vignettes/NLR-Dictionary.Rmd
NLR-Dictionary.RmdThis document is based on the NetLogo
Dictionary. It lists all the entries in the NetLogo Dictionary
(i.e., NetLogo primitives) and informs the best replacements to
use in R. Are suggested as replacements, functions from the
NetLogoR package, as well as functions from the R software
and of other packages (indicated below). To find how to use these
functions, please refers to their documentation by using
help("nameFunction").
When no NetLogoR function was built to translate a
NetLogo primitive and that, to our knowledge, no R function (or from
other packages) could easily recreate the primitive, we indicated “not
implemented”. The NetLogo primitives not implemented should not prevent
the users from building individual-based models involving patches and
turtles.
For the inverse dictionary (i.e., to find the NetLogo
equivalents of the NetLogoR functions) please look at the
NetLogoR documentation as the links to NetLogo Dictionary
entries for the equivalent primitives are provided in the “See Also”
section of each NetLogoR function.
e: exp().
pi: pi.
false: FALSE.
true: TRUE.
black: "black".
gray: "gray" or "grey".
white: "white".
red: "red".
orange: "orange".
brown: "brown".
yellow: "yellow".
green: "green".
lime: "limegreen".
turquoise: "turquoise".
cyan: "cyan".
sky: "skyblue".
blue: "blue".
violet: "violet".
magenta: "magenta".
pink: "pink".
See http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf for more colors.
abs: abs().
acos: acos(), returns value in radians. Use
deg() from CircStats to convert the result in
degrees.
all?: NLall() from NetLogoR.
and: &.
any?: NLany() from NetLogoR.
approximate-hsb: hsv().
approximate-rgb: rgb().
arithmetic operators: +, *,
-, /, ^, <,
>, = or == (depends if it is
for setting or testing), !=, <=,
>=.
asin: asin(), returns value in radians. Use
deg() from CircStats to convert the result in
degrees.
ask: not implemented. The agents running a NetLogoR
function is one of the function arguments that need to be
provided.
ask-concurrent: not implemented. When multiple agents are
provided in a NetLogoR function, they all execute the
function at the same time. To execute a function similarly as
ask-concurrent, the function needs to be provided with one agent at the
time.
at-points: turtlesAt() from NetLogoR or
patchAt() from NetLogoR.
atan: atan2(), returns value in radians. Use
deg() from CircStats to convert the result in
degrees.
autoplot?: not implemented.
auto-plot-off: not implemented.
auto-plot-on: not implemented.
back (bk): bk() from NetLogoR.
base-colors: see help(rainbow) for different ways of
creating colors.
beep: beep() from beepr.
behaviorspace-experiment-name: BehaviorSpace not implemented.
behaviorspace-run-number: BehaviorSpace not implemented.
both-ends: links not implemented.
breed: use of() from NetLogoR to access
turtles’ breeds.
but-first (butfirst, bf): nameList[-1] for lists;
substring(nameString, 2) for strings.
but-last (but-last, bl): head(nameList, -1) or
nameList[-length(nameList)] for lists;
substr(nameString, 1, nchar(nameString) - 1) for
strings.
can-move?: canMove() in
NetLogoR.
carefully: try().
ceiling: ceiling().
clear-all (ca): not implemented. See the NetLogoR
dictionary entries for clear-globals, clear-ticks, clear-turtles,
clear-patches, clear-drawing, clear-all-plots, and
clear-output.
clear-all-plots: graphics.off() closes all external
plot windows opened and clears the plot window of RStudio.
clear-drawing (cd): not implemented.
clear-globals: rm() removes the specified objects
(which can be of any class) from the R environment, these objects do not
longer exist afterwards. To reset objects to 0 instead, reassign the
objects (e.g., nameObject <- 0).
clear-links: links not implemented.
clear-output: cat("\014") clears the R
console.
clear-patches (cp): clearPatches() from
NetLogoR.
clear-plot: dev.off() closes the external plot
window opened or clears the plot window of RStudio, depending on which
one was active. clearPlot() from quickPlot
acts differently on the external plot window as it clears it but does
not close it.
