[R] combining data.frames with is.na & match (), two questions

[Drake Gossi]

Hello everyone,

I'm working through this book, *Humanities Data in R* (Arnold & Tilton),
and I'm just having trouble understanding this maneuver.

In sum, I'm trying to combine data in two different data.frames.

This data.frame is called fruitNutr

Fruit  Calories
1 banana 100
2 pear 100
3 mango 200

And this data.frame is called fruitData

Fruit Color Shape Juice
1 apple red round 1
2 banana yellow oblong 0
3 pear green pear 0.5
4 orange orange round 1
5 kiwi green round 0

So, as you can see, these two data.frames overlap insofar as they both have
banana and pear. So, what happens next is the book suggests this:

fruitData$calories <- NA


As a result, I've created a new column for the fruitData data.frame:

Fruit Color Shape Juice Calories
1 apple red round 1N/A
2 banana yellow oblong 0N/A
3 pear green pear 0.5N/A
4 orange orange round 1N/A
5 kiwi green round 0N/A

Then:

> index <- match (x=fruitData$Fruit, table=fruitNutr$Fruit)
> index
  [1]NA   1   2  NA  NA
> is.na(index)
  [1]TRUE   FALSEFALSE   TRUETRUE
> fruitData$Calories [!is.na(index)] <- fruitNutr$Calories[index[!is.na
(index)]]
> fruitData

Fruit Color Shape Juice Calories
1 apple red round 1N/A
2 banana yellow oblong 0 100
3 pear green pear 0.5 100
4 orange orange round 1N/A
5 kiwi green round 0N/A

I get what the first part means, that first part being this:
fruitData$Calories [!is.na(index)]
go into the fruitData data.frame, specifically into the calories column,
and only for what's true according to is.na(index). But I just literally
can't understand this last part.  fruitNutr$Calories[index[!is.na(index)]]

Two questions.


   1. I just literally don't understand how this code works. It does work,
   of course, but I don't know what it's doing, specifically this [index[!
   is.na(index)]] part. Could someone explain it to me like I'm five? I'm
   new at this...
   2. And then: is there any other way to combine these two data.frames so
   that we get this same result? maybe an easier to understand method?

That same result, again, is

Fruit Color Shape Juice Calories
1 apple red round 1N/A
2 banana yellow oblong 0 100
3 pear green pear 0.5 100
4 orange orange round 1N/A
5 kiwi green round 0N/A


Drake

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[R] Problem to find the Maximum likelihood estimates of generalized normal distribution in R

[jawad hussain via R-help]

First I estimated the parameters of exponentiated generalized normal 
distribution using the dataset (data1: generated from normal distribution). 
Then I used real dataset (data2) and tried to find the maximum likelihood 
estimates (MLE) using the AdequacyModel packages. It gives the error message 
(mentioned right below the code). 
Why does the same code estimate for first dataset (data1), but it doesn't 
estimate for the second dataset (data2)?
Is my way of plugging the baseline distribution (normal) in generalized class 
of distributions F(x)= [1-(1-G(x))^beta]^gamma introduced by Cordeiro et 
al.(2013) in R environment right? Am I defining the cdf and pdf of an 
generalized normal distribution in R in right way?

# First Problem

library(AdequacyModel)

data1 <- rnorm(100)

pdf_exps <- function(par,x){
beta = par[1]
gamma= par[2]
mean = par[3]
sd = par[4]
 ( beta*gamma* ((1-(1-(pnorm(x,mean,sd)))^beta)^(gamma-1)) * 
((1-(pnorm(x,mean,sd)))^(beta-1)) ) * (dnorm(x,mean,sd)) 
}


cdf_exps <- function(par,x){
beta = par[1]
gamma= par[2]
mean = par[3]
sd = par[4]
( 1-(1-(pnorm(x,mean,sd)))^beta)^gamma 
}


set.seed(1)
result_1 = goodness.fit(pdf = pdf_exps, cdf = cdf_exps,
starts = c(1,1,1,1),data = data1  , method = "BFGS",
domain = c(-Inf,Inf), lim_inf = c(0,0,0,0),
lim_sup = c(2,2,2,2), S = 250, prop=0.1, N=50)
result_1$mle

