Chapter 17 Univariate distribution checks

This section reports a series of univariate summary checks of the bacteremia dataset.

17.1 Data set overview

Using the Hmisc describe function, we provide an overview of the data set. The descriptive report also provides histograms of continuous variables. For ease of scanning the information, we group the report by measurement type.

17.1.1 Demographic variables

Demographic variables

2 Variables 14691 Observations

Alter: Patient Age years

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14691	0	85	1	56.17	20.78	24	29	43	58	70	79	84

lowest : 16 17 18 19 20 , highest: 96 97 98 99 101

sex: Patient Sex 1=male, 2=female

n	missing	distinct	Info	Mean	Gmd
14691	0	2	0.73	1.419	0.4869

 Value          1     2
 Frequency   8536  6155
 Proportion 0.581 0.419

17.1.2 Pivotal variables and very important predictors

Pivotal variables and VIPs

6 Variables 14691 Observations

WBC: White blood count G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14229	462	2710	1	11.23	7.602	2.66	4.26	6.63	9.60	13.53	18.22	22.27

lowest : 0.00 0.01 0.02 0.03 0.04 , highest: 365.30 383.74 387.73 433.83 604.47

Alter: Patient Age years

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14691	0	85	1	56.17	20.78	24	29	43	58	70	79	84

lowest : 16 17 18 19 20 , highest: 96 97 98 99 101

BUN: Blood urea nitrogen mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14519	172	947	1	22.66	16.92	7.1	8.6	11.6	16.6	26.9	44.8	60.8

lowest : 2.5 2.7 2.8 2.9 3.0 , highest: 160.6 171.3 171.9 176.0 184.8

KREA: Creatinine mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14532	159	674	1	1.329	0.8518	0.620	0.690	0.810	1.000	1.350	2.160	3.144

lowest : 0.26 0.27 0.28 0.29 0.30 , highest: 15.24 15.40 15.67 16.64 20.75

NEU: Neutrophiles G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13963	728	374	1	8.367	5.776	1.60	2.70	4.60	7.30	10.80	15.08	18.40

lowest : 0.0 0.1 0.2 0.3 0.4 , highest: 54.0 56.4 63.7 71.6 83.8

PLT: Blood platelets G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14649	42	718	1	220	130.1	50	81	140	204	277	369	445

lowest : 0 1 2 3 4 , highest: 1068 1211 1321 1639 2092

17.1.3 Further variables related to leukocyte types and leukocyte ratios

Leukocyte related variables and leukocyte ratios

11 Variables 14691 Observations

WBC: White blood count G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14229	462	2710	1	11.23	7.602	2.66	4.26	6.63	9.60	13.53	18.22	22.27

lowest : 0.00 0.01 0.02 0.03 0.04 , highest: 365.30 383.74 387.73 433.83 604.47

NEU: Neutrophiles G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13963	728	374	1	8.367	5.776	1.60	2.70	4.60	7.30	10.80	15.08	18.40

lowest : 0.0 0.1 0.2 0.3 0.4 , highest: 54.0 56.4 63.7 71.6 83.8

EOS: Eosinophils G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14556	135	36	0.867	0.1148	0.1585	0.0	0.0	0.0	0.1	0.1	0.3	0.4

lowest : 0.0 0.1 0.2 0.3 0.4 , highest: 3.8 5.3 9.6 11.5 15.8

BASO: Basophiles G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14545	146	18	0.337	0.01725	0.03111	0.0	0.0	0.0	0.0	0.0	0.1	0.1

lowest : 0.0 0.1 0.2 0.3 0.4 , highest: 1.3 1.4 1.5 2.2 6.5

 Value        0.0   0.1   0.2   0.3   0.4   0.5   0.6   0.7   0.8   0.9   1.0   1.1
 Frequency  12671  1636   109    59    31    14     6     7     1     2     1     2
 Proportion 0.871 0.112 0.007 0.004 0.002 0.001 0.000 0.000 0.000 0.000 0.000 0.000
                                               
 Value        1.2   1.3   1.4   1.5   2.2   6.5
 Frequency      1     1     1     1     1     1
 Proportion 0.000 0.000 0.000 0.000 0.000 0.000

