20240520 - fix blandr error

05-Reliability.Rmd

@@ -1164,8 +1164,8 @@ The Bland-Altman plot was created using the `blandr` package [@R-blandr].\index{
 
 ```{r}
 BAstats <- blandr.statistics(
-  method1 = mydata$time1,
-  method2 = mydata$time2)
+  mydata$time1, #method1
+  mydata$time2) #method2
 BAplotlimits <- blandr.plot.limits(BAstats)
 ```
 
@@ -1961,16 +1961,16 @@ cor.test(x = mydata$time1, y = mydata$time2)
 ```{r}
 qnorm(.975) * sd(
   blandr.statistics(
-    method1 = mydata$time1,
-    method2 = mydata$time2)$differences, na.rm = TRUE)
+    mydata$time1,
+    mydata$time2)$differences, na.rm = TRUE)
 ```
 
 #### Bias {#noError-bias}
 
 ```{r}
 blandr.statistics(
-  method1 = mydata$time1,
-  method2 = mydata$time2)$bias
+  mydata$time1,
+  mydata$time2)$bias
 ```
 
 ### Add within-person random error {#withinPersonRandomError-example}
@@ -2022,17 +2022,17 @@ cor.test(x = mydata$time1, y = mydata$time2)
 ```{r}
 qnorm(.975) * sd(
   blandr.statistics(
-    method1 = mydata$time1,
-    method2 = mydata$time2)$differences,
+    mydata$time1,
+    mydata$time2)$differences,
   na.rm = TRUE)
 ```
 
 #### Bias {#withinPersonRandomError-bias}
 
 ```{r}
 blandr.statistics(
-  method1 = mydata$time1,
-  method2 = mydata$time2)$bias
+  mydata$time1,
+  mydata$time2)$bias
 ```
 
 #### Findings {#withinPersonRandomError-findings}
@@ -2091,17 +2091,17 @@ cor.test(x = mydata$time1, y = mydata$time2)
 ```{r}
 qnorm(.975) * sd(
   blandr.statistics(
-    method1 = mydata$time1,
-    method2 = mydata$time2)$differences,
+    mydata$time1,
+    mydata$time2)$differences,
   na.rm = TRUE)
 ```
 
 #### Bias {#withinPersonSystematicError-bias}
 
 ```{r}
 blandr.statistics(
-  method1 = mydata$time1,
-  method2 = mydata$time2)$bias
+  mydata$time1,
+  mydata$time2)$bias
 ```
 
 #### Findings {#withinPersonSystematicError-findings}
@@ -2158,17 +2158,17 @@ cor.test(x = mydata$time1, y = mydata$time2)
 ```{r}
 qnorm(.975) * sd(
   blandr.statistics(
-    method1 = mydata$time1,
-    method2 = mydata$time2)$differences,
+    mydata$time1,
+    mydata$time2)$differences,
   na.rm = TRUE)
 ```
 
 #### Bias {#betweenPersonRandomError-bias}
 
 ```{r}
 blandr.statistics(
-  method1 = mydata$time1,
-  method2 = mydata$time2)$bias
+  mydata$time1,
+  mydata$time2)$bias
 ```
 
 #### Findings {#betweenPersonRandomError-findings}
@@ -2224,17 +2224,17 @@ cor.test(
 ```{r}
 qnorm(.975) * sd(
   blandr.statistics(
-    method1 = mydata$time1,
-    method2 = mydata$time2)$differences,
+    mydata$time1,
+    mydata$time2)$differences,
   na.rm = TRUE)
 ```
 
 #### Bias {#betweenPersonSystematicError-bias}
 
 ```{r}
 blandr.statistics(
-  method1 = mydata$time1,
-  method2 = mydata$time2)$bias
+  mydata$time1,
+  mydata$time2)$bias
 ```
 
 #### Findings {#betweenPersonSystematicError-findings}
@@ -2292,16 +2292,16 @@ cor.test(x = mydata$time1,
 ```{r}
 qnorm(.975) * sd(
   blandr.statistics(
-    method1 = mydata$time1,
-    method2 = mydata$time2)$differences, na.rm = TRUE)
+    mydata$time1,
+    mydata$time2)$differences, na.rm = TRUE)
 ```
 
 #### Bias {#constantVariance-bias}
 
 ```{r}
 blandr.statistics(
-  method1 = mydata$time1,
-  method2 = mydata$time2)$bias
+  mydata$time1,
+  mydata$time2)$bias
 ```
 
 #### Findings {#constantVariance-findings}
@@ -2717,7 +2717,7 @@ cor(cnlsy[,c("bpi_antisocialT1Sum","bpi_antisocialT2Sum")], use = "pairwise.comp
 # Repeatability -----------------------------------------------------------
 
 # Bland-Altman Plot
-BAstats_ex <- blandr.statistics(method1 = cnlsy$bpi_antisocialT1Sum, method2 = cnlsy$bpi_antisocialT2Sum)
+BAstats_ex <- blandr.statistics(cnlsy$bpi_antisocialT1Sum, cnlsy$bpi_antisocialT2Sum)
 BAplotlimits_ex <- blandr.plot.limits(BAstats_ex)
 
 blandr.plot.rplot(BAstats_ex, plot.limits = BAplotlimits_ex, annotate = TRUE, method1name = "BPI_T1", method2name = "BPI_T2")