Data frames

sample number	transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks	phosphates	nitrates	temperature	salinity
10	1	81	13/11/2013	01:00:00	140	Deep	-27.42	-44.72	3278	1232	0.20	0.26	17.3	35.9
11	1	85	13/11/2013	13:30:00	110	Deep	-26.80	-45.30	16312	1615	0.29	0.22	21.3	36.5
120	2	96	18/11/2013	23:50:00	5	Surf	-27.39	-47.82	1150	75	0.43	0.19	23.1	33.5
121	2		18/11/2013	23:50:00	30	Deep	-27.39	-47.82	1737	218	0.43	0.23	22.6	33.7
122	2		18/11/2013	23:50:00	50	Deep	-27.39	-47.82	853	234	0.56	0.21	20.3	35.9
125	2	98	18/11/2013	05:00:00	5	Surf	-27.59	-47.39	3086	1300	0.29	0.25	23.1	35.7
126	2		18/11/2013	05:00:00	50	Deep	-27.59	-47.39	1217	782	0.25	0.20	23.7	37.2
127	2		18/11/2013	05:00:00	85	Deep	-27.59	-47.39	3420	226	0.25	0.47	22.9	37.0
13	1	86	13/11/2013	17:00:00	105	Deep	-26.33	-45.41	6366	1007	0.34	0.15	20.9	36.3
140	2	101	18/11/2013	12:00:00	5	Surf	-27.79	-46.96	500	366	0.29	0.14	23.5	36.5

sample number	transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks	phosphates	nitrates	temperature	salinity
10	1	81	2013-11-13	1899-12-31 01:00:00	140	Deep	-27.42	-44.72	3278	1232	0.20	0.26	17.3	35.9
11	1	85	2013-11-13	1899-12-31 13:30:00	110	Deep	-26.80	-45.30	16312	1615	0.29	0.22	21.3	36.5
120	2	96	2013-11-18	1899-12-31 23:50:00	5	Surf	-27.39	-47.82	1150	75	0.43	0.19	23.1	33.5
121	2		2013-11-18	1899-12-31 23:50:00	30	Deep	-27.39	-47.82	1737	218	0.43	0.23	22.6	33.7
122	2		2013-11-18	1899-12-31 23:50:00	50	Deep	-27.39	-47.82	853	234	0.56	0.21	20.3	35.9
125	2	98	2013-11-18	1899-12-31 05:00:00	5	Surf	-27.59	-47.39	3086	1300	0.29	0.25	23.1	35.7
126	2		2013-11-18	1899-12-31 05:00:00	50	Deep	-27.59	-47.39	1217	782	0.25	0.20	23.7	37.2
127	2		2013-11-18	1899-12-31 05:00:00	85	Deep	-27.59	-47.39	3420	226	0.25	0.47	22.9	37.0
13	1	86	2013-11-13	1899-12-31 17:00:00	105	Deep	-26.33	-45.41	6366	1007	0.34	0.15	20.9	36.3
140	2	101	2013-11-18	1899-12-31 12:00:00	5	Surf	-27.79	-46.96	500	366	0.29	0.14	23.5	36.5

sample number	transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks	phosphates	nitrates	temperature	salinity
10	1	81	2013-11-13	1899-12-31 01:00:00	140	Deep	-27.42	-44.72	3278	1232	0.20	0.26	17.3	35.9
11	1	85	2013-11-13	1899-12-31 13:30:00	110	Deep	-26.80	-45.30	16312	1615	0.29	0.22	21.3	36.5
120	2	96	2013-11-18	1899-12-31 23:50:00	5	Surf	-27.39	-47.82	1150	75	0.43	0.19	23.1	33.5
121	2		2013-11-18	1899-12-31 23:50:00	30	Deep	-27.39	-47.82	1737	218	0.43	0.23	22.6	33.7
122	2		2013-11-18	1899-12-31 23:50:00	50	Deep	-27.39	-47.82	853	234	0.56	0.21	20.3	35.9
125	2	98	2013-11-18	1899-12-31 05:00:00	5	Surf	-27.59	-47.39	3086	1300	0.29	0.25	23.1	35.7
126	2		2013-11-18	1899-12-31 05:00:00	50	Deep	-27.59	-47.39	1217	782	0.25	0.20	23.7	37.2
127	2		2013-11-18	1899-12-31 05:00:00	85	Deep	-27.59	-47.39	3420	226	0.25	0.47	22.9	37.0
13	1	86	2013-11-13	1899-12-31 17:00:00	105	Deep	-26.33	-45.41	6366	1007	0.34	0.15	20.9	36.3
140	2	101	2013-11-18	1899-12-31 12:00:00	5	Surf	-27.79	-46.96	500	366	0.29	0.14	23.5	36.5

