How can I tell what arima model this code is running? - r

I'm reading over some R code, and I've come across a line that where the function prototype doesn't seem to match what I've seen in the library's api (fabletools).
fitted_model = a_time_series %>%
filter(date <= tsibble::year(someyear)) %>%
fabletools::model(arima = ARIMA(time)
...Where time is a column from a a_time_series. How do I tell what arima model this is using?
(e.g. arima(1,1,1) or arima(0,1,1) ,etc)
I've checked this documentation however, the function prototypes don't seem to match.


You can identify the ARIMA output by looking at the formatted output in the console. If you need to obtain this display as text, you can use the format() function.
library(fable)
#> Loading required package: fabletools
library(tsibble)
library(dplyr)
tourism %>%
group_by(Purpose) %>%
summarise(Trips = sum(Trips)) %>%
model(auto_arima = ARIMA(Trips)) %>%
mutate(format(auto_arima))
#> # A mable: 4 x 3
#> # Key: Purpose [4]
#> Purpose auto_arima `format(auto_arima)`
#> <chr> <model> <chr>
#> 1 Business <ARIMA(0,1,1)(0,1,1)[4]> <ARIMA(0,1,1)(0,1,1)[4]>
#> 2 Holiday <ARIMA(0,1,1)(0,1,1)[4]> <ARIMA(0,1,1)(0,1,1)[4]>
#> 3 Other <ARIMA(0,1,1)(1,0,0)[4]> <ARIMA(0,1,1)(1,0,0)[4]>
#> 4 Visiting <ARIMA(1,0,1)(2,1,0)[4]> <ARIMA(1,0,1)(2,1,0)[4]>
Created on 2020-06-12 by the reprex package (v0.3.0)
Session info
devtools::session_info()
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Related

GDCprepare() returns Error in function (classes, fdef, mtable)

I have downloaded Proteome Profiling data from the TCGA-LGG project with the Bioconductor package TCGAbiolinks.
Then I have the following error when running GDCprepare:
library("TCGAbiolinks")
query_lgg = GDCquery(
project = "TCGA-LGG",
data.category = "Proteome Profiling",
sample.type = "Primary Tumor",
legacy = FALSE)
#> --------------------------------------
#> o GDCquery: Searching in GDC database
#> --------------------------------------
#> Genome of reference: hg38
#> --------------------------------------------
#> oo Accessing GDC. This might take a while...
#> --------------------------------------------
#> ooo Project: TCGA-LGG
#> --------------------
#> oo Filtering results
#> --------------------
#> ooo By sample.type
#> ----------------
#> oo Checking data
#> ----------------
#> ooo Check if there are duplicated cases
#> ooo Check if there results for the query
#> -------------------
#> o Preparing output
#> -------------------
lgg_res <- getResults(query_lgg)
GDCdownload(query = query_lgg)
#> Downloading data for project TCGA-LGG
#> Of the 429 files for download 429 already exist.
#> All samples have been already downloaded
lgg_data <- GDCprepare(query_lgg)
#> Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'metadata<-' for signature '"function"'
Created on 2021-11-10 by the reprex package (v2.0.1)
Session info
sessioninfo::session_info()
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#> setting value
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#> os Ubuntu 20.04.2 LTS
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#> ui X11
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#> fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0)
#> generics 0.1.1 2021-10-25 [1] CRAN (R 4.1.0)
#> GenomeInfoDb 1.28.4 2021-09-05 [1] Bioconductor
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#> rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.1.0)
#> Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.0)
#> RCurl 1.98-1.5 2021-09-17 [1] CRAN (R 4.1.0)
#> readr 2.0.2 2021-09-27 [1] CRAN (R 4.1.0)
#> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.0)
#> rlang 0.4.12 2021-10-18 [1] CRAN (R 4.1.0)
#> rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.1.0)
#> RSQLite 2.2.8 2021-08-21 [1] CRAN (R 4.1.0)
#> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
#> rvest 1.0.2 2021-10-16 [1] CRAN (R 4.1.0)
#> S4Vectors 0.30.2 2021-10-03 [1] Bioconductor
#> scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.0)
#> sessioninfo 1.2.1 2021-11-02 [1] CRAN (R 4.1.0)
#> stringi 1.7.5 2021-10-04 [1] CRAN (R 4.1.0)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
#> styler 1.6.2 2021-09-23 [1] CRAN (R 4.1.0)
#> SummarizedExperiment 1.22.0 2021-05-19 [1] Bioconductor
#> TCGAbiolinks * 2.20.1 2021-10-07 [1] Bioconductor
#> TCGAbiolinksGUI.data 1.12.0 2021-05-20 [1] Bioconductor
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#> withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.0)
#> xfun 0.28 2021-11-04 [1] CRAN (R 4.1.0)
#> XML 3.99-0.8 2021-09-17 [1] CRAN (R 4.1.0)
#> xml2 1.3.2 2020-04-23 [1] CRAN (R 4.1.0)
#> XVector 0.32.0 2021-05-19 [1] Bioconductor
#> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0)
#> zlibbioc 1.38.0 2021-05-19 [1] Bioconductor
#>
#> [1] /home/matt/R/x86_64-pc-linux-gnu-library/4.1
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
I tried to investigate the error and it lead me to Issue #198, but with no success.
Also, I understand that this error is related to S4 generic function being applied to an object with no defined S4 method, as discussed here.
Am I missing something? Can somebody please help me?
Thanks in advance!

