1 Introduction

Here we are going to analyse the Annotation packages of Bioconductor. See the home of the analysis here.

2 Load data

First we read the latest data from the Bioconductor project. There are two files, one with the download stats from 2009 until today and another with the download stats of the software packages, we will only use the first one:

load("stats.RData")
stats <- stats[Category == "Annotation", ]
yearly <- yearly[Category == "Annotation", ]
stats
##                                   Package                Date Month Year
##      1:   BSgenome.Dmelanogaster.UCSC.dm3 2014-08-01 02:00:00    08 2014
##      2:   BSgenome.Dmelanogaster.UCSC.dm3 2017-01-01 01:00:00    01 2017
##      3:   BSgenome.Dmelanogaster.UCSC.dm3 2017-02-01 01:00:00    02 2017
##      4:   BSgenome.Dmelanogaster.UCSC.dm3 2017-03-01 01:00:00    03 2017
##      5:   BSgenome.Dmelanogaster.UCSC.dm3 2017-04-01 02:00:00    04 2017
##      6:   BSgenome.Dmelanogaster.UCSC.dm3 2017-05-01 02:00:00    05 2017
##      7:   BSgenome.Dmelanogaster.UCSC.dm3 2017-06-01 02:00:00    06 2017
##      8:   BSgenome.Dmelanogaster.UCSC.dm3 2017-07-01 02:00:00    07 2017
##      9:   BSgenome.Dmelanogaster.UCSC.dm3 2016-01-01 01:00:00    01 2016
##     10:   BSgenome.Dmelanogaster.UCSC.dm3 2016-02-01 01:00:00    02 2016
##     ---                                                                 
## 105857:  SNPlocs.Hsapiens.dbSNP149.GRCh38 2017-03-01 01:00:00    03 2017
## 105858:  SNPlocs.Hsapiens.dbSNP149.GRCh38 2017-04-01 02:00:00    04 2017
## 105859:  SNPlocs.Hsapiens.dbSNP149.GRCh38 2017-05-01 02:00:00    05 2017
## 105860:  SNPlocs.Hsapiens.dbSNP149.GRCh38 2017-06-01 02:00:00    06 2017
## 105861:  SNPlocs.Hsapiens.dbSNP149.GRCh38 2017-07-01 02:00:00    07 2017
## 105862:  SNPlocs.Hsapiens.dbSNP150.GRCh38 2017-07-01 02:00:00    07 2017
## 105863: TxDb.Ggallus.UCSC.galGal5.refGene 2017-04-01 02:00:00    04 2017
## 105864: TxDb.Ggallus.UCSC.galGal5.refGene 2017-05-01 02:00:00    05 2017
## 105865: TxDb.Ggallus.UCSC.galGal5.refGene 2017-06-01 02:00:00    06 2017
## 105866: TxDb.Ggallus.UCSC.galGal5.refGene 2017-07-01 02:00:00    07 2017
##           Category Nb_of_distinct_IPs Nb_of_downloads
##      1: Annotation                172             235
##      2: Annotation                 74             142
##      3: Annotation                163             285
##      4: Annotation                135             225
##      5: Annotation                125             207
##      6: Annotation                175             259
##      7: Annotation                217             438
##      8: Annotation                 65              85
##      9: Annotation                125             186
##     10: Annotation                221             297
##     ---                                              
## 105857: Annotation                  3               4
## 105858: Annotation                  3               3
## 105859: Annotation                 14              18
## 105860: Annotation                 18              21
## 105861: Annotation                  7               7
## 105862: Annotation                  1               1
## 105863: Annotation                  3               4
## 105864: Annotation                 15              18
## 105865: Annotation                 12              12
## 105866: Annotation                  4               5

There have been 2572 Experimental packages in Bioconductor. Some have been added recently and some later.

