Re: [R] Interactions in regression
I have no real idea what you are trying to do, but if a table is
what you want, you can probably get it using the table() function.
Or, more likely, the xtabs() function.
Using your example from an earlier post (adjusted to make it
comprehensible to the human mind):
set.seed(1000)
time <- factor(rep(c("Pre","Post"),each=200))
treatment <- factor(rep(rep(c("Control","Treatment"),each=100),2))
mu<- rep(rep(1:2,each=100),2)
response <- rnorm(400,mean=mu)
xmpldata <- data.frame(time=time,treatment=treatment,response)
mod <- lm(response~time*treatment,data=xmpldata)
yhat <- fitted(mod)
xtb <- with(xmpldata,xtabs(yhat ~ time+treatment))
print(xtb)
> treatment
> time Control Treatment
> Post 94.10501 201.99112
> Pre 101.63792 210.04248
Is that (something like) what you want?
cheers,
Rolf Turner
P.S. You said: "I usually use GUI software". Now *there* lies your
problem. A GUI is a black box that removes all control over what is
going on, from your hands.
R. T.
--
Honorary Research Fellow
Department of Statistics
University of Auckland
Stats. Dep't. (secretaries) phone:
+64-9-373-7599 ext. 89622
Home phone: +64-9-480-4619
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Re: [R] igraph_vertex
В Mon, 26 Feb 2024 11:52:13 +0100 пишет: > TIFFOpen: figures/AES_network_bymembership.tiff: Cannot open. > Warning message: > In dev.off() : > unable to open TIFF file 'figures/AES_network_bymembership.tiff' In the current directory (see getwd()), is there a subdirectory named "figures"? Do you have write access to this subdirectory? Is there a file named "AES_network_bymembership.tiff" in the subdirectory named "figures"? Could it be open by a different program and therefore locked? Unfortunately, libtiff doesn't seem to provide any more information regarding why it couldn't open the file at this point. -- Best regards, Ivan __ 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.
Re: [R] igraph_vertex
Dear Ivan
Thanks a lot.
I used:
windowsFonts(Helvetica = windowsFont("Helvetica"))
No warning now with Helvetica
Additionally I used "sans", similarly no warning in the first part.
But still not able to open tiff with both versions:
Using "stress" as default layout
> dev.off()
TIFFOpen: figures/AES_network_bymembership.tiff: Cannot open.
RStudioGD
2
Warning message:
In dev.off() :
unable to open TIFF file 'figures/AES_network_bymembership.tiff'
Kind regards
Sibylle
-Original Message-
From: Ivan Krylov
Sent: Monday, February 26, 2024 10:15 AM
To: SIBYLLE STÖCKLI via R-help
Cc: sibylle.stoec...@gmx.ch
Subject: Re: [R] igraph_vertex
В Mon, 26 Feb 2024 09:02:56 +0100
SIBYLLE STÖCKLI via R-help пишет:
> In the following code, which loads the tiff file, I get the following
> error
This warning is definitely worth investigating, but it shouldn't interrupt your
code. Does the figure come out wrong after you see this warning?
> In doTryCatch(return(expr), name, parentenv, handler) : Character set
> family not found in the Windows character set database
>
> --> I am unsure if mySQL is the right solution. I have no experience
> how to change mySQL.
I see you've tried to do the right thing and searched for the warning message.
Unfortunately, the search engines are wrong; this doesn't seem related to MySQL.
A similarly-worded warning message exists in the Windows-related font functions
inside R:
>> warning(_("font family not found in Windows font database"))
If running a sufficiently new version of R, try Sys.setLanguage('en') before
reproducing the problem and searching for the exact warning message in double
quotes. (Reset it back using
Sys.setLanguage(your_language_code) or restart R afterwards.) Translated error
and warning messages are good for understanding, but they fragment the search
engine results.
I see that a few messages back you set a font family:
> vertex.label.family="Helvetica",
R probably doesn't know where to get it in order to render the plot as TIFF. If
you have a copy of Helvetica installed in your system, try registering it using
windowsFonts(Helvetica = windowsFont("how the font is named in the system")).
(See help(windowsFonts) for more
information.) Otherwise you may be limited to R's predefined font families.
It's annoying that "Helvetica" exists for PDF plots and such seemingly without
a problem, but if you change the output format to TIFF, the set of fonts
available to you changes too. Unfortunately, there are multiple different font
rendering engines in play, and their predefined lists of fonts also differ.
--
Best regards,
Ivan
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] igraph_vertex
В Mon, 26 Feb 2024 09:02:56 +0100
SIBYLLE STÖCKLI via R-help пишет:
> In the following code, which loads the tiff file, I get the following
> error
This warning is definitely worth investigating, but it shouldn't
interrupt your code. Does the figure come out wrong after you see this
warning?