 5.688120 4.413153 1.115777 1.996108

#

data2 <-c( 20.56, 20.67, 21.86, 21.88, 18.96, 21.04, 21.69, 20.62, 22.64, 
19.44, 25.75, 21.20,
  22.03, 25.44, 22.63, 21.86, 22.27, 21.27, 23.47, 23.19, 23.17, 24.54, 22.96, 
19.76,
  23.36, 22.67, 24.24, 24.21, 20.46, 20.81, 20.17, 23.06, 24.40, 23.97, 22.62, 
19.16,
  21.15, 21.40, 21.03, 21.77, 21.38, 21.47, 24.45, 22.63, 22.80, 23.58, 20.06, 
23.01,
  24.64, 18.26, 24.47, 23.99, 26.24, 20.04, 25.72, 25.64, 19.87, 23.35, 22.42, 
20.42,
  22.13, 25.17, 23.72, 21.28, 20.87, 19.00, 22.04, 20.12, 21.35, 28.57, 26.95, 
28.13,
  26.85, 25.27, 31.93, 16.75, 19.54, 20.42, 22.76, 20.12, 22.35, 19.16, 20.77, 
19.37,
  22.37, 17.54, 19.06, 20.30, 20.15, 25.36, 22.12, 21.25, 20.53, 17.06, 18.29, 
18.37,
  18.93, 17.79, 17.05, 20.31, 22.46, 23.88, 23.68, 23.15, 22.32, 24.02, 23.29, 
25.11,
 22.81, 26.25, 21.38, 22.52, 26.73, 23.57, 25.84, 24.06, 23.85, 25.09, 23.84, 
25.31,
 19.69, 26.07, 25.50, 23.69, 26.79, 25.61, 25.06, 24.93, 22.96, 20.69, 23.97, 
24.64,
 25.93, 23.69, 25.38, 22.68, 23.36, 22.44, 22.57, 19.81, 21.19, 20.39, 21.12, 
21.89,
 29.97, 27.39, 23.11, 21.75, 20.89, 22.83, 22.02, 20.07, 20.15, 21.24, 19.63, 
23.58,
 21.65, 25.17, 23.25, 32.52, 22.59, 30.18, 34.42, 21.86, 23.99, 24.81, 21.68, 
21.04,
 23.12, 20.76, 23.13, 22.35, 22.28, 23.55, 19.85, 26.51, 24.78, 33.73, 30.18, 
23.31,
 24.51, 25.37, 23.67, 24.28, 25.82, 21.93, 23.38, 23.07, 25.21, 23.25, 22.93, 
26.86,
 21.26, 25.43, 24.54, 27.79, 23.58, 27.56, 23.76, 22.01, 22.34, 21.07)


set.seed(1)
result_2 = goodness.fit(pdf = pdf_exps, cdf = cdf_exps,
starts = c(1,1,1,1),data = data2  , method = "BFGS",
domain = c(-Inf,Inf), lim_inf = c(0,0,0,0),
lim_sup = c(2,2,2,2), S = 250, prop=0.1, N=50)
result_2$mle

Error in optim(par = starts, fn = likelihood, x = data, method = "BFGS",  : 
  non-finite finite-difference value [1]


JAWAD HUSSAIN ASHRAF

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Re: [R] Limiting the scope of RNGkind/set.seed

[Elizabeth Purdom]

