SKIM values in phenotype table

Load packages + make it so table always displays NA’s

Make sure kable extra not loaded (https://github.com/ropensci/skimr/issues/637)

suppressMessages(silent <- lapply(
    c("tidyverse","knitr", "skimr"), 
    library, character.only=T))
table = function (..., useNA = 'always') base::table(..., useNA = useNA)

SKIMR

new=as_tibble(read.csv("../VegMarkdown/pheno/BioxVeg_pheno_09112022.csv"))

colnames(new)[colnames(new)=="Veg5yr1"]="Vegetarian"
new$Vegetarian[new$Vegetarian==0]="Omnivore"
new$Vegetarian[new$Vegetarian==1]="Vegetarian"



factorthesecols=c("Sex", "Geno_batch", "AlcoholFreq",
                  "PreviousSmoker","CurrentSmoker",
                  "statins", "tookMed", "tookSSRI",
                  "Vegetarian")

new[factorthesecols] <- lapply(new[factorthesecols], as.factor)


my_skim <- skim_with(
    numeric = sfl(
        p25 = NULL,
        p50=NULL,
        p75=NULL,
        median = ~median(.x, na.rm=TRUE),
        min = ~min(.x, na.rm=TRUE), 
        max = ~max(.x, na.rm=TRUE), 
        `Data completeness (%)` = ~ (length(.x[!is.na(.x)]) / length(.x))*100
        ),
    factor = sfl(
        `Data completeness (%)` = ~ (length(.x[!is.na(.x)]) / length(.x))*100,
    pct = ~{
        prt <- prop.table(table(., useNA = "no"))*100
        val <- sprintf("%.3f", prt)
        nm1 <- tolower(substr(names(prt), 1, 3))
            stringr::str_c(nm1, val, sep = ": ", collapse = ", ")
        }
        )
)


new2=new%>%select(-c(FID, IID, center1:center22, SmokeStatus))
my_skim(new2)%>%focus(
    skim_variable, 
    `numeric.Data completeness (%)`,
    numeric.mean, 
    numeric.sd, 
    numeric.min, 
    numeric.median, 
    numeric.max, 
    numeric.hist, 
    `factor.Data completeness (%)`,
    factor.n_unique, 
    factor.pct,
    factor.top_counts,
    )

Data summary
Name	new2
Number of rows	155375
Number of columns	107
_______________________
Column type frequency:
factor	9
numeric	98
________________________
Group variables	None

Variable type: factor

skim_variable	Data completeness (%)	n_unique	pct	top_counts
Sex	100.000	2	1: 45.671, 2: 54.329	2: 84413, 1: 70962
Geno_batch	100.000	2	0: 10.259, 1: 89.741	1: 139435, 0: 15940
AlcoholFreq	99.942	2	0: 50.203, 1: 49.797	0: 77958, 1: 77327
Vegetarian	100.000	2	omn: 98.502, veg: 1.498	Omn: 153047, Veg: 2328
PreviousSmoker	100.000	2	0: 64.192, 1: 35.808	0: 99739, 1: 55636
CurrentSmoker	100.000	2	0: 92.428, 1: 7.572	0: 143610, 1: 11765
statins	99.721	2	0: 85.619, 1: 14.381	0: 132660, 1: 22282
tookMed	99.721	2	0: 97.222, 1: 2.778	0: 150638, 1: 4304
tookSSRI	99.721	2	0: 96.610, 1: 3.390	0: 149690, 1: 5252