LYM: Lymphocytes G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14429	262	114	0.998	1.366	1.162	0.2	0.4	0.7	1.0	1.6	2.1	2.6

lowest : 0.0 0.1 0.2 0.3 0.4 , highest: 149.9 357.5 366.8 375.1 578.1

 Value          0     5    10    15    20    30    35    40    45    75   100   115
 Frequency  13675   703    27     7     4     2     1     1     1     1     1     1
 Proportion 0.948 0.049 0.002 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
                                         
 Value        150   360   365   375   580
 Frequency      1     1     1     1     1
 Proportion 0.000 0.000 0.000 0.000 0.000

For the frequency table, variable is rounded to the nearest 5

MONO: Monocytes G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14445	246	67	0.996	0.8527	0.5965	0.1	0.3	0.5	0.8	1.1	1.5	1.8

lowest : 0.0 0.1 0.2 0.3 0.4 , highest: 13.9 14.6 16.2 17.3 20.4

NEUR: Neutrophile ratio %

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13959	732	3850	1	75.15	15.6	47.42	57.88	69.23	78.33	85.32	90.13	92.63

lowest :	0.000000	1.484829	1.935484	1.960784	2.413793
highest:	99.122807	99.166667	99.476440	99.484536	100.000000

EOSR: Eosinophil ratio %

        n  missing distinct     Info     Mean      Gmd      .05      .10      .25 
    13959      732      927    0.891    1.297    1.825   0.0000   0.0000   0.0000 
      .50      .75      .90      .95 
   0.5882   1.7857   3.4900   5.0000

lowest :	0.0000000	0.1834862	0.2028398	0.2178649	0.2188184
highest:	39.1752577	46.6019417	46.9026549	50.0000000	73.4883721

BASOR: Basophile ratio %

        n  missing distinct     Info     Mean      Gmd      .05      .10      .25 
    13959      732      419    0.322    0.145   0.2679   0.0000   0.0000   0.0000 
      .50      .75      .90      .95 
   0.0000   0.0000   0.5501   1.0526

lowest :	0.0000000	0.1358696	0.1545595	0.1652893	0.1818182
highest:	11.1111111	15.2173913	16.6666667	18.4210526	23.6559140

LYMR: Lymphocyte ratio % (mg/dl)

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13959	732	3121	1	14.61	11.87	2.752	4.000	6.757	11.340	18.182	27.869	36.620

lowest :	0.0000000	0.3215434	0.4484305	0.4608295	0.4636785
highest:	97.2413793	97.4193548	98.0000000	99.1847826	100.0000000

MONOR: Monocyte ratio %

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13959	732	2334	1	8.793	5.4	2.000	3.390	5.634	8.000	10.870	14.141	17.021

lowest :	0.0000000	0.2747253	0.3412969	0.3448276	0.4566210
highest:	68.5446009	69.2307692	70.3703704	72.7272727	100.0000000

17.1.4 Kidney function related variables

Kidney function related variables

5 Variables 14691 Observations

BUN: Blood urea nitrogen mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14519	172	947	1	22.66	16.92	7.1	8.6	11.6	16.6	26.9	44.8	60.8

lowest : 2.5 2.7 2.8 2.9 3.0 , highest: 160.6 171.3 171.9 176.0 184.8

K: Potassium mmol/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
12683	2008	408	1	4.003	0.6004	3.20	3.39	3.66	3.95	4.29	4.67	4.92

lowest : 1.92 2.07 2.11 2.12 2.21 , highest: 8.57 11.34 13.55 14.60 36.62

 Value        2.0   2.5   3.0   3.5   4.0   4.5   5.0   5.5   6.0   6.5   7.0   7.5
 Frequency      6    91   650  3385  5088  2455   692   201    73    26     7     2
 Proportion 0.000 0.007 0.051 0.267 0.401 0.194 0.055 0.016 0.006 0.002 0.001 0.000
                                               
 Value        8.0   8.5  11.5  13.5  14.5  36.5
 Frequency      2     1     1     1     1     1
 Proportion 0.000 0.000 0.000 0.000 0.000 0.000

For the frequency table, variable is rounded to the nearest 0.5

KREA: Creatinine mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14532	159	674	1	1.329	0.8518	0.620	0.690	0.810	1.000	1.350	2.160	3.144

lowest : 0.26 0.27 0.28 0.29 0.30 , highest: 15.24 15.40 15.67 16.64 20.75

eGFR: estimated glomerular filtration rate mL/min/1.73 m²

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14532	159	9708	1	72.14	35.06	17.52	27.21	49.70	75.59	95.22	109.76	118.09

lowest :	2.430496	2.644088	2.783769	2.874308	2.901780
highest:	162.497066	163.668639	165.504354	169.958856	175.747773

