Re: [R] if value is in vector, perform this function
I think the command you want is:
if(t %in% feed_days) C_A - 1.5 else C_A - 0
Do not confuse `%in%` (which is essentially
are the left-hand values in the right-hand
vector)
with
in of the `for` loop.
By the way,
if(t == TRUE)
is redundant -- better is:
if(t)
Pat
On 02/03/2013 23:57, Louise Stevenson wrote:
Hi,
I'm trying to set up R to run a simulation of two populations in which every 3.5 days,
the initial value of one of the populations is reset to 1.5. I'm simulation an experiment
we did in which we fed Daphnia populations twice a week with algae, so I want the initial
value of the algal population to reset to 1.5 twice a week to simulate that feeding. I've
use for loops and if/else loops before but I can't figure out how to syntax if t is
in this vector of possible t values, do this command, else, do this command if that
makes sense. Here's what I have (and it doesn't work):
params = c(1, 0.15, 0.164, 1)
init = c(1.5, 0.05)
t=seq(1,60, by=0.5) #all time values, experiment ran for 60 days
#feeding sequence - every 3.5 days
feed_days = seq(1,60,by=3.5)
Daphnia - function(t,x,params){
C_D = x[2];
C_A = 0;
for(t %in% feed_days){
if t == TRUE {
C_A = 1.5
}
else{
C_A = 0
}}
gamma = params[1]; m_D = params[2]; K_q = params[3]; q_max = params[4];
M_D = m_D * C_D
I_A = (C_D * q_max * C_A) / (K_q + C_A)
r_D = gamma * I_A
return(
list(c(
- I_A,
r_D - M_D
)))
}
library(deSolve)
results - ode(init, t, Daphnia, params, method = lsoda)
Let me know if there's any other info that would be helpful and thanks very
much for your help!
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'The R Inferno'
'Tao Te Programming')
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Re: [R] if value is in vector, perform this function
On 03-03-2013, at 00:57, Louise Stevenson louise.steven...@lifesci.ucsb.edu
wrote:
Hi,
I'm trying to set up R to run a simulation of two populations in which every
3.5 days, the initial value of one of the populations is reset to 1.5. I'm
simulation an experiment we did in which we fed Daphnia populations twice a
week with algae, so I want the initial value of the algal population to reset
to 1.5 twice a week to simulate that feeding. I've use for loops and if/else
loops before but I can't figure out how to syntax if t is in this vector of
possible t values, do this command, else, do this command if that makes
sense. Here's what I have (and it doesn't work):
params = c(1, 0.15, 0.164, 1)
init = c(1.5, 0.05)
t=seq(1,60, by=0.5) #all time values, experiment ran for 60 days
#feeding sequence - every 3.5 days
feed_days = seq(1,60,by=3.5)
Daphnia - function(t,x,params){
C_D = x[2];
C_A = 0;
for(t %in% feed_days){
if t == TRUE {
C_A = 1.5
}
else{
C_A = 0
}}
gamma = params[1]; m_D = params[2]; K_q = params[3]; q_max = params[4];
M_D = m_D * C_D
I_A = (C_D * q_max * C_A) / (K_q + C_A)
r_D = gamma * I_A
return(
list(c(
- I_A,
r_D - M_D
)))
}
library(deSolve)
results - ode(init, t, Daphnia, params, method = lsoda)
You have been given a correction for expression for (t %in% feed_days).
But even with that correction things will not do as you seem to want.
The argument t of function Daphnia is the integration time the ode solver is
passing and almost certainly is NOT an element of the vector t defined at the
start of your script. That t is the the time sequence for which output is
wanted (see ode help); it is what is put into the output of ode.
There is no reason to assume that the Daphnia argument t is an element of
feed_days. You can easily check this by inserting a print(t) in Daphnia. So C_A
will be 0 most of the time.
It would certainly help if you named the elements of the init vector and the
return list of Daphnia.
In Daphnia x[2] is C_D. But what is x[1] (C_A?)?
