# A couple of thoughts on biotech and food security

“What has {insert biotech here} done for food security?” This question starts at the wrong end of the problem, because food security is much larger than any biotechnology. I would suggest that governance, property rights and education are the fundamental issues for food security, followed by biotechnological options. For example, the best biotechnology is useless if one is trying to do agriculture in a war-ravaged country.

Once we have a relatively stable government and educated people can rely on property rights, the effects of different biotechnologies will be magnified and it will be possible to better assess them. I would say that matching the most appropriate technologies to the local environmental, economic and cultural conditions is a good sign of sustainable agriculture. I would also say that the broader the portfolio of biotechnology and agronomic practices the more likely a good match will be. That is, I would not a priori exclude any biotechnology from the table based on generic considerations.

Should the success of a biotechnology for food security be measured as yield? It could be one of the desired effects but it is not necessarily the most important one. For example, having less fluctuating production (that is reducing the variance rather than increasing the mean) could be more relevant. Or we could be interested in creating combinations of traits that are difficult to achieve by traditional breeding (e.g. biofortification), where yield is still the same but nutritional content differs. Or we would like to have a reduction of inputs (agrochemicals, for example) while maintaining yield. There are many potential answers and—coming back to matching practices to local requirements—using a simple average of all crops in a country (or a continent) is definitely the wrong scale of assessment. We do not want to work with an average farmer or an average consumer but to target specific needs with the best available practices. Some times this will include {insert biotech, agronomical practices here}, other times this will include {insert another biotech and set of agronomical practices here}.

And that is the way I think of improving food security.

# Should I reject a manuscript because the analyses weren’t done using open source software?

“Should I reject a manuscript because the analyses weren’t done using open software?” I overheard a couple of young researchers discussing. Initially I thought it was a joke but, to my surprise, it was not funny at all.

There is an unsettling, underlying idea in that question: the value of a scientific work can be reduced to its computability. If I, the reader, cannot replicate the computation the work is of little, if any, value. Even further, my verification has to have no software cost involved, because if that is not the case we are limiting the possibility of computation to only those who can afford it. Therefore, the almost unavoidable conclusion is that we should force the use of open software in science.

What happens if the analyses were run using a point-and-click interface? For example SPSS, JMP, Genstat, Statistica, and a few other programs allow access to fairly complex analytical algorithms via a system of menus and icons. Most of them are not open source nor generate code for the analyses. Should we ban their use in science? One could argue that if users only spend the time and learn a programming language (e.g. R or Python) they will be free of the limitations of point-and-click. Nevertheless, we would be shifting accessibility from people that can pay for an academic license for a software to people that can learn and moderately enjoy programming. Are we better off as research community by that shift?

There is another assumption: open software will always provide good (or even appropriate) analytical tools for any problem. I assume that in many cases OSS is good enough and that there is a subset of problems where it is the best option. However, there is another subset where it is suboptimal. For example, I deal a lot with linear mixed models used in quantitative genetics, an area where R is seriously deficient. In fact, I should have to ignore the last 15 years of statistical development to run large problems. Given that some of the data sets are worth millions of dollars and decades of work, Should I sacrifice the use of best models so a hypothetical someone, somewhere can actually run my code without paying for an academic software license? This was a rhetorical question, by the way, as I would not do it.

There are trade-offs and unintended consequences in all research policies. This is one case where I think the negative effects would outweigh the benefits.

Gratuitous picture: I smiled when I saw the sign with the rightful place for forestry (Photo: Luis).

P.S. 2013-12-20 16:13 NZST Timothée Poisot provides some counterarguments for a subset of articles: papers about software.

# Protectionism under another name

This morning Radio New Zealand covered a story (audio) where Tomatoes New Zealand (TNZ, the growers association) was asking the Government to introduce compulsory labeling for irradiated products (namely imported Australian tomatoes), stating that consumers deserve an informed choice (TNZ Press Release). Two points that I think merit attention:

• Food irradiation is perfectly safe: it does not make food radioactive, it does not alter the nutritional value of food and reduces the presence (or completely eliminates) the presence of microorganisms that cause disease or pests (the latter being the reason for irradiation in this case).
• The second point is that the call for labeling does not come from consumers (or an organization representing them) but from producers that face competition.

