adding pvals to strobe_diff_bygroup

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: daDoctoR
 Type: Package
 Title: FUNCTIONS FOR HEALTH RESEARCH
-Version: 0.1.0.9019
+Version: 0.1.0.9020
 Author@R: c(person("Andreas", "Gammelgaard Damsbo", email = "agdamsbo@pm.me", role = c("cre", "aut")))
 Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@pm.me>
 Description: I am a Danish medical doctor involved in neuropsychiatric research. 
@@ -15,4 +15,4 @@ Imports: broom,
 License: GPL (>= 2)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.0.9000
+RoxygenNote: 6.1.1

R/strobe_diff_bygroup.R

@@ -6,16 +6,13 @@
 #' @param groups groups to compare, as string.
 #' @param adj variables to adjust for, as string.
 #' @param data dataframe of data.
-#' @param dec decimals for results, standard is set to 2. Mean and sd is dec-1.
+#' @param dec decimals for results, standard is set to 2. Mean and sd is dec-1. pval has 3 decimals.
 #' @keywords strobe
 #' @export
 #' @examples
 #' strobe_diff_bygroup()
 
 strobe_diff_bygroup<-function(meas,var,group,adj,data,dec=2){
-  ## Wishlist:
-  ## -fix confint()
-
 
   ## meas: sdmt
   ## var: rtreat
@@ -26,70 +23,96 @@ strobe_diff_bygroup<-function(meas,var,group,adj,data,dec=2){
     m <- d[, c(meas)]
     v <- d[, c(var)]
     g <- d[, c(group)]
-
     ads <- d[, c(adj)]
-
     dat <- data.frame(m, v, g, ads)
-
+    df <- data.frame(matrix(ncol = 9))
-  df<-data.frame(matrix(ncol=7))
-
     if (!is.factor(m)) {
-
       for (i in 1:length(levels(g))) {
         grp <- levels(dat$g)[i]
         di <- dat[dat$g == grp, ][, -3]
-
         mod <- lm(m ~ v, data = di)
-      co<-round(coef(mod)[-1],dec)
-      lo<-round(confint(mod)[-1,1],dec)
-      up<-round(confint(mod)[-1,2],dec)
 
+        p <- coef(summary(mod))[2,4]
+        p<-ifelse(p<0.001,"<0.001",round(p,3))
+        p <- ifelse(p<=0.05|p=="<0.001",paste0("*",p),
+                    ifelse(p>0.05&p<=0.1,paste0(".",p),p))
+        pv<-p
+
+        co<-round(coef(mod),dec)[2]
+        ci<-round(confint(mod),dec)[2,]
+        lo<-ci[1]
+        up<-ci[2]
         ci<-paste0(co," (",lo," to ",up,")")
 
         amod <- lm(m ~ ., data = di)
-      aco<-round(coef(amod)[2],dec)
+        pa <- coef(summary(amod))[2,4]
-      alo<-round(confint(amod)[2,1],dec)
+        pa<-ifelse(pa<0.001,"<0.001",round(pa,3))
-      aup<-round(confint(amod)[2,2],dec)
+        pa <- ifelse(pa<=0.05|pa=="<0.001",paste0("*",pa),
+                     ifelse(pa>0.05&pa<=0.1,paste0(".",pa),pa))
+        apv<-pa
 
+        aco<-round(coef(amod),dec)[2]
+        aci<-round(confint(amod),dec)[2,]
+        alo<-aci[1]
+        aup<-aci[2]
         aci<-paste0(aco," (",alo," to ",aup,")")
 
         nr <- c()
-
         for (r in 1:2) {
           vr <- levels(di$v)[r]
           dr <- di[di$v == vr, ]
           n <- as.numeric(nrow(dr[!is.na(dr$m), ]))
-        mean<-round(mean(dr$m,na.rm = TRUE),dec-1)
+          mean <- round(mean(dr$m, na.rm = TRUE), dec -
+                          1)
           sd <- round(sd(dr$m, na.rm = TRUE), dec - 1)
           ms <- paste0(mean, " (", sd, ")")
-
           nr <- c(nr, n, ms)
         }
-      irl<-c(grp,nr,ci,aci)
+        irl <- c(grp, nr, ci, pv, aci, apv)
         df <- rbind(df, irl)
-      names(df)<-c("grp",paste0("N.",substr(levels(v)[1],1,3)),paste0("M.",substr(levels(v)[1],1,3)),paste0("N.",substr(levels(v)[2],1,3)),paste0("M.",substr(levels(v)[2],1,3)),"diff","ad.diff")
+        names(df) <- c("grp",
-    }}
+                       paste0("N.", substr(levels(v)[1], 1, 3)),
-
+                       paste0("M.", substr(levels(v)[1], 1, 3)),
+                       paste0("N.", substr(levels(v)[2], 1, 3)),
+                       paste0("M.", substr(levels(v)[2], 1, 3)),
+                       "diff",
+                       "pval",
+                       "ad.diff",
+                       "ad.pval")
+      }
+    }
     if (is.factor(m)) {
-
       for (i in 1:length(levels(g))) {
         grp <- levels(dat$g)[i]
         di <- dat[dat$g == grp, ][, -3]
 
