Re: [R] File corruption?
If your workflow involves debugging and rerunning the code, you may experience differences between starting from a clean RStudio session and simply restarting your application. This can be caused by your environment having variables, shared objects etc defined. It is generally quite quick to close and open a new RStudio session, so ... when in doubt it's probably best to do that. You should be able to organize your workflow so that stopping and starting RStudio does not require you to rewrite any scripts. (e.g. save your scripts as you go along) HTH, Eric On Thu, Apr 1, 2021 at 9:45 PM wrote: > Hello, > > I would like to know if anyone has encounter this problem before and what > they have done to solve the problem. I am not sure if the problem has to > do > with R itself or with RStudio. The problem is the following: sometimes > when > I am developing code in R, using R studio -script inside a Shiny > application- at one point my code does not work in the application. I > works > outside the application as a separate script, but it stops working inside > the application with the rest of the functions. So far, what I have done is > to start an entire new script and rewrite the entire code and this will > solve the problem, the code will work fine again. I wonder if files/script > get corrupted sometimes and need to be refreshed. > > > > Thank you > > > [[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 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] File corruption?
Hello, I would like to know if anyone has encounter this problem before and what they have done to solve the problem. I am not sure if the problem has to do with R itself or with RStudio. The problem is the following: sometimes when I am developing code in R, using R studio -script inside a Shiny application- at one point my code does not work in the application. I works outside the application as a separate script, but it stops working inside the application with the rest of the functions. So far, what I have done is to start an entire new script and rewrite the entire code and this will solve the problem, the code will work fine again. I wonder if files/script get corrupted sometimes and need to be refreshed. Thank you [[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.
Re: [R] cox.zph
While the statements below about cox.zph are true, plotting the cox.zph result does tell you what the HR is doing. I never use one without the other. -- Kevin E. Thorpe Head of Biostatistics, Applied Health Research Centre (AHRC) Li Ka Shing Knowledge Institute of St. Michael's Assistant Professor, Dalla Lana School of Public Health University of Toronto email: kevin.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 > On Apr 1, 2021, at 9:00 AM, Bendix Carstensen > wrote: > > EXTERNAL EMAIL: > > Further to John Sorkin's post on the cox.zph: > You get test(s) of whether there is an interaction between a variable, say, > sex, and time. > > Suppose it is significant. You will have no clue whether the M/W hazard ratio > is increasing or decreasing by time. > > Suppose it is not significant. You will have no clue whether the > (non-significant) M/W hazrad ratio exhibits a pattern that is worth looking > further into or not. > > In this sense the cox.zph is a perfect tool to allow you to write 'we checked > for non proportionality' instead of 'we have no clue of how the M/W ratio > varies by time'. > > If you label it what it is, namely a test of interaction, you might realize > that you should ESTIMATE the shape and size of the interaction before > deriving a test, either ad-hoc by the Shoenfeld residuals or by proper > modeling. > > See for example pp 202 ff. in 'Epidemiology with R' by (surprise, surprise) > me, published by OUP a few months ago. > > b.r. > Bendix Carstensen > Senior Statistician > Steno Diabetes Center Copenhagen > Clinical Epidemiology > Niels Steensens Vej 2-4 > DK-2820 Gentofte > Denmark > tel: +45 30 91 29 61 > b...@bxc.dk > bendix.carsten...@regionh.dk > http://BendixCarstensen.com > > > > > > Region Hovedstaden anvender de personoplysninger, du giver os i forbindelse > med din henvendelse. Du kan læse mere om formålet med anvendelsen samt dine > rettigheder på vores hjemmeside: www.regionh.dk/persondatapolitik > > __ > 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.
Re: [R] Violin plot with mean_sdl
help(stat_summary) suggests you use the fun.args=list(...) argument to
pass arguments to the fun.* functions. Try replacing mult=1 by
fun.args=list(mult=1).
It is possible that ggplot2::stat_summary changed its behavior since
that web page was written or that the web page was always wrong.
