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Conduct phylogenetic meta-analysis from R calling Phylometa - These are functions needed in the code in file phylometa_inR_run.R.
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| ##################################################################### | |
| # Created by Scott Chamberlain | |
| # Ecology and Evolutionary Biology Dept., Rice University | |
| # Houston, TX 77005, USA | |
| # [email protected] | |
| ##################################################################### | |
| # Function to split confidence intervals, this function is required in the below functions | |
| CI_split <- function(a){ | |
| dd<-c(gsub("\\(","",unlist(strsplit(a[5],","))[1]),gsub("\\)","",unlist(strsplit(a[5],","))[2])) | |
| b22<-a[2:8] | |
| b222<-b22[-4] | |
| b222<-append(b222,dd,after=3) | |
| b222 | |
| } | |
| ### Functions to run meta-analysis in Phylometa | |
| # 1 group in the moderator variable | |
| maketables_1group <- function(output){ #DONE IF/ELSE REFORMATTING | |
| #Table 1, traditional | |
| #a1<-unlist(strsplit(output[6]," +"))[-1] #Table header | |
| a2 <- unlist(strsplit(output[8]," +"))[-1] #Data row 1, between groups, fixed effects | |
| a3 <- unlist(strsplit(output[9]," +"))[-1] #Data row 2, within groups | |
| a4 <- if(length(unlist(strsplit(output[10]," +"))[-1]) == 6) {c(paste(unlist(strsplit(output[10]," +"))[-1][1],unlist(strsplit(output[10]," +"))[-1][2],unlist(strsplit(output[10]," +"))[-1][3]),unlist(strsplit(output[10]," +"))[-1][4:6])} else | |
| if(length(unlist(strsplit(output[10]," +"))[-1]) == 8) {c(paste(unlist(strsplit(output[10]," +"))[-1][1],unlist(strsplit(output[10]," +"))[-1][2],unlist(strsplit(output[10]," +"))[-1][3]),unlist(strsplit(output[10]," +"))[-1][4:8])} else | |
| end | |
| a7 <- unlist(strsplit(output[11]," +"))[-1] #Data row 6, Total | |
| a8 <- unlist(strsplit(output[14]," +"))[-1] #Data row 7, between groups, random effects | |
| rownaames<-c(a2[1],a3[1],a4[1],a7[1],a8[1]) #make vector of first column names | |
| numbers<-t(data.frame(as.numeric(a2[2:4]),as.numeric(a3[2:4]),as.numeric(a4[2:4]),append(as.numeric(a7[2]),c(-9999,-9999),after=1),as.numeric(a8[2:4]))) #make data frame of numbers | |
| numbers<-data.frame(numbers,rownaames) #Make data frame of row names and numbers | |
| colnames(numbers)<-c("Q","df","P","Source") #Assign column names | |
| summaryfitstats_table1_trad<-data.frame(Source=numbers$Source,Q=numbers$Q,df=numbers$df,P=numbers$P) #Reorder columns | |
| #summaryfitstats_table1_trad #See table | |
| #Table 2, traditional | |
| #b1<-unlist(strsplit(output[23]," +"))[-1] #Table header | |
| b2 <- if(length(unlist(strsplit(output[27]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[27]," +"))[-1])[1],(unlist(strsplit(output[27]," +"))[-1])[2]),unlist(strsplit(output[27]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[27]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[27]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[27]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[27]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[27]," +"))[-1][6:7])} else | |
| end | |
| b3 <- if(length(unlist(strsplit(output[28]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[28]," +"))[-1])[1],(unlist(strsplit(output[28]," +"))[-1])[2]),unlist(strsplit(output[28]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[28]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[28]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[28]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[28]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[28]," +"))[-1][6:7])} else | |
| end | |
| b6 <- if(length(unlist(strsplit(output[32]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[32]," +"))[-1])[1],(unlist(strsplit(output[32]," +"))[-1])[2]),unlist(strsplit(output[32]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[32]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[32]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[32]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[32]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[32]," +"))[-1][6:7])} else | |
| end | |
| b7 <- if(length(unlist(strsplit(output[33]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[33]," +"))[-1])[1],(unlist(strsplit(output[33]," +"))[-1])[2]),unlist(strsplit(output[33]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[33]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[33]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[33]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[33]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[33]," +"))[-1][6:7])} else | |
| end | |
| rownaames1<-c(b2[1],b3[1],b6[1],b7[1]) #make vector of first column names | |
| b22<-CI_split(b2) #Split confidence interval numbers apart and reinsert to vector of data | |
| b33<-CI_split(b3) | |
| b66<-CI_split(b6) | |
| b77<-CI_split(b7) | |
| numbers1<-t(data.frame(as.numeric(b22),as.numeric(b33),as.numeric(b66),as.numeric(b77))) #make data frame of numbers | |
| numbers1<-data.frame(numbers1,rownaames1) #Make data frame of row names and numbers | |
| colnames(numbers1)<-c("k","effsize","var","95CI_low","95CI_high","Z","df","P","Group") #Assign column names | |
| summaryeffsizes_table2_trad<-data.frame(Group=numbers1[,9],k=numbers1[,1],effsize=numbers1[,2],var=numbers1[,3],CI_low=numbers1[,4],CI_high=numbers1[,5],Z=numbers1[,6],df=numbers1[,7],P=numbers1[,8]) #Reorder columns | |
| #summaryeffsizes_table2_trad #See table | |
| #Table 1, phylogenetic | |
| #d1 <- unlist(strsplit(output[47]," +"))[-1] #Table header | |
| d2 <- unlist(strsplit(output[49]," +"))[-1] #Data row 1, between groups, fixed effects | |
| d3 <- unlist(strsplit(output[50]," +"))[-1] #Data row 2, within groups | |
| d4 <- if(length(unlist(strsplit(output[51]," +"))[-1]) == 6) {c(paste(unlist(strsplit(output[51]," +"))[-1][1],unlist(strsplit(output[51]," +"))[-1][2],unlist(strsplit(output[51]," +"))[-1][3]),unlist(strsplit(output[51]," +"))[-1][4:6])} else | |
| if(length(unlist(strsplit(output[51]," +"))[-1]) == 8) {c(paste(unlist(strsplit(output[51]," +"))[-1][1],unlist(strsplit(output[51]," +"))[-1][2],unlist(strsplit(output[51]," +"))[-1][3]),unlist(strsplit(output[51]," +"))[-1][4:8])} else | |
| end | |
| d7 <- unlist(strsplit(output[52]," +"))[-1] #Data row 6, Total | |
| d8 <- unlist(strsplit(output[55]," +"))[-1] #Data row 7, between groups, random effects | |
| rownaames2<-c(d2[1],d3[1],d4[1],d7[1],d8[1]) #make vector of first column names | |
| numbers2<-t(data.frame(append(as.numeric(d2[2:4]),c(-9999,-9999),after=3),as.numeric(d3[2:6]),as.numeric(d4[2:6]),append(as.numeric(d7[2]),c(-9999,-9999,-9999,-9999),after=1),append(as.numeric(d8[2:4]),c(-9999,-9999),after=3))) #make data frame of numbers | |
| numbers2<-data.frame(numbers2,rownaames2) #Make data frame of row names and numbers | |
| colnames(numbers2)<-c("Q","df","P","df_polytadj","P_polytadj","Source") #Assign column names | |
| summaryfitstats_table1_phyl<-data.frame(Source=numbers2[,6],Q=numbers2[,1],df=numbers2[,2],P=numbers2[,3],df_polytadj=numbers2[,4],P_polytadj=numbers2[,5]) #Reorder columns | |
| #summaryfitstats_table1_phyl #See table | |
| #Table 2, phylogenetic | |
| #e1<-unlist(strsplit(output[64]," +"))[-1] #Table header | |
| e2 <- if(length(unlist(strsplit(output[68]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[68]," +"))[-1])[1],(unlist(strsplit(output[68]," +"))[-1])[2]),unlist(strsplit(output[68]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[68]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[68]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[68]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[68]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[68]," +"))[-1][6:7])} else | |
| end | |
