Conditionally selecting sublists from a large JSON generated list - r

I have a list generated from an API pull and converted from JSON by the httr package.
It has 80-odd top level numbered elements / lists, each of which contains between 10 next-level elements / lists. At this next level I'd like to be able to filter so I only have the 1 from the 10 that has the name "My Color" , I don't want the other 9 that don't match.
Here is the output in R for the 2nd level, (1 of 10) list:
..$ data:List of 10
.. ..$ :List of 3
.. .. ..$ id : int 1
.. .. ..$ name : chr "My Color"
.. .. ..$ color:List of 1
.. .. .. ..$ data:List of 1
.. .. .. .. ..$ :List of 3
.. .. .. .. .. ..$ id : int 15
.. .. .. .. .. ..$ name: chr "Blue"
I'm struggling to get a reproducible data example due to the complexity of the list, but the end goal would be to preserve the 80 top level elements, but with each containing the 1 sublist whose 'name' element contains 'My Color'.
Again apologies for the lack of a reproducible example, but a pointer to the correct approach would be appreciated. I'm really struggling with manipulating lists.

Related

How to convert dataframe (or vector) to matrix to use R baseline package for data other than the sample data provided?

I have data in the form of a dataframe of x and y values that when plotted looks like this:
(The portion highlighted in green corresponds to the dput() data below).
I want to use the baseline package to experiment with the different baseline correction algorithms described in "Liland, K. H., Almøy, T., & Mevik, B.-H. (2010). Optimal Choice of Baseline Correction for Multivariate Calibration of Spectra. Applied Spectroscopy, 64(9), 1007–1016. doi:10.1366/000370210792434350".
The package specifies that "data must be organized as row vectors in a matrix or data.frame", however, simply converting my y values to a matrix doesn't work:
> baseline(as.matrix(y, byrow=T))
Error in rep(3, p - 4) : invalid 'times' argument
The example data that is provided with the package has a structure that I can't interpret or figure out how to emulate with my own data.
> library(baseline)
> data(milk)
> str(milk)
'data.frame': 45 obs. of 2 variables:
$ cow : num 0 0.25 0.375 0.875 0.5 0.75 0.5 0.125 0 0.125 ...
$ spectra: num [1:45, 1:21451] 1029 371 606 368 554 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:21451] "4999.94078628963" "5001.55954267662" "5003.17856106153" "5004.79784144435" ...
- attr(*, "terms")=Classes 'terms', 'formula' language cow ~ spectra
.. ..- attr(*, "variables")= language list(cow, spectra)
.. ..- attr(*, "factors")= int [1:2, 1] 0 1
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:2] "cow" "spectra"
.. .. .. ..$ : chr "spectra"
.. ..- attr(*, "term.labels")= chr "spectra"
.. ..- attr(*, "order")= int 1
.. ..- attr(*, "intercept")= int 1
.. ..- attr(*, "response")= int 1
.. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
.. ..- attr(*, "predvars")= language list(cow, spectra)
.. ..- attr(*, "dataClasses")= Named chr [1:2] "numeric" "nmatrix.21451"
.. .. ..- attr(*, "names")= chr [1:2] "cow" "spectra"
If anyone can tell me how I can call baseline() on my own data, I would greatly appreciate it.