BUN_KREA: BUN/Scr ratio unitless

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14517	174	9708	1	17.87	8.898	8.048	9.482	12.101	15.902	21.136	28.906	34.683

lowest :	2.101990	2.486957	2.674419	3.215339	3.222222
highest:	82.463768	83.625000	84.230769	90.526316	112.857143

17.1.5 Acute phase reaction related variables

Acute phase related variables

5 Variables 14691 Observations

FIB: Fibrinogen mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
12124	2567	1084	1	547.4	231	247	301	397	529	674	816	892

lowest : 55 60 66 67 69 , highest: 1506 1508 1529 1537 1593

CRP: C-reactive protein mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14536	155	3328	1	10.92	10.39	0.29	0.77	2.87	8.57	16.45	24.49	29.61

lowest : 0.00 0.01 0.02 0.03 0.04 , highest: 58.40 61.81 63.96 73.04 76.32

ASAT: Aspartate transaminase U/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13537	1154	650	1	86.9	115.6	15	17	22	31	56	121	218

lowest : 3 5 6 7 8 , highest: 10845 11928 12079 12380 13991

ALAT: Alanin transaminase U/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13704	987	578	1	67.66	90.07	9	11	16	26	48	101	175

lowest : 0 1 2 3 4 , highest: 7109 9136 9314 12329 15059

GGT: Γ-glutamyl transpeptidase G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13429	1262	858	1	115.1	141.3	13.0	16.0	25.0	49.0	117.0	262.2	429.0

lowest : 3 5 6 7 8 , highest: 2932 3303 3782 3919 5171

17.1.6 Remaining variables

Remaining variables

29 Variables 14691 Observations

MCV: Mean corpuscular volume pg

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14649	42	506	1	88.35	6.992	78.2	81.1	84.7	88.3	92.0	95.9	99.0

lowest : 51.0 52.6 54.9 56.3 57.5 , highest: 121.0 121.8 124.6 127.9 128.7

HGB: Haemoglobin G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14650	41	157	1	11.57	2.558	8.2	8.8	9.9	11.4	13.2	14.6	15.4

lowest : 3.0 3.1 3.5 3.9 4.1 , highest: 19.5 20.5 20.7 20.8 21.0

HCT: Haematocrit %

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14649	42	404	1	34.48	7.316	24.6	26.4	29.8	34.3	39.1	42.9	44.8

lowest : 0.0 0.1 0.2 9.7 9.8 , highest: 61.4 61.9 63.2 65.3 66.6

MCH: Mean corpuscular hemoglobin fl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14649	42	232	1	29.58	2.693	25.3	26.7	28.4	29.7	31.0	32.4	33.4

lowest : 14.9 15.6 15.9 16.0 16.5 , highest: 42.0 42.3 42.4 42.5 47.4

MCHC: Mean corpuscular hemoglobin concentration g/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14649	42	124	0.999	33.47	1.546	31.1	31.7	32.6	33.5	34.4	35.2	35.6

lowest : 23.7 24.4 24.8 25.1 26.1 , highest: 38.3 38.4 38.9 39.3 43.5

RDW: Red blood cell distribution width %

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14635	56	173	1	15	2.385	12.4	12.7	13.4	14.5	16.0	18.0	19.5

lowest : 10.6 11.1 11.2 11.3 11.4 , highest: 28.6 28.9 29.1 29.7 31.8

MPV: Mean platelet volume fl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13989	702	71	0.999	10.38	1.132	8.9	9.2	9.7	10.3	11.0	11.7	12.2

lowest : 7.3 7.7 7.8 7.9 8.0 , highest: 14.2 14.3 14.6 14.8 15.0

NT: Normotest %

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
12224	2467	149	1	83.22	30.56	35	48	67	83	101	118	128

lowest : 4 5 6 7 8 , highest: 148 149 150 151 152

APTT: Activated partial thromboplastin time sec

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
12142	2549	631	1	40.06	9.533	30.1	31.4	34.1	37.7	42.7	49.9	56.6