Variable type: numeric

skim_variable	Data completeness (%)	mean	sd	min	median	max	hist
Age	100.000	56.331	7.880	40.000	58.000	72.000	▅▅▇▇▃
Townsend	99.876	-1.734	2.779	-6.258	-2.436	10.461	▇▇▃▁▁
Alanine_aminotransferase	95.253	23.017	13.455	3.180	19.800	472.430	▇▁▁▁▁
Albumin	87.087	45.389	2.602	18.870	45.360	58.210	▁▁▁▇▁
Alkaline_phosphatase	95.278	81.651	25.099	8.800	78.700	1416.700	▇▁▁▁▁
Apolipoprotein_A	86.515	1.556	0.271	0.436	1.529	2.499	▁▂▇▃▁
Apolipoprotein_B	94.861	1.079	0.239	0.401	1.063	2.775	▂▇▂▁▁
Aspartate_aminotransferase	94.960	25.922	9.450	3.300	24.300	711.300	▇▁▁▁▁
C_reactive_protein	95.082	2.338	4.098	0.080	1.180	79.490	▇▁▁▁▁
Calcium	87.046	2.382	0.094	1.467	2.378	3.572	▁▂▇▁▁
Cholesterol	95.274	5.943	1.087	2.141	5.878	15.555	▂▇▁▁▁
Creatinine	95.228	72.095	17.253	10.800	70.300	1219.400	▇▁▁▁▁
Cystatin_C	95.274	0.893	0.159	0.360	0.875	7.415	▇▁▁▁▁
Direct_bilirubin	82.078	1.839	0.825	1.000	1.620	44.290	▇▁▁▁▁
Gamma_glutamyltransferase	95.224	34.967	36.439	5.000	25.100	1160.800	▇▁▁▁▁
Glucose	86.981	5.103	1.113	1.449	4.948	36.813	▇▁▁▁▁
HbA1c	95.131	35.517	5.905	15.400	34.900	265.600	▇▁▁▁▁
HDL_cholesterol	87.047	1.478	0.386	0.228	1.430	4.107	▁▇▂▁▁
IGF_1	94.770	21.727	5.635	1.445	21.568	125.096	▇▂▁▁▁
LDL_direct	95.088	3.749	0.841	0.798	3.693	12.959	▃▇▁▁▁
Lipoprotein_A	76.113	43.834	49.255	3.800	19.830	189.000	▇▂▁▁▁
Oestradiol	16.017	473.180	455.462	175.000	325.000	14233.300	▇▁▁▁▁
Phosphate	86.916	1.164	0.160	0.369	1.168	4.186	▆▇▁▁▁
Rheumatoid_factor	8.335	24.362	19.690	10.000	16.600	120.000	▇▁▁▁▁
SHBG	86.247	52.714	28.124	0.390	46.330	241.580	▇▆▁▁▁
Testosterone	84.478	6.677	6.057	0.350	5.718	52.642	▇▃▁▁▁
Total_bilirubin	94.919	9.308	4.481	1.660	8.230	94.030	▇▁▁▁▁
Total_protein	86.998	72.336	4.022	36.270	72.160	115.280	▁▁▇▁▁
Triglycerides	95.209	1.691	0.985	0.235	1.436	11.278	▇▂▁▁▁
Urate	95.165	305.843	78.994	89.300	299.500	927.000	▃▇▁▁▁
Urea	95.227	5.361	1.328	1.200	5.230	35.080	▇▁▁▁▁
Vitamin_D	91.354	50.750	20.830	10.000	49.300	340.000	▇▁▁▁▁
PCA1	100.000	-12.112	2.108	-19.270	-12.284	21.451	▇▂▁▁▁
PCA2	100.000	3.674	1.758	-29.773	3.742	11.079	▁▁▁▃▇
PCA3	100.000	-1.440	1.787	-17.284	-1.520	16.684	▁▁▇▁▁
PCA4	100.000	0.841	3.612	-30.796	0.876	14.251	▁▁▁▇▁
PCA5	100.000	-1.063	6.625	-21.960	-2.777	27.916	▁▇▅▂▁
PCA6	100.000	-0.299	1.699	-7.292	-0.329	17.257	▁▇▁▁▁
PCA7	100.000	0.283	2.036	-14.695	0.307	12.792	▁▁▇▂▁
PCA8	100.000	-0.376	2.073	-10.299	-0.411	16.092	▁▇▅▁▁
PCA9	100.000	-0.134	4.465	-34.596	0.534	12.613	▁▁▁▇▂
PCA10	100.000	0.021	2.295	-17.298	-0.033	11.295	▁▁▇▇▁
PCA11	100.000	-0.276	3.462	-10.982	-0.712	20.307	▁▇▃▁▁
PCA12	100.000	0.174	2.367	-13.935	0.244	10.131	▁▁▇▇▁
PCA13	100.000	-0.001	1.648	-8.302	-0.002	9.654	▁▃▇▁▁
PCA14	100.000	-0.125	3.262	-14.144	-0.341	16.926	▁▅▇▁▁
PCA15	100.000	0.002	1.916	-13.787	0.019	9.559	▁▁▇▇▁
PCA16	100.000	-0.055	3.091	-25.240	-0.135	19.981	▁▁▇▂▁
PCA17	100.000	0.019	1.995	-9.876	0.014	8.475	▁▁▇▃▁
PCA18	100.000	0.015	2.847	-14.216	-0.020	21.161	▁▇▇▁▁
PCA19	100.000	0.052	2.893	-11.423	-0.030	12.705	▁▃▇▂▁