This situation reminded me of Milton Friedman talking about professional licenses The justification offered is always the same: to protect the consumer. However, the reason is demonstrated by observing who lobbies. Who is doing the lobbying is very telling in this case, particularly because there is no real reason to induce fear on the consumer, except that irradiation sounds too close to radioactive, and therefore TNZ is hoping to steer consumers away from imported tomatoes. Given that TNZ is for informing the consumer they could label tomatoes with ‘many of the characteristics in this tomato are the product of mutations‘. Harmless but scary.

P.S. The media is now picking up the story. Shameful manipulation.
P.S.2 Give that TNZ is in favor of the right to know I want a list of all chemicals used in the production of New Zealand tomatoes, how good is their water management and the employment practices of tomato growers.

I have written a few posts discussing descriptive analyses of evaluation of National Standards for New Zealand primary schools.The data for roughly half of the schools was made available by the media, but the full version of the dataset is provided in a single-school basis. In the page for a given school there may be link to a PDF file with the information on standards sent by the school to the Ministry of Education.

I’d like to keep a copy of the PDF reports for all the schools for which I do not have performance information, so I decided to write an R script to download just over 1,000 PDF files. Once I can identify all the schools with missing information I just loop over the list, using the fact that all URL for the school pages start with the same prefix. I download the page, look for the name of the PDF file and then download the PDF file, which is named school_schoolnumber.pdf. And that’s it.

Of course life would be a lot simpler if the Ministry of Education made the information available in a usable form for analysis.

library(XML) # HTML processing options(stringsAsFactors = FALSE)   # Base URL base.url = 'http://www.educationcounts.govt.nz/find-a-school/school/national?school=' download.folder = '~/Downloads/schools/'   # Schools directory directory <- read.csv('Directory-Schools-Current.csv') directory <- subset(directory, !(school.type %in% c("Secondary (Year 9-15)", "Secondary (Year 11-15)")))   # Reading file obtained from stuff.co.nz obtained from here: # http://schoolreport.stuff.co.nz/index.html fairfax <- read.csv('SchoolReport_data_distributable.csv') fairfax <- subset(fairfax, !is.na(reading.WB))   # Defining schools with missing information to.get <- merge(directory, fairfax, by = 'school.id', all.x = TRUE) to.get <- subset(to.get, is.na(reading.WB))   # Looping over schools, to find name of PDF file # with information and download it   for(school in to.get$school.id){ # Read HTML file, extract PDF link name cat('Processing school ', school, '\n') doc.html <- htmlParse(paste(base.url, school, sep = '')) doc.links <- xpathSApply(doc.html, "//a/@href") pdf.url <- as.character(doc.links[grep('pdf', doc.links)]) if(length(pdf.url) > 0) { pdf.name <- paste(download.folder, 'school_', school, '.pdf', sep = '') download.file(pdf.url, pdf.name, method = 'auto', quiet = FALSE, mode = "w", cacheOK = TRUE, extra = getOption("download.file.extra")) } } ## Can you help? It would be great if you can help me to get the information from the reports. The following link randomly chooses a school, click on the “National Standards” tab and open the PDF file. Then type the achievement numbers for reading, writing and mathematics in this Google Spreadsheet. No need to worry about different values per sex or ethnicity; the total values will do. Gratuitous picture: a simple summer lunch (Photo: Luis). # A word of caution: the sample may have an effect This week I’ve tried to i-stay mostly in the descriptive statistics realm and ii-surround any simple(istic) models with caveats and pointing that they are very preliminary. We are working with a sample of ~1,000 schools that did reply to Fairfax’s request, while there is a number of schools that either ignored the request or told Fairfax to go and F themselves. Why am I saying this? If one goes and gets a simple table of the number of schools by type and decile there is something quite interesting: we have different percentages for different types of schools represented in the sample and the possibility of bias on the reporting to Fairfax, due to potential low performance (references to datasets correspond to the ones I used in this post): summary(standards$school.type) # Composite (Year 1-10) Composite (Year 1-15) Contributing (Year 1-6) # 1 29 403 # Full Primary (Year 1-8) Intermediate (year 7 and 8) Restricted Composite (Yr 7-10) # 458 62 1 # Secondary (Year 7-15) # 56

