Questions tagged [r]
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332
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Tools that is similar to Prython
I'm working on a biostatistics project using R. I have several datasets to work with. However, in the RStudio environment, I need to modify and execute each script one by one. Recently, I discovered ...
- 157
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11
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Error using mcp2atm function for robust pairwise comparisons - undefined columns selected
I used a robust two-way ANOVA using the WRS2 package (R v.4.4.1), using the following code as suggested by Mair and Wilcox (2020) - the full dataset is on the bottom of this message:
library(WRS2)
...
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0
answers
8
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How to get predicted probabilities of being in each class of three using xgboost in R?
I am trying to train a xgboost model using iris dataset. The training code is shown below, and both prediction functions produce the same results. However, the length of the results is 135, while ...
- 109
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votes
1
answer
15
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Using R to generate lifespan plots
I have a dataset that records the lifespan and generation time of individual cell that I would like to plot as below:
Example_RLS_plot
Reference:
https://doi.org/10.1186/s12951-022-01379-9
Here is my ...
-3
votes
1
answer
14
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What it the R function to remove a couple of empty columns from a csv file
So I am working on this:
a screen shot of a csv file
and I am trying to delete the last 4 columns, what code should I use? I have it open on Rstudio and running R.
I tried doing
Df$column <- NULL
...
0
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0
answers
11
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Predicted values in a Tweedie GLM-model
I need help with how to create an actual vs predicted plot for a Tweedie GLM model in R where weights are used.
I have a Tweedie GLM model in R where I have derived the coefficients/factors for a risk ...
- 139
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votes
2
answers
19
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Export nested simple feature collection to geoJSON in R
I have used R to calculate a Voronoi tessellation I now want to use in an OSM umap. Because I want different areas to be easily distinguishable, following some hint at their github, I need a nested ...
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18
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How to speed up R dist matrix for hierarchical clustering for large matrix input data?
I have a large matrix (approximately 35,000 x 35,000) and I'm preparing a distance object in R for hierarchical clustering. The base R function dist() is too slow, so I'm using the distances function ...
- 609
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1
answer
15
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Open with Python an R data.table saved as metadata in a Parquet file
With R, I created a Parquet file containing a data.table as main data, and another data.table as metadata.
library(data.table)
library(arrow)
dt = data.table(x = c(1, 2, 3), y = c("a", "...
- 970
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6
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I want to colorize the points of a Shapviz dependence output acording to the variable
I have been trying to change the colors of the points on each variable, but even though i've tried using scale_x_discrete, by and changing the colors, or using scale_color_manual(), nothing works for ...
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5
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cLDA constraint for discrete-time models in R formulas
I work with longitudinal (repeated measures) models of clinical trial data. Patients are randomized to different treatment groups and measured over multiple pre-specified points in time. An example ...
- 5,771
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12
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Displaying Bar Graph in Shiny Dashboard Based on Select Input
I’m working on an interactive Shiny dashboard in R and I’m encountering an issue with my bar graph when no specific input is selected.
Here’s what I’m trying to achieve:
I have a bar graph that ...
1
vote
2
answers
26
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Plot datetime data as just month not month-year
I have a data frame that looks like this:
structure(list(date = structure(c(1592611200, 1624665600, 1626480000,
1620086400, 1624147200, 1624752000, 1626566400, 1.566e+09, 1621036800,
1651536000), ...
- 153
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0
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16
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Regression with a 0-1 variable. Should be the same as running a t-test, but I get a different p-value [migrated]
I have a dataset in R where I have volatility estimates (in my case, just standard deviation of minute returns on that day) for different days:
Date, Volatility, DayType
The variable DayType is 0 or ...
- 86
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0
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17
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R: stat_density2d change color of density surface?
I'm using this example to create a heatmap in R:
https://www.sharpsightlabs.com/blog/how-to-create-a-crime-heatmap-in-r/
ggmap(map_sf) +
stat_density2d(data = sf_crime, aes(x = lon, y = lat, fill = ....
- 1,691
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0
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19
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How do I get rid of the weird long floating point error numbers that are shown when I convert a vector to a name of a vector [duplicate]
This function shows the floating point error when displaying the vector as names of another vector but not when it is displayed "normally"
test <- rep(NA, times = length(seq(from = -0.5, ...
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votes
2
answers
31
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Find average temperature from a range of datetime for each day in dataframe
This is a subset of the dataframe I have:
structure(list(name = c("waldorf", "waldorf", "waldorf", "waldorf",
"waldorf", "waldorf", "...
