I would like to extract a dataframe that shows how many years it takes for NInd variable (dataset p1) to recover due to some culling happening, which is showed in dataframe e1.
I have the following datasets (mine are much bigger, but just to give you something to play with):
# Dataset 1
Batch <- c(2,2,2,2,2,2,2,2,2,2)
Rep <- c(0,0,0,0,0,0,0,0,0,0)
Year <- c(0,0,1,1,2,2,3,3,4,4)
RepSeason <- c(0,0,0,0,0,0,0,0,0,0)
PatchID <- c(17,25,19,16,21,24,23,20,18,33)
Species <- c(0,0,0,0,0,0,0,0,0,0)
Selected <- c(1,1,1,1,1,1,1,1,1,1)
Nculled <- c(811,4068,1755,449,1195,1711,619,4332,457,5883)
e1 <- data.frame(Batch,Rep,Year,RepSeason,PatchID,Species,Selected,Nculled)
# Dataset 2
Batch <- c(2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2)
Rep <- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0)
Year <- c(0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2)
RepSeason <- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0)
PatchID <- c(17,25,19,16,21,24,23,20,18,33,17,25,19,16,21,24,23,20,18,33,17,25,19,16,21,24,23,20,18,33)
Ncells <- c(6,5,6,4,4,5,6,5,5,5,6,5,6,4,4,5,6,7,3,5,4,4,3,3,4,4,5,5,6,4)
Species <- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0)
NInd <- c(656,656,262,350,175,218,919,218,984,875,700,190,93,127,52,54,292,12,43,68,308,1000,98,29,656,656,262,350,175,300)
p1 <- data.frame(Batch, Rep, Year, RepSeason, PatchID, Ncells, Species, NInd)
The dataset called e1 shows only those year where some culled happened to the population on specific PatchID.
I have created the following script that basically use each row from e1 to create a Recovery number. Maybe there is an easier way to get to the end, but this is the one I managed to get...
When you run this, you are working on ONE row of e1, so we focus on the first PatchID encounter and then do some calculation to match that up with p1, and finally I get a number named Recovery.
Now, the thing is my dataframe has 50,000 rows, so doing this over and over looks quite tedious. So, that's where I thought a loop may be useful. But have tried and no luck on how to make it work at all...
#here is where I would like the loop
e2 <- e1[1,] # Trial for one row only # but the idea is having here a loop that keep doing of comes next for each row
e3 <- e2 %>%
select(1,2,4,5)
p2 <- p1[,c(1,2,4,5,3,6,7,8)] # Re-order
row2 <- which(apply(p2, 1, function(x) return(all(x == e3))))
p3 <- p1 %>%
slice(row2) # all years with that particular patch in that particular Batch
#How many times was this patch cull during this replicate?
e4 <- e2[,c(1,2,4,5,3,6,7,8)]
e4 <- e4 %>%
select(1,2,3,4)
c_batch <- e1[,c(1,2,4,5,3,6,7,8)]
row <- which(apply(c_batch, 1, function(x) return(all(x == e4))))
c4 <- c_batch %>%
slice(row)
# Number of year to recover to 95% that had before culled
c5 <- c4[1,] # extract the first time was culled
c5 <- c5 %>%
select(1:5)
row3 <- which(apply(p2, 1, function(x) return(all(x == c5))))
Before <- p2 %>%
slice(row3)
NInd <- Before[,8] # Before culling number of individuals
Year2 <- Before[,5] # Year number where first culling happened (that actually the number corresponds to individuals before culling, as the Pop file is developed during reproduction, while Cull file is developed after!)
Percent <- (95*NInd)/100 # 95% recovery we want to achieve would correspond to having 95% of NInd BEFORE culled happened (Year2)
After <- p3 %>%
filter(NInd >= Percent & Year > Year2) # Look rows that match number of ind and Year
After2 <- After[1,] # we just want the first year where the recovery was successfully achieved
Recovery <- After2$Year - Before$Year
# no. of years to reach 95% of the population immediately before the cull
I reckon that the end would have to change somehow to to tell R that we are creating a dataframe with the Recovery, something like:
Batch <- c(1,1,2,2)
Rep <- c(0,0,0,0)
PatchID <- c(17,25,30,12)
Recovery <- c(1,2,1,5)
Final <- data.frame(Batch, Rep, PatchID, Recovery)
Would that be possible? OR this is just too mess-up and I may should try a different way?
Does the following solve the problem correectly?