-Bill
On Wed, Mar 31, 2021 at 11:03 PM Mahmood Naderan-Tahan
wrote:
>
> Hi,
>
> I followed the example described at [1] but I don't know why I get the
> following warning
>
>
> > library(ggplot2)
> > library(Hmisc)
> > mydata <- read.csv('test.csv', header=T,row.names=1)
> > mydata
> V1 V2 V3 V4
> P1 73.6 0.7 74.6 R
> P2 75.2 0.7 75.8 R
> P3 6.5 0.0 7.3 R
> P4 41.4 0.3 39.2 C
> P5 5.4 0.1 18.2 C
> P6 18.8 0.3 30.3 C
> > p <- ggplot(mydata, aes(x=V4, y=V1)) + geom_violin(trim=FALSE)
> > p + stat_summary(fun.data="mean_sdl", mult=1,
> + geom="crossbar", width=0.2 )
> Warning message:
> Ignoring unknown parameters: mult
>
>
> How can I fix that?
>
>
>
> [1]
> http://www.sthda.com/english/wiki/ggplot2-violin-plot-quick-start-guide-r-software-and-data-visualization
>
>
> Regards,
> Mahmood
>
> [[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.
__
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] [EXT] Calculating the total change in shareprice over a time periond
Dear David, thanks so much for your time and suggestion. It has worked now. Kind regards Ahson > On 31 March 2021 at 19:17 David K Stevens wrote: > > > Mr. Blueyonder, > > There are a number of problems with this. > > 1) is the data below really in a data frame? I coerced your table into a > data frame, guessing at the structure and when I print out the 1st three > rows I get an alignment into proper columns > > COMPANY_NUMBER COMPANY_NAME CITY YEAR_END_DATE > CLOSE_SHARE_PRICE > 1 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY > (THE)Egham 30/09/2005 NA > 2 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY > (THE)Egham 30/09/2006 NA > 3 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY > (THE)Egham 30/09/2007 9.65 > > I'd guess that your PLC is actually a 1 column data frame based on how > you present it. Because what you gave is so small, I just added commas > where they seemed suitable and used > > PLC <- read.csv(file='clipboard',header=T,stringsAsFactors = T) > > to create the data frame above. It's likely that your actual problem is > much larger so I'd export the data as a CSV file, and read it into R in > a similar way using > > PLC <- read.csv(file='myfile.csv',header=T,stringsAsFactors = T) > > 2) Your code is incorrect as is for two reasons. a) for your approach to > work, you'll need to create an empty column CH_SH_PRICE before running > the loop, because your loop is trying to place data into a non-existent > column b) the code PLC$CH_SH_PRICE(i+1) has to use square brackets, > otherwise R thinks PCL$CH_SH_PRICE is a function rather than a reference > to column element i+1 as in PLC$CH_SH_PRICE[i+1] > > Also, the functionisTRUE is actually the following > > function (x) > is.logical(x) && length(x) == 1L && !is.na(x) && x > > Is this really what you want to do, rather than just checking the > company number, as inPLC[i,1] == PLC[i+1,1]? > > Assuming (tentatively) I guessed right, here's what I got > > COMPANY_NUMBER COMPANY_NAME CITY > YEAR_END_DATE CLOSE_SHARE_PRICE CH_SH_PRICE > 1 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY (THE)Egham > 30/09/2005 NA NA > 2 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY (THE)Egham > 30/09/2006 NA NA > 3 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY (THE)Egham > 30/09/2007 9.65 NA > 4 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY (THE)Egham > 30/09/2008 6.55 -3.10 > > Good luck. > > David Stevens > > On 3/31/2021 11:04 AM, e-mail ma015k3113 via R-help wrote: > > Dear All, I have a data frame which is structured as follows: > > > > > > COMPANY_NUMBER