An example
In this example, we will learn how to create a import function for a specific eem file generated by the software of a Cary Eclipse spectrofluorometer. First, lets have a look to the content of custom_cary.csv.
file <- system.file("extdata/custom_cary.csv", package = "eemR")
cat(readLines(file, n = 25), sep = "\n")
Wavelength (nm),Intensity (a.u.),Z Axis,
,01_SYN_50.00,01_SYN_55.00,01_SYN_60.00,01_SYN_65.00,01_SYN_70.00,01_SYN_75.00,01_SYN_80.00,01_SYN_85.00,01_SYN_90.00,01_SYN_95.00,01_SYN_100.00,01_SYN_105.00,01_SYN_110.00,01_SYN_115.00,01_SYN_120.00,01_SYN_125.00,01_SYN_130.00,01_SYN_135.00,01_SYN_140.00,01_SYN_145.00,01_SYN_150.00,01_SYN_155.00,01_SYN_160.00,01_SYN_165.00,01_SYN_170.00,01_SYN_175.00,01_SYN_180.00,01_SYN_185.00,01_SYN_190.00,01_SYN_195.00,01_SYN_200.00,01_SYN_205.00,01_SYN_210.00,01_SYN_215.00,01_SYN_220.00,01_SYN_225.00,01_SYN_230.00,01_SYN_235.00,01_SYN_240.00,01_SYN_245.00,01_SYN_250.00,01_SYN_255.00,01_SYN_260.00,01_SYN_265.00,01_SYN_270.00,01_SYN_275.00,01_SYN_280.00,01_SYN_285.00,01_SYN_290.00,01_SYN_295.00,01_SYN_300.00,01_SYN_305.00,01_SYN_310.00,01_SYN_315.00,01_SYN_320.00,01_SYN_325.00,01_SYN_330.00
,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57
250,1.85870516300201,2.80107355117798,3.22146272659302,3.60980105400085,4.71845960617065,5.5966010093689,6.45598602294922,7.89595937728882,10.0022115707397,12.8900260925293,16.6048526763916,21.7009887695313,26.7308120727539,33.5129280090332,39.6480255126953,46.94189453125,52.1451263427734,59.4381446838379,63.8430557250977,71.0080108642578,74.9123001098633,80.2605209350586,84.8504257202148,87.1108627319336,87.6054077148438,89.1303558349609,88.1718978881836,89.9914093017578,90.4588851928711,90.4412231445313,91.7687301635742,88.9126510620117,88.2239227294922,83.9044876098633,81.0552597045898,76.6695327758789,72.4987258911133,68.7890853881836,65.8365325927734,91.5800476074219,109.421615600586,93.5778274536133,53.0399932861328,44.5870552062988,40.4739570617676,37.5545845031738,33.1918907165527,30.9178428649902,30.7513618469238,28.8479671478271,26.2540702819824,22.5371971130371,19.1686763763428,16.6529712677002,14.7242202758789,13.7677135467529,12.4740467071533
252.029998779297,2.1434018611908,3.11827969551086,3.62917947769165,4.18700551986694,5.13205671310425,6.11557626724243,7.16383838653564,8.7924222946167,10.8015441894531,13.4013109207153,17.4247570037842,22.7168807983398,28.294412612915,34.4576759338379,40.9357948303223,47.6901092529297,52.4071464538574,59.475528717041,64.4546813964844,70.2739791870117,75.7940139770508,79.9471435546875,83.4396667480469,85.106819152832,85.8016052246094,88.5793075561523,89.0074234008789,90.2360687255859,89.7650833129883,89.8542327880859,89.0672988891602,86.7302703857422,85.7473220825195,82.5640640258789,78.6254653930664,74.7004547119141,70.4368133544922,66.7534103393555,63.1299095153809,68.2004776000977,97.5321884155273,110.740531921387,60.1052017211914,44.5394287109375,39.8698654174805,36.2816505432129,33.5453300476074,30.2543392181396,28.1765575408936,25.9400939941406,25.5557174682617,22.9261245727539,18.3974666595459,15.442798614502,14.079273223877,13.2750692367554,11.3828964233398
254.059997558594,2.67089176177979,3.40243530273438,4.01974630355835,4.44969749450684,5.22138166427612,6.35891437530518,7.62873458862305,8.98092174530029,11.4190607070923,14.5513143539429,18.3162021636963,22.9994773864746,29.7316246032715,35.4233589172363,40.9313850402832,47.1130867004395,52.6845245361328,57.915599822998,64.2642211914062,69.621696472168,75.6429672241211,79.4112930297852,81.478271484375,82.5389556884766,83.7636108398438,85.4523010253906,86.0060958862305,87.1970748901367,86.3537292480469,87.5455551147461,88.1553192138672,85.58642578125,82.3766632080078,80.1367340087891,76.2343978881836,72.2738418579102,69.6762390136719,63.6211624145508,60.3295249938965,57.2498016357422,83.7615737915039,99.1347885131836,79.7561416625977,50.3657913208008,38.2091522216797,34.9725761413574,31.6794929504395,29.0758800506592,25.7576103210449,24.2810916900635,24.3023662567139,22.0833225250244,18.9265155792236,16.1673259735107,14.3542861938477,12.8271722793579,11.319299697876
