-
Notifications
You must be signed in to change notification settings - Fork 0
/
Weeks of Depression Sensitivity Analsyses Final Code.R
197 lines (158 loc) · 9.44 KB
/
Weeks of Depression Sensitivity Analsyses Final Code.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
#linear regressions for weeks of depression analyses
rm(list = ls()) # command to clear all variables from R environment
# Load necessary packages
library(dplyr)
library(readxl)
library(lubridate)
library(openxlsx)
library(ggplot2)
library(tidyr)
library(gapminder)
library(writexl)
#dataset3 <- read_xlsx("W:/string-mbd/RA Instruction Manuals/Lily Eisner/Research/FH/Lisa Files/Family History Interview/FINALWODDATASETFORPAPER.xlsx" )
dataset3 <- read_xlsx("./data/FINALWODDATASETFORPAPER_PLUSDX_PLUSANX.xlsx" )
#If you were loading in the PII free dataset, use the following line of code instead:
#dataset3 <- read_xlsx("./data/PII Free WOD Dataset.xlsx" )
#Demographic Information
mean(dataset3$AgeatV1)
sd(dataset3$AgeatV1)
female <- dataset3 %>% filter(SEX == "FEMALE")
male <- dataset3 %>% filter(SEX == "MALE")
52/72
famhx <- dataset3 %>% filter(dep_immed == 1)
nofamhx <- dataset3 %>% filter(dep_immed == 0)
51/72
baseantidep <- dataset3 %>% filter(BaselineAntiDep == 1)
nobaseantidep <- dataset3 %>% filter(BaselineAntiDep == 0)
34/72
baseothermed <- dataset3 %>% filter(BaselineOtherMeds == 1)
nobaseothermed <- dataset3 %>% filter(BaselineOtherMeds == 0)
23/72
mean(dataset3$v1MFQScore)
sd(dataset3$v1MFQScore)
dataset3$c_ksadsdx_epset_annual_weeks_mdd <- as.numeric(dataset3$c_ksadsdx_epset_annual_weeks_mdd)
hist(dataset3$c_ksadsdx_epset_annual_weeks_mdd,
main = "Histogram of Weeks of Depression",
xlab = "Weeks of Depression",
breaks = c(0,5,10,15,20,25,30,35,40,45,50,55,60))
#Linear Regressions
#Null Model
truenull <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3)
summary(truenull)
#Model 1
nullwithbaselinemfq <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ v1MFQScore + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3)
summary(nullwithbaselinemfq)
#Model 2
baselinemfqplusfh <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ v1MFQScore + dep_immed + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3)
summary(baselinemfqplusfh)
#Model 3
mfqfhcase <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ v1MFQScore + (dep_immed*s_case__neg_tot) + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3)
summary(mfqfhcase)
#Model 4
familyhistoryonly <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ dep_immed + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3)
summary(familyhistoryonly)
# sensitivity analysis with only formal diagnosis of depression for supplemental analysis
#Linear Regressions
#Null Model
truenull_dx <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3)
summary(truenull_dx)
#Model 1
nullwithbaselinemfq_dx <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ v1MFQScore + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3)
summary(nullwithbaselinemfq_dx)
#Model 2
baselinemfqplusfh_dx <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ v1MFQScore + dep_immed_dx + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3)
summary(baselinemfqplusfh_dx)
#Model 3
mfqfhcase_dx <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ v1MFQScore + (dep_immed_dx*s_case__neg_tot) + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3)
summary(mfqfhcase_dx)
#Model 4
familyhistoryonly_dx <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ dep_immed_dx + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3)
summary(familyhistoryonly_dx)
#------------------------------------------------
# Anxiety Exploratory Analyses
#dataset3 <- read_xlsx("W:/string-mbd/RA Instruction Manuals/Lily Eisner/Research/FH/Lisa Files/Family History Interview/FINALWODDATASETFORPAPER.xlsx" )
dataset3_anx <- read_xlsx("./data/FINALWODDATASETFORPAPER_PLUSDX_PLUSANX.xlsx" )
#If you were loading in the PII free dataset, use the following line of code instead:
#dataset3 <- read_xlsx("./data/PII Free WOD Dataset.xlsx" )
#Demographic Information
mean(dataset3_anx$AgeatV1)
sd(dataset3_anx$AgeatV1)
female_anx <- dataset3_anx %>% filter(SEX == "FEMALE")
male_anx <- dataset3_anx %>% filter(SEX == "MALE")
52/72
famhx_anx <- dataset3_anx %>% filter(anx_immed == 1)