Now let’s compare this number with the school directory:

summary(factor(directory$school.type)) # Composite (Year 1-10) Composite (Year 1-15) Contributing (Year 1-6) # 4 149 775 # Correspondence School Full Primary (Year 1-8) Intermediate (year 7 and 8) # 1 1101 122 #Restricted Composite (Yr 7-10) Secondary (Year 11-15) Secondary (Year 7-10) # 4 2 2 # Secondary (Year 7-15) Secondary (Year 9-15) Special School # 100 238 39 # Teen Parent Unit # 20 As a proportion we are missing more secondary schools. We can use the following code to get an idea of how similar are school types, because the small number of different composite schools is a pain. If # Performance of Contributing (Year 1-6) and # Full Primary (Year 1-8) looks pretty much the # same. Composites could be safely merged qplot(school.type, reading.OK, data = standards, geom = 'jitter') qplot(school.type, writing.OK, data = standards, geom = 'jitter') qplot(school.type, math.OK, data = standards, geom = 'jitter') # Merging school types and plotting them colored # by decile standards$school.type.4 <- standards$school.type levels(standards$school.type.4) <- c('Composite', 'Composite', 'Primary', 'Primary', 'Intermediate', 'Composite', 'Secondary')   qplot(school.type.4, reading.OK, colour = decile, data = standards, geom = 'jitter')

Representation of different schools types and deciles is uneven.

Different participations in the sample for school types. This type is performance in mathematics.

I’m using jittering rather than box and whisker plots to i- depict all the schools and ii- get an idea of the different participation of school types in the dataset. Sigh. Another caveat to add in the discussion.

P.S. 2012-09-27 16:15. Originally I mentioned in this post the lack of secondary schools (Year 9-15) but, well, they are not supposed to be here, because National Standards apply to years 1 to 8 (Thanks to Michael MacAskill for pointing out my error.)

# Some regressions on school data

Eric and I have been exchanging emails about potential analyses for the school data and he published a first draft model in Offsetting Behaviour. I have kept on doing mostly data exploration while we get a definitive full dataset, and looking at some of the pictures I thought we could present a model with fewer predictors.

The starting point is the standards dataset I created in the previous post:

# Make authority a factor standards$authority <- factor(standards$authority)   # Plot relationship between school size and number of FTTE # There seems to be a separate trend for secondary schools qplot(total.roll, teachers.ftte, data = standards, color = school.type)

There seems to be a different trend for secondary vs non-secondary schools concerning the relationship between number of full time teacher equivalent and total roll. The presence of a small number of large schools suggests that log transforming the variables could be a good idea.

# Create a factor for secondary schools versus the rest standards$secondary <- factor(ifelse(standards$school.type == 'Secondary (Year 7-15)', 'Yes', 'No'))   # Plot the relationship between number of students per FTTE # and type of school qplot(secondary, total.roll/teachers.ftte, data = standards, geom = 'boxplot', ylab = 'Number of students per FTTE')

Difference on the number of students per FTTE between secondary and non-secondary schools.

Now we fit a model where we are trying to predict reading standards achievement per school accounting for decile, authority , proportion of non-european students, secondary schools versus the rest, and a different effect of number of students per FTTE
for secondary and non-secondary schools.