lowest : 21.4 21.6 23.4 23.5 23.6 , highest: 160.7 163.0 168.7 171.6 176.1

NA.: Sodium mmol/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13409	1282	58	0.994	137.2	5.034	129	132	135	137	140	142	144

lowest : 106 108 109 110 112 , highest: 161 165 166 168 170

CA: Calcium mmol/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13415	1276	185	1	2.214	0.2213	1.89	1.96	2.09	2.22	2.35	2.45	2.51

lowest : 1.03 1.15 1.18 1.20 1.23 , highest: 3.84 3.88 3.96 4.18 4.40

PHOS: Phosphate mmol/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13449	1242	306	1	1.048	0.3993	0.55	0.64	0.81	0.99	1.20	1.47	1.74

lowest : 0.30 0.31 0.32 0.33 0.34 , highest: 4.36 4.43 4.53 5.48 6.22

MG: Magnesium mmol/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
12822	1869	146	0.999	0.8136	0.1609	0.59	0.64	0.72	0.81	0.89	0.98	1.06

lowest : 0.20 0.21 0.22 0.26 0.28 , highest: 1.83 1.88 1.96 2.07 2.22

HS: Uric acid mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
11630	3061	169	1	5.413	2.625	2.2	2.7	3.7	5.0	6.6	8.5	10.0

lowest : 1.3 1.4 1.5 1.6 1.7 , highest: 19.8 20.2 22.2 22.3 22.7

GBIL: Bilirubin mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13250	1441	885	1	1.406	1.477	0.33	0.39	0.53	0.77	1.23	2.34	3.96

lowest : 0.11 0.12 0.13 0.14 0.15 , highest: 42.82 43.83 45.10 51.72 51.77

TP: Total protein G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13108	1583	649	1	64.9	12.97	45.20	49.47	56.90	65.70	73.30	78.80	82.00

lowest : 29.9 30.0 30.3 30.5 30.6 , highest: 107.8 108.1 108.7 112.8 120.9

ALB: Albumin G/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13015	1676	401	1	33.42	8.513	21.3	23.6	27.9	33.6	39.1	43.2	45.2

lowest : 10.0 10.2 10.5 10.6 10.7 , highest: 52.9 53.2 53.7 54.0 55.7

AMY: Amylase U/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
10778	3913	488	1	90.83	100.5	18	23	33	49	76	125	187

lowest : 8 9 10 11 12 , highest: 4984 5248 40372 43970 56146

 Value          0   500  1000  1500  2000  2500  4000  4500  5000 40500 44000 56000
 Frequency  10432   268    39    14    12     4     2     2     2     1     1     1
 Proportion 0.968 0.025 0.004 0.001 0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.000

For the frequency table, variable is rounded to the nearest 500

PAMY: Pancreas amylase U/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
7577	7114	280	0.999	41.66	47.28	7	9	14	22	36	64	97

lowest : 1 2 3 4 5 , highest: 1673 2083 2116 3066 38369

 Value          0   500  1000  1500  2000  3000 38500
 Frequency   7495    65     7     6     2     1     1
 Proportion 0.989 0.009 0.001 0.001 0.000 0.000 0.000

For the frequency table, variable is rounded to the nearest 500

LIP: Lipases U/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
10992	3699	444	1	63.82	89.88	6	8	14	23	40	79	135

lowest : 0 1 2 3 4 , highest: 11469 15843 18560 22339 45991

CHE: Cholinesterase kU/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
12244	2447	997	1	4.79	2.378	1.70	2.17	3.15	4.60	6.22	7.65	8.49

lowest : 0.98 0.99 1.00 1.01 1.02 , highest: 12.39 12.55 12.97 13.32 13.89

AP: Alkaline phosphatase U/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13291	1400	672	1	118.8	91.51	42	49	63	84	123	206	302

lowest : 11 14 15 16 17 , highest: 1980 2132 2549 2596 2995

LDH: Lactate dehydrogenase U/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
12977	1714	1137	1	331.2	240.9	136	152	187	239	332	508	724

lowest : 39 46 54 55 56 , highest: 10473 10784 10822 11246 13906

CK: Creatinine kinases U/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
12611	2080	1506	1	385	615.4	18	25	42	80	184	577	1155

lowest : 8 9 10 11 12 , highest: 60799 63011 82180 83880 98801

GLU: Glucoses mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
10499	4192	389	1	126.4	48.3	78	85	97	113	138	177	216