255.929992675781,2.72522306442261,3.28733682632446,4.19300174713135,4.97215986251831,6.1463885307312,7.02236175537109,7.71991062164307,9.6124849319458,11.823860168457,15.4190979003906,19.5648899078369,24.0559177398682,28.3993949890137,35.6616325378418,40.9907379150391,46.2872734069824,51.7886924743652,57.424259185791,62.3483505249023,67.7299957275391,72.0610275268555,75.5730285644531,78.332405090332,80.6701889038086,81.3849716186523,83.3349380493164,83.8467254638672,84.6118087768555,84.9456100463867,84.2068939208984,84.434455871582,82.4365921020508,79.8226165771484,76.500732421875,73.765251159668,68.90869140625,65.3082122802734,61.8021774291992,57.9347038269043,54.6737518310547,61.3831558227539,83.2965927124023,95.8872299194336,72.8872985839844,37.6438446044922,32.7891044616699,29.4536170959473,26.5586490631104,24.3266563415527,22.6301803588867,21.189245223999,20.526050567627,19.40260887146,16.4672718048096,13.1716690063477,11.8394460678101,10.4384927749634
257.959991455078,3.21290683746338,3.98891663551331,4.72322702407837,5.63693141937256,6.4882287979126,7.45437288284302,8.90002632141113,10.663013458252,13.262001991272,16.6105194091797,20.4600143432617,25.9285221099854,31.2529468536377,37.0466766357422,42.4403190612793,47.3480987548828,53.1885375976562,58.5294418334961,64.3140335083008,68.8223876953125,71.7386703491211,76.046875,78.0461196899414,80.7746047973633,81.7677764892578,82.95556640625,84.4830169677734,84.428337097168,85.2716369628906,84.8473205566406,84.114616394043,81.9455413818359,80.568977355957,76.8515625,72.9974594116211,68.9783782958984,64.455192565918,60.5049858093262,56.848274230957,52.9985847473145,50.7969512939453,66.1279907226563,105.358459472656,89.5109558105469,39.0232467651367,32.7334098815918,29.4105377197266,26.7679061889648,24.2018451690674,21.8511295318604,20.4381790161133,19.5665378570557,19.1251640319824,17.2594509124756,14.3079223632812,12.1065378189087,10.5271911621094
260,3.41055822372437,3.93557405471802,5.1127781867981,5.9223747253418,6.73870515823364,7.8412184715271,9.4288444519043,11.6463184356689,14.1108064651489,17.5000305175781,21.7909755706787,26.9293537139893,32.0226821899414,37.3111724853516,42.6441459655762,47.9842987060547,53.9838218688965,58.4067115783691,62.4811820983887,67.9415283203125,72.0176467895508,74.2498474121094,75.0730209350586,78.44287109375,79.1882476806641,81.2593536376953,81.8445281982422,82.8198699951172,83.2321472167969,83.5785369873047,82.0417556762695,79.4182510375977,76.4430236816406,73.7386322021484,69.5505447387695,64.676383972168,61.7696571350098,57.9401168823242,54.3826103210449,51.0335388183594,47.273078918457,56.4147033691406,113.201438903809,80.7597351074219,39.8838844299316,30.4663391113281,27.8390369415283,25.6157512664795,23.1932373046875,20.8993339538574,18.5871868133545,17.9609069824219,18.4881687164307,16.6580276489258,13.1956052780151,11.5353488922119,9.66449356079102
262.029998779297,3.82153797149658,4.68460035324097,5.47021532058716,6.31838464736938,7.08445405960083,8.41258716583252,9.51007556915283,11.8409414291382,14.6743392944336,18.2979602813721,21.9991550445557,27.3488578796387,32.1398429870605,37.7207489013672,41.5274200439453,47.5885772705078,51.7020034790039,57.099292755127,61.7406425476074,65.6555023193359,69.953987121582,71.0863876342773,72.1729507446289,74.046012878418,76.3831253051758,76.5245666503906,78.6100769042969,78.930061340332,78.9697952270508,78.8229598999023,77.4386367797852,74.3858337402344,72.0304260253906,69.0096817016602,64.5219955444336,61.5817642211914,57.9443168640137,54.1362762451172,50.5893630981445,47.3394966125488,43.4472389221191,49.5518836975098,97.0061645507812,81.2925109863281,47.1760177612305,29.0424575805664,26.0920829772949,23.7819023132324,20.9830074310303,19.6952857971191,17.1577033996582,16.684419631958,16.3815746307373,15.3087348937988,13.0794944763184,10.3042526245117,8.92405891418457
