diff --git a/README.md b/README.md index a9bca09d..d603a1c0 100644 --- a/README.md +++ b/README.md @@ -6,12 +6,14 @@ Status](https://travis-ci.com/arcaldwell49/SimplyAgree.svg?branch=master)](https [![Codecov test coverage](https://codecov.io/gh/arcaldwell49/SimplyAgree/branch/master/graph/badge.svg)](https://codecov.io/gh/arcaldwell49/SimplyAgree?branch=master) -**This Package is still in development and has only recently implemented -basic unit tests. USE WITH CAUTION** - -This is a R package for calculating absolute agreement and estimating -the required sample size for a study attempting to estimate absolute -agreement. +`SimplyAgree` is an R package, and [jamovi](https://www.jamovi.org/) +module, created to make agreement and reliability analyses easier for +the average researcher. The functions within this package include simple +tests of agreement (`agree_test`), agreement analysis for nested +(`agree_nest`) and replicate data (`agree_reps`), and provide robust +analyses of reliability (`reli_stats`). In addition, this package +contains a set of functions to help when planning studies looking to +assess measurement agreement (`blandPowerCurve`). ## Installing SimplyAgree @@ -35,12 +37,10 @@ quantitative measurements: Exact test procedure and sample size calculation. *Statistics in Biopharmaceutical Research*, 1-8. -Parker, R. A., Weir, C. J., Rubio, N., Rabinovich, R., Pinnock, H., -Hanley, J., McLoughan, L., Drost, E.M., Mantoani, L.C., MacNee, W., & -McKinstry, B. (2016). Application of mixed effects limits of agreement -in the presence of multiple sources of variability: exemplar from the -comparison of several devices to measure respiratory rate in COPD -patients. Plos one, 11(12), e0168321. +Parker, R. A., et al (2016). Application of mixed effects limits of +agreement in the presence of multiple sources of variability: exemplar +from the comparison of several devices to measure respiratory rate in +COPD patients. Plos one, 11(12), e0168321. Zou, G. Y. (2013). Confidence interval estimation for the Bland–Altman @@ -53,21 +53,19 @@ intraclass correlation coefficient and the SEM. *The Journal of Strength & Conditioning Research*, 19(1), 231-240. -Lu, Meng-Jie, Zhong, Wei-Hua, Liu, Yu-Xiu, Miao, Hua-Zhang, Li, -Yong-Chang and Ji, Mu-Huo. “Sample Size for Assessing Agreement between +Lu, Meng-Jie, et al (2016). “Sample Size for Assessing Agreement between Two Methods of Measurement by Bland−Altman Method” *The International -Journal of Biostatistics*, vol. 12, no. 2, 2016. +Journal of Biostatistics*, 12(2), King, TS and Chinchilli, VM. (2001). A generalized concordance correlation coefficient for continuous and categorical data. *Statistics in Medicine*, 20, 2131:2147. -King, TS; Chinchilli, VM; Carrasco, JL. (2007). A repeated measures +King, TS, Chinchilli, VM, and Carrasco, JL. (2007). A repeated measures concordance correlation coefficient. *Statistics in Medicine*, 26, 3095:3113. -Carrasco, JL; Phillips, BR; Puig-Martinez, J; King, TS; Chinchilli, VM. -(2013). Estimation of the concordance correlation coefficient for -repeated measures using SAS and R. *Computer Methods and Programs in -Biomedicine*, 109, 293-304. +Carrasco, JL, et al. (2013). Estimation of the concordance correlation +coefficient for repeated measures using SAS and R. *Computer Methods and +Programs in Biomedicine*, 109, 293-304. diff --git a/docs/articles/intro_vignette.html b/docs/articles/intro_vignette.html index 39100717..e99e123c 100644 --- a/docs/articles/intro_vignette.html +++ b/docs/articles/intro_vignette.html @@ -241,7 +241,7 @@ 

 
 plot(a3, type = 2)
-

### Calcuations for agree_reps & agree_nest

+

### Calculations for agree_reps & agree_nest

All the calculations for the limits of agreement in these two functions can be found in the article by Zou (2011).

In addition, the CCC calculations are derived from the cccUst function of the cccrm R package. The mathematics for this CCC calculation can be found in the work of King, Chinchilli, and Carrasco (2007) and Carrasco, King, and Chinchilli (2009).

diff --git a/docs/articles/reanalysis.html b/docs/articles/reanalysis.html index 60e4de2d..4f0f37c3 100644 --- a/docs/articles/reanalysis.html +++ b/docs/articles/reanalysis.html @@ -114,7 +114,7 @@

Rectal Temperature

-

Now, based on the typical thresholds (0.8 can be considered a “good” CCC), neither Trec as a raw value or a change score (Trec delta) is within acceptable degrees of agreement. As I will address later, this may not be an accurate and there are sometimes where there is a low CCC but the expected differences between conditions is acceptable (limits of agreemnt).

