Help on plotting probability density for calendar dates

gianmarco · Sep 12, 2013

Hi All,
I would like to have some hints on how to plot in R a chart similar to the one attached.
It is a figure from a Journal article of mine (JOURNAL OF QUATERNARY SCIENCE (2013) 28(6) 630–640; ISSN 0267-8179. DOI: 10.1002/jqs.2659). I made it with JMP.

The problem is that I would like to make something similar in R (ggplot2?), by the main issue for me is the fact that I am dealing with calendar dates, and I do not know how to tackle this issue in R.

The chart is actually plotting the probability density for the radiocarbon calendar dates for 4 different archaeological sites. The data on which is based are provided by a program used for Bayesian radiocarbon dating.

The program returns a file with two columns: one for the calendar date, one for the probability of each date. A third column could be used for a grouping variable, in case of more than 1 site.

In JMP it is quite straightforward to make the chart; but with R I am lost...
How is it possible to chart calendar dates on the x axis ?

Any help is appreciated.

Regards
Gm

p.s.
sample dataset

Code:

dates	prob	site
-1669,5	0,000006592	A
-1664,5	0,000008077	A
-1659,5	0,000010774	A
-1654,5	0,000013171	A
-1649,5	0,000013089	A
-1644,5	0,000014846	A
-1639,5	0,000020908	A
-1634,5	0,000025552	A
-1629,5	0,000030524	A
-1624,5	0,0000333	A
-1619,5	0,00003883	A
-1614,5	0,0000498	A
-1609,5	0,00006008	A
-1604,5	0,0000779	A
-1599,5	0,00009127	A
-1594,5	0,00011045	A
-1589,5	0,00013803	A
-1584,5	0,00016183	A
-1579,5	0,00020962	A
-1574,5	0,00024032	A
-1569,5	0,00029564	A
-1564,5	0,0003831	A
-1559,5	0,0005092	A
-1554,5	0,0006705	A
-1549,5	0,0008538	A
-1544,5	0,0011448	A
-1539,5	0,0014985	A
-1534,5	0,0020447	A
-1529,5	0,0027548	A
-1524,5	0,003599	A
-1519,5	0,004628	A
-1514,5	0,005829	A
-1509,5	0,007203	A
-1504,5	0,0088	A
-1499,5	0,010631	A
-1494,5	0,012035	A
-1489,5	0,012699	A
-1484,5	0,012967	A
-1479,5	0,01296	A
-1474,5	0,01316	A
-1469,5	0,013552	A
-1464,5	0,013621	A
-1459,5	0,013222	A
-1454,5	0,011972	A
-1449,5	0,010188	A
-1444,5	0,007949	A
-1439,5	0,005573	A
-1434,5	0,003478	A
-1429,5	0,0019968	A
-1424,5	0,0011756	A
-1419,5	0,0006661	A
-1414,5	0,0003989	A
-1409,5	0,00018489	A
-2824,5	2,07E-03	B
-2819,5	5,23E-04	B
-2814,5	1,03E-03	B
-2809,5	3,10E-03	B
-2804,5	6,26E-07	B
-2799,5	2,07E-03	B
-2794,5	3,10E-03	B
-2789,5	2,07E-03	B
-2784,5	8,33E-04	B
-2779,5	3,10E-03	B
-2774,5	2,07E-03	B
-2769,5	1,03E-03	B
-2764,5	4,19E-04	B
-2759,5	5,23E-04	B
-2754,5	1,03E-03	B
-2749,5	1,03E-03	B
-2744,5	1,03E-03	B
-2739,5	3,10E-03	B
-2734,5	3,10E-03	B
-2729,5	0	B
-2724,5	1,03E-03	B
-2719,5	0	B
-2714,5	4,19E-04	B
-2709,5	3,10E-03	B
-2704,5	2,07E-03	B
-2699,5	3,10E-03	B
-2694,5	3,10E-03	B
-2689,5	3,10E-03	B
-2684,5	2,07E-03	B
-2679,5	4,19E-04	B
-2674,5	2,07E-03	B
-2669,5	3,10E-03	B
-2664,5	4,19E-04	B
-2659,5	6,26E-07	B
-2654,5	0	B
-2649,5	4,19E-04	B
-2644,5	3,10E-03	B
-2639,5	4,19E-04	B
