K Amoatwi
2020-Jun-23 14:37 UTC
[R] Error message in meta-analysis package Metafor-weights =""
Dear Wolfgang, I have posted the requested information you asked for.> sessionInfo()R version 4.0.1 (2020-06-06) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] meta_4.12-0 reshape2_1.4.4 metafor_2.4-0 Matrix_1.2-18 loaded via a namespace (and not attached): [1] Rcpp_1.0.4.6 lattice_0.20-41 MASS_7.3-51.6 grid_4.0.1 [5] plyr_1.8.6 nlme_3.1-148 magrittr_1.5 stringi_1.4.6 [9] minqa_1.2.4 nloptr_1.2.2.1 boot_1.3-25 splines_4.0.1 [13] statmod_1.4.34 lme4_1.1-23 tools_4.0.1 stringr_1.4.0 [17] CompQuadForm_1.4.3 compiler_4.0.1>> class(result.md)[1] "rma.uni" "rma">Thank you Kobby On Tue, Jun 23, 2020 at 3:24 AM Viechtbauer, Wolfgang (SP) < wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:> Dear Kobby, > > Please post the output of sessionInfo() and class(result.md). > > Best, > Wolfgang > > >-----Original Message----- > >From: K Amoatwi [mailto:amoatwik20 at gmail.com] > >Sent: Monday, 22 June, 2020 22:30 > >To: Viechtbauer, Wolfgang (SP) > >Cc: r-help at r-project.org > >Subject: Re: [R] Error message in meta-analysis package Metafor-weights > ="" > > > >Hi Wolfgang and All, > >I am still practising my meta-analysis with the "Metafor" package, I tried > >to run the code for "Forest plot" and got error message as shown below: > >forest(result.md) > >> forest(result.md) > >Error in UseMethod("forest") : > > no applicable method for 'forest' applied to an object of class > >"c('rma.uni', 'rma')" > > > >Thank you in advance for your support > > > >regards > >Kobby > > > >On Tue, Jun 16, 2020 at 12:50 PM Viechtbauer, Wolfgang (SP) > ><wolfgang.viechtbauer at maastrichtuniversity.nl> wrote: > >Dear Amoatwi, > > > >This way of using the escalc() function has been deprecated. It might be > >added back once there is actually any benefit from having this > >functionality, but for years it just meant that I had to maintain two > >different ways of doing the exact same thing without any additional > >benefits. > > > >Best, > >Wolfgang > > > >-- > >Wolfgang Viechtbauer, Ph.D., Statistician | Department of Psychiatry and > >Neuropsychology | Maastricht University | P.O. Box 616 (VIJV1) | 6200 MD > >Maastricht, The Netherlands | +31 (43) 388-4170 | http://www.wvbauer.com > > > >>-----Original Message----- > >>From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of K > Amoatwi > >>Sent: Tuesday, 16 June, 2020 4:50 > >>To: r-help at r-project.org > >>Subject: [R] Error message in meta-analysis package Metafor-weights ="" > >> > >>Dear All, > >>I am using the example from one of the tutorial about "Metafor" package > and > >>"escalc" function, to learn how this package can be applied to do > >>meta-analysi; the code and the data is directly from the tutorials but > >>"weights=freq" option in the escalc function is given me error message > >>This is the code below: > >> > >>library(metafor) # Load package > >>#####DATASET 1: BCG Vaccine Trials > >>data(dat.bcg) # BCG meta-analytic dataset > >> > >>##Formula based Specification > >>##That is, what if I have multiple rows per study, corresponding to > >>difference treatment groups? > >> > >>library(reshape2) # Load package for data reshaping > >> > >>bcg.long <- melt(dat.bcg[, c("trial", "tpos", "tneg", "cpos", "cneg")], > id > >>= "trial") > >>bcg.long$pos <- ifelse(bcg.long$var == "tpos" | bcg.long$var == "cpos", > 1, > >>0) > >>bcg.long$group <- ifelse(bcg.long$var == "tpos" | bcg.long$var == "tneg", > >>1, 0) > >> > >>##sample of the data, the first 6 rows > >>head(bcg.long) > >> trial variable value pos group > >>1 1 tpos 4 1 1 > >>2 2 tpos 6 1 1 > >>3 3 tpos 3 1 1 > >>4 4 tpos 62 1 1 > >>5 5 tpos 33 1 1 > >>6 6 tpos 180 1 1 > >> > >>##Now applying the " escalc " function > >> > >>escalc(factor(pos)~factor(group)| factor(trial),weights = value,data > >>bcg.long, measure = "OR") > >> > >>##Then I got this error message > >>Error in escalc(factor(pos) ~ factor(group) | factor(trial), weights > >>value, : > >> object 'value' not found > >> > >>I used the same data with different example from another author and got a > >>similar error message > >>Second code with the same data but different coding > >>Sample data > >> > >>with the first 6 rows of the rearranged data shown below. (T=treatment, > >>C=Control group, Out=outcome whether positive or negative, and then > >>frequency) > >> study grp out freq > >>1 1 T + 4 > >>2 1 T - 119 > >>3 1 C + 11 > >>4 1 C - 128 > >>5 2 T + 6 > >>6 2 T - 300 > >> > >>>escalc(out ~ grp | study, weights = freq, data = dat.fm, measure > "OR") > >> > >>Error in escalc(out ~ grp | study, weights = freq, data = dat.fm, > measure > >>"OR") : > >> object 'freq' not found > >> > >>I am not sure what I am doing wrong since both authors were able to get > >>their results while I am getting error messages. > >> > >>Any help will be very much appreciated > >> > >>Amoatwi >[[alternative HTML version deleted]]
Viechtbauer, Wolfgang (SP)
2020-Jun-23 15:17 UTC
[R] Error message in meta-analysis package Metafor-weights =""
You have loaded the 'meta' package after 'metafor' and then forest() will try to use the corresponding function from the meta package and not metafor. With: metafor::forest(result.md) it should work. Best, Wolfgang>-----Original Message----- >From: K Amoatwi [mailto:amoatwik20 at gmail.com] >Sent: Tuesday, 23 June, 2020 16:37 >To: Viechtbauer, Wolfgang (SP) >Cc: r-help at r-project.org >Subject: Re: [R] Error message in meta-analysis package Metafor-weights ="" > >Dear Wolfgang, >I have posted the requested information you asked?for. > >> ?sessionInfo() >R version 4.0.1 (2020-06-06) >Platform: x86_64-w64-mingw32/x64 (64-bit) >Running under: Windows 10 x64 (build 18362) > >Matrix products: default > >locale: >[1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United >States.1252 >[3] LC_MONETARY=English_United States.1252 >LC_NUMERIC=C >[5] LC_TIME=English_United States.1252 > >attached base packages: >[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > >other attached packages: >[1] meta_4.12-0 ? ?reshape2_1.4.4 metafor_2.4-0 ?Matrix_1.2-18 > >loaded via a namespace (and not attached): >?[1] Rcpp_1.0.4.6 ? ? ? lattice_0.20-41 ? ?MASS_7.3- >51.6 ? ? ?grid_4.0.1 >?[5] plyr_1.8.6 ? ? ? ? nlme_3.1- >148 ? ? ? magrittr_1.5 ? ? ? stringi_1.4.6 >?[9] minqa_1.2.4 ? ? ? ?nloptr_1.2.2.1 ? ? boot_1.3- >25 ? ? ? ?splines_4.0.1 >[13] statmod_1.4.34 ? ? lme4_1.1- >23 ? ? ? ?tools_4.0.1 ? ? ? ?stringr_1.4.0 >[17] CompQuadForm_1.4.3 compiler_4.0.1 >> > >> class(result.md) >[1] "rma.uni" "rma" >> > >Thank you >Kobby > >On Tue, Jun 23, 2020 at 3:24 AM Viechtbauer, Wolfgang (SP) ><wolfgang.viechtbauer at maastrichtuniversity.nl> wrote: >Dear Kobby, > >Please post the output of sessionInfo() and class(result.md). > >Best, >Wolfgang > >>-----Original Message----- >>From: K Amoatwi [mailto:amoatwik20 at gmail.com] >>Sent: Monday, 22 June, 2020 22:30 >>To: Viechtbauer, Wolfgang (SP) >>Cc: r-help at r-project.org >>Subject: Re: [R] Error message in meta-analysis package Metafor-weights ="" >> >>Hi?Wolfgang and All, >>I am still practising my meta-analysis with the "Metafor" package, I tried >>to run the code for "Forest plot" and got error message as shown below: >>forest(result.md) >>> forest(result.md) >>Error in UseMethod("forest") : >>? no applicable method for 'forest' applied to an object of class >>"c('rma.uni', 'rma')" >> >>Thank you in advance for your support >> >>regards >>Kobby >> >>On Tue, Jun 16, 2020 at 12:50 PM Viechtbauer, Wolfgang (SP) >><wolfgang.viechtbauer at maastrichtuniversity.nl> wrote: >>Dear Amoatwi, >> >>This way of using the escalc() function has been deprecated. It might be >>added back once there is actually any benefit from having this >>functionality, but for years it just meant that I had to maintain two >>different ways of doing the exact same thing without any additional >>benefits. >> >>Best, >>Wolfgang >> >>-- >>Wolfgang Viechtbauer, Ph.D., Statistician | Department of Psychiatry and >>Neuropsychology | Maastricht University | P.O. Box 616 (VIJV1) | 6200 MD >>Maastricht, The Netherlands | +31 (43) 388-4170 | http://www.wvbauer.com >> >>>-----Original Message----- >>>From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of K Amoatwi >>>Sent: Tuesday, 16 June, 2020 4:50 >>>To: r-help at r-project.org >>>Subject: [R] Error message in meta-analysis package Metafor-weights ="" >>> >>>Dear All, >>>I am using the example from one of the tutorial about "Metafor" package >and >>>"escalc" function, to learn how this package can be applied to do >>>meta-analysi; the code and the data is directly from the tutorials but >>>"weights=freq" option in the escalc function is given me error message >>>This is the code below: >>> >>>library(metafor) # Load package >>>#####DATASET 1: BCG Vaccine Trials >>>data(dat.bcg) # BCG meta-analytic dataset >>> >>>##Formula based Specification >>>##That is, what if I have multiple rows per study, corresponding to >>>difference treatment groups? >>> >>>library(reshape2) # Load package for data reshaping >>> >>>bcg.long <- melt(dat.bcg[, c("trial", "tpos", "tneg", "cpos", "cneg")], id >>>= "trial") >>>bcg.long$pos <- ifelse(bcg.long$var == "tpos" | bcg.long$var == "cpos", 1, >>>0) >>>bcg.long$group <- ifelse(bcg.long$var == "tpos" | bcg.long$var == "tneg", >>>1, 0) >>> >>>##sample of the data, the first 6 rows >>>head(bcg.long) >>>? trial variable value pos group >>>1? ? ?1? ? ?tpos? ? ?4? ? ?1? ? ?1 >>>2? ? ?2? ? ?tpos? ? ?6? ? ?1? ? ?1 >>>3? ? ?3? ? ?tpos? ? ?3? ? ?1? ? ?1 >>>4? ? ?4? ? ?tpos? ? 62? ? 1? ? ?1 >>>5? ? ?5? ? ?tpos? ? 33? ? 1? ? ?1 >>>6? ? ?6? ? ?tpos? ?180? ?1? ? ?1 >>> >>>##Now applying the " escalc " function >>> >>>escalc(factor(pos)~factor(group)| factor(trial),weights = value,data >>>bcg.long, measure = "OR") >>> >>>##Then I got this error message >>>Error in escalc(factor(pos) ~ factor(group) | factor(trial), weights >>>value,? : >>>? object 'value' not found >>> >>>I used the same data with different example from another author and got a >>>similar error message >>>Second code with the same data but different coding >>>Sample data >>> >>>with the first 6 rows of the rearranged data shown below. (T=treatment, >>>C=Control group, Out=outcome whether positive or negative, and then >>>frequency) >>>? ? study grp out freq >>>1? ? ? ? 