PCA20	100.000	-0.105	2.843	-12.491	-0.136	13.297	▁▃▇▂▁
BMI	99.491	26.935	4.638	12.121	26.247	74.684	▅▇▁▁▁
Age2	100.000	3235.315	869.579	1600.000	3364.000	5184.000	▆▇▇▇▂
zblood	99.629	0.000	1.000	-2.030	0.000	2.350	▅▇▇▇▂
zTownsend	99.876	0.000	1.000	-1.628	-0.253	4.388	▇▇▃▁▁
zAge	100.000	0.000	1.000	-2.072	0.212	1.988	▅▅▇▇▃
logSHBG	86.247	3.838	0.507	-0.942	3.836	5.487	▁▁▁▇▂
Scr	95.228	0.815	0.195	0.122	0.795	13.791	▇▁▁▁▁
eGFR	95.156	95.906	13.851	15.000	97.075	149.490	▁▁▆▇▁
bioavailableTest	76.969	2.004	1.741	0.084	2.068	14.861	▇▅▁▁▁
freeTest	78.674	0.114	0.108	0.001	0.092	1.615	▇▁▁▁▁
Cholesterolold	95.274	5.720	1.121	1.770	5.680	15.460	▂▇▁▁▁
LDL_directold	95.088	3.566	0.853	0.546	3.525	9.797	▁▇▂▁▁
Apolipoprotein_Bold	94.861	1.031	0.234	0.401	1.016	1.998	▂▇▆▂▁
Alanine_aminotransferase_rint	95.253	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
Albumin_rint	87.087	0.000	1.000	-4.482	0.000	4.482	▁▂▇▂▁
Alkaline_phosphatase_rint	95.278	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
Apolipoprotein_A_rint	86.515	0.000	1.000	-4.481	0.000	4.481	▁▂▇▂▁
Apolipoprotein_B_rint	94.861	0.000	1.000	-4.500	0.000	4.500	▁▂▇▂▁
Aspartate_aminotransferase_rint	94.960	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
C_reactive_protein_rint	95.082	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
Calcium_rint	87.046	0.000	1.000	-4.482	0.000	4.482	▁▂▇▂▁
Cholesterol_rint	95.274	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
Creatinine_rint	95.228	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
Cystatin_C_rint	95.274	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
Direct_bilirubin_rint	82.078	0.000	1.000	-4.469	0.000	4.469	▁▂▇▂▁
Gamma_glutamyltransferase_rint	95.224	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
Glucose_rint	86.981	0.000	1.000	-4.482	0.000	4.482	▁▂▇▂▁
HbA1c_rint	95.131	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
HDL_cholesterol_rint	87.047	0.000	1.000	-4.482	0.000	4.482	▁▂▇▂▁
IGF_1_rint	94.770	0.000	1.000	-4.500	0.000	4.500	▁▂▇▂▁
LDL_direct_rint	95.088	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
Lipoprotein_A_rint	76.113	0.000	1.000	-4.453	0.000	4.453	▁▂▇▂▁
Oestradiol_rint	16.017	0.000	1.000	-4.106	0.000	4.106	▁▃▇▃▁
Phosphate_rint	86.916	0.000	1.000	-4.482	0.000	4.482	▁▂▇▂▁
Rheumatoid_factor_rint	8.335	0.000	1.000	-3.953	0.000	3.953	▁▃▇▃▁
SHBG_rint	86.247	0.000	1.000	-4.480	0.000	4.480	▁▂▇▂▁
Testosterone_rint	84.478	0.000	1.000	-4.476	0.000	4.476	▁▂▇▂▁
Total_bilirubin_rint	94.919	0.000	1.000	-4.500	0.000	4.500	▁▂▇▂▁
Total_protein_rint	86.998	0.000	1.000	-4.482	0.000	4.482	▁▂▇▂▁
Triglycerides_rint	95.209	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
Urate_rint	95.165	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
Urea_rint	95.227	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
Vitamin_D_rint	91.354	0.000	1.000	-4.492	0.000	4.492	▁▂▇▂▁
eGFR_rint	95.156	0.000	1.000	-4.501	0.000	4.501	▁▂▇▂▁
bioavailableTest_rint	76.969	0.000	1.000	-4.456	0.000	4.456	▁▂▇▂▁
freeTest_rint	78.674	0.000	1.000	-4.460	0.000	4.460	▁▂▇▂▁

