Storing results of a for loop from linear model for multiple datasets into a vector

General
1

Hello!

I am trying to store the results of a for loop into a vector.

I have 40 datasets in .csv files that I am formatting and performing some calculations on. What I want to do for each dataset is reformat it, run a linear model, remove the outliers, and then identify and store the r2 and slope coefficient results into a vector.

Below is my code:

files <- list.files(pattern="\\.csv$")
# Create a function which reads each csv file and stores it as a list
dfs <- lapply(files, function(i){
  read.csv(i, header=T)
})
# Determine how many entries are in the list to tell R how many times to iterate the function
N <- length(dfs)

r2vector <- vector(mode="numeric")
Kdvector <- vector(mode="numeric")

for(i in 1:N){
data <- dfs[[i]] %>% pivot_wider(id_cols = c(SITE_ID, LINE), names_from = PARAMETER, values_from = RESULT) %>%
  select(SITE_ID, CAST, LINE, DEPTH, TEMPERATURE, DO, PH, CONDUCTIVITY, LIGHT_AMB, LIGHT_UW) %>% 
  mutate(across(.cols = LINE:LIGHT_UW, as.numeric)) %>% arrange(LINE) %>% group_by(SITE_ID, DEPTH) %>% na.omit()
data$FRLIGHT <- data$LIGHT_UW/data$LIGHT_AMB
# Determine any outliers
outliers <- boxplot(data$FRLIGHT, plot=F)$out
Kdout <- data[-which(data$FRLIGHT %in% outliers),]
lm <- lm(Kdout$FRLIGHT~Kdout$DEPTH)
summary <- summary(lm)
# get r2 value from linear model to determine if the relationship is strong enough for Kd calculation
r2 <- summary$r.squared
# Store Kd value
Kd <- summary$coefficients[2,1]
# Store r2 and Kd values into vectors to add to list of means
r2vector <- append(r2vector, r2)
Kdvector <- append(Kdvector, Kd)
}

Unfortunately it only stores the results of one of the datasets into the vectors and stops there. How do I make it so that the results from each dataset get stored into the vector?

If it helps, here is one of the datasets that I run through my code:

df1 <- structure(list(UID = c("GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
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"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
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"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
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"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1", 
"GBA20-10501_1", "GBA20-10501_1", "GBA20-10501_1"), SITE_ID = c("GBA20-10501", 
"GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", 
"GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", 
"GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", 
"GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", 
"GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", 
"GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", 
"GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", 
"GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", 
"GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", 
"GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", "GBA20-10501", 
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4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 
4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5), SAMPLE_TYPE = c("HYDRO", 
"SECC", "SECC", "SECC", "SECC", "SECC", "SECC", "SECC", "SECC", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", 
"HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO", "HYDRO"), LINE = c(0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 
9L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 
11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 13L, 
13L, 13L, 13L, 13L, 13L, 13L, 13L, 14L, 14L, 14L, 14L, 14L, 14L, 
14L, 14L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 16L, 16L, 16L, 
16L, 16L, 16L, 16L, 16L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 
18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 19L, 19L, 19L, 19L, 19L, 
19L, 19L, 19L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 21L, 21L, 
21L, 21L, 21L, 21L, 21L, 21L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 
22L, 23L, 23L, 23L, 23L, 23L, 23L, 23L, 23L, 24L, 24L, 24L, 24L, 
24L, 24L, 24L, 24L, 25L, 25L, 25L, 25L, 25L, 25L, 25L, 25L, 26L, 
26L, 26L, 26L, 26L, 26L, 26L, 26L), PARAMETER = c("STATION_DEPTH", 
"SECCHI_TIME", "CLEAR_TO_BOTTOM", "DISAPPEARS_1", "REAPPEARS_1", 
"DISAPPEARS_2", "REAPPEARS_2", "DISAPPEARS_3", "REAPPEARS_3", 
"CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", 
"LIGHT_UW", "COMMENT", "CAST", "DEPTH", "TEMPERATURE", "PH", 
"DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW", "CAST", "DEPTH", 
"TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW", 
"CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", 
"LIGHT_UW", "CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", 
"LIGHT_AMB", "LIGHT_UW", "CAST", "DEPTH", "TEMPERATURE", "PH", 
"DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW", "CAST", "DEPTH", 
"TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW", 
"CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", 
"LIGHT_UW", "CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", 
"LIGHT_AMB", "LIGHT_UW", "CAST", "DEPTH", "TEMPERATURE", "PH", 
"DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW", "CAST", "DEPTH", 
"TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW", 
"CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", 
"LIGHT_UW", "CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", 
"LIGHT_AMB", "LIGHT_UW", "CAST", "DEPTH", "TEMPERATURE", "PH", 
"DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW", "CAST", "DEPTH", 
"TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW", 
"CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", 
"LIGHT_UW", "CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", 
"LIGHT_AMB", "LIGHT_UW", "CAST", "DEPTH", "TEMPERATURE", "PH", 
"DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW", "CAST", "DEPTH", 
"TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW", 
"CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", 
"LIGHT_UW", "CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", 
"LIGHT_AMB", "LIGHT_UW", "CAST", "DEPTH", "TEMPERATURE", "PH", 
"DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW", "CAST", "DEPTH", 
"TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW", 
"CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", "LIGHT_AMB", 
"LIGHT_UW", "CAST", "DEPTH", "TEMPERATURE", "PH", "DO", "CONDUCTIVITY", 
"LIGHT_AMB", "LIGHT_UW", "CAST", "DEPTH", "TEMPERATURE", "PH", 
"DO", "CONDUCTIVITY", "LIGHT_AMB", "LIGHT_UW"), RESULT = c("11.4", 
"09:47", "N", "2.3", "2.0", "2.2", "2.0", "2.2", "2.0", "DOWN", 
"0.1", "22.0", "8.58", "9.5", "308.4", "203.9", "1003.4", "Forgot cap on Amb light sensor resulting in low readings.", 
"DOWN", "0.5", "22.0", "8.59", "9.4", "308.6", "204.1", "957.9", 
"DOWN", "1", "22.0", "8.61", "9.6", "308.8", "204.0", "695.9", 
"DOWN", "2", "22.0", "8.62", "9.5", "308.6", "203.9", "397.4", 
"DOWN", "3", "21.8", "8.62", "9.4", "309.1", "204.2", "127.1", 
"DOWN", "4", "21.8", "8.62", "9.2", "309.6", "204.2", "64.3", 
"DOWN", "5", "21.8", "8.61", "9.0", "308.9", "204.2", "31.7", 
"DOWN", "6", "21.6", "8.59", "8.7", "309.0", "204.0", "15.1", 
"DOWN", "7", "20.4", "8.41", "6.3", "306.2", "204.2", "8.0", 
"DOWN", "8", "18.1", "8.22", "4.8", "293.4", "204.1", "3.8", 
"DOWN", "9", "17.2", "8.11", "2.3", "287.0", "204.2", "2.3", 
"DOWN", "10", "16.3", "8.02", "2.1", "285.5", "204.2", "0.9", 
"DOWN", "11", "15.7", "7.94", "2.0", "287.7", "204.2", "0.2", 
"UP", "11", "15.7", "7.93", "2.0", "287.9", "204.1", "0.3", "UP", 
"10", "15.6", "7.86", "2.0", "289.6", "204.2", "0.9", "UP", "9", 
"16.4", "7.80", "2.4", "298.1", "204.1", "2.2", "UP", "8", "18.5", 
"7.90", "4.9", "306.5", "204.1", "3.8", "UP", "7", "20.3", "8.10", 
"6.8", "311.8", "204.6", "7.3", "UP", "6", "21.0", "8.38", "8.5", 
"312.2", "204.3", "15.0", "UP", "5", "21.3", "8.52", "8.9", "311.8", 
"204.3", "30.5", "UP", "4", "21.5", "8.58", "9.4", "311.7", "204.4", 
"64.8", "UP", "3", "21.6", "8.62", "9.5", "311.0", "204.3", "122.3", 
"UP", "2", "21.7", "8.66", "9.6", "310.6", "204.4", "267.9", 
"UP", "1", "21.8", "8.68", "9.8", "310.7", "204.4", "973.1", 
"UP", "0.5", "21.8", "8.69", "9.8", "310.9", "204.6", "748.3", 
"UP", "0.1", "21.9", "8.70", "9.7", "311.1", "204.4", "967.4"
)), class = "data.frame", row.names = c(NA, -218L))

Thank you so much for your help!

2

Assuming that reading the files goes okay,what happens when you start defining the two vectors as list() ?

3

How about within the loop

r2vector[i] <- r2

1 Like
4

There was an issue earlier in my code that I figured out, but once I did, this worked!
Thanks so much for your help!

5

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