Here is a subsection of the data I'm working with, corresponding to the green highlighted portion of the plot above:
> dput(fid_df[fid_df$rt>12.5&fid_df$rt<12.8,])
structure(list(rt = c(12.5002866914485, 12.5011200182712, 12.5019533450939,
12.5027866719166, 12.5036199987393, 12.5044533255619, 12.5052866523846,
12.5061199792073, 12.50695330603, 12.5077866328527, 12.5086199596754,
12.5094532864981, 12.5102866133207, 12.5111199401434, 12.5119532669661,
12.5127865937888, 12.5136199206115, 12.5144532474342, 12.5152865742568,
12.5161199010795, 12.5169532279022, 12.5177865547249, 12.5186198815476,
12.5194532083703, 12.5202865351929, 12.5211198620156, 12.5219531888383,
12.522786515661, 12.5236198424837, 12.5244531693064, 12.5252864961291,
12.5261198229517, 12.5269531497744, 12.5277864765971, 12.5286198034198,
12.5294531302425, 12.5302864570652, 12.5311197838878, 12.5319531107105,
12.5327864375332, 12.5336197643559, 12.5344530911786, 12.5352864180013,
12.536119744824, 12.5369530716466, 12.5377863984693, 12.538619725292,
12.5394530521147, 12.5402863789374, 12.5411197057601, 12.5419530325827,
12.5427863594054, 12.5436196862281, 12.5444530130508, 12.5452863398735,
12.5461196666962, 12.5469529935189, 12.5477863203415, 12.5486196471642,
12.5494529739869, 12.5502863008096, 12.5511196276323, 12.551952954455,
12.5527862812776, 12.5536196081003, 12.554452934923, 12.5552862617457,
12.5561195885684, 12.5569529153911, 12.5577862422138, 12.5586195690364,
12.5594528958591, 12.5602862226818, 12.5611195495045, 12.5619528763272,
12.5627862031499, 12.5636195299725, 12.5644528567952, 12.5652861836179,
12.5661195104406, 12.5669528372633, 12.567786164086, 12.5686194909087,
12.5694528177313, 12.570286144554, 12.5711194713767, 12.5719527981994,
12.5727861250221, 12.5736194518448, 12.5744527786674, 12.5752861054901,
12.5761194323128, 12.5769527591355, 12.5777860859582, 12.5786194127809,
12.5794527396035, 12.5802860664262, 12.5811193932489, 12.5819527200716,
12.5827860468943, 12.583619373717, 12.5844527005397, 12.5852860273623,
12.586119354185, 12.5869526810077, 12.5877860078304, 12.5886193346531,
12.5894526614758, 12.5902859882984, 12.5911193151211, 12.5919526419438,
12.5927859687665, 12.5936192955892, 12.5944526224119, 12.5952859492346,
12.5961192760572, 12.5969526028799, 12.5977859297026, 12.5986192565253,
12.599452583348, 12.6002859101707, 12.6011192369933, 12.601952563816,
12.6027858906387, 12.6036192174614, 12.6044525442841, 12.6052858711068,
12.6061191979295, 12.6069525247521, 12.6077858515748, 12.6086191783975,
12.6094525052202, 12.6102858320429, 12.6111191588656, 12.6119524856882,
12.6127858125109, 12.6136191393336, 12.6144524661563, 12.615285792979,
12.6161191198017, 12.6169524466243, 12.617785773447, 12.6186191002697,
12.6194524270924, 12.6202857539151, 12.6211190807378, 12.6219524075605,
12.6227857343831, 12.6236190612058, 12.6244523880285, 12.6252857148512,
12.6261190416739, 12.6269523684966, 12.6277856953192, 12.6286190221419,
12.6294523489646, 12.6302856757873, 12.63111900261, 12.6319523294327,
12.6327856562554, 12.633618983078, 12.6344523099007, 12.6352856367234,
12.6361189635461, 12.6369522903688, 12.6377856171915, 12.6386189440141,