clear-ticks: tick counter not implemented. If a global variable
is used to store the time (e.g., time <- 0;
time <- time + 1), see NetLogoR dictionary
entry for clear-globals.
clear-turtles (ct): see NetLogoR dictionary entry
for clear-globals. If reassigning,
turtles <- noTurtles() can be used to kill all the
turtles in the agentset and replace it by an empty turtle
agentset.
color: use of() from NetLogoR to access
turtles’ colors.
cos: cos() takes an input value in radians. Use
rad() from CircStats to convert the input from
degrees to radians.
count: NLcount() from
NetLogoR.
create-ordered-turtles (cro): createOTurtles() from
NetLogoR. The created turtles must be assigned to an object
before they can run some functions.
create-ordered<breeds>: createOTurtles() from
NetLogoR. The created turtles must be assigned to an object
before they can run some functions.
create-<breed>-to: links not implemented.
create-<breeds>-to: links not implemented.
create-<breed>-from: links not implemented.
create-<breeds>-from: links not implemented.
create-<breed>-with: links not implemented.
create-<breeds>-with: links not implemented.
create-link-to: links not implemented.
create-links-to: links not implemented.
create-link-from: links not implemented.
create-links-from: links not implemented.
create-link-with: links not implemented.
create-links-with: links not implemented.
create-turtles (crt): createTurtles() from
NetLogoR. The created turtles must be assigned to an object
before they can run some functions.
create-<breeds>: createTurtles() from
NetLogoR. The created turtles must be assigned to an object
before they can run some functions.
create-temporary-plot-pen: not implemented.
date-and-time: Sys.time().
die: die() from NetLogoR.
diffuse: diffuse() from
NetLogoR.
diffuse4: diffuse() from
NetLogoR.
directed-link-breed: links not implemented.
display: not implemented.
distance: NLdist() from
NetLogoR.
distancexy: NLdist() from
NetLogoR.
downhill: downhill() from
NetLogoR.
downhill4: downhill() from
NetLogoR.
dx: dx() from NetLogoR.
dy: dy() from NetLogoR.
empty?: length(nameList) == 0 for lists and vectors;
nchar(nameString) == 0 or
length(nameString) == 0 for strings, depending if
nameString = "" or
nameString = character(0).
end: not implemented.
end1: links not implemented.
end2: links not implemented.
error: stop("errorMessage").
error-message: not implemented.
every: not implemented.
exp: exp().
export-view: not implemented.
export-interface: not implemented.
export-output: not implemented.
export-world: save() can save any created R objects
(worlds, turtles, patches, globals, etc.).
extensions: similar as using R packages. Load packages with
library(), then all the functions from the loaded package
are available.
extract-hsb: col2hsv() from IDPmisc.
extract-rgb: col2rgb().
face: face() from NetLogoR.
facexy: face() from NetLogoR.
file-at-end?: not implemented.
file-close: not implemented.
file-close-all: not implemented.
file-delete: file.remove().
file-exists?: file.exists().
file-flush: not implemented.
file-open: read.table(), read.csv,
load(), raster(), etc., depends on the file
format.
file-print: not implemented.
file-read: not implemented.
file-read-characters: not implemented.
file-read-line: not implemented.
file-show: not implemented.
file-type: not implemented.
file-write: not implemented.
filter: Filter().
first: nameList[[1]] for lists;
substr(nameString, 1, 1) for strings.
floor: floor().
follow: not implemented.
follow-me: not implemented.
foreach:
for(i in 1:length(nameList)) {task(nameList[[i]])},
lapply() or sapply() for single list or
mapply() for multiple lists. Functions are the same when
used with vectors, except for the for-loop :
for(i in 1:length(nameVector)) {task(nameVector[i])}.
forward (fd): fd() from
NetLogoR.
fput: c(newElement, nameList) for lists and
vectors.
hatch: hatch() from NetLogoR. The new
hatched turtles cannot directly run functions. The turtles agentset
containing the parent turtles and the new hatched turtles needs to be
assigned to an object, then the new hatched turtles must be identified
within that agentset to run some functions.
