Re: [R] Failure in predicting parameters

[Luigi Marongiu]

It worked. I re-written the equation as:
```
rutledge_param <- function(p, x, y) ( (p$M / ( 1 + exp(-(x-p$m)/p$s))
) + p$B ) - y
```
and used Desmos to estimate the slope, so:
```
estim <- nls.lm(par = list(m = halfCycle, s = 2.77, M = MaxFluo, B = high[1]),
fn = rutledge_param, x = 1:45, y = high)
summary(estim)
R <- rutledge(list(half_fluorescence = 27.1102, slope = 2.7680,
   max_fluorescence = 11839.7745, back_fluorescence =
-138.8615) , 1:45)
points(1:45, R, type="l", col="red")
```

Thanks

On Tue, Mar 16, 2021 at 8:29 AM Luigi Marongiu  wrote:
>
> Just an update:
> I tried with desmos and the fitting looks good. Desmos calculated the
> parameters as:
> Fmax = 11839.8
> Chalf = 27.1102 (with matches with my estimate of 27 cycles)
> k = 2.76798
> Fb = -138.864
> I forced R to accept the right parameters using a single named list
> and re-written the formula (it was a bit unclear in the paper):
> ```
> rutledge <- function(p, x) {
>   m = p$half_fluorescence
>   s = p$slope
>   M = p$max_fluorescence
>   B = p$back_fluorescence
>   y = (M / (1+exp( -((x-m)/s) )) ) + B
>   return(y)
> }
> ```
> but when I apply it I get a funny graph:
> ```
> desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
> max_fluorescence = 11839.8, back_fluorescence
> = -138.864) , high)
> ```
>
> On Mon, Mar 15, 2021 at 7:39 AM Luigi Marongiu  
> wrote:
> >
> > Hello,
> > the negative data comes from the machine. Probably I should use raw
> > data directly, although in the paper this requirement is not reported.
> > The p$x was a typo. Now I corrected it and I got this error:
> > ```
> >
> > > rutledge_param <- function(p, x, y) ((p$M / (1 + exp(-1*(x-p$m)/p$s))) + 
> > > p$B) - y
> > > estim <- nls.lm(par = list(m = halfFluo, s = slopes, M = MaxFluo, B = 
> > > high[1]),
> > + fn = rutledge_param, x = 1:45, y = high)
> > Error in dimnames(x) <- dn :
> >   length of 'dimnames' [2] not equal to array extent
> > ```
> > Probably because 'slopes' is a vector instead of a scalar. Since the
> > slope is changing, I don't think is right to use a scalar, but I tried
> > and I got:
> > ```
> > > estim <- nls.lm(par = list(m = halfFluo, s = 1, M = MaxFluo, B = high[1]),
> > + fn = rutledge_param, x = 1:45, y = high)
> > > estim
> > Nonlinear regression via the Levenberg-Marquardt algorithm
> > parameter estimates: 6010.94, 1, 12021.88, 4700.4928889
> > residual sum-of-squares: 1.14e+09
> > reason terminated: Relative error in the sum of squares is at most `ftol'.
> > ```
> > The values reported are the same I used at the beginning apart from
> > the last (the background parameter) which is 4700 instead of zero. If
> > I plug it, I get an L shaped plot that is worse than that at the
> > beginning:
> > ```
> > after = init = rutledge(halfFluo, 1, MaxFluo, 4700.4928889, high)
> > points(1:45, after, type="l", col="blue")
> > ```
> > What did I get wrong here?
> > Thanks
> >
> > On Sun, Mar 14, 2021 at 8:05 PM Bill Dunlap  
> > wrote:
> > >
> > > > rutledge_param <- function(p, x, y) ((p$M / (1 + 
> > > > exp(-1*(p$x-p$m)/p$s))) + p$B) - y
> > >
> > > Did you mean that p$x to be just x?  As is, this returns numeric(0)
> > > for the p that nls.lm gives it because p$x is NULL and NULL-aNumber is
> > > numeric().
> > >
> > > -Bill
> > >
> > > On Sun, Mar 14, 2021 at 9:46 AM Luigi Marongiu  
> > > wrote:
> > > >
> > > > Hello,
> > > > I would like to use the Rutledge equation
> > > > (https://pubmed.ncbi.nlm.nih.gov/15601990/) to model PCR data. The
> > > > equation is:
> > > > Fc = Fmax / (1+exp(-(C-Chalf)/k)) + Fb
> > > > I defined the equation and another that subtracts the values from the
> > > > expectations. I used minpack.lm to get the parameters, but I got an
> > > > error:
> > > > ```
> > > >
> > > > > library("minpack.lm")
> > > > > h <- c(120.64, 66.14, 34.87, 27.11, 8.87, -5.8, 4.52, -7.16, -17.39,
> > > > +-14.29, -20.26, -14.99, -21.05, -20.64, -8.03, -21.56, -1.28, 
> > > > 15.01,
> > > > +75.26, 191.76, 455.09, 985.96, 1825.59, 2908.08, 3993.18, 
> > > > 5059.94,
> > > > +6071.93, 6986.32, 7796.01, 8502.25, 9111.46, 9638.01, 10077.19,
> > > > +10452.02, 10751.81, 11017.49, 11240.37, 11427.47, 11570.07, 
> > > > 11684.96,
> > > > +11781.77, 11863.35, 11927.44, 11980.81, 12021.88, 12058.35, 
> > > > 12100.63,
> > > > +12133.57, 12148.89, 12137.09)
> > > > > high <- h[1:45]
> > > > > MaxFluo <- max(high)
> > > > > halfFluo <- MaxFluo/2
> > > > > halfCycle = 27
> > > > > find_slope <- function(X, Y) {
> > > > +   Slope <- c(0)
> > > > +   for (i in 2:length(X)) {
> > > > + delta_x <- X[i] - X[i-1]
> > > > + delta_y <- Y[i] - Y[i-1]
> > > > + Slope[i] <- delta_y/delta_x
> > > > +   }
> > > > +   return(Slope)
> > > > + }
> > > > > slopes <- find_slope(1:45, high)
> > > > >
> > > > > rutledge <- function(m, s, M, B, x) {
> > > > +   divisor = 1 + exp(-1* ((x-m)/s) )
> > > > +