         mod <- glm(m ~ v, family = binomial(), data = di)
-      co<-round(exp(coef(mod)[-1]),dec)
-      lo<-round(exp(confint(mod)[-1,1]),dec)
-      up<-round(exp(confint(mod)[-1,2]),dec)
 
+        p <- coef(summary(mod))[2,4]
+        p<-ifelse(p<0.001,"<0.001",round(p,3))
+        p <- ifelse(p<=0.05|p=="<0.001",paste0("*",p),
+                    ifelse(p>0.05&p<=0.1,paste0(".",p),p))
+        pv<-p
+
+        co <- round(exp(coef(mod)[-1]), dec)
+        ci<-round(exp(confint(mod)),dec)[2,]
+        lo<-ci[1]
+        up<-ci[2]
         ci <- paste0(co, " (", lo, " to ", up, ")")
 
         amod <- glm(m ~ ., family = binomial(), data = di)
+
+        pa <- coef(summary(amod))[2,4]
+        pa<-ifelse(pa<0.001,"<0.001",round(pa,3))
+        pa <- ifelse(pa<=0.05|pa=="<0.001",paste0("*",pa),
+                     ifelse(pa>0.05&pa<=0.1,paste0(".",pa),pa))
+        apv<-pa
+
         aco <- round(exp(coef(amod)[2]), dec)
-      alo<-suppressMessages(round(exp(confint(amod)[2,1]),dec))
+        aci<-suppressMessages(round(exp(confint(amod)),dec))[2,]
-      aup<-suppressMessages(round(exp(confint(amod)[2,2]),dec))
+        alo<-aci[1]
-
+        aup<-aci[2]
         aci <- paste0(aco, " (", alo, " to ", aup, ")")
-
         nr <- c()
 
         for (r in 1:2) {
@@ -100,13 +123,20 @@ strobe_diff_bygroup<-function(meas,var,group,adj,data,dec=2){
           out <- nrow(dr[dr$m == nl & !is.na(dr$m), ])
           pro <- round(out/n * 100, 0)
           rt <- paste0(out, " (", pro, "%)")
-
           nr <- c(nr, n, rt)
         }
-      irl<-c(grp,nr,ci,aci)
+        irl <- c(grp, nr, ci, pv, aci, apv)
         df <- rbind(df, irl)
-      names(df)<-c("grp",paste0("N.",substr(levels(v)[1],1,3)),paste0(nl,".",substr(levels(v)[1],1,3)),paste0("N.",substr(levels(v)[2],1,3)),paste0(nl,".",substr(levels(v)[2],1,3)),"OR","ad.OR")
+        names(df) <- c("grp",
-    }}
+                       paste0("N.", substr(levels(v)[1], 1, 3)),
-
+                       paste0(nl, ".", substr(levels(v)[1], 1, 3)),
+                       paste0("N.", substr(levels(v)[2], 1, 3)),
+                       paste0(nl, ".", substr(levels(v)[2], 1, 3)),
+                       "OR",
+                       "pval",
+                       "ad.OR",
+                       "ad.pval")
+      }
+    }
     return(df)
   }

man/strobe_diff_bygroup.Rd

@@ -15,7 +15,7 @@ strobe_diff_bygroup(meas, var, group, adj, data, dec = 2)
 
 \item{data}{dataframe of data.}
 
-\item{dec}{decimals for results, standard is set to 2. Mean and sd is dec-1.}
+\item{dec}{decimals for results, standard is set to 2. Mean and sd is dec-1. pval has 3 decimals.}
 
 \item{groups}{groups to compare, as string.}
 }