nofamhx_anx <- dataset3_anx %>% filter(anx_immed == 0)
51/72
baseantidep_anx <- dataset3_anx %>% filter(BaselineAntiDep == 1)
nobaseantidep_anx <- dataset3_anx %>% filter(BaselineAntiDep == 0)
34/72
baseothermed_anx <- dataset3_anx %>% filter(BaselineOtherMeds == 1)
nobaseothermed_anx <- dataset3_anx %>% filter(BaselineOtherMeds == 0)
23/72
mean(dataset3_anx$v1MFQScore)
sd(dataset3_anx$v1MFQScore)
dataset3_anx$c_ksadsdx_epset_annual_weeks_mdd <- as.numeric(dataset3_anx$c_ksadsdx_epset_annual_weeks_mdd)
hist(dataset3_anx$c_ksadsdx_epset_annual_weeks_mdd,
main = "Histogram of Weeks of Depression (Anxiety Analysis)",
xlab = "Weeks of Depression",
breaks = c(0,5,10,15,20,25,30,35,40,45,50,55,60))
#Linear Regressions
#Null Model
truenull_anx <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3_anx)
summary(truenull_anx)
#Model 1
nullwithbaselinemfq_anx <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ v1MFQScore + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3_anx)
summary(nullwithbaselinemfq_anx)
#Model 2
baselinemfqplusfh_anx <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ v1MFQScore + anx_immed + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3_anx)
summary(baselinemfqplusfh_anx)
#Model 3
mfqfhcase_anx <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ v1MFQScore + (anx_immed*s_case__neg_tot) + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3_anx)
summary(mfqfhcase_anx)
#Model 4
familyhistoryonly_anx <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ anx_immed + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3_anx)
summary(familyhistoryonly_anx)
#------------------------------------------------
# No Inpatient Sensitivity Analysis
#dataset3 <- read_xlsx("W:/string-mbd/RA Instruction Manuals/Lily Eisner/Research/FH/Lisa Files/Family History Interview/FINALWODDATASETFORPAPER.xlsx" )
dataset3_noinpatient <- read_xlsx("./data/FINALWODDATASETFORPAPER_NOINPATIENT.xlsx" )
#If you were loading in the PII free dataset, use the following line of code instead:
#dataset3 <- read_xlsx("./data/PII Free WOD Dataset.xlsx" )
#Demographic Information
mean(dataset3_noinpatient$AgeatV1)
sd(dataset3_noinpatient$AgeatV1)
female_noinpatient <- dataset3_noinpatient %>% filter(SEX == "FEMALE")
male_noinpatient <- dataset3_noinpatient %>% filter(SEX == "MALE")
52/72
famhx_noinpatient <- dataset3_noinpatient %>% filter(dep_immed == 1)
nofamhx_noinpatient <- dataset3_noinpatient %>% filter(dep_immed == 0)
51/72
baseantidep_noinpatient <- dataset3_noinpatient %>% filter(BaselineAntiDep == 1)
nobaseantidep_noinpatient <- dataset3_noinpatient %>% filter(BaselineAntiDep == 0)
34/72
baseothermed_noinpatient <- dataset3_noinpatient %>% filter(BaselineOtherMeds == 1)
nobaseothermed_noinpatient <- dataset3_noinpatient %>% filter(BaselineOtherMeds == 0)
23/72
mean(dataset3_noinpatient$v1MFQScore)
sd(dataset3_noinpatient$v1MFQScore)
dataset3_noinpatient$c_ksadsdx_epset_annual_weeks_mdd <- as.numeric(dataset3_noinpatient$c_ksadsdx_epset_annual_weeks_mdd)
hist(dataset3_noinpatient$c_ksadsdx_epset_annual_weeks_mdd,
main = "Histogram of Weeks of Depression (No Inpatient Analysis)",
xlab = "Weeks of Depression",
breaks = c(0,5,10,15,20,25,30,35,40,45,50,55,60))
#Linear Regressions
#Null Model
truenull_noinpatient <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3_noinpatient)
summary(truenull_noinpatient)
#Model 1
nullwithbaselinemfq_noinpatient <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ v1MFQScore + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3_noinpatient)
summary(nullwithbaselinemfq_noinpatient)
#Model 2
baselinemfqplusfh_noinpatient <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ v1MFQScore + dep_immed + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3_noinpatient)
summary(baselinemfqplusfh_noinpatient)
#Model 3
mfqfhcase_noinpatient <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ v1MFQScore + (dep_immed*s_case__neg_tot) + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3_noinpatient)
summary(mfqfhcase_noinpatient)
#Model 4
familyhistoryonly_noinpatient <- lm(c_ksadsdx_epset_annual_weeks_mdd ~ dep_immed + BaselineAntiDep + BaselineOtherMeds + FUAntiDep + FUOtherMeds + Inpatient + SEX + AgeatV1 + postpandemic, data = dataset3_noinpatient)
summary(familyhistoryonly_noinpatient)