I know it is fundamental but I can't find the trick ...
Here is an exemple :
Species <- c("dark frog",rep(c("elephant","tiger","boa"),3),"black mamba")
Year <- c(rep(2011,4),rep(2012,3),rep(2013,4))
Abundance <- c(2,4,5,6,9,2,1,5,6,8,4)
df <- data.frame(Species, Year, Abundance)
I would like to obtain another dataframe (3 rows *5 columns) with the abundance values in function of the species as the column names (each species appearing thus only one time) and the years as the row names (appearing one time also).
May someone help me please ?
You mean something like this?
> xtabs(Abundance~Year+Species, data=df)
Species
Year black mamba boa dark frog elephant tiger
2011 0 6 2 4 5
2012 0 1 0 9 2
2013 4 8 0 5 6
The class for the above is a table, so if you prefer a data.frame instead, you can try:
library(tidyr)
new.df<- spread(df, key = Species, value = Abundance)
Year black mamba boa dark frog elephant tiger
1 2011 NA 6 2 4 5
2 2012 NA 1 NA 9 2
3 2013 4 8 NA 5 6
If you want 0s instead of NA add the following line:
new.df[is.na(new.df)]<- 0
Related
I am working with a dataset that contains variables measured from permanent plots. These plots are continuously remeasured every couple of years. The data sort of looks like the table at the bottom. I used the following code to separate the dataset to slice the initial measurement at t1. Now, I want to slice t2 which is the remeasurement that is one step greater than the minimum_Cycle or minimum_Measured_year. This is particularly a problem for plots that have more than two remeasurements (num_obs > 2) and the measured_year intervals and cycle intervals are different.
I would really appreciate the help. I have stuck on this for quite sometime now.
df_Time1 <- df %>% group_by(State, County, Plot) %>% slice(which.min(Cycle))
State County Plot Measured_year basal_area tph Cycle num_obs
1 1 1 2006 10 10 8 2
2 1 2 2002 20 20 7 3
1 1 1 2009 30 30 9 2
2 1 1 2005 40 40 6 3
2 1 1 2010 50 50 8 3
2 1 2 2013 60 60 10 2
2 1 2 2021 70 70 12 3
2 1 1 2019 80 80 13 3
Create a t variable for yourself based on the Cycle order:
df_Time1 %>%
group_by(State, County, Plot) %>%
mutate(t = order(Cycle))
You can then filter on t == 1 or t == 2, etc.
So I have this first dataframe (fish18) which consists of data on fish specimens, and a column "grade" that is to be filled with conditions in an ifelse function.
species BIN collectors country grade species_frequency
1 Poecilothrissa congica BOLD:AAF7519 mljs et al, Democratic Republic of the Congo NA 2
2 Acanthurus triostegus BOLD:AAA9362 Vinothkumar S, Kaleshkumar K and Rajaram R. India NA 54
3 Pseudogramma polyacantha BOLD:AAC5137 Allan D. Connell South Africa NA 15
4 Pomadasys commersonnii BOLD:AAD1338 Allan D. Connell South Africa NA 12
5 Secutor insidiator BOLD:AAB2487 Allan D. Connell South Africa NA 18
6 Sebastes macdonaldi BOLD:AAJ7419 Merit McCrea United States NA 3
BIN_per_species collector_per_species countries_per_species species_per_bin
1 2 1 1 1
2 1 21 15 1
3 3 6 6 1
4 1 2 1 1
5 4 5 4 2
6 1 1 1 1
And after filling the grade column I have something like this (fish19)
species BIN collectors country grade species_frequency
1 Poecilothrissa congica BOLD:AAF7519 mljs et al, Democratic Republic of the Congo D 2
2 Acanthurus triostegus BOLD:AAA9362 Vinothkumar S, Kaleshkumar K and Rajaram R. India A 54
3 Pseudogramma polyacantha BOLD:AAC5137 Allan D. Connell South Africa C 15
4 Pomadasys commersonnii BOLD:AAD1338 Allan D. Connell South Africa A 12
5 Secutor insidiator BOLD:AAB2487 Allan D. Connell South Africa E 18
6 Sebastes macdonaldi BOLD:AAJ7419 Merit McCrea United States B 3
BIN_per_species collector_per_species countries_per_species species_per_bin
1 2 1 1 1
2 1 21 15 1
3 3 6 6 1
4 1 2 1 1
5 4 5 4 2
6 1 1 1 1
Both dataframes have many specimens belonging to the same species of fish, and the thing is that the grades are suposed to be assigned to each species for every specimen of that species. The problem I'm having is that some rows belonging to the same species are having different grades, specially in the case of the grades "C" and "E". What I want to incorporate into my ifelse function is: Change from grade "C" to "E" every occurrence of the dataframe where two or more specimens belonging to the same species are assigned "C" in one row and "E" in another row. Because if one species has grade "E", every other row with that species name should also have grade "E".
