Re: [R] dependent nested for loops in R

[David Winsemius]

On 1/31/21 1:26 PM, Berry, Charles wrote:



On Jan 30, 2021, at 9:32 PM, Shaami  wrote:

Hi
I have made the sample code again. Could you please guide how to use
vectorization for variables whose next value depends on the previous one?



I agree with Charles that I suspect your results are not what you 
expect. You should try using cat or print to output intermediate results 
to the console. I would suggest you limit your examination to a more 
manageable length, say the first 10 results while you are working out 
your logic. After you have the logic debugged, you can move on to long 
sequences.



This is my suggestion for a more compact solution (at least for the 
inner loop calculation):


set.seed(123)

x <- rnorm(2000)

z <- Reduce( function(x,y) { sum(y+5*x) }, x, accumulate=TRUE)

w<- numeric(2000)

w <-  (1:2000)[ z >4 | z < 1 ]  # In your version the w values get 
overwritten and end up all being 2000



I would also advise making a natural language statement of the problem 
and goals. I'm thinking that you may be missing certain aspects of the 
underying problem.


--

David.



Glad to help.

First, it could help you to trace your code.  I suspect that the results are 
not at all what you want and tracing would help you see that.

I suggest running this revision and printing out x, z, and w.

#+begin_src R
   w = NULL
   for(j in 1:2)
   {
 z = NULL
 x = rnorm(10)
 z[1] = x[1]
 for(i in 2:10)
 {
   z[i] = x[i]+5*z[i-1]
   if(z[i]>4 | z[i]<1) {
w[j]=i
   } else {
w[j] = 0
   }
 }
   }
#+end_src


You should be able to see that the value of w can easily be obtained outside of 
the `i' loop.



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Re: [R] union of two sets are smaller than one set?

[Avi Gross via R-help]

Martin,

You did not say your two starting objects were already sets. You said they
were vectors of strings. It may well be that your strings included
duplicates. For example, If I read in lots of text with a blank line between
paragraphs, I would have lots of seemingly empty and identical parts. Just
converting that into a set would shrink it.

You have not said how you created or processed your initial two vectors. It
is also possible parts were sort of DELETED as in removing the string
pointed to by some entry but leaving a null pointer of sorts which would
leave the length of the vector longer than the useful contents.

Your strings seem to be what may be filenames. Are they unique, especially
if they are files in different folders/directories?

There are many ways to check, but using your method, try this:

length(base::union(s1, s1))

-Original Message-
From: R-help  On Behalf Of Martin Møller
Skarbiniks Pedersen
Sent: Sunday, January 31, 2021 3:57 PM
To: R mailing list 
Subject: [R] union of two sets are smaller than one set?

This is really puzzling me and when I try to make a small example everything
works like expected.

The problem:

I got these two large vectors of strings.

> str(s1)
 chr [1:766608] "0.dk" ...
> str(s2)
 chr [1:59387] "043.dk" "0606.dk" "0618.dk" "0888.dk" "0iq.dk" "0it.dk" ...

And I need to create the union-set of s1 and s2.
I expect the size of the union-set to be between 766608 and 766608+59387.
However it is 681193 which is less that number of elements in s1!

> length(base::union(s1, s2))
[1] 681193

Any hints?

Regards
Martin

[[alternative HTML version deleted]]

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Re: [R] dependent nested for loops in R

[Berry, Charles]

> On Jan 30, 2021, at 9:32 PM, Shaami  wrote:
> 
> Hi
> I have made the sample code again. Could you please guide how to use
> vectorization for variables whose next value depends on the previous one?
> 


Glad to help.

First, it could help you to trace your code.  I suspect that the results are 
not at all what you want and tracing would help you see that.

I suggest running this revision and printing out x, z, and w.

#+begin_src R
  w = NULL
  for(j in 1:2)
  {
z = NULL
x = rnorm(10)
z[1] = x[1]
for(i in 2:10)
{
  z[i] = x[i]+5*z[i-1]
  if(z[i]>4 | z[i]<1) {
w[j]=i
  } else {
w[j] = 0
  }
}
  }
#+end_src


You should be able to see that the value of w can easily be obtained outside of 
the `i' loop.

-- 

If inspecting those results did not make you go back and rethink your approach, 
try writing the expression for 

z[n] = x[n] + ... + k * x[1]

If you are not good with algebra write out each of z[1], z[2], z[3] and z[4] in 
terms of x[1:4] and then look at what you have.

Perhaps the value of `k' will surprise you.

