General options

Packages

## [1] "/home/sergiouribe/Insync/sergio.uribe@gmail.com/Google Drive/Research Drive/2021-FAIRness-Dental-Research-Data/fairness-data-analysis-2021/analysis-fairness-dental-research"

Datasets

Select some columns for the analysis

Remove the open_data_all

Store local raw copy

add index number

##  [1] "id"                     "doi_publication"        "title"                 
##  [4] "journalTitle"           "pubYear"                "pubType"               
##  [7] "isOpenAccess"           "citedByCount"           "is_open_data"          
## [10] "open_data_category"     "is_open_code"           "true_open_data"        
## [13] "study_type"             "dataset_type"           "FAIR_level"            
## [16] "FAIRness"               "Findability"            "Accesibility"          
## [19] "Interoperability"       "Reusability"            "Findability_level"     
## [22] "Accesibility_level"     "Interoperability_level" "Reusability_level"     
## [25] "FsF_F1_01D"             "FsF_F1_02D"             "FsF_F2_01M"            
## [28] "FsF_F3_01M"             "FsF_F4_01M"             "FsF_A1_01M"            
## [31] "FsF_A1_03D"             "FsF_A1_02M"             "FsF_I1_01M"            
## [34] "FsF_I1_02M"             "FsF_I3_01M"             "FsF_R1_01MD"           
## [37] "FsF_R1.1_01M"           "FsF_R1.2_01M"           "FsF_R1.3_01M"          
## [40] "FsF_R1.3_02D"