| e3 <- if(length(unlist(strsplit(output[69]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[69]," +"))[-1])[1],(unlist(strsplit(output[69]," +"))[-1])[2]),unlist(strsplit(output[69]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[69]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[69]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[69]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[69]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[69]," +"))[-1][6:7])} else | |
| end | |
| e6 <- if(length(unlist(strsplit(output[73]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[73]," +"))[-1])[1],(unlist(strsplit(output[73]," +"))[-1])[2]),unlist(strsplit(output[73]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[73]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[73]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[73]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[73]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[73]," +"))[-1][6:7])} else | |
| end | |
| e7 <- if(length(unlist(strsplit(output[74]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[74]," +"))[-1])[1],(unlist(strsplit(output[74]," +"))[-1])[2]),unlist(strsplit(output[74]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[74]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[74]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[74]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[74]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[74]," +"))[-1][6:7])} else | |
| end | |
| rownaames3<-c(e2[1],e3[1],e6[1],e7[1]) #make vector of first column names | |
| e22<-CI_split(e2) #Split confidence interval numbers apart and reinsert to vector of data | |
| e33<-CI_split(e3) | |
| e66<-CI_split(e6) | |
| e77<-CI_split(e7) | |
| numbers3<-t(data.frame(as.numeric(e22),as.numeric(e33),as.numeric(e66),as.numeric(e77))) #make data frame of numbers | |
| numbers3<-data.frame(numbers3,rownaames3) #Make data frame of row names and numbers | |
| colnames(numbers3)<-c("k","effsize","var","95CI_low","95CI_high","Z","df","P","Group") #Assign column names | |
| summaryeffsizes_table2_phyl<-data.frame(Group=numbers3[,9],k=numbers3[,1],effsize=numbers3[,2],var=numbers3[,3],CI_low=numbers3[,4],CI_high=numbers3[,5],Z=numbers3[,6],df=numbers3[,7],P=numbers3[,8]) #Reorder columns | |
| #summaryeffsizes_table2_phyl #See table | |
| ### Model fit table, AIC | |
| f1<-unlist(strsplit(output[89]," +"))[-1] #Table header | |
| f2<-unlist(strsplit(output[90]," +"))[-1] #Data row 1, fixed effects, all studies | |
| rownaames4<-c(f1[1],f2[1]) #make vector of first column names | |
| numbers4<-t(data.frame(as.numeric(f1[2:3]),as.numeric(f2[2:3]))) #make data frame of numbers | |
| numbers4<-data.frame(numbers4,rownaames4) #Make data frame of row names and numbers | |
| colnames(numbers4)<-c("AIC_fixed","AIC_random","Analysis") #Assign column names | |
| summarymodelfits_AIC_table<-data.frame(Analysis=numbers4[,3],AIC_fixed=numbers4[,1],AIC_random=numbers4[,2]) #Reorder columns | |
| #summarymodelfits_table #See table | |
| ### Model fit table, -2(likelihood) | |
| g1 <- unlist(strsplit(output[101]," +"))[-1] #Traditional AIC data | |
| g2 <- unlist(strsplit(output[102]," +"))[-1] #Phylogenetically controlled AIC data | |
| rownaames5 <- c(g1[1],g2[1]) #make vector of first column names | |
| numbers5 <- t(data.frame(as.numeric(g1[2:3]), as.numeric(g2[2:3]))) #make data frame of numbers | |
| numbers5 <- data.frame(numbers5, rownaames5) #Make data frame of row names and numbers | |
| colnames(numbers5) <- c("twoln_fixed", "twoln_random", "Analysis") #Assign column names | |
| summarymodelfits_twoln_table <- data.frame(Analysis = numbers5[,3], twoln_fixed = numbers5[,1], twoln_random = numbers5[,2]) #Reorder columns | |
| #summarymodelfits_twoln_table #See table | |
| #Make list of tables | |
| tables <- list(summaryfitstats_table1_trad, summaryeffsizes_table2_trad, summaryfitstats_table1_phyl, summaryeffsizes_table2_phyl, summarymodelfits_AIC_table, summarymodelfits_twoln_table) | |
| tables | |
| } | |
| # 2 groups in the moderator variable | |
| maketables_2group <- function(output){ #DONE IF/ELSE REFORMATTING | |
| #Table 1, Traditional meta-analysis | |
| a1 <- unlist(strsplit(output[6]," +"))[-1] #Table header | |
| a2 <- unlist(strsplit(output[8]," +"))[-1] #Data row 1, between groups, fixed effects | |
| a3 <- unlist(strsplit(output[9]," +"))[-1] #Data row 2, within groups | |
| a4 <- if(length(unlist(strsplit(output[10]," +"))[-1]) == 6) {c(paste(unlist(strsplit(output[10]," +"))[-1][1],unlist(strsplit(output[10]," +"))[-1][2],unlist(strsplit(output[10]," +"))[-1][3]),unlist(strsplit(output[10]," +"))[-1][4:6])} else | |
| if(length(unlist(strsplit(output[10]," +"))[-1]) == 8) {c(paste(unlist(strsplit(output[10]," +"))[-1][1],unlist(strsplit(output[10]," +"))[-1][2],unlist(strsplit(output[10]," +"))[-1][3]),unlist(strsplit(output[10]," +"))[-1][4:8])} else | |
| end | |
| a5 <- if(length(unlist(strsplit(output[11]," +"))[-1]) == 6) {c(paste(unlist(strsplit(output[11]," +"))[-1][1],unlist(strsplit(output[11]," +"))[-1][2],unlist(strsplit(output[11]," +"))[-1][3]),unlist(strsplit(output[11]," +"))[-1][4:6])} else | |
| if(length(unlist(strsplit(output[11]," +"))[-1]) == 8) {c(paste(unlist(strsplit(output[11]," +"))[-1][1],unlist(strsplit(output[11]," +"))[-1][2],unlist(strsplit(output[11]," +"))[-1][3]),unlist(strsplit(output[11]," +"))[-1][4:8])} else | |
| end | |
| a7 <- unlist(strsplit(output[12]," +"))[-1] #Data row 6, Total | |
| a8 <- unlist(strsplit(output[15]," +"))[-1] #Data row 7, between groups, random effects | |
| rownaames<-c(a2[1],a3[1],a4[1],a5[1],a7[1],a8[1]) #make vector of first column names | |
| numbers<-t(data.frame(as.numeric(a2[2:4]),as.numeric(a3[2:4]),as.numeric(a4[2:4]),as.numeric(a5[2:4]),append(as.numeric(a7[2]),c(-9999,-9999),after=1),as.numeric(a8[2:4]))) #make data frame of numbers | |
| numbers<-data.frame(numbers,rownaames) #Make data frame of row names and numbers | |
| colnames(numbers)<-c("Q","df","P","Source") #Assign column names | |
| summaryfitstats_table1_trad<-data.frame(Source=numbers$Source,Q=numbers$Q,df=numbers$df,P=numbers$P) #Reorder columns | |
| #summaryfitstats_table1_trad #See table | |
| #Table 2, Traditional meta-analysis | |
| #b1<-unlist(strsplit(output[24]," +"))[-1] #Table header | |
| b2 <- if(length(unlist(strsplit(output[28]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[28]," +"))[-1])[1],(unlist(strsplit(output[28]," +"))[-1])[2]),unlist(strsplit(output[28]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[28]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[28]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[28]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[28]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[28]," +"))[-1][6:7])} else | |
| end | |
| b3 <- if(length(unlist(strsplit(output[29]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[29]," +"))[-1])[1],(unlist(strsplit(output[29]," +"))[-1])[2]),unlist(strsplit(output[29]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[29]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[29]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[29]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[29]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[29]," +"))[-1][6:7])} else | |
| end | |
| b4 <- if(length(unlist(strsplit(output[30]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[30]," +"))[-1])[1],(unlist(strsplit(output[30]," +"))[-1])[2]),unlist(strsplit(output[30]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[30]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[30]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[30]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[30]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[30]," +"))[-1][6:7])} else | |
| end | |