hatch-<breeds>: hatch() from
NetLogoR. The new hatched turtles cannot directly run
functions. The turtles agentset containing the parent turtles and the
new hatched turtles needs to be assigned to an object, then the new
hatched turtles must be identified within that agentset to run some
functions.
heading: use of() from NetLogoR to
access turtles’ headings.
hidden?: not implemented.
hide-link: links not implemented.
hide-turtle (ht): not implemented.
histogram: hist(). Use unlist() to
transform a list into a vector prior using hist(). Only
numeric values can be passed on to hist() (e.g., strings
cannot be used).
home: home() from NetLogoR.
hsb: col2rgb(hsv()).
hubnet-broadcast: HubNet not implemented.
hubnet-broadcast-clear-output: HubNet not implemented.
hubnet-broadcast-message: HubNet not implemented.
hubnet-clear-override: HubNet not implemented.
hubnet-clear-overrides: HubNet not implemented.
hubnet-clients-list: HubNet not implemented.
hubnet-enter-message?: HubNet not implemented.
hubnet-exit-message?: HubNet not implemented.
hubnet-fetch-message: HubNet not implemented.
hubnet-kick-client: HubNet not implemented.
hubnet-kick-all-clients: HubNet not implemented.
hubnet-message: HubNet not implemented.
hubnet-message-source: HubNet not implemented.
hubnet-message-tag: HubNet not implemented.
hubnet-message-waiting?: HubNet not implemented.
hubnet-reset: HubNet not implemented.
hubnet-reset-perspective: HubNet not implemented.
hubnet-send: HubNet not implemented.
hubnet-send-clear-output: HubNet not implemented.
hubnet-send-follow: HubNet not implemented.
hubnet-send-message: HubNet not implemented.
hubnet-send-override: HubNet not implemented.
hubnet-send-watch: HubNet not implemented.
hubnet-set-client-interface: HubNet not implemented.
if: if(){}.
ifelse: ifelse() or
if(){} else {}.
ifelse-value: ifelse() or
if(){} else {}.
import-drawing: not implemented.
import-pcolors: not implemented.
import-pcolors-rgb: not implemented.
import-world: not implemented.
in-cone: inCone() from
NetLogoR.
in-<breed>-neighbor?: links not implemented.
in-link-neighbor?: links not implemented.
in-<breed>-neighbors: links not implemented.
in-link-neighbors: links not implemented.
in-<breed>-from: links not implemented.
in-link-from: links not implemented.
__includes: not implemented.
in-radius: inRadius() from
NetLogoR.
inspect: inspect() from NetLogoR to
inspect turtles; or of() from NetLogoR to
obtain variables values for patches or turtles.
int: trunc().
is-agent?: isNLclass() from
NetLogoR.
is-agentset?: isNLclass() from
NetLogoR.
is-boolean?: is.logical().
is-command-task?: not implemented.
is-directed-link?: links not implemented.
is-link?: links not implemented.
is-link-set?: links not implemented.
is-list?: is.list().
is-number?: is.numeric().
is-patch?: isNLclass() from
NetLogoR.
is-patch-set?: isNLclass() from
NetLogoR.
is-reporter-task?: not implemented.
is-string?: is.character().
is-turtle?: isNLclass() from
NetLogoR.
is-turtle-set?: isNLclass() in
NetLogoR.
is-undirected-link?: links not implemented.
item: nameList[[index]] for lists;
substr(nameString, index, index) for strings;
nameVector[index] for vectors. Indices begin from 1, not 0
like in NetLogo.
label: text() to add labels on plot.
label-color: text() to add labels on plot.
last: nameList[[length(nameList)]] or
tail(nameList, n = 1) for lists;
substring(nameString, nchar(nameString)) for strings;
nameVector[length(nameVector)] or
tail(nameVector, n = 1) for vectors.
layout-circle: layoutCircle() from
NetLogoR.
layout-radial: links not implemented.
layout-spring: links not implemented.
layout-tutte: links not implemented.
left (lt): left() from
NetLogoR.
length: length() for lists and vectors;
nchar() for strings.
let: not implemented.
link: links not implemented.