So far I've tried the %in% function and just using "=="
Trying with %in%
assign_grades=function(fish18){
fish19<-fish18 %>%
mutate(grade = ifelse(species_frequency<3,"D",ifelse(BIN_per_species==1 & (collector_per_species>1 | countries_per_species>1),"A",ifelse(BIN_per_species==1 & collector_per_species==1 | countries_per_species==1,"B",ifelse(BIN_per_species>1 & species_per_bin==1,"C",ifelse(species_per_bin>1,"E",ifelse(fish19$species[fish19$grade=="E"]%in%fish19$species[fish19$grade=="C"]==TRUE,"E",NA))) ))))
assign('fish19',fish19,envir=.GlobalEnv)
}
assign_grades(fish18)
Trying with "=="
assign_grades=function(fish18){
fish19<-fish18 %>%
mutate(grade = ifelse(species_frequency<3,"D",ifelse(BIN_per_species==1 & (collector_per_species>1 | countries_per_species>1),"A",ifelse(BIN_per_species==1 & collector_per_species==1 | countries_per_species==1,"B",ifelse(BIN_per_species>1 & species_per_bin==1,"C",ifelse(species_per_bin>1,"E",ifelse(fish19$species[fish19$grade=="E"]==fish19$species[fish19$grade=="C"],"E",NA))) ))))
assign('fish19',fish19,envir=.GlobalEnv)
}
assign_grades(fish18)
Both these two options did not work and the output of this alteration should be that if one occurrence of a specific species name has the grade "E" assigned to it, so should all other occurences with that same species name.
I'm sorry if this was confusion but I tried to be as clear as I could, thank you in advance for any responses.
Kind of a long winded answer, but:
dat = data.frame('species'=c('a','b','c','a','a','b'),'grade'=c('E','E','C','C','C','D'))
dat %>% left_join(dat %>%
group_by(species) %>%
summarize(sum_e = sum(grade=='E')),by='species')
Then you could do an ifelse for sum_e>0
I have searched unsuccessfully for several days for an answer to this question: I have a dataframe with 279 columns and want to generate subtotals using aggregate(), or indeed, anything suitable. Here is a subset:
LGA off.cat sub.cat Jan1995 Feb1995
1 Albury Homicide Murder * 0 0
2 Albury Homicide Attempted murder 0 0
3 Albury Homicide Murder accessory, conspiracy 0 0
4 Albury Homicide Manslaughter * 0 0
5 Albury Assault Domestic violence related assault 7 7
6 Albury Assault Non-domestic violence related assault 29 20
7 Albury Assault Assault Police 12 3
8 Albury Sexual offences Sexual assault 4 3
The full dataframe contains dozens of LGA values, and many more date columns. I would like to obtain subtotals for each unique LGA value grouped by unique values of off.cat and sub.cat, summed over all dates. I tried using cbind in aggregate, but found no way to generate the 276 date column names that would not cause errors. Explicit column names worked fine. Apologies for the lack of clarity in the earlier post, and thanks to those who valiantly tried to interpret my meaning.
Your question is a bit unclear, but you may be successful using the formula syntax of aggregate. Here's an example:
df <- data.frame(group = letters[1:5],
x = 1:5,
y = 6:10,
z = 11:15)
group x y z
1 a 1 6 11
2 b 2 7 12
3 c 3 8 13
4 d 4 9 14
5 e 5 10 15
We now sum all three variables x, y and z by the levels of group, using setdiff to get a vector of column names except group, and pasting them together to use in as.formula:
aggregate(as.formula(paste(paste(setdiff(names(df), c("group")), collapse = "+"), "~ group")), data = df, sum)
group x + y + z
1 a 18
2 b 21
3 c 24
4 d 27
5 e 30
Hope this helps.