Recoding, relabelling, relevelling and cleaning

Replace all the TRUE and FALSE for YES/NO

Labelling variables

Recode variables

Change open access values

Relevel variables

EDA

Check the discrete variables

For the open data papers

##        id       doi_publication       title           journalTitle      
##  Min.   :   1   Length:7549        Length:7549        Length:7549       
##  1st Qu.:1888   Class :character   Class :character   Class :character  
##  Median :3775   Mode  :character   Mode  :character   Mode  :character  
##  Mean   :3775                                                           
##  3rd Qu.:5662                                                           
##  Max.   :7549                                                           
##                                                                         
##     pubYear       pubType          isOpenAccess        citedByCount    
##  Min.   :2016   Length:7549        Length:7549        Min.   :  0.000  
##  1st Qu.:2018   Class :character   Class :character   1st Qu.:  0.000  
##  Median :2020   Mode  :character   Mode  :character   Median :  1.000  
##  Mean   :2019                                         Mean   :  3.034  
##  3rd Qu.:2021                                         3rd Qu.:  3.000  
##  Max.   :2022                                         Max.   :812.000  
##                                                                        
##  open_data_category  study_type        dataset_type          FAIRness    
##  Length:7549        Length:7549        Length:7549        Min.   : 4.00  
##  Class :character   Class :character   Class :character   1st Qu.: 4.00  
##  Mode  :character   Mode  :character   Mode  :character   Median : 9.00  
##                                                           Mean   :32.55  
##                                                           3rd Qu.:70.00  
##                                                           Max.   :79.00  
##                                                           NA's   :7437   
##   Findability     Accesibility   Interoperability  Reusability   
##  Min.   :1.000   Min.   :0.000   Min.   :0.00     Min.   :0.000  
##  1st Qu.:1.000   1st Qu.:0.000   1st Qu.:0.00     1st Qu.:0.000  
##  Median :1.250   Median :0.500   Median :0.00     Median :0.500  
##  Mean   :3.438   Mean   :0.951   Mean   :1.08     Mean   :2.402  
##  3rd Qu.:7.000   3rd Qu.:2.000   3rd Qu.:3.00     3rd Qu.:5.000  
##  Max.   :7.000   Max.   :3.000   Max.   :3.00     Max.   :6.000  
##  NA's   :7437    NA's   :7437    NA's   :7437     NA's   :7437   
##    FsF_F1_01D     FsF_F1_02D      FsF_F2_01M      FsF_F3_01M      FsF_F4_01M   
##  Min.   :3      Min.   :0.000   Min.   :0.000   Min.   :0.000   Min.   :0.000  
##  1st Qu.:3      1st Qu.:0.000   1st Qu.:0.000   1st Qu.:0.000   1st Qu.:0.000  
##  Median :3      Median :0.000   Median :0.500   Median :0.000   Median :0.000  
##  Mean   :3      Mean   :1.241   Mean   :1.295   Mean   :1.018   Mean   :1.366  
##  3rd Qu.:3      3rd Qu.:3.000   3rd Qu.:3.000   3rd Qu.:3.000   3rd Qu.:3.000  
##  Max.   :3      Max.   :3.000   Max.   :3.000   Max.   :3.000   Max.   :3.000  
##  NA's   :7437   NA's   :7437    NA's   :7437    NA's   :7437    NA's   :7437   
##    FsF_A1_01M      FsF_A1_03D      FsF_A1_02M     FsF_I1_01M      FsF_I1_02M   
##  Min.   :0.000   Min.   :0.000   Min.   :0.0    Min.   :0.000   Min.   :0.000  
##  1st Qu.:0.000   1st Qu.:0.000   1st Qu.:0.0    1st Qu.:0.000   1st Qu.:0.000  
##  Median :0.000   Median :0.000   Median :1.5    Median :0.000   Median :0.000  
##  Mean   :0.321   Mean   :1.018   Mean   :1.5    Mean   :1.214   Mean   :0.393  
##  3rd Qu.:0.000   3rd Qu.:3.000   3rd Qu.:3.0    3rd Qu.:3.000   3rd Qu.:1.000  
##  Max.   :3.000   Max.   :3.000   Max.   :3.0    Max.   :3.000   Max.   :1.000  
##  NA's   :7437    NA's   :7437    NA's   :7437   NA's   :7437    NA's   :7437   
##    FsF_I3_01M     FsF_R1_01MD     FsF_R1.1_01M    FsF_R1.2_01M   FsF_R1.3_01M  
##  Min.   :0.000   Min.   :0.000   Min.   :0.000   Min.   :0      Min.   :0.000  
##  1st Qu.:0.000   1st Qu.:0.000   1st Qu.:0.000   1st Qu.:0      1st Qu.:0.000  
##  Median :0.000   Median :0.000   Median :0.000   Median :1      Median :0.000  
##  Mean   :0.938   Mean   :0.804   Mean   :1.214   Mean   :1      Mean   :1.143  
##  3rd Qu.:3.000   3rd Qu.:2.000   3rd Qu.:3.000   3rd Qu.:2      3rd Qu.:3.000  
##  Max.   :3.000   Max.   :2.000   Max.   :3.000   Max.   :2      Max.   :3.000  
##  NA's   :7437    NA's   :7437    NA's   :7437    NA's   :7437   NA's   :7437   
##   FsF_R1.3_02D   is_open_data       is_open_code       true_open_data    
##  Min.   :0.000   Length:7549        Length:7549        Length:7549       
##  1st Qu.:0.000   Class :character   Class :character   Class :character  
##  Median :0.000   Mode  :character   Mode  :character   Mode  :character  
##  Mean   :0.732                                                           
##  3rd Qu.:2.000                                                           
##  Max.   :3.000                                                           
##  NA's   :7437                                                            
##       FAIR_level    Findability_level  Accesibility_level
##  incomplete:   0   incomplete:   0    incomplete:  56    
##  initial   :  67   initial   :  64    initial   :  14    
##  moderate  :  21   moderate  :  10    moderate  :  34    
##  advanced  :  24   advanced  :  38    advanced  :   8    
##  NA's      :7437   NA's      :7437    NA's      :7437    
##                                                          
##                                                          
##  Interoperability_level  Reusability_level
##  incomplete:  64        incomplete:  56   
##  initial   :  13        initial   :  16   
##  moderate  :  35        moderate  :  17   
##  advanced  :   0        advanced  :  23   
##  NA's      :7437        NA's      :7437   
##                                           
##

all data

All articles

## # A tibble: 10 × 3
## # Groups:   journalTitle [10]
##    journalTitle                     No   Yes
##    <fct>                         <int> <int>
##  1 Other                          2483    25
##  2 BMC Oral Health                1724    67
##  3 Med Oral Patol Oral Cir Bucal   639     2
##  4 J Appl Oral Sci                 483     2
##  5 J Indian Prosthodont Soc        424    NA
##  6 Clin Exp Dent Res               387     4
##  7 Dental Press J Orthod           351    NA
##  8 Int J Implant Dent              350     5
##  9 Clin Oral Investig              343    NA
## 10 Prog Orthod                     253     7

Articles with data

##  isOpenAccess   No Yes Total
##            No  494   6   500
##           Yes 6855 194  7049
##         Total 7349 200  7549

## # A tibble: 8 × 2
## # Groups:   journalTitle [8]
##   journalTitle           n
##   <fct>              <int>
## 1 BMC Oral Health       67
## 2 Other                 18
## 3 Prog Orthod            7
## 4 Int J Implant Dent     5
## 5 Int J Oral Sci         5
## 6 Clin Exp Dent Res      4
## 7 J Clin Periodontol     3
## 8 J Dent Res             3

General

How many papers do we have?

## [1] 7541

How many are open access and how many are not?

Total papers

## [1] 7549   40

By open access status

##  isOpenAccess    n percent
##            No  500    6.6%
##           Yes 7049   93.4%
##         Total 7549       -

How many have open data according to the package?