lowest : 19 22 23 26 28 , highest: 843 848 890 1349 1403

TRIG: Triclyceride mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
9630	5061	538	1	141.7	90.33	54	64	83	115	165	241	307

lowest : 14 15 16 20 22 , highest: 1796 2247 2662 2918 5440

CHOL: Cholesterol mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
9646	5045	339	1	150.8	59.23	74	89	113	145	182	219	243

lowest : 25 26 27 28 29 , highest: 646 662 676 710 1104

PDW: Platelet distribution width %

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
13589	1102	167	1	12.29	2.375	9.3	9.8	10.8	12.0	13.4	15.1	16.4

lowest : 6.6 6.8 6.9 7.0 7.1 , highest: 24.1 24.7 24.9 25.2 25.3

RBC: Red blood count T/L

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
14230	461	65	0.999	3.936	0.8772	2.7	2.9	3.4	3.9	4.5	4.9	5.2

lowest : 1.0 1.1 1.2 1.3 1.4 , highest: 7.2 7.4 7.6 7.7 8.2

17.2 Categorical variables

We now provide a closer visual examination of the categorical predictors.

17.3 Continuous variables

17.3.1 Suggested transformations

Next we investigate whether a transformation of continuous variables may improve any further analyses to reduce disproportional impact of highly influential points, also in multivariate summaries. We employ a function ida_trans for this purpose, which optimises the parameter sigma of the pseudo-logarithm for that purpose. The optimization targets the best possible linear correlation of the transformed values with normal deviates. If no better transformation can be found, no transformation is suggested.

variables<- c("Alter", pivotal_vars, vip_vars, leuko_related_vars, leuko_ratio_vars, kidney_related_vars, acute_related_vars, remaining_vars)
unique.variables <- unique(variables)
#variables<- c("Alter", pivotal_vars, vip_vars)

res<-sapply(unique.variables, function(X) ida_trans(b_bact[,X])$const) #takes long, calculate once, and save?

res

##      Alter        WBC        BUN       KREA        NEU        PLT        EOS 
##         NA 2.51471408 0.03198339 0.03193846 2.30783002         NA 0.11873740 
##       BASO        LYM       MONO       NEUR       EOSR      BASOR       LYMR 
## 0.12980073 0.17957981 0.26505156         NA 0.42874860 0.17300902 1.77333947 
##      MONOR          K       eGFR   BUN_KREA        FIB        CRP       ASAT 
## 3.00040692 0.02677349         NA 0.03194543         NA         NA 0.03185536 
##       ALAT        GGT        MCV        HGB        HCT        MCH       MCHC 
## 1.02570312 0.03185702         NA         NA         NA         NA         NA 
##        RDW        MPV         NT       APTT        NA.         CA       PHOS 
##         NA         NA         NA 0.03047767         NA         NA 0.14534462 
##         MG         HS       GBIL         TP        ALB        AMY       PAMY 
##         NA         NA 0.03306450         NA         NA 0.02970893 0.03005131 
##        LIP        CHE         AP        LDH         CK        GLU       TRIG 
## 1.02558160         NA 0.02888640 0.02191602 0.02786388 0.01875994 0.02911146 
##       CHOL        PDW        RBC 
##         NA         NA         NA

for(j in 1:length(unique.variables)){
  if(!is.na(res[j])){
    newname <- paste("t_",unique.variables[j],sep="")
    newlabel <- paste("pseudo-log of",label(b_bact)[unique.variables[j]])
    names(newlabel)<-newname
    x<-pseudo_log(b_bact[[unique.variables[j]]], sigma=res[j], base=10)
    label(x)<-newlabel
    b_bact[[newname]] <- x
    upData(b_bact, labels=newlabel)
  }
}

## Input object size:    5575040 bytes;  57 variables    14691 observations
## New object size: 5574816 bytes;  57 variables    14691 observations
## Input object size:    5693696 bytes;  58 variables    14691 observations
## New object size: 5693472 bytes;  58 variables    14691 observations
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## New object size: 7235840 bytes;  71 variables    14691 observations
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## Input object size:    7947968 bytes;  77 variables    14691 observations
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## Input object size:    8066608 bytes;  78 variables    14691 observations
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## Input object size:    8185248 bytes;  79 variables    14691 observations
## New object size: 8185024 bytes;  79 variables    14691 observations
## Input object size:    8303904 bytes;  80 variables    14691 observations
## New object size: 8303680 bytes;  80 variables    14691 observations
## Input object size:    8422560 bytes;  81 variables    14691 observations
## New object size: 8422336 bytes;  81 variables    14691 observations
## Input object size:    8541216 bytes;  82 variables    14691 observations
## New object size: 8540992 bytes;  82 variables    14691 observations
## Input object size:    8659856 bytes;  83 variables    14691 observations
## New object size: 8659632 bytes;  83 variables    14691 observations
## Input object size:    8778496 bytes;  84 variables    14691 observations
## New object size: 8778272 bytes;  84 variables    14691 observations

