Data Variables’ Description

Descriptive Information

Original Data Set

  • Data set has 215 observations with 48 variables
  • Of the 48 variables, 5 are sums of subscores
    • 12 binary, 14 level categorical, 7 continuous, 28 cont/discrete
  • Full data missingess:
  • In the original data set, only 113 with complete data on all 48 variables.
  • Of the 215, 4 are missing conversion status - these subjects are dropped from subsequent analysis.
  • Of the 211 remaining, 12 are missing most/all SIPS variables (N, P, D, G vars - will drop these subjects from subsequent analyses).
  • Have removed 16/215 = 7.4% of the data.

Analysis Data Set

  • For the set of 199 subjects to be analyzed, missingness looks like:

Missingness per subject:

  • Number of variables missing and proportion of sample with that many missing:
## 
##     0     1     2     3     4     5     7     9    10    12    13    15 
## 0.568 0.141 0.111 0.060 0.005 0.035 0.020 0.020 0.015 0.005 0.015 0.005
## [1] 0.03213987
  • Cummulative proportion missing x or less
##     0     1     2     3     4     5     7     9    10    12    13    15 
## 0.568 0.709 0.820 0.880 0.885 0.920 0.940 0.960 0.975 0.980 0.995 1.000

Missingness per variable:

##                                         count  prop
## ID                                          0 0.000
## Idea_Sev_Base                               6 0.030
## Behav_Sev_Base                              6 0.030
## SI_Base                                     6 0.030
## SB_Base                                     6 0.030
## Trauma_NonSexual                            6 0.030
## Trauma_Sexual                               6 0.030
## race..AA.is.0..C.is.1..As.2..mixed.is.3     6 0.030
## race_bin..c.is.0..non.c.is.1                6 0.030
## schizotypal..scz.is.1..non.is.0             6 0.030
## X1..no.is.0..yes.is.1                      15 0.075
## famhx1..0.no..1.yes                        34 0.171
## Age                                         1 0.005
## Female                                      3 0.015
## Conversion                                  0 0.000
## P4a                                        15 0.075
## P4v                                        15 0.075
## P1                                          0 0.000
## P2                                          0 0.000
## P3                                          0 0.000
## P4                                          0 0.000
## P5                                          0 0.000
## Ptot                                        0 0.000
## N1                                          0 0.000
## N2                                          0 0.000
## N3                                          0 0.000
## N4                                          0 0.000
## N5                                          0 0.000
## N6                                          0 0.000
## N.Total                                     0 0.000
## D1                                          0 0.000
## D2                                          0 0.000
## D3                                          0 0.000
## D4                                          0 0.000
## D.Total                                     0 0.000
## G1                                          2 0.010
## G2                                          0 0.000
## G3                                          0 0.000
## G4                                          0 0.000
## G.Total                                     2 0.010
## SIPS.Total                                  0 0.000
## GAF                                         2 0.010
## GFS..Social                                41 0.206
## GFS..Role                                  41 0.206
## P1PD                                       16 0.080
## P1FR                                       16 0.080
## P1OB                                       16 0.080
## P1SNG                                      16 0.080
## P1NP                                       18 0.090


