[R] Passing arguments to a function within a function ...
Hallo Everybody
How do you specify arguments for a function used within another function?
Here is my problem:
I am reconstructing a calculator for the burden of disease due to air
pollution from publications and tools published by the WHO. The
calculations make use of published dose-response relationships for
particular health end-points. This is then applied to populations with
known or estimated levels of exposure and incidence rates to calcute
the number of cases of each end-point attributable to each pollutant.
I have functions that work on their own but when is have to use the
one within the other, I don't know how to specify its arguments
Here are example data and the functions:
## Example data frame with population, concentration and cases ##
x = data.frame(Name = LETTERS[1:10],
pop=sample(x=1000:1,size=10),
Xbabies = 0.106,
Xkids = 0.232,
Xteens = 0.375,
Xadults = 0.235,
Xaged = 0.52,
cases = sample(x=100:500,size=10),
conc = sample(x=20:125,size=10)
)
## Two of the published dose-response relationships
adult.CP.mortality = list(end.point = Cardiopulmanory mortality in
adults over 30,
pollutant = PM10,
relationship = log-linear,
beta = c(0.0562,0.1551,0.2541),
Xpop =
c(Xbabies,Xkids,Xteens,Xadults,Xaged)[4:5])
adult.LC.mortality = list(end.point = Lung Cancer mortality in adults over 30,
pollutant = PM10,
relationship = log-linear,
beta = c(0.0856, 0.2322,0.3787),
Xpop =
c(Xbabies,Xkids,Xteens,Xadults,Xaged)[4:5])
## Generic function to calculculate the Attributable cases for a
pollutant in a population
dose.response - function(pop,
Xpop = 1,
conc,
base.conc=7.5,
relationship = c(linear,log-linear)[1],
beta=c(0.0006,0.0008,0.0010),
cases=NULL,
incidence.rate=NULL,
par = c(low estimate,cental
estimate,high estimate),
verbose = FALSE
){
# Turn case rate into case number
d - cases
if(verbose==TRUE) message(d = , d)
if(verbose==TRUE) message(pop = , pop)
if(verbose==TRUE) message(beta = , beta)
if(verbose==TRUE) message(conc = , conc)
if(verbose==TRUE) message(base.coc = , base.conc)
if(verbose==TRUE) message(relationship = , relationship)
if(is.null(cases)==TRUE) {d - incidence.rate*pop} # use incidence
rate if cases are not available
if(relationship == linear) {RR = exp(beta*(conc-base.conc))}
#RR=exp[beta(X-Xo)]
if(relationship == log-linear) {RR = ((conc+1)/(base.conc+1))^beta}
if(verbose==TRUE) message(RR = , RR)
AF = (RR-1)/RR #AF=(RR-1)/RR
if(verbose==TRUE) message(AF = , AF)
AM = AF * d #AM = AF * cases
if(verbose==TRUE) message(AM = , AM)
out = data.frame(beta=beta,cases=d,
RelativeRisk=RR,AttributableFraction=AF,
AttributableInsidence=AM)
rownames(out) = c(low estimate,cental estimate,high estimate)
if(verbose==TRUE) message(dimentions of out = , dim(out))
out.idx = na.omit(match(par,rownames(out)))
out[out.idx,]
}
## Function using the published dose-response relationships with the
generic function
drep - function(pop.conc=x,sicklist=adult.CP.mortality,...){
dr.out=by(x,x$Name,function(x){z=as.data.frame((x))
dose.response(pop=z$pop*sum(z[,adult.CP.mortality$Xpop]),
conc=z$conc,
cases=z$cases,
relationship =
sicklist$relationship,
beta = sicklist$beta,
Xpop = sicklist$Xpop,
par = c(low
estimate,cental estimate,high estimate)[2]
, verbose=FALSE
)
} )
names(dr.out) - paste(sicklist$end.point,: , names(dr.out),sep=)
dr.out
}
#
This is where the trouble starts: What do I do if I need to pass the
argument base.conc=10 or a different option for par= to
dose.response() ? At the moment it works becuase it uses the default,
which will not be valid in all cases.
