KRRD Report 2018

Rheumatology Unit, Department of Internal Medicine, Al-Amiri Hospital
adeebaalherz@yahoo.com

Statistical Consultant, Advancement Consultant Solutions for Statistics (ACS)
admin@acs-kw.com

1. Overview

To find out whether comorbidity influence measures of RA activity. Significant number of patients in KRRD database have comorbidities (hypertension, DM, hyperlipidemia..etc). The presence of these comorbidities complicates the course of rheumatoid arthritis (RA). This study will shed the light on the relationship between comorbidity assessment with disease activity (DAS 28) and functional status (HAQ).

2. Method

the target sample is all patient enrolled into KRRD database from inception. We will use model called rheumatic dx comorbidity index (RDCI) and study the relation to DAS28 and HAQ. The RDCI, comorbidity counts, or by individual condition. Multivariate analysis model and Chi-Squaer test are conducted to assess this relationship. The odds of ever achieving at least low disease activity (DAS28 less than 3.2) will be examined using multivariate logistic regression

3. Statistical Analysis

This report is about visualising KRRD data into tables and figures. The statistical analysis of this report will cover the two main aspects:

1. Descriptive statistics (Frequancy tables, mean, standard deviation, 95% Confidence intervals, …, etc.)
2. Infrential statistics (t-test, ANOVA, Chi-Square, Regression, …, etc.)

3.1 Descriptive Table (Proposal for research) for first time visit

Summary descriptives table by groups of `DAS28.Group’

	DAS28 < 3.2 N=803	DAS28 >= 3.2 N=666	p.overall
Gender:			<0.001
female	448 (55.8%)	450 (67.6%)
male	355 (44.2%)	216 (32.4%)
AGE.years	52.2 (12.8)	52.8 (12.4)	0.387
DOD.years	11.6 (3.20)	11.7 (3.18)	0.431
ANA:			0.080
Negative	485 (75.1%)	380 (70.4%)
Positive	161 (24.9%)	160 (29.6%)
RF:			0.018
Negative	188 (25.5%)	123 (19.9%)
Positive	550 (74.5%)	495 (80.1%)
SICCA.Symptoms	108 (17.3%)	107 (19.1%)	0.451
Smoking	58 (10.7%)	52 (10.2%)	0.868
Current.Steroid	115 (15.3%)	177 (28.1%)	<0.001

Summary descriptives table by groups of `DAS28.Group’

	DAS28 < 3.2 N=803	DAS28 >= 3.2 N=666	p.overall	N
Gender: female	448 (55.8%)	450 (67.6%)	<0.001	1469
AGE.years	52.2 (12.8)	52.8 (12.4)	0.387	1453
DOD.years	11.6 (3.20)	11.7 (3.18)	0.431	1141
ANA: Positive	161 (24.9%)	160 (29.6%)	0.080	1186
RF: Positive	550 (74.5%)	495 (80.1%)	0.018	1356
SICCA.Symptoms: Yes	108 (17.3%)	107 (19.1%)	0.451	1184
Smoking	58 (10.7%)	52 (10.2%)	0.868	1052
Current.Steroid	115 (15.3%)	177 (28.1%)	<0.001	1383

3.1.1 Computing OR and HR for first time visit

Odds Ratio

For case control studies, it may be interesting to compute the Odds Ratio for each variable between cases and controls (DAS28 < 3.2 or DAS28 >= 3.2).

Note the use of fact.ratio argument to set an increment of 10 units for its OR. Also, to set the reference cathegory to “male” when displaying the OR set the ref.ratio argument.

## 
## --------Summary descriptives table by 'DAS28.Group'---------
## 
## ___________________________________________________________________________ 
##                 DAS28 < 3.2 DAS28 >= 3.2        OR        p-value p.overall 
##                    N=803       N=666                                        
## ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ 
## Gender:                                                            <0.001   
##     female         55.8%       67.6%           Ref.        Ref.             
##     male           44.2%       32.4%     0.61 [0.49;0.75] <0.001            
## AGE.years       52.2 (12.8) 52.8 (12.4)  1.00 [1.00;1.01]  0.388    0.387   
## DOD.years       11.6 (3.20) 11.7 (3.18)  1.01 [0.98;1.05]  0.431    0.431   
## ANA:                                                                0.080   
##     Negative       75.1%       70.4%           Ref.        Ref.             
##     Positive       24.9%       29.6%     1.27 [0.98;1.64]  0.070            
## RF:                                                                 0.018   
##     Negative       25.5%       19.9%           Ref.        Ref.             
##     Positive       74.5%       80.1%     1.37 [1.06;1.78]  0.015            
## SICCA.Symptoms     17.3%       19.1%     1.13 [0.84;1.52]  0.408    0.451   
## Smoking            10.7%       10.2%     0.95 [0.64;1.41]  0.791    0.868   
## Current.Steroid    15.3%       28.1%     2.16 [1.66;2.81] <0.001   <0.001   
## ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯

3.2 Descriptive Table (Proposal for research) for last time visit

Summary descriptives table by groups of `DAS28.Group’

	DAS28 < 3.2 N=1024	DAS28 >= 3.2 N=448	p.overall
Gender:			0.001
female	597 (58.3%)	302 (67.4%)
male	427 (41.7%)	146 (32.6%)
AGE.years	52.3 (12.7)	52.7 (12.4)	0.620
DOD.years	11.6 (3.25)	11.8 (3.06)	0.238
ANA:			<0.001
Negative	636 (77.1%)	229 (63.4%)
Positive	189 (22.9%)	132 (36.6%)
RF:			0.004
Negative	237 (25.1%)	74 (17.9%)
Positive	707 (74.9%)	340 (82.1%)
SICCA.Symptoms	153 (18.5%)	61 (17.0%)	0.590
Smoking	78 (10.9%)	33 (9.85%)	0.691
Current.Steroid	98 (10.2%)	85 (20.1%)	<0.001

Summary descriptives table by groups of `DAS28.Group’

	DAS28 < 3.2 N=1024	DAS28 >= 3.2 N=448	p.overall	N
Gender: female	597 (58.3%)	302 (67.4%)	0.001	1472
AGE.years	52.3 (12.7)	52.7 (12.4)	0.620	1456
DOD.years	11.6 (3.25)	11.8 (3.06)	0.238	1142
ANA: Positive	189 (22.9%)	132 (36.6%)	<0.001	1186
RF: Positive	707 (74.9%)	340 (82.1%)	0.004	1358
SICCA.Symptoms: Yes	153 (18.5%)	61 (17.0%)	0.590	1186
Smoking	78 (10.9%)	33 (9.85%)	0.691	1052
Current.Steroid	98 (10.2%)	85 (20.1%)	<0.001	1387

3.2.1 Computing OR and HR for last time visit

Odds Ratio

For case control studies, it may be interesting to compute the Odds Ratio for each variable between cases and controls (DAS28 < 3.2 or DAS28 >= 3.2).

Note the use of fact.ratio argument to set an increment of 10 units for its OR. Also, to set the reference cathegory to “male” when displaying the OR set the ref.ratio argument.

## 
## --------Summary descriptives table by 'DAS28.Group'---------
## 
## ___________________________________________________________________________ 
##                 DAS28 < 3.2 DAS28 >= 3.2        OR        p-value p.overall 
##                    N=803       N=666                                        
## ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ 
## Gender:                                                            <0.001   
##     female         55.8%       67.6%           Ref.        Ref.             
##     male           44.2%       32.4%     0.61 [0.49;0.75] <0.001            
## AGE.years       52.2 (12.8) 52.8 (12.4)  1.00 [1.00;1.01]  0.388    0.387   
## DOD.years       11.6 (3.20) 11.7 (3.18)  1.01 [0.98;1.05]  0.431    0.431   
## ANA:                                                                0.080   
##     Negative       75.1%       70.4%           Ref.        Ref.             
##     Positive       24.9%       29.6%     1.27 [0.98;1.64]  0.070            
## RF:                                                                 0.018   
##     Negative       25.5%       19.9%           Ref.        Ref.             
##     Positive       74.5%       80.1%     1.37 [1.06;1.78]  0.015            
## SICCA.Symptoms     17.3%       19.1%     1.13 [0.84;1.52]  0.408    0.451   
## Smoking            10.7%       10.2%     0.95 [0.64;1.41]  0.791    0.868   
## Current.Steroid    15.3%       28.1%     2.16 [1.66;2.81] <0.001   <0.001   
## ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯

3.3 Descriptive Table (Proposal for research) for all visits

Summary descriptives table by groups of `DAS28.Group’