standards$students.per.ftte <- with(standards, total.roll/teachers.ftte) # Decile2 is just a numeric version of decile (rather than a factor) m1e <- lm(reading.OK ~ decile2 + I(decile2^2) + authority + I(1 - prop.euro) + secondary*students.per.ftte, data = standards, weights = total.roll) summary(m1e) #Coefficients: # Estimate Std. Error t value Pr(>|t|) #(Intercept) 0.6164089 0.0305197 20.197 < 2e-16 *** #decile2 0.0422733 0.0060756 6.958 6.24e-12 *** #I(decile2^2) -0.0015441 0.0004532 -3.407 0.000682 *** #authorityState: Not integrated -0.0440261 0.0089038 -4.945 8.94e-07 *** #I(1 - prop.euro) -0.0834869 0.0181453 -4.601 4.74e-06 *** #secondaryYes -0.2847035 0.0587674 -4.845 1.47e-06 *** #students.per.ftte 0.0023512 0.0011706 2.009 0.044854 * #secondaryYes:students.per.ftte 0.0167085 0.0040847 4.091 4.65e-05 *** --- #Residual standard error: 1.535 on 999 degrees of freedom # (3 observations deleted due to missingness) #Multiple R-squared: 0.4942, Adjusted R-squared: 0.4906 #F-statistic: 139.4 on 7 and 999 DF, p-value: < 2.2e-16 The residuals are still a bit of a mess: Residuals for this linear model: still a bit of a mess. If we remember my previous post decile accounted for 45% of variation and we explain 4% more through the additional predictors. Non-integrated schools have lower performance, a higher proportion of non-European students reduce performance, secondary schools have lower performance and larger classes tend to perform better (Eric suggests reverse causality, I’m agnostic at this stage), although the rate of improvement changes between secondary and non-secondary schools. In contrast with Eric, I didn’t fit separate ethnicities as those predictors are related to each other and constrained to add up to one. Of course this model is very preliminary, and a quick look at the coefficients will show that changes on any predictors besides decile will move the response by a very small amount (despite the tiny p-values and numerous stars next to them). The distribution of residuals is still heavy-tailed and there are plenty of questions about data quality; I’ll quote Eric here: But differences in performance among schools of the same decile by definition have to be about something other than decile. I can’t tell from this data whether it’s differences in stat-juking, differences in unobserved characteristics of entering students, differences in school pedagogy, or something else. But there’s something here that bears explaining. # Updating and expanding New Zealand school data In two previous posts I put together a data set and presented some exploratory data analysis on school achievement for national standards. After those posts I exchanged emails with a few people about the sources of data and Jeremy Greenbrook-Held pointed out Education Counts as a good source of additional variables, including number of teachers per school and proportions for different ethnic groups. The code below call three files: Directory-Schools-Current.csv, teacher-numbers.csv and SchoolReport_data_distributable.csv, which you can download from the links. options(stringsAsFactors = FALSE) library(ggplot2) # Reading School directory and dropping some address information # for 2012 obtained from here: # http://www.educationcounts.govt.nz/directories/list-of-nz-schools directory <- read.csv('Directory-Schools-Current.csv') directory <- subset(directory, select = -1*c(3:9, 11:13)) # Reading teacher numbers for 2011 obtained from here: # http://www.educationcounts.govt.nz/statistics/schooling/teaching_staff teachers <- read.csv('teacher-numbers.csv') # Reading file obtained from stuff.co.nz obtained from here: # http://schoolreport.stuff.co.nz/index.html fairfax <- read.csv('SchoolReport_data_distributable.csv') # Merging directory and teachers info standards <- merge(directory, teachers, by = 'school.id', all.x = TRUE) # Checking that the school names match # This shows ten cases, some of them obviously the same school # e.g. Epsom Girls Grammar School vs Epsom Girls' Grammar School tocheck <- subset(standards, school.name.x != school.name.y) tocheck[, c(1:2, 29)] #school.id school.name.x school.name.y #61 64 Epsom Girls Grammar School Epsom Girls' Grammar School #125 135 Fraser High School Hamilton's Fraser High School #362 402 Waiau Area School Tuatapere Community College #442 559 Te Wainui a Rua Whanganui Awa School #920 1506 St Michael's Catholic School (Remuera) St Michael's School (Remuera) #929 1515 Sunnyhills School Sunny Hills School #985 1573 Willow Park School Willowpark School #1212 1865 Te Wharekura o Maniapoto Te Wharekura o Oparure #1926 2985 Sacred Heart Cathedral School Sacred Heart School (Thorndon) #2266 3554 Waitaha School Waitaha Learning Centre # Merging now with fairfax data standards <- merge(standards, fairfax, by = 'school.id', all.x = TRUE) # Four schools have a different name tocheck2 <- subset(standards, school.name.x != school.name) tocheck2[, c(1:2, 32)] #school.id school.name.x school.name #920 1506 St Michael's Catholic School (Remuera) St Michael's School (Remuera) #929 1515 Sunnyhills School Sunny Hills School #985 1573 Willow Park School Willowpark School #2266 3554 Waitaha School Waitaha Learning Centre # Checking the original spreadsheets it seems that, despite # the different name they are the same school (at least same # city) # Now start dropping a few observations that are of no use # for any analysis; e.g. schools without data standards <- subset(standards, !is.na(reading.WB)) # Dropping school 498 Te Aho o Te Kura Pounamu Wellington # http://www.tekura.school.nz/ # It is a correspondence school without decile information standards <- subset(standards, school.id != 498) # Converting variables to factors standards$decile <- factor(standards$decile) standards$school.type <- factor(standards$school.type) standards$education.region <- factor(standards$education.region, levels = c('Northern', 'Central North', 'Central South', 'Southern')) # Removing 8 special schools standards <- subset(standards, as.character(school.type) != 'Special School') standards$school.type <- standards$school.type[drop = TRUE] # Saving file for Eric # write.csv(standards, 'standardsUpdated.csv', # row.names = FALSE, quote = FALSE) # Create performance groups standards$math.OK <- with(standards, math.At + math.A) standards$reading.OK <- with(standards, reading.At + reading.A) standards$writing.OK <- with(standards, writing.At + writing.A)   # Creating a few proportions standards$prop.euro <- with(standards, european/total.roll) standards$prop.maori <- with(standards, maori/total.roll) standards$prop.pacific <- with(standards, pacific.island/total.roll) standards$prop.asian <- with(standards, asian/total.roll)