Thanks in advance
Christiaan
--
Christiaan Pauw
Nova Institute
www.nova.org.za
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Re: [R] Passing arguments to a function within a function ...
Hello,
Your problem seems simple, if I understand it correctly. Just add an
extra argument to the caller function, drep().
drep - function(pop.conc = x, sicklist = adult.CP.mortality,
par = cental estimate, ...) { # This extra
argument
dr.out = by(x, x$Name, function(x) {
z = as.data.frame((x))
dose.response(pop = z$pop * sum(z[, adult.CP.mortality$Xpop]),
conc = z$conc,
cases = z$cases,
relationship = sicklist$relationship,
beta = sicklist$beta,
Xpop = sicklist$Xpop,
par = par, # Note the difference (!)
verbose = FALSE)
})
names(dr.out) - paste(sicklist$end.point, : , names(dr.out), sep
= )
dr.out
}
In this case, the new argument has a default value.When the callee
dose.response() is called, the first 'par' is the name one of it's
arguments, the second 'par' is a value, the passed to value. The first
is a name, it does not have a value and can not, for instance, be
printed, only the second can. They are completely different in nature.
And the same for other arguments, like 'base.conc'.
Hope this helps,
Rui Barradas
Em 07-08-2012 09:52, christiaan pauw escreveu:
Hallo Everybody
How do you specify arguments for a function used within another function?
Here is my problem:
I am reconstructing a calculator for the burden of disease due to air
pollution from publications and tools published by the WHO. The
calculations make use of published dose-response relationships for
particular health end-points. This is then applied to populations with
known or estimated levels of exposure and incidence rates to calcute
the number of cases of each end-point attributable to each pollutant.
I have functions that work on their own but when is have to use the
one within the other, I don't know how to specify its arguments
Here are example data and the functions:
## Example data frame with population, concentration and cases ##
x = data.frame(Name = LETTERS[1:10],
pop=sample(x=1000:1,size=10),
Xbabies = 0.106,
Xkids = 0.232,
Xteens = 0.375,
Xadults = 0.235,
Xaged = 0.52,
cases = sample(x=100:500,size=10),
conc = sample(x=20:125,size=10)
)
## Two of the published dose-response relationships
adult.CP.mortality = list(end.point = Cardiopulmanory mortality in
adults over 30,
pollutant = PM10,
relationship = log-linear,
beta = c(0.0562,0.1551,0.2541),
Xpop =
c(Xbabies,Xkids,Xteens,Xadults,Xaged)[4:5])
adult.LC.mortality = list(end.point = Lung Cancer mortality in adults over 30,
pollutant = PM10,
relationship = log-linear,
beta = c(0.0856, 0.2322,0.3787),
Xpop =
c(Xbabies,Xkids,Xteens,Xadults,Xaged)[4:5])
## Generic function to calculculate the Attributable cases for a
pollutant in a population
dose.response - function(pop,
Xpop = 1,
conc,
base.conc=7.5,
relationship = c(linear,log-linear)[1],
beta=c(0.0006,0.0008,0.0010),
cases=NULL,
incidence.rate=NULL,
par = c(low estimate,cental
estimate,high estimate),
verbose = FALSE
){
# Turn case rate into case number
d - cases
if(verbose==TRUE) message(d = , d)
if(verbose==TRUE) message(pop = , pop)
if(verbose==TRUE) message(beta = , beta)
if(verbose==TRUE) message(conc = , conc)
if(verbose==TRUE) message(base.coc = , base.conc)
if(verbose==TRUE) message(relationship = , relationship)
if(is.null(cases)==TRUE) {d - incidence.rate*pop} # use incidence
rate if cases are not available
if(relationship == linear) {RR = exp(beta*(conc-base.conc))}
#RR=exp[beta(X-Xo)]
if(relationship == log-linear) {RR = ((conc+1)/(base.conc+1))^beta}
if(verbose==TRUE) message(RR = , RR)
AF = (RR-1)/RR #AF=(RR-1)/RR
if(verbose==TRUE) message(AF = , AF)
AM = AF * d #AM = AF * cases
if(verbose==TRUE) message(AM = , AM)
out = data.frame(beta=beta,cases=d,
RelativeRisk=RR,AttributableFraction=AF,
AttributableInsidence=AM)
rownames(out) = c(low estimate,cental estimate,high estimate)
if(verbose==TRUE) message(dimentions of out = , dim(out))
out.idx = na.omit(match(par,rownames(out)))
out[out.idx,]
}
## Function using the published dose-response relationships with the
generic function
drep - function(pop.conc=x,sicklist=adult.CP.mortality,...){
Re: [R] Passing arguments to a function within a function ...
