Related
I'm new to R and I'm trying to define a function in R where I call another function already in a R package (pgls and sma). I'm not sure how to do it or even if it is possible.
I have tried the following:
For pgls
getpgls <- function(P1, P2, dataf){
PGLSt <- pgls(log(P1)~log(P2), data = dataf, lambda = 'ML')
}
When I call the function:
getpgls(sym('Long'), sym('massAvg'), CompData)
I get:
Error in log(P1) : non-numeric argument to mathematical function
Something similar happens with the sma function:
getsma <- function(P1, P2, dataf){
SMAt <- sma(P1~P2,
log = "xy",
data = dataf,
)
}
when I call the function:
getsma(sym('Long'), sym('massAvg'), Data_Animal_de_pd)
I get the following error:
Error in model.frame.default(formula = P1 ~ P2, data = dataf, drop.unused.levels = TRUE) :
object is not a matrix
When I run both pgls and sma with the same argumerts, but outside the function, it runs just fine.
ie.
Long.SMA <- sma(Long~massAvg,
log = "xy",
data = Data_Animal_de_pd,
)
and
Long.PGLS = pgls(log(Long)~log(massAvg), data = CompData, lambda = 'ML')
EDIT:
Here I include small versions of CompData and Data_Animal_de_pd (only with 10 animals and the parameters massAvg and Long).
The class of CompData is "comparative.data" and comes from a function comparative.data which connects a phylogenetic tree with another data frame (Data_Animal_de_pd).
> dput(CompData)
structure(list(phy = structure(list(edge = structure(c(11L, 12L,
13L, 14L, 14L, 15L, 15L, 16L, 17L, 17L, 16L, 13L, 12L, 18L, 18L,
11L, 19L, 19L, 12L, 13L, 14L, 1L, 15L, 2L, 16L, 17L, 3L, 4L,
5L, 6L, 18L, 7L, 8L, 19L, 9L, 10L), dim = c(18L, 2L)), edge.length = c(100.597661,
5.254328, 4.311278, 71.0845800943, 34.327960646, 36.7566030561,
5.779375747, 15.0619109945, 15.9153248095, 15.9153245794, 30.9772360366,
75.39586827, 44.21113726, 36.439042146, 36.4390420969, 108.977279909,
72.27059073, 72.270578302), Nnode = 9L, tip.label = c("Tupaia_minor",
"Hystrix_cristata", "Geocapromys_brownii", "Myocastor_coypus",
"Hydrochoerus_hydrochaeris", "Rhinoceros_sondaicus", "Dasypus_hybridus",
"Tolypeutes_matacus", "Caluromysiops_irrupta", "Acrobates_pygmaeus"
), node.label = 11:19), class = "phylo", order = "cladewise"),
data = structure(list(massAvg = c(0.045, 20, 1.5, 7.5, 50.5,
1350, 5.5, 1.5, 0.45, 0.01), Long = c(21.565, 110.4, 55.52,
68.3266666666667, 175.2, 447.4, 47.02, 44.68, 38.58, 12.67
)), row.names = c("Tupaia_minor", "Hystrix_cristata", "Geocapromys_brownii",
"Myocastor_coypus", "Hydrochoerus_hydrochaeris", "Rhinoceros_sondaicus",
"Dasypus_hybridus", "Tolypeutes_matacus", "Caluromysiops_irrupta",
"Acrobates_pygmaeus"), class = "data.frame"), data.name = "datanm2[, c(\"massAvg\", \"Long\", \"Sci_name2\")]",
phy.name = "newphy", dropped = list(tips = character(0),
unmatched.rows = character(0))), class = "comparative.data")
Data_Animal_de_pd is a data frame that contains the information of the animals such as the length of the bones, etc.
> dput(Data_Animal_de_pd)
structure(list(massAvg = c(20, 50.5, 7.5, 1350, 0.45, 0.045,
1.5, 5.5, 1.5, 0.01), Long = c(110.4, 175.2, 68.3266666666667,
447.4, 38.58, 21.565, 55.52, 47.02, 44.68, 12.67), Sci_name = c("Hystrix cristata",
"Hydrochoerus hydrochaeris", "Myocastor coypus", "Rhinoceros sondaicus",
"Caluromysiops irrupta", "Tupaia minor", "Geocapromys brownii",
"Dasypus hybridus", "Tolypeutes matacus", "Acrobates pygmaeus"
), Sci_name2 = c("Hystrix_cristata", "Hydrochoerus_hydrochaeris",
"Myocastor_coypus", "Rhinoceros_sondaicus", "Caluromysiops_irrupta",
"Tupaia_minor", "Geocapromys_brownii", "Dasypus_hybridus", "Tolypeutes_matacus",
"Acrobates_pygmaeus")), row.names = c("10137", "10149", "10157",
"102233", "126286", "143289", "1543402", "1756220", "183749",
"190720"), class = "data.frame")```
To make your function work with symbols (i assume from rlang::sym) you must inject them with rlang::inject:
getsma <- function(P1, P2, dataf){
SMAt <- rlang::inject(sma(!!P1 ~ !!P2,
log = "xy",
data = dataf,
))
}
but you can instead substitute and inject arguments:
getsma <- function(P1, P2, dataf){
P1 <- rlang::enexpr(P1)
P2 <- rlang::enexpr(P2)
SMAt <- rlang::inject(sma(!!P1 ~ !!P2,
log = "xy",
data = dataf,
))
}
Then call them directly:
getsma(Long, massAvg, Data_Animal_de_pd)
Please, find my data q below.