Support for proteome profiling has been provided in the package. To obtain the newest version the package should be installed from Github with the following command BiocManager::install("BioinformaticsFMRP/TCGAbiolinks") (see here).

Column not being recognised as variable in R [duplicate]

This question already has answers here:
Convert row names into first column
(9 answers)
Closed 2 years ago.
Hi,
I just transposed a large data set and I realised that the first row doesn't have a column name. I have included an extract of the dataset, I tried to use names(df)[1] <- "Year" but it changed the variable name for the second column instead of the first. Is there a way I can include a variable name for the first column?
df <- structure(list(Construction = c("3209.4", "3307.0", "3519.3", "3693.0",
"3545.1", "3620.2"), Manufacturing = c(" 654.9", " 692.9", " 785.1",
" 810.1", " 744.8", " 793.6")), row.names = c("1975 1Q", "1975 2Q",
"1975 3Q", "1975 4Q", "1976 1Q", "1976 2Q"), class = "data.frame")
df
#> Construction Manufacturing
#> 1975 1Q 3209.4 654.9
#> 1975 2Q 3307.0 692.9
#> 1975 3Q 3519.3 785.1
#> 1975 4Q 3693.0 810.1
#> 1976 1Q 3545.1 744.8
#> 1976 2Q 3620.2 793.6
Created on 2020-09-03 by the reprex package (v0.3.0)
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.0.2 (2020-06-22)
#> os macOS Catalina 10.15.5
#> system x86_64, darwin17.0
#> ui X11
#> language (EN)
#> collate en_AU.UTF-8
#> ctype en_AU.UTF-8
#> tz Australia/Melbourne
#> date 2020-09-03
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date lib source
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#>
#> [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

It is the row.names and not a column. If we need to create a column with row names, use rownames_to_column from tibble
library(tibble)
library(dplyr)
df <- df %>%
rownames_to_column('Year')

Why does dplyr::mutate_at() on the first element in a rowwise-tibble also take effect on the rest of the elements?

