Forest Plots

knitr::opts_knit$set(root.dir = "../../")

suppressPackageStartupMessages(library(tidyverse))
library(gt)
library(targets)
source("src/R/forest_plots.R")

df_forest <- tar_read(df_forest)

df_forest

## # A tibble: 4 × 2
##   category_id tab          
##   <chr>       <list>       
## 1 cnsn        <gt_tbl [15]>
## 2 dtin        <gt_tbl [15]>
## 3 sfty        <gt_tbl [15]>
## 4 ptpe        <gt_tbl [15]>

Consent

df_forest %>%
  filter(category_id == "cnsn") %>%
  pull(tab) %>%
  htmltools::tagList()

Consent Related Audit and Inspection Findings
Adjusted Risk Factors
	Distribution	N¹	N with Findings¹	Coefficient (CI95)²	Odds Ratio (CI95)	P	Coefficient Over Time (CI95)^2,3
# Issues Late
[0 - 4)		172 (21.2%)	60 (34.9%)		0.6 (0.4-0.9)	0.01577 *
[4 - 8)		85 (10.5%)	33 (38.8%)		0.7 (0.5-1.2)	0.2554
[8 - 14)		60 (7.4%)	28 (46.7%)
[14 - 30)		71 (8.8%)	35 (49.3%)		1.2 (0.7-2.1)	0.47143
[30 - Inf)		47 (5.8%)	27 (57.4%)		1.7 (0.9-3.2)	0.12573
missing		376 (46.4%)	188 (50%)
# Minor Deviations Per Days on Study⁴
[0 - 0.0029)		281 (34.6%)	111 (39.5%)		0.7 (0.5-1)	0.0274 *
[0.0029 - Inf)		147 (18.1%)	68 (46.3%)
missing		383 (47.2%)	192 (50.1%)
Pediatric Study
Not Pediatric Study		756 (93.2%)	335 (44.3%)
Pediatric Study		55 (6.8%)	36 (65.5%)		2.4 (1.3-4.4)	0.00421 **
missing		0 (0%)	0 (0%)
Perc Visits Not Occured (Percent Rank)⁵
[0 - 0.5)		157 (19.4%)	59 (37.6%)		0.7 (0.5-1)	0.03882 *
[0.5 - 0.85)		131 (16.2%)	59 (45%)
[0.85 - Inf)		67 (8.3%)	33 (49.3%)		1.2 (0.7-2.1)	0.44656
missing		456 (56.2%)	220 (48.2%)
Total Population⁶
[8.16 thous. - 8.1 mil.)		436 (53.8%)	180 (41.3%)
[8.1 mil. - Inf)		205 (25.3%)	117 (57.1%)		2 (1.4-2.8)	6e-05 ***
missing		170 (21%)	74 (43.5%)
¹ Number of Clinical Trial Site Audits and Inspections ² Red Reference Line Indicates Zero ³ Coefficient Value as New Data is Successively Added from 2011-2019 ⁴ Sum of Days Since Enrollment of All Patients ⁵ Percent Rank of Site Within Study ⁶ Population Within 100 km Radius of Site

Data Integrity

df_forest %>%
  filter(category_id == "dtin") %>%
  pull(tab) %>%
  htmltools::tagList()

Data Integrity Related Audit and Inspection Findings
Adjusted Risk Factors
	Distribution	N¹	N with Findings¹	Coefficient (CI95)²	Odds Ratio (CI95)	P	Coefficient Over Time (CI95)^2,3
# Active Trials At Site In TA Past Year (Percent Rank)^4,5
[0 - 0.4)		313 (39.5%)	210 (67.1%)		0.6 (0.5-0.9)	0.00521 *
[0.4 - Inf)		391 (49.4%)	302 (77.2%)
missing		88 (11.1%)	63 (71.6%)
# Issues Due
[0 - 2)		288 (36.4%)	189 (65.6%)		0.6 (0.4-0.8)	0.00076 ***
[2 - Inf)		147 (18.6%)	109 (74.1%)
missing		357 (45.1%)	277 (77.6%)
# Open Queries Per Days On Study⁶
[0 - 0.0055)		179 (22.6%)	109 (60.9%)		0.5 (0.4-0.8)	0.00066 ***
[0.0055 - Inf)		162 (20.5%)	123 (75.9%)
missing		451 (56.9%)	343 (76.1%)
Male to Female Ratio in Population with Age 18-39⁷
[0.46 - 0.49)		34 (4.3%)	20 (58.8%)		0.6 (0.3-1.3)	0.20156
[0.49 - 0.5)		175 (22.1%)	121 (69.1%)		0.8 (0.5-1.2)	0.29585
[0.5 - 0.51)		249 (31.4%)	183 (73.5%)
[0.51 - 0.52)		149 (18.8%)	123 (82.6%)		1.8 (1.1-2.9)	0.01796 *
[0.52 - Inf)		34 (4.3%)	28 (82.4%)		2 (0.9-5.6)	0.12908
missing		151 (19.1%)	100 (66.2%)
¹ Number of Clinical Trial Site Audits and Inspections ² Red Reference Line Indicates Zero ³ Coefficient Value as New Data is Successively Added from 2011-2019 ⁴ Percent Rank of Site Within Study ⁵ Active Trials in the Past Year in the Same Theraputic Area ⁶ Sum of Days Since Enrollment of All Patients ⁷ Population Within 100 km Radius of Site