Re: [R] modelling 4-parameter curve in R does not match data - how to proceed?

[Luigi Marongiu]

Oh, I got it! I was sending the fluorescence instead of the cycles x.
Thank you

```
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
max_fluorescence = 11839.8, back_fluorescence
= -138.864) , 1:45)
```

On Wed, Mar 17, 2021 at 8:58 PM Duncan Murdoch  wrote:
>
> On 17/03/2021 12:37 p.m., Luigi Marongiu wrote:
> > sorry, I don't get it...
>
> Modify your rutledge function to print x, and you'll see the values of
> high printed.  x should be 1:45.
>
> Duncan Murdoch
>
> >
> > On Wed, Mar 17, 2021 at 2:35 PM Duncan Murdoch  
> > wrote:
> >>
> >> On 17/03/2021 6:59 a.m., Luigi Marongiu wrote:
> >>> yes, but in `rutledge` I model y as `y = (M / ( 1 + exp(-(x-m)/s)) ) +
> >>> B`, with x being 1:45. Isn't that the equivalent of what I fed Desmos
> >>> with? Tx
> >>
> >> No, it's not.
> >>
> >> Duncan Murdoch
> >>
> >>>
> >>> On Wed, Mar 17, 2021 at 11:31 AM Duncan Murdoch
> >>>  wrote:
> 
>  On 17/03/2021 5:41 a.m., Luigi Marongiu wrote:
> > Hello,
> > I have a dataset from a polymerase chain reaction. I am using the
> > equation given by Rutledge
> > (https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
> > does not match the data. I ran the same thing in Desmos and instead
> > the profile is correct (attached).
> > Why do I not get the same matching model as in Desmos? I believe the
> > formula in R is the same as the one in Desmos, and I am using the same
> > parameters.
> > Is there a procedure to debug models?
> > Thanks
> >
> > Here is the code:
> > ```
> > high <- c(120.64, 66.14, 34.87, 27.11, 8.87, -5.8, 4.52, -7.16, -17.39,
> >   -14.29, -20.26, -14.99, -21.05, -20.64, -8.03, -21.56, -1.28, 
> > 15.01,
> >   75.26, 191.76, 455.09, 985.96, 1825.59, 2908.08, 3993.18, 
> > 5059.94,
> >   6071.93, 6986.32, 7796.01, 8502.25, 9111.46, 9638.01, 
> > 10077.19,
> >   10452.02, 10751.81, 11017.49, 11240.37, 11427.47, 11570.07, 
> > 11684.96,
> >   11781.77, 11863.35, 11927.44, 11980.81, 12021.88)
> > plot(1:45, high, type = "l")
> > rutledge <- function(p, x) {
> >  m = p$half_fluorescence
> >  s = p$slope
> >  M = p$max_fluorescence
> >  B = p$back_fluorescence
> >  y = (M / ( 1 + exp(-(x-m)/s)) ) + B
> >  return(y)
> > }
> > desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
> >max_fluorescence = 11839.8, back_fluorescence
> > = -138.864) , high)
> >
> > points(1:45, desmos, type="l", col="blue")
> 
> 
>  In your calculation of desmos, you are using the Y variable for x in the
>  formula.  Calculate it this way instead:
> 
>  desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
>   max_fluorescence = 11839.8, 
>  back_fluorescence
>  = -138.864) , 1:45)
> 
>  Duncan Murdoch
> 
> >>>
> >>>
> >>
> >
> >
>


-- 
Best regards,
Luigi

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Re: [R] help

[hatice gürdil]

Thank you so much
I thought that ncol is for dimension .
ncol= 2, 2x2 matris for 2 dimension
ncol= 3, 3x3 matris for 3 dimention

I have to work a little more considering what you said.