- 153
-2
votes
1
answer
21
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Possible issues with text encoding
I'm having a strange problem when I read a .csv file using read_csv. I'm afraid I don't think I can produce a reproducible example because the issue may involve my current R/RStudio session and how ...
- 33
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16
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Google Cloud Platform Maps API key: Best practice to use in R to avoid incurring large API costs?
I'm using google maps API and ggmap to create a simple map of NYC in an RMarkdown document, in R:
install.packages("ggmap")
ggmap::register_google(key = "<your-api-key>", ...
- 1,691
-1
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0
answers
16
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Why does my mutate(across()) function not work in lapply? [duplicate]
I have a simple function that works just fine on one data frame but doesn't do anything when I use it in lapply.
For example:
df1 <- data.frame(x = c(1:5), y = c(11:14, NA))
df2 <- data.frame(...
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0
answers
25
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Dplyr ( count for total number/treatment) [closed]
I have data frame with two columns the first column is the number of children under the age of five that receive a treatment and the second column classifies the type of the treatment. I would like to ...
0
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0
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34
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How to extract from multiple zip files only the csv files whose name starts with a specific string of characters in r? [duplicate]
Let's consider a folder myfile containing more than a hundred zip files (z001.zip, z002.zip, z003.zip ...) each always including 4 distinct csv files whose names always start with these three letters ...
- 487
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votes
0
answers
18
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Increasing fontsize of numbers in forestplot in R
I am trying to prepare a forest plot for summarizing patient survival outcomes in multiple cohorts using the forestplot package in R. The plot comes out fine but I am struggling to increase the size ...
- 535
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0
answers
21
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Problems running accuracy metrics on Validation_Set using fable package
I am unable to let the ACCURACY function point only to the Validation_set. The code perfectly works only in case the first argument of Accuracy is the whole dataset("data_tsibble") but in ...
- 21
-1
votes
1
answer
36
views
Produce table with data bars in base R or ggplot2
I am looking to make a table with horizontal bar graphs in each cell to display continuous numeric data with 2 categorical independent variables. It would look similar to the below (fictional data):
...
- 151
-1
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0
answers
22
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Getting "invalid 'type' (character) of argument" error with numeric values when I do apply.weekly(data$x, sum) [closed]
I have a time series object and I am creating a list of the variables at different timesteps.
when I do apply.weekly( , mean) it works fine, but when I want to sum the values over a week it gives me..
...
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1
vote
4
answers
73
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Find row in Matrix A which is closest two Matrix B
Lets say I have two matrices A and B given by
set.seed(123)
m1 = matrix(runif(10*5), nrow = 10, ncol = 5)
m2 = matrix(runif(10*5), nrow = 10, ncol = 5)
I want to find for each row in matrix A the row ...
- 2,511
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0
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25
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Making a ggplot2 Sankey plot in R less crowded
If I have a dataframe in R (called connections_df), that shows the connections between the two endpoints (endpoint1 and endpoint2) with the corresponding chromosome (CHR):
endpoint1 ...
- 467
-1
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0
answers
38
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Making lines not overlap
I am creating a DGE plot for 2 samples. I want the lines in the resulting plot to NOT BE STACKED on top of each other, bot to be next to each other (so that both are visible).
## Load packages
if (! ...
1
vote
2
answers
33
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R function 'transform' ignoring argument 'check.names=FALSE'
I'm having issues with the function transform in R and the argument check.names.
For example:
df <- data.frame('A' = sample(1:10), 'B' = sample(1:10), 'C(%)' = NA, check.names = FALSE)
> names(...
- 47
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0
answers
47
views
Conditional variable for COMPLETE DATA [duplicate]
Attached data :
id = c (2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2)
vm = c("12", "13", "14", "15", "16", "17", "18" "19", &...
- 33
1
vote
2
answers
30
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Change the absolute value of elements in a dataframe without changing their sign (+ / -)
I have a dataframe of cumulative changes, which I am trying to convert into (multiplicative) factor values.
If all values were positive, I could simply add 1: e.g. a 25% increase would be 0.25, adding ...
- 219
1
vote
1
answer
15
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Pattern fill in highcharter bar chart
I would like to create a column or bar chart with pattern fill in an R shiny app. It seems to me that highcharts and related highcharter package should be able to do the job, but I could not find a ...
3
votes
1
answer
51
views
In R, how and where does the underlying C functions get their argument inputs?
I'm trying to understand what happens at the C level when I call a function in R. For instance, print("Hello, World!") will call UseMethod("print"). From the "table" in ...
