Jay Zola
2017-Jun-26 18:19 UTC
[R] Model studies in one analysis using treatment as a five level moderator in a meta-regression
Hello,
I am medical student, writing a meta-analysis on complication and reoperation
rates after the five most common treatments of distal radius fractures. I have
been busy with the statistics for months by my self, but find it quite hard
since our classes were very basic. Now I want to compare the treatment
modalities to see if there are significant differences. Using R I was able to
synthesize the complication rates and reoperation rates for each treatment
method. But I never had any R course and managed by trial and error, so the code
probably doesn't look that great. Someone told me I could best model the
data in one analysis using treatment as a five level moderator in a
meta-regression. Can some help me with the R code to do this? Your help would be
very much appreciated.
Thank you,
Jay
Study| Event Type| Treatment| Number of Events (n)| N| n/N|
Kumaravel| Complications| EF| 3| 23| 0,1304348|
Franck| Complications| EF| 2| 20| 0,1|
Schonnemann| Complications| EF| 8| 30| 0,2666667|
Aita| Complications| EF| 1| 16| 0,0625|
Hove| Complications| EF| 31| 39| 0,7948718|
Andersen| Complications| EF| 26| 75| 0,3466667|
Krughaug| Complications| EF| 22| 75| 0,2933333|
Moroni| Complications| EF| 0| 20| 0|
Plate| Complications| IMN| 3| 30| 0,1|
Chappuis| Complications| IMN| 4| 16| 0,25|
Gradl| Complications| IMN| 12| 66| 0,1818182|
Schonnemann| Complications| IMN| 6| 31| 0,1935484|
Aita| Complications| IMN| 1| 16| 0,0625|
Dremstrop| Complications| IMN| 17| 44| 0,3863636|
Wong| Complications| PC| 1| 30| 0,0333333|
Kumaravel| Complications| PC| 4| 25| 0,16|
Dataset on my dropbox:
https://www.dropbox.com/s/j1urqzr99bt76ip/Basics%20excel%20file%20complication%20and%20reoperation%20rate.xlsx?dl=0
Basics excel file complication and reoperation
rate.xlsx<https://www.dropbox.com/s/j1urqzr99bt76ip/Basics%20excel%20file%20complication%20and%20reoperation%20rate.xlsx?dl=0>
www.dropbox.com
Shared with Dropbox
library(meta)
library(stargazer)
library(foreign)
All <-read.spss("C:\\Users\\313635aa.STUDENT\\Desktop\\Meta-Analyse
Complications and Reoperations.sav",to.data.frame = T, use.value.labels =
T)
All <- na.omit(All)
Complications <- All[which(All[,"Event_Type"] ==
"Complications"),]
Re_operation <- All[which(All[,"Event_Type"] ==
"Reoperations"),]
EF <- All[which(All[,"Treatment"] == "EF"),]
IMN <- All[which(All[,"Treatment"] == "IMN"),]
pc <- All[which(All[,"Treatment"] == "PC"),]
KW <- All[which(All[,"Treatment"] == "KW"),]
VPO <- All[which(All[,"Treatment"] == "VPO"),]
EF_C <- EF[which(EF[,"Event_Type"] == "Complications"),]
EF_R <- EF[which(EF[,"Event_Type"] == "Reoperations"),]
IMN_C <- IMN[which(IMN[,"Event_Type"] ==
"Complications"),]
IMN_R <- IMN[which(IMN[,"Event_Type"] ==
"Reoperations"),]
pc_C <- pc[which(pc[,"Event_Type"] == "Complications"),]
pc_R <- pc[which(pc[,"Event_Type"] == "Reoperations"),]
KW_C <- KW[which(KW[,"Event_Type"] == "Complications"),]
KW_R <- KW[which(KW[,"Event_Type"] == "Reoperations"),]
VPO_C <- VPO[which(VPO[,"Event_Type"] ==