Cheers,

Hatice Gürdil.

Bill Dunlap , 16 Mar 2021 Sal, 21:09 tarihinde
şunu yazdı:

> The length of the mean vector must match the number of rows and
> columns of the sigma matrix.  Once you give 3 entries in the mean
> vector you will run into the problem that the sigma you are using is
> not positive (semi-)definite - a variance must be the product of a
> matrix and its transpose.
>
> -Bill
>
> On Tue, Mar 16, 2021 at 10:55 AM hatice gürdil
>  wrote:
> >
> > Code a is working. But code b is given error like given below. How can I
> > write code b?
> >
> > > a<-rmvnorm(750, mean=c(0, 0),
> > +sigma=matrix(c(1, .3, .3, 1), ncol=2))
> >
> > > head(a)
> > [,1][,2]
> > [1,] -0.97622921 -0.87129405
> > [2,]  0.54763494  0.16080131
> > [3,] -1.16627647  0.31225125
> > [4,]  1.72541168  2.06513939
> > [5,]  0.05372489 -0.07525197
> > [6,] -0.85062230 -1.02188473
> >
> > > b<-rmvnorm(round(500,0), mean=c(0,-1),
> > +sigma=matrix(c(.3, 1,1,1,.3, 1, 1,1, .3),
> ncol=3))
> >
> > Error in rmvnorm(round(500, 0), mean = c(0, -1), sigma = matrix(c(0.3,  :
> >   mean and sigma have non-conforming size
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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.
>

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[R] [R-pkgs] domir: Tools to Support Relative Importance Analysis

[Joseph Luchman]

Hello All,

  I am pleased to announce that {domir} is now available on CRAN.

  {domir} aims to provide broadly applicable tools for the relative 
importance analysis of facets of statistical models and machine 
learning algorithms.  The focus for this initial release is on 
Dominance Analysis/Shapley Value Decomposition as a methodology - which 
is to be expanded in future versions.

  I hope the community finds the tool(s) in this package of value and I 
look forward to further developing the package in collaboration with 
the community.

  Note: {domir} version 0.0.0 has a known bug that affects 
functionality in R versions < 4.  Working on a patch to revise.

  Cordially,

- Joseph

CRAN: 
GibHub: 


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[R] [R-pkgs] Splinets

[Krzysztof Podgórski]

Splinets -- a package with an efficient B-spline orthogonalization suitable for 
sparse functional data analysis.

See also: 

Liu, X., Nassar, H., Podgórski, K. (2019) "Splinets – efficient 
orthonormalization of the B-splines." .
Podgórski, K. (2021) "Splinets – splines through the Taylor expansion, their 
support sets and orthogonal bases." .
 

#
Krzysztof Podgorski
Professor
Department of Statistics 
Lund University
#
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[R] [R-pkgs] {miclust} Multiple imputation & cluster analysis

[Jose Barrera]

Dear all,

Want to perform cluster analysis but you have missing data?

Following researchers' suggestion, our R package miclust is now on CRAN:
https://CRAN.R-project.org/package=miclust

miclust implements a framework to integrate multiple imputed data sets due
to missing data in cluster analysis. Methods are described in the original
work: https://academic.oup.com/aje/article/177/7/718/91109

I hope you find it helpful.

On behalf of the authors,

Jose Barrera
Statistician, Associate Lecturer

*IS**Global*
Barcelona Institute for Global Health - Campus MAR
Barcelona Biomedical Research Park (PRBB) (Room Hypatia)

Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 2147383
jose.barr...@isglobal.org

Personal website: sites.google.com/view/josebarrera
www.isglobal.org

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Re: [R] modelling 4-parameter curve in R does not match data - how to proceed?

[Duncan Murdoch]

On 17/03/2021 12:37 p.m., Luigi Marongiu wrote:

sorry, I don't get it...


Modify your rutledge function to print x, and you'll see the values of 
high printed.  x should be 1:45.


Duncan Murdoch



On Wed, Mar 17, 2021 at 2:35 PM Duncan Murdoch  wrote:


On 17/03/2021 6:59 a.m., Luigi Marongiu wrote:

yes, but in `rutledge` I model y as `y = (M / ( 1 + exp(-(x-m)/s)) ) +
B`, with x being 1:45. Isn't that the equivalent of what I fed Desmos
with? Tx


No, it's not.