3 Packages

3.1 Number

First we explore the number of packages being downloaded by month:

theme_bw <- theme_bw(base_size = 16)
scal <- scale_x_datetime(date_breaks = "3 months")
theme <- theme(axis.text.x=element_text(angle=60, hjust=1))
ggplot(stats[, .(Downloads = .N), by = Date], aes(Date, Downloads)) +
  geom_bar(stat = "identity") + 
  theme_bw +
  ggtitle("Packages downloaded") +
  theme + 
  scal + 
  xlab("")

Figure 1: Packages in Bioconductor with downloads

The number of packages being downloaded is increasing with time almost exponentially. Partially explained with the incorporation of new packages

ggplot(stats[, .(Number = sum(Nb_of_downloads)), by = Date], aes(Date, Number)) +
  geom_bar(stat = "identity") + 
  theme_bw +
  ggtitle("Downloads") +
  scal +
  theme + 
  xlab("")

Figure 2: Downloads of packages

Even if the number of packages increase exponentially, the number of the downloads from 2011 grows linearly with time. Which indicates that each time a software package must compete with more packages to be downloaded.

pd <- position_dodge(0.1)
ggplot(stats[, .(Number = mean(Nb_of_downloads), 
                  sem = sd(Nb_of_downloads)/sqrt(.N)),
              by = Date], aes(Date, Number)) +
  geom_errorbar(aes(ymin = Number - sem, ymax = Number + sem), width = .1, position = pd) +
  geom_point() + 
  geom_line() +
  theme_bw +
  ggtitle("Downloads") +
  ylab("Mean download for a package") +
  scal +
  theme + 
  xlab("")

Figure 3: Downloads of packages per package
The error bar indicates the 95% confidence interval.

Here we can apreciate that the number of downloads per package hasn’t changed much with time. If something, now there is less dispersion between packages downloads.

3.2 Incorporations

This might be due to an increase in the usage of packages or that new packages bring more users. We start knowing how many packages has been introduced in Bioconductor each month.

today <- base::date()
year <- substr(today, 21, 25)
month <- monthsConvert(substr(today, 5, 7))
incorporation <- stats[ , .SD[which.min(Date)], by = Package, .SDcols = "Date"]
histincorporation <- incorporation[, .(Number = .N), by = Date, ]
ggplot(histincorporation, aes(Date, Number)) + 
  geom_bar(stat="identity") + 
  theme_bw + 
  ggtitle("Packages with first download") +
  scal +
  theme +
  xlab("")

Figure 4: New packages

We can see that At the beggining of 2009 many Annotation packages were added in Bioconductor, and since them occasionally there is a raise to 250 new downloads (Which would be new packages being added). This may be due to updates in the databases and new releases of data being incorporated.

ggplot(histincorporation, aes(Date, Number)) + 
  geom_bar(stat="identity") + 
  theme_bw + 
  ggtitle("Packages with first download") +
  scal +
  theme +
  xlab("") + 
  ylim(c(0, 250))
## Warning: Removed 2 rows containing missing values (position_stack).

Figure 5: New packages

Close view to the new packages not previously downloaded. ## Removed

Using a similar procedure we can approximate the packages deprecated and removed each month. In this case we look for the last date a package was downloaded, excluding the current month:

deprecation <- stats[, .SD[which.max(Date)], by = Package, .SDcols = c("Date",  "Year", "Month")]
deprecation <- deprecation[Month != month & Year == Year, , .SDcols = "Date"] # Before this month
histDeprecation <- deprecation[, .(Number = .N), by = Date, ]
ggplot(histDeprecation, aes(Date, Number)) + 
  geom_bar(stat = "identity") + 
  theme_bw + 
  ggtitle("Packages without downloads") +
  scal +
  theme + 
  ylab("Last seen packages") +
  xlab("")

Figure 6: Date where a package was last downloaded
Aproximates to the date when packages were removed from Bioconductor.

Here we can see the packages whose last download was in certain month, assuming that this means they are deprecated. It can happen that a package is no longer downloaded but is still in Bioconductor repository, this would be the reason of the spike to 500 packages as per last year. Although this last year many more packages has been left without downloading.

