Sampling distribution and sum of tables - r

I've made a few experiments and each experiment led to the apparition of color.
As I can't do more experiments, I want to sample by size=30 and see what frequency table (of colors) I could obtain for 1000 sampling. The resulting frequency table should be the sum of the 1000 frequency table.
I think about concatenating table as follows and try to agregate, but it did not work:
mydata=structure(list(Date = structure(c(11L, 1L, 9L, 9L, 10L, 1L, 2L,
3L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 6L, 7L, 4L, 4L, 4L, 6L, 6L, 11L,
5L, 4L, 7L, 10L, 6L, 6L, 2L, 5L, 7L, 11L, 1L, 9L, 11L, 11L, 11L,
1L, 1L), .Label = c("01/02/2016", "02/02/2016", "03/02/2016",
"08/02/2016", "10/02/2016", "11/02/2016", "16/02/2016", "22/02/2016",
"26/01/2016", "27/01/2016", "28/01/2016"), class = "factor"),
Color = structure(c(30L, 33L, 11L, 1L, 18L, 18L, 11L,
16L, 19L, 19L, 22L, 1L, 18L, 18L, 13L, 14L, 13L, 18L, 24L,
24L, 11L, 24L, 2L, 33L, 25L, 1L, 30L, 5L, 24L, 18L, 13L,
35L, 19L, 19L, 18L, 23L, 19L, 8L, 19L, 14L), .Label = c("ARD",
"ARP", "BBB", "BIE", "CFX", "CHR", "DDD", "DOO", "EAU", "ELY",
"EPI", "ETR", "GEN", "GER", "GGG", "GIS", "ISE", "JUV", "LER",
"LES", "LON", "LYR", "MON", "NER", "NGY", "NOJ", "NYO", "ORI",
"PEO", "RAY", "RRR", "RSI", "SEI", "SEP", "VIL", "XQU", "YYY",
"ZYZ"), class = "factor"), Categorie = structure(c(1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("1", "1,2", "1,2,3",
"1,3", "2", "2,3", "3", "4", "5"), class = "factor"), Portion_Longueur = c(3L,
4L, 1L, 1L, 2L, 4L, 5L, 6L, 7L, 7L, 8L, 8L, 9L, 8L, 8L, 9L,
11L, 7L, 7L, 7L, 9L, 8L, 3L, 8L, 7L, 11L, 2L, 9L, 8L, 5L,
8L, 12L, 3L, 4L, 1L, 3L, 3L, 3L, 4L, 5L)), .Names = c("Date",
"Color", "Categorie", "Portion_Longueur"), row.names = c(NA,
40L), class = "data.frame")
for (i in 1:1000) {
mysamp= sample(mydata$Color,size=30)
x=data.frame(table(mysamp))
if (i==1) w=x
else w <- c(w, x)
}
aggregate(w$Freq, by=list(Color=w$mysamp), FUN=sum)
Example, for 3 sampling, for (i in 1:3) I expect have sum as follow :
But I do not have Sum, instead I have:
Color x
1 ARD 2
2 ARP 1
3 BBB 0
4 BIE 0
5 CFX 0
6 CHR 0
7 DDD 0
8 DOO 1
9 EAU 0
10 ELY 0
11 EPI 3
12 ETR 0
13 GEN 2
14 GER 2
15 GGG 0
16 GIS 1
17 ISE 0
18 JUV 4
19 LER 5
20 LES 0
21 LON 0
22 LYR 1
23 MON 1
24 NER 2
25 NGY 1
26 NOJ 0
27 NYO 0
28 ORI 0
29 PEO 0
30 RAY 1
31 RRR 0
32 RSI 0
33 SEI 2
34 SEP 0
35 VIL 1
36 XQU 0
37 YYY 0
38 ZYZ 0
How to do this ?
Thanks a lot

Your for loop is what's causing your issues. You end up creating a big list that is somewhat difficult to perform calculations on (check out names(w) to see what I mean). A better data structure would allow for easier calculations:
x = NULL #initialize
for (i in 1:1000) {
mysamp = sample(mydata$Color,size=30) #sample
mysamp = data.frame(table(mysamp)) #frequency
x = rbind(x, mysamp) #bind to x
}
aggregate(Freq~mysamp, data = x, FUN = sum) #perform calculation
Note that this loop runs a bit slower than your loop. This is because of the rbind() function. See this post. Maybe someone will come along with a more efficient solution.