Duncan Murdoch



On Wed, Mar 17, 2021 at 11:31 AM Duncan Murdoch
 wrote:


On 17/03/2021 5:41 a.m., Luigi Marongiu wrote:

Hello,
I have a dataset from a polymerase chain reaction. I am using the
equation given by Rutledge
(https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
does not match the data. I ran the same thing in Desmos and instead
the profile is correct (attached).
Why do I not get the same matching model as in Desmos? I believe the
formula in R is the same as the one in Desmos, and I am using the same
parameters.
Is there a procedure to debug models?
Thanks

Here is the code:
```
high <- c(120.64, 66.14, 34.87, 27.11, 8.87, -5.8, 4.52, -7.16, -17.39,
  -14.29, -20.26, -14.99, -21.05, -20.64, -8.03, -21.56, -1.28, 15.01,
  75.26, 191.76, 455.09, 985.96, 1825.59, 2908.08, 3993.18, 5059.94,
  6071.93, 6986.32, 7796.01, 8502.25, 9111.46, 9638.01, 10077.19,
  10452.02, 10751.81, 11017.49, 11240.37, 11427.47, 11570.07, 11684.96,
  11781.77, 11863.35, 11927.44, 11980.81, 12021.88)
plot(1:45, high, type = "l")
rutledge <- function(p, x) {
 m = p$half_fluorescence
 s = p$slope
 M = p$max_fluorescence
 B = p$back_fluorescence
 y = (M / ( 1 + exp(-(x-m)/s)) ) + B
 return(y)
}
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
   max_fluorescence = 11839.8, back_fluorescence
= -138.864) , high)

points(1:45, desmos, type="l", col="blue")



In your calculation of desmos, you are using the Y variable for x in the
formula.  Calculate it this way instead:

desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
 max_fluorescence = 11839.8, back_fluorescence
= -138.864) , 1:45)

Duncan Murdoch











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Re: [R] library(hms)

[John Fox]

Dear Greg,

As I explained to you in a private email, and as others have told you, 
there is no Install.libraries() command, nor is there an 
install.libraries(0 command, but there is an install.packages() command.


So install.packages("hms") should work, on a Mac or on any other 
internet-connected computer on which R runs -- as you've also been told 
by others, this is not a Mac-specific issue. Note that the argument to 
install.packages must be quoted. See ?install.packages for details.


I'll also repeat the advice that I gave you privately to learn something 
about R before you try to use it, possibly starting with the "An 
Introduction to R" manual that ships with the standard R distribution.


Best,
 John

John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/

On 2021-03-17 1:07 p.m., Gregory Coats wrote:

On my MacBook, I do not have, and do not know how to install, library(hms).
Greg Coats


library(hms)

Error in library(hms) : there is no package called ‘hms’

Install.libraries(“hms”)

Error: unexpected input in "Install.libraries(“"




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Re: [R] library(hms)

[Gregory Coats via R-help]

It appears that 
install.libraries(“hms”)
is unsuccessful, but that
install.packages(“hms”)
is successful.

install.packages("lubridate")
downloaded 1.5 MB
install.packages("hms")
downloaded 95 KB
install.packages("data.table")
downloaded 2.2 MB
Greg
> On Mar 17, 2021, at 1:07 PM, Gregory Coats via R-help  
> wrote:
> 
> On my MacBook, I do not have, and do not know how to install, library(hms).
> Greg Coats
> 
>> library(hms)
> Error in library(hms) : there is no package called ‘hms’
>> Install.libraries(“hms”)
> Error: unexpected input in "Install.libraries(“"
>> 
>   [[alternative HTML version deleted]]
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> and provide commented, minimal, self-contained, reproducible code.


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Re: [R] library(hms)

[Caitlin Gibbons]

Your opening quote looks slightly different from the closing quote. This 
probably explains why you received the error message regarding “unexpected 
input”. 

I hope this helps. 


> On Mar 17, 2021, at 10:08 AM, Gregory Coats via R-help  
> wrote:
> 
> On my MacBook, I do not have, and do not know how to install, library(hms).
> Greg Coats
> 
>> library(hms)
> Error in library(hms) : there is no package called ‘hms’