> In doTryCatch(return(expr), name, parentenv, handler) : Character set
> family not found in the Windows character set database
>
> --> I am unsure if mySQL is the right solution. I have no experience
> how to change mySQL.
I see you've tried to do the right thing and searched for the warning
message. Unfortunately, the search engines are wrong; this doesn't seem
related to MySQL.
A similarly-worded warning message exists in the Windows-related font
functions inside R:
>> warning(_("font family not found in Windows font database"))
If running a sufficiently new version of R, try Sys.setLanguage('en')
before reproducing the problem and searching for the exact warning
message in double quotes. (Reset it back using
Sys.setLanguage(your_language_code) or restart R afterwards.)
Translated error and warning messages are good for understanding, but
they fragment the search engine results.
I see that a few messages back you set a font family:
> vertex.label.family="Helvetica",
R probably doesn't know where to get it in order to render the plot as
TIFF. If you have a copy of Helvetica installed in your system, try
registering it using windowsFonts(Helvetica = windowsFont("how the
font is named in the system")). (See help(windowsFonts) for more
information.) Otherwise you may be limited to R's predefined font
families.
It's annoying that "Helvetica" exists for PDF plots and such seemingly
without a problem, but if you change the output format to TIFF, the set
of fonts available to you changes too. Unfortunately, there are
multiple different font rendering engines in play, and their predefined
lists of fonts also differ.
--
Best regards,
Ivan
__
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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] Interactions in regression
Hi,
I do not want to make a plot, I try to make an output table in R, (in GUI
like Stata this is trivially easy task)
with regard to SO OP question. As I mentioned, in paper I would not do
this, but out of curiosity I use R this time trying to create it.
If in R this is trivial task as well, could you please show how to do it ?
After googling a lot I did not find solution.
regards,
Jacek
niedz., 25 lut 2024 o 17:00 Bert Gunter napisał(a):
> It is trivial in R to add whatever decorations to a plot that you would
> like, but that requires that you go beyond point and click production of
> graphics and write actual code. If you are unwilling or unable to do this,
> you are stuck with whatever various packaged graphics functionality
> provides.So you might want to search on "interaction plots for linear
> models in R" or similar at rseek.org or in your favorite web search
> engine if you haven't already done so. My minimal efforts brought up lots
> of hits, though none may be useful for your concerns, especially, as has
> already been pointed out, as your query doesn't seem to make much sense
> statistically.
>
> Cheers,
> Bert
>
>
> On Sun, Feb 25, 2024 at 7:46 AM Jacek Kownacki
> wrote:
>
>> Hi All,
>> I stumbled upon some topics regarding interactions in anova and regression
>> and packages for tabulating and visualizations the results of them.
>> Here we are:
>>
>> https://stackoverflow.com/questions/77933272/how-to-add-a-reference-level-for-interaction-in-gtsummary-and-sjplot/77935742#77935742
>> ,
>>
>> https://stackoverflow.com/questions/78016795/how-to-add-reference-levels-for-interaction-in-r?noredirect=1=1
>> .
>> I was wondering because I usually use GUI software and these questions did
>> not get answers, if from a technical point of view
>> how to do it, using these (sjPlot, gtsummary) or other ways to make such
>> tables, inserting the reference levels of these mentioned interactions.
>> This is not likely to be used in publications (including three base
>> levels), but from the point of view of solving the topics this questions
>> have interested me.
>> I tried myself to make it happen, but so far without success.
>> I recall this reprex based on SO:
>>
>> set.seed(1000)
>> my_data <- rbind(
>> data.frame(time = "Pre", treatment = "Control", response =
>> rnorm(100, mean=1)),
>> data.frame(time = "Pre", treatment = "Treatment", response =
>> rnorm(100, mean=2)),
>> data.frame(time = "Post", treatment = "Control", response =
>> rnorm(100, mean=1)),
>> data.frame(time = "Post", treatment = "Treatment", response =
>> rnorm(100, mean=2))
>> ) %>% mutate(time = factor(time, levels = c("Pre", "Post")))
>> %>%mutate(treatment = factor(treatment, levels = c("Control",
>> "Treatment")))
>> model3 <- lm(response ~ time * treatment, data = my_data)
>>
>> Thanks,
>> Jacek
>>
>> [[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.
>>
>
[[alternative HTML version deleted]]
__
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] igraph_vertex
Dear Kimmo
First of all many thanks for the valuable advice to publish code and csv.
Noted.
Yes, "edge.width= E(.)$weight" makes definitively sense.
In the following code, which loads the tiff file, I get the following error
tiff("figures/AES_network_bymembership.tiff", width=1000, height=700, res=120)
Warning message:
In doTryCatch(return(expr), name, parentenv, handler) : Character set family
not found in the Windows character set database
--> I am unsure if mySQL is the right solution. I have no experience how to
change mySQL.