In the following code, I defined a tibble df with two columns: name column contains a character vector of c("a", "b", "c"), and data column contains a list of tibbles, each with the column value. Then I'd like to change the column name of each tibble's value column to the character in the corresponding row, e.g. "a", "b" and "c". To manipulate the tibble in a row-wise manner, I used dplyr::rowwise(), but then I found that the changes taking effect on the first element (changing the column name to "a") also took effect on the rest of the elements (since after the first row, the printed tibble before the change of the column name showed the column name of "a"). And therefore, it can be expected that the change of column names to the following elements in the column failed, since there were no longer column names of "value" (all changed to "a"). Do I have to use a purrr::map() function here instead of the tidier row-wise tibble manipulation?
Would you please give me an answer using rowwise-mutate_at method? Thanks.
library(tidyverse)
#> Warning: 程辑包'tidyverse'是用R版本3.6.3 来建造的
#> Warning: 程辑包'ggplot2'是用R版本3.6.1 来建造的
#> Warning: 程辑包'tibble'是用R版本3.6.3 来建造的
#> Warning: 程辑包'tidyr'是用R版本3.6.1 来建造的
#> Warning: 程辑包'readr'是用R版本3.6.1 来建造的
#> Warning: 程辑包'purrr'是用R版本3.6.1 来建造的
#> Warning: 程辑包'dplyr'是用R版本3.6.3 来建造的
#> Warning: 程辑包'stringr'是用R版本3.6.1 来建造的
#> Warning: 程辑包'forcats'是用R版本3.6.3 来建造的
df <- tibble::tibble(name = c("a", "b", "c"),
data = list(tibble::tibble(value = 1:10)))
df_mutate <- df %>%
dplyr::rowwise() %>%
dplyr::mutate_at("data", ~ {
print(.x)
colnames(.x)[colnames(.x) %in% "value"] <- name
list(.x)
}) %>%
dplyr::ungroup()
#> # A tibble: 10 x 1
#> value
#> <int>
#> 1 1
#> 2 2
#> 3 3
#> 4 4
#> 5 5
#> 6 6
#> 7 7
#> 8 8
#> 9 9
#> 10 10
#> # A tibble: 10 x 1
#> a
#> <int>
#> 1 1
#> 2 2
#> 3 3
#> 4 4
#> 5 5
#> 6 6
#> 7 7
#> 8 8
#> 9 9
#> 10 10
#> # A tibble: 10 x 1
#> a
#> <int>
#> 1 1
#> 2 2
#> 3 3
#> 4 4
#> 5 5
#> 6 6
#> 7 7
#> 8 8
#> 9 9
#> 10 10
Created on 2020-06-19 by the reprex package (v0.3.0)
devtools::session_info()
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Yes, you can use map2 :
library(dplyr)
df %>% mutate(data = purrr::map2(name, data, ~{names(.y) <- .x;.y}))
Or Map in base R :
df$data <- Map(function(x, y) {names(y) <- x;y}, df$name, df$data)
If you want to use rowwise a similar approach would be :
df %>% rowwise() %>% mutate(data = {names(data) <- name;list(data)})

How to set the label for the point that bigger than their median in r?

I am new to R and I have problems with setting my labels that their coordinates are bigger than their median. Here is my dataframe:
dat <- data.frame(
time = factor(c("Breakfast","Breakfast","Breakfast","Lunch","Lunch","Lunch","Dinner","Dinner","Dinner","Snack","Snack","Snack","Snack"), levels=c("Breakfast","Lunch","Dinner","Snack")),
total_bill_x = c(12.75,14.89,20.5,17.23,30.3,27.8,20.7,32.3,25.4,14.5,13.7,14.2,15.7), total_bill_y= c(20.75,15.29,18.52,19.23,27.3,23.6,19.75,27.3,21.48,13.66,15.59,17.3,14.78)
)
Here is my code:
library (dplyr)
library(ggplot2)
c<-dat %>%
group_by(time) %>%
summarise(
x = sum(total_bill_x),
y = sum(total_bill_y)
)
#visualiser
ggplot(c,aes(x,y))+
geom_point()+
geom_vline(linetype="dashed",color="red",xintercept = median(c$x))+
geom_hline(linetype="dashed",color="red",yintercept = median(c$y))+
geom_text(aes(label=time),hjust=1, vjust=1.2)
In this case, Label that I want to display are only Lunch and Dinner. Which condition should I add to achieve this?
Any help would be much appreciated.

Try this:
library (dplyr)
library(ggplot2)
dat <- data.frame(
time = factor(c("Breakfast","Breakfast","Breakfast","Lunch","Lunch","Lunch","Dinner","Dinner","Dinner","Snack","Snack","Snack","Snack"), levels=c("Breakfast","Lunch","Dinner","Snack")),
total_bill_x = c(12.75,14.89,20.5,17.23,30.3,27.8,20.7,32.3,25.4,14.5,13.7,14.2,15.7), total_bill_y= c(20.75,15.29,18.52,19.23,27.3,23.6,19.75,27.3,21.48,13.66,15.59,17.3,14.78)
)
c<-dat %>%
group_by(time) %>%
summarise(x = sum(total_bill_x),
y = sum(total_bill_y)) %>%
mutate(med_x = median(x),
med_y = median(y),
lab = case_when(x > med_x & y > med_y ~ as.character(time),
TRUE ~ NA_character_))
#visualiser
ggplot(c,aes(x,y))+
geom_point()+
geom_vline(linetype="dashed",color="red",xintercept = median(c$x))+
geom_hline(linetype="dashed",color="red",yintercept = median(c$y))+
geom_text(aes(label=lab),hjust=1, vjust=1.2)
Which gives you:

Maybe something like this will work
library(tidyverse)
dat <- data.frame(
time = factor(c("Breakfast","Breakfast","Breakfast","Lunch","Lunch","Lunch","Dinner","Dinner","Dinner","Snack","Snack","Snack","Snack"), levels=c("Breakfast","Lunch","Dinner","Snack")),
total_bill_x = c(12.75,14.89,20.5,17.23,30.3,27.8,20.7,32.3,25.4,14.5,13.7,14.2,15.7), total_bill_y= c(20.75,15.29,18.52,19.23,27.3,23.6,19.75,27.3,21.48,13.66,15.59,17.3,14.78)
)
c<-dat %>%
group_by(time) %>%
summarise(
x = sum(total_bill_x),
y = sum(total_bill_y),
) %>%
mutate(median_x = median(x),median_y = median(y)) %>%
filter(x > median_x,y > median_y)
ggplot(data = c,aes(x,y))+
geom_point()+
geom_vline(linetype="dashed",color="red",xintercept = c$median_x)+
geom_hline(linetype="dashed",color="red",yintercept = c$median_y)+
geom_text(aes(label=time),hjust=1, vjust=1.2)
Created on 2020-05-08 by the reprex package (v0.3.0)
devtools::session_info()
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#> setting value
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R: ggplot2 plot with ggupset and hrbrthemes::theme_upsum(): Superfluous "at" appears at x-axis label

I am using hrbrthemes::theme_ipsum() with most of my plots, but now I'm encountering odd behaviour while using ggupset: An extra "at" above the x-axis label that I can neither find the origin of nor can get rid of.
If anyone could try to explain what's going on here (and how to get rid of it), that'd be great.
Note that I tried both the current CRAN and GitHub versions of hrbrthemes.
Demonstration:
library(ggplot2)
library(dplyr, warn.conflicts = FALSE)
library(ggupset) # https://github.com/const-ae/ggupset
library(hrbrthemes) # https://github.com/hrbrmstr/hrbrthemes
# starting with a perfectly normal upset plot from ggupset's README
p <- tidy_movies %>%
distinct(title, year, length, .keep_all = TRUE) %>%
head(100) %>% # smaller dataset for faster(ish) plotting
ggplot(aes(x=Genres)) +
geom_bar() +
scale_x_upset(order_by = "degree") +
labs(x = "x-label for demonstration purposes")
looks fine:
p
#> Warning: Removed 30 rows containing non-finite values (stat_count).
Now with theme_ipsum() the easy way
p_hrbr <- p + hrbrthemes::theme_ipsum()
But nope, something seems to conflict here.
p_hrbr
#> Warning: Removed 30 rows containing non-finite values (stat_count).
#> Error: Insufficient values in manual scale. 2 needed but only 0 provided.
But in my actual usecase I set the theme globally, like so:
theme_set(hrbrthemes::theme_ipsum())
The original plot, now with theme_ipsum. Notice the x-axis on the bottom right.
p
#> Warning: Removed 30 rows containing non-finite values (stat_count).
I can't find any label set to "at". at what?
p$labels
#> $x
#> [1] "x-label for demonstration purposes"
#>
#> $y
#> [1] "count"
#>
#> $weight
#> [1] "weight"
Resetting to the default theme:
theme_set(theme_gray())
It's gone
p
#> Warning: Removed 30 rows containing non-finite values (stat_count).
Session info
devtools::session_info(pkgs = c("ggplot2", "hrbrthemes", "ggupset"))
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 3.6.3 (2020-02-29)
#> os macOS Catalina 10.15.3
#> system x86_64, darwin15.6.0
#> ui X11
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#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Europe/Berlin
#> date 2020-03-24
#>
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#>
#> [1] /Users/Lukas/Library/R/3.6
#> [2] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
Created on 2020-03-24 by the reprex package (v0.3.0)
Update 2020-03-24: The author of ggupset has responded on GitHub and is taking a look.

The issue was caused by ggupset, and has since been fixed.
If anyone else has encountered this, you can use the current development version: remotes::install_github("const-ae/ggupset"), or wait for the CRAN release in the near future.

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