NB: This vignette is (still) work-in-progress and not yet complete.
TBD
digest() and
sha1()R FAQ 7.31 illustrates potential problems with floating point arithmetic. Mathematically the equality $x = \sqrt{x}^2$ should hold. But the precision of floating points numbers is finite. Hence some rounding is done, leading to numbers which are no longer identical.
An illustration:
> # FAQ 7.31
> a0 <- 2
> b <- sqrt(a0)
> a1 <- b ^ 2
> identical(a0, a1)
[1] FALSE
> a0 - a1
[1] -4.440892e-16
> a <- c(a0, a1)
> # hexadecimal representation
> sprintf("%a", a)
[1] "0x1p+1" "0x1.0000000000001p+1"Although the difference is small, any difference will result in
different hash when using the digest() function. However,
the sha1() function tackles this problem by using the
hexadecimal representation of the numbers and truncates that
representation to a certain number of digits prior to calculating the
hash function.
> library(digest)
> # different hashes with digest
> sapply(a, digest, algo = "sha1")
[1] "315a5aa84aa6cfa4f3fb4b652a596770be0365e8"
[2] "5e3999bf79c230f7430e97d7f30070a7eff5ec92"
> # same hash with sha1 with default digits (14)
> sapply(a, sha1)
[1] "8a938d8f5fb9b8ccb6893aa1068babcc517f32d4"
[2] "8a938d8f5fb9b8ccb6893aa1068babcc517f32d4"
> # larger digits can lead to different hashes
> sapply(a, sha1, digits = 15)
[1] "98eb1dc9fada00b945d3ef01c77049ee5a4b7b9c"
[2] "5a173e2445df1134908037f69ac005fbd8afee74"
> # decreasing the number of digits gives a stronger truncation
> # the hash will change when then truncation gives a different result
> # case where truncating gives same hexadecimal value
> sapply(a, sha1, digits = 13)
[1] "43b3b465c975af322c85473190a9214b79b79bf6"
[2] "43b3b465c975af322c85473190a9214b79b79bf6"
> sapply(a, sha1, digits = 10)
[1] "6b537a9693c750ed535ca90527152f06e358aa3a"
[2] "6b537a9693c750ed535ca90527152f06e358aa3a"
> # case where truncating gives different hexadecimal value
> c(sha1(pi), sha1(pi, digits = 13), sha1(pi, digits = 10))
[1] "169388cf1ce60dc4e9904a22bc934c5db33d975b"
[2] "20dc38536b6689d5f2d053f30efb09c44af78378"
[3] "3a727417bd1807af2f0148cf3de69abff32c23ec"The result of floating point arithematic on 32-bit and 64-bit can be
slightly different. E.g. print(pi ^ 11, 22) returns
294204.01797389047 on 32-bit and
294204.01797389053 on 64-bit. Note that only the last 2
digits are different.
| command | 32-bit | 64-bit |
|---|---|---|
print(pi ^ 11, 22) |
294204.01797389047 |
294204.01797389053 |
sprintf("%a", pi ^ 11) |
"0x1.1f4f01267bf5fp+18" |
"0x1.1f4f01267bf6p+18" |
digest(pi ^ 11, algo = "sha1") |
"c5efc7f167df1bb402b27cf9b405d7cebfba339a" |
"b61f6fea5e2a7952692cefe8bba86a00af3de713" |
sha1(pi ^ 11, digits = 14) |
"5c7740500b8f78ec2354ea6af58ea69634d9b7b1" |
"4f3e296b9922a7ddece2183b1478d0685609a359" |
sha1(pi ^ 11, digits = 13) |
"372289f87396b0877ccb4790cf40bcb5e658cad7" |
"372289f87396b0877ccb4790cf40bcb5e658cad7" |
sha1(pi ^ 11, digits = 10) |
"c05965af43f9566bfb5622f335817f674abfc9e4" |
"c05965af43f9566bfb5622f335817f674abfc9e4" |
digest() or sha1()TBD
sha1().
sha1.sha1() on the (list of) relevant
component(s).sha1()zapsmall = 7 is recommended.digits = 14 is recommended in case all numerics are
data.digits = 4 is recommended in case some numerics stem
from floating point arithmetic.Let’s illustrate this using the summary of a simple linear regression. Suppose that we want a hash that takes into account the coefficients, their standard error and sigma.