In total there are 1 packages downloaded. We further explore how many time between the incorporation of the package and the last download.

df <- merge(incorporation, deprecation, by = "Package")
timeBioconductor <- unclass(df$Date.y-df$Date.x)/(60*60*24*365) # Transform to years
hist(timeBioconductor, main = "Time in Bioconductor", xlab = "Years")
abline(v = mean(timeBioconductor), col = "red")
abline(v = median(timeBioconductor), col = "green")

(#fig:time.package)Time of packages between first and last download

Packages tend to stay up to 8 years. Not surprisingly the number of packages incorporated before 2009 and still in the repository are of 0 packages. But those packages not removed how do they do in Bioconductor?

4 Packages downloads

4.1 Ratio downloads per IP

We can start comparing the number of downloads (different from 0) by how many IPs download each package.

pd <- position_dodge(0.1)
ggplot(stats[, .(Number = mean(Nb_of_downloads/Nb_of_distinct_IPs),
                 sem = sd(Nb_of_downloads/Nb_of_distinct_IPs)/sqrt(.N)), 
              by = c("Date")], aes(Date, Number)) +
  geom_point() +
  geom_errorbar(aes(ymin = Number - sem, 
                    ymax = Number + sem),
                width = .1, position = pd) +
  geom_line() +
  theme_bw +
  ggtitle("Downloads per IP") +
  ylab("Mean downloads per IP") +
  xlab("") + 
  theme +
  scal +
  guides(col = FALSE)

Figure 7: Downloads and distinct IPs of all months and packages
Each color is a package, the black line represents 2 downloads per IP.

Not surprisingly most of the package has two downloads from the same IP, one for each Bioconductor release (black line). However, there are some packages where few IPs download many times the same package, which may indicate that these packages are mostly installed in a few locations.

ratio <- stats[, .(Mean = mean(Nb_of_downloads/Nb_of_distinct_IPs),
                   sd = sd(Nb_of_downloads/Nb_of_distinct_IPs),
                   max = max(Nb_of_downloads/Nb_of_distinct_IPs),
                   min = min(Nb_of_downloads/Nb_of_distinct_IPs)), 
              by = c("Package")]
ratio <- ratio[order(Mean, decreasing = TRUE), ]
ratio$Package <- as.character(ratio$Package)
ratio
##                                 Package      Mean       sd       max
##    1:                      hgfocusprobe 10.459925 5.199339 25.300000
##    2: BSgenome.Scerevisiae.UCSC.sacCer1  6.169985 2.540019 14.850000
##    3:                     pd.hg.u133a.2  3.607621 3.682459 15.266667
##    4:                        mirna10cdf  3.431727 2.104486  8.243243
##    5:                       hgu95aprobe  3.387250 3.650635 16.274194
##    6:   IlluminaHumanMethylation450k.db  3.030156 2.300729 10.768786
##    7:                        ath1attigr  3.000000 3.391165  9.000000
##    8:                    atgenomeattigr  2.800000 3.492850  9.000000
##    9:                 atgenomeattigrcdf  2.800000 3.492850  9.000000
##   10:               atgenomeattigrprobe  2.800000 3.492850  9.000000
##   ---                                                               
## 2563:                MeSH.Sau.MW2.eg.db  1.000000       NA  1.000000
## 2564:                MeSH.Sau.Mu3.eg.db  1.000000 0.000000  1.000000
## 2565:               MeSH.Sau.Mu50.eg.db  1.000000       NA  1.000000
## 2566:               MeSH.Sau.N315.eg.db  1.000000       NA  1.000000
## 2567:             MeSH.Sau.Newman.eg.db  1.000000       NA  1.000000
## 2568:              MeSH.Sau.RF122.eg.db  1.000000       NA  1.000000
## 2569:      MeSH.Sau.USA300FPR3757.eg.db  1.000000 0.000000  1.000000
## 2570:               MeSH.Sau.VC40.eg.db  1.000000       NA  1.000000
## 2571:                 o%2520rg.Hs.eg.db  1.000000       NA  1.000000
## 2572:  SNPlocs.Hsapiens.dbSNP150.GRCh38  1.000000       NA  1.000000
##            min
##    1: 1.179487
##    2: 1.111111
##    3: 1.000000
##    4: 1.000000
##    5: 1.000000
##    6: 1.243697
##    7: 1.000000
##    8: 1.000000
##    9: 1.000000
##   10: 1.000000
##   ---         
## 2563: 1.000000
## 2564: 1.000000
## 2565: 1.000000
## 2566: 1.000000
## 2567: 1.000000
## 2568: 1.000000
## 2569: 1.000000
## 2570: 1.000000
## 2571: 1.000000
## 2572: 1.000000

