[R] impute.transcan missing original variables
I’m trying to select only one dataframe, after performing an imputation with
aregImpute and impute.transcan. However, I cannot get back a variable that was
kept out of the imputation model. Can somebody tell me how to do it? If we
illustrate this problem using the following reproducible example, how could I
get the dataframe with all the variables that were not imputated, such as
Species and id variables?
Best !
Data
data("iris")
library(missForest)
library(tidyverse)
library(Hmisc)
# example
iris.missing <- iris %>%
group_by(Species) %>%
prodNA(noNA = 0.1) %>%
ungroup() %>%
mutate(id=row_number())
imputation_model <- aregImpute(~Sepal.Length+Sepal.Width+Petal.Width,
n.impute=3,
data=iris.missing,
pr=F,
type='pmm')
data_imp <- impute.transcan(imputation_model,
imputation=1,
data=iris.missing,
list.out=TRUE,
pr=FALSE,
check=FALSE)
datos_imp <- bind_rows(data_imp)
--
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[R] incidence_fit model for simulation
Hello How can I make a prediction with object type incidence_fit. incidence_fit object is returned by the function fit in library(incidence). Best regard maicel -- Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/ __ 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.
[R] purrr::map and xml2:: read_xml
Hi List, I am trying to extract the key words from 1403 papers in xml
format. I programmed such codes but they do not work but they only do
with the modification showed below. But that variation is not the one
I need because the 1403 xml files do not match to those in my folder.
Could you please tell me where are the mistakes in the codes list (A
or B) to help me to correct them? The data frame columns are an id and
the paths.
A-Does not work, but it is the one I need.
keyword <-
muestra %>%
select(path) %>%
read_xmlmap(.f = function(x) { read_xml(x) %>%
xml_find_all( ".//kwd") %>%
xml_text(trim=T) })
B-It works but only with a small number of papers.
keyword <-
muestra %>%
select(path) %>%
dplyr::sample_n(50) %>%
unlist() %>%
map(.f = function(x) { read_xml(x) %>%
xml_find_all( ".//kwd") %>%
xml_text(trim=T) })
Thank you,
Maicel Monzon MD, PHD
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Re: [R] dplyr : row total for all groups in dplyr summarise
Sorry, what I wanted to do was to add a total row at the end of the
summary. The marginal totals by columns correspond to 100% and the sum
of levels.
best reagard
Maicel Monzon
Ulrik Stervbo <ulrik.ster...@gmail.com> escribió:
Yes. But in the sample code the data is summarised. In which case you get 4
rows and not the correct 32.
On Tue, 5 Jul 2016, 07:48 David Winsemius, <dwinsem...@comcast.net> wrote:
nrow(mtcars)
Sent from my iPhone
On Jul 4, 2016, at 9:03 PM, Ulrik Stervbo <ulrik.ster...@gmail.com> wrote:
That will give you the wrong result when used on summarised data
David Winsemius <dwinsem...@comcast.net> schrieb am Di., 5. Juli 2016
02:10:
I thought there was an nrow() function?
Sent from my iPhone
On Jul 4, 2016, at 9:59 AM, Ulrik Stervbo <ulrik.ster...@gmail.com>
wrote:
If you want the total number of rows in the original data.frame after
counting the rows in each group, you can ungroup and sum the row counts,
like:
library("dplyr")
mtcars %>%
group_by (am, gear) %>%
summarise (n=n()) %>%
mutate(rel.freq = paste0(round(100 * n/sum(n), 0), "%")) %>%
ungroup() %>%
mutate(row.tot = sum(n))
HTH
Ulrik
On Mon, 4 Jul 2016 at 18:23 David Winsemius <dwinsem...@comcast.net>
wrote:
> On Jul 4, 2016, at 6:56 AM, mai...@infomed.sld.cu wrote:
>
> Hello,
> How can I aggregate row total for all groups in dplyr summarise ?
Row total ? of what? Aggregate ? how? What is the desired answer?
> library(dplyr)
> mtcars %>%
> group_by (am, gear) %>%
> summarise (n=n()) %>%
> mutate(rel.freq = paste0(round(100 * n/sum(n), 0), "%"))
>
> best regard
> Maicel Monzon
>
>
>
>
>
>
>
>
> --
> Este mensaje le ha llegado mediante el servicio de correo electronico
que ofrece Infomed para respaldar el cumplimiento de las misiones del
Sistema Nacional de Salud. La persona que envia este correo asume el
compromiso de usar el servicio a tales fines y cumplir con las
regulaciones
establecidas
>
> Infomed: http://www.sld.cu/
>
> __
> 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.
__
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.
--
Este mensaje le ha llegado mediante el servicio de correo electronico que
ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema
Nacional de Salud. La persona que envia este correo asume el compromiso de usar
el servicio a tales fines y cumplir con las regulaciones establecidas
Infomed: http://www.sld.cu/
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R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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Re: [R] dplyr : row total for all groups in dplyr summarise
Thank you!!! It's what I needed.
best regard
Maicel Monzon, PHD
Centro Nacional de Ensayos Clinicos
Ulrik Stervbo <ulrik.ster...@gmail.com> escribió:
If you want the total number of rows in the original data.frame after
counting the rows in each group, you can ungroup and sum the row counts,
like:
library("dplyr")
mtcars %>%
group_by (am, gear) %>%
summarise (n=n()) %>%
mutate(rel.freq = paste0(round(100 * n/sum(n), 0), "%")) %>%
ungroup() %>%
mutate(row.tot = sum(n))
HTH
Ulrik
On Mon, 4 Jul 2016 at 18:23 David Winsemius <dwinsem...@comcast.net> wrote:
> On Jul 4, 2016, at 6:56 AM, mai...@infomed.sld.cu wrote:
>
> Hello,
> How can I aggregate row total for all groups in dplyr summarise ?