This updated data set is more comprehensive but it doesn’t change the general picture presented in my previous post beyond the headlines. Now we can get some cool graphs to point out the obvious, for example the large proportion of Maori and Pacific Island students in low decile schools:

qplot(prop.maori, prop.pacific, data = standards, color = decile, xlab = 'Proportion of Maori', ylab = 'Proportion of Pacific Island')

Proportion of Pacific Island (vertical axis) and Maori students (horizontal axis) in schools with points colored by decile. Higher proportions for both are observed in low decile schools.

I have avoided ‘proper’ statistical modeling because i- there is substantial uncertainty in the data and ii- the national standards for all schools (as opposed to only 1,000 schools) will be released soon; we do’t know if the published data are a random sample. In any case, a quick linear model fitting the proportion of students that meet reading standards (reading.OK) as a function of decile and weighted by total school roll—to account for the varying school sizes—will explain roughly 45% of the observed variability on reading achievement.

m1 <- lm(reading.OK ~ decile, data = standards, weights = total.roll) summary(m1)   # Coefficients: # Estimate Std. Error t value Pr(>|t|) # (Intercept) 0.56164 0.01240 45.278 < 2e-16 *** # decile2 0.06238 0.01769 3.527 0.000439 *** # decile3 0.10890 0.01749 6.225 7.07e-10 *** # decile4 0.16434 0.01681 9.774 < 2e-16 *** # decile5 0.18579 0.01588 11.697 < 2e-16 *** # decile6 0.22849 0.01557 14.675 < 2e-16 *** # decile7 0.25138 0.01578 15.931 < 2e-16 *** # decile8 0.24849 0.01488 16.701 < 2e-16 *** # decile9 0.28861 0.01492 19.347 < 2e-16 *** # decile10 0.31074 0.01439 21.597 < 2e-16 *** # # Residual standard error: 1.594 on 999 degrees of freedom # (1 observation deleted due to missingness) # Multiple R-squared: 0.4548, Adjusted R-squared: 0.4499 # F-statistic: 92.58 on 9 and 999 DF, p-value: < 2.2e-16

Model fit has a few issues with distribution of residuals, we should probably use a power transformation for the response variable, but I wouldn’t spend much more time before getting the full data for national standards.

par(mfrow = c(2, 2)) plot(m1) par(mfrow = c(1, 1))

Residuals of a quick weighted linear model. The residuals show some heterogeneity of variance (top-left) and deviation from normality (top-right) with heavy tails.

Bonus plot: map of New Zealand based on school locations, colors depicting proportion of students meeting reading national standards.

[sourcecode lang="R"]
qplot(longitude, latitude,
data = standards, color = reading.OK)
[/sourcecode]

New Zealand drawn using school locations; color coding is for proportion of students meeting reading national standards.