##  isOpenAccess    n percent
##            No  500    6.6%
##           Yes 7049   93.4%
##         Total 7549       -

Cross tabulation open access vs open data

##  isOpenAccess  No Yes Total
##            No 494   6   500
##         Total 494   6   500

Open data vs true open data in open access

##  true_open_data   No Yes
##              No 6855  85
##             Yes    0 109

Check with https://www.medcalc.org/calc/diagnostic_test.php

any trend about open data by year?

Hoy many journals?

## # A tibble: 2 × 2
##   isOpenAccess count
##   <chr>        <int>
## 1 No              99
## 2 Yes             76

how many journal open access y non open access

Characteristic	No, N = 500¹	Yes, N = 7,049¹
Journal
BMC Oral Health	1 (0.2%)	1,790 (25%)
Med Oral Patol Oral Cir Bucal	0 (0%)	641 (9.1%)
J Appl Oral Sci	0 (0%)	485 (6.9%)
J Indian Prosthodont Soc	1 (0.2%)	423 (6.0%)
Clin Exp Dent Res	0 (0%)	391 (5.5%)
Int J Implant Dent	0 (0%)	355 (5.0%)
Dental Press J Orthod	0 (0%)	351 (5.0%)
Clin Oral Investig	19 (3.8%)	324 (4.6%)
Prog Orthod	0 (0%)	260 (3.7%)
Int J Oral Sci	0 (0%)	203 (2.9%)
Head Face Med	0 (0%)	196 (2.8%)
Br Dent J	6 (1.2%)	151 (2.1%)
Eur Endod J	0 (0%)	148 (2.1%)
J Craniofac Surg	41 (8.2%)	97 (1.4%)
Oral Dis	12 (2.4%)	75 (1.1%)
J Dent Educ	7 (1.4%)	74 (1.0%)
J Dent Res	10 (2.0%)	70 (1.0%)
Br J Oral Maxillofac Surg	11 (2.2%)	61 (0.9%)
J Clin Periodontol	9 (1.8%)	62 (0.9%)
J Oral Rehabil	9 (1.8%)	54 (0.8%)
J Oral Maxillofac Surg	19 (3.8%)	38 (0.5%)
Eur Arch Paediatr Dent	3 (0.6%)	52 (0.7%)
Odontology	4 (0.8%)	42 (0.6%)
Clin Oral Implants Res	4 (0.8%)	41 (0.6%)
Evid Based Dent	4 (0.8%)	41 (0.6%)
Clin Implant Dent Relat Res	5 (1.0%)	32 (0.5%)
J Orofac Orthop	1 (0.2%)	34 (0.5%)
Oral Maxillofac Surg	7 (1.4%)	28 (0.4%)
J Am Dent Assoc	3 (0.6%)	31 (0.4%)
Int Dent J	3 (0.6%)	28 (0.4%)
J Endod	18 (3.6%)	13 (0.2%)
J Periodontal Res	4 (0.8%)	27 (0.4%)
Cleft Palate Craniofac J	8 (1.6%)	22 (0.3%)
Eur J Dent Educ	4 (0.8%)	26 (0.4%)
Eur J Oral Sci	2 (0.4%)	27 (0.4%)
Int J Dent Hyg	0 (0%)	29 (0.4%)
JDR Clin Trans Res	3 (0.6%)	24 (0.3%)
Oral Surg Oral Med Oral Pathol Oral Radiol	16 (3.2%)	11 (0.2%)
J Periodontol	4 (0.8%)	20 (0.3%)
Community Dent Oral Epidemiol	2 (0.4%)	21 (0.3%)
Eur J Orthod	3 (0.6%)	20 (0.3%)
Am J Orthod Dentofacial Orthop	8 (1.6%)	14 (0.2%)
Int J Oral Maxillofac Surg	15 (3.0%)	7 (<0.1%)
J Dent	6 (1.2%)	15 (0.2%)
Periodontol 2000	1 (0.2%)	20 (0.3%)
