I don't get how to use the optim() function. I tried something simple (at least i thought so). Here is the code:
w<-c(0.5,0.5)
A<-runif(100)
B<-runif(100)
c<-function(w,A,B) sqrt(w[1]*A + w[2]*B)
optim(w,c)
Error in w[1]*A:'A' is missing
I have seen various questions of this type but I still don't know what is wrong. What am I missing here?
There are two separate things to look at in the code above.
First, in the optim function you need to pass in the other arguments to c (as part of the ... argument to optim:
optim(w, c, A = A, B = B)
But that still won't run because the function your trying to optimise returns a vector (optim tries to minimise the value of the function by default).
Because you say it's an example, it's not clear what to do with the function c but just to show something that should work, you could try the sum of the squared differences between A & B:
c <- function(w, A, B) sum((w[1] * A - w[2] * B)^2)
optim(w, c, A = A, B = B)
Related
I have a function whose value is the integral of another well-established function. Then I want to create a new function whose value is the integral of the function, whose value is the integral :) The first step is OK, but then the second gives a error. Here's the code:
A <- 1
f <- function(a) a^2
g <- function(a,b) integrate(f,a,b)$value
h <- function(s) g(s,A)
integrate(h,0,A)
The error I get is:
Error in integrate(f, a, b) : length(lower) == 1 is not TRUE
What am I doing wrong? Thanks a lot!
I tried to Google and did not find this specific situation.
I also tried to actually integrate g to obtain h, numerically ad hoc: take dx>0, then dx*sum(sapply(seq(a,b,by=dx),h)) just to obtain a number, but I would like to do it with an integrated function.
The problem is that integrate will not accept an array of values for the lower bound, only a single number. That means your function h(s) cannot accept a vector of values. But integrate also requires that the function to be integrated is vectorized. You can fix this with the function Vectorize.
If you change the definition of h, your code will work.
h <- Vectorize(function(s) g(s,A))
integrate(h,0,A)
0.25 with absolute error < 2.8e-15
Look at the ?integrate
integrate(f, lower, upper)
f should be a function taking a numeric and returning a numeric
your f <- function(a) a^2 is ok.
the next 2 arguments should be the limits of integration ("numbers")
integrate(f,2,5)
39 with absolute error < 4.3e-13
(1/3) * (5^3-2^3)
39
the error message length(lower) == 1 is not TRUE
means that the second argument is not "one" number
I want to integrate a function involving while loop in R. I have pasted here an MWE. Could anyone please guide about how to get rid of warning messages when integrating such a function?
Thank You
myfun <- function(X, a, b, kmin, kmax){
term <- 0
k <- 1
while(k < kmax | term < 10000){
term <- term + a * b * X^k
k <- k+1
}
fx <- exp(X) * term
return(fx)
}
a <- 5
b <- 4
kmax <- 20
integrate(myfun, lower = 0, upper = 10, a = a, b = b, kmax = kmax)
Produces a warning, accessed via warnings():
In while (k < kmax | term < 10000) { ... :
the condition has length > 1 and only the first element will be used
From the integrate() documentation:
f must accept a vector of inputs and produce a vector of function evaluations at those points.
This is the crux of the problem here, which you can see by running myfun(c(1, 2), a, b, kmin, kmax) and reproducing a similar warning. What's happening is that integrate() wants to pass a vector of inputs to myfun in X; this means that inside your while loop, term will become a vector as well. This creates a problem when the while loop kicks back to the evaluation stage, because now the condition k < kmax | term < 10000 has a vector structure as well (since term does), which while doesn't like.
This warning is very good in this case, because it strongly suggests that integrate() isn't doing what you want it to do. Your goal here isn't to get rid of the warning messages; the function as written simply won't work with integrate() due to the while loop structure.
Your choices for how to proceed are to either (1) rewrite the function in a way that doesn't use a while loop, or (2) just hard-code some numeric integration yourself, perhaps with a for loop. The best way to use R is to vectorize everything and to avoid things like while and for when at all possible.
