## ----echo = FALSE, warning = FALSE, results = 'hide'-------------------------- library(metaumbrella) library(DT) ## ----eval=FALSE--------------------------------------------------------------- # umb <- umbrella(df.SMD) ## ----eval=FALSE--------------------------------------------------------------- # umb <- umbrella(df.SMD) # strat.io <- add.evidence(umb.SMD, criteria = "Ioannidis") ## ----eval=FALSE--------------------------------------------------------------- # umb <- umbrella(df.SMD) # strat.grd <- add.evidence(umb.SMD, criteria = "GRADE") ## ----eval=FALSE--------------------------------------------------------------- # umb <- umbrella(df.SMD) # strat.prso <- add.evidence(umb, criteria = "Personalized", # class_I = c(total_n = 600, I2 = 25, rob = 75), # class_II = c(total_n = 400, I2 = 50, rob = 50), # class_III = c(total_n = 200, I2 = 75, rob = 25), # class_IV = c(total_n = 100)) ## ----eval=FALSE--------------------------------------------------------------- # umb <- umbrella(df.SMD) # strat.io <- add.evidence(umb.SMD, criteria = "Ioannidis") # forest(strat.io) ## ----eval=FALSE--------------------------------------------------------------- # df.OR ## ----echo=FALSE, warning=FALSE------------------------------------------------ DT::datatable(df.OR, options = list( scrollX = TRUE, dom = c('pt'), ordering = FALSE, scrollY = "300px", pageLength = 100, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) ## ----eval=FALSE--------------------------------------------------------------- # umb.OR <- umbrella(df.OR) # summary(umb.OR) ## ----echo=FALSE, warning=FALSE------------------------------------------------ umb.OR <- metaumbrella:::.quiet(umbrella(df.OR)) DT::datatable(summary(umb.OR), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 5, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) ## ----eval=FALSE--------------------------------------------------------------- # strat.io <- add.evidence(umb.OR, criteria = "Ioannidis") # summary(strat.io) ## ----echo=FALSE, message=FALSE------------------------------------------------ strat.io <- metaumbrella:::.quiet(add.evidence(umb.OR, criteria = "Ioannidis")) DT::datatable(summary(strat.io), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 5, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) ## ----eval = FALSE------------------------------------------------------------- # forest(strat.io, # measure = "eOR", # smlab = "umbrella review of risk \nfactors for NDD") ## ----fig.width = 8, fig.height = 7.2, echo=FALSE, warning=FALSE--------------- metaumbrella:::.quiet(forest(strat.io, measure = "eOR", smlab = "umbrella review of risk \nfactors for NDD")) ## ----eval=FALSE--------------------------------------------------------------- # df.RR ## ----echo=FALSE, warning=FALSE------------------------------------------------ DT::datatable(df.RR, options = list( scrollX = TRUE, dom = c('pt'), ordering = FALSE, scrollY = "300px", pageLength = 30, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) ## ----eval=FALSE--------------------------------------------------------------- # umb.RR <- umbrella(df.RR) # summary(umb.RR) ## ----echo=FALSE, message=FALSE, warning=FALSE--------------------------------- umb.RR <- metaumbrella:::.quiet(umbrella(df.RR)) DT::datatable(summary(umb.RR), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 2, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) ## ----eval=FALSE--------------------------------------------------------------- # strat.grade <- add.evidence(umb.RR, criteria = "GRADE") # summary(strat.grade) ## ----echo=FALSE, message=FALSE------------------------------------------------ strat.grade <- metaumbrella:::.quiet(add.evidence(umb.RR, criteria = "GRADE")) DT::datatable(summary(strat.grade), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 5, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) ## ----eval = FALSE------------------------------------------------------------- # forest(strat.grade, # measure = "eOR", # smlab = "umbrella review of adverse events\n of SSRI treatment.") ## ----echo = FALSE, fig.width = 8, fig.height = 7------------------------------ metaumbrella:::.quiet(forest(strat.grade, measure = "eOR", smlab = "umbrella review of adverse events\n of SSRI treatment.")) ## ----eval=FALSE--------------------------------------------------------------- # df.SMD ## ----echo=FALSE, warning=FALSE------------------------------------------------ DT::datatable(df.SMD, options = list( scrollX = TRUE, dom = c('pt'), ordering = FALSE, scrollY = "300px", pageLength = 50, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) ## ----eval=FALSE--------------------------------------------------------------- # umb.SMD <- umbrella(df.SMD) # summary(umb.SMD) ## ----echo=FALSE, message=FALSE------------------------------------------------ umb.SMD <- metaumbrella:::.quiet(umbrella(df.SMD)) DT::datatable(summary(umb.SMD), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 5, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) ## ----eval=FALSE--------------------------------------------------------------- # strat.pers1 <- add.evidence(umb.SMD, criteria = "Personalized", # class_I = c(n_cases = 800), # class_II = c(n_cases = 500), # class_III = c(n_cases = 200), # class_IV = c(n_cases = 100)) ## ----eval=FALSE--------------------------------------------------------------- # strat.pers1 <- add.evidence(umb.SMD, criteria = "Personalized", # class_I = c(n_cases = 800, esb_p = .10), # class_II = c(n_cases = 500, esb_p = .05), # class_III = c(n_cases = 200, esb_p = .01), # class_IV = c(n_cases = 100)) ## ----eval = FALSE------------------------------------------------------------- # strat.pers1 <- add.evidence(umb.SMD, criteria = "Personalized", # class_I = c(n_cases = 800, esb_p = .10, rob = 80), # class_II = c(n_cases = 500, esb_p = .05, rob = 65), # class_III = c(n_cases = 200, esb_p = .01, rob = 50), # class_IV = c(n_cases = 100, rob = 35)) ## ----eval=FALSE--------------------------------------------------------------- # summary(strat.pers1) ## ----echo=FALSE, message=FALSE------------------------------------------------ strat.pers1 <- metaumbrella:::.quiet(add.evidence(umb.SMD, criteria = "Personalized", class_I = c(n_cases = 800, esb_p = .10, rob = 80), class_II = c(n_cases = 500, esb_p = .05, rob = 65), class_III = c(n_cases = 200, esb_p = .01, rob = 50), class_IV = c(n_cases = 100, rob = 35))) DT::datatable(summary(strat.pers1), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 5, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) ## ----eval = FALSE------------------------------------------------------------- # forest(strat.pers1, # measure = "eG", # smlab = "Umbrella review of interventions\n on a numeric outcome.") ## ----echo = FALSE, fig.width = 8, fig.height = 7.2---------------------------- metaumbrella:::.quiet(forest(strat.pers1, measure = "eG", smlab = "Umbrella review of interventions\n on a numeric outcome.")) ## ----eval=FALSE--------------------------------------------------------------- # df.OR.multi ## ----echo=FALSE, warning=FALSE------------------------------------------------ DT::datatable(df.OR.multi, options = list( scrollX = TRUE, dom = c('pt'), ordering=FALSE, scrollY = "300px", pageLength = 40, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) ## ----eval=FALSE--------------------------------------------------------------- # df.OR.multi$r <- NA # we initialize the r column in the dataset # df.OR.multi[df.OR.multi$author == "el-Hariri", ]$r <- .30 # we indicate a mean correlation of .30 for the study of Godebu # # # option 1: we specify - via the r argument of the umbrella function - that all studies with multiple outcomes # # but no r values in the dataset are assigned with a correlation of .60. # umb.OR.multi_1 <- umbrella(df.OR.multi, mult.level = TRUE, r = 0.6) # # # option 2: we manually specify - via the r argument of the dataset - the correlation for other studies # df.OR.multi[df.OR.multi$multiple_es == "outcomes" & # !is.na(df.OR.multi$multiple_es) & # !df.OR.multi$author %in% c("el-Hariri"), ]$r <- .60 # # you no longer have to specify the r value in the umbrella function as it is already specified for all studies in the dataset # umb.OR.multi_2 <- umbrella(df.OR.multi, mult.level = TRUE) # # # as usual, you can