J Orthod	2 (0.4%)	18 (0.3%)
Arch Oral Biol	15 (3.0%)	3 (<0.1%)
Int J Paediatr Dent	2 (0.4%)	14 (0.2%)
J Oral Pathol Med	5 (1.0%)	11 (0.2%)
Int Endod J	3 (0.6%)	12 (0.2%)
J Prosthet Dent	10 (2.0%)	5 (<0.1%)
Mol Oral Microbiol	2 (0.4%)	12 (0.2%)
Orthod Craniofac Res	5 (1.0%)	9 (0.1%)
J Prosthodont	5 (1.0%)	8 (0.1%)
Spec Care Dentist	2 (0.4%)	11 (0.2%)
J Stomatol Oral Maxillofac Surg	6 (1.2%)	6 (<0.1%)
Dentomaxillofac Radiol	4 (0.8%)	7 (<0.1%)
Pediatr Dent	11 (2.2%)	0 (0%)
Gerodontology	1 (0.2%)	9 (0.1%)
Dent Mater	2 (0.4%)	7 (<0.1%)
Dent Mater J	9 (1.8%)	0 (0%)
J Craniomaxillofac Surg	6 (1.2%)	3 (<0.1%)
J Evid Based Dent Pract	5 (1.0%)	4 (<0.1%)
Acta Odontol Scand	7 (1.4%)	1 (<0.1%)
Aust Dent J	4 (0.8%)	4 (<0.1%)
Facial Plast Surg	6 (1.2%)	2 (<0.1%)
J Contemp Dent Pract	7 (1.4%)	0 (0%)
J World Fed Orthod	0 (0%)	7 (<0.1%)
Dent Traumatol	2 (0.4%)	4 (<0.1%)
Int J Periodontics Restorative Dent	6 (1.2%)	0 (0%)
J Esthet Restor Dent	2 (0.4%)	4 (<0.1%)
Am J Dent	5 (1.0%)	0 (0%)
Braz Oral Res	5 (1.0%)	0 (0%)
Int J Prosthodont	5 (1.0%)	0 (0%)
J Oral Implantol	5 (1.0%)	0 (0%)
J Oral Sci	5 (1.0%)	0 (0%)
J Public Health Dent	1 (0.2%)	4 (<0.1%)
Oral Health Prev Dent	5 (1.0%)	0 (0%)
Angle Orthod	4 (0.8%)	0 (0%)
Aust Endod J	2 (0.4%)	2 (<0.1%)
Compend Contin Educ Dent	4 (0.8%)	0 (0%)
Cranio	4 (0.8%)	0 (0%)
J Prosthodont Res	4 (0.8%)	0 (0%)
Oral Maxillofac Surg Clin North Am	2 (0.4%)	2 (<0.1%)
Braz Dent J	3 (0.6%)	0 (0%)
Dent Med Probl	3 (0.6%)	0 (0%)
Eur J Paediatr Dent	3 (0.6%)	0 (0%)
Indian J Dent Res	3 (0.6%)	0 (0%)
Int J Oral Maxillofac Implants	3 (0.6%)	0 (0%)
J Adhes Dent	3 (0.6%)	0 (0%)
J Clin Pediatr Dent	3 (0.6%)	0 (0%)
Anesth Prog	1 (0.2%)	1 (<0.1%)
Caries Res	2 (0.4%)	0 (0%)
Dent Clin North Am	1 (0.2%)	1 (<0.1%)
Gen Dent	2 (0.4%)	0 (0%)
Hua Xi Kou Qiang Yi Xue Za Zhi	2 (0.4%)	0 (0%)
Int J Esthet Dent	2 (0.4%)	0 (0%)
J Clin Orthod	2 (0.4%)	0 (0%)
J Indian Soc Pedod Prev Dent	2 (0.4%)	0 (0%)
J Oral Facial Pain Headache	1 (0.2%)	1 (<0.1%)
J Vet Dent	1 (0.2%)	1 (<0.1%)
Swiss Dent J	2 (0.4%)	0 (0%)
Acta Odontol Latinoam	1 (0.2%)	0 (0%)
Can Med Educ J	0 (0%)	1 (<0.1%)
Eur J Prosthodont Restor Dent	1 (0.2%)	0 (0%)
Int J Comput Dent	1 (0.2%)	0 (0%)
J Dent Hyg	1 (0.2%)	0 (0%)
J Forensic Odontostomatol	1 (0.2%)	0 (0%)
J Oral Biosci	0 (0%)	1 (<0.1%)
Minerva Dent Oral Sci	1 (0.2%)	0 (0%)
Oper Dent	1 (0.2%)	0 (0%)
Quintessence Int	1 (0.2%)	0 (0%)
¹ n (%)