Safety

df_forest %>%
  filter(category_id == "sfty") %>%
  pull(tab) %>%
  htmltools::tagList()

Safety Related Audit and Inspection Findings
Adjusted Risk Factors
	Distribution	N¹	N with Findings¹	Coefficient (CI95)²	Odds Ratio (CI95)	P	Coefficient Over Time (CI95)^2,3
% Population with Age over 60⁴
[0.043 - 0.14)		75 (9.2%)	33 (44%)		1 (0.6-1.6)	0.96856
[0.14 - 0.28)		485 (59.8%)	234 (48.2%)
[0.28 - Inf)		37 (4.6%)	26 (70.3%)		2.3 (1.1-5)	0.02759 *
missing		214 (26.4%)	98 (45.8%)
AE Per Visit
[0 - 0.52)		325 (40.1%)	144 (44.3%)
[0.52 - Inf)		82 (10.1%)	50 (61%)		1.7 (1.1-2.9)	0.02567 *
missing		404 (49.8%)	197 (48.8%)
SAE Per Visit
[0 - 0.0075)		171 (21.1%)	62 (36.3%)		0.6 (0.4-0.8)	0.00362 **
[0.0075 - Inf)		236 (29.1%)	132 (55.9%)
missing		404 (49.8%)	197 (48.8%)
Therapeutic Area
Autoimmune Disease Study		109 (13.4%)	41 (37.6%)		0.9 (0.5-1.5)	0.72133
Cancer Study		460 (56.7%)	262 (57%)		1.7 (1.2-2.6)	0.00815 *
Neuro- Psychiatric Study		112 (13.8%)	36 (32.1%)		0.6 (0.4-1.1)	0.1131
other Therapeutic Area Study		130 (16%)	52 (40%)
missing		0 (0%)	0 (0%)
¹ Number of Clinical Trial Site Audits and Inspections ² Red Reference Line Indicates Zero ³ Coefficient Value as New Data is Successively Added from 2011-2019 ⁴ Population Within 100 km Radius of Site

Protecting Endpoints

df_forest %>%
  filter(category_id == "ptpe") %>%
  pull(tab) %>%
  htmltools::tagList()

Protecting The Primary Endpoint Related Audit and Inspection Findings
Adjusted Risk Factors
	Distribution	N¹	N with Findings¹	Coefficient (CI95)²	Odds Ratio (CI95)	P	Coefficient Over Time (CI95)^2,3
# Issues Late
[0 - 4)		172 (27.6%)	116 (67.4%)		0.9 (0.6-1.3)	0.60298
[4 - 30)		216 (34.6%)	152 (70.4%)
[30 - Inf)		47 (7.5%)	37 (78.7%)		1.5 (0.7-3.4)	0.27818
missing		189 (30.3%)	134 (70.9%)
# Minor Deviations Per Days on Study⁴
[0 - 0.011)		355 (56.9%)	247 (69.6%)
[0.011 - Inf)		73 (11.7%)	58 (79.5%)		1.9 (1.1-3.7)	0.03814 *
missing		196 (31.4%)	134 (68.4%)
Median AE Reporting Delay (days)
[0 - 27)		206 (33%)	131 (63.6%)		0.6 (0.4-0.8)	0.00541 *
[27 - Inf)		179 (28.7%)	136 (76%)
missing		239 (38.3%)	172 (72%)
Median Query Processing Time (days)
[0 - 2)		207 (33.2%)	140 (67.6%)
[2 - 5)		52 (8.3%)	40 (76.9%)		1.6 (0.8-3.3)	0.18389
[5 - Inf)		19 (3%)	16 (84.2%)		2.2 (0.7-9.9)	0.21083
missing		346 (55.4%)	243 (70.2%)
¹ Number of Clinical Trial Site Audits and Inspections ² Red Reference Line Indicates Zero ³ Coefficient Value as New Data is Successively Added from 2011-2019 ⁴ Sum of Days Since Enrollment of All Patients