sample number	transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks	phosphates	nitrates	temperature	salinity
10	1	81	2013-11-13	1899-12-31 01:00:00	140	Deep	-27.42	-44.72	3278	1232	0.20	0.26	17.3	35.9
11	1	85	2013-11-13	1899-12-31 13:30:00	110	Deep	-26.80	-45.30	16312	1615	0.29	0.22	21.3	36.5
120	2	96	2013-11-18	1899-12-31 23:50:00	5	Surf	-27.39	-47.82	1150	75	0.43	0.19	23.1	33.5
121	2	96	2013-11-18	1899-12-31 23:50:00	30	Deep	-27.39	-47.82	1737	218	0.43	0.23	22.6	33.7
122	2	96	2013-11-18	1899-12-31 23:50:00	50	Deep	-27.39	-47.82	853	234	0.56	0.21	20.3	35.9
125	2	98	2013-11-18	1899-12-31 05:00:00	5	Surf	-27.59	-47.39	3086	1300	0.29	0.25	23.1	35.7
126	2	98	2013-11-18	1899-12-31 05:00:00	50	Deep	-27.59	-47.39	1217	782	0.25	0.20	23.7	37.2
127	2	98	2013-11-18	1899-12-31 05:00:00	85	Deep	-27.59	-47.39	3420	226	0.25	0.47	22.9	37.0
13	1	86	2013-11-13	1899-12-31 17:00:00	105	Deep	-26.33	-45.41	6366	1007	0.34	0.15	20.9	36.3
140	2	101	2013-11-18	1899-12-31 12:00:00	5	Surf	-27.79	-46.96	500	366	0.29	0.14	23.5	36.5

transect	sample number	station	depth	latitude	longitude	picoeuks	nanoeuks
1	10	81	140	-27.42	-44.72	3278	1232
1	11	85	110	-26.80	-45.30	16312	1615
2	120	96	5	-27.39	-47.82	1150	75
2	121	96	30	-27.39	-47.82	1737	218
2	122	96	50	-27.39	-47.82	853	234
2	125	98	5	-27.59	-47.39	3086	1300
2	126	98	50	-27.59	-47.39	1217	782
2	127	98	85	-27.59	-47.39	3420	226
1	13	86	105	-26.33	-45.41	6366	1007
2	140	101	5	-27.79	-46.96	500	366

transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks
1	81	2013-11-13	1899-12-31 01:00:00	140	Deep	-27.42	-44.72	3278	1232
1	85	2013-11-13	1899-12-31 13:30:00	110	Deep	-26.80	-45.30	16312	1615
2	96	2013-11-18	1899-12-31 23:50:00	5	Surf	-27.39	-47.82	1150	75
2	96	2013-11-18	1899-12-31 23:50:00	30	Deep	-27.39	-47.82	1737	218
2	96	2013-11-18	1899-12-31 23:50:00	50	Deep	-27.39	-47.82	853	234
2	98	2013-11-18	1899-12-31 05:00:00	5	Surf	-27.59	-47.39	3086	1300
2	98	2013-11-18	1899-12-31 05:00:00	50	Deep	-27.59	-47.39	1217	782
2	98	2013-11-18	1899-12-31 05:00:00	85	Deep	-27.59	-47.39	3420	226
1	86	2013-11-13	1899-12-31 17:00:00	105	Deep	-26.33	-45.41	6366	1007
2	101	2013-11-18	1899-12-31 12:00:00	5	Surf	-27.79	-46.96	500	366

