How to show frequencies in discrete categories with range data in R?

Assuming your data frames are named genus

and stage

, first create a list containing, for each, the stage

names of the genera that lived during this stage

. Then we'll add this to the dataframe stage

and also add another column that counts the number of births alive during each stage

.

The code below sapply

takes each value in turn stage

and checks which values genus

fall within that time range stage

, comparing stage

ma_max

both ma_min

with ma_max

and ma_min

for each genus

.

# List of genera that lived during each Stage
stages.genus = sapply(stage$Stage, function(x){
  genus$GENUS[which((stage$ma_max[stage$Stage==x] <= genus$ma_max & 
                       stage$ma_max[stage$Stage==x] >= genus$ma_min) |
                      (stage$ma_min[stage$Stage==x] >= genus$ma_min & 
                         stage$ma_min[stage$Stage==x] <= genus$ma_max))]
})

      

        
        
        
      

    

For each element, stages.genus

insert together all the values genus

that apply to this stage

, separated by commas, giving us a vector containing the genders that come with each value stage

. Assign this vector as a new column stage

, which we'll call genera

.

# Add list of genera by stage to the stage data frame
stage$genera = lapply(stages.genus, paste, sep=", ")

      

        
        
        
      

    

To get the number of numbers in each stage

, simply count the number of genera in each element stages.genus

and assign it to a new column stage

, which we will callNgenera

# Add count of genera for each Stage to the stage data frame
stage$Ngenera = lapply(stages.genus, length)

      

        
        
        
      

    

And here's the result:

> stage

           Stage ma_max ma_min ma_mid                      genera Ngenera
1     Hettangian  201.6  197.0 199.30                                   0
2     Sinemurian  197.0  190.0 193.50                                   0
...
16        Aptian  125.0  112.0 118.50                                   0
17        Albian  112.0   99.6 105.80                 Abydosaurus       1
18    Cenomanian   99.6   93.5  96.55                 Abydosaurus       1
19      Turonian   93.5   89.3  91.40                                   0
20     Coniacian   89.3   85.8  87.55                                   0
21     Santonian   85.8   83.5  84.65               Achelousaurus       1
22     Campanian   83.5   70.6  77.05 Achelousaurus, Acheroraptor       2
23 Maastrichtian   70.6   66.5  68.05 Achelousaurus, Acheroraptor       2

      

        
        
        
      

    

An additional option is to create a column in stage

for each genus

and set the value to 1 if genus

lived at this stage or zero otherwise:

stage[, genus$GENUS] = lapply(genus$GENUS, function(x) {
  ifelse(grepl(x, stages.genus), 1, 0)
})

      

        
        
        
      

    

Here are the additional columns we just added:

> stage[ , c(1,7:9)]   # Just show the Stage plus the three new GENUS columns

           Stage Abydosaurus Achelousaurus Acheroraptor
1     Hettangian           0             0            0
2     Sinemurian           0             0            0
...
16        Aptian           0             0            0
17        Albian           1             0            0
18    Cenomanian           1             0            0
19      Turonian           0             0            0
20     Coniacian           0             0            0
21     Santonian           0             1            0
22     Campanian           0             1            1
23 Maastrichtian           0             1            1

      

        
        
        
      

    

The last step will also help you get a stage-by-stage visualization of labor. For example:

library(reshape2)
library(ggplot2)

# Melt data into long format
stage.m = melt(stage[,c(1:4,7:9)], id.var=1:4)

# Tile plot where height of each Stage is proportional to how long it lasted
ggplot(stage.m, aes(variable, ma_mid, fill=factor(value))) +
  geom_tile(aes(height=ma_max - ma_min), colour="grey20", lwd=0.2) +
  scale_fill_manual(values=c("white","blue")) +
  scale_y_continuous(breaks=stage$ma_mid, labels=stage$Stage) +
  xlab("Genus") + ylab("Stage") +
  theme_bw(base_size=15) +
  guides(fill=FALSE)

      

        
        
        
      

    

The previous code can also be modified to use time ranges from data frames stage

and genus

if you want the blue to only cover the time range when each genus

lived, not the full range of each one stage

they lived in.