12.6394522708368, 12.6402855976595, 12.6411189244822, 12.6419522513049,
12.6427855781276, 12.6436189049503, 12.6444522317729, 12.6452855585956,
12.6461188854183, 12.646952212241, 12.6477855390637, 12.6486188658864,
12.649452192709, 12.6502855195317, 12.6511188463544, 12.6519521731771,
12.6527854999998, 12.6536188268225, 12.6544521536452, 12.6552854804678,
12.6561188072905, 12.6569521341132, 12.6577854609359, 12.6586187877586,
12.6594521145813, 12.6602854414039, 12.6611187682266, 12.6619520950493,
12.662785421872, 12.6636187486947, 12.6644520755174, 12.6652854023401,
12.6661187291627, 12.6669520559854, 12.6677853828081, 12.6686187096308,
12.6694520364535, 12.6702853632762, 12.6711186900988, 12.6719520169215,
12.6727853437442, 12.6736186705669, 12.6744519973896, 12.6752853242123,
12.6761186510349, 12.6769519778576, 12.6777853046803, 12.678618631503,
12.6794519583257, 12.6802852851484, 12.6811186119711, 12.6819519387937,
12.6827852656164, 12.6836185924391, 12.6844519192618, 12.6852852460845,
12.6861185729072, 12.6869518997298, 12.6877852265525, 12.6886185533752,
12.6894518801979, 12.6902852070206, 12.6911185338433, 12.691951860666,
12.6927851874886, 12.6936185143113, 12.694451841134, 12.6952851679567,
12.6961184947794, 12.6969518216021, 12.6977851484247, 12.6986184752474,
12.6994518020701, 12.7002851288928, 12.7011184557155, 12.7019517825382,
12.7027851093609, 12.7036184361835, 12.7044517630062, 12.7052850898289,
12.7061184166516, 12.7069517434743, 12.707785070297, 12.7086183971196,
12.7094517239423, 12.710285050765, 12.7111183775877, 12.7119517044104,
12.7127850312331, 12.7136183580558, 12.7144516848784, 12.7152850117011,
12.7161183385238, 12.7169516653465, 12.7177849921692, 12.7186183189919,
12.7194516458145, 12.7202849726372, 12.7211182994599, 12.7219516262826,
12.7227849531053, 12.723618279928, 12.7244516067506, 12.7252849335733,
12.726118260396, 12.7269515872187, 12.7277849140414, 12.7286182408641,
12.7294515676868, 12.7302848945094, 12.7311182213321, 12.7319515481548,
12.7327848749775, 12.7336182018002, 12.7344515286229, 12.7352848554455,
12.7361181822682, 12.7369515090909, 12.7377848359136, 12.7386181627363,
12.739451489559, 12.7402848163817, 12.7411181432043, 12.741951470027,
12.7427847968497, 12.7436181236724, 12.7444514504951, 12.7452847773178,
12.7461181041404, 12.7469514309631, 12.7477847577858, 12.7486180846085,
12.7494514114312, 12.7502847382539, 12.7511180650766, 12.7519513918992,
12.7527847187219, 12.7536180455446, 12.7544513723673, 12.75528469919,
12.7561180260127, 12.7569513528353, 12.757784679658, 12.7586180064807,
12.7594513333034, 12.7602846601261, 12.7611179869488, 12.7619513137715,
12.7627846405941, 12.7636179674168, 12.7644512942395, 12.7652846210622,
12.7661179478849, 12.7669512747076, 12.7677846015302, 12.7686179283529,
12.7694512551756, 12.7702845819983, 12.771117908821, 12.7719512356437,
12.7727845624663, 12.773617889289, 12.7744512161117, 12.7752845429344,
12.7761178697571, 12.7769511965798, 12.7777845234025, 12.7786178502251,
12.7794511770478, 12.7802845038705, 12.7811178306932, 12.7819511575159,
12.7827844843386, 12.7836178111612, 12.7844511379839, 12.7852844648066,
12.7861177916293, 12.786951118452, 12.7877844452747, 12.7886177720974,