TABLE 1

Characteristic	Overall, N = 7,549¹	No, N = 500¹	Yes, N = 7,049¹
journalTitle
BMC Oral Health	1,791 (24%)	1 (0.2%)	1,790 (25%)
Other	1,418 (19%)	403 (81%)	1,015 (14%)
Med Oral Patol Oral Cir Bucal	641 (8.5%)	0 (0%)	641 (9.1%)
J Appl Oral Sci	485 (6.4%)	0 (0%)	485 (6.9%)
J Indian Prosthodont Soc	424 (5.6%)	1 (0.2%)	423 (6.0%)
Clin Exp Dent Res	391 (5.2%)	0 (0%)	391 (5.5%)
Int J Implant Dent	355 (4.7%)	0 (0%)	355 (5.0%)
Dental Press J Orthod	351 (4.6%)	0 (0%)	351 (5.0%)
Clin Oral Investig	343 (4.5%)	19 (3.8%)	324 (4.6%)
Prog Orthod	260 (3.4%)	0 (0%)	260 (3.7%)
Int J Oral Sci	203 (2.7%)	0 (0%)	203 (2.9%)
Head Face Med	196 (2.6%)	0 (0%)	196 (2.8%)
Br Dent J	157 (2.1%)	6 (1.2%)	151 (2.1%)
Eur Endod J	148 (2.0%)	0 (0%)	148 (2.1%)
J Craniofac Surg	138 (1.8%)	41 (8.2%)	97 (1.4%)
Oral Dis	87 (1.2%)	12 (2.4%)	75 (1.1%)
J Dent Educ	81 (1.1%)	7 (1.4%)	74 (1.0%)
J Dent Res	80 (1.1%)	10 (2.0%)	70 (1.0%)
Pub Year
2021	2,233 (30%)	102 (20%)	2,131 (30%)
2020	1,571 (21%)	96 (19%)	1,475 (21%)
2018	1,135 (15%)	71 (14%)	1,064 (15%)
2019	1,037 (14%)	82 (16%)	955 (14%)
2017	823 (11%)	87 (17%)	736 (10%)
2016	747 (9.9%)	61 (12%)	686 (9.7%)
2022	3 (<0.1%)	1 (0.2%)	2 (<0.1%)
true_open_data	112 (1.5%)	3 (0.6%)	109 (1.5%)
¹ n (%)

TABLE 2

Characteristic	No, N = 7,437¹	Yes, N = 112¹
journalTitle
BMC Oral Health	1,724 (23%)	67 (60%)
Other	1,202 (16%)	10 (8.9%)
Med Oral Patol Oral Cir Bucal	639 (8.6%)	2 (1.8%)
J Appl Oral Sci	483 (6.5%)	2 (1.8%)
J Indian Prosthodont Soc	424 (5.7%)	0 (0%)
Clin Exp Dent Res	387 (5.2%)	4 (3.6%)
Int J Implant Dent	350 (4.7%)	5 (4.5%)
Dental Press J Orthod	351 (4.7%)	0 (0%)
Clin Oral Investig	343 (4.6%)	0 (0%)
Prog Orthod	253 (3.4%)	7 (6.2%)
Int J Oral Sci	198 (2.7%)	5 (4.5%)
Head Face Med	194 (2.6%)	2 (1.8%)
Br Dent J	157 (2.1%)	0 (0%)
Eur Endod J	148 (2.0%)	0 (0%)
J Craniofac Surg	138 (1.9%)	0 (0%)
Oral Dis	86 (1.2%)	1 (0.9%)
J Dent Educ	81 (1.1%)	0 (0%)
J Dent Res	77 (1.0%)	3 (2.7%)
Br J Oral Maxillofac Surg	72 (1.0%)	0 (0%)
J Clin Periodontol	68 (0.9%)	3 (2.7%)
J Oral Rehabil	62 (0.8%)	1 (0.9%)
Pub Year
2021	2,195 (30%)	38 (34%)
2020	1,556 (21%)	15 (13%)
2018	1,117 (15%)	18 (16%)
2019	1,018 (14%)	19 (17%)
2017	815 (11%)	8 (7.1%)
2016	733 (9.9%)	14 (12%)
2022	3 (<0.1%)	0 (0%)
¹ n (%)

Now select only those with opendata, to fill the Table 2

## # A tibble: 21 × 2
## # Groups:   journalTitle [21]
##    journalTitle                      n
##    <chr>                         <int>
##  1 BMC Oral Health                  67
##  2 Prog Orthod                       7
##  3 Int J Implant Dent                5
##  4 Int J Oral Sci                    5
##  5 Clin Exp Dent Res                 4
##  6 J Clin Periodontol                3
##  7 J Dent Res                        3
##  8 Head Face Med                     2
##  9 J Appl Oral Sci                   2
## 10 Med Oral Patol Oral Cir Bucal     2
## # … with 11 more rows

Characteristic	No, N = 68¹	Yes, N = 3¹
Journal
J Clin Periodontol	68 (100%)	3 (100%)
¹ n (%)

Check the journals without open data

##  true_open_data  No  Yes
##              No 497 6940
##             Yes   3  109

FAIRness

Overall FAIRness

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
##    4.00    4.00    9.00   32.55   70.00   79.00    7437

## # A tibble: 1 × 3
##       n  mean    sd
##   <int> <dbl> <dbl>
## 1   112  32.5  31.9

Overall FAIRness by domain

## # A tibble: 4 × 4
##   FAIR_item            n  mean    sd
##   <fct>            <int> <dbl> <dbl>
## 1 Accesibility       112 0.951  1.05
## 2 Interoperability   112 1.08   1.36
## 3 Reusability        112 2.40   2.63
## 4 Findability        112 3.44   2.76