- 51
-1
votes
0
answers
21
views
In ggHoriPlot, geom_horizon will create fill Categories. What the meanning? [closed]
In ggHoriPlot,geom_horizon will create fill Categories ypos3 .. yneg1 ..yneg13 ,refer to the legend in attached image.
How to understand Categories and it's created according what kind of logic ？ ...
- 2,281
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0
answers
5
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KFAS package: Why I can't pass SSMCustom state space object to SSModel formula?
I am trying to create SSModel from KFAS package in R. In the code I got from someone it was done this way:
model <- KFAS::SSModel(ts ~ -1 + SSMcustom(Z = Z_t,T = T_t, R = R_t, Q = Q_t, a1 = a1_t, ...
- 403
2
votes
1
answer
81
views
lme4 (glmer): Something buggy with treatment of factors in 4-way interactions
I have a dataset for which I am making a series of complex generalized linear mixed-effects models with the lme4 package in R. I have experience with glmer and this type of experimental data, but I'...
0
votes
1
answer
21
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how can I force the scale in ggplot to be in the middle of the data range?
In the plot below, the range in a goes from 0.001 to 0.7 but the legend doesn't have the middle value in the cyan color. Is there a way I can force that the middle value in the range of a be in the ...
- 215
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0
answers
12
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How to change the line-height only in the code chunk when using Rmd in Rstudio
I'm looking for a way to modify the .rstheme file and adjust the line-height in a R markdown document. Specifically I want the code chunk in the Rmd file to have a line-height of 1.2 and for the other ...
- 1
3
votes
0
answers
25
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R parallel: Stopping a cluster you don't have the object for?
I am working with a function that starts with parallel::makeCluster() and ends with parallel::stopCluster(). Sometimes it crashes in the middle and does not stop the cluster.
Demonstration code:
...
- 452
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0
answers
28
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How to remove real-time NA rows?
I'm writing a code in shiny to input data in real time and download a csv file, but I want to remove rows with NA in the final output file.
Is it difficult to remove rows in real time in shiny?
Is it ...
- 1
0
votes
0
answers
11
views
RStudio: Failure to install 'imager'
I am attempting to do the tutortial "Getting started with imager", but the very first instruction library(imager) generates a long error message, with only the first part shown below
Error: ...
- 57
1
vote
1
answer
33
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Fix order of stacks but allow colour to change
The data and code for this question were adapted from:
How to fill colors of stacked bar plot depending on colors column of df in R using ggplot
I want to fix the order of country appearance in each ...
- 15.5k
-1
votes
0
answers
37
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Exact same line of code not working between 2 PCs [closed]
On my home PC with R4.4.0
avg_demand_per_yearday <- aggregate(demand ~ yearday, df, 'mean')
it works as expexted. On my work machine with R4.4.1 an error occurs
Error in UseMethod("aggregate&...
2
votes
2
answers
61
views
Efficiently standardize a large matrix in R with foreach/doParallel?
I need to standardize (subtract the mean and divide by the standard deviation) the columns of several large matrices in R (roughly 300,000 rows by 10,000-20,000 columns).
The process has been very ...
- 452
0
votes
0
answers
22
views
Issues in my script to analyze a list of stock ticker symbols
The purpose of this script is to gather basic information about all S&P listed stocks from Wikipedia. It then uses the get symbol to extract price data over time, calculates log.return over that ...
0
votes
0
answers
13
views
Error in system(cmd, intern = intern, ignore.stdout = ignore.stdout, ignore.stderr = ignore.stderr)
I am running an R script that uses cifti and am getting this error:
Error in system(cmd, intern = intern, ignore.stdout = ignore.stdout, ignore.stderr = ignore.stderr) :
error in running command
...
- 1
0
votes
0
answers
58
views
aggregation based upon multiple criteria and time range (R)
Ultimately, I want to aggregate the amount column in my data over modular groups that do not yet exist but that are the composite of two existing groups and a time difference dimension.
I have a ...
- 25
0
votes
0
answers
10
views
Which versions to install to make RandomFields, RandomFieldsUtils, rpy2 compatible?
I am hoping to install some packages that people no longer update.
I need RandomFields (https://cran.r-project.org/src/contrib/Archive/RandomFields/), RandomFieldsUtils (https://cran.r-project.org/src/...
- 101
0
votes
2
answers
42
views
Why is this part of my code not adding the new columns to my data frame?
I have 13 datasets that are in .XPT format called data2010, data2011, data2012.. data2022. These are the BRFSS datasets from the CDC website. I have been trying to add three new columns to each of my ...
- 1