264.059997558594,4.36516094207764,5.05646896362305,5.99236488342285,6.88891792297363,7.66924381256104,8.91412544250488,10.5313968658447,12.7600231170654,15.3796339035034,18.8983612060547,23.2077102661133,27.7346801757813,32.7493743896484,36.8162002563477,40.5715980529785,44.7855911254883,49.5624198913574,55.0984649658203,58.7350540161133,62.1021461486816,64.7838287353516,66.2831573486328,67.974983215332,70.7058715820312,72.8498764038086,73.0734939575195,73.7861175537109,74.3114700317383,73.9988327026367,73.8561782836914,72.9426727294922,70.1829071044922,67.5993118286133,63.5668411254883,60.2468490600586,57.487232208252,53.2839546203613,50.6836357116699,47.6183319091797,43.991138458252,40.4820938110352,41.5865783691406,62.2503547668457,82.8523406982422,69.3785705566406,30.143440246582,24.3638820648193,21.5016860961914,19.6230926513672,17.3148403167725,16.195442199707,14.6696329116821,14.4185476303101,13.9425964355469,13.0310144424438,10.9795207977295,8.76940536499023
265.929992675781,4.78284692764282,5.76570892333984,6.2163519859314,7.07550430297852,8.39108276367187,9.84166526794434,11.565936088562,13.7092056274414,16.5279941558838,19.7648601531982,24.1468276977539,28.073486328125,32.7102127075195,36.1343002319336,40.6638031005859,44.9474601745605,48.9677352905273,54.0034446716309,57.4265022277832,60.7783851623535,63.1089515686035,64.493408203125,66.729118347168,68.4787445068359,69.8424453735352,71.2379989624023,71.7714996337891,72.2129440307617,72.8810653686523,70.9214553833008,70.215950012207,67.907600402832,64.2173004150391,61.1582298278809,57.5839424133301,54.9184608459473,51.5932540893555,49.202579498291,45.0264625549316,42.5927276611328,37.9131355285645,36.7271995544434,45.6402282714844,78.1432647705078,84.2446899414062,38.4780883789063,23.1993026733398,20.8801803588867,19.0665664672852,17.3067398071289,15.101203918457,13.9566831588745,12.7976837158203,12.8941488265991,12.8284616470337,11.0452766418457,8.81198501586914
267.959991455078,5.27589845657349,6.1521725654602,7.36993169784546,7.90959119796753,9.15065383911133,10.7644720077515,12.6431379318237,14.7186260223389,17.5145130157471,20.7577228546143,25.0087203979492,29.0566215515137,33.0576438903809,36.3420867919922,39.9359664916992,44.4382171630859,48.8775634765625,51.8091201782227,56.0869331359863,59.6242942810059,60.5920906066895,62.274055480957,63.9864654541016,65.7647094726563,66.7045593261719,67.7906265258789,68.4980087280273,69.54052734375,69.0837554931641,68.0009613037109,66.1260986328125,63.7568168640137,61.0248680114746,57.8305931091309,54.5320739746094,52.4861183166504,48.8132286071777,45.8495101928711,42.258113861084,39.0966682434082,36.7507438659668,34.2593154907227,33.8393821716309,63.0026969909668,84.1991577148438,56.4019622802734,24.9062767028809,19.6142807006836,18.051815032959,15.8577184677124,14.0769367218018,12.82164478302,11.6376247406006,11.5235414505005,11.8738603591919,10.9061365127563,9.20903587341309