Table 3 FAIRness by journal

## # A tibble: 8 × 6
##   journalTitle           n FAIRmean    sd   min   max
##   <fct>              <int>    <dbl> <dbl> <dbl> <dbl>
## 1 Prog Orthod            7     41.4 35.5      4    75
## 2 BMC Oral Health       67     37.7 32.5      4    79
## 3 Int J Implant Dent     5     32.4 38.9      4    75
## 4 Other                 18     28.3 29.9      4    75
## 5 Int J Oral Sci         5     18.2 31.8      4    75
## 6 Clin Exp Dent Res      4     11    8.08     4    18
## 7 J Clin Periodontol     3      4    0        4     4
## 8 J Dent Res             3      4    0        4     4

Table FAIRness by year

## # A tibble: 6 × 6
##   pubYear     n FAIRmean    sd   min   max
##     <dbl> <int>    <dbl> <dbl> <dbl> <dbl>
## 1    2016    14     44    34.0     4    75
## 2    2017     8     31.8  34.8     4    75
## 3    2018    18     28.4  32.1     4    75
## 4    2019    19     35.1  33.6     4    75
## 5    2020    15     24.1  27.8     4    79
## 6    2021    38     32.5  32.0     4    75

SUPP FIG FAIRness by journal

Are differences by journal or year?

Characteristic	Beta	95% CI¹	p-value
Journal
Prog Orthod	—	—
BMC Oral Health	-4.0	-29, 21	0.8
Clin Exp Dent Res	-32	-70, 7.3	0.11
Int J Implant Dent	-9.0	-45, 27	0.6
Int J Oral Sci	-23	-59, 13	0.2
J Clin Periodontol	-38	-80, 5.0	0.087
J Dent Res	-36	-79, 6.4	0.10
Other	-12	-40, 15	0.4
Pub Year	-1.3	-4.7, 2.1	0.5
¹ CI = Confidence Interval

SUPP FIG FAIRness by year

With FAIRness assessment

Publications by year by journal with open data

## # A tibble: 8 × 7
## # Groups:   Journal [8]
##   Journal            `2016` `2017` `2018` `2019` `2020` `2021`
##   <fct>               <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>
## 1 BMC Oral Health      44.8   39.5   23.3   49.2     32   37.3
## 2 Clin Exp Dent Res    NA     18     11     NA        4   NA  
## 3 Int J Implant Dent   NA      4     75      4       NA   39.5
## 4 Int J Oral Sci       NA     NA     75      4        4    4  
## 5 J Clin Periodontol    4     NA     NA     NA        4    4  
## 6 J Dent Res           NA     NA     NA      4        4    4  
## 7 Prog Orthod          NA     NA     39.5   45.7     70    4  
## 8 Other                75     37      4     11       17   31.6

Analysis by FAIRness items

Analysis by FAIR metrics in detail

FIG 1

## # A tibble: 4 × 5
## # Groups:   item [4]
##   item             initial moderate advanced incomplete
##   <fct>              <int>    <int>    <int>      <int>
## 1 Findability           64       10       38         NA
## 2 Accesibility          14       34        8         56
## 3 Interoperability      13       35       NA         64
## 4 Reusability           16       17       23         56

Save the plot

which dataset is more FAIR? Some examples

## # A tibble: 6 × 6
##   doi_publication            title      journalTitle pubYear FAIRness FAIR_level
##   <chr>                      <chr>      <chr>          <dbl>    <dbl> <fct>     
## 1 10.1186/s12903-020-01151-1 Pre-appli… BMC Oral He…    2020       79 advanced  
## 2 10.1186/s12903-016-0231-y  Does eros… BMC Oral He…    2016       75 advanced  
## 3 10.1186/s12903-016-0239-3  Influence… BMC Oral He…    2016       75 advanced  
## 4 10.1186/s12903-016-0264-2  Parallel … BMC Oral He…    2016       75 advanced  
## 5 10.1186/s12903-016-0294-9  Oral hygi… BMC Oral He…    2016       75 advanced  
## 6 10.1186/s13005-016-0127-8  Classific… Head Face M…    2016       75 advanced

## # A tibble: 6 × 6
##   doi_publication            title      journalTitle pubYear FAIRness FAIR_level
##   <chr>                      <chr>      <chr>          <dbl>    <dbl> <fct>     
## 1 10.1186/s12903-021-01828-1 Old age a… BMC Oral He…    2021        4 initial   
## 2 10.1186/s12903-021-01847-y Evaluatio… BMC Oral He…    2021        4 initial   
## 3 10.1186/s12903-021-01867-8 Detection… BMC Oral He…    2021        4 initial   
## 4 10.1186/s12903-021-01970-w Influence… BMC Oral He…    2021        4 initial   
## 5 10.1007/s10266-021-00594-4 Age-relat… Odontology      2021        4 initial   
## 6 10.1111/odi.13933          Expressio… Oral Dis        2021        4 initial