| b6 <- if(length(unlist(strsplit(output[34]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[34]," +"))[-1])[1],(unlist(strsplit(output[34]," +"))[-1])[2]),unlist(strsplit(output[34]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[34]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[34]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[34]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[34]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[34]," +"))[-1][6:7])} else | |
| end | |
| b7 <- if(length(unlist(strsplit(output[35]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[35]," +"))[-1])[1],(unlist(strsplit(output[35]," +"))[-1])[2]),unlist(strsplit(output[35]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[35]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[35]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[35]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[35]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[35]," +"))[-1][6:7])} else | |
| end | |
| b8 <- if(length(unlist(strsplit(output[36]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[36]," +"))[-1])[1],(unlist(strsplit(output[36]," +"))[-1])[2]),unlist(strsplit(output[36]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[36]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[36]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[36]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[36]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[36]," +"))[-1][6:7])} else | |
| end | |
| rownaames1<-c(b2[1],b3[1],b4[1],b6[1],b7[1],b8[1]) #make vector of first column names | |
| b22<-CI_split(b2) #Split confidence interval numbers apart and reinsert to vector of data | |
| b33<-CI_split(b3) | |
| b44<-CI_split(b4) | |
| b66<-CI_split(b6) | |
| b77<-CI_split(b7) | |
| b88<-CI_split(b8) | |
| numbers1<-t(data.frame(as.numeric(b22),as.numeric(b33),as.numeric(b44),as.numeric(b66),as.numeric(b77),as.numeric(b88))) #make data frame of numbers | |
| numbers1<-data.frame(numbers1,rownaames1) #Make data frame of row names and numbers | |
| colnames(numbers1)<-c("k","effsize","var","95CI_low","95CI_high","Z","df","P","Group") #Assign column names | |
| summaryeffsizes_table2_trad<-data.frame(Group=numbers1[,9],k=numbers1[,1],effsize=numbers1[,2],var=numbers1[,3],CI_low=numbers1[,4],CI_high=numbers1[,5],Z=numbers1[,6],df=numbers1[,7],P=numbers1[,8]) #Reorder columns | |
| #summaryeffsizes_table2_trad #See table | |
| ###Phylogenetic meta-analysis | |
| #Table 1, Phylogenetic meta-analysis | |
| d1<-unlist(strsplit(output[50]," +"))[-1] #Table header | |
| d2<-unlist(strsplit(output[52]," +"))[-1] #Data row 1, between groups, fixed effects | |
| d3<-unlist(strsplit(output[53]," +"))[-1] #Data row 2, within groups | |
| d4 <- if(length(unlist(strsplit(output[54]," +"))[-1]) == 6) {c(paste(unlist(strsplit(output[54]," +"))[-1][1],unlist(strsplit(output[54]," +"))[-1][2],unlist(strsplit(output[54]," +"))[-1][3]),unlist(strsplit(output[54]," +"))[-1][4:6])} else | |
| if(length(unlist(strsplit(output[54]," +"))[-1]) == 8) {c(paste(unlist(strsplit(output[54]," +"))[-1][1],unlist(strsplit(output[54]," +"))[-1][2],unlist(strsplit(output[54]," +"))[-1][3]),unlist(strsplit(output[54]," +"))[-1][4:8])} else | |
| end | |
| d5 <- if(length(unlist(strsplit(output[55]," +"))[-1]) == 6) {c(paste(unlist(strsplit(output[55]," +"))[-1][1],unlist(strsplit(output[55]," +"))[-1][2],unlist(strsplit(output[55]," +"))[-1][3]),unlist(strsplit(output[55]," +"))[-1][4:6])} else | |
| if(length(unlist(strsplit(output[55]," +"))[-1]) == 8) {c(paste(unlist(strsplit(output[55]," +"))[-1][1],unlist(strsplit(output[55]," +"))[-1][2],unlist(strsplit(output[55]," +"))[-1][3]),unlist(strsplit(output[55]," +"))[-1][4:8])} else | |
| end | |
| d7<-unlist(strsplit(output[56]," +"))[-1] #Data row 6, Total | |
| d8<-unlist(strsplit(output[59]," +"))[-1] #Data row 7, between groups, random effects | |
| rownaames2<-c(d2[1],d3[1],d4[1],d5[1],d7[1],d8[1]) #make vector of first column names | |
| numbers2<-t(data.frame(append(as.numeric(d2[2:4]),c(-9999,-9999),after=3),as.numeric(d3[2:6]),as.numeric(d4[2:6]),as.numeric(d5[2:6]),append(as.numeric(d7[2]),c(-9999,-9999,-9999,-9999),after=1),append(as.numeric(d8[2:4]),c(-9999,-9999),after=3))) #make data frame of numbers | |
| numbers2<-data.frame(numbers2,rownaames2) #Make data frame of row names and numbers | |
| colnames(numbers2)<-c("Q","df","P","df_polytadj","P_polytadj","Source") #Assign column names | |
| summaryfitstats_table1_phyl<-data.frame(Source=numbers2[,6],Q=numbers2[,1],df=numbers2[,2],P=numbers2[,3],df_polytadj=numbers2[,4],P_polytadj=numbers2[,5]) #Reorder columns | |
| #summaryfitstats_table1_phyl #See table | |
| #Table 2, Phylogenetic meta-analysis | |
| #e1<-unlist(strsplit(output[68]," +"))[-1] #Table header | |
| e2 <- if(length(unlist(strsplit(output[72]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[72]," +"))[-1])[1],(unlist(strsplit(output[72]," +"))[-1])[2]),unlist(strsplit(output[72]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[72]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[72]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[72]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[72]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[72]," +"))[-1][6:7])} else | |
| end | |
| e3 <- if(length(unlist(strsplit(output[73]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[73]," +"))[-1])[1],(unlist(strsplit(output[73]," +"))[-1])[2]),unlist(strsplit(output[73]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[73]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[73]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[73]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[73]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[73]," +"))[-1][6:7])} else | |
| end | |
| e4 <- if(length(unlist(strsplit(output[74]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[74]," +"))[-1])[1],(unlist(strsplit(output[74]," +"))[-1])[2]),unlist(strsplit(output[74]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[74]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[74]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[74]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[74]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[74]," +"))[-1][6:7])} else | |
| end | |
| e6 <- if(length(unlist(strsplit(output[78]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[78]," +"))[-1])[1],(unlist(strsplit(output[78]," +"))[-1])[2]),unlist(strsplit(output[78]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[78]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[78]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[78]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[78]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[78]," +"))[-1][6:7])} else | |
| end | |
| e7 <- if(length(unlist(strsplit(output[79]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[79]," +"))[-1])[1],(unlist(strsplit(output[79]," +"))[-1])[2]),unlist(strsplit(output[79]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[79]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[79]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[79]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[79]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[79]," +"))[-1][6:7])} else | |
| end | |
| e8 <- if(length(unlist(strsplit(output[80]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[80]," +"))[-1])[1],(unlist(strsplit(output[80]," +"))[-1])[2]),unlist(strsplit(output[80]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[80]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[80]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[80]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[80]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[80]," +"))[-1][6:7])} else | |
| end | |
| rownaames3<-c(e2[1],e3[1],e4[1],e6[1],e7[1],e8[1]) #make vector of first column names | |
| e22<-CI_split(e2) #Split confidence interval numbers apart and reinsert to vector of data | |
| e33<-CI_split(e3) | |
| e44<-CI_split(e4) | |
| e66<-CI_split(e6) | |
| e77<-CI_split(e7) | |