270,6.14943790435791,7.03985548019409,7.82888746261597,8.69509792327881,10.0348987579346,11.407787322998,13.8408660888672,16.1221160888672,19.270845413208,22.557897567749,26.3853607177734,30.0097217559814,33.4600219726562,36.7038192749023,40.4986381530762,44.0181198120117,48.4642143249512,51.684268951416,54.5989532470703,56.839973449707,58.0130996704102,60.3085708618164,61.4368782043457,63.4444274902344,64.6917724609375,65.7073593139648,66.4018783569336,66.8043670654297,67.0418167114258,65.5020904541016,63.2610092163086,60.4115867614746,58.1661643981934,54.9642066955566,52.1002922058105,48.9184417724609,46.8931655883789,43.8339691162109,40.0859375,37.0245361328125,34.6409759521484,31.8849487304687,29.64133644104,46.5233955383301,78.053840637207,78.1692810058594,30.5129566192627,18.7718601226807,16.6673927307129,14.9790945053101,13.4591083526611,12.3086795806885,11.1659564971924,10.3124408721924,10.6833515167236,10.7682857513428,9.91868877410889
272,6.62944889068604,7.28008651733398,8.23663997650146,9.39974975585938,10.8453950881958,12.5571994781494,14.8496608734131,17.1337718963623,20.1834678649902,23.6731014251709,26.8694725036621,30.5808620452881,33.4804801940918,37.2322463989258,40.7571868896484,45.3029975891113,48.3478355407715,51.3533744812012,53.493595123291,55.5847282409668,56.5123901367188,58.6008949279785,59.9544448852539,60.9591674804687,62.7969284057617,63.1091804504394,63.6809539794922,64.250114440918,64.0958023071289,62.4899787902832,59.6733245849609,57.6421966552734,55.0552520751953,52.0735054016113,49.5760650634766,46.2068748474121,43.8879890441895,41.0317001342773,37.9778289794922,35.1745529174805,32.847469329834,30.0689926147461,27.9124813079834,31.8812732696533,69.2128677368164,84.668212890625,41.0692863464355,18.4481716156006,15.9182415008545,13.7189950942993,12.7896699905396,11.7229051589966,10.3710126876831,9.50142669677734,9.04445457458496,9.81654357910156,9.39487934112549
274,7.41603326797485,7.92876625061035,9.13995933532715,10.2568235397339,11.953724861145,13.8516931533813,15.7398204803467,18.3624038696289,21.2710933685303,24.2195739746094,28.0204486846924,31.9226016998291,34.0879936218262,37.4483108520508,40.7658996582031,44.8349075317383,47.6915893554687,50.3293609619141,52.4713935852051,54.3359985351562,55.314868927002,56.9962730407715,58.7051849365234,59.1122741699219,60.3003120422363,60.6139450073242,61.6620941162109,61.2050857543945,60.4748229980469,58.348991394043,56.3800582885742,54.2810173034668,51.5368804931641,48.6399345397949,47.0471572875977,44.1619453430176,40.654842376709,38.0979270935059,35.6526527404785,32.2819633483887,31.1417274475098,28.2369842529297,25.169584274292,25.4083862304687,49.8596458435059,77.0573043823242,57.9296760559082,21.5218982696533,14.3651523590088,13.397910118103,11.8990306854248,10.8816595077515,9.66688537597656,9.02763938903809,8.11851406097412,8.73623752593994,8.61113166809082
276,7.81372547149658,8.81320190429688,9.60810375213623,11.5968799591064,13.3157911300659,14.7510061264038,17.3492660522461,19.8856315612793,22.6171913146973,26.2505836486816,29.3080310821533,32.4245719909668,35.5392189025879,37.9935836791992,42.1229972839355,44.591682434082,47.7093734741211,49.8665771484375,51.4108963012695,51.8842506408691,53.9039878845215,55.3751754760742,56.5443649291992,56.7629547119141,57.7544288635254,58.5337409973145,58.6556930541992,58.5977973937988,57.6518936157227,55.8751831054687,53.748291015625,50.9336585998535,48.9919013977051,46.54736328125,43.7442855834961,41.5843887329102,38.3376770019531,35.5525932312012,33.3607788085937,31.7255821228027,28.9991931915283,26.7983951568604,24.3347206115723,22.1110553741455,31.2014274597168,65.520637512207,72.6701965332031,30.4517059326172,14.4962472915649,12.1989126205444,11.0809707641602,10.0885620117187,9.45803165435791,8.29226207733154,7.64368200302124,7.52702045440674,7.91528081893921