"Complications"),]
VPO_R <- VPO[which(VPO[,"Event_Type"] ==
"Reoperations"),]
Output <- function(x, y, k.min=10){
file <- metaprop(Events_n, N, Study_ID, data = x)
forest.meta(file, studlab = T, pooled.totals = T, bysort = F)
dev.copy2pdf(file=y, width = 11.69, height = 8.27)
print(file)
}
R code on my dropbox:
https://www.dropbox.com/s/67pnfpi10qu110v/R%20code%20voor%20forrest%20en%20funnel%20plots.rtf?dl=0
[https://cfl.dropboxstatic.com/static/images/icons128/page_white_word.png]<https://www.dropbox.com/s/67pnfpi10qu110v/R%20code%20voor%20forrest%20en%20funnel%20plots.rtf?dl=0>
R code voor forrest en funnel
plots.rtf<https://www.dropbox.com/s/67pnfpi10qu110v/R%20code%20voor%20forrest%20en%20funnel%20plots.rtf?dl=0>
www.dropbox.com
Shared with Dropbox
[[alternative HTML version deleted]]
Vito Michele Rosario Muggeo
2017-Jun-26 20:05 UTC
[R] Model studies in one analysis using treatment as a five level moderator in a meta-regression
hi Jay, Consult a local statistician. Statistics is not you think is (namely simple computations, R and probably plotting..). regards, vito Jay Zola <jayjay.1988 at hotmail.nl> ha scritto:> Hello, > > > I am medical student, writing a meta-analysis on complication and > reoperation rates after the five most common treatments of distal > radius fractures. I have been busy with the statistics for months by > my self, but find it quite hard since our classes were very basic. > Now I want to compare the treatment modalities to see if there are > significant differences. Using R I was able to synthesize the > complication rates and reoperation rates for each treatment method. > But I never had any R course and managed by trial and error, so the > code probably doesn't look that great. Someone told me I could best > model the data in one analysis using treatment as a five level > moderator in a meta-regression. Can some help me with the R code to > do this? Your help would be very much appreciated. > > > Thank you, > > > Jay > > > Study| Event Type| Treatment| Number of Events (n)| N| n/N| > > Kumaravel| Complications| EF| 3| 23| 0,1304348| > > Franck| Complications| EF| 2| 20| 0,1| > > Schonnemann| Complications| EF| 8| 30| 0,2666667| > > Aita| Complications| EF| 1| 16| 0,0625| > > Hove| Complications| EF| 31| 39| 0,7948718| > > Andersen| Complications| EF| 26| 75| 0,3466667| > > Krughaug| Complications| EF| 22| 75| 0,2933333| > > Moroni| Complications| EF| 0| 20| 0| > > Plate| Complications| IMN| 3| 30| 0,1| > > Chappuis| Complications| IMN| 4| 16| 0,25| > > Gradl| Complications| IMN| 12| 66| 0,1818182| > > Schonnemann| Complications| IMN| 6| 31| 0,1935484| > > Aita| Complications| IMN| 1| 16| 0,0625| > > Dremstrop| Complications| IMN| 17| 44| 0,3863636| > > Wong| Complications| PC| 1| 30| 0,0333333| > > Kumaravel| Complications| PC| 4| 25| 0,16| > > > Dataset on my dropbox: > https://urlsand.esvalabs.com/?u=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fj1urqzr99bt76ip%2FBasics%2520excel%2520file%2520complication%2520and%2520reoperation%2520rate.xlsx%3Fdl%3D0&e=541e9c83&h=065e9ef9&f=y > > Basics excel