Help with looping a function over a list of dataframes:
Perhaps the following will be helpful (you can ignore the warning message here):
set.seed(1001) x <- sample(1:5,10, rep = TRUE) y <- sample(1:5,12, rep = TRUE) n <- seq_len(min(length(x), length(y))) flag <- as.numeric(abs(x-y)[n] <= 1)
Warning message: In x - y : longer object length is not a multiple of shorter object length
cbind(x[n], y[n], flag)
flag [1,] 3 2 1 [2,] 3 2 1 [3,] 4 4 1 [4,] 4 3 1 [5,] 4 4 1 [6,] 4 1 0 [7,] 4 2 0 [8,] 5 3 0 [9,] 5 5 1 [10,] 3 1 0 Do note that all columns in a data frame must have the same length, so maybe you'll need to pad with NA's -- I do not entirely get what you are trying to do. Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Sat, Jul 4, 2020 at 8:04 AM Kathan Desai <kdesai1 at sheffield.ac.uk> wrote:
*I hope this is more succinct.*
*I have the following code: *
list_df$position_tab_5$ID <- unlist(lapply(list_df$position_tab_5$midpoint,
function(x) ifelse(any(abs(x - list_df$position_tab_4$midpoint) <=
1),1,0)))
It compares every observation from the midpoint column from dataframe 2 to
every observation from the midpoint column from dataframe 1. It does this
in order to find any values within +/- 1 of the value, and if it satisfies
this criteria then it assigns it a unique id of 1. If not then a value of
0.
In the example below, pos_tab_5 is being compared to pos_tab_4:
Pos tab 4:
Object minimum maximum midpoint
2600 4 22 13
2604 42 85 63.5
2606 142 172 157
2609 223 241 232
2611 393 421 407
Pos tab 5:
Object minimum maximum midpoint ID
2580 3 21 12 1
2581 43 85 64 1
2585 132 168 150 0
2586 223 241 232 1
2589 391 419 405 0
The reason it compares every observation from pos_tab_(n) to pos_tab_(n-1)
is because some of the dataframes are of different row length, and so by
comparing every observation from one DF to another, it can find any values
that are within +/- 1 of each other. (which is the main thing i'm looking
for)
I need help looping this function over a list of dataframes. The list of
dataframes called: list_df contains 121 different dataframes all
representing a different time point of the object.
This is what i have so far:
for(i in seq_along(list_df)){
list_df$position_tab_[[i]]$ID <-
unlist(lapply(list_df$position_tab_[[i]]$midpoint, function(x)
ifelse(any(abs(x - list_df$position_tab_[[i-1]]$midpoint)
<= 1),1,0)
))
}
On Sat, 4 Jul 2020 at 14:44, Eric Berger <ericjberger at gmail.com> wrote:
Hi Kathan, How about trying to create a *minimal* reproducible example, e.g. with a list of two data frames, where each data frame has 5 rows,? My guess is that there is a good chance that when you try to create such an example, you will discover the problem yourself. In the event that you create the example but still cannot solve your issue, you will find more people on this list willing to look into your question, as it will be much faster for them to do that (compared to the original formulation.) Eric On Sat, Jul 4, 2020 at 4:33 PM Kathan Desai <kdesai1 at sheffield.ac.uk> wrote:
---------- Forwarded message --------- From: Kathan Desai <kdesai1 at sheffield.ac.uk> Date: Sat, 4 Jul 2020 at 14:31 Subject: Re: [R] Help with looping a function over a list of dataframes: To: Jim Lemon <drjimlemon at gmail.com> Hi Jim, Thankyou for your reply, I tried the function you suggested and it doesn't seem to work. There are again no error messages produced,
however
the transformation to each position_tab_n table isn't being applied. Cheers, Kathan On Sat, 4 Jul 2020 at 11:14, Jim Lemon <drjimlemon at gmail.com> wrote:
Hi Kathan,
This is a very lazy answer as I haven't tested it. I think you will
need to wrap your loop in a function and return the modified list_df
to assign it like this:
add_IDs<-function(xdf) {
for(i in seq_along(xdf)) {
xdf$position_tab_[[i]]$ID <-
unlist(lapply(xdf$position_tab_[[i]]$midpoint, function(x)
ifelse(any(abs(x - xdf$position_tab_[[i-1]]$midpoint)<= 1),1,0)))
}
return(xdf)
}
list_df<-add_IDs(list_df)
Jim
On Sat, Jul 4, 2020 at 4:48 PM Kathan Desai <kdesai1 at sheffield.ac.uk>
wrote:
I have been trying to run a forloop for a function that compares
dataframe n
with dataframe n-1, across a list of dataframes. It does this by
checking
each midpoint of dataframe n with each midpoint of dataframe n-1.