sigma_values <- res


c_bact <- b_bact

# update variable lists - generate a second list with transformed variables replacing the originals

bact_transformed <- bact_variables

for(j in 1:length(bact_variables)){
  for(jj in 1:length(bact_variables[[j]])){
      if(!is.na(res[bact_variables[[j]][jj]])) bact_transformed[[j]][jj] <- paste("t_", bact_variables[[j]][jj], sep="")
  }
}

17.3.2 Univariate distribution with variables using the original variable and the suggested transformations

for(j in 1:length(unique.variables)){
  print(ida_plot_univar(b_bact, unique.variables[j], sigma=res[j], n_bars=100))
#  if(!is.na(res[j])){
#    print(ida_plot_univar(b_bact, paste("t_",variables[j],sep="")))
#  }
}

## Warning: Removed 4 rows containing missing values (geom_point).

## Warning: Removed 95 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).

## Warning: Removed 5 rows containing missing values (geom_point).

## Warning: Removed 162 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 3483 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 6249 rows containing missing values (geom_point).
## Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 56 rows containing missing values (geom_point).

## Warning: Removed 233 rows containing missing values (geom_point).

## Warning: Removed 76 rows containing missing values (geom_point).

## Warning: Removed 3325 rows containing missing values (geom_point).

## Warning: Removed 6233 rows containing missing values (geom_point).

## Warning: Removed 92 rows containing missing values (geom_point).

## Warning: Removed 204 rows containing missing values (geom_point).

## Warning: Removed 6 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).
## Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 57 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).
## Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 7 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).
## Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 12 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).
## Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 27 rows containing missing values (geom_point).

## Warning: Removed 5 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 4 rows containing missing values (geom_point).
## Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 9 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).
## Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 17 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 7 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

save(list=c("c_bact", "bact_variables", "sigma_values", "bact_transformed"), 
     file=here::here("data", "bact_env_c.rda"))

17.3.3 Univariate distribution with variables using only the original variable without the suggested transformations

for(j in 1:length(unique.variables)){
  print(ida_plot_univar(b_bact, unique.variables[j], sigma=res[j], n_bars=100, transform = FALSE))
#  if(!is.na(res[j])){
#    print(ida_plot_univar(b_bact, paste("t_",variables[j],sep="")))
#  }
}

## Warning: Removed 3 rows containing missing values (geom_point).

## Warning: Removed 6 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).

## Warning: Removed 59 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 3 rows containing missing values (geom_point).

## Warning: Removed 3407 rows containing missing values (geom_point).

## Warning: Removed 6332 rows containing missing values (geom_point).

## Warning: Removed 54 rows containing missing values (geom_point).

## Warning: Removed 188 rows containing missing values (geom_point).

## Warning: Removed 82 rows containing missing values (geom_point).

## Warning: Removed 3333 rows containing missing values (geom_point).

## Warning: Removed 6181 rows containing missing values (geom_point).

## Warning: Removed 68 rows containing missing values (geom_point).

## Warning: Removed 177 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).
## Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 46 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 7 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).
## Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 1 rows containing missing values (geom_point).
## Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 28 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 5 rows containing missing values (geom_point).
## Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 18 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).

17.3.4 Comparison of univariate distributions with and without pseudo-log transformation

The comparison is only shown for variables where a transformation is suggested.

for(j in 1:length(unique.variables)){
#  print(ida_plot_univar_orig_vs_trans(b_bact, unique.variables[j], sigma=res[j], n_bars=100))
 if(!is.na(res[j])){
   print(ida_plot_univar_orig_vs_trans(b_bact, unique.variables[j], sigma=res[j], n_bars=100))
 }
}

## Warning: Removed 5 rows containing missing values (geom_point).

## Warning: Removed 91 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 8 rows containing missing values (geom_point).

