8 Univariate distribution checks

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

8.1 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.

8.1.1 Demographic variables

Demographic variables

2 Variables 14691 Observations

AGE: 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

8.1.2 Structural covariates and key predictors

Structural covariates and key predictors

7 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

AGE: 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

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

CREA: 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

8.1.3 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

8.1.4 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

POTASS: 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

CREA: 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_CREA: 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

8.1.5 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

8.1.6 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

SODIUM: 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

8.2 Categorical variables

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

8.3 Continuous variables

8.3.1 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.

Show the code

variables<- c("AGE", structural_vars, key_predictors, leuko_related_vars, leuko_ratio_vars, kidney_related_vars, acute_related_vars, remaining_vars)
unique.variables <- unique(variables)

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

res

       AGE        WBC        SEX        BUN       CREA        NEU        PLT 
        NA 2.14364604         NA 0.03198339 0.03193846         NA         NA 
       EOS       BASO        LYM       MONO       NEUR       EOSR      BASOR 
0.12561255 0.13215999 0.17979933 0.23679427         NA 0.47139320 0.19315481 
      LYMR      MONOR     POTASS       eGFR   BUN_CREA        FIB        CRP 
1.70910135 3.11197362         NA         NA 0.01953382         NA         NA 
      ASAT       ALAT        GGT        MCV        HGB        HCT        MCH 
0.02818736 1.01761807 0.02827878         NA         NA         NA         NA 
      MCHC        RDW        MPV         NT       APTT     SODIUM         CA 
        NA         NA         NA         NA 0.03047767         NA         NA 
      PHOS         MG         HS       GBIL         TP        ALB        AMY 
0.12526560         NA         NA 0.03306450         NA         NA 0.01844397 
      PAMY        LIP        CHE         AP        LDH         CK        GLU 
0.03036179 1.02765958         NA 0.02384583 0.03166182 0.03282045 0.02766430 
      TRIG       CHOL        PDW        RBC 
0.03242708         NA         NA         NA

Show the code

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
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Input object size:   8422576 bytes;  81 variables    14691 observations
New object size:    8422352 bytes;  81 variables    14691 observations
Input object size:   8541216 bytes;  82 variables    14691 observations
New object size:    8540992 bytes;  82 variables    14691 observations

Show the code

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="")
  }
}

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

Show the code

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 1 rows containing missing values (geom_bar).

Warning: 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_bar).

Warning: 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_bar).

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

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

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

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

Show the code

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 1 rows containing missing values (geom_bar).
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_bar).

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

Show the code

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

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

Show the code

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 1 rows containing missing values (geom_bar).

Warning: 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_bar).

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

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

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

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

Show the code

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 1 rows containing missing values (geom_bar).
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Warning: 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_bar).

8.4 Section session info

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     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_1.0.9     purrr_0.3.4    
 [9] readr_2.1.1     tidyr_1.2.0     tibble_3.1.7    ggplot2_3.3.6  
[13] tidyverse_1.3.1 here_1.0.1     

loaded via a namespace (and not attached):
 [1] httr_1.4.2          jsonlite_1.7.2      splines_4.1.2      
 [4] modelr_0.1.8        assertthat_0.2.1    latticeExtra_0.6-29
 [7] renv_0.15.5         cellranger_1.1.0    pillar_1.7.0       
[10] backports_1.4.1     glue_1.6.2          digest_0.6.29      
[13] checkmate_2.1.0     RColorBrewer_1.1-3  rvest_1.0.2        
[16] colorspace_2.0-3    htmltools_0.5.2     Matrix_1.3-4       
[19] pkgconfig_2.0.3     broom_0.8.0         haven_2.4.3        
[22] patchwork_1.1.1     scales_1.2.0        jpeg_0.1-9         
[25] tzdb_0.2.0          htmlTable_2.3.0     farver_2.1.0       
[28] generics_0.1.2      ellipsis_0.3.2      withr_2.5.0        
[31] nnet_7.3-16         cli_3.3.0           magrittr_2.0.3     
[34] crayon_1.5.1        readxl_1.3.1        evaluate_0.14      
[37] fs_1.5.2            fansi_1.0.3         xml2_1.3.3         
[40] foreign_0.8-81      data.table_1.14.2   tools_4.1.2        
[43] hms_1.1.1           lifecycle_1.0.1     munsell_0.5.0      
[46] reprex_2.0.1        cluster_2.1.2       compiler_4.1.2     
[49] rlang_1.0.3         grid_4.1.2          rstudioapi_0.13    
[52] htmlwidgets_1.5.4   labeling_0.4.2      base64enc_0.1-3    
[55] rmarkdown_2.11      gtable_0.3.0        DBI_1.1.2          
[58] R6_2.5.1            gridExtra_2.3       lubridate_1.8.0    
[61] knitr_1.37          fastmap_1.1.0       utf8_1.2.2         
[64] rprojroot_2.0.2     stringi_1.7.6       Rcpp_1.0.8.3       
[67] vctrs_0.4.1         rpart_4.1-15        png_0.1-7          
[70] dbplyr_2.1.1        tidyselect_1.1.2    xfun_0.31