This is
done to make up for an disparity in row length. The idea of this
code
is
to
identify any objects that are stationary, and assign them an id of
1,
and
the dynamic objects are assigned an id of 0 (examples can be found
below).
*This is what i have so far:*
for(i in seq_along(list_df)){
list_df$position_tab_[[i]]$ID <-
unlist(lapply(list_df$position_tab_[[i]]$midpoint, function(x)
ifelse(any(abs(x -
list_df$position_tab_[[i-1]]$midpoint)
<= 1),1,0)
))
}
There is no error message being produced so theres nothing to debug,
i am
quite new to R programming in general so excuse any silly mistakes i
may
have made. The function doesnt seem to be adding the ID columns and comparing the data as it should. my list of dataframes contain dataframes named: position_tab_1, position_tab_2 .... position_tab_121. Each position_tab represents a timepoints, so in total there are 121 timepoints (frames). I need
the
loop
to run so that pos_tab_2 compares to pos_tab_1 and this continues
all
the
way to pos_tab_121 comparing to pos_tab_120. The function adds a column named "id" to each of these dataframes as
it
compares to the dataframe before it, so all dataframes apart from position_tab_1 (as it has nothing to compare to) should have this
added.
*Some of my data (first 10 dataframes in list):*
dput(list_df[1:10])
list(position_tab_1 = structure(list(Object = c(2666L, 2668L, 2671L, 2674L, 2676L, 2677L, 2678L, 2679L, 2680L, 2682L, 2683L, 2684L, 2685L, 2686L, 2687L, 2689L, 2692L, 2693L, 2694L, 2695L, 2696L), minimum = c(4L, 39L, 147L, 224L, 419L, 531L, 595L, 641L, 669L, 723L, 810L, 836L, 907L, 978L, 1061L, 1129L, 1290L, 1519L, 1749L, 1843L, 1897L), maximum = c(22L, 85L, 173L, 242L, 449L, 587L, 627L, 655L, 702L, 740L, 828L, 890L, 923L, 1024L, 1086L, 1144L, 1302L, 1544L, 1780L, 1870L, 1925L), midpoint = c(13, 62, 160, 233, 434, 559, 611, 648, 685.5, 731.5, 819, 863, 915, 1001, 1073.5, 1136.5, 1296, 1531.5, 1764.5, 1856.5, 1911)), row.names =
c(NA,
-21L), class = c("tbl_df", "tbl", "data.frame")), position_tab_2 =
structure(list(
Object = c(2645L, 2646L, 2650L, 2652L, 2655L, 2656L, 2657L,
2658L, 2659L, 2661L, 2662L, 2663L, 2664L, 2665L, 2667L, 2670L,
2675L, 2681L, 2688L, 2690L, 2691L), minimum = c(4L, 40L,
147L, 224L, 415L, 532L, 595L, 641L, 670L, 722L, 811L, 835L,
907L, 978L, 1061L, 1128L, 1289L, 1520L, 1748L, 1843L, 1897L
), maximum = c(22L, 85L, 173L, 242L, 445L, 588L, 627L, 655L,
702L, 739L, 828L, 891L, 923L, 1022L, 1085L, 1143L, 1302L,
1544L, 1779L, 1870L, 1925L), midpoint = c(13, 62.5, 160,
233, 430, 560, 611, 648, 686, 730.5, 819.5, 863, 915, 1000,
1073, 1135.5, 1295.5, 1532, 1763.5, 1856.5, 1911)), row.names =
c(NA,