>> Install.libraries(“hms”)
> Error: unexpected input in "Install.libraries(“"
>> 
>[[alternative HTML version deleted]]
> 
> __
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> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] [External] unanticipated axis labels

[Richard M. Heiberger]

exactly!
a warning when running would be very helpful.

Thank you.

Rich

> On Mar 17, 2021, at 02:41, Deepayan Sarkar  wrote:
> 
> On Tue, Mar 16, 2021 at 11:35 PM Richard M. Heiberger  wrote:
>> 
>> library(lattice)
>> library(latticeExtra)
>> 
>> barchart(matrix(c(1:6, 5:6)), main="unanticipated left axis labels", 
>> ylab="unanticipated inside labels") +
>>  latticeExtra::layer(panel.axis("left", half=FALSE, labels=1:8))
> 
> So to summarize, your problem case happens when you explicitly specify
> 'labels' but not 'at' in panel.axis(), right?
> 
> Unfortunately, this is not intended to work at all, so what you are
> seeing is undefined behaviour. This is hinted at, but not quite
> explicitly spelled out, in the documentation. I will fix that, and
> maybe add a warning as well.
> 
> -Deepayan
> 
>> barchart(matrix(c(1:6, 5:6)), main="ok 1", ylab="anticipated") +
>>  latticeExtra::layer(panel.axis("left", half=FALSE, labels=1:8, at=1:8))
>> 
>> barchart(matrix(c(1:6, 5:6)), main="ok 2", ylab="anticipated") +
>>  latticeExtra::layer(panel.axis("left", half=FALSE, at=1:8))
>> 
>> barchart(matrix(c(1:6, 5:6)), main="ok 3", ylab="anticipated") +
>>  latticeExtra::layer(panel.axis("left", half=FALSE))
>> 
>> 
>> 
>> __
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>> https://stat.ethz.ch/mailman/listinfo/r-help
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>> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] library(hms)

[Caitlin Gibbons]

Maybe you used the wrong quotes with the parentheses? 

> On Mar 17, 2021, at 10:08 AM, Gregory Coats via R-help  
> wrote:
> 
> On my MacBook, I do not have, and do not know how to install, library(hms).
> Greg Coats
> 
>> library(hms)
> Error in library(hms) : there is no package called ‘hms’
>> Install.libraries(“hms”)
> Error: unexpected input in "Install.libraries(“"
>> 
>[[alternative HTML version deleted]]
> 
> __
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> 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.

[[alternative HTML version deleted]]

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Re: [R] library(hms)

[Mark Leeds]

Hi: install.packages("hms") should work if you have R installed along with
an internet connection.

When you do above, if you get a message about other packages needing to be
installed, then use

install.packages("hms", dependencies = TRUE).





On Wed, Mar 17, 2021 at 1:08 PM Gregory Coats via R-help <
r-help@r-project.org> wrote:

> On my MacBook, I do not have, and do not know how to install, library(hms).
> Greg Coats
>
> > library(hms)
> Error in library(hms) : there is no package called ‘hms’
> > Install.libraries(“hms”)
> Error: unexpected input in "Install.libraries(“"
> >
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
>

[[alternative HTML version deleted]]

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Re: [R] library(hms)

[Bill Dunlap]

install.packages("hms")

A 'library' is a directory (aka folder) that contains installed
'packages'.  I.e., one installs packages into a library, but one does
not install a library.

-Bill

On Wed, Mar 17, 2021 at 10:08 AM Gregory Coats via R-help
 wrote:
>
> On my MacBook, I do not have, and do not know how to install, library(hms).
> Greg Coats
>
> > library(hms)
> Error in library(hms) : there is no package called ‘hms’
> > Install.libraries(“hms”)
> Error: unexpected input in "Install.libraries(“"
> >
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.

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[R] library(hms)

[Gregory Coats via R-help]

On my MacBook, I do not have, and do not know how to install, library(hms).
Greg Coats

> library(hms)
Error in library(hms) : there is no package called ‘hms’
> Install.libraries(“hms”)
Error: unexpected input in "Install.libraries(“"