link-heading: links not implemented.
link-length: links not implemented.
link-set: links not implemented.
link-shapes: links not implemented.
links: links not implemented.
links-own: links not implemented.
list: list().
ln: log().
loop: repeat{}.
lput: c(nameList, newElement) for lists and
vectors.
map:
for(i in 1:length(nameList)) {task(nameList[[i]])},
lapply() for single list or mapply() for
multiple lists. Functions are the same when used with vectors, except
for the for-loop :
for(i in 1:length(nameVector)) {task(nameVector[i])}.
max: max(). Use unlist() to transform a
list into a vector prior using max().
max-n-of: maxNof() from
NetLogoR.
max-one-of: maxOneOf() from
NetLogoR.
max-pxcor: maxPxcor() from
NetLogoR.
max-pycor: maxPycor() from
NetLogoR.
mean: mean(). Use unlist() to transform
a list into a vector prior using mean().
median: median(). Use unlist() to
transform a list into a vector prior using
median().
member?: pExist() or tExist(), both
from NetLogoR to test patches or turtles existence in an
agentset. element %in% nameList for lists and vectors;
grepl() for strings.
min: min(). Use unlist() to transform a
list into a vector prior using min().
min-n-of: minNof() from
NetLogoR.
min-one-of: minOneOf() from
NetLogoR.
min-pxcor: minPxcor() from
NetLogoR.
min-pycor: minPycor() from
NetLogoR.
mod: %%.
modes: mlv() from modeest.
mouse-down?: not implemented.
mouse-inside?: not implemented.
mouse-xcor: not implemented.
mouse-ycor:not implemented.
move-to: moveTo() from
NetLogoR.
movie-cancel: see package animation.
movie-close: see package animation.
movie-grab-view: see package animation.
movie-grab-interface: see package animation.
movie-set-frame-rate: see package animation.
movie-start: see package animation.
movie-status: see package animation.
my-<breeds>: links not implemented.
my-links: links not implemented.
my-in-<breeds>: links not implemented.
my-in-links: links not implemented.
my-out-<breeds>: links not implemented.
my-out-links: links not implemented.
myself: not implemented.
n-of: nOf() from NetLogoR.
n-values: rep() or
(for i in 1:n){}.
neighbors: neighbors() from
NetLogoR.
neighbors4: neighbors() from
NetLogoR.
<breed>-neighbors: links not implemented.
link-neighbors: links not implemented.
<breed>-neighbor?: links not implemented.
link-neighbor?: links not implemented.
netlogo-applet?: not implemented.
netlogo-version: R.Version().
netlogo-web?: not implemented.
new-seed: rm(.Random.seed) removes the old seed and
automatically select a random new one.
no-display: not implemented.
nobody: not implemented.
no-links: links not implemented.
no-patches: noPatches() from
NetLogoR.
not: !.
no-turtles: noTurtles() from
NetLogoR.
of: of() from NetLogoR.
world[pxcor, pycor] can also be used to report the value(s)
of a single patch.
one-of: oneOf() from NetLogoR to select
agent in an agentset; sample() for lists and
vectors.
or: |.
other: other() from NetLogoR.
other-end: links not implemented.
out-<breed>-neighbor?: links not implemented.
out-link-neighbor?: links not implemented.
out-<breed>-neighbors: links not implemented.
out-link-neighbors: links not implemented.
out-<breed>-to: links not implemented.
out-link-to: links not implemented.
output-print: not implemented.
output-show: not implemented.
output-type: not implemented.
output-write: not implemented.
patch: patch() from NetLogoR.
patch-ahead: patchAhead() from
NetLogoR.
patch-at: patchAt() from
NetLogoR.
patch-at-heading-and-distance: patchDistDir() from
NetLogoR.
patch-here: patchHere() from
NetLogoR.
patch-left-and-ahead: patchLeft() from
NetLogoR.
patch-right-and-ahead: patchRight() from
NetLogoR.
patch-set: patchSet() from
NetLogoR.
patch-size: not implemented.
patches: patches() from
NetLogoR.