12.78945109892, 12.7902844257427, 12.7911177525654, 12.7919510793881,
12.7927844062108, 12.7936177330335, 12.7944510598561, 12.7952843866788,
12.7961177135015, 12.7969510403242, 12.7977843671469, 12.7986176939696,
12.7994510207923), value = c(17.3893229166667, 17.394140625,
17.3994791666667, 17.3966145833333, 17.397265625, 17.4009114583333,
17.4036458333333, 17.400390625, 17.3940104166667, 17.3908854166667,
17.3873697916667, 17.3858072916667, 17.3841145833333, 17.3834635416667,
17.383984375, 17.3837239583333, 17.3838541666667, 17.3850260416667,
17.3904947916667, 17.3954427083333, 17.39375, 17.3897135416667,
17.387109375, 17.3890625, 17.3876302083333, 17.385546875, 17.3850260416667,
17.390234375, 17.39921875, 17.4076822916667, 17.4131510416667,
17.41484375, 17.4111979166667, 17.402734375, 17.3953125, 17.3915364583333,
17.3934895833333, 17.3923177083333, 17.3938802083333, 17.3967447916667,
17.398828125, 17.4, 17.396484375, 17.4, 17.39921875, 17.4032552083333,
17.4138020833333, 17.4260416666667, 17.4364583333333, 17.4458333333333,
17.4639322916667, 17.491015625, 17.5239583333333, 17.5647135416667,
17.6229166666667, 17.6997395833333, 17.7994791666667, 17.916015625,
18.0544270833333, 18.2184895833333, 18.4170572916667, 18.6494791666667,
18.914453125, 19.2151041666667, 19.5665364583333, 19.9688802083333,
20.4143229166667, 20.8876302083333, 21.3850260416667, 21.9104166666667,
22.4467447916667, 23.0069010416667, 23.5716145833333, 24.1360677083333,
24.6528645833333, 25.1217447916667, 25.5454427083333, 25.9471354166667,
26.2817708333333, 26.5583333333333, 26.7454427083333, 26.8537760416667,
26.9045572916667, 26.889453125, 26.82734375, 26.6755208333333,
26.442578125, 26.1438802083333, 25.7912760416667, 25.437109375,
25.0861979166667, 24.7126302083333, 24.262890625, 23.73359375,
23.1990885416667, 22.7178385416667, 22.28359375, 21.8391927083333,
21.3856770833333, 20.9497395833333, 20.56640625, 20.2286458333333,
19.9221354166667, 19.6524739583333, 19.3998697916667, 19.1759114583333,
18.9670572916667, 18.7893229166667, 18.640625, 18.5109375, 18.401171875,
18.3026041666667, 18.2216145833333, 18.1454427083333, 18.0764322916667,
18.0162760416667, 17.9623697916667, 17.9102864583333, 17.8688802083333,
17.8309895833333, 17.8029947916667, 17.7690104166667, 17.7415364583333,
17.7149739583333, 17.693359375, 17.6713541666667, 17.6526041666667,
17.631640625, 17.6157552083333, 17.6013020833333, 17.5877604166667,
17.5740885416667, 17.5670572916667, 17.55703125, 17.545703125,
17.5307291666667, 17.527734375, 17.5272135416667, 17.5216145833333,
17.5140625, 17.5040364583333, 17.4944010416667, 17.4796875, 17.469921875,
17.4647135416667, 17.4657552083333, 17.46640625, 17.4638020833333,
17.4580729166667, 17.4485677083333, 17.4446614583333, 17.4430989583333,
17.4475260416667, 17.4428385416667, 17.4401041666667, 17.433984375,
17.4352864583333, 17.4342447916667, 17.4309895833333, 17.42890625,
17.4265625, 17.4248697916667, 17.42109375, 17.4109375, 17.4052083333333,
17.403125, 17.4092447916667, 17.413671875, 17.4153645833333,
17.4123697916667, 17.4123697916667, 17.4091145833333, 17.4052083333333,
17.401953125, 17.4052083333333, 17.40703125, 17.410546875, 17.4084635416667,
