Thnaks a lot, Ben.
I really like your suggestion about taking the the log. I'll
definitely play with optim - since it seems to work very fast.
Actually, I did take a look at the function - I created a grid of
function results for many different values of a crossed with many
different values of b. Then looked in what direction the results of
the function grow and focused on that area (or the area that is next
to it if it looked like things were growing towards outside my area).
But that was a very manual process and (I thought) prone to lead me to
local maxima - something I was trying to avoid.
Thanks again!
Dimitri
On Mon, Mar 7, 2011 at 9:32 PM, Ben Bolker <bbol...@gmail.com> wrote:
> Dimitri Liakhovitski <dimitri.liakhovitski <at> gmail.com> writes:
>
>> I have 2 variables - predictor "pred" and response variable "DV":
>>
>> pred<-c(439635.053, 222925.718, 668434.755, 194242.330, 5786.321, 115537.344,
>> 100835.368, 7133.206, 159058.286, 4079991.629, 3380078.060, 2661279.136,
>> 2698324.478, 1245213.965, 1901815.503, 1517019.451, 1396857.736, 1034030.988,
>> 432249.574, 342329.325, 1831335.792, 2209578.859, 1641709.754, 1329308.669,
>> 1251794.367, 731368.430, 1705626.983, 673535.171, 242519.280, 57251.998,
>> 5728.821, 2054514.244, 301954.819, 773955.355, 735497.506, 347355.976,
>> 1678175.153, 133082.395, 591326.289, 30866.182, 27235.846, 118372.342,
>> 71590.969, 84813.299, 366146.153, 1391725.205, 763199.746, 1216661.202,
>> 263878.157, 930832.769, 261270.130, 589303.561, 455137.946,
>> 954655.201, 873434.054)
>> (pred)
>> DV<-c(0.55351297,0.27616943,0.58134926,0.33887159,0.03092546,0.14928061,
>> 0.11836759,0.01719463,0.03258188,1.81205587,2.86657699,2.49491195,
>> 3.09727230,1.95648776,2.28106268,1.78978179,1.74003678,1.22520393,
>> 0.54245878,0.41483039,1.08731493,2.19581289,1.60516129,1.30723431,
>> 1.41822649,1.31530539,2.02406576,1.22211412,0.52055790,0.12975522,
>> 0.01416903,0.61043485,0.44141748,0.64327070,0.53607039,0.32603820,
>> 1.77261016,0.42035756,0.37853917,0.12342486,0.06607710,0.02383682,
>> 0.08421590,0.09255332,0.23644909,1.67921092,1.26864432,1.38654574,
>> 1.29833020,1.76873555,0.93363677,1.01857658,0.81359775,2.14758239,2.41583852)
>> (DV)
>>
>> Both "pred" and "DV" above are time series (observed across 55
>> months). The relationship between them is pre-specified. In this
>> relationship, the (predicted) "DV" at time t is a specific function of
>> itself at time t-1, of "pred" at time t, and of 2 scalars - a and b.
>> I have to find optimal a and b that would ensure the best fit between
>> the observed DV and the predicted DV. Below is the function I have to
>> optimize:
>>
>> my.function <- function(param){
>> a<-param[1]
>> b<-param[2]
>> DV_pred <- rep(0,length(pred))
>> for(i in 2:length(pred)){
>> DV_pred[i] <- 1 - ( (1 - DV_pred[i-1] * a) / (exp(pred[i] * b)) )
>> }
>> DV_pred[1]<-DV[1]
>> correl <- cor(DV,DV_pred)
>> return(correl)
>> }
>>
>> a has to be between 0.001 and 0.75
>> b has to be positive.
>
> Rather than worry about optimization routines, I think
> you need to think more carefully about what your objective
> function is actually doing. I played around with this a bit
> and got something reasonable. You only have two parameters, so it shouldn't
> be too hard to figure out what's going on by appropriate exploration.
>
> matplot(cbind(pred,DV),log="y")
>
> ## split objective function into two parts, one that computes
> ## the predicted value ...
> calc_DV_pred <- function(a,b) {
> DV_pred <- rep(0,length(pred))
> DV_pred[1]<-DV[1]
> for(i in 2:length(pred)){
> DV_pred[i] <- 1 - ( (1 - DV_pred[i-1] * a) / (exp(pred[i] * b)) )
> }
> DV_pred
> }
>
>
> ## ... and the other (wrapper) to compute the correlation
> ## I switched to estimating b on a logarithmic scale
>
> my.function <- function(param){
> a<-param[1]
> b<-exp(param[2])
> correl <- cor(DV,calc_DV_pred(a,b))
> return(correl)
> }
>
> ## try out the function for various values
> my.function(c(0.5,-5))
> my.function(c(0.5,-6))
> my.function(c(0.5,-9))
> my.function(c(0.5,1.1))
> my.function(c(0.5,1.2))
>
> ## try to fit
> opt1 <- optim(fn=my.function,par=c(a=0.5,b=-9),
> method="L-BFGS-B",
> lower=c(0.001,-17),
> upper=c(0.75,Inf),
> control=list(fnscale=-1))
>
> ## look at objective function surface
> library(emdbook)
> cc <- curve3d(my.function(c(x,y)),xlim=c(0.001,0.75),ylim=c(-18,1),
> n=c(50,50),sys3d="contour")
>
> cc2 <- curve3d(my.function(c(x,y)),xlim=c(0.001,0.75),ylim=c(-16,-12),
> n=c(50,50),sys3d="contour")
> points(opt1$par[1],opt1$par[2])
>
> DV_pred <- calc_DV_pred(opt1$par[1],exp(opt1$par[2]))
>
> matplot(cbind(pred,DV,DV_pred),log="y",type="l",col=c(1,2,4))
>
> In hindsight, my initial difficulty (and possibly yours as well)
> was starting with a value of b that was much too large.
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Dimitri Liakhovitski
Ninah Consulting
www.ninah.com
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