Tag: running

Garmonbozia: Using R to look at Garmin CSV data

Garmin Connect has a number of plots built in, but to take a deeper dive into all your fitness data, you need to export a CSV and fire up R. This post is a quick guide to some possibilities for running data. 

There’s a few things that I wanted to look at. For example, how does my speed change through the year? How does that compare to previous years? If I see some trends, is that the same for short runs and long runs? I wanted to look at the cumulative distance I’d run each year… There’s a lot of things that would be good to analyse.

Garmin Connect has a simple way to export data as a CSV. There are other ways to get your data, but the web interface is pretty straightforward. To export a CSV of your data, head to the Garmin Connect website, login and select Activities, All Activities. On this page, filter the activities for whatever you want to export. I clicked Running (you can filter some more if you want), and then scrolled down letting the data load onto the page until I went back as far as I wanted. In the top right corner, you click Export CSV and you will download whatever is displayed on the page.

The code to generate these plots, together with some fake data to play with can be found here.

Now in R, load in the CSV file

require(ggplot2)
require(dplyr)
require(hms)
file_name <- file.choose()
df1 <- read.csv(file_name, header = TRUE, stringsAsFactors = FALSE)

We have a data frame, but we need to rejig the Dates and a few other columns before we can start making plots.

# format Date column to POSIXct
df1$Date <- as.POSIXct(strptime(df1$Date, format = "%Y-%m-%d %H:%M:%S"))
# format Avg.Pace to POSIXct
df1$Avg.Pace <- as.POSIXct(strptime(df1$Avg.Pace, format = "%M:%S"))
# make groups of different distances using ifelse
df1$Type <- ifelse(df1$Distance < 5, "< 5 km", ifelse(df1$Distance < 8, "5-8 km", ifelse(df1$Distance < 15, "8-15 km", ">15 km")))
# make factors for these so that they're in the right order when we make the plot
df1$Type_f = factor(df1$Type, levels=c("< 5 km","5-8 km","8-15 km", ">15 km"))

Now we can make the first plot. The code for the first one is below, with all the code for the other plots shown below that.

# plot out average pace over time
p1 <- ggplot( data = df1, aes(x = Date,y = Avg.Pace, color = Distance)) + 
  geom_point() +
  scale_y_datetime(date_labels = "%M:%S") +
  geom_smooth(color = "orange") +
  labs(x = "Date", y = "Average Pace (min/km)")

The remainder of the code for the other plots is shown below. The code is commented. For some of the plots, a bit of extra work on the data frame is required.