FIG 2 Journal and Year

FAIR Items per journal

Note that these are the LEVEL values, not the SCORES

Convert the scores to their ordinal meanings

FAIR Items per year

### ggasve fig 2

FIG 3 FAIR Maturity details

ggsave fig 3

Remove graphs

Tables to check

## # A tibble: 16 × 4
## # Groups:   item [16]
##    item                                               adv_mod Incomplete Initial
##    <fct>                                                <dbl>      <dbl>   <dbl>
##  1 F1-01D - Data is assigned a globally unique ident…   100         NA    NA    
##  2 F1-02D - Data is assigned a persistent identifier     41.1       58.0   0.893
##  3 F2-01M - Metadata includes descriptive core eleme…    42.0       50     8.04 
##  4 F3-01M - Metadata includes the identifier of the …    33.9       66.1  NA    
##  5 F4-01M - Metadata is offered in such a way that i…    45.5       54.5  NA    
##  6 A1-01M - Metadata contains access level and acces…    10.7       88.4   0.893
##  7 A1-02M - Metadata is accessible through a standar…    33.9       66.1  NA    
##  8 A1-03D - Data is accessible through a standardize…    50         50    NA    
##  9 I1-01M - Metadata is represented using a formal k…    41.1       58.9  NA    
## 10 I1-02M - Metadata uses semantic resources             NA         60.7  39.3  
## 11 I3-01M - Metadata includes links between the data…    31.2       68.8  NA    
## 12 R1-01MD - Metadata specifies the content of the d…    33.9       53.6  12.5  
## 13 R1.1-01M - Metadata includes license information …    39.3       57.1   3.57 
## 14 R1.2-01M - Metadata includes provenance informati…    50         50    NA    
## 15 R1.3-01M - Metadata follows a standard recommende…    35.7       55.4   8.93 
## 16 R1.3-02D - Data is available in a file format rec…    25.9       74.1  NA

levels by journal

## # A tibble: 8 × 17
## # Groups:   journalTitle [8]
##   journalTitle FsF_F1_01D FsF_F1_02D FsF_F2_01M FsF_F3_01M FsF_F4_01M FsF_A1_01M
##   <fct>             <dbl>      <dbl>      <dbl>      <dbl>      <dbl>      <dbl>
## 1 BMC Oral He…          3       1.48       1.55      1.21        1.66      0.269
## 2 Clin Exp De…          3       0          0.5       0           0         0    
## 3 Int J Impla…          3       1.2        1.2       1.2         1.2       0    
## 4 Int J Oral …          3       0.6        0.6       0.6         0.6       0    
## 5 J Clin Peri…          3       0          0         0           0         0    
## 6 J Dent Res            3       0          0         0           0         0    
## 7 Prog Orthod           3       1.71       1.57      1.71        1.71      0.857
## 8 Other                 3       1.06       1.06      0.667       1.17      0.667
## # … with 10 more variables: FsF_A1_03D <dbl>, FsF_A1_02M <dbl>,
## #   FsF_I1_01M <dbl>, FsF_I1_02M <dbl>, FsF_I3_01M <dbl>, FsF_R1_01MD <dbl>,
## #   FsF_R1.1_01M <dbl>, FsF_R1.2_01M <dbl>, FsF_R1.3_01M <dbl>,
## #   FsF_R1.3_02D <dbl>

## # A tibble: 6 × 17
## # Groups:   pubYear [6]
##   pubYear FsF_F1_01D FsF_F1_02D FsF_F2_01M FsF_F3_01M FsF_F4_01M FsF_A1_01M
##     <dbl>      <dbl>      <dbl>      <dbl>      <dbl>      <dbl>      <dbl>
## 1    2016          3      1.71       1.79       1.5         1.93      0.143
## 2    2017          3      1.12       1.12       1.12        1.12      0.375
## 3    2018          3      1          1.11       1           1.17      0    
## 4    2019          3      1.26       1.42       1.26        1.42      0.368
## 5    2020          3      0.867      0.867      0.6         1.2       0.4  
## 6    2021          3      1.34       1.34       0.868       1.34      0.474
## # … with 10 more variables: FsF_A1_03D <dbl>, FsF_A1_02M <dbl>,
## #   FsF_I1_01M <dbl>, FsF_I1_02M <dbl>, FsF_I3_01M <dbl>, FsF_R1_01MD <dbl>,
## #   FsF_R1.1_01M <dbl>, FsF_R1.2_01M <dbl>, FsF_R1.3_01M <dbl>,
## #   FsF_R1.3_02D <dbl>

Extras

Open access by year

### open data by year

Open access has more citations per year?