1? ? T? ? +? ? ? 4 >>>2? ? ? ? 1? ? T? ? -? ? 119 >>>3? ? ? ? 1? ? C? ?+? ? ? 11 >>>4? ? ? ? 1? ? C? ?-? ? ?128 >>>5? ? ? ? 2? ? T? ?+? ? ? ? 6 >>>6? ? ? ? 2? ? T? ?-? ? ? 300 >>> >>>>escalc(out ~ grp | study, weights = freq, data = dat.fm, measure = "OR") >>> >>>Error in escalc(out ~ grp | study, weights = freq, data = dat.fm, measure >>>>"OR") : >>>? object 'freq' not found >>> >>>I am not sure what I am doing wrong since both authors were able to get >>>their results while I am getting error messages. >>> >>>Any help will be very much appreciated >>> >>>Amoatwi
K Amoatwi
2020-Jun-23 15:29 UTC
[R] Error message in meta-analysis package Metafor-weights =""
Dear Wolfgang, Yes! The "metafor::forest(result.md)" works Thank you very much. Any reason why "forest(result.md)" was not working? Kobby On Tue, Jun 23, 2020 at 11:18 AM Viechtbauer, Wolfgang (SP) < wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:> You have loaded the 'meta' package after 'metafor' and then forest() will > try to use the corresponding function from the meta package and not > metafor. With: > > metafor::forest(result.md) > > it should work. > > Best, > Wolfgang > > >-----Original Message----- > >From: K Amoatwi [mailto:amoatwik20 at gmail.com] > >Sent: Tuesday, 23 June, 2020 16:37 > >To: Viechtbauer, Wolfgang (SP) > >Cc: r-help at r-project.org > >Subject: Re: [R] Error message in meta-analysis package Metafor-weights > ="" > > > >Dear Wolfgang, > >I have posted the requested information you asked for. > > > >> sessionInfo() > >R version 4.0.1 (2020-06-06) > >Platform: x86_64-w64-mingw32/x64 (64-bit) > >Running under: Windows 10 x64 (build 18362) > > > >Matrix products: default > > > >locale: > >[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > >States.1252 > >[3] LC_MONETARY=English_United States.1252 > >LC_NUMERIC=C > >[5] LC_TIME=English_United States.1252 > > > >attached base packages: > >[1] stats graphics grDevices utils datasets methods base > > > >other attached packages: > >[1] meta_4.12-0 reshape2_1.4.4 metafor_2.4-0 Matrix_1.2-18 > > > >loaded via a namespace (and not attached): > > [1] Rcpp_1.0.4.6 lattice_0.20-41 MASS_7.3- > >51.6 grid_4.0.1 > > [5] plyr_1.8.6 nlme_3.1- > >148 magrittr_1.5 stringi_1.4.6 > > [9] minqa_1.2.4 nloptr_1.2.2.1 boot_1.3- > >25 splines_4.0.1 > >[13] statmod_1.4.34 lme4_1.1- > >23 tools_4.0.1 stringr_1.4.0 > >[17] CompQuadForm_1.4.3 compiler_4.0.1 > >> > > > >> class(result.md) > >[1] "rma.uni" "rma" > >> > > > >Thank you > >Kobby > > > >On Tue, Jun 23, 2020 at 3:24 AM Viechtbauer, Wolfgang (SP) > ><wolfgang.viechtbauer at maastrichtuniversity.nl> wrote: > >Dear Kobby, > > > >Please post the output of sessionInfo() and class(result.md). > > > >Best, > >Wolfgang > > > >>-----Original Message----- > >>From: K Amoatwi [mailto:amoatwik20 at gmail.com] > >>Sent: Monday, 22 June, 2020 22:30 > >>To: Viechtbauer, Wolfgang (SP) > >>Cc: r-help at r-project.org > >>Subject: Re: [R] Error message in meta-analysis package Metafor-weights > ="" > >> > >>Hi Wolfgang and All, > >>I am still practising my meta-analysis with the "Metafor" package, I > tried > >>to run the code for "Forest plot" and got error message as shown below: > >>forest(result.md) > >>> forest(result.md) > >>Error in UseMethod("forest") : > >> no applicable method for 'forest' applied to an object of class > >>"c('rma.uni', 'rma')" > >> > >>Thank you in advance for your support > >> > >>regards > >>Kobby > >> > >>On