file complication and reoperation > rate.xlsx<https://urlsand.esvalabs.com/?u=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fj1urqzr99bt76ip%2FBasics%2520excel%2520file%2520complication%2520and%2520reoperation%2520rate.xlsx%3Fdl%3D0&e=541e9c83&h=065e9ef9&f=y> > https://urlsand.esvalabs.com/?u=http%3A%2F%2Fwww.dropbox.com&e=541e9c83&h=4bc36151&f=y > Shared with Dropbox > > > > > library(meta) > library(stargazer) > library(foreign) > > All <-read.spss("C:\\Users\\313635aa.STUDENT\\Desktop\\Meta-Analyse > Complications and Reoperations.sav",to.data.frame = T, > use.value.labels = T) > All <- na.omit(All) > > Complications <- All[which(All[,"Event_Type"] == "Complications"),] > Re_operation <- All[which(All[,"Event_Type"] == "Reoperations"),] > > EF <- All[which(All[,"Treatment"] == "EF"),] > IMN <- All[which(All[,"Treatment"] == "IMN"),] > pc <- All[which(All[,"Treatment"] == "PC"),] > KW <- All[which(All[,"Treatment"] == "KW"),] > VPO <- All[which(All[,"Treatment"] == "VPO"),] > > EF_C <- EF[which(EF[,"Event_Type"] == "Complications"),] > EF_R <- EF[which(EF[,"Event_Type"] == "Reoperations"),] > > IMN_C <- IMN[which(IMN[,"Event_Type"] == "Complications"),] > IMN_R <- IMN[which(IMN[,"Event_Type"] == "Reoperations"),] > > pc_C <- pc[which(pc[,"Event_Type"] == "Complications"),] > pc_R <- pc[which(pc[,"Event_Type"] == "Reoperations"),] > > KW_C <- KW[which(KW[,"Event_Type"] == "Complications"),] > KW_R <- KW[which(KW[,"Event_Type"] == "Reoperations"),] > > VPO_C <- VPO[which(VPO[,"Event_Type"] == "Complications"),] > VPO_R <- VPO[which(VPO[,"Event_Type"] == "Reoperations"),] > > Output <- function(x, y, k.min=10){ > file <- metaprop(Events_n, N, Study_ID, data = x) > > forest.meta(file, studlab = T, pooled.totals = T, bysort = F) > > dev.copy2pdf(file=y, width = 11.69, height = 8.27) > print(file) > } > > R code on my dropbox: > https://urlsand.esvalabs.com/?u=https%3A%2F%2Fwww.dropbox.com%2Fs%2F67pnfpi10qu110v%2FR%2520code%2520voor%2520forrest%2520en%2520funnel%2520plots.rtf%3Fdl%3D0&e=541e9c83&h=1df77562&f=y > > [https://urlsand.esvalabs.com/?u=https%3A%2F%2Fcfl.dropboxstatic.com%2Fstatic%2Fimages%2Ficons128%2Fpage_white_word.png&e=541e9c83&h=b0ed7c54&f=y]<https://urlsand.esvalabs.com/?u=https%3A%2F%2Fwww.dropbox.com%2Fs%2F67pnfpi10qu110v%2FR%2520code%2520voor%2520forrest%2520en%2520funnel%2520plots.rtf%3Fdl%3D0&e=541e9c83&h=1df77562&f=y> > > R code voor forrest en funnel > plots.rtf<https://urlsand.esvalabs.com/?u=https%3A%2F%2Fwww.dropbox.com%2Fs%2F67pnfpi10qu110v%2FR%2520code%2520voor%2520forrest%2520en%2520funnel%2520plots.rtf%3Fdl%3D0&e=541e9c83&h=1df77562&f=y> > https://urlsand.esvalabs.com/?u=http%3A%2F%2Fwww.dropbox.com&e=541e9c83&h=4bc36151&f=y > Shared with Dropbox > > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://urlsand.esvalabs.com/?u=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help&e=541e9c83&h=16efca0d&f=y > PLEASE do read the posting guide > https://urlsand.esvalabs.com/?u=http%3A%2F%2Fwww.R-project.org%2Fposting-guide.html&e=541e9c83&h=0c678195&f=y > and provide commented, minimal, self-contained, reproducible code.