obtain results of the calculations using the summary command # summary(umb.OR.multi_2) # # # check: you can check results are equal regardless of the method used # all(summary(umb.OR.multi_1) == summary(umb.OR.multi_2), na.rm = TRUE) # ## ----echo=FALSE, message=FALSE------------------------------------------------ df.OR.multi$r <- NA # we initialize the r column in the dataset df.OR.multi[df.OR.multi$author == "el-Hariri", ]$r <- .30 # we indicate a mean correlation of .30 for the study of el-Hariri # option 1: we specify - via the r argument of the umbrella function - that all studies with multiple outcomes # but no r values in the dataset are assigned with a correlation of .60. umb.OR.multi_1 <- metaumbrella:::.quiet(umbrella(df.OR.multi, mult.level = TRUE, r = 0.6)) # option 2: we manually specify - via the r argument of the dataset - the correlation for other studies df.OR.multi[df.OR.multi$multiple_es == "outcomes" & !is.na(df.OR.multi$multiple_es) & !df.OR.multi$author %in% c("el-Hariri"), ]$r <- .60 # you no longer have to specify the r value in the umbrella function as it is already specified for all studies in the dataset # you no longer have to specify the r value in the umbrella function as it is already specified for all studies in the dataset umb.OR.multi_2 <- metaumbrella:::.quiet(umbrella(df.OR.multi, mult.level = TRUE)) DT::datatable(summary(umb.OR.multi_2), options = list( scrollX = TRUE, dom = c('t'), ordering = FALSE, pageLength = 5, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) paste0("all(summary(umb.OR.multi_1) == summary(umb.OR.multi_2), na.rm = TRUE) returns " , all(summary(umb.OR.multi_1) == summary(umb.OR.multi_2), na.rm = TRUE)) ## ----eval = FALSE------------------------------------------------------------- # strat.pers2 <- add.evidence(umb.OR.multi_1, criteria = "Personalized", # class_I = c(I2 = 20), # class_II = c(I2 = 40), # class_III = c(I2 = 60), # class_IV = c(I2 = 80)) ## ----eval = FALSE------------------------------------------------------------- # strat.pers2 <- add.evidence(umb.OR.multi_1, criteria = "Personalized", # class_I = c(I2 = 20, egger_p = .10), # class_II = c(I2 = 40, egger_p = .10), # class_III = c(I2 = 60, egger_p = .05), # class_IV = c(I2 = 80, egger_p = .05)) ## ----eval = FALSE------------------------------------------------------------- # strat.pers2 <- add.evidence(umb.OR.multi_1, criteria = "Personalized", # class_I = c(I2 = 20, egger_p = .10, largest_CI = "notnull"), # class_II = c(I2 = 40, egger_p = .10, largest_CI = "notnull"), # class_III = c(I2 = 60, egger_p = .05, largest_CI = "notnull"), # class_IV = c(I2 = 80, egger_p = .05)) # ## ----eval = FALSE------------------------------------------------------------- # strat.pers2 <- add.evidence(umb.OR.multi_1, criteria = "Personalized", # class_I = c(I2 = 20, egger_p = .10, largest_CI = "notnull", imprecision = 0.2), # class_II = c(I2 = 40, egger_p = .10, largest_CI = "notnull", imprecision = 0.4), # class_III = c(I2 = 60, egger_p = .05, largest_CI = "notnull", imprecision = 0.6), # class_IV = c(I2 = 80, egger_p = .05, imprecision = 0.8)) ## ----eval=FALSE--------------------------------------------------------------- # summary(strat.pers2) ## ----echo=FALSE, message=FALSE------------------------------------------------ strat.pers2 <- metaumbrella:::.quiet(add.evidence(umb.OR.multi_1, criteria = "Personalized", class_I = c(I2 = 20, egger_p = .10, largest_CI = "notnull", imprecision = 0.2), class_II = c(I2 = 40, egger_p = .10, largest_CI = "notnull", imprecision = 0.4), class_III = c(I2 = 60, egger_p = .05, largest_CI = "notnull", imprecision = 0.6), class_IV = c(I2 = 80, egger_p = .05, imprecision = 0.8))) DT::datatable(summary(strat.pers2), options = list( scrollX = TRUE, scrollY = "600px", dom = c('t'), ordering = FALSE, columnDefs = list( list(width = '110px', targets = "_all"), list(className = 'dt-center', targets = "_all")))) ## ----eval = FALSE------------------------------------------------------------- # forest(strat.pers2, measure = "eOR") ## ----echo = FALSE, fig.width = 8, fig.height = 7.2---------------------------- metaumbrella:::.quiet(forest(strat.pers2))