> # taken from the help file of lm.influence
> lm_SR <- lm(sr ~ pop15 + pop75 + dpi + ddpi, data = LifeCycleSavings)
> lm_sum <- summary(lm_SR)
> class(lm_sum)
[1] "summary.lm"
> # str() gives the structure of the lm object
> str(lm_sum)
List of 11
$ call : language lm(formula = sr ~ pop15 + pop75 + dpi + ddpi, data = LifeCycleSavings)
$ terms :Classes 'terms', 'formula' language sr ~ pop15 + pop75 + dpi + ddpi
.. ..- attr(*, "variables")= language list(sr, pop15, pop75, dpi, ddpi)
.. ..- attr(*, "factors")= int [1:5, 1:4] 0 1 0 0 0 0 0 1 0 0 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:5] "sr" "pop15" "pop75" "dpi" ...
.. .. .. ..$ : chr [1:4] "pop15" "pop75" "dpi" "ddpi"
.. ..- attr(*, "term.labels")= chr [1:4] "pop15" "pop75" "dpi" "ddpi"
.. ..- attr(*, "order")= int [1:4] 1 1 1 1
.. ..- attr(*, "intercept")= int 1
.. ..- attr(*, "response")= int 1
.. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
.. ..- attr(*, "predvars")= language list(sr, pop15, pop75, dpi, ddpi)
.. ..- attr(*, "dataClasses")= Named chr [1:5] "numeric" "numeric" "numeric" "numeric" ...
.. .. ..- attr(*, "names")= chr [1:5] "sr" "pop15" "pop75" "dpi" ...
$ residuals : Named num [1:50] 0.864 0.616 2.219 -0.698 3.553 ...
..- attr(*, "names")= chr [1:50] "Australia" "Austria" "Belgium" "Bolivia" ...
$ coefficients : num [1:5, 1:4] 28.566087 -0.461193 -1.691498 -0.000337 0.409695 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:5] "(Intercept)" "pop15" "pop75" "dpi" ...
.. ..$ : chr [1:4] "Estimate" "Std. Error" "t value" "Pr(>|t|)"
$ aliased : Named logi [1:5] FALSE FALSE FALSE FALSE FALSE
..- attr(*, "names")= chr [1:5] "(Intercept)" "pop15" "pop75" "dpi" ...
$ sigma : num 3.8
$ df : int [1:3] 5 45 5
$ r.squared : num 0.338
$ adj.r.squared: num 0.28
$ fstatistic : Named num [1:3] 5.76 4 45
..- attr(*, "names")= chr [1:3] "value" "numdf" "dendf"
$ cov.unscaled : num [1:5, 1:5] 3.74 -7.24e-02 -4.46e-01 -7.86e-05 -1.88e-02 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:5] "(Intercept)" "pop15" "pop75" "dpi" ...
.. ..$ : chr [1:5] "(Intercept)" "pop15" "pop75" "dpi" ...