+

Now, based on the typical thresholds (0.8 can be considered a “good” CCC), neither Trec as a raw value or a change score (Trec delta) is within acceptable degrees of agreement. As I will address later, this may not be an accurate and there are sometimes where there is a low CCC but the expected differences between conditions is acceptable (limits of agreement).

 ccc_rec.post = cccrm::cccUst(dataset = df_temps,
                             ry = "trec_post",
diff --git a/docs/index.html b/docs/index.html
index f43aba66..e8056e06 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -12,7 +12,7 @@
 
 
 
-
+
 
@@ -39,9 +39,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -119,14 +118,13 @@
 

   

     

-    
Simple Test of Agreement in jamovi

+    
Simple Agreement Analysis in jamovi

     
     
     

 
     

-    
Simple Test of Agreement in jamovi

-
Simple Test of Agreement in jamovi

+    
Simple Agreement Analysis in jamovi

     

 
     
jmvagree(
@@ -139,18 +137,6 @@ 
Simple Test of Agreement in jamovi

   CCC = TRUE,
   plotbland = FALSE,
   plotcon = FALSE
-)
-
-jmvagree(
-  data,
-  method1,
-  method2,
-  ciWidth = 0.95,
-  agreeWidth = 0.95,
-  testValue = 2,
-  CCC = TRUE,
-  plotbland = FALSE,
-  plotcon = FALSE
 )

 
     
Arguments

@@ -158,15 +144,15 @@ 
Arg
     
     
       data
-      
.

+      
Data

     
     
       method1
-      
.

+      
Name of column containing 1st Vector of data

     
     
       method2
-      
.

+      
Name of column containing Vector of data

     
     
       ciWidth
@@ -208,18 +194,6 @@ 
Value

 
 
 
-
Tables can be converted to data frames with asDF or as.data.frame. For example:

-
results$blandtab$asDF

-
as.data.frame(results$blandtab)

-
A results object containing:

-
-
-
-
-
-
results$texta preformatted
results$blandtaba table
results$ccctaba table
results$plotbaan image
results$plotconan image

-
-
 
Tables can be converted to data frames with asDF or as.data.frame. For example:

 
results$blandtab$asDF

 
as.data.frame(results$blandtab)

diff --git a/docs/reference/jmvagreemulti.html b/docs/reference/jmvagreemulti.html
index 59d56942..123a30e7 100644
--- a/docs/reference/jmvagreemulti.html
+++ b/docs/reference/jmvagreemulti.html
@@ -6,7 +6,7 @@
 
 
 
-Agreement Analysis for Nested or Replicate Data — jmvagreemulti • SimplyAgree
+Nested/Replicate Data Agreement Analysis in jamovi — jmvagreemulti • SimplyAgree
 
 
 
@@ -39,8 +39,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -118,13 +118,13 @@
 

   

     

-    
Agreement Analysis for Nested or Replicate Data

+    
Nested/Replicate Data Agreement Analysis in jamovi

     
     
     

 
     

-    
Agreement Analysis for Nested or Replicate Data

+    
Nested/Replicate Data Agreement Analysis in jamovi

     

 
     
jmvagreemulti(
diff --git a/docs/reference/jmvreli.html b/docs/reference/jmvreli.html
index 02858309..b5e59591 100644
--- a/docs/reference/jmvreli.html
+++ b/docs/reference/jmvreli.html
@@ -6,7 +6,7 @@
 
 
 
-Reliability Analysis — jmvreli • SimplyAgree
+Reliability Analysis in jamovi — jmvreli • SimplyAgree
 
 
 
@@ -39,8 +39,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -118,13 +118,13 @@
 

   

     

-    
Reliability Analysis

+    
Reliability Analysis in jamovi

     
     
     

 
     

-    
Reliability Analysis

+    
Reliability Analysis in jamovi

     

 
     
jmvreli(data, vars, ciWidth = 0.95, desc = FALSE, plots = FALSE)

diff --git a/docs/reference/simple_agree-methods.html b/docs/reference/simple_agree-methods.html
index 8e67718e..e60b852f 100644
--- a/docs/reference/simple_agree-methods.html
+++ b/docs/reference/simple_agree-methods.html
@@ -138,7 +138,7 @@ 
Arg
     
     
       x
-      
object of class simple_agree as returned from a fucntion starting with 'agree'

+      
object of class simple_agree as returned from a function starting with 'agree'

     
     
       ...
diff --git a/docs/reference/temps.html b/docs/reference/temps.html
index 5f663c8b..ee22d72a 100644
--- a/docs/reference/temps.html
+++ b/docs/reference/temps.html
@@ -40,7 +40,7 @@
 
 
 
-
 
 
@@ -125,7 +125,7 @@ 
temps

     

 
     

-    
A dataset from a study on the reliability of human body temperature at diferents times of day before and after exercise.

+    
A dataset from a study on the reliability of human body temperature at different times of day before and after exercise.

 
A fake data set of a agreement study where both measures have replicates.

     

 
@@ -156,7 +156,7 @@ 
FormatAn object of class tbl_df (inherits from tbl, data.frame) with 30 rows and 6 columns.

 
A data frame with 20 rows with 3 variables

   
id
Subject identifier

-  
X
X measurment

+  
X
X measurement

   
Y
Y measurement

 
 
@@ -165,7 +165,7 @@ 
FormatSource

 
-    
https://doi.org/10.1249/MSS.0000000000002575

+    
Ravanelli N, Jay O. The Change in Core Temperature and Sweating Response during Exercise Are Unaffected by Time of Day within the Wake Period. Med Sci Sports Exerc. 2020 Dec 1. doi: 10.1249/MSS.0000000000002575. Epub ahead of print. PMID: 33273272.