I think you will have to look at deSolve events but I'm not sure if that is
possible or required/desired with your model.
Berend
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Re: [R] if value is in vector, perform this function
I forgot to say:
Also do not depend on equality in this situation.
You want to test equality with a tolerance.
See Circle 1 of 'The R Inferno':
http://www.burns-stat.com/documents/books/the-r-inferno/
I also see that 't' is a vector unlike what I was
thinking before, thus you want to use 'ifelse':
C_A - ifelse(t %in% feed_days, 1.5, 0)
except that still leaves out the tolerance. If
you are always only going to go by half-days, then
the following should work:
C_A - ifelse( round(2*t) %in% round(2 * feed_days), 1.5, 0)
Pat
On 02/03/2013 23:57, Louise Stevenson wrote:
Hi,
I'm trying to set up R to run a simulation of two populations in which every 3.5 days,
the initial value of one of the populations is reset to 1.5. I'm simulation an experiment
we did in which we fed Daphnia populations twice a week with algae, so I want the initial
value of the algal population to reset to 1.5 twice a week to simulate that feeding. I've
use for loops and if/else loops before but I can't figure out how to syntax if t is
in this vector of possible t values, do this command, else, do this command if that
makes sense. Here's what I have (and it doesn't work):
params = c(1, 0.15, 0.164, 1)
init = c(1.5, 0.05)
t=seq(1,60, by=0.5) #all time values, experiment ran for 60 days
#feeding sequence - every 3.5 days
feed_days = seq(1,60,by=3.5)
Daphnia - function(t,x,params){
C_D = x[2];
C_A = 0;
for(t %in% feed_days){
if t == TRUE {
C_A = 1.5
}
else{
C_A = 0
}}
gamma = params[1]; m_D = params[2]; K_q = params[3]; q_max = params[4];
M_D = m_D * C_D
I_A = (C_D * q_max * C_A) / (K_q + C_A)
r_D = gamma * I_A
return(
list(c(
- I_A,
r_D - M_D
)))
}
library(deSolve)
results - ode(init, t, Daphnia, params, method = lsoda)
Let me know if there's any other info that would be helpful and thanks very
much for your help!
[[alternative HTML version deleted]]
__
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.
--
Patrick Burns
pbu...@pburns.seanet.com
twitter: @burnsstat @portfolioprobe
http://www.portfolioprobe.com/blog
http://www.burns-stat.com
(home of:
'Impatient R'
'The R Inferno'
'Tao Te Programming')
__
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.
[R] if value is in vector, perform this function
Hi,
I'm trying to set up R to run a simulation of two populations in which every
3.5 days, the initial value of one of the populations is reset to 1.5. I'm
simulation an experiment we did in which we fed Daphnia populations twice a
week with algae, so I want the initial value of the algal population to reset
to 1.5 twice a week to simulate that feeding. I've use for loops and if/else
loops before but I can't figure out how to syntax if t is in this vector of
possible t values, do this command, else, do this command if that makes sense.
Here's what I have (and it doesn't work):
params = c(1, 0.15, 0.164, 1)
init = c(1.5, 0.05)
t=seq(1,60, by=0.5) #all time values, experiment ran for 60 days
#feeding sequence - every 3.5 days
feed_days = seq(1,60,by=3.5)
Daphnia - function(t,x,params){
C_D = x[2];
C_A = 0;
for(t %in% feed_days){
if t == TRUE {
C_A = 1.5
}
else{
C_A = 0
}}
gamma = params[1]; m_D = params[2]; K_q = params[3]; q_max = params[4];
M_D = m_D * C_D
I_A = (C_D * q_max * C_A) / (K_q + C_A)
r_D = gamma * I_A
return(
list(c(
- I_A,
r_D - M_D
)))
}
library(deSolve)
results - ode(init, t, Daphnia, params, method = lsoda)
Let me know if there's any other info that would be helpful and thanks very
much for your help!
[[alternative HTML version deleted]]
__
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.