Compsrisons between converters/non-converters

  • Numbers of converters and non-converters:
## 
##   0   1 
## 135  64
  • Mean (sd) reported for each continous variable and n (%) for each categorical variable. t-tests used to compare converters and non-converters on continuous measures and Fisher’s exact test used for categorical measures.
Variables Variable Names N Range Full Non-Converter Converter Stat p
(n = 199) (n = 135) (n = 64)
Age Age 198 Age 20.08 (3.82) 20.11 (3.86) 20.02 (3.76) -0.16 0.871
P4a P4a 184 auditory hallucations 2.48 (1.59) 2.54 (1.58) 2.36 (1.61) -0.71 0.482
P4v P4v 184 visual hallucinations 1.89 (1.49) 2.12 (1.47) 1.40 (1.41) -3.14 0.002
P1 P1 199 unusual thought content 3.58 (1.03) 3.43 (1.01) 3.91 (0.99) 3.13 0.002
P2 P2 199 paranoia 3.34 (1.24) 3.27 (1.22) 3.48 (1.27) 1.12 0.264
P3 P3 199 grandiosity 2.09 (1.59) 2.04 (1.57) 2.20 (1.64) 0.69 0.493
P4 P4 199 overall hallucinations 2.85 (1.43) 2.87 (1.40) 2.83 (1.51) -0.18 0.860
P5 P5 199 disorganization 2.70 (1.31) 2.50 (1.29) 3.11 (1.27) 3.1 0.002
Ptot Ptot 199 total positive symptoms sum of P1 P5 14.57 (4.00) 14.11 (3.99) 15.53 (3.87) 2.37 0.019
N1 N1 199 Social anhedonia 3.54 (1.57) 3.30 (1.54) 4.03 (1.53) 3.12 0.002
N2 N2 199 avolition 3.38 (1.63) 3.28 (1.66) 3.59 (1.56) 1.26 0.208
N3 N3 199 expression of emotion 2.09 (1.72) 1.87 (1.64) 2.55 (1.83) 2.61 0.010
N4 N4 199 experience of emotions and self 2.49 (1.89) 2.40 (1.94) 2.67 (1.77) 0.95 0.343
N5 N5 199 ideational richness 1.85 (1.42) 1.67 (1.30) 2.25 (1.56) 2.76 0.006
N6 N6 199 occupational functioning 3.79 (1.70) 3.69 (1.73) 4.00 (1.61) 1.21 0.228
N.Total N Total 199 total negative symptoms sum of N1 N6 17.14 (6.65) 16.21 (6.39) 19.09 (6.82) 2.91 0.004
D1 D1 199 odd behavior 2.57 (1.36) 2.36 (1.34) 3.02 (1.32) 3.26 0.001
D2 D2 199 bizarre thinking 2.53 (1.46) 2.44 (1.42) 2.72 (1.55) 1.27 0.205
D3 D3 199 trouble with focus and attention 3.17 (1.20) 3.01 (1.16) 3.48 (1.23) 2.61 0.010
D4 D4 199 impairments in hygiene 1.62 (1.63) 1.59 (1.65) 1.69 (1.59) 0.38 0.702
D.Total D Total 199 total disorganization symptoms sum of D1 D4 9.88 (3.82) 9.40 (3.76) 10.91 (3.77) 2.64 0.009
G1 G1 197 sleep disturbance 2.69 (1.74) 2.65 (1.75) 2.77 (1.73) 0.42 0.674
G2 G2 199 dysphoric mood 3.23 (1.55) 3.40 (1.53) 2.86 (1.55) -2.32 0.021
G3 G3 199 motor disturbance 1.92 (1.58) 1.70 (1.47) 2.39 (1.72) 2.94 0.004
G4 G4 199 impaired tolerance to stress 3.91 (1.83) 3.91 (1.84) 3.91 (1.83) -0.02 0.986
G.Total G Total 197 total general symptoms sum of G1 G4 11.74 (4.25) 11.65 (4.47) 11.92 (3.77) 0.42 0.672
SIPS.Total SIPS Total 199 sum of all total scores 53.53 (13.75) 51.67 (14.14) 57.45 (12.07) 2.82 0.005
GAF GAF 197 global assessment of functioning 0 100 45.18 (6.84) 46.10 (7.08) 43.18 (5.86) -2.84 0.005
GFS..Social GFS 158 Social social functioning 5.35 (1.77) 5.35 (1.76) 5.37 (1.82) 0.07 0.945
GFS..Role GFS 158 Role role functioning 5.16 (2.35) 5.12 (2.29) 5.28 (2.49) 0.39 0.697
P1PD P1PD 183 P1 subsymptom perplexity and delusional mood 2.70 (1.12) 2.64 (1.11) 2.84 (1.15) 1.12 0.266
P1FR P1FR 183 p1 subsymptom first rank symptoms 1.73 (1.73) 1.70 (1.72) 1.81 (1.75) 0.39 0.694
P1OB P1OB 183 P1 subsymptom overvalued beliefs 2.14 (1.16) 2.11 (1.08) 2.19 (1.32) 0.44 0.659
P1SNG P1SNG 183 p1 subsymptom somatic nihilistic and very guilty ideas 1.96 (1.29) 1.98 (1.27) 1.93 (1.36) -0.22 0.823
P1NP P1NP 181 P1 non persecutory ideas of reference 1.27 (1.35) 1.29 (1.36) 1.21 (1.35) -0.37 0.713
Idea_Sev_Base Idea_Sev_Base 193 Baseline Violent Ideation 0 is no 1 is yes 56 (29.0) 28 (21.5) 28 (44.4) 0.002
Behav_Sev_Base Behav_Sev_Base 193 Baseline Violent Behavior 0 is no 1 is yes 12 ( 6.2) 4 ( 3.1) 8 (12.7) 0.023
SI_Base SI_Base 193 baseline suicidal ideation 0 is no 1 is yes 13 ( 6.7) 7 ( 5.4) 6 ( 9.5) 0.442
SB_Base SB_Base 193 baseline suicidal behavior 0 is no 1 is yes 5 ( 2.6) 2 ( 1.5) 3 ( 4.8) 0.402
Trauma_NonSexual Trauma_NonSexual 193 any history of nonsexual trauma at baseline 0 is no 1 is yes 29 (15.0) 20 (15.4) 9 (14.3) 1.000