Thanks Rui It works. On 7 August 2012 11:34, Rui Barradas ruipbarra...@sapo.pt wrote: Hello, Your problem seems simple, if I understand it correctly. Just add an extra argument to the caller function, drep(). Christiaan Pauw Nova Institute www.nova.org.za __ 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] Passing Arguments in a function
Hi All,
I'm having some trouble assigning arguments inside a function to
produce a plot from a model
Can anyone help me? Below I've outlined the situation and examples of
failing and working code.
Regards
Mike
## data ##
decay.data - ...
behaviors lift reach.uu estimated.conversions.uu total.reach
1 1 432.0083 770 7700.00
2 2 432.008329660296600.03
3 3 429.98643298500.03
4 4 427.859930320300200.03
5 5 424.010530680301100.03
6 6 418.471031180302000.03
7 7 412.002231840303600.03
8 8 405.455332340303500.03
9 9 397.008333260305600.03
1010 393.238233600305800.03
1111 385.543134940311800.03
1212 384.294235050311700.03
1313 374.029936110312600.03
1414 363.305737290313500.03
1515 353.118538450314200.03
1616 342.21904316800.03
1717 338.923240470317400.04
1818 328.866641880318800.04
1919 318.321945510335300.04
2020 308.120047230336800.04
If i use:
library(nlrwr)
# Build a model.
decay.model - nls(lift ~ SSexp(total.reach, y0, b), data = decay.data)
# plot the model
plot(decay.data[[total.reach]], decay.data[[lift]])
xv - seq(min(decay.data[[lift]]), max(decay.data[[total.reach]]), 0.02)
yv - predict(decay.model, newdata = list(total.reach = xv))
lines(xv,yv)
This works.
If i try and wrap this in a function and pass the argument values i fail when
i reach the list(total.reach = xv) i've tried various flavours or paste(),
but again can't figure out where i am going wrong, any help appreciated.
PlotDecayModel - function(x = total.reach,
y = lift,
data) {
decay.model - BuildDecayModel(x= total.reach,
y = lift,
data = data)
# Plot the lift Vs reach plot.
plot(data[[x]], data[[y]])
# Add the model curve to the plot.
xv - seq(min(data[[x]]), max(data[[x]]), 0.02)
yv - predict(decay.model, newdata = list(x = xv))
lines(xv,yv)
}
I return the error
Error in xy.coords(x, y) : 'x' and 'y' lengths differ
I can see this is because the function ignores the 'newdata = list(x = xv)'
as it is trying ot assign x on the data to be xv,
(which doesn't exist in the model), so how can i use the arg total.reach so
the argument 'newdata = list(x = xv)' is evaluated as
'newdata = list(total.reach = xv)'
Many thanks in advance
Mike
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Passing Arguments in a function
Hi Michael,
On Tue, Feb 15, 2011 at 7:15 AM, Michael Pearmain
michael.pearm...@gmail.com wrote:
Hi All,
I'm having some trouble assigning arguments inside a function to
produce a plot from a model
Can anyone help me? Below I've outlined the situation and examples of
failing and working code.