Open data has more citations per year?

Let’s check

Characteristic	exp(Beta)	95% CI¹	p-value
Pub Year	0.42	0.35, 0.50	<0.001
true_open_data
No	—	—
Yes	0.39	0.00, 1,631,710	>0.9
isOpenAccess
No	—	—
Yes	2.24	0.66, 7.62	0.2
true_open_data * isOpenAccess
Yes * Yes	2.76	0.00, 14,253,609	0.9
¹ CI = Confidence Interval

Codebook

(run only once at the end of the analysis)

## R version 4.0.4 (2021-02-15)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Pop!_OS 21.10
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] dataMaid_1.4.0     labelled_2.9.0     scales_1.1.1       DataExplorer_0.8.2
##  [5] visdat_0.5.3       ggeasy_0.1.3       patchwork_1.1.1    gtsummary_1.5.0   
##  [9] here_1.0.1         janitor_2.0.1      forcats_0.5.1      stringr_1.4.0     
## [13] dplyr_1.0.7        purrr_0.3.4        readr_2.1.1        tidyr_1.1.4       
## [17] tibble_3.1.6       ggplot2_3.3.5      tidyverse_1.3.0   
## 
## loaded via a namespace (and not attached):
##   [1] colorspace_2.0-2     ggsignif_0.6.0       rio_0.5.16          
##   [4] ellipsis_0.3.2       rprojroot_2.0.2      htmlTable_2.3.0     
##   [7] snakecase_0.11.0     base64enc_0.1-3      fs_1.5.0            
##  [10] rstudioapi_0.13      ggpubr_0.4.0         farver_2.1.0        
##  [13] bit64_4.0.5          fansi_0.5.0          lubridate_1.8.0     
##  [16] xml2_1.3.3           splines_4.0.4        robustbase_0.93-6   
##  [19] knitr_1.36           Formula_1.2-4        jsonlite_1.7.2      
##  [22] gt_0.3.1             broom_0.7.10.9000    cluster_2.1.1       
##  [25] dbplyr_2.0.0         png_0.1-7            broom.mixed_0.2.6   
##  [28] compiler_4.0.4       httr_1.4.2           backports_1.3.0     
##  [31] assertthat_0.2.1     Matrix_1.3-2         fastmap_1.1.0       
##  [34] cli_3.1.0            htmltools_0.5.2.9000 tools_4.0.4         
##  [37] igraph_1.2.6         coda_0.19-4          gtable_0.3.0        
##  [40] glue_1.5.1           reshape2_1.4.4       Rcpp_1.0.7          
##  [43] carData_3.0-4        cellranger_1.1.0     jquerylib_0.1.3     
##  [46] vctrs_0.3.8          nlme_3.1-152         broom.helpers_1.4.0 
##  [49] xfun_0.28            networkD3_0.4        openxlsx_4.2.3      
##  [52] rvest_1.0.2          lifecycle_1.0.1      pacman_0.5.1        
##  [55] rstatix_0.6.0        DEoptimR_1.0-8       MASS_7.3-53.1       
##  [58] vroom_1.5.7          hms_1.1.1            parallel_4.0.4      
##  [61] TMB_1.7.22           RColorBrewer_1.1-2   yaml_2.2.1          
##  [64] curl_4.3.2           gridExtra_2.3        pander_0.6.3        
##  [67] sass_0.4.0           rpart_4.1-15         latticeExtra_0.6-29 
##  [70] stringi_1.7.6        highr_0.9            checkmate_2.0.0     
##  [73] zip_2.1.1            rlang_0.4.12         pkgconfig_2.0.3     
##  [76] commonmark_1.7       evaluate_0.14        lattice_0.20-41     
##  [79] htmlwidgets_1.5.4    labeling_0.4.2       cowplot_1.1.0       
##  [82] bit_4.0.4            tidyselect_1.1.1     plyr_1.8.6          
##  [85] magrittr_2.0.1       R6_2.5.1             generics_0.1.1      
##  [88] Hmisc_4.6-0          DBI_1.1.0            foreign_0.8-81      
##  [91] pillar_1.6.4         haven_2.4.3          withr_2.4.3         
##  [94] abind_1.4-5          nnet_7.3-15          survival_3.2-13     
##  [97] car_3.0-10           modelr_0.1.8         crayon_1.4.2        
## [100] utf8_1.2.2           tzdb_0.2.0           rmarkdown_2.11      
## [103] jpeg_0.1-9           grid_4.0.4           readxl_1.3.1        
## [106] data.table_1.14.2    reprex_0.3.0         digest_0.6.28       
## [109] munsell_0.5.0        bslib_0.2.4

Data Analysis FAIRness of Dental Research Data

Uribe, Sofi-Mahmudi, Raittio, Maldupa and Vilne

11 April, 2022