-21L), class = c("tbl_df", "tbl", "data.frame")), position_tab_3 =
structure(list(
Object = c(2623L, 2624L, 2627L, 2631L, 2633L, 2635L, 2636L,
2637L, 2638L, 2640L, 2641L, 2642L, 2643L, 2644L, 2647L, 2649L,
2654L, 2660L, 2669L, 2672L, 2673L), minimum = c(3L, 39L,
149L, 223L, 402L, 539L, 594L, 639L, 669L, 722L, 811L, 834L,
907L, 979L, 1060L, 1129L, 1289L, 1520L, 1749L, 1842L, 1897L
), maximum = c(22L, 86L, 175L, 241L, 431L, 587L, 627L, 653L,
700L, 738L, 828L, 894L, 925L, 1021L, 1084L, 1144L, 1302L,
1544L, 1779L, 1869L, 1925L), midpoint = c(12.5, 62.5, 162,
232, 416.5, 563, 610.5, 646, 684.5, 730, 819.5, 864, 916,
1000, 1072, 1136.5, 1295.5, 1532, 1764, 1855.5, 1911)),
row.names
=
c(NA,
-21L), class = c("tbl_df", "tbl", "data.frame")), position_tab_4 =
structure(list(
Object = c(2600L, 2604L, 2606L, 2609L, 2611L, 2613L, 2614L,
2615L, 2617L, 2618L, 2619L, 2620L, 2621L, 2622L, 2626L, 2628L,
2632L, 2639L, 2648L, 2651L, 2653L), minimum = c(4L, 42L,
142L, 223L, 393L, 547L, 595L, 641L, 669L, 720L, 809L, 835L,
908L, 979L, 1059L, 1127L, 1289L, 1519L, 1749L, 1841L, 1897L
), maximum = c(22L, 85L, 172L, 241L, 421L, 587L, 629L, 655L,
701L, 738L, 826L, 890L, 925L, 1019L, 1084L, 1143L, 1301L,
1544L, 1780L, 1868L, 1925L), midpoint = c(13, 63.5, 157,
232, 407, 567, 612, 648, 685, 729, 817.5, 862.5, 916.5, 999,
1071.5, 1135, 1295, 1531.5, 1764.5, 1854.5, 1911)), row.names =
c(NA,
-21L), class = c("tbl_df", "tbl", "data.frame")), position_tab_5 =
structure(list(
Object = c(2580L, 2581L, 2585L, 2586L, 2589L, 2590L, 2592L,
2593L, 2594L, 2595L, 2596L, 2597L, 2598L, 2599L, 2601L, 2603L,
2605L, 2610L, 2616L, 2625L, 2629L, 2630L, 2634L), minimum =
c(3L,
43L, 132L, 223L, 391L, 547L, 643L, 669L, 721L, 808L, 836L,
861L, 908L, 978L, 1028L, 1057L, 1127L, 1288L, 1519L, 1748L,
1842L, 1893L, 2148L), maximum = c(21L, 85L, 168L, 241L, 419L,
629L, 656L, 701L, 738L, 828L, 858L, 890L, 925L, 1013L, 1050L,
1083L, 1143L, 1301L, 1544L, 1780L, 1869L, 1925L, 2148L),
midpoint = c(12, 64, 150, 232, 405, 588, 649.5, 685, 729.5,
818, 847, 875.5, 916.5, 995.5, 1039, 1070, 1135, 1294.5,
1531.5, 1764, 1855.5, 1909, 2148)), row.names = c(NA, -23L
), class = c("tbl_df", "tbl", "data.frame")), position_tab_6 =
structure(list(
Object = c(2555L, 2559L, 2562L, 2563L, 2564L, 2567L, 2569L,
2570L, 2571L, 2572L, 2573L, 2574L, 2575L, 2576L, 2577L, 2579L,
2583L, 2587L, 2591L, 2602L, 2607L, 2608L, 2612L), minimum =
c(4L,
45L, 123L, 154L, 224L, 390L, 546L, 600L, 643L, 669L, 720L,
804L, 836L, 908L, 967L, 1058L, 1129L, 1289L, 1519L, 1748L,
1843L, 1893L, 2147L), maximum = c(23L, 86L, 150L, 171L, 241L,
419L, 589L, 636L, 657L, 701L, 738L, 827L, 879L, 925L, 1011L,