Trauma_Sexual Trauma_Sexual 193 any history of sexual trauma at baseline 0 is no 1 is yes 21 (10.9) 12 ( 9.2) 9 (14.3) 0.417
Race (4 Category) race 193 AA is 0, C is 1, As 2, mixed is 3 0.020
Afr. Am. 43 (22.3) 26 (20.0) 17 (27.0)
Cauc. 87 (45.1) 67 (51.5) 20 (31.7)
Asian 15 ( 7.8) 6 ( 4.6) 9 (14.3)
Other 48 (24.9) 31 (23.8) 17 (27.0)
Race (Binary) race_bin 193 c is 0 non c is 1 106 (54.9) 63 (48.5) 43 (68.3) 0.015
Schizotypal schizotypal 193 scz is 1 non is 0 111 (57.5) 70 (53.8) 41 (65.1) 0.185
GRDS GRDS 184 Genetic Risk and Deterioration syndrome no is 0 yes is 1 8 ( 4.3) 5 ( 4.0) 3 ( 5.0) 1.000
Family History famhx1 165 fam hx of psychosis 0 no 1 yes 61 (37.0) 41 (38.3) 20 (34.5) 0.750
Female Female 196 0 is no 1 is yes 53 (27.0) 41 (30.6) 12 (19.4) 0.140
  • Below table shows similar info with Cohen’s d calculated for each continuous measure
    • Note it’s computed as nonconverter - converter (take opposite for paper)
##             no_conv  conv     t  df    p n1  n2     d min max
## Age           20.11 20.02 -0.16 196 0.87 63 135 -0.02  13  29
## P4a            2.54  2.36 -0.71 182 0.48 58 126 -0.11   0   5
## P4v            2.12  1.40 -3.14 182 0.00 58 126 -0.50   0   4
## P1             3.43  3.91  3.13 197 0.00 64 135  0.47   0   5
## P2             3.27  3.48  1.12 197 0.26 64 135  0.17   0   5
## P3             2.04  2.20  0.69 197 0.49 64 135  0.10   0   5
## P4             2.87  2.83 -0.18 197 0.86 64 135 -0.03   0   5
## P5             2.50  3.11  3.10 197 0.00 64 135  0.47   0   5
## Ptot          14.11 15.53  2.37 197 0.02 64 135  0.36   4  22
## N1             3.30  4.03  3.12 197 0.00 64 135  0.47   0   6
## N2             3.28  3.59  1.26 197 0.21 64 135  0.19   0   6
## N3             1.87  2.55  2.61 197 0.01 64 135  0.40   0   6
## N4             2.40  2.67  0.95 197 0.34 64 135  0.14   0   6
## N5             1.67  2.25  2.76 197 0.01 64 135  0.42   0   5
## N6             3.69  4.00  1.21 197 0.23 64 135  0.18   0   6
## N.Total       16.21 19.09  2.91 197 0.00 64 135  0.44   0  31
## D1             2.36  3.02  3.26 197 0.00 64 135  0.50   0   5
## D2             2.44  2.72  1.27 197 0.21 64 135  0.19   0   5
## D3             3.01  3.48  2.61 197 0.01 64 135  0.40   0   6
## D4             1.59  1.69  0.38 197 0.70 64 135  0.06   0   6
## D.Total        9.40 10.91  2.64 197 0.01 64 135  0.40   1  18
## G1             2.65  2.77  0.42 195 0.67 64 133  0.06   0   6
## G2             3.40  2.86 -2.32 197 0.02 64 135 -0.35   0   6
## G3             1.70  2.39  2.94 197 0.00 64 135  0.45   0   6
## G4             3.91  3.91 -0.02 197 0.99 64 135  0.00   0   6
## G.Total       11.65 11.92  0.42 195 0.67 64 133  0.06   0  20
## SIPS.Total    51.67 57.45  2.82 197 0.01 64 135  0.43  16  82
## GAF           46.10 43.18 -2.84 195 0.01 62 135 -0.44  31  60
## GFS..Social    5.35  5.37  0.07 156 0.95 46 112  0.01   1  10
## GFS..Role      5.12  5.28  0.39 156 0.70 47 111  0.07   1  10
## P1PD           2.64  2.84  1.12 181 0.27 57 126  0.18   0   5
## P1FR           1.70  1.81  0.39 181 0.69 57 126  0.06   0   5
## P1OB           2.11  2.19  0.44 181 0.66 57 126  0.07   0   4
## P1SNG          1.98  1.93 -0.22 181 0.82 57 126 -0.04   0   5
## P1NP           1.29  1.21 -0.37 179 0.71 57 124 -0.06   0   5

Data Preparation for Modeling

  • For constructing the the predictive model we consider all covariates from the descriptive table except:
    • we remove the 4 category race variable (leave in the binary one)
    • we remove total scores (Ptot, N.Total, D.Total, G.Total and SIPS.Total) since we include the components of each
  • We employ K Nearest Neighbors (kNN) Imputaion (k = 5) using the VIM package (kNN function) in R to ``fill in’’ missing data, which handles both continuous and categorical variables. (A. Kowarik, M. Templ (2016) Imputation with R package VIM. Journal of Statistical Software, 74(7), 1-16.)