sample number	transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks	temperature	salinity
10	1	81	2013-11-13	1899-12-31 01:00:00	140	Deep	-27.42	-44.72	3278	1232	17.3	35.9
11	1	85	2013-11-13	1899-12-31 13:30:00	110	Deep	-26.80	-45.30	16312	1615	21.3	36.5
120	2	96	2013-11-18	1899-12-31 23:50:00	5	Surf	-27.39	-47.82	1150	75	23.1	33.5
121	2	96	2013-11-18	1899-12-31 23:50:00	30	Deep	-27.39	-47.82	1737	218	22.6	33.7
122	2	96	2013-11-18	1899-12-31 23:50:00	50	Deep	-27.39	-47.82	853	234	20.3	35.9
125	2	98	2013-11-18	1899-12-31 05:00:00	5	Surf	-27.59	-47.39	3086	1300	23.1	35.7
126	2	98	2013-11-18	1899-12-31 05:00:00	50	Deep	-27.59	-47.39	1217	782	23.7	37.2
127	2	98	2013-11-18	1899-12-31 05:00:00	85	Deep	-27.59	-47.39	3420	226	22.9	37.0
13	1	86	2013-11-13	1899-12-31 17:00:00	105	Deep	-26.33	-45.41	6366	1007	20.9	36.3
140	2	101	2013-11-18	1899-12-31 12:00:00	5	Surf	-27.79	-46.96	500	366	23.5	36.5

transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks
1	81	2013-11-13	1899-12-31 01:00:00	140	Deep	-27.42	-44.72	3278	1232
1	85	2013-11-13	1899-12-31 13:30:00	110	Deep	-26.80	-45.30	16312	1615
2	96	2013-11-18	1899-12-31 23:50:00	5	Surf	-27.39	-47.82	1150	75
2	96	2013-11-18	1899-12-31 23:50:00	30	Deep	-27.39	-47.82	1737	218
2	96	2013-11-18	1899-12-31 23:50:00	50	Deep	-27.39	-47.82	853	234
2	98	2013-11-18	1899-12-31 05:00:00	5	Surf	-27.59	-47.39	3086	1300
2	98	2013-11-18	1899-12-31 05:00:00	50	Deep	-27.59	-47.39	1217	782
2	98	2013-11-18	1899-12-31 05:00:00	85	Deep	-27.59	-47.39	3420	226
1	86	2013-11-13	1899-12-31 17:00:00	105	Deep	-26.33	-45.41	6366	1007
2	101	2013-11-18	1899-12-31 12:00:00	5	Surf	-27.79	-46.96	500	366

sample_number	transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks	phosphates	nitrates	temperature	salinity
10	1	81	2013-11-13	1899-12-31 01:00:00	140	Deep	-27.42	-44.72	3278	1232	0.20	0.26	17.3	35.9
11	1	85	2013-11-13	1899-12-31 13:30:00	110	Deep	-26.80	-45.30	16312	1615	0.29	0.22	21.3	36.5
120	2	96	2013-11-18	1899-12-31 23:50:00	5	Surf	-27.39	-47.82	1150	75	0.43	0.19	23.1	33.5
121	2	96	2013-11-18	1899-12-31 23:50:00	30	Deep	-27.39	-47.82	1737	218	0.43	0.23	22.6	33.7
122	2	96	2013-11-18	1899-12-31 23:50:00	50	Deep	-27.39	-47.82	853	234	0.56	0.21	20.3	35.9
125	2	98	2013-11-18	1899-12-31 05:00:00	5	Surf	-27.59	-47.39	3086	1300	0.29	0.25	23.1	35.7
126	2	98	2013-11-18	1899-12-31 05:00:00	50	Deep	-27.59	-47.39	1217	782	0.25	0.20	23.7	37.2
127	2	98	2013-11-18	1899-12-31 05:00:00	85	Deep	-27.59	-47.39	3420	226	0.25	0.47	22.9	37.0
13	1	86	2013-11-13	1899-12-31 17:00:00	105	Deep	-26.33	-45.41	6366	1007	0.34	0.15	20.9	36.3
140	2	101	2013-11-18	1899-12-31 12:00:00	5	Surf	-27.79	-46.96	500	366	0.29	0.14	23.5	36.5