Finally, I'll note that there seems to be some problem with the underlying function, since myfun(0.5, a, b, kmin, kmax) does not converge (note the problem with the mathematics when the supplied X term is less than 1), so you won't be able to integrate it on the interval [0, 10] no matter what you do.
I've got a function, KozakTaper, that returns the diameter of a tree trunk at a given height (DHT). There's no algebraic way to rearrange the original taper equation to return DHT at a given diameter (4 inches, for my purposes)...enter R! (using 3.4.3 on Windows 10)
My approach was to use a for loop to iterate likely values of DHT (25-100% of total tree height, HT), and then use optimize to choose the one that returns a diameter closest to 4". Too bad I get the error message Error in f(arg, ...) : could not find function "f".
Here's a shortened definition of KozakTaper along with my best attempt so far.
KozakTaper=function(Bark,SPP,DHT,DBH,HT,Planted){
if(Bark=='ob' & SPP=='AB'){
a0_tap=1.0693567631
a1_tap=0.9975021951
a2_tap=-0.01282775
b1_tap=0.3921013594
b2_tap=-1.054622304
b3_tap=0.7758393514
b4_tap=4.1034897617
b5_tap=0.1185960455
b6_tap=-1.080697381
b7_tap=0}
else if(Bark=='ob' & SPP=='RS'){
a0_tap=0.8758
a1_tap=0.992
a2_tap=0.0633
b1_tap=0.4128
b2_tap=-0.6877
b3_tap=0.4413
b4_tap=1.1818
b5_tap=0.1131
b6_tap=-0.4356
b7_tap=0.1042}
else{
a0_tap=1.1263776728
a1_tap=0.9485083275
a2_tap=0.0371321602
b1_tap=0.7662525552
b2_tap=-0.028147685
b3_tap=0.2334044323
b4_tap=4.8569609081
b5_tap=0.0753180483
b6_tap=-0.205052535
b7_tap=0}
p = 1.3/HT
z = DHT/HT
Xi = (1 - z^(1/3))/(1 - p^(1/3))
Qi = 1 - z^(1/3)
y = (a0_tap * (DBH^a1_tap) * (HT^a2_tap)) * Xi^(b1_tap * z^4 + b2_tap * (exp(-DBH/HT)) +
b3_tap * Xi^0.1 + b4_tap * (1/DBH) + b5_tap * HT^Qi + b6_tap * Xi + b7_tap*Planted)
return(y=round(y,4))}
HT <- .3048*85 #converting from english to metric (sorry, it's forestry)
for (i in c((HT*.25):(HT+1))) {
d <- KozakTaper(Bark='ob',SPP='RS',DHT=i,DBH=2.54*19,HT=.3048*85,Planted=0)
frame <- na.omit(d)
optimize(f=abs(10.16-d), interval=frame, lower=1, upper=90,
maximum = FALSE,
tol = .Machine$double.eps^0.25)
}
Eventually I would like this code to iterate through a csv and return i for the best d, which will require some rearranging, but I figured I should make it work for one tree first.
When I print d I get multiple values, so it is iterating through i, but it gets held up at the optimize function.
Defining frame was my most recent tactic, because d returns one NaN at the end, but it may not be the best input for interval. I've tried interval=c((HT*.25):(HT+1)), defining KozakTaper within the for loop, and defining f prior to the optimize, but I get the same error. Suggestions for what part I should target (or other approaches) are appreciated!
-KB
Forestry Research Fellow, Appalachian Mountain Club.
MS, University of Maine
**Edit with a follow-up question:
I'm now trying to run this script for each row of a csv, "Input." The row contains the values for KozakTaper, and I've called them with this:
Input=read.csv...
Input$Opt=0
o <- optimize(f = function(x) abs(10.16 - KozakTaper(Bark='ob',
SPP='Input$Species',
DHT=x,
DBH=(2.54*Input$DBH),
HT=(.3048*Input$Ht),
Planted=0)),
lower=Input$Ht*.25, upper=Input$Ht+1,
maximum = FALSE, tol = .Machine$double.eps^0.25)
Input$Opt <- o$minimum
Input$Mht <- Input$Opt/.3048. # converting back to English
Input$Ht and Input$DBH are numeric; Input$Species is factor.
