Hello R-helpers,
Thanks to Ravi Varadhan, I have improve the function I am working on top
optimize two equations. Now, my objective is to do a series of optimization
from a data table, where each row is one data serie (i.e data from one plant)
to be optimized.
The function below works up to the for loops. Before that, it outputs the
desired values. However, what I want to do is to loop the function (fun() in
this case) where each of the loop should optimize the functions using the ith
elements. I am working with a data table, so each of the elements that are used
in the testF (below) are vectors, since each of them are columns of the data
table.
I am new at writing function and looping, and ?for and ?apply did not help me
understand my error, as well as R help etc. I was wondering if the apply family
functions could be of any help here.
Also, I might not be handling my data correctly (is the data frame correct or
should I convert the data into a matrix?). Any improvement is warmly welcome.
Thank you for your help.
Guillaume
Guillaume Théroux Rancourt
Ph.D. candidate --- Plant Biology
Université Laval, Québec, QC, Canada
guillaume.theroux-rancour...@ulaval.ca
#####
Here is my complete code:
testF = function(A.a, A.b, Ci.a, Ci.b, O.a, O.b, Rd, Sco, id)
{
fun=function(x) {
f=function(x) {
Vcmax = x[2]
gi = x[1]
# First
f.1=(-((Vcmax-Rd)/gi+Ci.a+272.38*(1+O.a*10/165.82))+sqrt(((Vcmax-Rd)/gi+Ci.a+272.38*(1+O.a*10/165.82))^2-4*(-1/gi)*(Rd*(Ci.a+272.38*(1+O.a*10/165.82))-Vcmax*(Ci.a-(5*O.a/Sco)))))/(-2/gi)
if (is.nan(f.1)) f.1 = 1e30
# Second
f.2=(-((Vcmax-Rd)/gi+Ci.b+272.38*(1+O.b*10/165.82))+sqrt(((Vcmax-Rd)/gi+Ci.b+272.38*(1+O.b*10/165.82))^2-4*(-1/gi)*(Rd*(Ci.b+272.38*(1+O.b*10/165.82))-Vcmax*(Ci.b-(5*O.b/Sco)))))/(-2/gi)
if (is.nan(f.2)) f.2 = 1e30
# Verification with measured A values
y.1 = A.a - f.1
y.2 = A.b - f.2
y = y.1^2 + y.2^2
return(y)
}
res <- optim(par=c(0.15,50), fn=f, lower=c(0,0), upper=c(1,250),
method="L-BFGS-B")
output = data.frame(res$par[2],res$par[1])
colnames(output) = c("Vcmax", "gi")
return(output)
}
# Looping
n = length(A.a)
for (i in 1:n) {
A.a = A.a[i]
A.b = A.b[i]
Ci.a = Ci.a[i]
Ci.b = Ci.b[i]
O.a = O.a[i]
O.b = O.b[i]
Rd = Rd[i]
Sco = Sco[i]
fn = fun(i)
fn
}
}
#### SAMPLE DATA
O.21 A.21 Ci.21 O.2 A.2 Ci.2 O.10 A.10 Ci.10
Vcmax Rd gi Gamma.s Sco Ci.s
1 21 7.478326633 164.6573484 2 12.73133946
164.3076501 10 10.52935048 161.6103191 64.48 0.89189 0.2835
40.3 2.605459057 37.15400353
2 21 5.797166726 162.4292412 2 11.12480648
165.8296147 10 8.704447278 165.0450986 53.232 0.9703 0.22335
40.3 2.605459057 35.95569734
pop=read.table("file.name", header=T)
testF(pop$A.21, pop$A.2, pop$Ci.21, pop$Ci.2, pop$O.21, pop$O.2, pop$Rd,
pop$Sco)
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