1084L, 1144L, 1301L, 1543L, 1780L, 1871L, 1924L, 2148L),
midpoint = c(13.5, 65.5, 136.5, 162.5, 232.5, 404.5, 567.5,
618, 650, 685, 729, 815.5, 857.5, 916.5, 989, 1071, 1136.5,
1295, 1531, 1764, 1857, 1908.5, 2147.5)), row.names = c(NA,
-23L), class = c("tbl_df", "tbl", "data.frame")), position_tab_7 =
structure(list(
Object = c(2537L, 2539L, 2540L, 2541L, 2542L, 2544L, 2546L,
2547L, 2548L, 2549L, 2550L, 2551L, 2552L, 2554L, 2556L, 2558L,
2560L, 2565L, 2568L, 2578L, 2582L, 2584L, 2588L), minimum =
c(3L,
45L, 122L, 156L, 224L, 387L, 546L, 601L, 669L, 719L, 803L,
837L, 908L, 959L, 1059L, 1096L, 1128L, 1289L, 1519L, 1748L,
1844L, 1892L, 2147L), maximum = c(22L, 86L, 147L, 172L, 241L,
415L, 590L, 656L, 699L, 738L, 830L, 871L, 924L, 1014L, 1082L,
1119L, 1144L, 1301L, 1543L, 1781L, 1872L, 1925L, 2148L),
midpoint = c(12.5, 65.5, 134.5, 164, 232.5, 401, 568, 628.5,
684, 728.5, 816.5, 854, 916, 986.5, 1070.5, 1107.5, 1136,
1295, 1531, 1764.5, 1858, 1908.5, 2147.5)), row.names = c(NA,
-23L), class = c("tbl_df", "tbl", "data.frame")), position_tab_8 =
structure(list(
Object = c(2514L, 2517L, 2519L, 2520L, 2521L, 2523L, 2525L,
2526L, 2527L, 2528L, 2529L, 2530L, 2531L, 2532L, 2533L, 2534L,
2536L, 2543L, 2545L, 2553L, 2557L, 2561L, 2566L), minimum =
c(5L,
44L, 121L, 153L, 224L, 380L, 546L, 603L, 668L, 721L, 802L,
841L, 907L, 960L, 1006L, 1060L, 1106L, 1288L, 1518L, 1748L,
1843L, 1893L, 2148L), maximum = c(23L, 86L, 146L, 170L, 242L,
409L, 588L, 655L, 699L, 738L, 830L, 872L, 924L, 994L, 1029L,
1084L, 1143L, 1302L, 1543L, 1781L, 1870L, 1925L, 2148L),
midpoint = c(14, 65, 133.5, 161.5, 233, 394.5, 567, 629,
683.5, 729.5, 816, 856.5, 915.5, 977, 1017.5, 1072, 1124.5,
1295, 1530.5, 1764.5, 1856.5, 1909, 2148)), row.names = c(NA,
-23L), class = c("tbl_df", "tbl", "data.frame")), position_tab_9 =
structure(list(
Object = c(2492L, 2493L, 2497L, 2498L, 2499L, 2501L, 2503L,
2504L, 2505L, 2506L, 2507L, 2508L, 2509L, 2510L, 2511L, 2513L,
2516L, 2522L, 2524L, 2532L, 2535L, 2538L), minimum = c(6L,
44L, 111L, 149L, 224L, 375L, 548L, 596L, 668L, 722L, 800L,
840L, 908L, 960L, 1005L, 1058L, 1127L, 1289L, 1519L, 1748L,
1842L, 1891L), maximum = c(24L, 81L, 137L, 167L, 242L, 403L,
589L, 656L, 699L, 738L, 828L, 872L, 925L, 994L, 1028L, 1081L,
1149L, 1302L, 1544L, 1780L, 1868L, 1924L), midpoint = c(15,
62.5, 124, 158, 233, 389, 568.5, 626, 683.5, 730, 814, 856,
916.5, 977, 1016.5, 1069.5, 1138, 1295.5, 1531.5, 1764, 1855,
1907.5)), row.names = c(NA, -22L), class = c("tbl_df", "tbl",
"data.frame")), position_tab_10 = structure(list(Object = c(2469L,
2471L, 2474L, 2475L, 2476L, 2478L, 2481L, 2482L, 2483L, 2484L,
2485L, 2486L, 2487L, 2488L, 2489L, 2491L, 2495L, 2500L, 2502L,