P.S. 2012-09-26 16:01. The simple model above could be fitted taking into account the order of the decile factor (using ordered()) or just fitting linear and quadratic terms for a numeric expression of decile. Anyway, that would account for 45% of the observed variability.

m1d <- lm(reading.OK ~ as.numeric(decile) + I(as.numeric(decile)^2), data = standards, weights = total.roll) summary(m1d)   #Coefficients: # Estimate Std. Error t value Pr(>|t|) #(Intercept) 0.5154954 0.0136715 37.706 < 2e-16 *** #as.numeric(decile) 0.0583659 0.0051233 11.392 < 2e-16 *** #I(as.numeric(decile)^2) -0.0023453 0.0004251 -5.517 4.39e-08 *** #--- #Residual standard error: 1.598 on 1006 degrees of freedom # (1 observation deleted due to missingness) #Multiple R-squared: 0.4483, Adjusted R-squared: 0.4472 #F-statistic: 408.8 on 2 and 1006 DF, p-value: < 2.2e-16

P.S. 2012-09-26 18:17. Eric Crampton has posted preliminary analyses based on this dataset in Offsetting Behaviour.

# New Zealand school performance: beyond the headlines

I like the idea of having data on school performance, not to directly rank schools—hard, to say the least, at this stage—but because we can start having a look at the factors influencing test results. I imagine the opportunity in the not so distant future to run hierarchical models combining Ministry of Education data with Census/Statistics New Zealand data.

At the same time, there is the temptation to come up with very simple analyses that would make appealing newspaper headlines. I’ll read the data and create a headline and then I’ll move to something that, personally, seems more important. In my previous post I combined the national standards for around 1,000 schools with decile information to create the standards.csv file.