| e88<-CI_split(e8) | |
| numbers3<-t(data.frame(as.numeric(e22),as.numeric(e33),as.numeric(e44),as.numeric(e66),as.numeric(e77),as.numeric(e88))) #make data frame of numbers | |
| numbers3<-data.frame(numbers3,rownaames3) #Make data frame of row names and numbers | |
| colnames(numbers3)<-c("k","effsize","var","95CI_low","95CI_high","Z","df","P","Group") #Assign column names | |
| summaryeffsizes_table2_phyl<-data.frame(Group=numbers3[,9],k=numbers3[,1],effsize=numbers3[,2],var=numbers3[,3],CI_low=numbers3[,4],CI_high=numbers3[,5],Z=numbers3[,6],df=numbers3[,7],P=numbers3[,8]) #Reorder columns | |
| #summaryeffsizes_table2_phyl #See table | |
| ### Model fit table, AIC | |
| f1<-unlist(strsplit(output[95]," +"))[-1] #Traditional AIC data | |
| f2<-unlist(strsplit(output[96]," +"))[-1] #Phylogenetically controlled AIC data | |
| rownaames4<-c(f1[1],f2[1]) #make vector of first column names | |
| numbers4<-t(data.frame(as.numeric(f1[2:3]),as.numeric(f2[2:3]))) #make data frame of numbers | |
| numbers4<-data.frame(numbers4,rownaames4) #Make data frame of row names and numbers | |
| colnames(numbers4)<-c("AIC_fixed","AIC_random","Analysis") #Assign column names | |
| summarymodelfits_AIC_table<-data.frame(Analysis=numbers4[,3],AIC_fixed=numbers4[,1],AIC_random=numbers4[,2]) #Reorder columns | |
| #summarymodelfits_AIC_table #See table | |
| ### Model fit table, -2(likelihood) | |
| g1 <- unlist(strsplit(output[107]," +"))[-1] #Traditional AIC data | |
| g2 <- unlist(strsplit(output[108]," +"))[-1] #Phylogenetically controlled AIC data | |
| rownaames5 <- c(g1[1],g2[1]) #make vector of first column names | |
| numbers5 <- t(data.frame(as.numeric(g1[2:3]), as.numeric(g2[2:3]))) #make data frame of numbers | |
| numbers5 <- data.frame(numbers5, rownaames5) #Make data frame of row names and numbers | |
| colnames(numbers5) <- c("twoln_fixed", "twoln_random", "Analysis") #Assign column names | |
| summarymodelfits_twoln_table <- data.frame(Analysis = numbers5[,3], twoln_fixed = numbers5[,1], twoln_random = numbers5[,2]) #Reorder columns | |
| #summarymodelfits_twoln_table #See table | |
| #Make list of tables | |
| tables <- list(summaryfitstats_table1_trad, summaryeffsizes_table2_trad, summaryfitstats_table1_phyl, summaryeffsizes_table2_phyl, summarymodelfits_AIC_table, summarymodelfits_twoln_table) | |
| tables | |
| } | |
| # 3 groups in the moderator variable | |
| maketables_3group <- function(output){ #DONE IF/ELSE REFORMATTING | |
| #Table 1, Traditional meta-analysis | |
| #a1<-unlist(strsplit(output[6]," +"))[-1] #Table header | |
| a2<-unlist(strsplit(output[8]," +"))[-1] #Data row 1, between groups, fixed effects | |
| a3<-unlist(strsplit(output[9]," +"))[-1] #Data row 2, within groups | |
| a4 <- if(length(unlist(strsplit(output[10]," +"))[-1]) == 6) {c(paste(unlist(strsplit(output[10]," +"))[-1][1],unlist(strsplit(output[10]," +"))[-1][2],unlist(strsplit(output[10]," +"))[-1][3]),unlist(strsplit(output[10]," +"))[-1][4:6])} else | |
| if(length(unlist(strsplit(output[10]," +"))[-1]) == 8) {c(paste(unlist(strsplit(output[10]," +"))[-1][1],unlist(strsplit(output[10]," +"))[-1][2],unlist(strsplit(output[10]," +"))[-1][3]),unlist(strsplit(output[10]," +"))[-1][4:8])} else | |
| end | |
| a5 <- if(length(unlist(strsplit(output[11]," +"))[-1]) == 6) {c(paste(unlist(strsplit(output[11]," +"))[-1][1],unlist(strsplit(output[11]," +"))[-1][2],unlist(strsplit(output[11]," +"))[-1][3]),unlist(strsplit(output[11]," +"))[-1][4:6])} else | |
| if(length(unlist(strsplit(output[11]," +"))[-1]) == 8) {c(paste(unlist(strsplit(output[11]," +"))[-1][1],unlist(strsplit(output[11]," +"))[-1][2],unlist(strsplit(output[11]," +"))[-1][3]),unlist(strsplit(output[11]," +"))[-1][4:8])} else | |
| end | |
| a6 <- if(length(unlist(strsplit(output[12]," +"))[-1]) == 6) {c(paste(unlist(strsplit(output[12]," +"))[-1][1],unlist(strsplit(output[12]," +"))[-1][2],unlist(strsplit(output[12]," +"))[-1][3]),unlist(strsplit(output[12]," +"))[-1][4:6])} else | |
| if(length(unlist(strsplit(output[12]," +"))[-1]) == 8) {c(paste(unlist(strsplit(output[12]," +"))[-1][1],unlist(strsplit(output[12]," +"))[-1][2],unlist(strsplit(output[12]," +"))[-1][3]),unlist(strsplit(output[12]," +"))[-1][4:8])} else | |
| end | |
| a7<-unlist(strsplit(output[13]," +"))[-1] #Data row 6, Total | |
| a8<-unlist(strsplit(output[16]," +"))[-1] #Data row 7, between groups, random effects | |
| rownaames<-c(a2[1],a3[1],a4[1],a5[1],a6[1],a7[1],a8[1]) #make vector of first column names | |
| numbers<-t(data.frame(as.numeric(a2[2:4]),as.numeric(a3[2:4]),as.numeric(a4[2:4]),as.numeric(a5[2:4]),as.numeric(a6[2:4]),append(as.numeric(a7[2]),c(-9999,-9999),after=1),as.numeric(a8[2:4]))) #make data frame of numbers | |
| numbers<-data.frame(numbers,rownaames) #Make data frame of row names and numbers | |
| colnames(numbers)<-c("Q","df","P","Source") #Assign column names | |
| summaryfitstats_table1_trad<-data.frame(Source=numbers$Source,Q=numbers$Q,df=numbers$df,P=numbers$P) #Reorder columns | |
| #summaryfitstats_table1_trad #See table | |
| #Table 2, Traditional meta-analysis | |
| #b1<-unlist(strsplit(output[25]," +"))[-1] #Table header | |
| b2 <- if(length(unlist(strsplit(output[29]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[29]," +"))[-1])[1],(unlist(strsplit(output[29]," +"))[-1])[2]),unlist(strsplit(output[29]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[29]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[29]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[29]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[29]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[29]," +"))[-1][6:7])} else | |
| end | |
| b3 <- if(length(unlist(strsplit(output[30]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[30]," +"))[-1])[1],(unlist(strsplit(output[30]," +"))[-1])[2]),unlist(strsplit(output[30]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[30]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[30]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[30]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[30]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[30]," +"))[-1][6:7])} else | |
| end | |
| b4 <- if(length(unlist(strsplit(output[31]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[31]," +"))[-1])[1],(unlist(strsplit(output[31]," +"))[-1])[2]),unlist(strsplit(output[31]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[31]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[31]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[31]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[31]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[31]," +"))[-1][6:7])} else | |
| end | |
| b5 <- if(length(unlist(strsplit(output[32]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[32]," +"))[-1])[1],(unlist(strsplit(output[32]," +"))[-1])[2]),unlist(strsplit(output[32]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[32]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[32]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[32]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[32]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[32]," +"))[-1][6:7])} else | |
| end | |
| b6 <- if(length(unlist(strsplit(output[36]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[36]," +"))[-1])[1],(unlist(strsplit(output[36]," +"))[-1])[2]),unlist(strsplit(output[36]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[36]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[36]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[36]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[36]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[36]," +"))[-1][6:7])} else | |
| end | |