We can see that the package with more downloads from the same IP is hgfocusprobe, followed by, BSgenome.Scerevisiae.UCSC.sacCer1, pd.hg.u133a.2 and the forth one is mirna10cdf.

Now we explore if there is some seasons cycles in the downloads, as in figure 2 seems to be some cicles.

4.2 By date

First we can explore the number of IPs per month downloading each package:

ggplot(stats, aes(Date, Nb_of_distinct_IPs, col = Package)) + 
  geom_line() + 
  theme_bw +
  ggtitle("IPs") +
  ylab("Distinct IP downloads") +
  scal +
  theme + 
  guides(col = FALSE)

Figure 8: Distinct IP per package

As we can see there are two groups of packages at the 2009 years, some with low number of IPs and some with bigger number of IPs. As time progress the number of distinct IPs increases for some packages. But is the spread in IPs associated with an increase in downloads?

ggplot(stats, aes(Date, Nb_of_downloads, col = Package)) + 
  geom_line() + 
  theme_bw +
  ggtitle("Downloads per IP") +
  ylab("Downloads") +
  scal +
  theme + 
  guides(col = FALSE)

Figure 9: Downloads per year

Surprisingly some package have a big outburst of downloads to 400k downloads, others to just 100k downloads. But lets focus on the lower end:

ggplot(stats, aes(Date, Nb_of_downloads, col = Package)) + 
  geom_line() + 
  theme_bw +
  ggtitle("Downloads per package every three months") +
  ylab("Downloads") +
  scal +
  ylim(0, 10000)+
  theme + 
  guides(col = FALSE)

Figure 10: Downloads per year

There are many packages close to 0 downloads each month, but most packages has less than 10000 downloads per month:

ggplot(stats, aes(Date, Nb_of_downloads, col = Package)) + 
  geom_line() + 
  theme_bw+
  ggtitle("Downloads per package every three months") +
  ylab("Downloads") +
  scal +
  ylim(0, 2500)+
  theme + 
  guides(col = FALSE)
## Warning: Removed 169 rows containing missing values (geom_path).

Figure 11: Downloads per year

As we can see, in general the month of the year also influences the number of downloads. So we have that from 2010 the factors influencing the downloads are the year, and the month.

Maybe there is a relationship between the downloads and the number of IPs per date

ggplot(stats, aes(Date, Nb_of_downloads/Nb_of_distinct_IPs, col = Package)) + 
  geom_line() + 
  theme_bw +
  ggtitle("IPs") +
  ylab("Ratio") +
  scal +
  theme + 
  guides(col = FALSE)

Figure 12: Ratio downloads per IP per package

We can see some packages have ocasional raises of downloads per IP. But for small ranges we miss a lot of packages:

ggplot(stats, aes(Date, Nb_of_downloads/Nb_of_distinct_IPs, col = Package)) + 
  geom_line() + 
  theme_bw +
  ggtitle("IPs") +
  ylab("Ratio") +
  scal +
  theme + 
  guides(col = FALSE) +
  ylim(1, 5)

Figure 13: Ratio downloads per IP per package

But most of the packages seem to be more or less constant and around 2.