Related

Add a column and repeat every 16 dplyr

I need to add a column, column name "type", and for every 16 rows, change the row name to "type1, type 2 etc".
I tried book1$ID %/% 16 but not quite right.
This is the original data:
book1 <- structure(list(ID = 1:34, per_section = c(1L, 2L, 3L, 4L, 5L,
6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 1L, 2L, 3L,
4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 1L,
2L)), class = "data.frame", row.names = c(NA, -34L))
This is my desired output:
output <- structure(list(ID = 1:34, Type = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L), per_section = c(1L,
2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L,
16L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L,
14L, 15L, 16L, 1L, 2L)), class = "data.frame", row.names = c(NA,
-34L))
With %/% we may need to adjust by subtracting 1 and adding 1
book1$Type <- with(book1, (ID-1) %/% 16 + 1)
Or maybe more easier with gl
library(dplyr)
book1 <- book1 %>%
mutate(Type = as.integer(gl(n(), 16, n())), .after = 1)
Try this
book1$type <-ifelse(1:nrow(book1) %% 16 != 0 ,
1:nrow(book1) %% 16 , 16)

R:Error in `[.data.frame` undefined columns selected

I have this data sample
dput()
timeseries=structure(list(sales_point_id = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L), calendar_id_operday = c(1L, 2L, 3L, 4L, 5L, 6L,
7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L,
20L, 21L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L,
13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L), line_fact_amt = c(55767L,
59913L, 36363L, 48558L, 505L, 76344L, 22533L, 11965L, 78944L,
36754L, 30621L, 55716L, 32470L, 62165L, 57986L, 2652L, 16487L,
72849L, 73715L, 65656L, 64411L, 47460L, 61866L, 10877L, 72392L,
53011L, 23544L, 76692L, 10388L, 24255L, 56684L, 59329L, 6655L,
65612L, 17495L, 10389L, 63702L, 47407L, 78782L, 22898L, 21151L,
32587L)), class = "data.frame", row.names = c(NA, -42L))
calendar_id_operday=1 its mean range of week 20210101-20210108(ymd) but here there is no date format only week, just such a specificity of these data . I try transform my data.
library(reshape)
df <- cast(melt(timeseries, id=c("calendar_id_operday"), na.rm=TRUE),
line_fact_amt + calendar_id_operday)[, c("line_fact_amt", "calendar_id_operday", substring(month.name, 1, 3))]
colnames(df)[1] <- "sales_point_id"
df[, substring(month.name, 1, 3)] <- lapply(timeseries[, substring(month.name, 1, 3)],
function(x) as.numeric(as.character(x)))
But something goes wrong
Error in `[.data.frame`(timeseries, , substring(month.name, 1, 3)) :
undefined columns selected
I want that as the result i got this data.frame
sales_point_id year jan-1 jan-2 jan-3 jan-4 feb1
1 1 2021 8034.843 7485.725 8238.493 8446.994 134
2 1 2021 7810.315 7261.198 8013.965 8222.466 346
3 1 2021 7585.788 7036.670 7789.438 7997.938 54364
4 1 2021 7361.260 6812.142 7564.910 7773.411 34546
5 1 2021 7136.733 6587.615 7340.382 7548.883 46436
jan-1 is data for firts week of jan. jan2- is the second week of jan and so on.
What should i do to get desired result?
Thanks for your valuable help

Create unique ID based on repeated IDs [duplicate]

This question already has answers here:
Create group number for contiguous runs of equal values
(4 answers)
Closed 4 days ago.
I received some data from a colleague who is working with animal observations recorded in several transects. However my colleague used the same three ID codes for identifying each transect: 1, 7, 13 and 19. I would like to replace the repeated IDs with unique IDs. This image shows what I want to do:
Here's the corresponding code:
example_data<-structure(list(ID_Transect = c(1L, 1L, 1L, 1L, 1L, 1L, 7L, 7L,
7L, 7L, 7L, 7L, 13L, 13L, 13L, 13L, 13L, 13L, 19L, 19L, 19L,
19L, 19L, 19L, 1L, 1L, 1L, 1L, 1L, 1L, 7L, 7L, 7L, 7L, 7L, 7L),
transect_id = c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L,
5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L)), class = "data.frame", row.names = c(NA,
-36L))
We can also do
library(data.table)
setDT(example_data)[, transect_id := rleid(ID_Transect)]
You can use data.table rleid -
example_data$transect_id <- data.table::rleid(example_data$ID_Transect)
#[1] 1 1 1 1 1 1 2 2 2 2 2 2 3 3 3 3 3 3 4 4 4 4 4 4 5 5 5 5 5 5 6 6 6 6 6 6
In base R we can use rle -
with(rle(example_data$ID_Transect), rep(seq_along(values), lengths))
Or diff + cumsum -
cumsum(c(TRUE, diff(example_data$ID_Transect) != 0))