patches-own: a new world must be created with
createWorld() to create a new patch variable. This new
world can then be stacked with others using stackWorlds()
to create a single object with the different patch values.
pcolor: not implemented.
pen-down (pd): SpatialLines objects from sp should be derived from the turtles object to plot their trajectories, by using their current and previous coordiantes.
pen-erase (pe): not implemented.
pen-up (pu): not implemented.
pen-mode: not implemented.
pen-size: plot(..., lwd = x).
plabel: text() to add labels on plot.
plabel-color: text() to add labels on plot.
plot-name: dev.cur() returns the name and number of
the active device/window where to plot. plot(..., main = x)
gives a title to the plot.
plot-pen-exists?: not implemented.
plot-pen-down: SpatialLines objects from sp should be derived from the turtles object to plot their trajectories, by using their current and previous coordiantes.
plot-pen-up: not implemented.
plot-pen-reset: not implemented.
plotxy: not implemented.
plot-x-min: not implemented.
plot-x-max: not implemented.
plot-y-min: not implemented.
plot-y-max: not implemented.
position: match() for lists and vectors;
regexpr()[1] or StrPos() from DescTools for
strings.
precision: round().
print: print().
pxcor: use patch() from NetLogoR to
access patches’ coordinates at any [x, y] locations.
pycor: use patch() from NetLogoR to
access patches’ coordinates at any [x, y] locations.
random: sample().
random-float: runif().
random-exponential: rexp().
random-gamma: rgamma().
random-normal: rnorm().
random-poisson: rpois().
random-pxcor: randomPxcor() from
NetLogoR.
random-pycor: randomPycor() from
NetLogoR.
random-seed: set.seed().
random-xcor: randomXcor() from
NetLogoR. Use randomXYcor() from
NetLogoR to generate random xcor and ycor at the same
time.
random-ycor: randomYcor() from
NetLogoR. Use randomXYcor() from
NetLogoR to generate random xcor and ycor at the same
time.
read-from-string: get().
reduce: Reduce().
remainder: %/%.
remove: nameList[nameList != element] for list and
vectors; gsub(element, "", nameString) for
strings.
remove-duplicate: unique() for lists and
vectors.
remove-item: nameList[-index] for list and vectors;
gsub(substr(nameString, index, index), "", nameString) for
strings.
repeat: for(i in 1:n){task}.
replace-item: nameList[[index]] <- value for
lists;
gsub(substr(nameString, index, index), characters, nameString)
for strings; nameVector[index] <- value for
vectors.
report: return().
reset-perspective (rp): not implemented.
reset-ticks: not implemented.
reset-timer: not implemented.
resize-world: create a new world with createWorld()
and assign it to the object name of the previous world to overwrite it.
Patches values from the previous world are then lost. To kill all the
turtles, see the NetLogoR Dictionary entry for
clear-turtles.
reverse: rev() for lists and vectors;
paste(rev(unlist(strsplit(nameString, split=""))), collapse=""))
for strings.
rgb: rgb2hsv().
ride: not implemented.
ride-me: not implemented.
right (rt): right() from
NetLogoR.
round: round().
run: not implemented.
runresult: not implemented.
scale-color: gray.colors or
grey.colors, rainbow() or see
RColorBrewer package.
self: not implemented.
; (semicolon): #.
sentence (se): c().
set: NLset() from NetLogoR.
set-current-directory: setwd().
set-current-plot: dev.set().
set-current-plot-pen: not implemented.
set-default-shape: not implemented.
set-histogram-num-bars:
hist(..., breaks = x).