	DAS28 < 3.2 N=5410	DAS28 >= 3.2 N=2433	p.overall
Gender:			<0.001
female	3056 (56.5%)	1587 (65.2%)
male	2354 (43.5%)	846 (34.8%)
AGE.years	52.9 (12.8)	53.8 (12.3)	0.003
DOD.years	11.6 (3.01)	11.7 (2.96)	0.070
ANA:			0.062
Negative	3661 (79.1%)	1589 (77.0%)
Positive	970 (20.9%)	475 (23.0%)
RF:			<0.001
Negative	1411 (28.1%)	465 (20.3%)
Positive	3612 (71.9%)	1831 (79.7%)
SICCA.Symptoms	745 (16.9%)	363 (18.1%)	0.260
Smoking	291 (8.74%)	154 (9.30%)	0.545
Current.Steroid	428 (8.23%)	456 (19.5%)	<0.001

Summary descriptives table by groups of `DAS28.Group’

	DAS28 < 3.2 N=5410	DAS28 >= 3.2 N=2433	p.overall	N
Gender: female	3056 (56.5%)	1587 (65.2%)	<0.001	7843
AGE.years	52.9 (12.8)	53.8 (12.3)	0.003	7798
DOD.years	11.6 (3.01)	11.7 (2.96)	0.070	5818
ANA: Positive	970 (20.9%)	475 (23.0%)	0.062	6695
RF: Positive	3612 (71.9%)	1831 (79.7%)	<0.001	7319
SICCA.Symptoms: Yes	745 (16.9%)	363 (18.1%)	0.260	6398
Smoking	291 (8.74%)	154 (9.30%)	0.545	4987
Current.Steroid	428 (8.23%)	456 (19.5%)	<0.001	7536

3.3.1 Computing OR and HR for all visits

Odds Ratio

For case control studies, it may be interesting to compute the Odds Ratio for each variable between cases and controls (DAS28 < 3.2 or DAS28 >= 3.2).

Note the use of fact.ratio argument to set an increment of 10 units for its OR. Also, to set the reference cathegory to “male” when displaying the OR set the ref.ratio argument.

## 
## --------Summary descriptives table by 'DAS28.Group'---------
## 
## ___________________________________________________________________________ 
##                 DAS28 < 3.2 DAS28 >= 3.2        OR        p-value p.overall 
##                    N=803       N=666                                        
## ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ 
## Gender:                                                            <0.001   
##     female         55.8%       67.6%           Ref.        Ref.             
##     male           44.2%       32.4%     0.61 [0.49;0.75] <0.001            
## AGE.years       52.2 (12.8) 52.8 (12.4)  1.00 [1.00;1.01]  0.388    0.387   
## DOD.years       11.6 (3.20) 11.7 (3.18)  1.01 [0.98;1.05]  0.431    0.431   
## ANA:                                                                0.080   
##     Negative       75.1%       70.4%           Ref.        Ref.             
##     Positive       24.9%       29.6%     1.27 [0.98;1.64]  0.070            
## RF:                                                                 0.018   
##     Negative       25.5%       19.9%           Ref.        Ref.             
##     Positive       74.5%       80.1%     1.37 [1.06;1.78]  0.015            
## SICCA.Symptoms     17.3%       19.1%     1.13 [0.84;1.52]  0.408    0.451   
## Smoking            10.7%       10.2%     0.95 [0.64;1.41]  0.791    0.868   
## Current.Steroid    15.3%       28.1%     2.16 [1.66;2.81] <0.001   <0.001   
## ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯

3.4.1 Comparison on DAS28-Groups for all visits with Comorbid factors

Summary descriptives table by groups of `krrd.date.DAS28.Group’

	DAS28 < 3.2 N=5410	DAS28 >= 3.2 N=2433	p.overall
krrd.date.MedCond.Hypertension	1088 (20.1%)	591 (24.3%)	<0.001
krrd.date.MedCond.Hyperlipidemia	601 (11.1%)	286 (11.8%)	0.425
krrd.date.MedCond.DM	1001 (18.5%)	578 (23.8%)	<0.001
krrd.date.MedCond.CAD	166 (3.07%)	67 (2.75%)	0.492
COPD	12 (0.22%)	9 (0.37%)	0.348
Cancer	8 (0.15%)	5 (0.21%)	0.557
Kidney	9 (0.17%)	7 (0.29%)	0.285
ILD	36 (0.67%)	23 (0.95%)	0.236
Como	1847 (34.1%)	952 (39.1%)	<0.001