Kind regards
Sibylle
tiff("figures/AES_network_bymembership.tiff", width=1000, height=700, res=120)
network %>%
ggraph(., layout = "auto")+
geom_edge_arc(curvature=0.3, aes(width=(E(network)$weight/10), color=from,
alpha=0.5)) +
geom_node_point(aes(size = V(network)$hub_score*200, color=
as.factor(V(network)$community))) +
geom_node_text(aes(label = V(network)$name), size=5, color="white", repel=T)+
scale_color_scico_d(palette = "batlow")+
scale_edge_width(range = c(0.2,4))+
scale_size(range = c(0.5,20)) +
#scale_edge_color_manual(values = c(scico(21, palette="batlow")))+
theme(plot.background = element_rect(fill = "black"),
legend.position = "right",
panel.background = element_rect(fill = "black"))
dev.off()
-Original Message-
From: R-help On Behalf Of Kimmo Elo
Sent: Monday, February 26, 2024 8:10 AM
To: r-help@r-project.org
Subject: Re: [R] igraph_vertex
Hi,
a quick additional note: try
"edge.width= E(.)$weight"
instead of the current "edge.width= network". Seems to work and makes a visible
difference...
HTH,
Kimmo
su, 2024-02-25 kello 19:11 +, Kimmo Elo kirjoitti:
>
> Hi again,
>
> your code is still not reproducible without modifications, but I
> succeed in getting the data straight. All read.csv-command are missing
> 'sep="\t"', it is need to read you tsv-data.
>
> And it could be more reproducible if you used e.g.
>
> --- snip ---
> aes<-read.csv(text="A.A B.B C.C D.D E.E F.F
> A.A 0 0 5 5 5 5 B.B 4 0
> 1 1 1 1 C.C 5 5 0 5 4
> 2 D.D 5 0 5 0 5 3 E.E 5 1
> 5 5 0 4 F.F 1 2 3 4 5
> 5", sep="\t", row.names = 1)
> --- snip ---
>
> This would save us from unnecessary copy-pasting :-)
>
> However, the error is still the same I mentioned in my first reply,
> i.e.:
>
> network %>% plot(
> vertex.color=clrs[V(.)$community],
> vertex.size=V(.)$hub_score*5,
> vertex.frame.color=V(.)$color,
> vertex.label.color="white",
> vertex.label.cex=0.5,
> vertex.label.family="Helvetica",
> vertex.label.font=1,
> edge.curved=0.5,
> HERE -->edge.width= network, <-- HERE
> layout=layout_with_mds(.))
>
> Try to comment out his line and see what happens. What network data
> variable should be mapped to edge width?
>
> Best,
> Kimmo
>
> su, 2024-02-25 kello 09:59 +0100, sibylle.stoec...@gmx.ch kirjoitti:
> > Dear coummunity
> >
> > Thanks a lot to David and Kimmo. Yes I see now that I need to
> > provide the two raw tables. Find here the reproducible example.
> >
> > Kind regards
> > Sibylle
> >
> > # R-labraries
> > library(circlize)
> > library(ggplot2)
> > library(igraph)
> > library(tidyverse)
> > library(RColorBrewer)
> > library(stringi)
> > library(scico)
> > library(plotly)
> > library(ggraph)
> >
> >
> > # Tables
> > aes<-read.csv("Test_adjac.csv", row.names = 1)
> > details<-read.csv("Test_cat.csv")
> >
> > # Edge table, reorganisation
> > aes_collapsed<-aes %>%
> > rownames_to_column(var='Names') %>%
> > tidyr::gather(target, weight, 1:ncol(aes)+1) %>%
> > dplyr::filter(weight != 0) %>%
> > mutate(weight = ifelse(weight == "-1", 0, weight)) # here 0 =
> > negative values
> >
> > write.csv(aes_collapsed, "edges_table_Test.csv", row.names = F)
> > edge_list<-read.csv("edges_table_Test.csv")
> >
> > # Network attributes
> > network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
> > vertices = details)
> >
> >
> > temp<-cluster_optimal(network)
> > temp<-cbind(membership=temp$membership, Names=temp$name)
> > aes_collapsed <- aes_collapsed %>%
> > merge(temp, by="Names")
> >
> >
> > network <- network %>%
> > set_edge_attr(name = "type", value = factor(aes_collapsed$Names,
> > ordered =
> > is.ordered(V(network)$name))) %>%
> > set_edge_attr(name = "membership", value =
> > aes_collapsed$membership) %>%
> > set_edge_attr(name = "color",
> > value = c(viridis::viridis(5))
> > [match(E(.)$type, c(factor(V(.)$name)))]) %>%
> > set_vertex_attr(name = "trans_v_net", value = c(transitivity(.,
> > type = "local"))) %>%
> > set_vertex_attr(name = "hub_score", value =
> > c(hub_score(.)$vector))
>