new2%>%group_by(Vegetarian)%>%my_skim()%>%focus(
    skim_variable, 
    Vegetarian,
    `numeric.Data completeness (%)`,
    numeric.mean, 
    numeric.sd, 
    numeric.min, 
    numeric.median, 
    numeric.max, 
    numeric.hist, 
    `factor.Data completeness (%)`,
    factor.n_unique, 
    factor.pct,
    factor.top_counts,)

Data summary
Name	Piped data
Number of rows	155375
Number of columns	107
_______________________
Column type frequency:
factor	8
numeric	98
________________________
Group variables	Vegetarian

Variable type: factor

skim_variable	Vegetarian	Data completeness (%)	n_unique	pct	top_counts
Sex	Omnivore	100.00	2	1: 45.851, 2: 54.149	2: 82873, 1: 70174
Sex	Vegetarian	100.00	2	1: 33.849, 2: 66.151	2: 1540, 1: 788
Geno_batch	Omnivore	100.00	2	0: 10.290, 1: 89.710	1: 137298, 0: 15749
Geno_batch	Vegetarian	100.00	2	0: 8.204, 1: 91.796	1: 2137, 0: 191
AlcoholFreq	Omnivore	99.94	2	0: 50.118, 1: 49.882	0: 76659, 1: 76298
AlcoholFreq	Vegetarian	100.00	2	0: 55.799, 1: 44.201	0: 1299, 1: 1029
PreviousSmoker	Omnivore	100.00	2	0: 64.161, 1: 35.839	0: 98197, 1: 54850
PreviousSmoker	Vegetarian	100.00	2	0: 66.237, 1: 33.763	0: 1542, 1: 786
CurrentSmoker	Omnivore	100.00	2	0: 92.414, 1: 7.586	0: 141437, 1: 11610
CurrentSmoker	Vegetarian	100.00	2	0: 93.342, 1: 6.658	0: 2173, 1: 155
statins	Omnivore	99.72	2	0: 85.473, 1: 14.527	0: 130450, 1: 22172
statins	Vegetarian	99.66	2	0: 95.259, 1: 4.741	0: 2210, 1: 110
tookMed	Omnivore	99.72	2	0: 97.225, 1: 2.775	0: 148386, 1: 4236
tookMed	Vegetarian	99.66	2	0: 97.069, 1: 2.931	0: 2252, 1: 68
tookSSRI	Omnivore	99.72	2	0: 96.609, 1: 3.391	0: 147446, 1: 5176
tookSSRI	Vegetarian	99.66	2	0: 96.724, 1: 3.276	0: 2244, 1: 76