library(ggplot2)   # Reading data, building factors standards <- read.csv('standards.csv') standards$decile.2008 <- factor(standards$decile.2008) standards$electorate <- factor(standards$electorate) standards$school.type <- factor(standards$school.type)   # Removing special schools (all 8 of them) because their # performance is not representative of the overall school # system standards <- subset(standards, as.character(school.type) != 'Special School') standards$school.type <- standards$school.type[drop = TRUE]   # Create performance variables. Proportion of the students that # at least meet the standards (i.e. meet + above) # Only using all students, because subsets are not reported # by many schools standards$math.OK <- with(standards, math.At + math.A) standards$reading.OK <- with(standards, reading.At + reading.A) standards$writing.OK <- with(standards, writing.At + writing.A) Up to this point we have read the data, removed special schools and created variables that represent the proportion of students that al least meet standards. Now I’ll do something very misleading: calculate the average for reading.OK for each school decile and plot it, showing the direct relationship between socio-economic decile and school performance. mislead <- aggregate(reading.OK ~ decile.2008, data = standards, mean) qplot(decile.2008, reading.OK , data = mislead) Scatterplot of average proportion of students at least meeting the reading national standards for each socioeconomic decile. Using only the average strengthens the relationship, but it hides something extremely important: the variability within each decile. The following code will display box and whisker plots for each decile: the horizontal line is the median, the box contains the middle 50% of the schools and the vertical lines 1.5 times the interquantile range (pretty much the range in most cases): qplot(decile.2008, reading.OK, data = standards, geom = 'boxplot', xlab = 'Decile in 2008', ylab = 'Reading at or above National Standard') Box and whisker plot for proportion of students at least meeting the reading national standard for each decile. Notice the variability for each decile. A quick look at the previous graph shows a few interesting things: • the lower the decile the more variable school performance, • there is pretty much no difference between deciles 6, 7, 8 and 9, and a minor increase for decile 10. • there is a trend for decreasing performance for lower deciles; however, there is also a huge variability within those deciles. We can repeat the same process for writing.OK and math.OK with similar trends, although the level of standard achievement is lower than for reading: qplot(decile.2008, writing.OK, data = standards, geom = 'boxplot', xlab = 'Decile in 2008', ylab = 'Writing at or above National Standard') qplot(decile.2008, math.OK, data = standards, geom = 'boxplot', xlab = 'Decile in 2008', ylab = 'Mathematics at or above National Standard') Box and whisker plot for proportion of students at least meeting the writing national standard for each decile. Box and whisker plot for proportion of students at least meeting the mathematics national standard for each decile. Achievement in different areas (reading, writing, mathematics) is highly correlated: cor(standards[, c('reading.OK', 'writing.OK', 'math.OK')], use = 'pairwise.complete.obs') # reading.OK writing.OK math.OK #reading.OK 1.0000000 0.7886292 0.7749094 #writing.OK 0.7886292 1.0000000 0.7522446 #math.OK 0.7749094 0.7522446 1.0000000 # We can plot an example and highlight decile groups # 1-5 vs 6-10 qplot(reading.OK, math.OK, data = standards, color = ifelse(as.numeric(decile.2008) > 5, 1, 0)) + opts(legend.position = 'none') Scatterplot for proportion meeting mathematics and reading national standards. Dark points are deciles 1 to 5, while light points are deciles 6 to 10. Notice the large overlap for performance between the two groups. All these graphs are only descriptive/exploratory; however, once we had more data we could move to hierarchical models to start adjusting performance by socioeconomic aspects, geographic location, type of school, urban or rural setting, school size, ethnicity, etc. Potentially, this would let us target resources on schools that could be struggling to perform; nevertheless, any attempt at creating a ‘quick & dirty’ ranking ignoring the previously mentioned covariates would be, at the very least, misleading. Note 2012-09-26: I have updated data and added a few plots in this post. # New Zealand School data Some people have the naive idea that the national standards data and the decile data will not be put together. Given that at some point in time all data will be available, there is no technical reason to not have merged the data, which I have done in this post for an early release. Stuff made data for the National Standards for a bit over 1,000 schools available here as an Excel File. I cleaned it up a bit to read it in R, saved it to csv format, of which you can get a copy here. Decile data is available from the Ministry of Education, which I transformed to csv and uploaded here. We can now merge the datasets using R: options(stringsAsFactors = FALSE) deciles <- read.csv('DecileChanges20072008.csv') standards <- read.csv('SchoolReport_data_distributable.csv') standards <- merge(standards, deciles, by = 'school.id') But there are some name discrepancies in the merge, which we can check using: standards$name.discrepancy <- factor(ifelse(standards$school.name.x != standards$school.name.y, 1, 0))   tocheck <- subset(standards[, c(1, 2, 64, 77)], name.discrepancy == 1) # school.id school.name.x school.name.y name.discrepancy #9 82 Aidanfield Christian School Canterbury Christian College 1 #33 266 Waipa Christian School Bethel Christian School 1 #73 429 Excellere College Kamo Christian College 1 #143 1245 Christ the King Catholic School (Owairak Christ The King School (Mt Roskill) 1 #150 1256 Cornwall Park District School Cornwall Park School 1 #211 1360 Marist Catholic School (Herne Bay) Marist School (Herne Bay) 1 #270 1500 St Leo's Catholic School (Devonport) St Leos School (Devonport) 1 #297 1588 St Francis Xavier Catholic School (Whang St Francis Xavier School (Whangarei) 1 #305 1650 Drummond Primary School Central Southland Rural Primary School 1 #314 1678 Te Kura o Waikaremoana Te Kura O Waikaremoana 1 #335 1744 Horahora School (Cambridge) Horahora School 1 #389 1991 Tauranga Primary School Tauranga School 1 #511 2424 Parkland School (P North) Parkland School 1 #587 2663 Reignier Catholic School Reignier School (Taradale) 1 #627 2841 Fergusson Intermediate (Trentham) Fergusson Intermediate 1 #771 3213 Parklands School (Motueka) Parklands School 1 #956 3801 Pine Hill School (Dunedin) Pine Hill School 1

There are four schools that have very different names in the dataset: 82, 266, 429 and 1650. They may just have changed names or something could be wrong. At this point one may choose to drop them from any analysis; up to you. We then just rename the second variable to school.name and save the file to csv (available here standards.csv for your enjoyment).

names(standards)[2] <- 'school.name' write.csv(standards, 'standards.csv', row.names = FALSE, quote = FALSE)

Now we should try to merge any other economic and social information available in Statistics New Zealand.

Note 2012-09-26: I have updated data and added a few plots in this post.