In any case, if the code is truly what you intended, you only need x[1:25] to 
get z[n] to double precision for any n.  So, 

Also, you will hardly ever be able to compute the value of z[n] for n > 450. 

If these last two statements are puzzling, see 
https://en.wikipedia.org/wiki/Floating-point_arithmetic

HTH,
Chuck

> w = NULL
> 
> for(j in 1:1000)
> 
> {
> 
>  z = NULL
> 
>  x = rnorm(2000)
> 
>  z[1] = x[1]
> 
>  for(i in 2:2000)
> 
>  {
> 
>z[i] = x[i]+5*z[i-1]
> 
>if(z[i]>4 | z[i]<1) {
> 
>  w[j]=i
> 
>} else {
> 
>  w[j] = 0
> 
>}
> 
>  }
> 
> }
> 

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Re: [R] union of two sets are smaller than one set?

[Enrico Schumann]

On Sun, 31 Jan 2021, Martin Møller Skarbiniks Pedersen writes:

> This is really puzzling me and when I try to make a small example
> everything works like expected.
>
> The problem:
>
> I got these two large vectors of strings.
>
>> str(s1)
>  chr [1:766608] "0.dk" ...
>> str(s2)
>  chr [1:59387] "043.dk" "0606.dk" "0618.dk" "0888.dk" "0iq.dk" "0it.dk" ...
>
> And I need to create the union-set of s1 and s2.
> I expect the size of the union-set to be between 766608 and 766608+59387.
> However it is 681193 which is less that number of elements in s1!
>
>> length(base::union(s1, s2))
> [1] 681193
>
> Any hints?
>
> Regards
> Martin
>

Duplicates?

kind regards
Enrico

-- 
Enrico Schumann
Lucerne, Switzerland
http://enricoschumann.net

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Re: [R] union of two sets are smaller than one set?

[Duncan Murdoch]

On 31/01/2021 3:57 p.m., Martin Møller Skarbiniks Pedersen wrote:

This is really puzzling me and when I try to make a small example
everything works like expected.

The problem:

I got these two large vectors of strings.


str(s1)

  chr [1:766608] "0.dk" ...

str(s2)

  chr [1:59387] "043.dk" "0606.dk" "0618.dk" "0888.dk" "0iq.dk" "0it.dk" ...

And I need to create the union-set of s1 and s2.
I expect the size of the union-set to be between 766608 and 766608+59387.
However it is 681193 which is less that number of elements in s1!


length(base::union(s1, s2))

[1] 681193

Any hints?


I imagine unique(s1) is shorter than s1.  The union function is the same as

unique(c(s1, s2))

for your data.  (The only difference is if s1 or s2 is named:  the names 
are dropped.)


Duncan Murdoch

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[R] union of two sets are smaller than one set?

[Martin Møller Skarbiniks Pedersen]

This is really puzzling me and when I try to make a small example
everything works like expected.

The problem:

I got these two large vectors of strings.

> str(s1)
 chr [1:766608] "0.dk" ...
> str(s2)
 chr [1:59387] "043.dk" "0606.dk" "0618.dk" "0888.dk" "0iq.dk" "0it.dk" ...

And I need to create the union-set of s1 and s2.
I expect the size of the union-set to be between 766608 and 766608+59387.
However it is 681193 which is less that number of elements in s1!

> length(base::union(s1, s2))
[1] 681193

Any hints?

Regards
Martin

[[alternative HTML version deleted]]

__
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Help with Using spTimer or spTDyn to estimate "GP" Model

[Bert Gunter]

Also note that you should have a higher likelihood of getting a helpful
response on the r-sig-geo list rather than here.

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Sun, Jan 31, 2021 at 12:34 PM Bert Gunter  wrote:

> Please not per the posting guide linked below:
>
> "For questions about functions in standard packages distributed with R
> (see the FAQ Add-on packages in R
> ),
> ask questions on R-help.
> If the question relates to a *contributed package* , e.g., one downloaded
> from CRAN, try contacting the package maintainer first. You can also use
> find("functionname") and packageDescription("packagename") to find this
> information. *Only* send such questions to R-help or R-devel if you get
> no reply or need further assistance. This applies to both requests for help
> and to bug reports."
>
> So do not be disappointed if you do not receive a (helpful) response here.
> You could, but ... There are, after all, around 25,000 R packages out
> there, and this list cannot possibly support them all.
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Sun, Jan 31, 2021 at 11:26 AM alex_rugu--- via R-help <
> r-help@r-project.org> wrote:
>
>> When I run the following scripts I get the following error and I do not
>> understand the source. I believe N is specified as the number of
>> observations by year in the time series variables.  The error is
>> ###
>> Output: GP models
>> Error in spGP.Gibbs(formula = formula, data = data, time.data =
>> time.data,  :
>>Error: Years, Months, and Days are misspecified,
>>  i.e., total number of observations in the data set should be equal to N
>>   : N = n * r * T
>>where, N = total number of observations in the data,
>>   n = total number of sites,
>>   r = total number of years,
>>   T = total number of days.
>> ## Check spT.time function.
>>
>> The scrip is
>> ##
>> library(spTimer)
>> library(spTDyn)
>> library(tidyverse)
>> library(ggmap)
>>
>>
>> register_google(key=" your key ") # for use with ggmap
>> getOption("ggmap")
>>
>>
>> #Data to analyze is from plm package
>> #The data include US States Production, which is a panel of 48
>> observations from 1970 to 1986
>> #A data frame containing :
>> #state: the state
>> #year : the year
>> #region : the region
>> #pcap : public capital stock
>> #hwy :  highway and streets
>> #water : water and sewer facilities
>> #util : other public buildings and structures
>> #pc : private capital stock
>> #gsp : gross state product
>> #emp :labor input measured by the employment in non–agricultural payrolls
>> #unemp : state unemployment rateA panel of 48 observations from 1970 to
>> 1986
>>
>>
>> data("Produc", package = "plm")
>> glimpse(Produc)
>>
>>
>> #Estimate Geolocation of states to account for spill over effects
>> states_df <- data.frame(as.character(unique(Produc$state)))
>> names(states_df)<- c("state")
>>
>>
>> state_geo_df <- mutate_geocode(states_df, state)
>>
>> #Join the data
>>
>> Product_geo <- full_join(state_geo_df, Produc)
>> glimpse(Product_geo)
>>
>>
>> #Create the time series variable
>> #number of state
>> ns <- length(unique(Product_geo$state))
>>
>>
>> #number of year
>> ny <- length(unique(Product_geo$year))
>> 
>> # I want to do Spatio-Temporal Bayesian Modeling Using spTimer or spTDyn
>> #defines the time series in the Spatio-temporal data.
>>
>>
>> ts_STD <- def.time(t.series=ns, segments=ny)
>>
>>
>> ##Estimate the model using spTDyn package
>> #Also note that the spT.Gibbs in spTimer gives the same error
>>
>>
>> GibbsDyn(gsp ~ pcap + hwy + water + util + pc ,
>>data=Product_geo, model="GP",
>>  time.data=ts_STD,
>>  coords=~lon + lat,
>>   nItr=5000, nBurn=1000, report=1, tol.dist=0.05,
>> distance.method="geodetic:km", cov.fnc="exponential",
>>
>>  
>> spatial.decay=decay(distribution="FIXED"),truncation.para=list(at=0,lambda=2))
>>
>>
>> #Also I will appreciate showing how to deal with unbalanced panel data
>> #Delete some of the rows
>> Product_geo$cond = with(Product_geo,  if_else(state=="ALABAMA" &
>> year==1971, 0,
>>  if_else(state=="COLORADO" &
>> year==1971 | year==1973 , 0,
>>  if_else(state=="TEXAS" &
>> year==1971 | year==1973 | year==1985, 0, 1
>>
>> #Create an unbalanced panel
>> Product_geo_unb <- Product_geo %>% filter(cond==1) %>% select(-cond)
>> glimpse(Product_geo_unb)
>>
>>
>> #How to use GibbsDyn or spT.Gibbs function to estimate the "GP" 

Re: [R] Help with Using spTimer or spTDyn to estimate "GP" Model

[Bert Gunter]

Please not per the posting guide linked below:

"For questions about functions in standard packages distributed with R (see
the FAQ Add-on packages in R
), ask
questions on R-help.
If the question relates to a *contributed package* , e.g., one downloaded
from CRAN, try contacting the package maintainer first. You can also use
find("functionname") and packageDescription("packagename") to find this
information. *Only* send such questions to R-help or R-devel if you get no
reply or need further assistance. This applies to both requests for help
and to bug reports."

So do not be disappointed if you do not receive a (helpful) response here.
You could, but ... There are, after all, around 25,000 R packages out
there, and this list cannot possibly support them all.