COMPANY_NAMECITYYEAR_END_DATE CLOSE_SHARE_PRICE > > 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY (THE)Egham > > 30/09/2005 NA > > 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY (THE)Egham > > 30/09/2006 NA > > 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY (THE)Egham > > 30/09/2007 9.65 > > 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY (THE)Egham > > 30/09/2008 6.55 > > 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY (THE)Egham > > 30/09/2009 6.55 > > 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY (THE)Egham > > 30/09/2010 7.5 > > 10395804TOC PROPERTY BACKED LENDING TRUST PLC Newcastle Upon Tyne > > 30/11/2016 NA > > 10395804TOC PROPERTY BACKED LENDING TRUST PLC Newcastle Upon Tyne > > 30/11/2017 1.04 > > 10395804TOC PROPERTY BACKED LENDING TRUST PLC Newcastle Upon Tyne > > 30/11/2018 1.04 > > SC192761MARTIN CURRIE GLOBAL PORTFOLIO TRUST PLCEdinburgh > > 31/01/2000 NA > > SC192761MARTIN CURRIE GLOBAL PORTFOLIO TRUST PLCEdinburgh > > 31/01/2001 NA > > SC192761MARTIN CURRIE GLOBAL PORTFOLIO TRUST PLCEdinburgh > > 31/01/2003 NA > > SC192761MARTIN CURRIE GLOBAL PORTFOLIO TRUST PLCEdinburgh > > 31/01/2004 NA > > SC192761MARTIN CURRIE GLOBAL PORTFOLIO TRUST PLCEdinburgh > > 31/01/2005 NA > > SC192761MARTIN CURRIE GLOBAL PORTFOLIO TRUST PLCEdinburgh > > 31/01/2006 1.09 > > SC192761MARTIN CURRIE GLOBAL PORTFOLIO TRUST PLCEdinburgh > > 31/01/2007 1.17 > > SC192761MARTIN CURRIE GLOBAL PORTFOLIO TRUST PLCEdinburgh > > 31/01/2008 1.24 > > SC192761MARTIN CURRIE GLOBAL PORTFOLIO TRUST PLCEdinburgh > > 31/01/2009 0.9 > > SC192761MARTIN CURRIE GLOBAL PORTFOLIO TRUST PLCEdinburgh > > 31/01/2010 1.14 > > > > > > > > I am trying to calculate the
Re: [R] FD package_dbFD error
Hi Sara, Thank you for your advice and apologies for spamming. I will try to reorganise the arguments and if it doesn't work, will try r-sig-ecology. Kind regards, Vesna On 2021-04-01 0:58, Sarah Goslee wrote: Hi, While Bert is right that this would be a good question for r-sig-ecology, I think you might have made a very simple-to-fix mistake: According to https://www.rdocumentation.org/packages/FD/versions/1.0-12/topics/dbFD if you don't name the arguments, traits should come BEFORE sites. If that doesn't help, take a look at the site and trait data frames used in the examples and see if you can figure out where you went wrong. If you can't, then try r-sig-ecology. Sarah On Wed, Mar 31, 2021 at 6:33 PM Vesna Gulin wrote: Hi everyone, I am trying to conduct dbFD from the FD package, but it keeps giving me the same error: ex1 <- dbFD(sites, traits) Error in dbFD(sites, traits) : Different number of species in 'x' and 'a'. Ab, bb, Ci are species names. I have tried rewriting the species names so many times and ways, but nothing seems to work. I also checked for blank space but can't seem to find one. Does anyone have and idea what am I doing wrong? My data consists of two data frames: sites X Ab Bb Ci Cb Cbm Cdo Cm Cdi Dv Edi Ee Ede Es Eb Gc La Mm Op Oc Oh Or Pgr Ps Pgi Pf Pgri Po Pp Rr Ss Sl Ts Tv Tr 1 A 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 2 B 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 2 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 3 C 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 1 0 0 0 0 0 0 0 4 D 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 5 E 0 0 0 0 0 0 0 3 2 3 0 0 0 0 0 0 0 0 0 4 0 0 0 0 00 0 0 0 0 0 0 0 0 6 F 0 0 0 0 0 0 0 0 3 0 1 0 0 4 1 8 0 1 3 2 0 0 0 0 00 0 0 0 0 0 0 0 2 7 G 0 0 0 0 0 0 1 1 1 2 0 0 0 0 0 0 0 0 1 4 0 0 0 0 00 0 