| b7 <- if(length(unlist(strsplit(output[37]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[37]," +"))[-1])[1],(unlist(strsplit(output[37]," +"))[-1])[2]),unlist(strsplit(output[37]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[37]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[37]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[37]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[37]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[37]," +"))[-1][6:7])} else | |
| end | |
| b8 <- if(length(unlist(strsplit(output[38]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[38]," +"))[-1])[1],(unlist(strsplit(output[38]," +"))[-1])[2]),unlist(strsplit(output[38]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[38]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[38]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[38]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[38]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[38]," +"))[-1][6:7])} else | |
| end | |
| b9 <- if(length(unlist(strsplit(output[39]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[39]," +"))[-1])[1],(unlist(strsplit(output[39]," +"))[-1])[2]),unlist(strsplit(output[39]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[39]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[39]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[39]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[39]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[39]," +"))[-1][6:7])} else | |
| end | |
| rownaames1<-c(b2[1],b3[1],b4[1],b5[1],b6[1],b7[1],b8[1],b9[1]) #make vector of first column names | |
| b22<-CI_split(b2) #Split confidence interval numbers apart and reinsert to vector of data | |
| b33<-CI_split(b3) | |
| b44<-CI_split(b4) | |
| b55<-CI_split(b5) | |
| b66<-CI_split(b6) | |
| b77<-CI_split(b7) | |
| b88<-CI_split(b8) | |
| b99<-CI_split(b9) | |
| numbers1<-t(data.frame(as.numeric(b22),as.numeric(b33),as.numeric(b44),as.numeric(b55),as.numeric(b66),as.numeric(b77),as.numeric(b88),as.numeric(b99))) #make data frame of numbers | |
| numbers1<-data.frame(numbers1,rownaames1) #Make data frame of row names and numbers | |
| colnames(numbers1)<-c("k","effsize","var","95CI_low","95CI_high","Z","df","P","Group") #Assign column names | |
| summaryeffsizes_table2_trad<-data.frame(Group=numbers1[,9],k=numbers1[,1],effsize=numbers1[,2],var=numbers1[,3],CI_low=numbers1[,4],CI_high=numbers1[,5],Z=numbers1[,6],df=numbers1[,7],P=numbers1[,8]) #Reorder columns | |
| #summaryeffsizes_table2_trad #See table | |
| ###Phylogenetic meta-analysis | |
| #Table 1, Phylogenetic meta-analysis | |
| #d1<-unlist(strsplit(output[53]," +"))[-1] #Table header | |
| d2 <- unlist(strsplit(output[55]," +"))[-1] #Data row 1, between groups, fixed effects | |
| d3 <- unlist(strsplit(output[56]," +"))[-1] #Data row 2, within groups | |
| d4 <- if(length(unlist(strsplit(output[57]," +"))[-1]) == 6) {c(paste(unlist(strsplit(output[57]," +"))[-1][1],unlist(strsplit(output[57]," +"))[-1][2],unlist(strsplit(output[57]," +"))[-1][3]),unlist(strsplit(output[57]," +"))[-1][4:6])} else | |
| if(length(unlist(strsplit(output[57]," +"))[-1]) == 8) {c(paste(unlist(strsplit(output[57]," +"))[-1][1],unlist(strsplit(output[57]," +"))[-1][2],unlist(strsplit(output[57]," +"))[-1][3]),unlist(strsplit(output[57]," +"))[-1][4:8])} else | |
| end | |
| d5 <- if(length(unlist(strsplit(output[58]," +"))[-1]) == 6) {c(paste(unlist(strsplit(output[58]," +"))[-1][1],unlist(strsplit(output[58]," +"))[-1][2],unlist(strsplit(output[58]," +"))[-1][3]),unlist(strsplit(output[58]," +"))[-1][4:6])} else | |
| if(length(unlist(strsplit(output[58]," +"))[-1]) == 8) {c(paste(unlist(strsplit(output[58]," +"))[-1][1],unlist(strsplit(output[58]," +"))[-1][2],unlist(strsplit(output[58]," +"))[-1][3]),unlist(strsplit(output[58]," +"))[-1][4:8])} else | |
| end | |
| d6 <- if(length(unlist(strsplit(output[59]," +"))[-1]) == 6) {c(paste(unlist(strsplit(output[59]," +"))[-1][1],unlist(strsplit(output[59]," +"))[-1][2],unlist(strsplit(output[59]," +"))[-1][3]),unlist(strsplit(output[59]," +"))[-1][4:6])} else | |
| if(length(unlist(strsplit(output[59]," +"))[-1]) == 8) {c(paste(unlist(strsplit(output[59]," +"))[-1][1],unlist(strsplit(output[59]," +"))[-1][2],unlist(strsplit(output[59]," +"))[-1][3]),unlist(strsplit(output[59]," +"))[-1][4:8])} else | |
| end | |
| d7 <- unlist(strsplit(output[60]," +"))[-1] #Data row 6, Total | |
| d8 <- unlist(strsplit(output[63]," +"))[-1] #Data row 7, between groups, random effects | |
| rownaames2<-c(d2[1],d3[1],d4[1],d5[1],d6[1],d7[1],d8[1]) #make vector of first column names | |
| numbers2<-t(data.frame(append(as.numeric(d2[2:4]),c(-9999,-9999),after=3),as.numeric(d3[2:6]),as.numeric(d4[2:6]),as.numeric(d5[2:6]),as.numeric(d6[2:6]),append(as.numeric(d7[2]),c(-9999,-9999,-9999,-9999),after=1),append(as.numeric(d8[2:4]),c(-9999,-9999),after=3))) #make data frame of numbers | |
| numbers2<-data.frame(numbers2,rownaames2) #Make data frame of row names and numbers | |
| colnames(numbers2)<-c("Q","df","P","df_polytadj","P_polytadj","Source") #Assign column names | |
| summaryfitstats_table1_phyl<-data.frame(Source=numbers2[,6],Q=numbers2[,1],df=numbers2[,2],P=numbers2[,3],df_polytadj=numbers2[,4],P_polytadj=numbers2[,5]) #Reorder columns | |
| #summaryfitstats_table1_phyl #See table | |
| #Table 2, Phylogenetic meta-analysis | |
| #e1<-unlist(strsplit(output[72]," +"))[-1] #Table header | |
| e2 <- if(length(unlist(strsplit(output[76]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[76]," +"))[-1])[1],(unlist(strsplit(output[76]," +"))[-1])[2]),unlist(strsplit(output[76]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[76]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[76]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[76]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[76]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[76]," +"))[-1][6:7])} else | |
| end | |
| e3 <- if(length(unlist(strsplit(output[77]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[77]," +"))[-1])[1],(unlist(strsplit(output[77]," +"))[-1])[2]),unlist(strsplit(output[77]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[77]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[77]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[77]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[77]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[77]," +"))[-1][6:7])} else | |
| end | |
| e4 <- if(length(unlist(strsplit(output[78]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[78]," +"))[-1])[1],(unlist(strsplit(output[78]," +"))[-1])[2]),unlist(strsplit(output[78]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[78]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[78]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[78]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[78]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[78]," +"))[-1][6:7])} else | |
| end | |
| e5 <- if(length(unlist(strsplit(output[79]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[79]," +"))[-1])[1],(unlist(strsplit(output[79]," +"))[-1])[2]),unlist(strsplit(output[79]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[79]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[79]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[79]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[79]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[79]," +"))[-1][6:7])} else | |
| end | |
| e6 <- if(length(unlist(strsplit(output[83]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[83]," +"))[-1])[1],(unlist(strsplit(output[83]," +"))[-1])[2]),unlist(strsplit(output[83]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[83]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[83]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[83]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[83]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[83]," +"))[-1][6:7])} else | |
| end | |