Variable type: numeric

skim_variable	Vegetarian	Data completeness (%)	mean	sd	min	median	max	hist
Age	Omnivore	100.00	56.39	7.87	40.00	58.00	72.00	▃▅▇▇▃
Age	Vegetarian	100.00	52.65	7.77	40.00	53.00	70.00	▇▆▆▆▂
Townsend	Omnivore	99.87	-1.74	2.78	-6.26	-2.45	10.27	▇▇▃▁▁
Townsend	Vegetarian	99.96	-1.12	2.96	-6.18	-1.74	10.46	▇▇▅▁▁
Alanine_aminotransferase	Omnivore	95.25	23.07	13.49	3.18	19.85	472.43	▇▁▁▁▁
Alanine_aminotransferase	Vegetarian	95.70	19.27	10.54	5.40	16.74	138.10	▇▁▁▁▁
Albumin	Omnivore	87.08	45.39	2.60	18.87	45.36	57.97	▁▁▁▇▁
Albumin	Vegetarian	87.67	45.39	2.58	33.28	45.36	58.21	▁▂▇▂▁
Alkaline_phosphatase	Omnivore	95.27	81.66	25.12	8.80	78.70	1416.70	▇▁▁▁▁
Alkaline_phosphatase	Vegetarian	95.83	80.90	23.70	25.80	77.80	333.60	▇▅▁▁▁
Apolipoprotein_A	Omnivore	86.51	1.56	0.27	0.44	1.53	2.50	▁▂▇▃▁
Apolipoprotein_A	Vegetarian	87.03	1.57	0.27	0.77	1.55	2.47	▁▆▇▂▁
Apolipoprotein_B	Omnivore	94.86	1.08	0.24	0.40	1.06	2.77	▂▇▂▁▁
Apolipoprotein_B	Vegetarian	95.06	0.99	0.23	0.41	0.97	2.33	▂▇▂▁▁
Aspartate_aminotransferase	Omnivore	94.95	25.94	9.47	3.30	24.30	711.30	▇▁▁▁▁
Aspartate_aminotransferase	Vegetarian	95.45	24.97	8.32	8.10	23.60	184.10	▇▁▁▁▁
C_reactive_protein	Omnivore	95.08	2.35	4.11	0.08	1.19	79.49	▇▁▁▁▁
C_reactive_protein	Vegetarian	95.27	1.79	3.41	0.08	0.88	49.48	▇▁▁▁▁
Calcium	Omnivore	87.04	2.38	0.09	1.47	2.38	3.57	▁▂▇▁▁
Calcium	Vegetarian	87.63	2.37	0.09	2.06	2.37	2.83	▁▇▇▁▁
Cholesterol	Omnivore	95.27	5.95	1.09	2.14	5.88	15.56	▂▇▁▁▁
Cholesterol	Vegetarian	95.83	5.60	1.05	2.30	5.52	11.53	▁▇▅▁▁
Creatinine	Omnivore	95.22	72.23	17.30	10.80	70.50	1219.40	▇▁▁▁▁
Creatinine	Vegetarian	95.70	63.33	10.67	35.10	62.30	140.70	▃▇▁▁▁
Cystatin_C	Omnivore	95.27	0.89	0.16	0.36	0.88	7.42	▇▁▁▁▁
Cystatin_C	Vegetarian	95.75	0.89	0.13	0.47	0.88	1.51	▁▇▆▁▁
Direct_bilirubin	Omnivore	82.09	1.84	0.82	1.00	1.62	44.29	▇▁▁▁▁
Direct_bilirubin	Vegetarian	81.53	1.84	1.15	1.00	1.61	37.33	▇▁▁▁▁
Gamma_glutamyltransferase	Omnivore	95.22	35.09	36.49	5.00	25.20	1160.80	▇▁▁▁▁
Gamma_glutamyltransferase	Vegetarian	95.70	26.77	32.23	6.80	19.60	800.90	▇▁▁▁▁
Glucose	Omnivore	86.97	5.11	1.12	1.45	4.95	36.81	▇▁▁▁▁
Glucose	Vegetarian	87.67	4.93	0.70	2.57	4.86	11.84	▂▇▁▁▁
HbA1c	Omnivore	95.13	35.53	5.92	15.40	34.90	265.60	▇▁▁▁▁
HbA1c	Vegetarian	95.06	34.39	4.30	22.70	34.20	84.40	▇▅▁▁▁
HDL_cholesterol	Omnivore	87.04	1.48	0.39	0.23	1.43	4.11	▁▇▂▁▁
HDL_cholesterol	Vegetarian	87.67	1.50	0.38	0.61	1.47	3.69	▃▇▂▁▁
IGF_1	Omnivore	94.76	21.73	5.64	1.45	21.57	125.10	▇▂▁▁▁
IGF_1	Vegetarian	95.23	21.30	5.46	4.62	21.30	50.45	▁▇▅▁▁
LDL_direct	Omnivore	95.08	3.75	0.84	0.80	3.70	12.96	▃▇▁▁▁
LDL_direct	Vegetarian	95.70	3.45	0.80	0.80	3.40	8.57	▁▇▃▁▁
Lipoprotein_A	Omnivore	76.10	43.88	49.28	3.80	19.90	189.00	▇▂▁▁▁
Lipoprotein_A	Vegetarian	76.76	40.94	47.35	3.80	18.80	187.60	▇▁▁▁▁
Oestradiol	Omnivore	15.89	471.53	454.91	175.00	324.00	14233.30	▇▁▁▁▁
Oestradiol	Vegetarian	24.40	543.79	473.62	175.00	380.75	5067.10	▇▁▁▁▁
Phosphate	Omnivore	86.91	1.16	0.16	0.37	1.17	4.19	▆▇▁▁▁
Phosphate	Vegetarian	87.54	1.17	0.17	0.57	1.18	1.82	▁▃▇▂▁
Rheumatoid_factor	Omnivore	8.35	24.36	19.69	10.00	16.60	120.00	▇▁▁▁▁