sample_number	transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks	phosphates	nitrates	temperature	salinity	pico_pct
10	1	81	2013-11-13	1899-12-31 01:00:00	140	Deep	-27.42	-44.72	3278	1232	0.20	0.26	17.3	35.9	72.68293
11	1	85	2013-11-13	1899-12-31 13:30:00	110	Deep	-26.80	-45.30	16312	1615	0.29	0.22	21.3	36.5	90.99124
120	2	96	2013-11-18	1899-12-31 23:50:00	5	Surf	-27.39	-47.82	1150	75	0.43	0.19	23.1	33.5	93.87755
121	2	96	2013-11-18	1899-12-31 23:50:00	30	Deep	-27.39	-47.82	1737	218	0.43	0.23	22.6	33.7	88.84910
122	2	96	2013-11-18	1899-12-31 23:50:00	50	Deep	-27.39	-47.82	853	234	0.56	0.21	20.3	35.9	78.47286
125	2	98	2013-11-18	1899-12-31 05:00:00	5	Surf	-27.59	-47.39	3086	1300	0.29	0.25	23.1	35.7	70.36024
126	2	98	2013-11-18	1899-12-31 05:00:00	50	Deep	-27.59	-47.39	1217	782	0.25	0.20	23.7	37.2	60.88044
127	2	98	2013-11-18	1899-12-31 05:00:00	85	Deep	-27.59	-47.39	3420	226	0.25	0.47	22.9	37.0	93.80143
13	1	86	2013-11-13	1899-12-31 17:00:00	105	Deep	-26.33	-45.41	6366	1007	0.34	0.15	20.9	36.3	86.34206
140	2	101	2013-11-18	1899-12-31 12:00:00	5	Surf	-27.79	-46.96	500	366	0.29	0.14	23.5	36.5	57.73672

sample_number	transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks	pico_pct
10	1	81	2013-11-13	1899-12-31 01:00:00	140	Deep	-27.42	-44.72	3278	1232	72.68293
11	1	85	2013-11-13	1899-12-31 13:30:00	110	Deep	-26.80	-45.30	16312	1615	90.99124
120	2	96	2013-11-18	1899-12-31 23:50:00	5	Surf	-27.39	-47.82	1150	75	93.87755
121	2	96	2013-11-18	1899-12-31 23:50:00	30	Deep	-27.39	-47.82	1737	218	88.84910
122	2	96	2013-11-18	1899-12-31 23:50:00	50	Deep	-27.39	-47.82	853	234	78.47286
125	2	98	2013-11-18	1899-12-31 05:00:00	5	Surf	-27.59	-47.39	3086	1300	70.36024
126	2	98	2013-11-18	1899-12-31 05:00:00	50	Deep	-27.59	-47.39	1217	782	60.88044
127	2	98	2013-11-18	1899-12-31 05:00:00	85	Deep	-27.59	-47.39	3420	226	93.80143
13	1	86	2013-11-13	1899-12-31 17:00:00	105	Deep	-26.33	-45.41	6366	1007	86.34206
140	2	101	2013-11-18	1899-12-31 12:00:00	5	Surf	-27.79	-46.96	500	366	57.73672

sample_number	transect	station	date	time	sample_label
10	1	81	2013-11-13	1899-12-31 01:00:00	TR_1_St_81
11	1	85	2013-11-13	1899-12-31 13:30:00	TR_1_St_85
120	2	96	2013-11-18	1899-12-31 23:50:00	TR_2_St_96
121	2	96	2013-11-18	1899-12-31 23:50:00	TR_2_St_96
122	2	96	2013-11-18	1899-12-31 23:50:00	TR_2_St_96
125	2	98	2013-11-18	1899-12-31 05:00:00	TR_2_St_98
126	2	98	2013-11-18	1899-12-31 05:00:00	TR_2_St_98
127	2	98	2013-11-18	1899-12-31 05:00:00	TR_2_St_98
13	1	86	2013-11-13	1899-12-31 17:00:00	TR_1_St_86
140	2	101	2013-11-18	1899-12-31 12:00:00	TR_2_St_101