| e7 <- if(length(unlist(strsplit(output[84]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[84]," +"))[-1])[1],(unlist(strsplit(output[84]," +"))[-1])[2]),unlist(strsplit(output[84]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[84]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[84]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[84]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[84]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[84]," +"))[-1][6:7])} else | |
| end | |
| e8 <- if(length(unlist(strsplit(output[85]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[85]," +"))[-1])[1],(unlist(strsplit(output[85]," +"))[-1])[2]),unlist(strsplit(output[85]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[85]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[85]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[85]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[85]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[85]," +"))[-1][6:7])} else | |
| end | |
| e9 <- if(length(unlist(strsplit(output[86]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[86]," +"))[-1])[1],(unlist(strsplit(output[86]," +"))[-1])[2]),unlist(strsplit(output[86]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[86]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[86]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[86]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[86]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[86]," +"))[-1][6:7])} else | |
| end | |
| rownaames3<-c(e2[1],e3[1],e4[1],e5[1],e6[1],e7[1],e8[1],e9[1]) #make vector of first column names | |
| e22<-CI_split(e2) #Split confidence interval numbers apart and reinsert to vector of data | |
| e33<-CI_split(e3) | |
| e44<-CI_split(e4) | |
| e55<-CI_split(e5) | |
| e66<-CI_split(e6) | |
| e77<-CI_split(e7) | |
| e88<-CI_split(e8) | |
| e99<-CI_split(e9) | |
| numbers3<-t(data.frame(as.numeric(e22),as.numeric(e33),as.numeric(e44),as.numeric(e55),as.numeric(e66),as.numeric(e77),as.numeric(e88),as.numeric(e99))) #make data frame of numbers | |
| numbers3<-data.frame(numbers3,rownaames3) #Make data frame of row names and numbers | |
| colnames(numbers3)<-c("k","effsize","var","95CI_low","95CI_high","Z","df","P","Group") #Assign column names | |
| summaryeffsizes_table2_phyl<-data.frame(Group=numbers3[,9],k=numbers3[,1],effsize=numbers3[,2],var=numbers3[,3],CI_low=numbers3[,4],CI_high=numbers3[,5],Z=numbers3[,6],df=numbers3[,7],P=numbers3[,8]) #Reorder columns | |
| #summaryeffsizes_table2_phyl #See table | |
| ### Model fit table, AIC | |
| f1<-unlist(strsplit(output[101]," +"))[-1] #Table header | |
| f2<-unlist(strsplit(output[102]," +"))[-1] #Data row 1, fixed effects, all studies | |
| rownaames4<-c(f1[1],f2[1]) #make vector of first column names | |
| numbers4<-t(data.frame(as.numeric(f1[2:3]),as.numeric(f2[2:3]))) #make data frame of numbers | |
| numbers4<-data.frame(numbers4,rownaames4) #Make data frame of row names and numbers | |
| colnames(numbers4)<-c("AIC_fixed","AIC_random","Analysis") #Assign column names | |
| summarymodelfits_AIC_table<-data.frame(Analysis=numbers4[,3],AIC_fixed=numbers4[,1],AIC_random=numbers4[,2]) #Reorder columns | |
| #summarymodelfits_AIC_table #See table | |
| ### Model fit table, -2(likelihood) | |
| g1 <- unlist(strsplit(output[113]," +"))[-1] #Traditional AIC data | |
| g2 <- unlist(strsplit(output[114]," +"))[-1] #Phylogenetically controlled AIC data | |
| rownaames5 <- c(g1[1],g2[1]) #make vector of first column names | |
| numbers5 <- t(data.frame(as.numeric(g1[2:3]), as.numeric(g2[2:3]))) #make data frame of numbers | |
| numbers5 <- data.frame(numbers5, rownaames5) #Make data frame of row names and numbers | |
| colnames(numbers5) <- c("twoln_fixed", "twoln_random", "Analysis") #Assign column names | |
| summarymodelfits_twoln_table <- data.frame(Analysis = numbers5[,3], twoln_fixed = numbers5[,1], twoln_random = numbers5[,2]) #Reorder columns | |
| #summarymodelfits_twoln_table #See table | |
| #Make list of tables | |
| tables <- list(summaryfitstats_table1_trad, summaryeffsizes_table2_trad, summaryfitstats_table1_phyl, summaryeffsizes_table2_phyl, summarymodelfits_AIC_table, summarymodelfits_twoln_table) | |
| tables | |
| } | |
| # 4 groups in the moderator variable | |
| maketables_4group <- function(output){ #DONE IF/ELSE REFORMATTING | |
| #Table 1, Traditional meta-analysis | |
| a1<-unlist(strsplit(output[6]," +"))[-1] #Table header | |
| a2<-unlist(strsplit(output[8]," +"))[-1] #Data row 1, between groups, fixed effects | |
| a3<-unlist(strsplit(output[9]," +"))[-1] #Data row 2, within groups | |
| a4<-unlist(strsplit(output[10]," +"))[-1] #Data row 3, within goup 0 | |
| a5<-unlist(strsplit(output[11]," +"))[-1] #Data row 4, within goup 1 | |
| a6<-unlist(strsplit(output[12]," +"))[-1] #Data row 5, within goup 2 | |
| a7<-unlist(strsplit(output[13]," +"))[-1] #Data row 6, Total | |
| a8<-unlist(strsplit(output[14]," +"))[-1] #Data row 7, between groups, random effects | |
| a9<-unlist(strsplit(output[17]," +"))[-1] #Data row 7, between groups, random effects | |
| rownaames<-c(a2[1],a3[1],a4[1],a5[1],a6[1],a7[1],a8[1],a9[1]) #make vector of first column names | |
| numbers<-t(data.frame(as.numeric(a2[2:4]),as.numeric(a3[2:4]),as.numeric(a4[2:4]),as.numeric(a5[2:4]),as.numeric(a6[2:4]),as.numeric(a7[2:4]),append(as.numeric(a8[2]),c(-9999,-9999),after=1),as.numeric(a9[2:4]))) #make data frame of numbers | |
| numbers<-data.frame(numbers,rownaames) #Make data frame of row names and numbers | |
| colnames(numbers)<-c("Q","df","P","Source") #Assign column names | |
| summaryfitstats_table1_trad<-data.frame(Source=numbers$Source,Q=numbers$Q,df=numbers$df,P=numbers$P) #Reorder columns | |
| #summaryfitstats_table1_trad #See table | |
| #Table 2, Traditional meta-analysis | |
| b1<-unlist(strsplit(output[26]," +"))[-1] #Table header | |
| b2 <- if(length(unlist(strsplit(output[30]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[30]," +"))[-1])[1],(unlist(strsplit(output[30]," +"))[-1])[2]),unlist(strsplit(output[30]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[30]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[30]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[30]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[30]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[30]," +"))[-1][6:7])} else | |
| end | |
| b3 <- if(length(unlist(strsplit(output[31]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[31]," +"))[-1])[1],(unlist(strsplit(output[31]," +"))[-1])[2]),unlist(strsplit(output[31]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[31]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[31]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[31]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[31]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[31]," +"))[-1][6:7])} else | |
| end | |
| b4 <- if(length(unlist(strsplit(output[32]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[32]," +"))[-1])[1],(unlist(strsplit(output[32]," +"))[-1])[2]),unlist(strsplit(output[32]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[32]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[32]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[32]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[32]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[32]," +"))[-1][6:7])} else | |
| end | |
| b5 <- if(length(unlist(strsplit(output[33]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[33]," +"))[-1])[1],(unlist(strsplit(output[33]," +"))[-1])[2]),unlist(strsplit(output[33]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[33]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[33]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[33]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[33]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[33]," +"))[-1][6:7])} else | |
| end | |