> 
[[alternative HTML version deleted]]

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Re: [R] modelling 4-parameter curve in R does not match data - how to proceed?

[Luigi Marongiu]

sorry, I don't get it...

On Wed, Mar 17, 2021 at 2:35 PM Duncan Murdoch  wrote:
>
> On 17/03/2021 6:59 a.m., Luigi Marongiu wrote:
> > yes, but in `rutledge` I model y as `y = (M / ( 1 + exp(-(x-m)/s)) ) +
> > B`, with x being 1:45. Isn't that the equivalent of what I fed Desmos
> > with? Tx
>
> No, it's not.
>
> Duncan Murdoch
>
> >
> > On Wed, Mar 17, 2021 at 11:31 AM Duncan Murdoch
> >  wrote:
> >>
> >> On 17/03/2021 5:41 a.m., Luigi Marongiu wrote:
> >>> Hello,
> >>> I have a dataset from a polymerase chain reaction. I am using the
> >>> equation given by Rutledge
> >>> (https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
> >>> does not match the data. I ran the same thing in Desmos and instead
> >>> the profile is correct (attached).
> >>> Why do I not get the same matching model as in Desmos? I believe the
> >>> formula in R is the same as the one in Desmos, and I am using the same
> >>> parameters.
> >>> Is there a procedure to debug models?
> >>> Thanks
> >>>
> >>> Here is the code:
> >>> ```
> >>> high <- c(120.64, 66.14, 34.87, 27.11, 8.87, -5.8, 4.52, -7.16, -17.39,
> >>>  -14.29, -20.26, -14.99, -21.05, -20.64, -8.03, -21.56, -1.28, 
> >>> 15.01,
> >>>  75.26, 191.76, 455.09, 985.96, 1825.59, 2908.08, 3993.18, 
> >>> 5059.94,
> >>>  6071.93, 6986.32, 7796.01, 8502.25, 9111.46, 9638.01, 10077.19,
> >>>  10452.02, 10751.81, 11017.49, 11240.37, 11427.47, 11570.07, 
> >>> 11684.96,
> >>>  11781.77, 11863.35, 11927.44, 11980.81, 12021.88)
> >>> plot(1:45, high, type = "l")
> >>> rutledge <- function(p, x) {
> >>> m = p$half_fluorescence
> >>> s = p$slope
> >>> M = p$max_fluorescence
> >>> B = p$back_fluorescence
> >>> y = (M / ( 1 + exp(-(x-m)/s)) ) + B
> >>> return(y)
> >>> }
> >>> desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
> >>>   max_fluorescence = 11839.8, back_fluorescence
> >>> = -138.864) , high)
> >>>
> >>> points(1:45, desmos, type="l", col="blue")
> >>
> >>
> >> In your calculation of desmos, you are using the Y variable for x in the
> >> formula.  Calculate it this way instead:
> >>
> >> desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
> >> max_fluorescence = 11839.8, back_fluorescence
> >>= -138.864) , 1:45)
> >>
> >> Duncan Murdoch
> >>
> >
> >
>


-- 
Best regards,
Luigi

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Re: [R] modelling 4-parameter curve in R does not match data - how to proceed?

[Duncan Murdoch]

On 17/03/2021 6:59 a.m., Luigi Marongiu wrote:

yes, but in `rutledge` I model y as `y = (M / ( 1 + exp(-(x-m)/s)) ) +
B`, with x being 1:45. Isn't that the equivalent of what I fed Desmos
with? Tx


No, it's not.

Duncan Murdoch



On Wed, Mar 17, 2021 at 11:31 AM Duncan Murdoch
 wrote:


On 17/03/2021 5:41 a.m., Luigi Marongiu wrote:

Hello,
I have a dataset from a polymerase chain reaction. I am using the
equation given by Rutledge
(https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
does not match the data. I ran the same thing in Desmos and instead
the profile is correct (attached).
Why do I not get the same matching model as in Desmos? I believe the
formula in R is the same as the one in Desmos, and I am using the same
parameters.
Is there a procedure to debug models?
Thanks

Here is the code:
```
high <- c(120.64, 66.14, 34.87, 27.11, 8.87, -5.8, 4.52, -7.16, -17.39,
 -14.29, -20.26, -14.99, -21.05, -20.64, -8.03, -21.56, -1.28, 15.01,
 75.26, 191.76, 455.09, 985.96, 1825.59, 2908.08, 3993.18, 5059.94,
 6071.93, 6986.32, 7796.01, 8502.25, 9111.46, 9638.01, 10077.19,
 10452.02, 10751.81, 11017.49, 11240.37, 11427.47, 11570.07, 11684.96,
 11781.77, 11863.35, 11927.44, 11980.81, 12021.88)
plot(1:45, high, type = "l")
rutledge <- function(p, x) {
m = p$half_fluorescence
s = p$slope
M = p$max_fluorescence
B = p$back_fluorescence
y = (M / ( 1 + exp(-(x-m)/s)) ) + B
return(y)
}
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
  max_fluorescence = 11839.8, back_fluorescence
= -138.864) , high)