I have first added a unique ID to your data.frames to allow matching of the cull and population files (this saves most of you complicated look-up code):
# Add a unique ID for the patch/replicate etc. (as done in the example code)
e1$RepID = paste(e1$Batch, e1$Rep, e1$RepSeason, e1$PatchID, sep = ":")
p1$RepID = paste(p1$Batch, p1$Rep, p1$RepSeason, p1$PatchID, sep = ":")
If you want a quick overview of the number of times each patch was culled, the new RepID makes this easy:
# How many times was each patch culled?
table(p1$RepID)
Then you want a loop to check the recovery time after each cull.
My solutions uses an sapply loop (which also retains the RepIDs so you can match to other metadata later):
sapply(unique(e1$RepID), function(rep_id){
all_cull_events = e1[e1$RepID == rep_id, , drop = F]
first_year = order(all_cull_events$Year)[1] # The first cull year (assuming data might not be in temporal order)
first_cull_event = all_cull_events[first_year, ] # The row corresponding to the first cull event
population_counts = p1[p1$RepID == first_cull_event$RepID, ] # The population counts for this plot/replicate
population_counts = population_counts[order(population_counts$Year), ] # Order by year (assuming data might not be in temporal order)
pop_at_first_cull_event = population_counts[population_counts$Year == first_cull_event$Year, "NInd"]
population_counts_after_cull = population_counts[population_counts$Year > first_cull_event$Year, , drop = F]
years_to_recovery = which(population_counts_after_cull$NInd >= (pop_at_first_cull_event * .95))[1] # First year to pass 95% threshold
return(years_to_recovery)
})
2:0:0:17 2:0:0:25 2:0:0:19 2:0:0:16 2:0:0:21 2:0:0:24 2:0:0:23 2:0:0:20 2:0:0:18 2:0:0:33
1 2 1 NA NA NA NA NA NA NA
(The output contains some NAs because the first cull year was outside the range of population counts in the data you gave us)
Please check this against your expected output though. There were some aspects of the question and example code that were not clear (see comments).
I'm lost on how to combine my data into a usable data frame. I have a list of lists of character and number vectors Here is a working example of my code so far:
remove(list=ls())
# Headers for each of my column names
headers <- c("name","p","c","prophylaxis","control","inclusion","exclusion","conversion excluded","infection criteria","age criteria","mean age","age sd")
#_name = author and year
#_p = no. in experimental arm.
#_c = no. in control arm
#_abx = antibiotic used
#_con = control used
#_inc = inclusion criteria
#_exc = exclusion criteria
#_coexc = was conversion to open excluded?
#_infxn = infection criteria
#_agecrit = age criteria
#_agemean = mean age of study
#_agesd = sd age of study
# Passos 2016
passos_name <- c("Passos","2016")
passos_p <- 50
passos_c <- 50
passos_abx <- "cefazolin 1g at induction"
passos_con <- "none"
passos_inc <- c("elective LC","symptomatic cholelithiasis","low risk")
passos_exc <- c("renal impairment","hepatic impairment","immunosuppression","regular steroid use","antibiotics within 48H","acute cholecystitis","choledocolithiasis")
passos_coexc <- TRUE
passos_infxn <- c("temperature >37.8C","tachycardia","asthenia","local pain","local purulence")
passos_agecrit <- NULL
passos_agemean <- 48
passos_agesd <- 13.63
passos <- list(passos_name,passos_p,passos_c,passos_abx,passos_con,passos_inc,passos_exc,passos_coexc,passos_infxn,passos_agecrit,passos_agemean,passos_agesd)
names(passos) <- headers
# Darzi 2016
darzi_name <- c("Darzi","2016")
darzi_p <- 182
darzi_c <- 247
darzi_abx <- c("cefazolin 1g 30min prior to induction","cefazolin 1g 6H after induction","cefazolin 1g 12H after induction")
darzi_con <- "NaCl"
darzi_inc <- c("elective LC","first time abdominal surgery")
darzi_exc <- c("antibiotics within 7 days","immunosuppression","acute cholecystitis","choledocolithiasis","cholangitis","obstructive jaundice",
"pancreatitis","previous biliary tract surgery","previous ERCP","DM","massive intraoperative bleeding","antibiotic allergy","major thalassemia",
"empyema")
darzi_coexc <- TRUE
darzi_infxn <- c("temperature >38C","local purulence","intra-abdominal collection")
darzi_agecrit <- c(">18", "<75")
darzi_agemean <- 43.75
darzi_agesd <- 13.30
darzi <- list(darzi_name,darzi_p,darzi_c,darzi_abx,darzi_con,darzi_inc,darzi_exc,darzi_coexc,darzi_infxn,darzi_agecrit,darzi_agemean,darzi_agesd)
names(darzi) <- headers
# Matsui 2014
matsui_name <- c("Matsui","2014")
matsui_p <- 504
matsui_c <- 505
matsui_abx <- c("cefazolin 1g at induction","cefazolin 1g 12H after induction","cefazolin 1g 24H after induction")
matsui_con <- "none"