# plot out same data grouped by distance
p2 <- ggplot( data = df1, aes(x = Date,y = Avg.Pace, group = Type_f, color = Type_f)) + 
  geom_point() +
  scale_y_datetime(date_labels = "%M:%S") +
  geom_smooth() +
  labs(x = "Date", y = "Average Pace (min/km)", colour = NULL) +
  facet_grid(~Type_f)
# now look at stride length. first remove zeros
df1[df1 == 0] <- NA
# now find earliest valid date
date_v <- df1$Date
# change dates to NA where there is no avg stride data
date_v <- as.Date.POSIXct(ifelse(df1$Avg.Stride.Length > 0, df1$Date, NA))
# find min and max for x-axis
earliest_date <- min(date_v, na.rm = TRUE)
latest_date <- max(date_v, na.rm = TRUE)
# make the plot
p3 <- ggplot(data = df1, aes(x = Date,y = Avg.Stride.Length, group = Type_f, color = Type_f)) +
  geom_point() + 
  ylim(0, NA) + xlim(as.POSIXct(earliest_date), as.POSIXct(latest_date)) +
  geom_smooth() +
  labs(x = "Date", y = "Average stride length (m)", colour = NULL) +
  facet_grid(~Type_f)
df1$Avg.HR <- as.numeric(as.character(df1$Avg.HR))
p4 <- ggplot(data = df1, aes(x = Date,y = Avg.HR, group = Type_f, color = Type_f)) +
  geom_point() +
  ylim(0, NA) + xlim(as.POSIXct(earliest_date), as.POSIXct(latest_date)) +
  geom_smooth() +
  labs(x = "Date", y = "Average heart rate (bpm)", colour = NULL) +
  facet_grid(~Type_f)
# plot out average pace per distance coloured by year
p5 <- ggplot( data = df1, aes(x = Distance,y = Avg.Pace, color = Date)) + 
  geom_point() +
  scale_y_datetime(date_labels = "%M:%S") +
  geom_smooth(color = "orange") +
  labs(x = "Distance (km)", y = "Average Pace (min/km)")
# make a date factor for year to group the plots
df1$Year <- format(as.Date(df1$Date, format="%d/%m/%Y"),"%Y")
p6 <- ggplot( data = df1, aes(x = Distance,y = Avg.Pace, group = Year, color = Year)) + 
  geom_point() +
  scale_y_datetime(date_labels = "%M:%S") +
  geom_smooth() +
  labs(x = "Distance", y = "Average Pace (min/km)") +
  facet_grid(~Year)
# Cumulative sum over years
df1 <- df1[order(as.Date(df1$Date)),]
df1 <- df1 %>% group_by(Year) %>% mutate(cumsum = cumsum(Distance))
p7 <- ggplot( data = df1, aes(x = Date,y = cumsum, group = Year, color = Year)) + 
  geom_line() +
  labs(x = "Date", y = "Cumulative distance (km)")
# Plot these cumulative sums overlaid
# Find New Year's Day for each and then work out how many days have elapsed since
df1$nyd <- paste(df1$Year,"-01-01",sep = "")
df1$Days <- as.Date(df1$Date, format="%Y-%m-%d") - as.Date(as.character(df1$nyd), format="%Y-%m-%d")
# Make the plot
p8 <- ggplot( data = df1, aes(x = Days,y = cumsum, group = Year, color = Year)) + 
  geom_line() +
  scale_x_continuous() +
  labs(x = "Days", y = "Cumulative distance (km)")

Finally, we can save all of the plots using ggsave.

# save all plots
ggsave("allPace.png", plot = p1, width = 8, height = 4, dpi = "print")
ggsave("paceByDist.png", plot = p2, width = 8, height = 4, dpi = "print")
ggsave("strideByDist.png", plot = p3, width = 8, height = 4, dpi = "print")
ggsave("HRByDist.png", plot = p4, width = 8, height = 4, dpi = "print")
ggsave("allPaceByDist.png", plot = p5, width = 8, height = 4, dpi = "print")
ggsave("paceByDistByYear.png", plot = p6, width = 8, height = 4, dpi = "print")
ggsave("cumulativeDistByYear.png", plot = p7, width = 8, height = 4, dpi = "print")
ggsave("cumulativeDistOverlay.png", plot = p8, width = 8, height = 4, dpi = "print")

I think the code might fail if you don’t record all of the fields that I do. For example if heart rate data is missing or stride length is not recorded, I’m not sure what the code will do. The aim here is to give an idea of what sorts of plots can be generated just using the summary data in the CSV provided by Garmin. Feel free to make suggestions in the comments below.

—

The post title comes from “Garmonbozia” by Superdrag from the Regretfully Yours album. Apparently Garmonbozia is something eaten by the demons in the Black Lodge in the TV series Twin Peaks.

By adventures in code, computing , , One Comment

Plotlines: the story behind the graph

On a whim a posted a plot on Twitter. It shows a marathon training schedule. This post explains the story behind the graph.

I downloaded a few different 17-week marathon training schedules. Most were in imperial measurement and/or were written for time at a certain pace, e.g. 30 min Easy Run etc. I wanted to convert one of these schedules into a proper plan where I input my pace and get an idea of the distance I need to run (in metric). This means I can pick routes to run each day without having to think too much about it.

Calculating the running paces was simple using Jack Daniels’ VDot calculator and verifying the predicted paces with my running database. I constructed a spreadsheet from the plan, and then did the calculations to get the distances out. Once this was done I wondered what the rationale behind the schedule is, and the best way to see that is to plot it out.

No colour-coding

From this plot the way that the long run on each Sunday is extended or tapered is reasonably clear. However, I was wondering about how intense each of the runs will be. Running 5K at threshold is more intense than a 10K easy run. To look at this I just took the average pace for the session. This doesn’t quite tell us about intensity, because a 10 min easy run + 2 intervals + 10 min easy run is not as intense as doing 4 intervals, yet the average pace would be similar. But it would be close enough. I used a colourscale called VioletOrangeYellow and the result was quite intuitive.