Rheumatoid_factor	Vegetarian	7.56	24.60	19.69	10.00	16.15	116.70	▇▁▁▁▁
SHBG	Omnivore	86.24	52.60	28.05	0.39	46.23	241.58	▇▆▁▁▁
SHBG	Vegetarian	86.68	60.26	31.55	7.95	54.19	240.77	▇▆▂▁▁
Testosterone	Omnivore	84.50	6.69	6.06	0.35	5.90	52.64	▇▃▁▁▁
Testosterone	Vegetarian	83.12	5.53	6.07	0.35	1.48	26.73	▇▂▂▁▁
Total_bilirubin	Omnivore	94.91	9.31	4.48	1.66	8.24	94.03	▇▁▁▁▁
Total_bilirubin	Vegetarian	95.45	9.17	4.82	3.22	7.96	92.84	▇▁▁▁▁
Total_protein	Omnivore	86.99	72.34	4.02	36.27	72.17	115.28	▁▁▇▁▁
Total_protein	Vegetarian	87.67	72.04	3.97	53.59	71.88	92.77	▁▃▇▁▁
Triglycerides	Omnivore	95.20	1.69	0.98	0.23	1.44	11.28	▇▂▁▁▁
Triglycerides	Vegetarian	95.70	1.65	1.04	0.33	1.37	10.59	▇▁▁▁▁
Urate	Omnivore	95.16	306.41	78.99	89.30	300.20	927.00	▃▇▁▁▁
Urate	Vegetarian	95.58	268.84	70.12	104.90	259.90	574.40	▂▇▅▁▁
Urea	Omnivore	95.22	5.37	1.33	1.20	5.24	35.08	▇▁▁▁▁
Urea	Vegetarian	95.70	4.45	1.12	1.40	4.35	11.11	▂▇▂▁▁
Vitamin_D	Omnivore	91.34	50.86	20.81	10.00	49.40	340.00	▇▁▁▁▁
Vitamin_D	Vegetarian	92.18	43.74	21.03	10.00	40.90	169.00	▇▆▁▁▁
PCA1	Omnivore	100.00	-12.11	2.11	-19.27	-12.28	21.45	▇▂▁▁▁
PCA1	Vegetarian	100.00	-12.10	2.11	-17.51	-12.26	12.21	▇▃▁▁▁
PCA2	Omnivore	100.00	3.68	1.76	-28.41	3.74	11.08	▁▁▁▅▇
PCA2	Vegetarian	100.00	3.61	1.85	-29.77	3.68	9.29	▁▁▁▁▇
PCA3	Omnivore	100.00	-1.44	1.79	-17.28	-1.52	16.68	▁▁▇▁▁
PCA3	Vegetarian	100.00	-1.41	1.88	-17.13	-1.51	9.45	▁▁▇▆▁
PCA4	Omnivore	100.00	0.84	3.61	-30.80	0.88	14.25	▁▁▁▇▁
PCA4	Vegetarian	100.00	0.68	3.84	-24.50	0.76	13.22	▁▁▂▇▁
PCA5	Omnivore	100.00	-1.06	6.63	-21.96	-2.78	27.92	▁▇▅▂▁
PCA5	Vegetarian	100.00	-0.98	6.46	-18.00	-2.64	25.78	▁▇▃▁▁
PCA6	Omnivore	100.00	-0.30	1.70	-7.29	-0.33	17.26	▁▇▁▁▁
PCA6	Vegetarian	100.00	-0.28	1.70	-6.02	-0.30	7.77	▁▇▇▁▁
PCA7	Omnivore	100.00	0.28	2.03	-14.70	0.31	12.79	▁▁▇▂▁
PCA7	Vegetarian	100.00	0.26	2.14	-11.70	0.25	12.08	▁▁▇▂▁
PCA8	Omnivore	100.00	-0.38	2.07	-10.30	-0.41	16.09	▁▇▅▁▁
PCA8	Vegetarian	100.00	-0.33	2.06	-6.42	-0.44	11.86	▁▇▂▁▁
PCA9	Omnivore	100.00	-0.13	4.46	-34.60	0.54	12.61	▁▁▁▇▂
PCA9	Vegetarian	100.00	-0.44	4.53	-29.48	0.24	9.89	▁▁▁▇▃
PCA10	Omnivore	100.00	0.02	2.30	-17.30	-0.03	11.30	▁▁▇▇▁
PCA10	Vegetarian	100.00	-0.07	2.27	-9.33	-0.16	9.04	▁▂▇▂▁
PCA11	Omnivore	100.00	-0.27	3.47	-10.98	-0.71	20.31	▁▇▃▁▁
PCA11	Vegetarian	100.00	-0.42	3.22	-8.56	-0.78	13.13	▂▇▅▁▁
PCA12	Omnivore	100.00	0.17	2.37	-13.93	0.24	10.13	▁▁▇▇▁
PCA12	Vegetarian	100.00	0.25	2.28	-9.44	0.30	8.58	▁▂▇▅▁
PCA13	Omnivore	100.00	0.00	1.65	-8.30	0.00	9.65	▁▃▇▁▁
PCA13	Vegetarian	100.00	0.00	1.65	-5.88	0.04	6.55	▁▃▇▂▁
PCA14	Omnivore	100.00	-0.12	3.26	-14.14	-0.34	16.93	▁▅▇▁▁
PCA14	Vegetarian	100.00	-0.33	3.23	-10.18	-0.62	16.83	▁▇▅▁▁
PCA15	Omnivore	100.00	0.00	1.92	-13.79	0.02	9.56	▁▁▇▇▁
PCA15	Vegetarian	100.00	-0.03	1.88	-11.15	-0.01	6.73	▁▁▆▇▁
PCA16	Omnivore	100.00	-0.05	3.09	-23.73	-0.13	19.98	▁▁▇▂▁
PCA16	Vegetarian	100.00	-0.13	2.99	-25.24	-0.21	14.86	▁▁▅▇▁
PCA17	Omnivore	100.00	0.02	1.99	-9.88	0.01	8.47	▁▁▇▃▁
PCA17	Vegetarian	100.00	0.01	1.98	-7.30	0.05	6.49	▁▃▇▅▁
PCA18	Omnivore	100.00	0.02	2.85	-14.22	-0.02	21.16	▁▇▇▁▁
PCA18	Vegetarian	100.00	0.01	2.73	-9.78	0.03	16.10	▁▇▆▁▁
PCA19	Omnivore	100.00	0.05	2.89	-11.42	-0.03	12.70	▁▃▇▂▁