| b6 <- if(length(unlist(strsplit(output[34]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[34]," +"))[-1])[1],(unlist(strsplit(output[34]," +"))[-1])[2]),unlist(strsplit(output[34]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[34]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[34]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[34]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[34]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[34]," +"))[-1][6:7])} else | |
| end | |
| b7 <- if(length(unlist(strsplit(output[38]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[38]," +"))[-1])[1],(unlist(strsplit(output[38]," +"))[-1])[2]),unlist(strsplit(output[38]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[38]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[38]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[38]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[38]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[38]," +"))[-1][6:7])} else | |
| end | |
| b8 <- if(length(unlist(strsplit(output[39]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[39]," +"))[-1])[1],(unlist(strsplit(output[39]," +"))[-1])[2]),unlist(strsplit(output[39]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[39]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[39]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[39]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[39]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[39]," +"))[-1][6:7])} else | |
| end | |
| b9 <- if(length(unlist(strsplit(output[40]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[40]," +"))[-1])[1],(unlist(strsplit(output[40]," +"))[-1])[2]),unlist(strsplit(output[40]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[40]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[40]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[40]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[40]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[40]," +"))[-1][6:7])} else | |
| end | |
| b10 <- if(length(unlist(strsplit(output[41]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[41]," +"))[-1])[1],(unlist(strsplit(output[41]," +"))[-1])[2]),unlist(strsplit(output[41]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[41]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[41]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[41]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[41]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[41]," +"))[-1][6:7])} else | |
| end | |
| b11 <- if(length(unlist(strsplit(output[42]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[42]," +"))[-1])[1],(unlist(strsplit(output[42]," +"))[-1])[2]),unlist(strsplit(output[42]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[42]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[42]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[42]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[42]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[42]," +"))[-1][6:7])} else | |
| end | |
| rownaames1<-c(b2[1],b3[1],b4[1],b5[1],b6[1],b7[1],b8[1],b9[1],b10[1],b11[1]) #make vector of first column names | |
| b22<-CI_split(b2) #Split confidence interval numbers apart and reinsert to vector of data | |
| b33<-CI_split(b3) | |
| b44<-CI_split(b4) | |
| b55<-CI_split(b5) | |
| b66<-CI_split(b6) | |
| b77<-CI_split(b7) | |
| b88<-CI_split(b8) | |
| b99<-CI_split(b9) | |
| b1010<-CI_split(b10) | |
| b1111<-CI_split(b11) | |
| numbers1<-t(data.frame(as.numeric(b22),as.numeric(b33),as.numeric(b44),as.numeric(b55),as.numeric(b66),as.numeric(b77),as.numeric(b88),as.numeric(b99),as.numeric(b1010),as.numeric(b1111))) #make data frame of numbers | |
| numbers1<-data.frame(numbers1,rownaames1) #Make data frame of row names and numbers | |
| colnames(numbers1)<-c("k","effsize","var","95CI_low","95CI_high","Z","df","P","Group") #Assign column names | |
| summaryeffsizes_table2_trad<-data.frame(Group=numbers1[,9],k=numbers1[,1],effsize=numbers1[,2],var=numbers1[,3],CI_low=numbers1[,4],CI_high=numbers1[,5],Z=numbers1[,6],df=numbers1[,7],P=numbers1[,8]) #Reorder columns | |
| #summaryeffsizes_table2_trad #See table | |
| ###Phylogenetic meta-analysis | |
| #Table 1, Phylogenetic meta-analysis | |
| d1<-unlist(strsplit(output[56]," +"))[-1] #Table header | |
| d2<-unlist(strsplit(output[58]," +"))[-1] #Data row 1, between groups, fixed effects | |
| d3<-unlist(strsplit(output[59]," +"))[-1] #Data row 2, within groups | |
| d4<-unlist(strsplit(output[60]," +"))[-1] #Data row 3, within goup 0 | |
| d5<-unlist(strsplit(output[61]," +"))[-1] #Data row 4, within goup 1 | |
| d6<-unlist(strsplit(output[62]," +"))[-1] #Data row 5, within goup 2 | |
| d7<-unlist(strsplit(output[63]," +"))[-1] #Data row 6, Total | |
| d8<-unlist(strsplit(output[64]," +"))[-1] #Data row 7, between groups, random effects | |
| d9<-unlist(strsplit(output[67]," +"))[-1] #Data row 7, between groups, random effects | |
| rownaames2<-c(d2[1],d3[1],d4[1],d5[1],d6[1],d7[1],d8[1],d9[1]) #make vector of first column names | |
| numbers2<-t(data.frame(append(as.numeric(d2[2:4]),c(-9999,-9999),after=3),as.numeric(d3[2:6]),as.numeric(d4[2:6]),as.numeric(d5[2:6]),as.numeric(d6[2:6]),as.numeric(d7[2:6]),append(as.numeric(d8[2]),c(-9999,-9999,-9999,-9999),after=3),append(as.numeric(d9[2:4]),c(-9999,-9999),after=3))) #make data frame of numbers | |
| numbers2<-data.frame(numbers2,rownaames2) #Make data frame of row names and numbers | |
| colnames(numbers2)<-c("Q","df","P","df_polytadj","P_polytadj","Source") #Assign column names | |
| summaryfitstats_table1_phyl<-data.frame(Source=numbers2[,6],Q=numbers2[,1],df=numbers2[,2],P=numbers2[,3],df_polytadj=numbers2[,4],P_polytadj=numbers2[,5]) #Reorder columns | |
| #summaryfitstats_table1_phyl #See table | |
| #Table 2, Phylogenetic meta-analysis | |
| e1 <- unlist(strsplit(output[76]," +"))[-1] #Table header | |
| e2 <- if(length(unlist(strsplit(output[80]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[80]," +"))[-1])[1],(unlist(strsplit(output[80]," +"))[-1])[2]),unlist(strsplit(output[80]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[80]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[80]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[80]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[80]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[80]," +"))[-1][6:7])} else | |
| end | |
| e3 <- if(length(unlist(strsplit(output[81]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[81]," +"))[-1])[1],(unlist(strsplit(output[81]," +"))[-1])[2]),unlist(strsplit(output[81]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[81]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[81]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[81]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[81]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[81]," +"))[-1][6:7])} else | |
| end | |
| e4 <- if(length(unlist(strsplit(output[82]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[82]," +"))[-1])[1],(unlist(strsplit(output[82]," +"))[-1])[2]),unlist(strsplit(output[82]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[82]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[82]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[82]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[82]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[82]," +"))[-1][6:7])} else | |
| end | |
| e5 <- if(length(unlist(strsplit(output[83]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[83]," +"))[-1])[1],(unlist(strsplit(output[83]," +"))[-1])[2]),unlist(strsplit(output[83]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[83]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[83]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[83]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[83]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[83]," +"))[-1][6:7])} else | |
| end | |