Marathon training schedule
A menu of pain – marathon training schedule

The shorter runs are organised in blocks of intensity while the long runs are about building endurance. From what I understand, the blocks are to do with adapting to the stresses of increasing running load/intensity.

Feedback on the plot was good: runners liked it, non-runners thought it was psychotic.

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Pledging My Time IV

 

The Green Leek 10.5 km run is a mixed terrain race now in its third year. Today’s was a wet and muddy edition. The chip times were posted this afternoon and using my previous code, I took a look at the results.

I was a bit disappointed with my time, which was about 24 s slower than last year. Considering that I’m running faster this year than last, I wondered whether the conditions affected my time. To look at this I quickly retrieved times for people who’d run it all three editions and looked to see if this edition was generally slower than previous editions.

Excuse the formatting of the plot. It looked pretty flat but then we’re probably only considering very small differences over 10.5 km. So I looked at the difference in time from the 2016 edition. Again the formatting is bad (23:55 is 5 minutes faster than 2016, 00:05 is 5 minutes slower).

Three people recorded much slower times this year, but the majority are within the difference from 2016 to 2017. Obviously this is just a few people that could be easily picked out using a script, more runners might reveal more of a pattern. Anyway, here’s hoping for better weather next year!

Well done to Andy Crabtree and Rachel Miller who were fastest male and female, respectively. Thanks to the organisers and volunteers.

—

The post title is taken from “Pledging My Time” a track from Blonde on Blonde by Bob Dylan

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Pledging My Time III

I’ve previously crunched times for local Half and Full Marathons here on quantixed. Last weekend was the Kenilworth Half Marathon (2018) over a new course. I thought I’d have a look at the distributions of times and paces of the runners. The times are available here. If the Time and Category for finishers are saved as a csv, the script below works to generate the following plots.

Aggregated stats for the race are here. The beeswarm plot nicely shows the distribution of runners times and paces per category. There’s a bimodality to some of the age groups which is interesting. You can see from the average times that people get slower as they get older, as expected.

There was a roughly 2:1 split of M:F runners with a similar proportion in all categories. The ratio is similar for DNSers. The winning times were Andrew Savery of Leamington C A & C in MV35 with 01:12:51 and Polly Keen of Nuneaton Harriers in F sen with 01:23:46.

Congrats to everyone who ran and thanks to the organisers and all the supporters out on the course.


require(ggplot2)
require(ggbeeswarm)
file_name <- file.choose()
df1 <- read.csv(file_name, header = TRUE, stringsAsFactors = FALSE)
# aggregate M and F to a new category called Gender
df1$Gender <- ifelse(startsWith(df1$Category,"F"),"F","M")
# format Date column to POSIXct
df1$Time <- as.POSIXct(strptime(df1$Time, format = "%H:%M:%S"))
orig_var <- as.POSIXct("00:00:00", format = "%H:%M:%S")
p1 <- ggplot( data = df1, aes(x = Category,y = Time, color = Category)) + 
  geom_quasirandom(alpha = 0.5, stroke = 0) +
  stat_summary(fun.y = mean, geom = "point", size=2, aes(group = 1)) +
  scale_y_datetime(date_labels = "%H:%M:%S", limits = c(orig_var,NA))
p1
# instead of finishing time, let's look at pace (min/km)
df1$Pace <- as.numeric(difftime(df1$Time, orig_var) / 21.1) * 3600
df1$Pace <- as.POSIXct(df1$Pace, origin = orig_var, format = "%H:%M:%S")
p2 <- ggplot( data = df1, aes(x = Category,y = Pace, color = Category)) + 
  geom_quasirandom(alpha = 0.5, stroke = 0) +
  stat_summary(fun.y = mean, geom = "point", size=2, aes(group = 1)) +
  scale_y_datetime(date_labels = "%M:%S", limits = c(orig_var,NA))
p2
# calculate speeds rather than pace
df1$Speed <- 21.1 / as.numeric(difftime(df1$Time, orig_var))
p3 <- ggplot( data = df1, aes(x = Category, y = Speed, color = Category)) + 
  geom_quasirandom(alpha = 0.5, stroke = 0) +
  stat_summary(fun.y = mean, geom = "point", size=2, aes(group = 1)) +
  ylim(0,NA) + ylab("Speed (km/h)")
p3
# now make the same plots but by Gender rather than Category
p4 <- ggplot( data = df1, aes(x = Gender,y = Time, color = Gender)) + 
  geom_quasirandom(alpha = 0.5, stroke = 0) +
  stat_summary(fun.y = mean, geom = "point", size=2, aes(group = 1)) +
  scale_y_datetime(date_labels = "%H:%M:%S", limits = c(orig_var,NA))
p4
p5 <- ggplot( data = df1, aes(x = Gender,y = Pace, color = Gender)) + 
  geom_quasirandom(alpha = 0.5, stroke = 0) +
  stat_summary(fun.y = mean, geom = "point", size=2, aes(group = 1)) +
  scale_y_datetime(date_labels = "%M:%S", limits = c(orig_var,NA))
p5
p6 <- ggplot( data = df1, aes(x = Gender, y = Speed, color = Gender)) + 
  geom_quasirandom(alpha = 0.5, stroke = 0) +
  stat_summary(fun.y = mean, geom = "point", size=2, aes(group = 1)) +
  ylim(0,NA) + ylab("Speed (km/h)")
p6
ggsave("raceTimeByCat.png", plot = p1)
ggsave("racePaceByCat.png", plot = p2)
ggsave("raceSpeedByCat.png", plot = p3)
ggsave("raceTimeByGen.png", plot = p4)
ggsave("racePaceByGen.png", plot = p5)
ggsave("raceSpeedByGen.png", plot = p6)