-2634,5	4,19E-04	B
-2629,5	1,03E-03	B
-2624,5	3,10E-03	B
-2619,5	5,23E-04	B
-2614,5	6,26E-07	B
-2609,5	2,07E-03	B
-2604,5	5,23E-04	B
-2599,5	2,07E-03	B
-2594,5	1,03E-03	B
-2589,5	8,33E-04	B
-2584,5	3,10E-03	B
-2579,5	5,23E-04	B
-2574,5	5,23E-04	B
-2569,5	1,03E-03	B
-2564,5	8,33E-04	B
-2559,5	7,30E-04	B
-2554,5	6,26E-07	B
-2549,5	3,10E-03	B
-2544,5	4,19E-04	B
-2539,5	5,23E-04	B
-2534,5	4,19E-04	B
-2529,5	5,23E-04	B
-2524,5	3,10E-03	B
-2519,5	5,23E-04	B
-2514,5	4,19E-04	B
-2509,5	9,36E-04	B
-2504,5	4,19E-04	B
-2499,5	4,19E-04	B
-2494,5	3,10E-03	B
-2489,5	8,33E-04	B
-2484,5	4,19E-04	B
-2479,5	8,33E-04	B
-2474,5	4,19E-04	B
-2469,5	1,03E-03	B
-2464,5	3,10E-03	B
-2459,5	4,19E-04	B
-2454,5	5,23E-04	B
-2449,5	2,07E-03	B
-2444,5	5,23E-04	B
-2439,5	5,23E-04	B
-2434,5	9,36E-04	B
-2429,5	4,19E-04	B
-2424,5	4,19E-04	B
-2419,5	6,26E-07	B
-2414,5	5,23E-04	B
-2409,5	6,26E-07	B
-2404,5	6,26E-07	B
-2399,5	6,26E-07	B
-2394,5	4,19E-04	B
-2389,5	1,0399E-006	B
-2384,5	1,0399E-006	B
-2379,5	4,19E-04	B
-2374,5	7,30E-04	B
-2369,5	7,30E-04	B
-2364,5	5,23E-04	B
-2359,5	8,33E-04	B
-2354,5	8,33E-04	B
-2349,5	1,3555E-006	B
-2344,5	6,26E-07	B
-2339,5	1,1485E-006	B
-2334,5	7,30E-04	B
-2329,5	0,000001252	B
-2324,5	8,33E-04	B
-2319,5	9,36E-04	B
-2314,5	1,1433E-006	B
-2309,5	1,0399E-006	B
-2304,5	0,000001252	B
-2299,5	0,000001252	B
-2294,5	2,3953E-006	B
-2289,5	1,1485E-006	B
-2284,5	1,3555E-006	B
-2279,5	1,4589E-006	B
-2274,5	2,1884E-006	B
-2269,5	1,0399E-006	B
-2264,5	4,19E-04	B
-2259,5	2,3953E-006	B
-2254,5	9,36E-04	B
-2249,5	1,9815E-006	B
-2244,5	1,7693E-006	B
-2239,5	2,4988E-006	B
-2234,5	2,0849E-006	B
-2229,5	1,9815E-006	B
-2224,5	2,1884E-006	B
-2219,5	2,1884E-006	B
-2214,5	1,3555E-006	B
-2209,5	2,2919E-006	B
-2204,5	1,0399E-006	B
-2199,5	1,7693E-006	B
-2194,5	0,000003228	B
-2189,5	1,7693E-006	B
-2184,5	2,3953E-006	B
-2179,5	1,7693E-006	B
-2174,5	2,7109E-006	B
-2169,5	2,0849E-006	B
-2164,5	2,1884E-006	B
-2159,5	2,9179E-006	B
-2154,5	3,1248E-006	B
-2149,5	2,7109E-006	B
-2144,5	2,8144E-006	B
-2139,5	2,7109E-006	B
-2134,5	0,00000344	B
-2129,5	0,000003958	B
-2124,5	3,0213E-006	B
-2119,5	0,000003647	B
-2114,5	0,000003544	B
-2109,5	0,000003958	B
-2104,5	0,000005003	B
-2099,5	0,000003751	B
-2094,5	0,00000344	B
-2089,5	0,00000344	B
-2084,5	0,000003751	B
-2079,5	0,000005106	B
-2074,5	0,00000552	B
-2069,5	0,000006669	B
-2064,5	0,000004687	B
-2059,5	0,000006146	B
-2054,5	0,00000552	B
-2049,5	0,000005624	B
-2044,5	0,000003958	B
-2039,5	0,000004899	B
-2034,5	0,000004687	B
-2029,5	0,00000448	B
-2024,5	0,000005417	B
-2019,5	0,00000521	B
-2014,5	0,000006565	B
-2009,5	0,000005629	B
-2004,5	0,000006565	B
-1999,5	0,000006043	B
-1994,5	0,000008438	B
-1989,5	0,00000865	B
-1984,5	0,000008231	B
-1979,5	0,000009897	B
-1974,5	0,000007812	B
-1969,5	0,000009586	B
-1964,5	0,000009064	B
-1959,5	0,000011563	B
-1954,5	0,000011045	B
-1949,5	0,000009374	B
-1944,5	0,000008857	B
-1939,5	0,000010942	B
-1934,5	0,000010626	B
-1929,5	0,000013441	B