- attr(*, "class")= chr "summary.lm"
> # extract the coefficients and their standard error
> coef_sum <- coef(lm_sum)[, c("Estimate", "Std. Error")]
> # extract sigma
> sigma <- lm_sum$sigma
> # check the class of each component
> class(coef_sum)
[1] "matrix" "array"
> class(sigma)
[1] "numeric"
> # sha1() has methods for both matrix and numeric
> # because the values originate from floating point arithmetic it is better to use a low number of digits
> sha1(coef_sum, digits = 4)
[1] "3f0b0c552f94d753fcc8deb4d3e9fc11a83197af"
> sha1(sigma, digits = 4)
[1] "cbc83d1791ef1eeadd824ea9a038891b5889056b"
> # we want a single hash
> # combining the components in a list is a solution that works
> sha1(list(coef_sum, sigma), digits = 4)
[1] "476d27265365cd41662eedf059b335d38a221cc2"
> # now turn everything into an S3 method
> # - a function with name "sha1.classname"
> # - must have the same arguments as sha1()
> sha1.summary.lm <- function(x, digits = 4, zapsmall = 7){
+ coef_sum <- coef(x)[, c("Estimate", "Std. Error")]
+ sigma <- x$sigma
+ combined <- list(coef_sum, sigma)
+ sha1(combined, digits = digits, zapsmall = zapsmall)
+ }
> sha1(lm_sum)
[1] "476d27265365cd41662eedf059b335d38a221cc2"
> # try an altered dataset
> LCS2 <- LifeCycleSavings[rownames(LifeCycleSavings) != "Zambia", ]
> lm_SR2 <- lm(sr ~ pop15 + pop75 + dpi + ddpi, data = LCS2)
> sha1(summary(lm_SR2))
[1] "90beb028833bf0542997fde7c3f19e5b9fdfeef4"Let’s illustrate this using the summary of a simple linear regression. Suppose that we want a hash that takes into account the coefficients, their standard error and sigma.
> class(lm_SR)
[1] "lm"
> # str() gives the structure of the lm object
> str(lm_SR)
List of 12
$ coefficients : Named num [1:5] 28.566087 -0.461193 -1.691498 -0.000337 0.409695
..- attr(*, "names")= chr [1:5] "(Intercept)" "pop15" "pop75" "dpi" ...
$ residuals : Named num [1:50] 0.864 0.616 2.219 -0.698 3.553 ...
..- attr(*, "names")= chr [1:50] "Australia" "Austria" "Belgium" "Bolivia" ...
$ effects : Named num [1:50] -68.38 -14.29 7.3 -3.52 -7.94 ...
..- attr(*, "names")= chr [1:50] "(Intercept)" "pop15" "pop75" "dpi" ...
$ rank : int 5
$ fitted.values: Named num [1:50] 10.57 11.45 10.95 6.45 9.33 ...
..- attr(*, "names")= chr [1:50] "Australia" "Austria" "Belgium" "Bolivia" ...
$ assign : int [1:5] 0 1 2 3 4
$ qr :List of 5
..$ qr : num [1:50, 1:5] -7.071 0.141 0.141 0.141 0.141 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:50] "Australia" "Austria" "Belgium" "Bolivia" ...
.. .. ..$ : chr [1:5] "(Intercept)" "pop15" "pop75" "dpi" ...
.. ..- attr(*, "assign")= int [1:5] 0 1 2 3 4
..$ qraux: num [1:5] 1.14 1.17 1.16 1.15 1.05
..$ pivot: int [1:5] 1 2 3 4 5
..$ tol : num 1e-07
..$ rank : int 5
..- attr(*, "class")= chr "qr"
$ df.residual : int 45
$ xlevels : Named list()
$ call : language lm(formula = sr ~ pop15 + pop75 + dpi + ddpi, data = LifeCycleSavings)
$ terms :Classes 'terms', 'formula' language sr ~ pop15 + pop75 + dpi + ddpi
.. ..- attr(*, "variables")= language list(sr, pop15, pop75, dpi, ddpi)
.. ..- attr(*, "factors")= int [1:5, 1:4] 0 1 0 0 0 0 0 1 0 0 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:5] "sr" "pop15" "pop75" "dpi" ...
.. .. .. ..$ : chr [1:4] "pop15" "pop75" "dpi" "ddpi"
.. ..- attr(*, "term.labels")= chr [1:4] "pop15" "pop75" "dpi" "ddpi"
.. ..- attr(*, "order")= int [1:4] 1 1 1 1
.. ..- attr(*, "intercept")= int 1
.. ..- attr(*, "response")= int 1
.. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
.. ..- attr(*, "predvars")= language list(sr, pop15, pop75, dpi, ddpi)
.. ..- attr(*, "dataClasses")= Named chr [1:5] "numeric" "numeric" "numeric" "numeric" ...