3.4.2 Comparison on DAS28-Groups for first visit with Comorbid factors

Summary descriptives table by groups of `krrd.date.DAS28.Group’

	DAS28 < 3.2 N=801	DAS28 >= 3.2 N=662	p.overall
krrd.date.MedCond.Hypertension	159 (19.9%)	157 (23.7%)	0.085
krrd.date.MedCond.Hyperlipidemia	99 (12.4%)	86 (13.0%)	0.777
krrd.date.MedCond.DM	163 (20.3%)	141 (21.3%)	0.703
krrd.date.MedCond.CAD	29 (3.62%)	26 (3.93%)	0.866
COPD	0 (0.00%)	4 (0.60%)	0.042
Cancer	2 (0.25%)	4 (0.60%)	0.419
Kidney	3 (0.37%)	1 (0.15%)	0.631
ILD	6 (0.75%)	6 (0.91%)	0.967
Como	269 (33.6%)	252 (38.1%)	0.084

3.5.1 Comparison between Comorbid levels for all visits

Summary descriptives table by groups of `Como’

	No N=5092	yes N=2801	p.overall
krrd.date.AGE.years	49.0 (12.0)	60.9 (9.93)	0.000
krrd.date.DOD.years	11.4 (2.92)	12.1 (3.09)	<0.001
krrd.date.Gender:			<0.001
female	2767 (54.3%)	1901 (67.9%)
male	2325 (45.7%)	900 (32.1%)
krrd.date.RF:			<0.001
Negative	1104 (23.7%)	772 (28.9%)
Positive	3550 (76.3%)	1902 (71.1%)
krrd.date.ANA:			0.015
Negative	3357 (79.4%)	1899 (76.8%)
Positive	872 (20.6%)	573 (23.2%)
krrd.date.SICCA.Symptoms	571 (14.7%)	539 (21.3%)	<0.001
krrd.date.Smoking	315 (10.3%)	134 (6.95%)	<0.001
krrd.date.Current.Steroid	562 (11.5%)	326 (12.2%)	0.450
krrd.date.VAS	1.35 (2.22)	1.99 (2.60)	<0.001
krrd.date.CDAI	6.06 (9.72)	7.81 (11.0)	<0.001
krrd.date.Uric.acid	267 (99.0)	296 (154)	<0.001
krrd.date.DAS28	2.73 (1.25)	2.80 (1.28)	0.018

3.5.2 Comparison between Comorbid levels for first visit

Summary descriptives table by groups of `Como’

	No N=989	yes N=522	p.overall
krrd.date.AGE.years	48.5 (11.8)	59.8 (10.5)	<0.001
krrd.date.DOD.years	11.6 (3.13)	11.8 (3.32)	0.297
krrd.date.Gender:			<0.001
female	558 (56.4%)	359 (68.8%)
male	431 (43.6%)	163 (31.2%)
krrd.date.RF:			0.746
Negative	202 (23.2%)	109 (22.3%)
Positive	668 (76.8%)	380 (77.7%)
krrd.date.ANA:			0.727
Negative	562 (73.5%)	306 (72.3%)
Positive	203 (26.5%)	117 (27.7%)
krrd.date.SICCA.Symptoms	115 (15.5%)	100 (22.4%)	0.004
krrd.date.Smoking	71 (10.7%)	43 (11.0%)	0.957
krrd.date.Current.Steroid	188 (21.0%)	107 (21.9%)	0.740
krrd.date.VAS	2.16 (2.67)	2.63 (2.76)	0.001
krrd.date.CDAI	9.74 (12.2)	10.7 (12.7)	0.139
krrd.date.Uric.acid	280 (170)	307 (270)	0.197
krrd.date.DAS28	3.18 (1.37)	3.30 (1.30)	0.097

4. Demographics Profile (Baseline Patients)

3.1 Gender

The following table and figure shows the percentages of KRRD gender distribution:

3.2 Hospital

The following table and figure shows the percentages of KRRD Hospital distribution:

3.3 Rheumatologist

The following table and figure shows the percentages of KRRD Rheumatologist distribution:

3.4 Nationality

The following table and figure shows the percentages of KRRD Nationality distribution:

3.5 Governorate

The following table and figure shows the percentages of KRRD Governorate distribution:

3.6 Governorate

The following table and figure shows the percentages of KRRD Governorate distribution:

Including Plots

You can also embed plots, for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.