-1924,5	0,000014377	B
-1919,5	0,000014067	B
-1914,5	0,000013022	B
-1909,5	0,000013337	B
-1904,5	0,00001594	B
-1899,5	0,000014688	B
-1894,5	0,000015733	B
-1889,5	0,000015526	B
-1884,5	0,000017818	B
-1879,5	0,000022194	B
-1874,5	0,000021149	B
-1869,5	0,000019276	B
-1864,5	0,000020001	B
-1859,5	0,000021568	B
-1854,5	0,000023027	B
-1849,5	0,000026152	B
-1844,5	0,000026462	B
-1839,5	0,00003407	B
-1834,5	0,000030524	B
-1829,5	0,000035	B
-1824,5	0,00003167	B
-1819,5	0,00003522	B
-1814,5	0,00003646	B
-1809,5	0,00003855	B
-1804,5	0,00003959	B
-1799,5	0,00004418	B
-1794,5	0,0000473	B
-1789,5	0,00005126	B
-1784,5	0,0000522	B
-1779,5	0,0000548	B
-1774,5	0,00005657	B
-1769,5	0,00006074	B
-1764,5	0,0000573	B
-1759,5	0,00006772	B
-1754,5	0,00006657	B
-1749,5	0,00007793	B
-1744,5	0,00007168	B
-1739,5	0,00007689	B
-1734,5	0,00008648	B
-1729,5	0,0000848	B
-1724,5	0,00009679	B
-1719,5	0,00010085	B
-1714,5	0,00011648	B
-1709,5	0,00011387	B
-1704,5	0,00012752	B
-1699,5	0,00013367	B
-1694,5	0,00014638	B
-1689,5	0,00014461	B
-1684,5	0,00015117	B
-1679,5	0,00016607	B
-1674,5	0,00017003	B
-1669,5	0,00018649	B
-1664,5	0,00017888	B
-1659,5	0,00020837	B
-1654,5	0,00022014	B
-1649,5	0,00023264	B
-1644,5	0,00024056	B
-1639,5	0,00026161	B
-1634,5	0,00029442	B
-1629,5	0,0003231	B
-1624,5	0,0003187	B
-1619,5	0,0003336	B
-1614,5	0,0003764	B
-1609,5	0,0003985	B
-1604,5	0,0004431	B
-1599,5	0,0004504	B
-1594,5	0,0004956	B
-1589,5	0,0005266	B
-1584,5	0,0005724	B
-1579,5	0,0006123	B
-1574,5	0,0006592	B
-1569,5	0,0007033	B
-1564,5	0,0007509	B
-1559,5	0,0008106	B
-1554,5	0,0008934	B
-1549,5	0,0009358	B
-1544,5	0,0009987	B
-1539,5	0,0011179	B
-1534,5	0,0012024	B
-1529,5	0,0013187	B
-1524,5	0,0014093	B
-1519,5	0,0015659	B
-1514,5	0,0016589	B
-1509,5	0,0017676	B
-1504,5	0,0019496	B
-1499,5	0,0021323	B
-1494,5	0,0022801	B
-1489,5	0,0023411	B
-1484,5	0,002507	B
-1479,5	0,0027229	B
-1474,5	0,0028387	B
-1469,5	0,0030357	B
-1464,5	0,003263	B
-1459,5	0,003509	B
-1454,5	0,003735	B
-1449,5	0,004069	B
-1444,5	0,004223	B
-1439,5	0,004461	B
-1434,5	0,004785	B
-1429,5	0,004897	B
-1424,5	0,004994	B
-1419,5	0,005062	B
-1414,5	0,005134	B
-1409,5	0,005106	B
-1404,5	0,005174	B
-1399,5	0,005048	B
-1394,5	0,004985	B
-1389,5	0,004902	B
-1384,5	0,004888	B
-1379,5	0,004844	B
-1374,5	0,004814	B
-1369,5	0,00474	B
-1364,5	0,004588	B
-1359,5	0,004551	B
-1354,5	0,004453	B
-1349,5	0,004202	B
-1344,5	0,004184	B
-1339,5	0,003915	B
-1334,5	0,003701	B
-1329,5	0,00346	B
-1324,5	0,003254	B
-1319,5	0,0029803	B
-1314,5	0,0027911	B
-1309,5	0,0025808	B
-1304,5	0,0025583	B
-1299,5	0,0023674	B
-1294,5	0,0020454	B
-1289,5	0,0017832	B
-1284,5	0,0016215	B
-1279,5	0,0013817	B
-1274,5	0,001173	B
-1269,5	0,0008482	B
-1264,5	0,0007464	B
-1259,5	0,0004251	B
-1254,5	0,00031495	B
-1249,5	0,00024087	B
-1244,5	0,00022628	B
-1239,5	0,00027098	B
-1234,5	0,0003194	B
-1229,5	0,00027858	B
-1224,5	0,00020951	B
-1219,5	0,00011721	B
-1214,5	0,00006886	B
-1209,5	0,000017192	B
-1204,5	0,000013022	B