Edit 2018-09-12T18:52:43Z I wasn’t happy with the plots and added a few more lines to look at gender as well as category. And show speed as well as pace and finishing time.

—

The post title is taken from “Pledging My Time” a track from Blonde on Blonde by Bob Dylan

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Measured Steps: Garmin step adjustment algorithm

I recently got a new GPS running watch, a Garmin Fēnix 5. As well as tracking runs, cycling and swimming, it does “activity tracking” – number of steps taken in a day, sleep, and so on. The step goals are set to move automatically and I wondered how it worked. With a quick number crunch, the algorithm revealed itself. Read on if you are interested how it works.

Step screen on the Garmin Fēnix 5

The watch started out with a step target of 7500 steps in one day. I missed this by 2801 and the target got reduced by 560 to 6940 for the next day. That day I managed 12480, i.e. 5540 over the target. So the target went up by 560 to 7500. With me so far? Good. So next I went over the target and it went up again (but this time by 590 steps). I missed that target by a lot and the target was reduced by 530 steps. This told me that I’d need to collect a bit more data to figure out how the goal is set. Here are the first few days to help you see the problem.

Actual steps Goal Deficit/Surplus Adjustment for Tomorrow
4699 7500 -2801 -560
12480 6940 5540 560
10417 7500 2917 590
2726 8090 -5364 -530
6451 7560 -1109 -220
8843 7340 1503 150
8984 7490 1494 300
9216 7790 1426 290

The data is available for download as a csv via the Garmin Connect website. After waiting to accumulate some more data, I plotted out the adjustment vs step deficit/surplus. The pattern was pretty clear.

There are two slopes here that pass through the origin. It doesn’t matter what the target was, the adjustment applied is scaled according to how close to the target I was, i.e. the step deficit or surplus. There was either a small (0.1) or large (0.2) scaling used to adjust the step target for the next day, but how did the watch decide which scale to use?

The answer was to look back at the previous day’s activity as well as the current day.

So if today you exceeded the target and you also exceeded the target yesterday then you get a small scale increase. Likewise if you fell short today and yesterday, you get a small scale decrease. However, if you’ve exceeded today but fell short yesterday, your target goes up by the big scaling. Falling short after exceeding yesterday is rewarded with a big scale decrease. The actual size of the decrease depends on the deficit or surplus on that day. The above plot is coloured according to the four possibilities described here.

I guess there is a logic to this. The goal could quickly get unreachable if it increased by 20% on a run of two days exceeding the target, and conversely, too easy if the decreases went down rapidly with consecutive inactivity. It’s only when there’s been a swing in activity that the goal should get moved by the large scaling. Otherwise, 10% in the direction of attainment is fine.