2512L, 2515L, 2518L), minimum = c(6L, 38L, 109L, 147L, 223L,
363L, 548L, 597L, 668L, 719L, 803L, 839L, 908L, 958L, 1004L,
1058L, 1126L, 1288L, 1519L, 1746L, 1841L, 1892L), maximum = c(24L,
76L, 134L, 165L, 240L, 394L, 591L, 656L, 698L, 737L, 829L, 869L,
924L, 996L, 1027L, 1081L, 1147L, 1301L, 1543L, 1781L, 1868L,
1925L), midpoint = c(15, 57, 121.5, 156, 231.5, 378.5, 569.5,
626.5, 683, 728, 816, 854, 916, 977, 1015.5, 1069.5, 1136.5,
1294.5, 1531, 1763.5, 1854.5, 1908.5)), row.names = c(NA, -22L
), class = c("tbl_df", "tbl", "data.frame")))
*What is produced when running the base code without any loops:*
This is the base code without me trying to loop it in anyway, below
is
what
it produces when its used with dataframe 4 and 5: #the code: list_df$position_tab_5$ID <-
unlist(lapply(list_df$position_tab_5$midpoint,
function(x) ifelse(any(abs(x - list_df$position_tab_4$midpoint) <=
1),1,0)))
##position_tab_5 after manipulations have occured:
structure(list(Object = c(2580L, 2581L, 2585L, 2586L, 2589L,
2590L, 2592L, 2593L, 2594L, 2595L, 2596L, 2597L, 2598L, 2599L,
2601L, 2603L, 2605L, 2610L, 2616L, 2625L, 2629L, 2630L, 2634L
), minimum = c(3L, 43L, 132L, 223L, 391L, 547L, 643L, 669L, 721L,
808L, 836L, 861L, 908L, 978L, 1028L, 1057L, 1127L, 1288L, 1519L,
1748L, 1842L, 1893L, 2148L), maximum = c(21L, 85L, 168L, 241L,
419L, 629L, 656L, 701L, 738L, 828L, 858L, 890L, 925L, 1013L,
1050L, 1083L, 1143L, 1301L, 1544L, 1780L, 1869L, 1925L, 2148L
), midpoint = c(12, 64, 150, 232, 405, 588, 649.5, 685, 729.5,
818, 847, 875.5, 916.5, 995.5, 1039, 1070, 1135, 1294.5, 1531.5,
1764, 1855.5, 1909, 2148), ID = c(1, 1, 0, 1, 0, 0, 0, 1, 1,
1, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0)), row.names = c(NA,
-23L), class = c("tbl_df", "tbl", "data.frame"))
#position_tab_4 (the DF pos_tab_5 is being compared to)
structure(list(Object = c(2600L, 2604L, 2606L, 2609L, 2611L,
2613L, 2614L, 2615L, 2617L, 2618L, 2619L, 2620L, 2621L, 2622L,
2626L, 2628L, 2632L, 2639L, 2648L, 2651L, 2653L), minimum = c(4L,
42L, 142L, 223L, 393L, 547L, 595L, 641L, 669L, 720L, 809L, 835L,
908L, 979L, 1059L, 1127L, 1289L, 1519L, 1749L, 1841L, 1897L),
maximum = c(22L, 85L, 172L, 241L, 421L, 587L, 629L, 655L,
701L, 738L, 826L, 890L, 925L, 1019L, 1084L, 1143L, 1301L,
1544L, 1780L, 1868L, 1925L), midpoint = c(13, 63.5, 157,
232, 407, 567, 612, 648, 685, 729, 817.5, 862.5, 916.5, 999,
1071.5, 1135, 1295, 1531.5, 1764.5, 1854.5, 1911)), row.names =
c(NA,
-21L), class = c("tbl_df", "tbl", "data.frame"))
*Appreciate any help, anyone can provide!*
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______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.