Tue, Jun 16, 2020 at 12:50 PM Viechtbauer, Wolfgang (SP) > >><wolfgang.viechtbauer at maastrichtuniversity.nl> wrote: > >>Dear Amoatwi, > >> > >>This way of using the escalc() function has been deprecated. It might be > >>added back once there is actually any benefit from having this > >>functionality, but for years it just meant that I had to maintain two > >>different ways of doing the exact same thing without any additional > >>benefits. > >> > >>Best, > >>Wolfgang > >> > >>-- > >>Wolfgang Viechtbauer, Ph.D., Statistician | Department of Psychiatry and > >>Neuropsychology | Maastricht University | P.O. Box 616 (VIJV1) | 6200 MD > >>Maastricht, The Netherlands | +31 (43) 388-4170 | http://www.wvbauer.com > >> > >>>-----Original Message----- > >>>From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of K > Amoatwi > >>>Sent: Tuesday, 16 June, 2020 4:50 > >>>To: r-help at r-project.org > >>>Subject: [R] Error message in meta-analysis package Metafor-weights ="" > >>> > >>>Dear All, > >>>I am using the example from one of the tutorial about "Metafor" package > >and > >>>"escalc" function, to learn how this package can be applied to do > >>>meta-analysi; the code and the data is directly from the tutorials but > >>>"weights=freq" option in the escalc function is given me error message > >>>This is the code below: > >>> > >>>library(metafor) # Load package > >>>#####DATASET 1: BCG Vaccine Trials > >>>data(dat.bcg) # BCG meta-analytic dataset > >>> > >>>##Formula based Specification > >>>##That is, what if I have multiple rows per study, corresponding to > >>>difference treatment groups? > >>> > >>>library(reshape2) # Load package for data reshaping > >>> > >>>bcg.long <- melt(dat.bcg[, c("trial", "tpos", "tneg", "cpos", "cneg")], > id > >>>= "trial") > >>>bcg.long$pos <- ifelse(bcg.long$var == "tpos" | bcg.long$var == "cpos", > 1, > >>>0) > >>>bcg.long$group <- ifelse(bcg.long$var == "tpos" | bcg.long$var => "tneg", > >>>1, 0) > >>> > >>>##sample of the data, the first 6 rows > >>>head(bcg.long) > >>> trial variable value pos group > >>>1 1 tpos 4 1 1 > >>>2 2 tpos 6 1 1 > >>>3 3 tpos 3 1 1 > >>>4 4 tpos 62 1 1 > >>>5 5 tpos 33 1 1 > >>>6 6 tpos 180 1 1 > >>> > >>>##Now applying the " escalc " function > >>> > >>>escalc(factor(pos)~factor(group)| factor(trial),weights = value,data > >>>bcg.long, measure = "OR") > >>> > >>>##Then I got this error message > >>>Error in escalc(factor(pos) ~ factor(group) | factor(trial), weights > >>>value, : > >>> object 'value' not found > >>> > >>>I used the same data with different example from another author and got > a > >>>similar error message > >>>Second code with the same data but different coding > >>>Sample data > >>> > >>>with the first 6 rows of the rearranged data shown below. (T=treatment, > >>>C=Control group, Out=outcome whether positive or negative, and then > >>>frequency) > >>> study grp out freq > >>>1 1 T + 4 > >>>2 1 T - 119 > >>>3 1 C + 11 > >>>4 1 C - 128 > >>>5 2 T + 6 > >>>6 2 T - 300 > >>> > >>>>escalc(out ~ grp | study, weights = freq, data = dat.fm, measure > "OR") > >>> > >>>Error in escalc(out ~ grp | study, weights = freq, data = dat.fm, > measure > >> >>>"OR") : > >>> object 'freq' not found > >>> > >>>I am not sure what I am doing wrong since both authors were able to get > >>>their results while I am getting error messages. > >>> > >>>Any help will be very much appreciated > >>> > >>>Amoatwi >[[alternative HTML version deleted]]