I have no idea if this is the algorithm used across all of Garmin’s watches or if other watch manufacturer’s use different target-setting algorithms.

—

The post title comes from “Measured Steps” by Edsel from their Techniques of Speed Hypnosis album.

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Colours Running Out: Analysis of 2016 running

Towards the end of 2015, I started distance running. I thought it’d be fun to look at the frequency of my runs over the course of 2016.

Most of my runs were recorded with a GPS watch. I log my cycling data using Rubitrack, so I just added my running data to this. This software is great but to do any serious number crunching, other software is needed. Yes, I know that if I used strava I can do lots of things with my data… but I don’t. I also know that there are tools for R to do this, but I wrote something in Igor instead. The GitHub repo is here. There’s a technical description below, as well as some random thoughts on running (and cycling).

The animation shows the tracks I recorded as 2016 rolled by. The routes won’t mean much to you, but I can recognise most of them. You can see how I built up the distance to run a marathon and then how the runs became less frequent through late summer to October. I logged 975 km with probably another 50 km or so not logged.

run2016

Technical description

To pull the data out of rubiTrack 4 Pro is actually quite difficult since there is no automated export. An applescript did the job of going through all the run activities and exporting them as gpx. There is an API provided by Garmin to take the data straight from the FIT files recorded by the watch, but everything is saved and tagged in rubiTrack, so gpx is a good starting point. GPX is an xml format which can be read into Igor using XMLutils XOP written by andyfaff. Previously, I’ve used nokogiri for reading XML, but this XOP keeps everything within Igor. This worked OK, but I had some trouble with namespaces which I didn’t resolve properly and what is in the code is a slight hack. I wrote some code which imported all the files and then processed the time frame I wanted to look at. It basically looks at a.m. and p.m. for each day in the timeframe. Igor deals with date/time nicely and so this was quite easy. Two lookups per day were needed because I often went for two runs per day (run commuting). I set the lat/lon at the start of each track as 0,0. I used the new alpha tools in IP7 to fade the tracks so that they decay away over time. They disappear with 1/8 reduction in opacity over a four day period. Igor writes out to mov which worked really nicely, but wordpress can’t host movies, so I added a line to write out TIFFs of each frame of the animation and assembled a nice gif using FIJI.

Getting started with running

Getting into running was almost accidental. I am a committed cyclist and had always been of the opinion: since running doesn’t improve aerobic cycling performance (only cycling does that), any activity other than cycling is a waste of time. However, I realised that finding time for cycling was getting more difficult and also my goal is to keep fit and not to actually be a pro-cyclist, so running had to be worth a try. Roughly speaking, running is about three times more time efficient compared to cycling. One hour of running approximates to three hours of cycling. I thought, I would just try it. Over the winter. No more than that. Of course, I soon got the running bug and ran through most of 2016. Taking part in a few running events (marathon, half marathons, 10K). A quick four notes on my experience.

  1. The key thing to keeping running is staying healthy and uninjured. That means building up distance and frequency of running very slowly. In fact, the limitation to running is the body’s ability to actually do the distance. In cycling this is different, as long as you fuel adequately and you’re reasonably fit, you could cycle all day if you wanted. This not true of running, and so, building up to doing longer distances is essential and the ramp up shouldn’t be rushed. Injuries will cost you lost weeks on a training schedule.
  2. There’s lots of things “people don’t tell you” about running. Blisters and things everyone knows about, but losing a toenail during a 20 km run? Encountering runner’s GI problems? There’s lots of surprises as you start out. Joining a club or reading running forums probably helps (I didn’t bother!). In case you are wondering, the respective answers are getting decent shoes fitted and well, there is no cure.
  3. Going from cycling to running meant going from very little upper body mass to gaining extra muscle. This means gaining weight. This is something of a shock to a cyclist and seems counterintuitive, since more activity should really equate to weight loss. I maintained cycling through the year, but was not expecting a gain of ~3 kilos.
  4. As with any sport, having something to aim for is essential. Training for training’s sake can become pointless, so line up something to shoot for. Sign up for an event or at least have an achievement (distance, average speed) in your mind that you want to achieve.