17.4096354166667, 17.4084635416667, 17.4135416666667, 17.4209635416667,
17.42265625, 17.42265625, 17.4223958333333, 17.4248697916667,
17.418359375, 17.4127604166667, 17.4125, 17.4184895833333, 17.4180989583333,
17.4111979166667, 17.4076822916667, 17.4158854166667, 17.425390625,
17.4279947916667, 17.424609375, 17.4229166666667, 17.4147135416667,
17.40625, 17.4014322916667, 17.4071614583333, 17.4125, 17.416796875,
17.415234375, 17.4084635416667, 17.402734375, 17.4018229166667,
17.4032552083333, 17.4009114583333, 17.40078125, 17.40078125,
17.4015625, 17.4002604166667, 17.4006510416667, 17.4001302083333,
17.398046875, 17.399609375, 17.4014322916667, 17.4, 17.39765625,
17.394140625, 17.3958333333333, 17.3985677083333, 17.399609375,
17.3979166666667, 17.3924479166667, 17.3860677083333, 17.3852864583333,
17.3834635416667, 17.3805989583333, 17.3751302083333, 17.3782552083333,
17.3834635416667, 17.3848958333333, 17.3802083333333, 17.3809895833333,
17.3842447916667, 17.3846354166667, 17.3779947916667, 17.3703125,
17.372265625, 17.3786458333333, 17.3860677083333, 17.38203125,
17.3813802083333, 17.38203125, 17.3881510416667, 17.38984375,
17.394921875, 17.3963541666667, 17.3998697916667, 17.3963541666667,
17.3932291666667, 17.3854166666667, 17.3725260416667, 17.3647135416667,
17.36328125, 17.372265625, 17.3756510416667, 17.380078125, 17.3766927083333,
17.378515625, 17.37578125, 17.382421875, 17.38359375, 17.379296875,
17.3759114583333, 17.37578125, 17.3803385416667, 17.378515625,
17.3837239583333, 17.3829427083333, 17.38359375, 17.3768229166667,
17.3790364583333, 17.380078125, 17.3846354166667, 17.3837239583333,
17.3869791666667, 17.3813802083333, 17.3889322916667, 17.388671875,
17.39375, 17.3911458333333, 17.3891927083333, 17.3889322916667,
17.386328125, 17.3830729166667, 17.3783854166667, 17.3748697916667,
17.3796875, 17.3830729166667, 17.383203125, 17.3755208333333,
17.37421875, 17.371875, 17.3735677083333, 17.37109375, 17.373046875,
17.3774739583333, 17.3782552083333, 17.3748697916667, 17.3764322916667,
17.3807291666667, 17.3876302083333, 17.3846354166667, 17.3802083333333,
17.376171875, 17.3727864583333, 17.3735677083333, 17.3796875,
17.3864583333333, 17.3876302083333, 17.3845052083333, 17.3850260416667,
17.3880208333333, 17.3891927083333, 17.3880208333333, 17.3830729166667,
17.3782552083333, 17.3765625, 17.379296875, 17.3829427083333,
17.3869791666667, 17.3881510416667, 17.384765625, 17.3763020833333,
17.376953125, 17.3786458333333, 17.3817708333333, 17.3821614583333,
17.3859375, 17.3876302083333, 17.3837239583333, 17.381640625,
17.37890625, 17.3802083333333, 17.3825520833333, 17.3881510416667,
17.3888020833333, 17.3864583333333, 17.3825520833333, 17.3834635416667,
17.386328125, 17.3854166666667, 17.384375, 17.3852864583333,
17.390234375, 17.3916666666667, 17.38828125, 17.3891927083333,
17.3901041666667, 17.3950520833333, 17.3963541666667, 17.3970052083333,
17.3907552083333, 17.3846354166667, 17.3760416666667, 17.3743489583333
)), row.names = 15002:15361, class = "data.frame")
(p.s the question here: R-package(baseline) application to sample dataset seems to have a similar problem, but doesn't address how to turn simple x,y data into the format required by the baseline package).