__set-line-thickness: not implemented.
set-patch-size: not implemented.
set-plot-pen-color: plot(..., col = x) or
Plot(..., cols = x) from quickPlot.
set-plot-pen-interval: not implemented.
set-plot-pen-mode: not implemented.
setup-plots: not implemented.
set-plot-x-range:
plot(..., xlim = c(x, x)).
set-plot-y-range:
plot(..., ylim = c(x, x)).
setxy: setXY() from NetLogoR.
shade-of?: not implemented.
shape: plot(..., pch = x).
shapes: not implemented.
show: not implemented
show-turtle (st): not implemented.
show-link: links not implemented.
shuffle: sample().
sin: sin() takes an input value in radians. Use
rad() from CircStats to convert the input from
degrees to radians.
sort: sort(). Use unlist() to transform
a list into a vector prior using sort().
sort-by: sort(..., decreasing = x). Use
unlist() to transform a list into a vector prior using
sort().
sort-on: sortOn() from
NetLogoR.
sprout:sprout() from NetLogoR. The new
sprouted turtles cannot directly run functions. The turtles agentset
containing the parent turtles and the new sprouted turtles needs to be
assigned to an object, then the new sprouted turtles must be identified
within the agentset to run some functions.
sprout-<breeds>: sprout() from
NetLogoR. The new sprouted turtles cannot directly run
functions. The turtles agentset containing the parent turtles and the
new sprouted turtles needs to be assigned to an object, then the new
sprouted turtles must be identified within the agentset to run some
functions.
sqrt: sqrt().
stamp: points() or Plot(..., addTo = x)
from quickPlot.
stamp-erase: not implemented.
standard-deviation: sd(). Use unlist()
to transform a list into a vector prior using
sd().
startup: not implemented.
stop: stop().
stop-inspecting: not implemented.
stop-inspecting-dead-agents: not implemented.
subject: not implemented.
sublist: nameList[index1:index2] for lists and
vectors. Indices begin from 1, not 0 like in NetLogo.
substring: substr(nameString, index1, index2).
Indices begin from 1, not 0 like in NetLogo.
subtract-headings: subHeadings() from
NetLogoR.
sum: sum(). Use unlist() to transform a
list into a vector prior using sum().
tan: tan() takes an input value in radians. Use
rad() from CircStats to convert the input from
degrees to radians.
task: not implemented.
thickness: links not implemented.
tick: not implemented.
tick-advance: not implemented.
ticks: not implemented.
tie: links not implemented.
tie-mode: links not implemented.
timer: not implemented.
to: function(){}.
to-report: function(){}.
towards: towards() from
NetLogoR.
towardsxy: towards() from
NetLogoR.
turtle: turtle() from
NetLogoR.
turtle-set: turtleSet() from
NetLogoR.
turtles: not implemented. Calling the name of the turtles agentset reports all the turtles in it.
turtles-at: turtlesAt() from
NetLogoR.
<breeds>-at: turtlesAt() from
NetLogoR.
turtles-here: turtlesOn() from
NetLogoR.
<breeds>-here: turtlesOn() from
NetLogoR.
turtles-on: turtlesOn() from
NetLogoR.
<breeds>-on: turtlesOn() from
NetLogoR.
turtles-own: turtlesOwn() from
NetLogoR.
<breeds>-own: turtlesOwn() from
NetLogoR.
type: print(paste()).
undirected-link-breed: links not implemented.
untie: links not implemented.
update-plots: not implemented.
uphill: uphill() from
NetLogoR.
uphill4: uphill() from
NetLogoR.
user-directory: not implemented.
user-file: not implemented.
user-new-file: not implemented.
user-input: not implemented.
user-message: not implemented.
user-one-of: not implemented.
user-yes-or-no?: not implemented.
wait: not implemented.
watch: not implemented.
watch-me: not implemented.
while: while(){}.
who: use of() from NetLogoR to access
turtles’ who numbers.
with: NLwith() from NetLogoR.
<breed>-with: links not implemented.
link-with: links not implemented.
with-max: withMax() from
NetLogoR.
with-min: withMin() from
NetLogoR.
with-local-randomness: save the current seed and RNG with
oldSeed <- get(".Random.seed", envir = .GlobalEnv) and
oldRNGkind <- RNGkind(), and reassign it later with
do.call("RNGkind", as.list(oldRNGkind)) and
assign(".Random.seed", oldSeed, envir = .GlobalEnv).
without-interruption: not implemented.
word: paste().
world-width: worldWidth() in
NetLogoR.
world-height: worldHeight() in
NetLogoR.
wrap-color: not implemented.
write: print(paste()).
of() from NetLogoR to access
turtles’ ycor coordinates.