Jay Zola
2017-Jun-26 21:43 UTC
[R] Model studies in one analysis using treatment as a five level moderator in a meta-regression
Dear Vito, Thank you for your reply. I tried to contact the statistics departement numerous times, but did not receive any reply. That is why I started to look on the internet for help. Yours sincerely, Jay Verstuurd vanaf mijn iPhone> Op 26 jun. 2017 om 22:05 heeft Vito Michele Rosario Muggeo <vito.muggeo at unipa.it> het volgende geschreven: > > hi Jay, > Consult a local statistician. Statistics is not you think is (namely simple computations, R and probably plotting..). > > regards, > vito > > > > Jay Zola <jayjay.1988 at hotmail.nl> ha scritto: > >> Hello, >> >> >> I am medical student, writing a meta-analysis on complication and reoperation rates after the five most common treatments of distal radius fractures. I have been busy with the statistics for months by my self, but find it quite hard since our classes were very basic. Now I want to compare the treatment modalities to see if there are significant differences. Using R I was able to synthesize the complication rates and reoperation rates for each treatment method. But I never had any R course and managed by trial and error, so the code probably doesn't look that great. Someone told me I could best model the data in one analysis using treatment as a five level moderator in a meta-regression. Can some help me with the R code to do this? Your help would be very much appreciated. >> >> >> Thank you, >> >> >> Jay >> >> >> Study| Event Type| Treatment| Number of Events (n)| N| n/N| >> >> Kumaravel| Complications| EF| 3| 23| 0,1304348| >> >> Franck| Complications| EF| 2| 20| 0,1| >> >> Schonnemann| Complications| EF| 8| 30| 0,2666667| >> >> Aita| Complications| EF| 1| 16| 0,0625| >> >> Hove| Complications| EF| 31| 39| 0,7948718| >> >> Andersen| Complications| EF| 26| 75| 0,3466667| >> >> Krughaug| Complications| EF| 22| 75| 0,2933333| >> >> Moroni| Complications| EF| 0| 20| 0| >> >> Plate| Complications| IMN| 3| 30| 0,1| >> >> Chappuis| Complications| IMN| 4| 16| 0,25| >> >> Gradl| Complications| IMN| 12| 66| 0,1818182| >> >> Schonnemann| Complications| IMN| 6| 31| 0,1935484| >> >> Aita| Complications| IMN| 1| 16| 0,0625| >> >> Dremstrop| Complications| IMN| 17| 44| 0,3863636| >> >> Wong| Complications| PC| 1| 30| 0,0333333| >> >> Kumaravel| Complications| PC| 4| 25| 0,16| >> >> >> Dataset on my dropbox: https://urlsand.esvalabs.com/?u=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fj1urqzr99bt76ip%2FBasics%2520excel%2520file%2520complication%2520and%2520reoperation%2520rate.xlsx%3Fdl%3D0&e=541e9c83&h=065e9ef9&f=y >> >> Basics excel file complication and reoperation rate.xlsx<https://urlsand.esvalabs.com/?u=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fj1urqzr99bt76ip%2FBasics%2520excel%2520file%2520complication%2520and%2520reoperation%2520rate.xlsx%3Fdl%3D0&e=541e9c83&h=065e9ef9&f=y> >> https://urlsand.esvalabs.com/?u=http%3A%2F%2Fwww.dropbox.com&e=541e9c83&h=4bc36151&f=y >> Shared with Dropbox >> >> >> >> >> library(meta) >> library(stargazer) >> library(foreign) >> >> All <-read.spss("C:\\Users\\313635aa.STUDENT\\Desktop\\Meta-Analyse Complications and Reoperations.sav",to.data.frame = T, use.value.labels = T) >> All <- na.omit(All) >> >> Complications <- All[which(All[,"Event_Type"] == "Complications"),] >> Re_operation <- All[which(All[,"Event_Type"] == "Reoperations"),] >> >> EF <- All[which(All[,"Treatment"] == "EF"),] >> IMN <- All[which(All[,"Treatment"] == "IMN"),] >> pc <- All[which(All[,"Treatment"] == "PC"),] >> KW <- All[which(All[,"Treatment"] == "KW"),] >> VPO <- All[which(All[,"Treatment"] == "VPO"),] >> >> EF_C <- EF[which(EF[,"Event_Type"] == "Complications"),] >> EF_R <- EF[which(EF[,"Event_Type"] == "Reoperations"),] >> >> IMN_C <- IMN[which(IMN[,"Event_Type"] == "Complications"),] >> IMN_R <- IMN[which(IMN[,"Event_Type"] == "Reoperations"),] >> >> pc_C <- pc[which(pc[,"Event_Type"] == "Complications"),] >> pc_R <- pc[which(pc[,"Event_Type"] == "Reoperations"),] >> >> KW_C <- KW[which(KW[,"Event_Type"] == "Complications"),] >> KW_R <- KW[which(KW[,"Event_Type"] == "Reoperations"),] >> >> VPO_C <- VPO[which(VPO[,"Event_Type"] == "Complications"),] >> VPO_R <- VPO[which(VPO[,"Event_Type"] == "Reoperations"),] >> >> Output <- function(x, y, k.min=10){ >> file <- metaprop(Events_n, N, Study_ID, data = x) >> >> forest.meta(file, studlab = T, pooled.totals = T, bysort = F) >> >> dev.copy2pdf(file=y, width = 11.69, height = 8.27) >> print(file) >> } >> >> R code on my dropbox: https://urlsand.esvalabs.com/?u=https%3A%2F%2Fwww.dropbox.com%2Fs%2F67pnfpi10qu110v%2FR%2520code%2520voor%2520forrest%2520en%2520funnel%2520plots.rtf%3Fdl%3D0&e=541e9c83&h=1df77562&f=y >> >> [https://urlsand.esvalabs.com/?u=https%3A%2F%2Fcfl.dropboxstatic.com%2Fstatic%2Fimages%2Ficons128%2Fpage_white_word.png&e=541e9c83&h=b0ed7c54&f=y]<https://urlsand.esvalabs.com/?u=https%3A%2F%2Fwww.dropbox.com%2Fs%2F67pnfpi10qu110v%2FR%2520code%2520voor%2520forrest%2520en%2520funnel%2520plots.rtf%3Fdl%3D0&e=541e9c83&h=1df77562&f=y> >> >> R code voor forrest en funnel plots.rtf<https://urlsand.esvalabs.com/?u=https%3A%2F%2Fwww.dropbox.com%2Fs%2F67pnfpi10qu110v%2FR%2520code%2520voor%2520forrest%2520en%2520funnel%2520plots.rtf%3Fdl%3D0&e=541e9c83&h=1df77562&f=y> >> https://urlsand.esvalabs.com/?u=http%3A%2F%2Fwww.dropbox.com&e=541e9c83&h=4bc36151&f=y >> Shared with Dropbox >> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://urlsand.esvalabs.com/?u=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help&e=541e9c83&h=16efca0d&f=y >> PLEASE do read the posting guide https://urlsand.esvalabs.com/?u=http%3A%2F%2Fwww.R-project.org%2Fposting-guide.html&e=541e9c83&h=0c678195&f=y >> and provide commented, minimal, self-contained, reproducible code. > > >
Michael Dewey
2017-Jun-28 15:05 UTC
[R] Model studies in one analysis using treatment as a five level moderator in a meta-regression
Dear Jay I am not that familiar with the meta package but it looks as though it does not allow you to do a meta-regression within metaprop. However there is a function metareg which takes the object you created with metaprop and allows you to add a moderator so i would try that next. By moderator in this case I mean your variable Treatment. On 26/06/2017 19:19, Jay Zola wrote:> Hello, > > > I am medical student, writing a meta-analysis on complication and reoperation rates after the five most common treatments of distal radius fractures. I have been busy with the statistics for months by my self, but find it quite hard since our classes were very basic. Now I want to compare the treatment modalities to see if there are significant differences. Using R I was able to synthesize the complication rates and reoperation rates for each treatment method. But I never had any R course and managed by trial and error, so the code probably doesn't look that great. Someone told me I could best model the data in one analysis using treatment as a five level moderator in a meta-regression. Can some help me with