Regards
Mike
## data ##
decay.data - ...
behaviors lift reach.uu estimated.conversions.uu total.reach
1 1 432.0083 770 770 0.00
2 2 432.0083 29660 29660 0.03
3 3 429.9864 3 29850 0.03
4 4 427.8599 30320 30020 0.03
5 5 424.0105 30680 30110 0.03
6 6 418.4710 31180 30200 0.03
7 7 412.0022 31840 30360 0.03
8 8 405.4553 32340 30350 0.03
9 9 397.0083 33260 30560 0.03
10 10 393.2382 33600 30580 0.03
11 11 385.5431 34940 31180 0.03
12 12 384.2942 35050 31170 0.03
13 13 374.0299 36110 31260 0.03
14 14 363.3057 37290 31350 0.03
15 15 353.1185 38450 31420 0.03
16 16 342.2190 4 31680 0.03
17 17 338.9232 40470 31740 0.04
18 18 328.8666 41880 31880 0.04
19 19 318.3219 45510 33530 0.04
20 20 308.1200 47230 33680 0.04
If i use:
library(nlrwr)
# Build a model.
decay.model - nls(lift ~ SSexp(total.reach, y0, b), data = decay.data)
# plot the model
plot(decay.data[[total.reach]], decay.data[[lift]])
xv - seq(min(decay.data[[lift]]), max(decay.data[[total.reach]]), 0.02)
yv - predict(decay.model, newdata = list(total.reach = xv))
lines(xv,yv)
This works.
Actually it doesn't work for me. I get
xv - seq(min(decay.data[[lift]]), max(decay.data[[total.reach]]), 0.02)
Error in seq.default(min(decay.data[[lift]]),
max(decay.data[[total.reach]]), :
wrong sign in 'by' argument
If i try and wrap this in a function and pass the argument values i fail when
i reach the list(total.reach = xv) i've tried various flavours or paste(),
but again can't figure out where i am going wrong, any help appreciated.
Your example is not reproducible (you don't define the BuildDecayModel
function for us...) which makes it harder to help. But just by
eyeballing...
PlotDecayModel - function(x = total.reach,
y = lift,
data) {
decay.model - BuildDecayModel(x= total.reach,
Putting total.reach in quotes like this just sets x equal to the
text string total.reach, not to the value of x passed to the
function. If you want the x to be passed from the function remove the
quotes.
y = lift,
data = data)
# Plot the lift Vs reach plot.
plot(data[[x]], data[[y]])
# Add the model curve to the plot.
xv - seq(min(data[[x]]), max(data[[x]]), 0.02)
yv - predict(decay.model, newdata = list(x = xv))
lines(xv,yv)
}
I return the error
Error in xy.coords(x, y) : 'x' and 'y' lengths differ
I can see this is because the function ignores the 'newdata = list(x = xv)'
as it is trying ot assign x on the data to be xv,
(which doesn't exist in the model), so how can i use the arg total.reach so
the argument 'newdata = list(x = xv)' is evaluated as
'newdata = list(total.reach = xv)'
I would try something like
nd - list(xv)
names(nd) - x
yv - predict(decay.model, newdata = nd)
Many thanks in advance
HTH, if you still have difficulty please post a reproducible example.
Best,
Ista
Mike
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--
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org
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[R] passing arguments to a function problem
Dear R-users,
is there some way how to pass various colnames to the following code for
sorting data.frames?
mydf.ordered-with(mydf, mydf[order(colname1,colname2, colnameX, decreasing
= TRUE), ])
I was trying something like
Afunction-function (mydf,colnames,decreasing=T){
mydf.ordered-with(mydf, mydf[order(colnames, decreasing = decreasing),
])
}
but it didnt work
please help
thank you
Jiri Voller
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] passing arguments to a function problem
See orderBy in the doBy package.
On Sat, Jun 21, 2008 at 7:58 PM, Jiří Voller [EMAIL PROTECTED] wrote:
Dear R-users,
is there some way how to pass various colnames to the following code for
sorting data.frames?
mydf.ordered-with(mydf, mydf[order(colname1,colname2, colnameX, decreasing
= TRUE), ])
I was trying something like
Afunction-function (mydf,colnames,decreasing=T){
mydf.ordered-with(mydf, mydf[order(colnames, decreasing = decreasing),
])
}
but it didnt work
please help
thank you
Jiri Voller
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
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