sample_number	transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks	phosphates	nitrates	temperature	salinity	pico_pct
10	1	81	2013-11-13	1:0	140	Deep	-27.42	-44.72	3278	1232	0.20	0.26	17.3	35.9	72.68293
11	1	85	2013-11-13	13:30	110	Deep	-26.80	-45.30	16312	1615	0.29	0.22	21.3	36.5	90.99124
120	2	96	2013-11-18	23:50	5	Surf	-27.39	-47.82	1150	75	0.43	0.19	23.1	33.5	93.87755
121	2	96	2013-11-18	23:50	30	Deep	-27.39	-47.82	1737	218	0.43	0.23	22.6	33.7	88.84910
122	2	96	2013-11-18	23:50	50	Deep	-27.39	-47.82	853	234	0.56	0.21	20.3	35.9	78.47286
125	2	98	2013-11-18	5:0	5	Surf	-27.59	-47.39	3086	1300	0.29	0.25	23.1	35.7	70.36024
126	2	98	2013-11-18	5:0	50	Deep	-27.59	-47.39	1217	782	0.25	0.20	23.7	37.2	60.88044
127	2	98	2013-11-18	5:0	85	Deep	-27.59	-47.39	3420	226	0.25	0.47	22.9	37.0	93.80143
13	1	86	2013-11-13	17:0	105	Deep	-26.33	-45.41	6366	1007	0.34	0.15	20.9	36.3	86.34206
140	2	101	2013-11-18	12:0	5	Surf	-27.79	-46.96	500	366	0.29	0.14	23.5	36.5	57.73672

sample_number	transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks	phosphates	nitrates	temperature	salinity	pico_pct
3	0	19	2013-11-02	13:30	5	Surf	-25.79	-40.36	1005	898	0.29	0.48	22.7	36.9	52.81135
5	0	21	2013-11-02	0:0	5	Surf	-26.23	-40.09	793	660	0.16	0.90	22.8	36.9	54.57674
7	0	26	2013-11-03	19:30	5	Surf	-27.31	-39.38	907	856	0.20	0.50	21.2	36.4	51.44640
1	0	6	2013-10-31	5:20	45	Deep	-23.58	-41.78	7651	4845	0.47	1.07	19.7	36.3	61.22759
2	0	6	2013-10-31	5:20	45	Deep	-23.58	-41.78	7343	3258	0.47	1.07	19.7	36.3	69.26705
10	1	81	2013-11-13	1:0	140	Deep	-27.42	-44.72	3278	1232	0.20	0.26	17.3	35.9	72.68293
9	1	81	2013-11-13	1:0	140	Deep	-27.42	-44.72	3181	1235	0.20	0.26	17.3	35.9	72.03351
11	1	85	2013-11-13	13:30	110	Deep	-26.80	-45.30	16312	1615	0.29	0.22	21.3	36.5	90.99124
13	1	86	2013-11-13	17:0	105	Deep	-26.33	-45.41	6366	1007	0.34	0.15	20.9	36.3	86.34206
15	1	87	2013-11-13	19:30	105	Deep	-26.22	-45.48	6189	622	0.47	1.51	19.5	36.1	90.86771