4.3 By year

To measure if the same IP has downloaded the same package in several months we can compare if the IPs per year are closer to the IP per month.

staty <- stats[, .(Nb_of_distinct_IPs = sum(Nb_of_distinct_IPs)), by = c("Year", "Package")]
year <- staty[yearly, , on = c("Package", "Year")]
year <- year[, Repeated_IP := Nb_of_distinct_IPs-i.Nb_of_distinct_IPs, by = c("Package", "Year")]
year <- year[, Repeated_IP_per := Repeated_IP/Nb_of_distinct_IPs*100, by = c("Package", "Year")]
ggplot(year, aes(Year, Repeated_IP_per)) + 
  geom_violin() +
  xlab("") +
  ylab("Percentatge of repeated IPs") +
  theme_bw +
  guides(col = FALSE)

Figure 14: Mean percentage of updates of the packages

This gives an idea that most of the IPs don’t update all their packages to the newest version of each package, or it could be that as most of the IPs are dynamic they change the measure is not completely reliable

year2 <- year[, .(m = mean(Repeated_IP_per), sem = sd(Repeated_IP_per)/sqrt(.N)), by = "Year"]
ggplot(year2, aes(Year, m)) +
  geom_bar(stat = "identity") +
  geom_errorbar(aes(ymin = m - sem, ymax = m + sem), 
                width = .1, position = pd) + 
  ylab("Percentatge") +
  xlab("") +
  ggtitle("Mean download per ") + 
  theme_bw

Figure 15: Mean percentage of updates of the packages
The error bar are the SEM.

We can see however that the percentatge of IPs which download the package quite similar for the packages in Bioconductor. It remains also around 17% of the total IPs.

year$Year <- as.numeric(year$Year)
d <- date()
thisYear <- as.numeric(substr(d, nchar(d)-3, nchar(d)))
ggplot(year, aes(Year, Repeated_IP_per, col = Package)) +
  geom_point() +
  geom_line() +
  guides(col = FALSE) + 
  scale_x_continuous(breaks = seq(2009, thisYear, 1)) + 
  ylab("Percentatge") +
  ggtitle("Update from the same IP") +
  theme_bw

Figure 16: Percentatge of updates from the same IP by package

We can see that some packages ocassionaly raise above the mean.

5 Models

5.1 Position in Bioconductor

We can observe if the packages has been consistently the most downloaded package of Bioconductor:

PercDate <- stats[, .(Package, Downloads = Nb_of_downloads/sum(Nb_of_downloads)), by = Date]
PercDate <- PercDate[order(Date, order(Downloads)), ]
ggplot(PercDate, aes(Date, Downloads, col = Package)) + 
  geom_line() + 
  theme_bw + 
  ggtitle("Downloads of packages by dates") +
  xlab("") + 
  ylab("% of downloads") +
  guides(col = FALSE) +
  scal + 
  theme

Figure 17: Downloads of packages in Bioconductor

We can see that usually the percentatge of downloads of a packages doesn’t reach 5% of downloads of the category. And that there is a huge differences between packages in the number of downloads. Let’s compare the most downloaded package to the other package:

OrdDate <- PercDate[, .(Package, Ord = Downloads/max(Downloads)), by = Date]
ggplot(OrdDate, aes(Date, Ord, col = Package)) + 
  geom_line() + 
  theme_bw + 
  ggtitle("Downloads of packages by dates") +
  xlab("") + 
  ylab("% of the Package more downloaded") +
  guides(col = FALSE) +
  scal + 
  theme

Figure 18: Position of packages in Bioconductor

We can observe that usually there are few package that are closer to the most downloaded packages and lots of them are far from it. We can see the rank between them to be able to see the evolution of downloads along time of a package:

rankDate <- OrdDate[, .(Package, rank = rank(Ord)/.N), by = Date]
ggplot(rankDate, aes(Date, rank, col = Package)) + 
  geom_line() + 
  theme_bw + 
  ggtitle("Rank of packages by downloads") +
  xlab("") + 
  ylab("Position by downloads") +
  guides(col = FALSE) +
  scal + 
  theme

Figure 19: % of packages in Bioconductor
Closer to 1 indicates the top downloaded packages.