matsui_inc <- "elective LC"
matsui_exc <- c("emergent","concurrent surgery","regular insulin use","regular steroid use","antibiotic allergy","HD","antibiotics within 7 days","hepatic impairment","chemotherapy")
matsui_coexc <- FALSE
matsui_infxn <- c("local purulence","intra-abdominal collection","distant infection","temperature >38C")
matsui_agecrit <- ">18"
matsui_agemean <- NULL
matsui_agesd <- NULL
matsui <- list(matsui_name,matsui_p,matsui_c,matsui_abx,matsui_con,matsui_inc,matsui_exc,matsui_coexc,matsui_infxn,matsui_agecrit,matsui_agemean,matsui_agesd)
names(matsui) <- headers
# Find unique exclusion critieria in order to create the list of all possible levels
exc <- ls()[grepl("_exc",ls())]
exclist <- sapply(exc,get)
exc.levels <- unique(unlist(exclist,use.names = F))
# Find unique inclusion critieria in order to create the list of all possible levels
inc <- ls()[grepl("_inc",ls())]
inclist <- sapply(inc,get)
inc.levels <- unique(unlist(inclist,use.names = F))
# Find unique antibiotics order to create the list of all possible levels
abx <- ls()[grepl("_abx",ls())]
abxlist <- sapply(abx,get)
abx.levels <- unique(unlist(abxlist,use.names = F))
# Find unique controls in order to create the list of all possible levels
con <- ls()[grepl("_con",ls())]
conlist <- sapply(con,get)
con.levels <- unique(unlist(conlist,use.names = F))
# Find unique age critieria in order to create the list of all possible levels
agecrit <- ls()[grepl("_agecrit",ls())]
agecritlist <- sapply(agecrit,get)
agecrit.levels <- unique(unlist(agecritlist,use.names = F))
I have been struggling with:
1) Turn each of the _exc, _inc, _abx, _con, _agecrit lists into factors using the levels generated at the end of the code block. I have been trying to use a for loop such as:
for (x in exc) {
as.name(x) <- factor(get(x),levels = exc.levels)
}
This only creates a variable, x, that stores the last parsed list as a factor.
2) Combine all of my data into a data frame formatted as such:
name, p, c, prophylaxis, control, inclusion, exclusion, conversion excluded, infection criteria, age criteria, mean age, age sd
"Passos 2016", 50, 50, "cefazolin 1g at induction", "none", ["elective LC","symptomatic cholelithiasis","low risk"], ["renal impairment","hepatic impairment","immunosuppression","regular steroid use","antibiotics within 48H","acute cholecystitis","choledocolithiasis"], TRUE, ["temperature >37.8C","tachycardia","asthenia","local pain","local purulence"], NULL, 48, 13.63
...
# [] = factors
# columns correspond to each studies variables (i.e. passos_name, passos_p, passos_c, etc..)
# rows correspond to each study (i.e., passos, darzi, matsui)
I have tried various solutions on StackOverflow, but have not found any that work; for example:
studies <- list(passos,darzi,matsui,ruangsin,turk,naqvi,hassan,sharma,uludag,yildiz,kuthe,koc,maha,tocchi,higgins,mahmoud,kumar)
library(data.table)
rbindlist(lapply(studies,as.data.frame.list))
I suspect my data may not be exactly amenable to a data frame? Primarily because of trying to store a list of factors in a column. Is that allowed? If not, how is this type of data normally stored? My goal is to be able to meaningfully compare these various criterion across studies.
This is too long for a comment, so I turn it into an "answer":
To start with, have a look at what happens here:
data.frame(name = "Passos, 2016", p = 50)
name p
1 Passos, 2016 50
data.frame(name = c("Passos", "2016"), p = 50)
name p
1 Passos 50
2 2016 50
In the first one, we created a dataframe with the column "name" which contained one entry "Passos, 2016", i.e. one character containing both pieces of information, and the column "p". All fine. Now, in the second version, I specified the column "name" as you did above, using c(Passos, 2016). This is a two-element vector, and hence we get two rows in the dataframe: one with name Passos, one with name 2016, and the column p gets recycled.
Clearly, the latter is probably not what you intended. But it works anyway because R just recycles the shorter vector. Now, what do you think happens if I add a vector that contains three elements?
And this highlights the main issue with what you are doing: you are trying to get a dataframe from many vectors with different lengths. Now, in some cases this is fine if you want the shorter vector to be repeated (in R speech, we call this "recycled"), but it does not look like something you want to do here.
So, my recommendation would be this: try to imagine a matrix and make sure you understand what each element (row and column) is supposed to be. Then specify your data accordingly. If in doubt, look up "tidy data".