the R code to do this? Your help would be very much appreciated. > > > Thank you, > > > Jay > > > Study| Event Type| Treatment| Number of Events (n)| N| n/N| > > Kumaravel| Complications| EF| 3| 23| 0,1304348| > > Franck| Complications| EF| 2| 20| 0,1| > > Schonnemann| Complications| EF| 8| 30| 0,2666667| > > Aita| Complications| EF| 1| 16| 0,0625| > > Hove| Complications| EF| 31| 39| 0,7948718| > > Andersen| Complications| EF| 26| 75| 0,3466667| > > Krughaug| Complications| EF| 22| 75| 0,2933333| > > Moroni| Complications| EF| 0| 20| 0| > > Plate| Complications| IMN| 3| 30| 0,1| > > Chappuis| Complications| IMN| 4| 16| 0,25| > > Gradl| Complications| IMN| 12| 66| 0,1818182| > > Schonnemann| Complications| IMN| 6| 31| 0,1935484| > > Aita| Complications| IMN| 1| 16| 0,0625| > > Dremstrop| Complications| IMN| 17| 44| 0,3863636| > > Wong| Complications| PC| 1| 30| 0,0333333| > > Kumaravel| Complications| PC| 4| 25| 0,16| > > > Dataset on my dropbox: https://www.dropbox.com/s/j1urqzr99bt76ip/Basics%20excel%20file%20complication%20and%20reoperation%20rate.xlsx?dl=0 > > Basics excel file complication and reoperation rate.xlsx<https://www.dropbox.com/s/j1urqzr99bt76ip/Basics%20excel%20file%20complication%20and%20reoperation%20rate.xlsx?dl=0> > www.dropbox.com > Shared with Dropbox > > > > > library(meta) > library(stargazer) > library(foreign) > > All <-read.spss("C:\\Users\\313635aa.STUDENT\\Desktop\\Meta-Analyse Complications and Reoperations.sav",to.data.frame = T, use.value.labels = T) > All <- na.omit(All) > > Complications <- All[which(All[,"Event_Type"] == "Complications"),] > Re_operation <- All[which(All[,"Event_Type"] == "Reoperations"),] > > EF <- All[which(All[,"Treatment"] == "EF"),] > IMN <- All[which(All[,"Treatment"] == "IMN"),] > pc <- All[which(All[,"Treatment"] == "PC"),] > KW <- All[which(All[,"Treatment"] == "KW"),] > VPO <- All[which(All[,"Treatment"] == "VPO"),] > > EF_C <- EF[which(EF[,"Event_Type"] == "Complications"),] > EF_R <- EF[which(EF[,"Event_Type"] == "Reoperations"),] > > IMN_C <- IMN[which(IMN[,"Event_Type"] == "Complications"),] > IMN_R <- IMN[which(IMN[,"Event_Type"] == "Reoperations"),] > > pc_C <- pc[which(pc[,"Event_Type"] == "Complications"),] > pc_R <- pc[which(pc[,"Event_Type"] == "Reoperations"),] > > KW_C <- KW[which(KW[,"Event_Type"] == "Complications"),] > KW_R <- KW[which(KW[,"Event_Type"] == "Reoperations"),] > > VPO_C <- VPO[which(VPO[,"Event_Type"] == "Complications"),] > VPO_R <- VPO[which(VPO[,"Event_Type"] == "Reoperations"),] > > Output <- function(x, y, k.min=10){ > file <- metaprop(Events_n, N, Study_ID, data = x) > > forest.meta(file, studlab = T, pooled.totals = T, bysort = F) > > dev.copy2pdf(file=y, width = 11.69, height = 8.27) > print(file) > } > > R code on my dropbox: https://www.dropbox.com/s/67pnfpi10qu110v/R%20code%20voor%20forrest%20en%20funnel%20plots.rtf?dl=0 > > [https://cfl.dropboxstatic.com/static/images/icons128/page_white_word.png]<https://www.dropbox.com/s/67pnfpi10qu110v/R%20code%20voor%20forrest%20en%20funnel%20plots.rtf?dl=0> > > R code voor forrest en funnel plots.rtf<https://www.dropbox.com/s/67pnfpi10qu110v/R%20code%20voor%20forrest%20en%20funnel%20plots.rtf?dl=0> > www.dropbox.com > Shared with Dropbox > > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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. > > --- > This email has been checked for viruses by AVG. > http://www.avg.com > >-- Michael http://www.dewey.myzen.co.uk/home.html
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