278,8.48977661132813,9.72201824188232,10.9945764541626,12.3502340316772,14.6449317932129,16.5595989227295,18.747974395752,21.2034740447998,24.3064498901367,27.6277103424072,30.4052429199219,33.8209686279297,36.1396217346191,39.385196685791,42.7643585205078,45.4900398254395,47.948673248291,49.6876640319824,50.9636993408203,52.3083076477051,53.5917663574219,54.0611381530762,55.3604202270508,55.7568016052246,56.2939567565918,57.7520179748535,56.8129348754883,56.0606842041016,55.2115783691406,53.1221351623535,50.9379577636719,49.4548149108887,46.8170204162598,44.3587074279785,41.6488952636719,39.3058090209961,36.089183807373,33.8585624694824,31.6063346862793,29.3909339904785,27.0542392730713,24.8800773620605,22.6839694976807,21.0330677032471,21.5759353637695,46.9133758544922,73.185661315918,49.4711151123047,17.0408706665039,11.9908084869385,10.5606393814087,9.47162628173828,8.83677864074707,8.19705486297607,7.32574367523193,6.79376029968262,6.77574682235718
280,9.17060279846191,10.7361602783203,11.9468517303467,13.7060613632202,15.5742597579956,18.0546531677246,20.4713668823242,23.7345409393311,26.4405708312988,29.5096549987793,32.8378601074219,34.5172424316406,38.207218170166,41.8863258361816,44.4178733825684,47.1293525695801,49.3283500671387,50.4015922546387,51.2054824829102,52.1976928710937,53.2793464660645,54.1178741455078,54.5313758850098,54.9432258605957,55.8546295166016,55.7861747741699,55.2872047424316,54.3410720825195,53.1083488464355,51.0687599182129,48.7317733764648,46.8424453735352,44.4959030151367,42.7631225585937,39.6353950500488,37.2586402893066,34.5268287658691,32.335823059082,30.0511512756348,27.9724884033203,25.4165897369385,22.9819965362549,21.0822505950928,19.606632232666,18.7149105072021,29.8068771362305,64.5562973022461,67.0754699707031,25.1678047180176,11.4009189605713,9.83836936950684,9.01907253265381,8.37013435363769,7.81657075881958,7.19332599639893,6.66719484329224,6.11242961883545
282,10.1019287109375,11.5800104141235,12.9970426559448,14.8697080612183,16.7626628875732,19.2185344696045,21.8908138275146,24.7509365081787,27.8465919494629,31.2070140838623,34.1463890075684,37.0135650634766,39.6970901489258,43.4160842895508,45.342357635498,47.8797187805176,49.8394889831543,50.3688507080078,50.4839782714844,52.2149238586426,52.8301200866699,53.2352714538574,54.1411628723145,54.8820114135742,54.8560218811035,55.3460540771484,53.9031372070313,53.0047569274902,51.1480407714844,49.4790000915527,46.8833351135254,44.6873245239258,42.497917175293,39.9358444213867,37.9777565002441,35.3452682495117,32.9601249694824,30.4906444549561,28.3763179779053,26.1937122344971,24.0974254608154,21.8326168060303,20.3651542663574,18.9013957977295,17.3187465667725,18.7819938659668,53.0021514892578,71.5673294067383,42.6870040893555,12.9425649642944,9.78479480743408,8.45710563659668,7.94507169723511,7.23891258239746,6.70252704620361,6.16295576095581,5.49235391616821
284,10.4421472549438,12.0179777145386,13.8513479232788,16.1304492950439,18.0575847625732,20.7996673583984,24.1695022583008,26.6093864440918,30.0439910888672,32.5205383300781,35.3260383605957,38.5231170654297,41.2779159545898,44.2526016235352,46.2045631408691,48.5946846008301,50.4220352172852,50.7044219970703,51.5091133117676,51.6817779541016,53.2729721069336,52.9527969360352,53.5108604431152,53.4884338378906,54.0079193115234,53.1847801208496,52.2562294006348,50.9408912658691,48.9856147766113,47.726390838623,44.9403762817383,42.6372413635254,40.4396896362305,38.6279335021973,36.564884185791,33.3923530578613,31.1226139068604,29.0496425628662,26.8141498565674,25.467809677124,23.0671539306641,20.7443943023682,19.1811771392822,17.7717571258545,15.8602781295776,15.4107141494751,35.026912689209,67.0927581787109,60.3559799194336,18.6382484436035,9.50141620635986,8.14902019500732,7.78250789642334,6.95368623733521,6.33366012573242,5.82480907440186,5.3531494140625