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Sun, Jan 31, 2021 at 11:26 AM alex_rugu--- via R-help <
r-help@r-project.org> wrote:

> When I run the following scripts I get the following error and I do not
> understand the source. I believe N is specified as the number of
> observations by year in the time series variables.  The error is
> ###
> Output: GP models
> Error in spGP.Gibbs(formula = formula, data = data, time.data =
> time.data,  :
>Error: Years, Months, and Days are misspecified,
>  i.e., total number of observations in the data set should be equal to N
>   : N = n * r * T
>where, N = total number of observations in the data,
>   n = total number of sites,
>   r = total number of years,
>   T = total number of days.
> ## Check spT.time function.
>
> The scrip is
> ##
> library(spTimer)
> library(spTDyn)
> library(tidyverse)
> library(ggmap)
>
>
> register_google(key=" your key ") # for use with ggmap
> getOption("ggmap")
>
>
> #Data to analyze is from plm package
> #The data include US States Production, which is a panel of 48
> observations from 1970 to 1986
> #A data frame containing :
> #state: the state
> #year : the year
> #region : the region
> #pcap : public capital stock
> #hwy :  highway and streets
> #water : water and sewer facilities
> #util : other public buildings and structures
> #pc : private capital stock
> #gsp : gross state product
> #emp :labor input measured by the employment in non–agricultural payrolls
> #unemp : state unemployment rateA panel of 48 observations from 1970 to
> 1986
>
>
> data("Produc", package = "plm")
> glimpse(Produc)
>
>
> #Estimate Geolocation of states to account for spill over effects
> states_df <- data.frame(as.character(unique(Produc$state)))
> names(states_df)<- c("state")
>
>
> state_geo_df <- mutate_geocode(states_df, state)
>
> #Join the data
>
> Product_geo <- full_join(state_geo_df, Produc)
> glimpse(Product_geo)
>
>
> #Create the time series variable
> #number of state
> ns <- length(unique(Product_geo$state))
>
>
> #number of year
> ny <- length(unique(Product_geo$year))
> 
> # I want to do Spatio-Temporal Bayesian Modeling Using spTimer or spTDyn
> #defines the time series in the Spatio-temporal data.
>
>
> ts_STD <- def.time(t.series=ns, segments=ny)
>
>
> ##Estimate the model using spTDyn package
> #Also note that the spT.Gibbs in spTimer gives the same error
>
>
> GibbsDyn(gsp ~ pcap + hwy + water + util + pc ,
>data=Product_geo, model="GP",
>  time.data=ts_STD,
>  coords=~lon + lat,
>   nItr=5000, nBurn=1000, report=1, tol.dist=0.05,
> distance.method="geodetic:km", cov.fnc="exponential",
>
>  
> spatial.decay=decay(distribution="FIXED"),truncation.para=list(at=0,lambda=2))
>
>
> #Also I will appreciate showing how to deal with unbalanced panel data
> #Delete some of the rows
> Product_geo$cond = with(Product_geo,  if_else(state=="ALABAMA" &
> year==1971, 0,
>  if_else(state=="COLORADO" &
> year==1971 | year==1973 , 0,
>  if_else(state=="TEXAS" &
> year==1971 | year==1973 | year==1985, 0, 1
>
> #Create an unbalanced panel
> Product_geo_unb <- Product_geo %>% filter(cond==1) %>% select(-cond)
> glimpse(Product_geo_unb)
>
>
> #How to use GibbsDyn or spT.Gibbs function to estimate the "GP" model for
> such unbalanced panel data?
>
> __
> 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] Help with Using spTimer or spTDyn to estimate "GP" Model

[alex_rugu--- via R-help]

When I run the following scripts I get the following error and I do not 
understand the source. I believe N is specified as the number of observations 
by year in the time series variables.  The error is
###
Output: GP models 
Error in spGP.Gibbs(formula = formula, data = data, time.data = time.data,  : 
   Error: Years, Months, and Days are misspecified,
 i.e., total number of observations in the data set should be equal to N
  : N = n * r * T 
   where, N = total number of observations in the data,
          n = total number of sites,
          r = total number of years,
          T = total number of days. 
## Check spT.time function.