Thanks Martin, this seems much better. All of the best, Elizabeth

> On Apr 16, 2019, at 10:22 AM, Martin Maechler  
> wrote:
> 
>> Elizabeth Purdom 
>>on Tue, 16 Apr 2019 09:45:45 -0700 writes:
> 
>> Hi Bert, Thanks for your response. What you suggest is
>> more or less the fix I suggested in my email (my second
>> version of .rcolors). I writing more because I was
>> wondering if there was a better way to work with RNG that
>> would avoid doing that. It doesn’t feel very friendly for
>> my package to be making changes to the user’s global
>> environment, even though I am setting them back (and if it
>> weren’t for the fact that setting the new R 3.6 argument
>> `sample.kind=“Rounding”` creates a warning, I wouldn’t
>> have even realized I was affecting the user’s settings, so
>> it seems potentially hazardous that packages could be
>> changing users settings without them being aware of
>> it). So I was wondering if there was a way to more fully
>> isolate the command.  Thanks, Elizabeth
> 
> Hi Elizabeth,
> 
> there's actually something better -- I think -- that you can do:
> 
> You store .Random.seed  before doing an RNGkind() & set.seed()
> setting, do all that, and make sure that .Random.seed is
> restored when leaving your function.
> 
> This works because the (typically quite long) .Random.seed
> stores the full state of the RNG, i.e., all RNGkind() settings
> *and* the result of set.seed() , calling r(n, ..)  etc.
> 
> If you additionally use  on.exit()  instead of manually reset
> things, you have the additional advantage, that things are also
> reset when your functions ends because the user interrupts its
> computations, or an error happens, etc.
> 
> So, your function would more elegantly (and robustly!)  look like
> 
> .rcolors <- function(seed = 23589) {
>if(!exists(".Random.seed", envir = .GlobalEnv)) {
>message("calling runif(1)"); runif(1) }
>old.R.s <- .Random.seed
>## will reset everything on exiting this function:
>on.exit(assign(".Random.seed", old.R.s, envir=.GlobalEnv))
>## set seed for sample() "back compatibly":
>suppressWarnings(RNGversion("3.5.0"))
>set.seed(seed)
>## return random permutation of "my colors"
>sample(colors()[-c(152:361)])
> }
> 
> BTW, you can look at  simulate() methods in standard R, e.g.,
> 
>  stats:::simulate.lm
> 
> to see the same method use [optionally, with slightly more sophistication]
> 
> 
> Best,
> Martin
> 
> Martin Mächler
> ETH Zurich, Switzerland

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Re: [R] Why I can not get work the "tidyverse" and "corrr" libraries

[Hadley Wickham]

On Wed, Apr 17, 2019 at 1:06 PM Jeff Newmiller  wrote:
>
> From reading
>
> > namespace ‘rlang’ 0.3.0 is already loaded, but >= 0.3.1 is required
>
> it would seem that you need to upgrade your rlang package...

Typically this indicates you need to restart R.

Hadley

-- 
http://hadley.nz

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Re: [R] Why I can not get work the "tidyverse" and "corrr" libraries

[Jeff Newmiller]

>From reading

> namespace ‘rlang’ 0.3.0 is already loaded, but >= 0.3.1 is required

it would seem that you need to upgrade your rlang package...

On April 17, 2019 10:19:48 AM PDT, greg holly  wrote:
>;
>
>I need work on libraries "tidyverse" and "corrr". When I cal these, I
>am
>getting the following error message. What can be done? Your help is
>highly
>appreciated.
>
>Greg
>
>Error: package or namespace load failed for ‘tidyverse’ in
>loadNamespace(i,
>c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
> namespace ‘rlang’ 0.3.0 is already loaded, but >= 0.3.1 is required
>In addition: Warning message:
>package ‘tidyverse’ was built under R version 3.5.3
>
>   [[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.

-- 
Sent from my phone. Please excuse my brevity.

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Re: [R] Limiting the scope of RNGkind/set.seed

[Paul Gilbert]

Elizabeth

There is a package (of mine) setRNG on CRAN that may be a helpful 
example (code/tests/examples/vignette). Most of the package is testing 
designed to fail if the RNG in R is changed in a way that will affect my 
other package testing. Martin's function in the previous reply has most 
of the import parts and adds warning suppression, so you might want to 
consider small adjustments on a combination of the two. Just to 
summarize the issues, from memory:


0/ Using a preset default seed in a function's argument makes the 
function not random by default. If you are doing that then maybe you 
need to consider carefully whether the function should be using random 
number generation.