## Warning: Removed 6 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 55 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 188 rows containing missing values (geom_point).

## Warning: Removed 3437 rows containing missing values (geom_point).

## Warning: Removed 3417 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 6396 rows containing missing values (geom_point).

## Warning: Removed 6306 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 57 rows containing missing values (geom_point).

## Warning: Removed 57 rows containing missing values (geom_point).

## Warning: Removed 188 rows containing missing values (geom_point).

## Warning: Removed 222 rows containing missing values (geom_point).

## Warning: Removed 3361 rows containing missing values (geom_point).

## Warning: Removed 3381 rows containing missing values (geom_point).

## Warning: Removed 5993 rows containing missing values (geom_point).

## Warning: Removed 6175 rows containing missing values (geom_point).

## Warning: Removed 76 rows containing missing values (geom_point).

## Warning: Removed 87 rows containing missing values (geom_point).

## Warning: Removed 193 rows containing missing values (geom_point).

## Warning: Removed 204 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 6 rows containing missing values (geom_point).

## Warning: Removed 32 rows containing missing values (geom_point).

## Warning: Removed 22 rows containing missing values (geom_point).

## Warning: Removed 7 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 5 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 7 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).
## Removed 1 rows containing missing values (geom_bar).

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 5 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 2 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).

17.4 Section session info

## R version 4.1.3 (2022-03-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 17763)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_Austria.1252  LC_CTYPE=English_Austria.1252   
## [3] LC_MONETARY=English_Austria.1252 LC_NUMERIC=C                    
## [5] LC_TIME=English_Austria.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] Hmisc_4.6-0     Formula_1.2-4   survival_3.2-13 lattice_0.20-45
##  [5] forcats_0.5.1   stringr_1.4.0   dplyr_1.0.8     purrr_0.3.4    
##  [9] readr_2.1.2     tidyr_1.2.0     tibble_3.1.6    ggplot2_3.3.5  
## [13] tidyverse_1.3.1 here_1.0.1     
## 
## loaded via a namespace (and not attached):
##  [1] fs_1.5.2            lubridate_1.8.0     RColorBrewer_1.1-2 
##  [4] httr_1.4.2          rprojroot_2.0.2     tools_4.1.3        
##  [7] backports_1.4.1     bslib_0.3.1         utf8_1.2.2         
## [10] R6_2.5.1            rpart_4.1.16        DBI_1.1.2          
## [13] colorspace_2.0-3    nnet_7.3-17         withr_2.5.0        
## [16] tidyselect_1.1.2    gridExtra_2.3       compiler_4.1.3     
## [19] cli_3.2.0           rvest_1.0.2         htmlTable_2.4.0    
## [22] xml2_1.3.3          labeling_0.4.2      bookdown_0.25      
## [25] sass_0.4.1          scales_1.1.1        checkmate_2.0.0    
## [28] digest_0.6.29       foreign_0.8-82      rmarkdown_2.13     
## [31] base64enc_0.1-3     jpeg_0.1-9          pkgconfig_2.0.3    
## [34] htmltools_0.5.2     highr_0.9           dbplyr_2.1.1       
## [37] fastmap_1.1.0       htmlwidgets_1.5.4   rlang_1.0.2        
## [40] readxl_1.3.1        rstudioapi_0.13     jquerylib_0.1.4    
## [43] generics_0.1.2      farver_2.1.0        jsonlite_1.8.0     
## [46] magrittr_2.0.2      patchwork_1.1.1     Matrix_1.4-0       
## [49] Rcpp_1.0.8.3        munsell_0.5.0       fansi_1.0.3        
## [52] lifecycle_1.0.1     stringi_1.7.6       yaml_2.3.5         
## [55] grid_4.1.3          crayon_1.5.1        haven_2.4.3        
## [58] splines_4.1.3       hms_1.1.1           knitr_1.38         
## [61] pillar_1.7.0        reprex_2.0.1        glue_1.6.2         
## [64] evaluate_0.15       latticeExtra_0.6-29 data.table_1.14.2  
## [67] modelr_0.1.8        png_0.1-7           vctrs_0.3.8        
## [70] tzdb_0.2.0          cellranger_1.1.0    gtable_0.3.0       
## [73] assertthat_0.2.1    xfun_0.30           broom_0.7.12       
## [76] cluster_2.1.2       ellipsis_0.3.2