0 0 0 0 0 0 0 traits X bodyration flight feeding lifestyle moisture 1Ab 29.5 0.6203390none herbivorous geo-chortobiont xerophilous 2Bb 16.0 1.0625000 reduced omnivorous chortobiont mesophilous 3Ci 23.5 0.5829787full omnivorous geo-chortobiont xerophilous 4Cb 18.0 0.600full herbivorous chortobiont mesophilous 5 Cbm 18.0 0.600full herbivorous chortobiont mesophilous 6 Cdo 17.5 0.6342857 reduced herbivorous chortobiont mesophilous 7Cm 17.5 0.5914286full herbivorous chortobiont mesophilous 8 Cdi 21.5 0.5883721 reduced herbivorous chortobiont hygrophilous 9Dv 34.0 0.9044118 reduced carnivorous geo-chortobiont mesophilous 10 Edi 27.0 0.722none omnivorous thamnobiont xerophilous 11 Ee 25.0 0.640none omnivorous thamnobiont mesophilous 12 Ede 20.5 0.5902439none herbivorous chortobiont xerophilous 13 Es 25.5 0.9803922none omnivorous thamnobiont mesophilous 14 Eb 18.0 0.6416667 reduced herbivorous chortobiont mesophilous 15 Gc 22.5 0.456none omnivorousgeobiont mesophilous 16 La 13.0 0.9807692none herbivorous chortobiont mesophilous 17 Mm 18.0 1.097none omnivorous geo-chortobiont xerophilous 18 Op 12.0 0.667full omnivorous thamnobiont xerophilous 19 Oc 21.0 0.5690476full herbivorousgeobiont xerophilous 20 Oh 15.5 0.5967742 reduced herbivorous chortobiont mesophilous 21 Or 15.5 0.7193548 reduced herbivorous chortobiont mesophilous 22 Pgr 17.0 1.0588235none omnivorous thamnobiont mesophilous 23 Ps 21.5 1.0465116none omnivorous thamnobiont mesophilous 24 Pgi 14.0 0.550none herbivorous chortobiont mesophilous 25 Pf 26.5 0.9622642none omnivorous thamnobiont mesophilous 26 Pgri 17.5 1.0428571none omnivorous thamnobiont mesophilous 27 Po 17.0 0.8970588none herbivorous chortobiont mesophilous 28 Pp 17.5 0.6542857 reduced herbivorous chortobiont mesophilous 29 Rr 17.5 0.8857143 reduced omnivorous chortobiont mesophilous 30 Ss 22.5 0.573full herbivorous chortobiont mesophilous 31 Sl 20.5 0.6268293 reduced herbivorous chortobiont mesophilous 32 Ts 12.5 0.472 reduced herbivorousgeobiont hygrophilous 33 Tv 33.0 0.7803030full carnivorous thamnobiont mesophilous 34 Tr 20.0 0.900none omnivorousgeobiont hygrophilous Thank you in advance and kind regards, Vesna -- Vesna Gulin, Research and Teaching Assistant Department of Biology Faculty of Science University of Zagreb Rooseveltov trg 6, 1 Zagreb, Croatia __
Re: [R] pie3D.labels
Dear Dr. Lemon, Thank you for the rapid response and suggestions as well. BestCollins On Tuesday, March 30, 2021, 11:46:08 PM GMT+2, Jim Lemon wrote: Hi Collins, pie3D draws a pseudo-3D pie and then places 2D labels around it. If you put the labels on top of the pie, it is not going to look right. The labels will be displayed with an orthogonal viewing angle, while the pie will be tilted. pie3D is one of those functions that I wrote for those who might otherwise think that if R can't produce 3D pie charts, then R is no good. You can do fulsomely decorative plots in R, and if your boss demands a 3D pie chart, you can do it. If you really want to create a 3D pie chart with 3D labels, do it with a 3D rendering program like POVray. I'm afraid that I don't have the time to provide you with an example right now. Jim On Tue, Mar 30, 2021 at 11:42 PM Collins Boahen wrote: > > Dear Dr. Lemon, > > Thank you for developing such a fantastic package. > > I would like to find out if there is a way to insert the labels inside the > pie and manipulate the labels for fit perfectly. > > Please any tips or suggestions will be appreciated. > > Thank you > > Best > Collins > [[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.