1/ It is good practice to use on.exit() in your function to reset 
things, so the state remains unaltered if your function fails.


2/ Saving the old seed does not work when it is unset, as it is by 
default in a new session, so you need to do something that insures it is 
set.


3/ You may need to save and reset not only the seed but also the RNG 
kind and the normal.kind, and possibly the kind for some other 
distributions. (setRNG does not handle other distributions.) It looks 
like you need to save and reset sample.kind.


4/ You should add the capability to pass all settings to your functions 
so that you can reproduce things when you want.


5/ I have found it useful to always pass back the settings in objects 
returned by functions like simulations. That way you always have a 
record when you discover something you want to reproduce.


6/ If parallel computing is considered then for reproducibility you need 
to save the number of nodes in the cluster. (I think this point is not 
as widely known as it should be.)


No doubt I have forgotten a few things.

Paul Gilbert

On 4/17/19 6:00 AM, r-help-requ...@r-project.org wrote:
> Date: Tue, 16 Apr 2019 19:22:34 +0200
> From: Martin Maechler
> To: Elizabeth Purdom
> Cc: Bert Gunter, R-help
> 
> Subject: Re: [R] Limiting the scope of RNGkind/set.seed
> Message-ID:<23734.3930.10744.126...@stat.math.ethz.ch>
> Content-Type: text/plain; charset="utf-8"
>
>> Elizabeth Purdom
>>  on Tue, 16 Apr 2019 09:45:45 -0700 writes:
>  > Hi Bert, Thanks for your response. What you suggest is
>  > more or less the fix I suggested in my email (my second
>  > version of .rcolors). I writing more because I was
>  > wondering if there was a better way to work with RNG that
>  > would avoid doing that. It doesn’t feel very friendly for
>  > my package to be making changes to the user’s global
>  > environment, even though I am setting them back (and if it
>  > weren’t for the fact that setting the new R 3.6 argument
>  > `sample.kind=“Rounding”` creates a warning, I wouldn’t
>  > have even realized I was affecting the user’s settings, so
>  > it seems potentially hazardous that packages could be
>  > changing users settings without them being aware of
>  > it). So I was wondering if there was a way to more fully
>  > isolate the command.  Thanks, Elizabeth
>
> Hi Elizabeth,
>
> there's actually something better -- I think -- that you can do:
>
> You store .Random.seed  before doing an RNGkind() & set.seed()
> setting, do all that, and make sure that .Random.seed is
> restored when leaving your function.
>
> This works because the (typically quite long) .Random.seed
> stores the full state of the RNG, i.e., all RNGkind() settings
> *and*  the result of set.seed() , calling r(n, ..)  etc.
>
> If you additionally use  on.exit()  instead of manually reset
> things, you have the additional advantage, that things are also
> reset when your functions ends because the user interrupts its
> computations, or an error happens, etc.
>
> So, your function would more elegantly (and robustly!)  look like
>
> .rcolors <- function(seed = 23589) {
>  if(!exists(".Random.seed", envir = .GlobalEnv)) {
>  message("calling runif(1)"); runif(1) }
>  old.R.s <- .Random.seed
>  ## will reset everything on exiting this function:
>  on.exit(assign(".Random.seed", old.R.s, envir=.GlobalEnv))
>  ## set seed for sample() "back compatibly":
>  suppressWarnings(RNGversion("3.5.0"))
>  set.seed(seed)
>  ## return random permutation of "my colors"
>  sample(colors()[-c(152:361)])
> }
>
> BTW, you can look at  simulate() methods in standard R, e.g.,
>
>stats:::simulate.lm
>
> to see the same method use [optionally, with slightly more 
sophistication]

>
>
> Best,
> Martin
>
> Martin Mächler
> ETH Zurich, Switzerland

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[R] Why I can not get work the "tidyverse" and "corrr" libraries

[greg holly]

;

I need work on libraries "tidyverse" and "corrr". When I cal these, I am
getting the following error message. What can be done? Your help is highly
appreciated.