PCA19	Vegetarian	100.00	0.05	2.86	-10.94	-0.03	10.39	▁▃▇▃▁
PCA20	Omnivore	100.00	-0.11	2.84	-12.49	-0.14	13.30	▁▃▇▂▁
PCA20	Vegetarian	100.00	-0.05	2.77	-12.12	0.04	8.96	▁▂▇▆▁
BMI	Omnivore	99.49	26.97	4.64	12.12	26.27	74.68	▅▇▁▁▁
BMI	Vegetarian	99.36	24.82	4.24	15.26	24.20	52.54	▅▇▁▁▁
Age2	Omnivore	100.00	3241.45	868.78	1600.00	3364.00	5184.00	▆▇▇▇▂
Age2	Vegetarian	100.00	2831.79	825.84	1600.00	2809.00	4900.00	▇▆▅▅▁
zblood	Omnivore	99.63	0.00	1.00	-2.03	-0.01	2.35	▅▇▇▇▂
zblood	Vegetarian	99.48	0.01	1.04	-2.00	0.01	2.01	▅▇▇▇▆
zTownsend	Omnivore	99.87	0.00	1.00	-1.63	-0.26	4.32	▇▇▃▁▁
zTownsend	Vegetarian	99.96	0.22	1.07	-1.60	0.00	4.39	▇▇▅▁▁
zAge	Omnivore	100.00	0.01	1.00	-2.07	0.21	1.99	▃▅▇▇▃
zAge	Vegetarian	100.00	-0.47	0.99	-2.07	-0.42	1.73	▇▇▇▇▂
logSHBG	Omnivore	86.24	3.84	0.51	-0.94	3.83	5.49	▁▁▁▇▂
logSHBG	Vegetarian	86.68	3.97	0.52	2.07	3.99	5.48	▁▂▇▆▁
Scr	Omnivore	95.22	0.82	0.20	0.12	0.80	13.79	▇▁▁▁▁
Scr	Vegetarian	95.70	0.72	0.12	0.40	0.70	1.59	▃▇▁▁▁
eGFR	Omnivore	95.15	95.84	13.86	15.00	97.02	149.49	▁▁▆▇▁
eGFR	Vegetarian	95.62	100.01	12.63	49.31	100.79	131.01	▁▂▆▇▂
bioavailableTest	Omnivore	76.99	2.01	1.74	0.08	2.11	14.86	▇▅▁▁▁
bioavailableTest	Vegetarian	75.43	1.63	1.75	0.09	0.43	7.66	▇▁▃▁▁
freeTest	Omnivore	78.70	0.11	0.11	0.00	0.10	1.62	▇▁▁▁▁
freeTest	Vegetarian	77.19	0.09	0.11	0.00	0.02	0.63	▇▃▁▁▁
Cholesterolold	Omnivore	95.27	5.72	1.12	1.77	5.68	15.46	▂▇▁▁▁
Cholesterolold	Vegetarian	95.83	5.52	1.03	2.30	5.44	10.54	▁▇▆▁▁
LDL_directold	Omnivore	95.08	3.57	0.85	0.55	3.53	9.80	▁▇▂▁▁
LDL_directold	Vegetarian	95.70	3.39	0.78	0.80	3.35	6.88	▁▇▇▂▁
Apolipoprotein_Bold	Omnivore	94.86	1.03	0.23	0.40	1.02	2.00	▂▇▆▂▁
Apolipoprotein_Bold	Vegetarian	95.06	0.97	0.22	0.41	0.95	1.87	▂▇▆▁▁
Alanine_aminotransferase_rint	Omnivore	95.25	0.01	1.00	-4.50	0.01	4.50	▁▂▇▂▁
Alanine_aminotransferase_rint	Vegetarian	95.70	-0.39	0.98	-2.99	-0.42	3.11	▂▇▇▂▁
Albumin_rint	Omnivore	87.08	0.00	1.00	-4.48	0.00	4.24	▁▂▇▃▁
Albumin_rint	Vegetarian	87.67	0.00	0.99	-3.57	0.00	4.48	▁▅▇▂▁
Alkaline_phosphatase_rint	Omnivore	95.27	0.00	1.00	-4.50	0.00	4.50	▁▂▇▂▁
Alkaline_phosphatase_rint	Vegetarian	95.83	-0.03	1.02	-3.26	-0.04	3.36	▁▅▇▃▁
Apolipoprotein_A_rint	Omnivore	86.51	0.00	1.00	-4.48	0.00	4.48	▁▂▇▂▁
Apolipoprotein_A_rint	Vegetarian	87.03	0.07	0.97	-3.52	0.08	3.25	▁▃▇▅▁
Apolipoprotein_B_rint	Omnivore	94.86	0.01	1.00	-4.50	0.01	4.50	▁▂▇▂▁
Apolipoprotein_B_rint	Vegetarian	95.06	-0.40	1.00	-3.78	-0.41	3.41	▁▅▇▂▁
Aspartate_aminotransferase_rint	Omnivore	94.95	0.00	1.00	-4.50	0.00	4.50	▁▂▇▂▁
Aspartate_aminotransferase_rint	Vegetarian	95.45	-0.13	0.98	-3.83	-0.13	3.52	▁▃▇▃▁
C_reactive_protein_rint	Omnivore	95.08	0.00	1.00	-4.50	0.00	4.50	▁▂▇▂▁
C_reactive_protein_rint	Vegetarian	95.27	-0.31	1.05	-3.48	-0.28	3.06	▁▅▇▃▁
Calcium_rint	Omnivore	87.04	0.00	1.00	-4.48	0.00	4.48	▁▂▇▂▁
Calcium_rint	Vegetarian	87.63	-0.10	1.01	-3.18	-0.10	3.15	▁▅▇▃▁
Cholesterol_rint	Omnivore	95.27	0.01	1.00	-4.50	0.01	4.50	▁▂▇▂▁
Cholesterol_rint	Vegetarian	95.83	-0.33	1.00	-3.92	-0.35	3.43	▁▃▇▃▁
Creatinine_rint	Omnivore	95.22	0.01	1.00	-4.50	0.01	4.50	▁▂▇▂▁
Creatinine_rint	Vegetarian	95.70	-0.63	0.87	-3.51	-0.61	2.87	▁▅▇▂▁