array manipulation: calculate odds ratios for a layer in a 3-way table

This is a question about array and data frame manipulation and calculation, in the
context of models for log odds in contingency tables. The closest question I've found to this is How can i calculate odds ratio in many table, but mine is more general.
I have a data frame representing a 3-way frequency table, of size 5 (litter) x 2 (treatment) x 3 (deaths).
"Freq" is the frequency in each cell, and deaths is the response variable.
Mice <-
structure(list(litter = c(7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L,
11L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 7L, 7L, 8L,
8L, 9L, 9L, 10L, 10L, 11L, 11L), treatment = structure(c(1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L), .Label = c("A",
"B"), class = "factor"), deaths = structure(c(1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("0", "1",
"2+"), class = "factor"), Freq = c(58L, 75L, 49L, 58L, 33L, 45L,
15L, 39L, 4L, 5L, 11L, 19L, 14L, 17L, 18L, 22L, 13L, 22L, 12L,
15L, 5L, 7L, 10L, 8L, 15L, 10L, 15L, 18L, 17L, 8L)), .Names = c("litter",
"treatment", "deaths", "Freq"), row.names = c(NA, 30L), class = "data.frame")
From this, I want to calculate the log odds for adjacent categories of the last variable (deaths)
and have this value in a data frame with factors litter (5), treatment (2), and contrast (2), as detailed below.
The data can be seen in xtabs() form:
mice.tab <- xtabs(Freq ~ litter + treatment + deaths, data=Mice)
ftable(mice.tab)
deaths 0 1 2+
litter treatment
7 A 58 11 5
B 75 19 7
8 A 49 14 10
B 58 17 8
9 A 33 18 15
B 45 22 10
10 A 15 13 15
B 39 22 18
11 A 4 12 17
B 5 15 8
>
From this, I want to calculate the (adjacent) log odds of 0 vs. 1 and 1 vs.2+ deaths, which is easy in
array format,
odds1 <- log(mice.tab[,,1]/mice.tab[,,2]) # contrast 0:1
odds2 <- log(mice.tab[,,2]/mice.tab[,,3]) # contrast 1:2+
odds1
treatment
litter A B
7 1.6625477 1.3730491
8 1.2527630 1.2272297
9 0.6061358 0.7156200
10 0.1431008 0.5725192
11 -1.0986123 -1.0986123
>
But, for analysis, I want to have these in a data frame, with factors litter, treatment and contrast
and a column, 'logodds' containing the entries in the odds1 and odds2 tables, suitably strung out.
More generally, for an I x J x K table, where the last factor is the response, my desired result
is a data frame of IJ(K-1) rows, with adjacent log odds in a 'logodds' column, and ideally, I'd like
to have a general function to do this.
Note that if T is the 10 x 3 matrix of frequencies shown by ftable(), the calculation is essentially
log(T) %*% matrix(c(1, -1, 0,
0, 1, -1))
followed by reshaping and labeling.
Can anyone help with this?

Showing data.frame as table or matrix in R

I want to show the following data.frame
df <- structure(list(Variety = structure(c(2L, 3L, 4L, 5L, 6L, 7L,
1L, 2L, 3L, 4L, 5L, 6L, 7L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 1L, 2L,
3L, 4L, 5L, 6L, 7L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 1L, 2L, 3L, 4L,
5L, 6L, 7L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 1L), .Label = c("F2022",
"F9917", "Hegari", "JS2002", "JS263", "PC1", "Sadabahar"), class = "factor"),
Priming = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L,
6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 1L), .Label = c("CaCl2",
"Dry", "Hydro", "KCL", "KNO3", "NaCl", "Onfarm"), class = "factor"),
Letters = structure(c(1L, 3L, 10L, 11L, 10L, 19L, 27L, 5L,
28L, 11L, 18L, 20L, 9L, 1L, 22L, 14L, 30L, 26L, 24L, 3L,
22L, 9L, 16L, 10L, 15L, 25L, 6L, 7L, 17L, 30L, 18L, 13L,
20L, 27L, 19L, 29L, 23L, 2L, 8L, 12L, 6L, 31L, 8L, 22L, 4L,
32L, 21L, 33L, 2L), .Label = c("a", "at", "bcd", "bclq",
"bcq", "bd", "bds", "chlq", "ds", "e", "efg", "efgmnor",
"efgnor", "efgnr", "efgr", "eg", "fgmnor", "fmnor", "hijkl",
"hijkp", "hikl", "hklq", "ijkmp", "ijmop", "jmop", "mno",
"mnop", "mnor", "su", "t", "uv", "v", "w"), class = "factor")), .Names = c("Variety",
"Priming", "Letters"), row.names = c(NA, -49L), class = "data.frame")
as Table or matrix with Ordered Variety names along rows and Ordered Priming names along columns and showing Letter column in the main body of the table in R.
I could not figure out how to do this. Any help will be highly appreciated. Thanks in advance.
This should do it.
d <- d[order(d$Variety,d$Priming),]
dw <- reshape(data = d, idvar = 'Variety', timevar = 'Priming', direction = 'wide')
dw
You might want to edit the column names.
names(dw) <- gsub('Letters.', '', names(dw), fixed = TRUE)
Simple one
library(reshape2)
acast(data=df, formula=Variety~Priming)
CaCl2 Dry Hydro KCL KNO3 NaCl Onfarm
F2022 at mnop a hklq bds hijkl uv
F9917 a bcq hklq ds fgmnor su chlq
Hegari bcd mnor efgnr eg t ijkmp hklq
JS2002 e efg t e fmnor at bclq
JS263 efg fmnor mno efgr efgnor chlq v
PC1 e hijkp ijmop jmop hijkp efgmnor hikl
Sadabahar hijkl ds bcd bd mnop bd w

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