Only if we select to follow some package we can track them:

packages <- c("GO.db", "org.Hs.eg.db", "org.MeSH.Hsa.db", "GenomeInfoDbData", 
              "BSgenome.Dmelanogaster.UCSC.dm3", "PFAM.db", "PFAM", 
              "KEGG", "reactome.db")
ggplot(rankDate[Package %in% packages, ], aes(Date, rank, col = Package))+ 
  geom_line() + 
  theme_bw + 
  ggtitle("Relative rank of packages by downloads") +
  xlab("") + 
  ylab("Position by downloads") +
  scal + 
  theme

Figure 20: Evolution of downloads of packages in Bioconductor

Here we can see that ALL and affydata are on the top downloaded packages since 2009. Recently airway has grown to reach the top downloaded packages, while other packages haven’t reached the top 25% packages by downloads on a month.

5.2 Package cycle

We can also observe when did a package reach the maximum number of downloads:

PercPack <- stats[, .(Date, Downloads = Nb_of_downloads/sum(Nb_of_downloads)), by = Package]
ggplot(PercPack, aes(Date, Downloads, col = Package)) + 
  geom_line() + 
  theme_bw + 
  ggtitle("Growth of the packages") +
  xlab("") + 
  ylab("Downloads/max(Downloads)") +
  guides(col = FALSE) +
  scal + 
  theme

$Cycle of packages. Percentatge of downloads of a package along time.$

Figure 21: Cycle of packages
Percentatge of downloads of a package along time.

Here we can see the date when a package reached the highest number of downloads. For most packages the higher downloads are on the recent months.

OrdPack <- PercPack[, .(Date, rank = Downloads/max(Downloads)), by = Package]
ggplot(OrdPack, aes(Date, rank, col = Package)) + 
  geom_line() + 
  theme_bw + 
  ggtitle("Growth of the packages") +
  xlab("") + 
  ylab("Downloads/max(Downloads)") +
  guides(col = FALSE) +
  scal + 
  theme

Here we can see when the package hast the most downloads along time. As usuall we need to focus on fewer packages to be able to distinguish between package to see their evolution:

ggplot(OrdPack[Package %in% packages, ], 
       aes(Date, rank, col = Package)) + 
  geom_line() + 
  theme_bw + 
  ggtitle("Growth of the packages") +
  xlab("") + 
  ylab("Downloads/max(Downloads)") +
  scal + 
  theme

Figure 22: Cycle of few packages
Position of package downloads respect the maximum downloads of the packages along time.

As expected the packages that keep up with Bioconductor growth have a peak near the end of the serie.

We can combine both models into a single one to have a timeless comparison of the packages. So we will know if the max position reached in Bioconductor is done when there are more downloads.

model <- rankDate[OrdPack, on = c("Package", "Date")]
setnames(model, "i.rank", "rank.P")
setnames(model, "rank", "rank.B")
ggplot(model[Package %in% packages], aes(rank.P, rank.B, col = Package)) +
  geom_point() + 
  theme_bw + 
  geom_line() +
  ylab("Position in Bioconductor") + 
  xlab("Position in package")

Figure 23: Relative position of the package
Position in Bioconductor downloads and position of package downloads.

This is a timeless comparison of the growth of packages in Bioconductor and against themselfs. The higher on the y-axis the higher they have been on Bioconductor, and the higher on the x-axis the most downloads they had.

Next we add the time as a factor so we standarize by the time a package has been in Bioconductor. We have omitted months with 0 downloads of a package so this might bias a bit the ranking.

model[, rank.D := rank(as.numeric(Date))/.N, by = Package]
ggplot(model[Package %in% packages], aes(rank.D, rank.B, col = Package)) +
  geom_point() + 
  theme_bw + 
  geom_line() +
  xlab("By date") + 
  ylab("Position in Bioconductor")

Figure 24: Relative position of the packages
Position relative to Bioconductor and itself compared to date.

  
ggplot(model[Package %in%  packages], aes(rank.D, rank.P, col = Package)) +
  geom_point() + 
  theme_bw + 
  geom_line() +
  xlab("By date") + 
  ylab("Position in Package")