Greg

Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(i,
c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 namespace ‘rlang’ 0.3.0 is already loaded, but >= 0.3.1 is required
In addition: Warning message:
package ‘tidyverse’ was built under R version 3.5.3

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[R-es] Gráfica de barras apilada ggplot2

[Alberto Segovia]

Hola
Estoy haciendo una gráfica de barras apiladas en ggplot2 pero la leyendas
tiene muchos nombres y desplazan la gráfica
Alguien que me ayude con un script para solo sacar las leyendas o que se
ajuste el tamaño de la gráfica

Muchas gracias :)

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Re: [R-es] leer registros de una determinada longitu

[Jesús Para Fernández]

Me imagino q tienew q leer todos y luego filtrar por aquellos que tengan la 
longitud que quieres.

Para eso , despues de leer todos quedate con ellos es con nchar

Obtener Outlook para Android


From: R-help-es  on behalf of Belén Cillero 
Jiménez 
Sent: Wednesday, April 17, 2019 11:57:42 AM
To: r-help-es@r-project.org
Subject: [R-es] leer registros de una determinada longitu

Buenos días
Quiero leer de un txt SOLO los registros que tengan una determinada longitud. 
¿Podéis ayudarme?

Gracias



Belén Cillero Jiménez

Técnico de Estadística

Instituto de Estadística de La Rioja



bcill...@larioja.org

oɯsıɯ ol ǝɹdɯǝıs sɐƃɐɥ ou ,soʇuıʇsıp sopɐʇlnsǝɹ sɐɔsnq ıS



GOBIERNO DE LA RIOJA
AVISO LEGAL: La información contenida en este mensaje es confidencial y está 
destinada a ser leída sólo por la persona a la que va dirigida. Si Ud. no es el 
destinatario señalado le informamos que está prohibida, y puede ser ilegal, 
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[R-es] leer registros de una determinada longitu

[Belén Cillero Jiménez]

Buenos días
Quiero leer de un txt SOLO los registros que tengan una determinada longitud. 
¿Podéis ayudarme?

Gracias



Belén Cillero Jiménez

Técnico de Estadística

Instituto de Estadística de La Rioja



bcill...@larioja.org

oɯsıɯ ol ǝɹdɯǝıs sɐƃɐɥ ou ,soʇuıʇsıp sopɐʇlnsǝɹ sɐɔsnq ıS



GOBIERNO DE LA RIOJA
AVISO LEGAL: La información contenida en este mensaje es confidencial y está 
destinada a ser leída sólo por la persona a la que va dirigida. Si Ud. no es el 
destinatario señalado le informamos que está prohibida, y puede ser ilegal, 
cualquier divulgación o reproducción de este mensaje.
Antes de imprimir este e-mail piense bien si es necesario hacerlo.

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[R] [R-pkgs] dbparser v1.0.1: DrugBank XML Database Parser

[mohammed ibrahim via R-packages]

Hello,I am pleased to announce the release of dbparser v1.0.1 on CRAN 
https://cran.r-project.org/web/packages/dbparser/index.htmlThe new release 
include:    * Check if drugbank database exist before parsing    * Add support 
for international_brands and salts elements    * Properly rename some features 
to have clear names    * Reduce datasets size by getting unique rows only    * 
Support reading zip file containing DrugBank xml database    * Fix previous 
version CRAN Note    * Improve functions documentation    * Refactor unused 
functions    * Remove Count features from drug data set    * Fix several typos 
in documentation and code    * Fix consistency issue of CLASS of Data Frames 
Returned by dbparser
As always, contributions and bug reports are welcome on 
https://dainanahan.github.io/dbparser/index.html

Best Regards,Mohammed Ali
MSc in Applied Data Science & Big Data
mohammed@edu.dsti.institute
+20 01000481973
eg.linkedin.com/in/mohammedali85
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