.. .. ..- attr(*, "names")= chr [1:5] "sr" "pop15" "pop75" "dpi" ...
$ model :'data.frame': 50 obs. of 5 variables:
..$ sr : num [1:50] 11.43 12.07 13.17 5.75 12.88 ...
..$ pop15: num [1:50] 29.4 23.3 23.8 41.9 42.2 ...
..$ pop75: num [1:50] 2.87 4.41 4.43 1.67 0.83 2.85 1.34 0.67 1.06 1.14 ...
..$ dpi : num [1:50] 2330 1508 2108 189 728 ...
..$ ddpi : num [1:50] 2.87 3.93 3.82 0.22 4.56 2.43 2.67 6.51 3.08 2.8 ...
..- attr(*, "terms")=Classes 'terms', 'formula' language sr ~ pop15 + pop75 + dpi + ddpi
.. .. ..- attr(*, "variables")= language list(sr, pop15, pop75, dpi, ddpi)
.. .. ..- attr(*, "factors")= int [1:5, 1:4] 0 1 0 0 0 0 0 1 0 0 ...
.. .. .. ..- attr(*, "dimnames")=List of 2
.. .. .. .. ..$ : chr [1:5] "sr" "pop15" "pop75" "dpi" ...
.. .. .. .. ..$ : chr [1:4] "pop15" "pop75" "dpi" "ddpi"
.. .. ..- attr(*, "term.labels")= chr [1:4] "pop15" "pop75" "dpi" "ddpi"
.. .. ..- attr(*, "order")= int [1:4] 1 1 1 1
.. .. ..- attr(*, "intercept")= int 1
.. .. ..- attr(*, "response")= int 1
.. .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
.. .. ..- attr(*, "predvars")= language list(sr, pop15, pop75, dpi, ddpi)
.. .. ..- attr(*, "dataClasses")= Named chr [1:5] "numeric" "numeric" "numeric" "numeric" ...
.. .. .. ..- attr(*, "names")= chr [1:5] "sr" "pop15" "pop75" "dpi" ...
- attr(*, "class")= chr "lm"
> # extract the model and the terms
> lm_model <- lm_SR$model
> lm_terms <- lm_SR$terms
> # check their class
> class(lm_model) # handled by sha1()
[1] "data.frame"
> class(lm_terms) # not handled by sha1()
[1] "terms" "formula"
> # define a method for formula
> sha1.formula <- function(x, digits = 14, zapsmall = 7, ..., algo = "sha1"){
+ sha1(as.character(x), digits = digits, zapsmall = zapsmall, algo = algo)
+ }
> sha1(lm_terms)
[1] "2737d209720aa7d1c0555050ad06ebe89f3850cd"
> sha1(lm_model)
[1] "27b7dd9e3e09b9577da6947b8473b63a1d0b6eb4"
> # define a method for lm
> sha1.lm <- function(x, digits = 14, zapsmall = 7, ..., algo = "sha1"){
+ lm_model <- x$model
+ lm_terms <- x$terms
+ combined <- list(lm_model, lm_terms)
+ sha1(combined, digits = digits, zapsmall = zapsmall, ..., algo = algo)
+ }
> sha1(lm_SR)
[1] "7eda2a9d58e458c8e782e40ce140d62b836b2a2f"
> sha1(lm_SR2)
[1] "4d3abdb1f17bd12fdf9d9b91a2ad04c07824fe4a"Use case
automated analysis
update frequency of the data might be lower than the frequency of automated analysis
similar analyses on many datasets (e.g. many species in ecology)
analyses that require a lot of computing time
Bundle all relevant information on an analysis in a class
calculate sha1()
file fingerprint ~ sha1() on the stable parts
status fingerprint ~ sha1() on the parts that result for
the model