The scrip is
##
library(spTimer)
library(spTDyn)
library(tidyverse)
library(ggmap)


register_google(key=" your key ") # for use with ggmap
getOption("ggmap")


#Data to analyze is from plm package
#The data include US States Production, which is a panel of 48 observations 
from 1970 to 1986
#A data frame containing :
#state: the state
#year : the year
#region : the region
#pcap : public capital stock
#hwy :  highway and streets
#water : water and sewer facilities
#util : other public buildings and structures
#pc : private capital stock
#gsp : gross state product
#emp :labor input measured by the employment in non–agricultural payrolls
#unemp : state unemployment rateA panel of 48 observations from 1970 to 1986


data("Produc", package = "plm")
glimpse(Produc)


#Estimate Geolocation of states to account for spill over effects
states_df <- data.frame(as.character(unique(Produc$state)))
names(states_df)<- c("state")


state_geo_df <- mutate_geocode(states_df, state)

#Join the data

Product_geo <- full_join(state_geo_df, Produc)
glimpse(Product_geo)


#Create the time series variable
#number of state
ns <- length(unique(Product_geo$state))


#number of year
ny <- length(unique(Product_geo$year))

# I want to do Spatio-Temporal Bayesian Modeling Using spTimer or spTDyn
#defines the time series in the Spatio-temporal data.


ts_STD <- def.time(t.series=ns, segments=ny)


##Estimate the model using spTDyn package
#Also note that the spT.Gibbs in spTimer gives the same error


GibbsDyn(gsp ~ pcap + hwy + water + util + pc , 
       data=Product_geo, model="GP", 
         time.data=ts_STD, 
         coords=~lon + lat,
          nItr=5000, nBurn=1000, report=1, tol.dist=0.05,
            distance.method="geodetic:km", cov.fnc="exponential", 
             
spatial.decay=decay(distribution="FIXED"),truncation.para=list(at=0,lambda=2))


#Also I will appreciate showing how to deal with unbalanced panel data
#Delete some of the rows
Product_geo$cond = with(Product_geo,  if_else(state=="ALABAMA" & year==1971, 0,
                                         if_else(state=="COLORADO" & year==1971 
| year==1973 , 0,
                                         if_else(state=="TEXAS" & year==1971 | 
year==1973 | year==1985, 0, 1

#Create an unbalanced panel
Product_geo_unb <- Product_geo %>% filter(cond==1) %>% select(-cond)
glimpse(Product_geo_unb)


#How to use GibbsDyn or spT.Gibbs function to estimate the "GP" model for such 
unbalanced panel data?

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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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] dependent nested for loops in R

[Shaami]

Hi
I have made the sample code again. Could you please guide how to use
vectorization for variables whose next value depends on the previous one?

w = NULL

for(j in 1:1000)

{

  z = NULL

  x = rnorm(2000)

  z[1] = x[1]

  for(i in 2:2000)

  {

z[i] = x[i]+5*z[i-1]

if(z[i]>4 | z[i]<1) {

  w[j]=i

} else {

  w[j] = 0

}

  }

}


On Sun, Jan 31, 2021 at 10:01 AM David Winsemius 
wrote:

>
> On 1/30/21 8:26 PM, Shaami wrote:
> > Hi
> > I have very large dependent nested for loops that are quite expensive
> > computationally. It takes weeks and does not end to give me results.
> Could
> > anyone please guide how could I use apply function or any other
> suggestion
> > for such big and dependent loops in R? A sample code is as follows.
> >
> > w = NULL
> > for(j in 1:1000)
> > {
> >x = rnorm(2000)
> >z = x[1]
> >for(i in 2:2000)
> >{
> >  z = x[i]+5*z[i-1]
>
> I'm guessing you meant to type:
>
>  z[i] <- x[i]+5*z[i-1]
>
> >  if(z>4 | z<1) {
>
> And more guesses (in the absence of any sort of problem description)
> that you really wanted:
>
>
>   if(z[i]>4 | z[i]<1) {  
>
>
> >w[j]=i
> >break
> >  } else {
> >w[j] = 0
> >  }
> >}
> > }
>
>
> Are you sure you need a for-loop? Seems like you could have done this
> with a couple of vectorized operations. And the `break` looked entirely
> superfluous.
>
>
>
> > Thank you
> >
> >   [[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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [ESS] unexpected behavior for Emacs-27.1-1-modified-1 for two MacBooks.

[Sparapani, Rodney via ESS-help]

Hi Rich et al.:

I just got a new MBP Intel.  And I have been fighting with 27.1 too!

But, I just wanted to say that you don’t need homebrew for aspell.
If you have the Xcode CLT, aspell install’s quite easily from source.
Grab it from directory.fsf.org and a dictionary.

The easiest way to install the Xcode CLT that I have found is just
try one of the commands like git and it will offer to install it.
In 10 minutes I had Xcode and aspell installed and working.

Rodney

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