sample_number	transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks	phosphates	nitrates	temperature	salinity	pico_pct
1	0	6	2013-10-31	5:20	45	Deep	-23.58	-41.78	7651	4845	0.47	1.07	19.7	36.3	61.22759
2	0	6	2013-10-31	5:20	45	Deep	-23.58	-41.78	7343	3258	0.47	1.07	19.7	36.3	69.26705
3	0	19	2013-11-02	13:30	5	Surf	-25.79	-40.36	1005	898	0.29	0.48	22.7	36.9	52.81135
5	0	21	2013-11-02	0:0	5	Surf	-26.23	-40.09	793	660	0.16	0.90	22.8	36.9	54.57674
7	0	26	2013-11-03	19:30	5	Surf	-27.31	-39.38	907	856	0.20	0.50	21.2	36.4	51.44640
10	1	81	2013-11-13	1:0	140	Deep	-27.42	-44.72	3278	1232	0.20	0.26	17.3	35.9	72.68293
9	1	81	2013-11-13	1:0	140	Deep	-27.42	-44.72	3181	1235	0.20	0.26	17.3	35.9	72.03351
11	1	85	2013-11-13	13:30	110	Deep	-26.80	-45.30	16312	1615	0.29	0.22	21.3	36.5	90.99124
13	1	86	2013-11-13	17:0	105	Deep	-26.33	-45.41	6366	1007	0.34	0.15	20.9	36.3	86.34206
15	1	87	2013-11-13	19:30	105	Deep	-26.22	-45.48	6189	622	0.47	1.51	19.5	36.1	90.86771

transect	n
0	5
1	5
2	18

transect	station	n_samples	mean_pico_percent
0	6	2	65.24732
0	19	1	52.81135
0	21	1	54.57674
0	26	1	51.44640
1	81	2	72.35822
1	85	1	90.99124
1	86	1	86.34206
1	87	1	90.86771
2	96	3	87.06651
2	98	3	75.01403

sample_number	transect	station	date	time	depth	level	latitude	longitude	picoeuks	nanoeuks	phosphates	nitrates	temperature	salinity	pico_pct
3	0	19	2013-11-02	13:30	5	Surf	-25.79	-40.36	1005	898	0.29	0.48	22.7	36.9	52.81135
5	0	21	2013-11-02	0:0	5	Surf	-26.23	-40.09	793	660	0.16	0.90	22.8	36.9	54.57674
7	0	26	2013-11-03	19:30	5	Surf	-27.31	-39.38	907	856	0.20	0.50	21.2	36.4	51.44640
120	2	96	2013-11-18	23:50	5	Surf	-27.39	-47.82	1150	75	0.43	0.19	23.1	33.5	93.87755
125	2	98	2013-11-18	5:0	5	Surf	-27.59	-47.39	3086	1300	0.29	0.25	23.1	35.7	70.36024
140	2	101	2013-11-18	12:0	5	Surf	-27.79	-46.96	500	366	0.29	0.14	23.5	36.5	57.73672
155	2	106	2013-11-19	2:30	5	Surf	-28.12	-46.17	355	18	0.25	0.37	23.0	36.9	95.17426
165	2	114	2013-11-19	21:40	5	Surf	-28.65	-44.99	728	226	0.29	0.28	22.4	36.4	76.31027
Trichod.1	2					Surf	-27.80	-47.10	1002	194					83.77926
Trichod.2	2					Surf	-27.80	-47.10	744	206					78.31579

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R course Daniel Vaulot 2023-01-19 Data wrangling

R course Daniel Vaulot...
R - Session 02
Data frames
R objects
Data frames
Useful functions
Access specific value
Access specific column
Access row
Tidy data
Installation and Resources
Basic concepts
Load necessary libraries
Read and Write data
Oceanographic data
Microbial populations
Read data
Reading a text file
Excel sheet
Read the data - read_excel
Bad data input under Excel
Filling missing values - fill
Write data
Write data
dplyr - Manipulate tables
@allison_horst...
Manipulate columns
List and Summarize columns
Select specific columns - select
Select a range of columns - select
Unselect columns - select
Using the pipe operator - %>%
Renaming variables - rename
Creating new variables - mutate
Using the pipe operator you can chain operations
Creating labels with mutate and stringr functions
Changing type of some columns - mutate
Manipulating rows
Order rows - arrange
Order rows - transform to numeric
Summarize rows - count
Summarize rows - group_by / summarize
Filtering rows - filter
Recap
Next time: Data visualization (ggplot2)