vinux · Sep 12, 2013

Initially I got confued with the comma (decimal point). You could plot this easily in ggplot. Since dates are in years, you don't need a special treatment.

Code:

ggplot(data=yourdata)+geom_line(aes(x=dates,y=prob,color=site))

gianmarco · Sep 12, 2013

Hi Vinux,
thanks for putting me on the right track.
As you can see from the attached .pdf, I managed to make the plot.

Now, I would like to:
1) zoom-in, i.e. setting the limits for the x axis between -1700 and -1300
2) if possible, to fill the area under the curves

Any idea?

Thanks again.
Gm

vinux · Sep 12, 2013

1. Add

Code:

scale_x_continuous(limits =c(-1700,-1300))

to the ggplot
2. You could try

Code:

geom_area(aes(x=dates,y=prob,fill=site))

instead of geom_line. You need to be careful on the intersection of two curves.

gianmarco · Sep 12, 2013

Thanks Vinux,
(2) works fine, even though I have to search further on how one can set some transparency.

As for (1), I do not get where the piece of code must be put within the main command???

Code:

scale_x_continuous(limits =c(-1700,-1300))

Gm

vinux · Sep 12, 2013

This way

Code:

ggplot(data=yourdata)+ geom_line(aes(x=dates,y=prob,color=site)) + scale_x_continuous(limits =c(-1700,-1300))

gianmarco · Sep 12, 2013

Unfortunately, upon further inspection, the following code does not produce the right plot.
Compare the previously attached plot to the new one. The dataset is, quite obviously, the same.
In the second plot, I notice that the curves are all the same (i.e., the first repeated 3 times).
I do not get why?

Code:

ggplot(data=data)+geom_area(aes(x=dates,y=prob,fill=site))

gianmarco · Sep 12, 2013

Vinux,
thanks.
Just to summarize the achievements:

Code:

ggplot(data=yourdata)+ geom_line(aes(x=dates,y=prob,color=site)) + scale_x_continuous(limits =c(-1700,-1300))

This works fine.

What remains to do is to fill the area under the curve.

vinux · Sep 13, 2013

You can do the transparency by adding alpha parameters. Here is an example.

Code:

ggplot(data=yourdata)+geom_area(aes(x=dates,y=prob,fill=site), alpha=0.3) +
  scale_x_continuous(limits =c(-1700,-1300))

gianmarco · Sep 13, 2013

Vinux,
thanks.
But there is an issue: I do not get why the plot made with code (1) is correct (=JPG_1), while the plot done with code (2) is wrong (=JPG_2).
code 1

Code:

ggplot(data=data)+ geom_line(aes(x=dates,y=prob,color=site)) + scale_x_continuous(limits =c(-1700,-1200))

code 2

Code:

ggplot(data=data)+geom_area(aes(x=dates,y=prob,fill=site), alpha=0.5) + scale_x_continuous(limits =c(-1700,-1200))

(dataset attached)

Any idea?

Gm

vinux · Sep 13, 2013

Sorry. I guess the default option in geom_area is "stack". Good observation.

Change the position you can get the graph you want. I have added position="identity" in the geom_area.
Try this

Code:

  ggplot(data=yourdata)+  geom_area(position="identity", aes(x=dates,y=prob,fill=site), alpha=0.3) +  scale_x_continuous(limits =c(-1700,-1300))

or

Code:

 ggplot(data=yourdata)+geom_line(aes(x=dates,y=prob,color=site)) + geom_area(position="identity",aes(x=dates,y=prob,fill=site), alpha=0.3) +
  scale_x_continuous(limits =c(-1700,-1300))

gianmarco · Sep 13, 2013

Many Thanks, Vinux !!!!
Both worked like a charm.

Regards
Gm

Help on plotting probability density for calendar dates

gianmarco

TS Contributor

vinux

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gianmarco

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vinux

Dark Knight

gianmarco

TS Contributor

vinux

Dark Knight

gianmarco

TS Contributor

gianmarco

TS Contributor

vinux

Dark Knight

gianmarco

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vinux

Dark Knight

gianmarco

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