However, I get the error invalid function value in 'optimize'. I get it whether I define "o" or just run optimize. Oddly, when I don't call values from the row but instead use the code from the answer, it tells me object 'HT' not found. I have the awful feeling this is due to some obvious/careless error on my part, but I'm not finding posts about this error with optimize. If you notice what I've done wrong, your explanation will be appreciated!
I'm not an expert on optimize, but I see three issues: 1) your call to KozakTaper does not iterate through the range you specify in the loop. 2) KozakTaper returns a a single number not a vector. 3) You haven't given optimize a function but an expression.
So what is happening is that you are not giving optimize anything to iterate over.
All you should need is this:
optimize(f = function(x) abs(10.16 - KozakTaper(Bark='ob',
SPP='RS',
DHT=x,
DBH=2.54*19,
HT=.3048*85,
Planted=0)),
lower=HT*.25, upper=HT+1,
maximum = FALSE, tol = .Machine$double.eps^0.25)
$minimum
[1] 22.67713 ##Hopefully this is the right answer
$objective
[1] 0
Optimize will now substitute x in from lower to higher, trying to minimize the difference
I am having the hardest time trying to implement this equation into a nonlinear solver in R. I am trying both the nleqslv and BB packages but so far getting nothing but errors. I have searched and read documentation until my eyes have bled, but I cannot wrap my brain around it. The equation itself works like this:
The Equation
s2 * sum(price^(2*x+2)) - s2.bar * sum(price^(2*x)) = 0
Where s2, s2.bar and price are known vectors of equal length.
The last attempt I tried in BB was this:
gamma = function(x){
n = len(x)
f = numeric(n)
f[n] = s2*sum(price^(2*x[n]+2)) - s2.bar*sum(price^(2*x[n]))
f
}
g0 = rnorm(length(price))
results = BBsolve(par=g0, fn=gamma)
From you description of the various parts used in the function you seem to have muddled up the formula.
Your function gamma should most probably be written as
gamma <- function(x){
f <- s2*sum(price^(2*x+2)) - s2.bar*sum(price^(2*x))
f
}
s2, price and s2.bar are vectors from your description so the formula you gave will return a vector.
Since you have not given any data we cannot test. I have tried testing with randomly generated values for s2, price, s2.bar. Sometimes one gets a solution with both nleqslv and BB but not always.
In the case of package nleqslv the default method will not always work.
Since the package has different methods you should use the function testnslv from the package to see if any of the provided methods does find a solution.
Let's say I have a function that is nlogn in space requirements, I want to work out the maximum size of input for that function for a given available space. i.e. I want to find n where nlogn=c.
I followed an approach to calculate n, that looks like this in R:
step = function(R, z) { log(log(R)-z)}
guess = function(R) log(log(R))
inverse_nlogn = function(R, accuracy=1e-10) {
zi_1 = 0
z = guess(R)
while(abs(z - zi_1)>accuracy) {
zi_1 = z
z = step(R, z)
}
exp(exp(z))
}
But I can't get understand why it must be solved iteratively. For the range we are interested (n>1), the function is non singular.
There's nothing special about n log n — nearly all elementary functions fail to have elementary inverses, and so have to be solved by some other means: bisection, Newton's method, Lagrange inversion theorem, series reversion, Lambert W function...
As Gareth hinted the Lambert W function (eg here) gets you almost there, indeed n = c/W(c)
A wee google found this, which might be helpful.
Following up (being completely explicit):
library(emdbook)
n <- 2.5
c <- 2.5*log(2.5)
exp(lambertW(c)) ## 2.5
library(gsl)
exp(lambert_W0(c)) ## 2.5
There are probably minor differences in speed, accuracy, etc. of the two implementations. I haven't tested/benchmarked them extensively. (Now that I tried
library(sos)
findFn("lambert W")
I discover that it's implemented all over the place: the games package, and a whole package that's called LambertW ...