So there you have it. I’ll probably continue to mix running with cycling in 2017. I’ll probably extend the repo to do more with cycling data if I have the time.

—

The post title is taken from “Colours Running Out” by TOY from their eponymous LP.

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Pledging My Time II

2016 was the 400 year anniversary of William Shakespeare’s death. Stratford-upon-Avon Rotary Club held the Shakespeare Marathon on the same weekend. Runners had an option of half or full marathon. There were apparently 3.5 K runners. Only 700 of whom were doing the full marathon. The chip results were uploaded last night and can be found here. Similar to my post on the Coventry Half Marathon, I thought I’d quickly analyse the data.

rsm16violins

rsm16barsThe breakdown of runners by category. M and F are male and female runners under 35 years of age. M35 is 35-45, F55 is 55-65 etc. Only a single runner in the F65 category!

The best time was 02:34:51 by Adam Holland of Notfast. Fastest female runner was 3:14:39 by Josie Hinton of London Heathside.

Congrats to everyone who ran and thanks to the organisers and all the supporters out on the course.

—

The post title is taken from “Pledging My Time” a track from Blonde on Blonde by Bob Dylan

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Pledging My Time

The end of the month sees the Coventry Half Marathon. I looked at what constitutes a good time over this course, based on 2015 results. I thought I’d post this here in case any one is interested.

covhalfviolins

covhalfbars

The breakdown of runners by category for the 2015 event. Male Senior (MSEN) category has the most runners, constituting a wide age grouping. There were 3565 runners in total, 5 in an undetermined category and 9 DNFs. These 14 were not included in the analysis.

The best time last year was 01:10:21!

Good luck to everyone running this (or any other event) this year.

Edit: The 2016 Coventry Half Marathon happened today. I’m updating this post with the new data.

CH2016Violins.png

The width of violins has no special significance compared to 2015. Fastest time this year was 1:08:40 in the MSEN category.

CH2016bars

There were more runners this year than last (4212 finishers), across all categories. Also this year there was a wheelchair category, which is not included here as there were only four competitors. FWIW, I placed somewhere in the first violin, in the lower whisker :-).

Congrats to everyone who ran and thanks to the all the supporters out on the course.

—

The post title is taken from “Pledging My Time” a track from Blonde on Blonde by Bob Dylan

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Tips from the blog IX: running route

University of Warwick is a popular conference destination, with thousands of visitors per year. Next time you visit and stay on campus, why not bring your running shoes and try out these routes?

Route 1

track1

This is just over 10K and it takes you from main campus out towards Cryfield Pavilion. A path goes to the Greenway (a former railway), which is a nice flat gravel track. It goes up to Burton Green and back to campus via Westwood Heath Road. To exit the Greenway at Burton Green you need to take the “offramp” at the bridge otherwise you will end up heading to Berkswell. If you want to run totally off-road*, just turn back at this point (probably ~12K). The path out to the Greenway and the Greenway itself is unlit, so be careful early in the morning or late at night.

GPX of a trace put together on gpsies.

Track 2

track2

This is a variation on Track 1. Instead of heading up the Greenway to Burton Green, take a left and head towards Kenilworth Common. With a bit of navigation you can run on alongside a brook and pop out in Abbey Fields and see the ruins of Kenilworth Abbey. This is out-and-back, 12K. Obviously you can turn back sooner if you prefer. It’s all off-road apart from a few 100m on quiet residential streets as you navigate from the Common to Abbey Fields. GPX from Uni to around the lake at Abbey Fields.

Track 3

track3

 

This is a variation on Track 1 where you exit the Greenway and take a loop around Crackley Wood. The Wood is nice and has wild deer and other interesting wildlife. This route is totally off-road and is shorter at ~8K. GPX from Uni to around the Wood.

 

Other Routes

There is a footpath next to a bike lane down the A429 which is popular for runners heading to do a lap or two of Memorial Park in Coventry. This is OK, but means that you run alongside cars a lot.

If you don’t have time for these routes, the official Warwick page has three very short running routes of around 3 to 5 km (1, 2 and 3). I think that these routes are the ones that are on the signpost near the Sports Centre.

* Here, off-road means on paths but not alongside a road on a pavement. It doesn’t mean across fields.

—

This post is part of a series of tips.

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