| e6 <- if(length(unlist(strsplit(output[84]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[84]," +"))[-1])[1],(unlist(strsplit(output[84]," +"))[-1])[2]),unlist(strsplit(output[84]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[84]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[84]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[84]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[84]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[84]," +"))[-1][6:7])} else | |
| end | |
| e7 <- if(length(unlist(strsplit(output[88]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[88]," +"))[-1])[1],(unlist(strsplit(output[88]," +"))[-1])[2]),unlist(strsplit(output[88]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[88]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[88]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[88]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[88]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[88]," +"))[-1][6:7])} else | |
| end | |
| e8 <- if(length(unlist(strsplit(output[89]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[89]," +"))[-1])[1],(unlist(strsplit(output[89]," +"))[-1])[2]),unlist(strsplit(output[89]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[89]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[89]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[89]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[89]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[89]," +"))[-1][6:7])} else | |
| end | |
| e9 <- if(length(unlist(strsplit(output[90]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[90]," +"))[-1])[1],(unlist(strsplit(output[90]," +"))[-1])[2]),unlist(strsplit(output[90]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[90]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[90]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[90]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[90]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[90]," +"))[-1][6:7])} else | |
| end | |
| e10 <- if(length(unlist(strsplit(output[91]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[91]," +"))[-1])[1],(unlist(strsplit(output[91]," +"))[-1])[2]),unlist(strsplit(output[91]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[91]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[91]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[91]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[91]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[91]," +"))[-1][6:7])} else | |
| end | |
| e11 <- if(length(unlist(strsplit(output[92]," +"))[-1]) == 9) {c(paste((unlist(strsplit(output[92]," +"))[-1])[1],(unlist(strsplit(output[92]," +"))[-1])[2]),unlist(strsplit(output[92]," +"))[-1][3:9])} else | |
| if(str_detect(unlist(strsplit(output[92]," +"))[-1][6], ")") == "TRUE") {c(unlist(strsplit(output[92]," +"))[-1][1:4], paste(str_split(unlist(strsplit(output[92]," +"))[-1][6], ")")[[1]][1],")", sep=""), str_split(unlist(strsplit(output[92]," +"))[-1][6], ")")[[1]][2], unlist(strsplit(output[92]," +"))[-1][6:7])} else | |
| end | |
| rownaames3<-c(e2[1],e3[1],e4[1],e5[1],e6[1],e7[1],e8[1],e9[1],e10[1],e11[1]) #make vector of first column names | |
| e22<-CI_split(e2) #Split confidence interval numbers apart and reinsert to vector of data | |
| e33<-CI_split(e3) | |
| e44<-CI_split(e4) | |
| e55<-CI_split(e5) | |
| e66<-CI_split(e6) | |
| e77<-CI_split(e7) | |
| e88<-CI_split(e8) | |
| e99<-CI_split(e9) | |
| e1010<-CI_split(e10) | |
| e1111<-CI_split(e11) | |
| numbers3<-t(data.frame(as.numeric(e22),as.numeric(e33),as.numeric(e44),as.numeric(e55),as.numeric(e66),as.numeric(e77),as.numeric(e88),as.numeric(e99),as.numeric(e1010),as.numeric(e1111))) #make data frame of numbers | |
| numbers3<-data.frame(numbers3,rownaames3) #Make data frame of row names and numbers | |
| colnames(numbers3)<-c("k","effsize","var","95CI_low","95CI_high","Z","df","P","Group") #Assign column names | |
| summaryeffsizes_table2_phyl<-data.frame(Group=numbers3[,9],k=numbers3[,1],effsize=numbers3[,2],var=numbers3[,3],CI_low=numbers3[,4],CI_high=numbers3[,5],Z=numbers3[,6],df=numbers3[,7],P=numbers3[,8]) #Reorder columns | |
| #summaryeffsizes_table2_phyl #See table | |
| ###Model fit table | |
| f1<-unlist(strsplit(output[107]," +"))[-1] #Table header | |
| f2<-unlist(strsplit(output[108]," +"))[-1] #Data row 1, fixed effects, all studies | |
| rownaames4<-c(f1[1],f2[1]) #make vector of first column names | |
| numbers4<-t(data.frame(as.numeric(f1[2:3]),as.numeric(f2[2:3]))) #make data frame of numbers | |
| numbers4<-data.frame(numbers4,rownaames4) #Make data frame of row names and numbers | |
| colnames(numbers4)<-c("AIC_fixed","AIC_random","Analysis") #Assign column names | |
| summarymodelfits_AIC_table<-data.frame(Analysis=numbers4[,3],AIC_fixed=numbers4[,1],AIC_random=numbers4[,2]) #Reorder columns | |
| #summarymodelfits_table #See table | |
| ### Model fit table, -2(likelihood) | |
| g1 <- unlist(strsplit(output[119]," +"))[-1] #Traditional AIC data | |
| g2 <- unlist(strsplit(output[120]," +"))[-1] #Phylogenetically controlled AIC data | |
| rownaames5 <- c(g1[1],g2[1]) #make vector of first column names | |
| numbers5 <- t(data.frame(as.numeric(g1[2:3]), as.numeric(g2[2:3]))) #make data frame of numbers | |
| numbers5 <- data.frame(numbers5, rownaames5) #Make data frame of row names and numbers | |
| colnames(numbers5) <- c("twoln_fixed", "twoln_random", "Analysis") #Assign column names | |
| summarymodelfits_twoln_table <- data.frame(Analysis = numbers5[,3], twoln_fixed = numbers5[,1], twoln_random = numbers5[,2]) #Reorder columns | |
| #summarymodelfits_twoln_table #See table | |
| #Make list of tables | |
| tables <- list(summaryfitstats_table1_trad, summaryeffsizes_table2_trad, summaryfitstats_table1_phyl, summaryeffsizes_table2_phyl, summarymodelfits_AIC_table, summarymodelfits_twoln_table) | |
| tables | |
| } | |
| # Process phylometa output | |
| phylometa.process <- function(phylometa.run,groups){ | |
| aaa <- data.frame(phylometa.run) | |
| if(length(subset(aaa,aaa[,1]=="poly")[,1]) == 1) {phylometa.run <- phylometa.run[-as.numeric(rownames(subset(aaa,aaa[,1]=="poly")))]} else (phylometa.run <- phylometa.run) | |
| aaaa <- data.frame(phylometa.run) | |
| x <- as.numeric(rownames(subset(aaaa,aaaa[,1]=="RESULTS SECTION A. Traditional meta-analysis."))) | |
| y <- as.numeric(rownames(subset(aaaa,aaaa[,1]=="For further details on these methods see:"))) | |
| bbb <- phylometa.run[x:y] | |
| outputtables <- ( | |
| if (groups == 1) {maketables_1group(bbb)} else | |
| if (groups == 2) {maketables_2group(bbb)} else | |
| if (groups == 3) {maketables_3group(bbb)} else | |
| if (groups == 4) {maketables_4group(bbb)} else | |
| end) | |
| outputtables | |
| } | |
| # Get output from phylometa.process | |
| phylometa.output <- function(a) { | |
| a | |
| } | |
| phylometa.output.table <- function(a,b) { | |
| a[[b]] | |
| } | |
| # Function used below in the function 'arrange' | |
| vp.layout <- function(x, y) viewport(layout.pos.row=x, layout.pos.col=y) | |
| arrange_ <- function(..., nrow=NULL, ncol=NULL, as.table=FALSE) { | |
| dots <- list(...) | |
| n <- length(dots) | |
| if(is.null(nrow) & is.null(ncol)) { nrow = floor(n/2) ; ncol = ceiling(n/nrow)} | |
| if(is.null(nrow)) { nrow = ceiling(n/ncol)} | |
| if(is.null(ncol)) { ncol = ceiling(n/nrow)} | |
| ## NOTE see n2mfrow in grDevices for possible alternative | |
| grid.newpage() | |
| pushViewport(viewport(layout=grid.layout(nrow,ncol) ) ) | |
| ii.p <- 1 | |
| for(ii.row in seq(1, nrow)){ | |
| ii.table.row <- ii.row | |
| if(as.table) {ii.table.row <- nrow - ii.table.row + 1} | |
| for(ii.col in seq(1, ncol)){ | |
| ii.table <- ii.p | |
| if(ii.p > n) break | |
| print(dots[[ii.table]], vp=vp.layout(ii.table.row, ii.col)) | |
| ii.p <- ii.p + 1 | |
| } | |
| } | |
| } | |
| # Function to write trees to directory for use by Phylometa | |
| WriteTrees2 <- function(xxx) { | |
| for(i in 1:length(xxx)){ | |
| write.tree(xxx[[i]], paste("tree",i,".txt","",sep="")) | |
| } | |
| } | |
| Created by Pretty R at inside-R.org |
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