points(1:45, desmos, type="l", col="blue")



In your calculation of desmos, you are using the Y variable for x in the
formula.  Calculate it this way instead:

desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
max_fluorescence = 11839.8, back_fluorescence
   = -138.864) , 1:45)

Duncan Murdoch






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Re: [R] Problem with the str_replace function

[phil]

Your help is much appreciated. I now understand what my problem was and 
can move forward.


Philip


On 2021-03-17 01:19, Hervé Pagès wrote:

Hi,

stringr::str_replace() treats the 2nd argument ('pattern') as a
regular expression and some characters have a special meaning when
they are used in a regular expression. For example the dot plays the
role of a wildcard (i.e. it means "any character"):

  > str_replace("aaXcc", "a.c", "ZZ")
  [1] "aZZc"

If you want to treat a special character literally, you need to escape
it with a double backslahe '\\':

  > str_replace(c("aaXcc", "aa.cc"), "a.c", "ZZ")
  [1] "aZZc" "aZZc"

  > str_replace(c("aaXcc", "aa.cc"), "a\\.c", "ZZ")
  [1] "aaXcc" "aZZc"

Turns out that parenthesis are also special characters so you also
need to escape them:

  > str_replace("aa(X)cc", "a(X)c", "ZZ")
  [1] "aa(X)cc"

  > str_replace("aa(X)cc", "a\\(X\\)c", "ZZ")
  [1] "aZZc"

There are plenty of example in the man page for str_replace() (see
'?str_replace') including examples showing the use of parenthesis in
the pattern.

Hope this helps,

H.


On 3/16/21 5:34 PM, p...@philipsmith.ca wrote:
I have a problem with the str_replace() function in the stringr 
package. Please refer to my reprex below.


I start with a vector of strings, called x. Some of the strings 
contain apostrophes and brackets. I make a simple replacement as with 
x1, and there is no problem. I make another simple replacement, x2, 
where the pattern string has an apostrophe. Again no problem. Then I 
make a third replacement, x3, where the pattern has opening and 
closing brackets and the function still works fine. Finally I make a 
replacement where the pattern has both an apostrophe and opening and 
closing brackets and the replacement does not work. I tried to solve 
this by putting backslashes before the apostrophe and/or the brackets, 
but that accomplished nothing. I am stumped.


# Reprex for str_replace problem

library(stringr)

x <- c(
   "Clothing and footwear",
   "Women's clothing",
   "Women's footwear (excluding athletic)",
   "Clothing accessories (belts and so on)",
   "Clothing and footwear",
   "Women's clothing",
   "Women's footwear (excluding athletic)",
   "Clothing accessories (belts and so on)"
)
x
x1 <- str_replace(x,
   "Clothing and footwear",
   "Clothing and shoes"
)
x1
x2 <- str_replace(x,
   "Women's clothing",
   "Women's clothing goods"
)
x2
x3 <- str_replace(x,
   "Clothing accessories (belts and so on)",
   "Clothing accessories")
x3
x4 <- str_replace(x,
   "Women's footwear (excluding athletic)",
   "Women's footwear")
x4

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Re: [R] modelling 4-parameter curve in R does not match data - how to proceed?

[Luigi Marongiu]

yes, but in `rutledge` I model y as `y = (M / ( 1 + exp(-(x-m)/s)) ) +
B`, with x being 1:45. Isn't that the equivalent of what I fed Desmos
with? Tx

On Wed, Mar 17, 2021 at 11:31 AM Duncan Murdoch
 wrote:
>
> On 17/03/2021 5:41 a.m., Luigi Marongiu wrote:
> > Hello,
> > I have a dataset from a polymerase chain reaction. I am using the
> > equation given by Rutledge
> > (https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
> > does not match the data. I ran the same thing in Desmos and instead
> > the profile is correct (attached).
> > Why do I not get the same matching model as in Desmos? I believe the
> > formula in R is the same as the one in Desmos, and I am using the same
> > parameters.
> > Is there a procedure to debug models?
> > Thanks
> >
> > Here is the code:
> > ```
> > high <- c(120.64, 66.14, 34.87, 27.11, 8.87, -5.8, 4.52, -7.16, -17.39,
> > -14.29, -20.26, -14.99, -21.05, -20.64, -8.03, -21.56, -1.28, 15.01,
> > 75.26, 191.76, 455.09, 985.96, 1825.59, 2908.08, 3993.18, 5059.94,
> > 6071.93, 6986.32, 7796.01, 8502.25, 9111.46, 9638.01, 10077.19,
> > 10452.02, 10751.81, 11017.49, 11240.37, 11427.47, 11570.07, 
> > 11684.96,
> > 11781.77, 11863.35, 11927.44, 11980.81, 12021.88)
> > plot(1:45, high, type = "l")
> > rutledge <- function(p, x) {
> >m = p$half_fluorescence
> >s = p$slope
> >M = p$max_fluorescence
> >B = p$back_fluorescence
> >y = (M / ( 1 + exp(-(x-m)/s)) ) + B
> >return(y)
> > }
> > desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
> >  max_fluorescence = 11839.8, back_fluorescence
> > = -138.864) , high)
> >
> > points(1:45, desmos, type="l", col="blue")
>
>
> In your calculation of desmos, you are using the Y variable for x in the
> formula.  Calculate it this way instead:
>
> desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
>max_fluorescence = 11839.8, back_fluorescence
>   = -138.864) , 1:45)
>
> Duncan Murdoch
>


-- 
Best regards,
Luigi

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Re: [R] modelling 4-parameter curve in R does not match data - how to proceed?