286,11.1862163543701,12.5576801300049,14.7683629989624,17.4937152862549,19.7286758422852,22.4737720489502,25.3906593322754,28.5470027923584,31.3895568847656,34.1828346252441,36.8001937866211,40.9202270507812,42.842700958252,45.3932800292969,48.1626968383789,49.2899055480957,50.6819648742676,51.6555786132812,50.9963874816895,51.641471862793,52.2208023071289,52.3825531005859,52.6477203369141,52.536060333252,53.2410163879395,51.7915420532227,50.9816284179687,49.817985534668,48.2453765869141,45.4916687011719,42.9353523254395,40.9983291625977,39.0420150756836,36.6315498352051,34.1375885009766,31.8135585784912,29.7591304779053,27.8124866485596,25.1664371490479,23.2535800933838,21.4422187805176,19.5025844573975,18.1085643768311,16.3618869781494,15.3263788223267,13.9953851699829,21.2125186920166,59.00048828125,67.0372848510742,28.2929344177246,9.06644630432129,7.53646755218506,7.2679705619812,6.53416347503662,5.90030336380005,5.24513149261475,5.02353954315186
288,11.418137550354,13.4024925231934,16.1324062347412,18.5914611816406,20.8604259490967,24.2508201599121,27.0655269622803,30.1565170288086,33.5743141174316,36.5337982177734,38.3620414733887,41.7550888061523,45.4048347473145,47.3766479492188,49.3450202941895,50.6066551208496,51.1274299621582,51.0591278076172,51.7542839050293,51.8490257263184,52.4329261779785,52.7435836791992,51.958667755127,52.1096992492676,51.6449012756348,50.8255767822266,49.5630569458008,48.119441986084,45.8649291992188,43.289966583252,41.3925895690918,39.0771675109863,37.5333633422852,35.1679000854492,32.8708381652832,30.4508457183838,28.3584594726562,26.4721431732178,24.2980518341064,22.1344432830811,20.2115783691406,18.611270904541,17.2335796356201,15.7603769302368,14.0518999099731,13.3108510971069,14.1540794372559,42.4813041687012,63.6471290588379,45.0498695373535,10.7297897338867,7.17738008499145,6.67493677139282,6.13038015365601,5.46122550964355,5.14815235137939,4.59314632415771
290,12.3915195465088,14.5368547439575,16.925220489502,19.987886428833,22.2329254150391,25.9109668731689,28.910343170166,32.4790954589844,35.4773635864258,38.0293235778809,40.3983268737793,43.6618843078613,46.437801361084,49.0418014526367,50.770393371582,51.6063423156738,51.665714263916,52.2079315185547,52.2347183227539,52.7055702209473,52.302661895752,52.0769920349121,52.2918472290039,52.1205558776855,51.725341796875,50.3940391540527,48.1075820922852,46.3073348999023,44.0949325561523,42.2608528137207,40.0914421081543,37.5530967712402,35.2090759277344,33.1373252868652,30.7469062805176,28.5165481567383,26.9057102203369,25.0044822692871,23.2345237731934,20.8397541046143,19.2261028289795,17.8055305480957,16.3429832458496,15.173300743103,13.3189630508423,12.1194944381714,11.6675472259521,22.9568252563477,61.9389266967773,54.2313270568848,16.8328342437744,7.14372968673706,6.36283874511719,5.68834257125854,5.20053243637085,4.70265054702759,4.49306154251099
292.029998779297,12.5515785217285,15.2342157363892,17.860668182373,20.7128601074219,24.3374519348145,27.5379524230957,31.0039157867432,34.2450523376465,36.4704704284668,40.5526542663574,43.319953918457,46.0796546936035,48.8112182617188,50.504524230957,51.8680000305176,52.7387886047363,52.4364356994629,52.8608703613281,52.6561698913574,52.7649803161621,52.4214401245117,52.9266395568848,52.6539840698242,51.4566917419434,50.7894897460937,49.0688552856445,47.0725212097168,44.8861274719238,42.5015525817871,40.313404083252,39.0502815246582,36.427318572998,34.2075347900391,31.843147277832,29.8690223693848,27.5666332244873,25.7452583312988,23.8300094604492,22.0810394287109,20.0860576629639,18.3934192657471,17.1226806640625,15.5786418914795,14.1440734863281,12.6415157318115,11.5818395614624,10.4505929946899,13.283164024353,48.3891334533691,58.9646949768066,29.2827930450439,8.54113674163818,5.85121726989746,5.40816020965576,4.68171501159668,4.27833843231201,3.89794135093689From this output, we see that:
- The emission wavelengths are contained in the first column (250, 252, …).