Re: [R] cox.zph
Further to John Sorkin's post on the cox.zph: You get test(s) of whether there is an interaction between a variable, say, sex, and time. Suppose it is significant. You will have no clue whether the M/W hazard ratio is increasing or decreasing by time. Suppose it is not significant. You will have no clue whether the (non-significant) M/W hazrad ratio exhibits a pattern that is worth looking further into or not. In this sense the cox.zph is a perfect tool to allow you to write 'we checked for non proportionality' instead of 'we have no clue of how the M/W ratio varies by time'. If you label it what it is, namely a test of interaction, you might realize that you should ESTIMATE the shape and size of the interaction before deriving a test, either ad-hoc by the Shoenfeld residuals or by proper modeling. See for example pp 202 ff. in 'Epidemiology with R' by (surprise, surprise) me, published by OUP a few months ago. b.r. Bendix Carstensen Senior Statistician Steno Diabetes Center Copenhagen Clinical Epidemiology Niels Steensens Vej 2-4 DK-2820 Gentofte Denmark tel: +45 30 91 29 61 b...@bxc.dk bendix.carsten...@regionh.dk http://BendixCarstensen.com Region Hovedstaden anvender de personoplysninger, du giver os i forbindelse med din henvendelse. Du kan læse mere om formålet med anvendelsen samt dine rettigheder på vores hjemmeside: www.regionh.dk/persondatapolitik __ 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] How can certain variables be automatically excluded from being saved?
Am Thu, 1 Apr 2021 08:39:45 -0400
schrieb Duncan Murdoch :
> On 01/04/2021 4:05 a.m., Ralf Goertz wrote:
> > Hi,
> >
> > after having read here about the "seed problem" I wonder if there
> > is a way to automatically exclude certain variables from being
> > saved when the workspace image is saved at the end of an
> > interactive session. I have been using .First() and .Last() for
> > ages but apparently they are of no help as .First() gets called
> > before loading the workspace and .Last() after it has been saved.
> > At least the line
> >
> > if (".Random.seed" %in% ls(all.names=T)) rm(.Random.seed, pos=1)
> >
> > in either of those functions doesn't have the desired effect.
>
> Jim suggested a way to do that, but I don't think it's really a good
> idea: it just fixes one aspect of the problem, it doesn't solve the
> whole thing.
>
> The real problem is saving the workspace occasionally, but always
> loading it. The "always loading" part is automatic, so I think the
> real solution should address the "occasionally saving" part.
Yes, that is exactly what I quite often do. I have to work in different
projects and I usually start R in the project directory. When I do
serious stuff I save afterwards. But quite often I want to check
something quickly and then I don't want to clutter up my workspace.
> If you always save the workspace, things are fine. You'll save the
> seed at the end of one session, and load it at the beginning of the
> next.
>
> If you never save the workspace, things are also fine. You'll always
> generate a new seed in each session that needs one.
>
> Personally, I believe in the "never save it" workflow. I think it
> has lots of benefits besides the random seed issue: you won't get a
> more-and-more cluttered workspace over time, you end up with more
> reproducible results, etc. However, I can understand that some
> people use a different workflow, so "always save it" is sometimes a
> reasonable choice.
>
> So the real problem is the "sometimes save it" workflow, which is
> **encouraged** by the default q(save = "default") option, which asks
> when interactive. Changing the default to act like q(save = "no")
> would be my preference (and that's how I configure things), but
> changing it to act like q(save = "yes") would be an improvement over
> the current choice.
I would prefer to be able to only save the history since that is where
the work is done. Usually, my data is easily restored using commands
from the history. I could probably accomplish that by linking .RData to
/dev/null or making it an empty readonly file. However, I would have to
do that in every directory I happen to use R in.
__
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] How can certain variables be automatically excluded from being saved?