Row total ? of what? Aggregate ? how? What is the desired answer?
> library(dplyr)
> mtcars %>%
> group_by (am, gear) %>%
> summarise (n=n()) %>%
> mutate(rel.freq = paste0(round(100 * n/sum(n), 0), "%"))
>
> best regard
> Maicel Monzon
>
>
>
>
>
>
>
>
> --
> Este mensaje le ha llegado mediante el servicio de correo electronico
que ofrece Infomed para respaldar el cumplimiento de las misiones del
Sistema Nacional de Salud. La persona que envia este correo asume el
compromiso de usar el servicio a tales fines y cumplir con las regulaciones
establecidas
>
> Infomed: http://www.sld.cu/
>
> __
> 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.
__
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.
--
Este mensaje le ha llegado mediante el servicio de correo electronico que
ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema
Nacional de Salud. La persona que envia este correo asume el compromiso de usar
el servicio a tales fines y cumplir con las regulaciones establecidas
Infomed: http://www.sld.cu/
__
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and provide commented, minimal, self-contained, reproducible code.
[R] dplyr : row total for all groups in dplyr summarise
Hello, How can I aggregate row total for all groups in dplyr summarise ? library(dplyr) mtcars %>% group_by (am, gear) %>% summarise (n=n()) %>% mutate(rel.freq = paste0(round(100 * n/sum(n), 0), "%")) best regard Maicel Monzon -- Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/ __ 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.
[R] extract all dataframes from list
Hello List, I have list of named dataframe. How can I extract all dataframes from this list? The dataframe names should be the same of the original list. May I use the lapply function? Thanks for your help. Best regards, Maicel Monzon, MD National Center of Clinical Trials Havana, Cuba -- Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/ __ 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.
[R] read Epidata level labels from R
Hello List, I need import data from Epidata version 3.1 to R data frame. My problem is that I need to import the level labels of from categorical variables to factors. Epidata has two files, .red and .chk. I read on a post that the best choice was to export them to .dta in epidat, and them to read the data from R. I've used the functions stata.get from the library Hmisc, read_statafrom library haven and read.dta from library foreign. Two of this functions allow me to import the labels of the dataframe variables, not the level labels of the factors I would like to get. How can I do it? Thanks for your help. Best regards, Maicel Monzon ,MD National Center of Clinical Trials Havana, Cuba -- Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/ __ 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.
[R] table
Hello List, I am trying to obtain a table containing absolute and relative frequencies but it must be done by strata. Each strata have to contain totals and subtotals being the sum of the subtotals equal to the total in upper strata in same column. As this could be some vague I am including an example of such table: data-data.frame(Provincial=rep(c(Prov1,Prov2,Prov1,Prov3),10), Municipios=rep(c(Mun1,Mun2,Mun3,Mun4),10),unit=rep(c(unit1,unit2,unit3,unit4),10)) VariableN % Province (i) Municipalities (j) Health units (k) #8721;i, #8721;j, #8721;k And so on i = 1 to 16 #8721;i, #8721;j, #8721;k If you could help me to obtain a function to get such table I would appreciate very much. Best and thank you . maicel monzon MD. MSc. -- Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/ __ 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.
[R] Unique values in dataframe columns
Hello list I would like to know how can i detect dataframe columns that have as unique values elements of a list. For example, at a given dataframe to look for columns that unique values are elements of a list like this one dataframe-data.frame( x = c(yes, 1, no, no), y = c(black, red, NA, white), z= c(T,F,T,T), J= c(2,7,8,9)) Library(DescTools) list-GetAllSubsets(c(NA,0,1,2,yes,y,no),min.n = 2, max.n = 5) ..and to obtain the following vector.. TRUE,FALSE, FALSE, FALSE Best regards Maicel Monzon -- Nunca digas nunca, di mejor: gracias, permiso, disculpe. Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/ __ 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] script to data clear
Hello List,
I did this script to clear data after import (I dont know is ok ). After
its execution levels and label values got lost. Could some explain me to
reassign levels again in the script (new depurate value)?
Best regard
Maicel Monzon MD, PHD
Center of Cybernetic Apply to Medicine
# data cleaning script
library(stringr)
for(i in 1:length(data)) {
if (is.factor(data[[i]])==T)
{for(j in 1:sum(str_detect(data[,i], )))
{data[[i]]-str_replace_all(data[[i]], , )}}
data[[i]]-str_trim (data[[i]],side = both)
data[[i]]-tolower(data[[i]])
}
Note: is 2 blank space and only one
--
Nunca digas nunca, di mejor: gracias, permiso, disculpe.
Este mensaje le ha llegado mediante el servicio de correo electronico que
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el servicio a tales fines y cumplir con las regulaciones establecidas
Infomed: http://www.sld.cu/
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