[Duncan Murdoch]

On 17/03/2021 5:41 a.m., Luigi Marongiu wrote:

Hello,
I have a dataset from a polymerase chain reaction. I am using the
equation given by Rutledge
(https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
does not match the data. I ran the same thing in Desmos and instead
the profile is correct (attached).
Why do I not get the same matching model as in Desmos? I believe the
formula in R is the same as the one in Desmos, and I am using the same
parameters.
Is there a procedure to debug models?
Thanks

Here is the code:
```
high <- c(120.64, 66.14, 34.87, 27.11, 8.87, -5.8, 4.52, -7.16, -17.39,
-14.29, -20.26, -14.99, -21.05, -20.64, -8.03, -21.56, -1.28, 15.01,
75.26, 191.76, 455.09, 985.96, 1825.59, 2908.08, 3993.18, 5059.94,
6071.93, 6986.32, 7796.01, 8502.25, 9111.46, 9638.01, 10077.19,
10452.02, 10751.81, 11017.49, 11240.37, 11427.47, 11570.07, 11684.96,
11781.77, 11863.35, 11927.44, 11980.81, 12021.88)
plot(1:45, high, type = "l")
rutledge <- function(p, x) {
   m = p$half_fluorescence
   s = p$slope
   M = p$max_fluorescence
   B = p$back_fluorescence
   y = (M / ( 1 + exp(-(x-m)/s)) ) + B
   return(y)
}
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
 max_fluorescence = 11839.8, back_fluorescence
= -138.864) , high)

points(1:45, desmos, type="l", col="blue")



In your calculation of desmos, you are using the Y variable for x in the 
formula.  Calculate it this way instead:


desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
  max_fluorescence = 11839.8, back_fluorescence
 = -138.864) , 1:45)

Duncan Murdoch

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[R] modelling 4-parameter curve in R does not match data - how to proceed?

[Luigi Marongiu]

Hello,
I have a dataset from a polymerase chain reaction. I am using the
equation given by Rutledge
(https://pubmed.ncbi.nlm.nih.gov/15601990/) but the profile I get in R
does not match the data. I ran the same thing in Desmos and instead
the profile is correct (attached).
Why do I not get the same matching model as in Desmos? I believe the
formula in R is the same as the one in Desmos, and I am using the same
parameters.
Is there a procedure to debug models?
Thanks

Here is the code:
```
high <- c(120.64, 66.14, 34.87, 27.11, 8.87, -5.8, 4.52, -7.16, -17.39,
   -14.29, -20.26, -14.99, -21.05, -20.64, -8.03, -21.56, -1.28, 15.01,
   75.26, 191.76, 455.09, 985.96, 1825.59, 2908.08, 3993.18, 5059.94,
   6071.93, 6986.32, 7796.01, 8502.25, 9111.46, 9638.01, 10077.19,
   10452.02, 10751.81, 11017.49, 11240.37, 11427.47, 11570.07, 11684.96,
   11781.77, 11863.35, 11927.44, 11980.81, 12021.88)
plot(1:45, high, type = "l")
rutledge <- function(p, x) {
  m = p$half_fluorescence
  s = p$slope
  M = p$max_fluorescence
  B = p$back_fluorescence
  y = (M / ( 1 + exp(-(x-m)/s)) ) + B
  return(y)
}
desmos <- rutledge(list(half_fluorescence = 27.1102, slope = 2.76798,
max_fluorescence = 11839.8, back_fluorescence
= -138.864) , high)

points(1:45, desmos, type="l", col="blue")
```

-- 
Best regards,
Luigi
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Re: [R] How to plot dates

[PIKAL Petr]

Hi

install.packages("lubridate") does not work on Mac?

Cheers
Petr


> -Original Message-
> From: R-help  On Behalf Of Gregory Coats
> via R-help
> Sent: Wednesday, March 17, 2021 1:11 AM
> To: Daniel Nordlund 
> Cc: r-help mailing list 
> Subject: Re: [R] How to plot dates
> 
> Dan, Thank you for this guidance.
> Unfortunately, I do not have the library lubridate, and I do not at this
> moment know where to go to get this library for an Apple MacBook.
> 
> > library(lubridate)
> Error in library(lubridate) : there is no package called ‘lubridate’
> 
> Greg Coats
> Reston, Virginia USA
> 
> > On Mar 16, 2021, at 7:49 PM, Daniel Nordlund 
> wrote:
> >
> > # create timepart variable - tme
> > library(lubridate)
> 
> 
>   [[alternative HTML version deleted]]
> 
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