On 01/04/2021 4:05 a.m., Ralf Goertz wrote:
Hi,
after having read here about the "seed problem" I wonder if there is a
way to automatically exclude certain variables from being saved when the
workspace image is saved at the end of an interactive session. I have
been using .First() and .Last() for ages but apparently they are of no
help as .First() gets called before loading the workspace and .Last()
after it has been saved. At least the line
if (".Random.seed" %in% ls(all.names=T)) rm(.Random.seed, pos=1)
in either of those functions doesn't have the desired effect.
Jim suggested a way to do that, but I don't think it's really a good
idea: it just fixes one aspect of the problem, it doesn't solve the
whole thing.
The real problem is saving the workspace occasionally, but always
loading it. The "always loading" part is automatic, so I think the real
solution should address the "occasionally saving" part.
If you always save the workspace, things are fine. You'll save the seed
at the end of one session, and load it at the beginning of the next.
If you never save the workspace, things are also fine. You'll always
generate a new seed in each session that needs one.
Personally, I believe in the "never save it" workflow. I think it has
lots of benefits besides the random seed issue: you won't get a
more-and-more cluttered workspace over time, you end up with more
reproducible results, etc. However, I can understand that some people
use a different workflow, so "always save it" is sometimes a reasonable
choice.
So the real problem is the "sometimes save it" workflow, which is
**encouraged** by the default q(save = "default") option, which asks
when interactive. Changing the default to act like q(save = "no") would
be my preference (and that's how I configure things), but changing it to
act like q(save = "yes") would be an improvement over the current choice.
Duncan Murdoch
__
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] How can certain variables be automatically excluded from being saved?
Hi Ralph,
I suppose you could write a wrapper for q():
byebye<-function(drop=".Random.seed",save = "default", status = 0,
runLast = TRUE) {
if(drop %in% ls(all.names=TRUE)) rm(drop,pos=1)
q(save=save,status=status,runLast=runLast)
)
warning: untested
Jim
On Thu, Apr 1, 2021 at 7:05 PM Ralf Goertz wrote:
>
> Hi,
>
> after having read here about the "seed problem" I wonder if there is a
> way to automatically exclude certain variables from being saved when the
> workspace image is saved at the end of an interactive session. I have
> been using .First() and .Last() for ages but apparently they are of no
> help as .First() gets called before loading the workspace and .Last()
> after it has been saved. At least the line
>
> if (".Random.seed" %in% ls(all.names=T)) rm(.Random.seed, pos=1)
>
> in either of those functions doesn't have the desired effect.
>
> __
> 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.
[R] How can certain variables be automatically excluded from being saved?
Hi,
after having read here about the "seed problem" I wonder if there is a
way to automatically exclude certain variables from being saved when the
workspace image is saved at the end of an interactive session. I have
been using .First() and .Last() for ages but apparently they are of no
help as .First() gets called before loading the workspace and .Last()
after it has been saved. At least the line
if (".Random.seed" %in% ls(all.names=T)) rm(.Random.seed, pos=1)
in either of those functions doesn't have the desired effect.
__
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] Violin plot with mean_sdl
Hi,
I followed the example described at [1] but I don't know why I get the
following warning
> library(ggplot2)
> library(Hmisc)
> mydata <- read.csv('test.csv', header=T,row.names=1)
> mydata
V1 V2 V3 V4
P1 73.6 0.7 74.6 R
P2 75.2 0.7 75.8 R
P3 6.5 0.0 7.3 R
P4 41.4 0.3 39.2 C
P5 5.4 0.1 18.2 C
P6 18.8 0.3 30.3 C
> p <- ggplot(mydata, aes(x=V4, y=V1)) + geom_violin(trim=FALSE)
> p + stat_summary(fun.data="mean_sdl", mult=1,
+ geom="crossbar", width=0.2 )
Warning message:
Ignoring unknown parameters: mult
How can I fix that?
[1]
http://www.sthda.com/english/wiki/ggplot2-violin-plot-quick-start-guide-r-software-and-data-visualization
Regards,
Mahmood
[[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.
