({Sys.sleep(0.1)}, time_out = 0.01, on_timeout = {print("It takes too long")}) # final call back try(timeout({Sys.sleep(0.1)}, time_out = 0.01, on_final = {print("some final words")})) # on error timeout({123}, on_final = {print("runs even success")}) # on success # assign to value my_val <- timeout({10 + 1}) my_val# The `try` command in following examples are here to make sure the # R CMD check will pass on package check. In a real case, you do not # need it. # default try(timeout({Sys.sleep(0.1)}, time_out = 0.01)) # timeout is evaluating expressions the same level as you call it timeout({abc <- 123}) # so you should get `abc` even outside the function call abc # custom timeout callback timeout({Sys.sleep(0.1)}, time_out = 0.01, on_timeout = {print("It takes too long")}) # final call back try(timeout({Sys.sleep(0.1)}, time_out = 0.01, on_final = {print("some final words")})) # on error timeout({123}, on_final = {print("runs even success")}) # on success # assign to value my_val <- timeout({10 + 1}) my_val