- The excitation wavelengths are in the first row (50, 55, …). They are offsets to be applied to each excitation. For examples:
- The emissions at excitation 250 nm are 250 + 50, 250 + 55, 250 + 60, …
- The emissions at excitation 252 nm are 252 + 50, 252 + 55, 252 + 60, …
- The fluorescence data start at row 3 and column 2.
The first thing we need to do is to create a function that will read this data in a format that can be used by eemR. The function needs to meet these flowing criteria:
- Have an argument
filethat will contains the path of the file(s) to read. - Return a list containing the flowing elements:
file: the path of the fileem: a numeric vector containing emission wavelengths.ex: a numeric vector containing excitation wavelengths.x: a matrix oflength(em)rows bylength(ex)columns.
Further more, the x matrix of the list need to be arranged as follow:
Let’s now write a function that will read the eem file and format the data accordingly. In this particular example, fluorescence has been measured in asynchronous mode. Hence, extra manipulations are needed to get the data on a regular grid.
library(dplyr)
library(tidyr)
library(eemR)
import_cary <- function(file) {
dat <- read.csv(file, nrows = 102, skip = 1)
ex <- na.omit(dat[, 1])
em <- seq(50, 330, by = 5)
em <- outer(ex, em, "+")
em <- as.vector(em)
ex <- rep(ex, 57)
x <- dat[, -1]
x <- x[-1, ]
x <- matrix(as.numeric(unlist(x, use.names = FALSE)), ncol = 101, byrow = FALSE)
res <- tibble(ex, em, x = as.vector(x)) %>%
arrange(ex, em) %>%
complete(ex, em, fill = list(x = NA))
ex <- sort(unique(ex))
em <- sort(unique(em))
x <- matrix(res$x, ncol = length(ex), byrow = TRUE)
# We need to interpolate because you do not have a regular grid (i.e. asynchronous)
r <- MBA::mba.surf(res %>% drop_na(), no.X = 200, no.Y = 200, extend = FALSE)
l <- list(
file = file,
x = t(r$xyz.est$z),
ex = r$xyz.est$x,
em = r$xyz.est$y
)
return(l)
}We can now try our function and have a look to the structure of the returned list.
str(import_cary(file))
#> List of 4
#> $ file: chr "/tmp/RtmpZobmZw/Rinst5602ac3da4e/eemR/extdata/custom_cary.csv"
#> $ x : num [1:200, 1:200] 1.91 2.29 2.73 3.04 3.27 ...
#> $ ex : num [1:200] 250 251 252 253 254 ...
#> $ em : num [1:200] 300 302 305 307 310 ...We will use the import_function argument of the eem_read() function to tell eemR how to read our file.
eem <- eem_read(file, import_function = import_cary)
eem
#> sample ex_min ex_max em_min em_max is_blank_corrected
#> 1 custom_cary 250 450 300 780 FALSE
#> is_scatter_corrected is_ife_corrected is_raman_normalized
#> 1 FALSE FALSE FALSEWe can visualize the eem by using the plot() function:
All other functions of the eemR package can now be used on the created eem. For example, we can remove the second order scattering.
# Remove second order Rayleigh scattering
plot(eem_remove_scattering(eem, "rayleigh", order = 2, width = 15))