Cystatin_C_rint	Omnivore	95.27	0.00	1.00	-4.50	0.00	4.50	▁▂▇▂▁
Cystatin_C_rint	Vegetarian	95.75	0.00	0.95	-3.40	0.01	2.62	▁▂▇▆▁
Direct_bilirubin_rint	Omnivore	82.09	0.00	1.00	-4.47	0.00	4.47	▁▂▇▂▁
Direct_bilirubin_rint	Vegetarian	81.53	-0.02	1.00	-3.93	-0.03	4.23	▁▃▇▂▁
Gamma_glutamyltransferase_rint	Omnivore	95.22	0.01	1.00	-4.50	0.01	4.50	▁▂▇▂▁
Gamma_glutamyltransferase_rint	Vegetarian	95.70	-0.43	1.00	-3.44	-0.47	3.64	▁▇▇▂▁
Glucose_rint	Omnivore	86.97	0.00	1.00	-4.48	0.00	4.48	▁▂▇▂▁
Glucose_rint	Vegetarian	87.67	-0.17	0.96	-3.34	-0.17	2.57	▁▃▇▆▁
HbA1c_rint	Omnivore	95.13	0.00	1.00	-4.50	0.00	4.50	▁▂▇▂▁
HbA1c_rint	Vegetarian	95.06	-0.21	0.93	-2.90	-0.20	2.98	▁▆▇▃▁
HDL_cholesterol_rint	Omnivore	87.04	0.00	1.00	-4.48	0.00	4.48	▁▂▇▂▁
HDL_cholesterol_rint	Vegetarian	87.67	0.06	0.97	-3.27	0.11	3.76	▁▃▇▂▁
IGF_1_rint	Omnivore	94.76	0.00	1.00	-4.50	0.00	4.50	▁▂▇▂▁
IGF_1_rint	Vegetarian	95.23	-0.08	1.00	-3.52	-0.05	3.24	▁▃▇▃▁
LDL_direct_rint	Omnivore	95.08	0.01	1.00	-4.50	0.01	4.50	▁▂▇▂▁
LDL_direct_rint	Vegetarian	95.70	-0.37	1.00	-4.26	-0.36	3.48	▁▃▇▃▁
Lipoprotein_A_rint	Omnivore	76.10	0.00	1.00	-4.45	0.00	4.45	▁▂▇▂▁
Lipoprotein_A_rint	Vegetarian	76.76	-0.06	0.99	-3.28	-0.04	2.81	▁▃▇▅▁
Oestradiol_rint	Omnivore	15.89	0.00	1.00	-4.11	0.00	4.11	▁▃▇▃▁
Oestradiol_rint	Vegetarian	24.40	0.21	0.99	-3.85	0.21	3.25	▁▂▇▆▁
Phosphate_rint	Omnivore	86.91	0.00	1.00	-4.48	0.00	4.48	▁▂▇▂▁
Phosphate_rint	Vegetarian	87.54	0.07	1.05	-3.50	0.09	3.63	▁▃▇▃▁
Rheumatoid_factor_rint	Omnivore	8.35	0.00	1.00	-3.95	0.00	3.95	▁▃▇▃▁
Rheumatoid_factor_rint	Vegetarian	7.56	0.03	1.00	-3.39	-0.04	2.79	▁▂▇▆▁
SHBG_rint	Omnivore	86.24	0.00	1.00	-4.48	0.00	4.48	▁▂▇▂▁
SHBG_rint	Vegetarian	86.68	0.26	1.03	-3.16	0.31	4.12	▁▅▇▃▁
Testosterone_rint	Omnivore	84.50	0.00	1.00	-4.48	0.00	4.48	▁▂▇▂▁
Testosterone_rint	Vegetarian	83.12	-0.17	1.03	-3.29	-0.27	3.13	▁▅▇▃▁
Total_bilirubin_rint	Omnivore	94.91	0.00	1.00	-4.50	0.00	4.50	▁▂▇▂▁
Total_bilirubin_rint	Vegetarian	95.45	-0.05	0.99	-3.08	-0.10	4.26	▁▇▇▂▁
Total_protein_rint	Omnivore	86.99	0.00	1.00	-4.48	0.00	4.48	▁▂▇▂▁
Total_protein_rint	Vegetarian	87.67	-0.07	0.99	-3.76	-0.07	3.48	▁▃▇▃▁
Triglycerides_rint	Omnivore	95.20	0.00	1.00	-4.50	0.00	4.50	▁▂▇▂▁
Triglycerides_rint	Vegetarian	95.70	-0.06	1.01	-3.64	-0.09	3.74	▁▃▇▂▁
Urate_rint	Omnivore	95.16	0.01	1.00	-4.50	0.01	4.50	▁▂▇▂▁
Urate_rint	Vegetarian	95.58	-0.48	0.95	-3.43	-0.51	2.88	▁▅▇▃▁
Urea_rint	Omnivore	95.22	0.01	1.00	-4.50	0.01	4.50	▁▂▇▂▁
Urea_rint	Vegetarian	95.70	-0.78	1.00	-3.96	-0.80	2.83	▁▅▇▃▁
Vitamin_D_rint	Omnivore	91.34	0.01	1.00	-4.49	0.01	4.49	▁▂▇▂▁
Vitamin_D_rint	Vegetarian	92.18	-0.38	1.10	-4.25	-0.38	3.64	▁▃▇▃▁
eGFR_rint	Omnivore	95.15	0.00	1.00	-4.50	0.00	4.50	▁▂▇▂▁
eGFR_rint	Vegetarian	95.62	0.31	0.98	-2.66	0.26	3.35	▁▅▇▅▁
bioavailableTest_rint	Omnivore	76.99	0.00	1.00	-4.46	0.00	4.46	▁▂▇▂▁
bioavailableTest_rint	Vegetarian	75.43	-0.20	1.05	-3.69	-0.31	3.35	▁▅▇▃▁
freeTest_rint	Omnivore	78.70	0.00	1.00	-4.46	0.00	4.46	▁▂▇▂▁
freeTest_rint	Vegetarian	77.19	-0.23	1.04	-3.88	-0.35	3.39	▁▃▇▃▁

Phenotype table SKIM

Mike Francis

2022-10-09 22:11:18

SKIM values in phenotype table

Load packages + make it so table always displays NA’s

SKIMR