The baseline package expects spectra to appear in rows, but your code creates a matrix with the spectrum in a single column. If you change the conversion from data.frame to matrix to the following it should work:
baseline(matrix(y, nrow=1))
The problem was caused by two things, using as.matrix(), which does not take the arguments you need, and using byrow=T instead of nrow=1. byrow controls the direction in which the matrix is filled, either by rows or by columns, but has no effect on the output dimensions.
The extra fuzz in the milk data is not helping here, so I will remove it in the next package update. I will also look into the possibility of allowing single spectra to be handled in vector format instead of explicitly forcing matrix input.
P.S. I was able to copy out your data with a tiny extra effort, but suspect that you need the raw data to directly copy-paste from this page as the dput line contains som subsetting.

R adding slots to existing S4 object

I am trying to follow this answer but getting lost with what to change for my example. Please can someone spell out specifically for the below?
I have the following S4 object called "classic":
> str(classic)
Formal class 'topGOresult' [package "topGO"] with 5 slots
..# description: chr "Custom Afol today"
..# score : Named num [1:7633] 0.5735 0.0883 0.8081 0.8005 0.4941 ...
.. ..- attr(*, "names")= chr [1:7633] "GO:0000002" "GO:0000003" "GO:0000018" "GO:0000027" ...
..# testName : chr "fisher"
..# algorithm : chr "classic"
.. ..- attr(*, "testClass")= chr "classicCount"
..# geneData : Named int [1:4] 9171 620 5 5361
.. ..- attr(*, "names")= chr [1:4] "Annotated" "Significant" "NodeSize" "SigTerms"
I am able to edit contents of existing slots, such as:
classic#description = "Custom Afol today"
However, I would like to add a new slot called "ontology" with character input of "BP". Is there a way to add a new slot to an existing object such as this?
Many thanks in advance for help.

understanding the output of str function in R

I use the str to print out information for a calculate variable
str(samples)
'mcmc' num [1:1000, 1:228] 0.1079 -0.2367 -0.0757 -0.3414 -0.3382 ...
- attr(*, "dimnames")=List of 2
..$ : NULL
..$ : chr [1:228] "B[1,1,1]" "B[2,1,1]" "B[3,1,1]" "B[4,1,1]" ...
- attr(*, "mcpar")= num [1:3] 20005 25000 5
But how to read these information, or what does this output can tell us? For instance, the third component is attr(*, "mcpar")= num [1:3] 20005 25000 5, what does it mean?

The attr implies there is an attribute named 'mcpar' which is a numeric vector
attributes(samples)
returns a list of all the attributes of the samples i.e. it will return dimnames as one attribute and the 'mcpar' as another one
According to documentation
The ‘mcpar’ attribute of an MCMC object gives the start iteration the end iteration and the thinning interval of the chain.

How to reference .. .. elements in list in R?

How do you access list elements prefaced with double dots .. ..?
I am trying to isolate the $attr part of the html to help in another question into a variable, and then place it another mime variable. x$parts$attr gives me NULL.
Thanks for your help.
EXAMPLE
library(gmailr)
test_email <- mime()
x <- html_body(mime = test_email, body = "I wish I had a nice body")
str(x)
List of 5
$ parts :List of 2
..$ : NULL
..$ :List of 4
.. ..$ parts : list()
.. ..$ header:List of 2
.. .. ..$ MIME-Version: chr "1.0"
.. .. ..$ Date : chr "Sun, 24 May 2015 09:44:59 GMT"
.. ..$ body : chr "I wish I had a nice body"
.. ..$ attr :List of 3 # << HOW do I get this?
.. .. ..$ content_type: chr "text/html"
.. .. ..$ charset : chr "utf-8"
.. .. ..$ encoding : chr "base64"
.. ..- attr(*, "class")= chr "mime"

Try this:
str(x$parts[[2]]$attr)
List of 3
$ content_type: chr "text/html"
$ charset : chr "utf-8"
$ encoding : chr "base64"

R understanding and access a nested object by reading from str

Hi I have a nested object which I think contains tables. I used str to see how it looks like,
> str(test)
Formal class 'CuffData' [package "cummeRbund"] with 5 slots
..# DB :Formal class 'SQLiteConnection' [package "RSQLite"] with 5 slots
.. .. ..# Id :<externalptr>
.. .. ..# dbname : chr "C:/temp/cuffData.db"
.. .. ..# loadable.extensions: logi TRUE
.. .. ..# flags : int 6
.. .. ..# vfs : chr ""
..# tables :List of 6
.. ..$ mainTable : chr "genes"
.. ..$ dataTable : chr "geneData"
.. ..$ expDiffTable : chr "geneExpDiffData"
.. ..$ featureTable : chr "geneFeatures"
.. ..$ countTable : chr "geneCount"
.. ..$ replicateTable: chr "geneReplicateData"
..# filters: list()
..# type : chr "genes"
..# idField: chr "gene_id"
however when I tried to to read the table mainTable all I get is this,
> test#tables$mainTable
[1] "genes"
is there any way I can read what is in this table?
Not sure if I'm even interpreting the str output correctly though. I'm a newbie at this and I'm also wondering if there is a good tutorial on how to interpret objects like these in R? Examples would be even better.
thanks you much in advance.
Ahdee

Resources