This question already has answers here:
How to reshape data from long to wide format
(14 answers)
Closed 5 years ago.
I'm trying to change a dataframe in R to group multiple rows by a measurement. The table has a location (km), a size (mm) a count of things in that size bin, a site and year. I want to take the sizes, make a column from each one (2, 4 and 6 in this example), and place the corresponding count into each the row for that location, site and year.
It seems like a combination of transposing and grouping, but I can't figure out a way to accomplish this in R. I've looked at t(), dcast() and aggregate(), but those aren't really close at all.
So I would go from something like this:
df <- data.frame(km=c(rep(32,3),rep(50,3)), mm=rep(c(2,4,6),2), count=sample(1:25,6), site=rep("A", 6), year=rep(2013, 6))
km mm count site year
1 32 2 18 A 2013
2 32 4 2 A 2013
3 32 6 12 A 2013
4 50 2 3 A 2013
5 50 4 17 A 2013
6 50 6 21 A 2013
To this:
km site year mm_2 mm_4 mm_6
1 32 A 2013 18 2 12
2 50 A 2013 3 17 21
Edit: I tried the solution in a suggested duplicate, but I did not work for me, not really sure why. The answer below worked better.
As suggested in the comment above, we can use the sep argument in spread:
library(tidyr)
spread(df, mm, count, sep = "_")
km site year mm_2 mm_4 mm_6
1 32 A 2013 4 20 1
2 50 A 2013 15 14 22
As you mentioned dcast(), here is a method using it.
set.seed(1)
df <- data.frame(km=c(rep(32,3),rep(50,3)),
mm=rep(c(2,4,6),2),
count=sample(1:25,6),
site=rep("A", 6),
year=rep(2013, 6))
library(reshape2)
dcast(df, ... ~ mm, value.var="count")
# km site year 2 4 6
# 1 32 A 2013 13 10 20
# 2 50 A 2013 3 17 1
And if you want a bit of a challenge you can try the base function reshape().
df2 <- reshape(df, v.names="count", idvar="km", timevar="mm", ids="mm", direction="wide")
colnames(df2) <- sub("count.", "mm_", colnames(df2))
df2
# km site year mm_2 mm_4 mm_6
# 1 32 A 2013 13 10 20
# 4 50 A 2013 3 17 1
I have a dataframe:
X Year Dependent.variable.1 Forecast.Dependent.variable.1
1 2009 12.42669703 12.41831191
2 2010 12.39309563 12.40043599
3 2011 12.36596964 12.38256006
4 2012 12.32067284 12.36468414
5 2013 12.303095 12.34680822
6 2014 NA 12.32893229
7 2015 NA 12.31105637
8 2016 NA 12.29318044
9 2017 NA 12.27530452
10 2018 NA 12.25742859
I want to calulate the exponential of the third and fourth columns. How can I do that?
In case your dataframe is called dfs, you can do the following:
dfs[c('Dependent.variable.1','Forecast.Dependent.variable.1')] <- exp(dfs[c('Dependent.variable.1','Forecast.Dependent.variable.1')])
which gives you:
X Year Dependent.variable.1 Forecast.Dependent.variable.1
1 1 2009 249371 247288.7
2 2 2010 241131 242907.5
3 3 2011 234678 238603.9
4 4 2012 224285 234376.5
5 5 2013 220377 230224.0
6 6 2014 NA 226145.1
7 7 2015 NA 222138.5
8 8 2016 NA 218202.9
9 9 2017 NA 214336.9
10 10 2018 NA 210539.5
In case you know the column numbers, this could then also simply be done by using:
dfs[,3:4] <- exp(dfs[,3:4])
which gives you the same result as above. I usually prefer to use the actual column names as the indices might change when the data frame is further processed (e.g. I delete columns, then the indices change).
Or you could do:
dfs$Dependent.variable.1 <- exp(dfs$Dependent.variable.1)
dfs$Forecast.Dependent.variable.1 <- exp(dfs$Forecast.Dependent.variable.1)
In case you want to store these columns in new variables (below they are called exp1 and exp2, respectively), you can do:
exp1 <- exp(dfs$Forecast.Dependent.variable.1)
exp2 <- exp(dfs$Dependent.variable.1)
In case you want to apply it to more than two columns and/or use more complicated functions, I highly recommend to look at apply/lappy.
Does that answer your question?