I have produced this Forest Plot, and I would like the encircled text to be red instead of black. Can this be done?
My script
q <- escalc(measure="IRR", x1i=x1i, t1i=t1i, x2i=x2i, t2i=t2i, data=q)
q1 <- rma(yi, vi, data=q, slab=paste(study, sep=", "), method = "REML")
## Forest
forest(q1, xlim=c(-27,8), atransf=exp, showweights = FALSE, psize = 1.6, refline=log(1),
cex=0.5, ylim=c(0.1, 17), font=1, col="white", border="white", order=order(q$order),
ilab=cbind(q$x1i, q$t1i, q$ir1, q$x2i, q$t2i,q$ir2),
ilab.xpos=c(-19.3,-17,-15,-12.3,-10,-8),
rows=c(2:7,11:13),xlab="Rate ratios", mlab="")
# Headlines
text(c(-19,-16.8,-15,-12,-9.8,-8) ,15.7,font=1, cex=0.5, c("Events\n per total\n", "Person-\nyrs\n", "IR\n", "Events\n per total\n", "Person-\nyrs\n","IR\n"))
text(c(-18.75,-18.75,-18.65) ,c(13,12,11),font=1, cex=0.54, c("/ 32", "/ 32", " / 23"))
text(c(-18.75,-18.75,-18.75) ,c(7,6,5),font=1, cex=0.54, c("/ 37", "/ 37", "/ 37"))
text(c(-18.65,-18.65,-18.65) ,c(4,3,2),font=1, cex=0.54, c(" / 29", " / 29", " / 19"))
text(c(-11.65,-11.65,-11.65) ,c(13,12,11),font=1, cex=0.54, c(" /23", " /16", " /16"))
text(c(-11.65,-11.65,-11.75) ,c(7,6,5),font=1, cex=0.54, c(" /29", "/19", " /25"))
text(c(-11.65,-11.75,-11.75) ,c(4,3,2),font=1, cex=0.54, c("/19", " / 25", " / 25"))
text(8 ,15.7,font=1, "Rate ratio [95% CI]", pos=2, cex=0.5)
text(-27 ,c(14,8),font=2, c("Progression rates","Mortality rates"), pos=4, cex=0.5)
text(-27 ,c(1,10),font=1, c("\nCohort: 110 patients included","\nCohort: 76 patients included"), pos=4, cex=0.45)
My data q
q <- structure(list(study = structure(c(2L, 4L, 7L, 3L, 5L, 1L, 8L,
6L, 9L), .Label = c("WHO-I versus Unknown ", "WHO-I versus WHO-II",
"WHO-I versus WHO-II ", "WHO-I versus WHO-III", "WHO-I versus WHO-III ",
"WHO-II versus Unknown", "WHO-II versus WHO-III", "WHO-II versus WHO-III ",
"WHO-III versus Unknown"), class = "factor"), order = 9:1, x1i = c(4L,
4L, 15L, 9L, 9L, 9L, 15L, 15L, 12L), n1i = c(32L, 32L, 23L, 37L,
37L, 37L, 29L, 29L, 19L), t1i = c(74.7, 74.7, 22.8, 108.1, 108.1,
108.1, 48.3, 48.3, 27.9), x2i = c(15L, 15L, 15L, 15L, 12L, 9L,
12L, 9L, 9L), n2i = c(23L, 16L, 16L, 29L, 19L, 25L, 19L, 25L,
25L), t2i = c(22.8, 4.4, 4.4, 48.3, 27.9, 79.1, 27.9, 79.1, 79.1
), ir1 = c(5.4, 5.4, 65.7, 8.3, 8.3, 8.3, 31.1, 31.1, 43.1),
ir2 = c(65.7, 339.6, 339.6, 31.1, 43.1, 11.4, 43.1, 11.4,
11.4)), class = "data.frame", row.names = c(NA, -9L))
Changing the color of what's added via ilab isn't possible, but you can always just add the text yourself using text() (e.g., on top of the existing text). This will do it:
text(-15, rev(c(2:7,11:13)), q$ir1, col="red", font=1, cex=0.5)
text( -8, rev(c(2:7,11:13)), q$ir2, col="red", font=1, cex=0.5)
I have the following data in a csv file.
y,x1,x2,x3,x4,x5,x6,x7,x8,x9
10,2113,1985,38.9,64.7,4,868,59.7,2205,1917
11,2003,2855,38.8,61.3,3,615,55,2096,1575
11,2957,1737,40.1,60,14,914,65.6,1847,2175
13,2285,2905,41.6,45.3,-4,957,61.4,1903,2476
10,2971,1666,39.2,53.8,15,836,66.1,1457,1866
11,2309,2927,39.7,74.1,8,786,61,1848,2339
10,2528,2341,38.1,65.4,12,754,66.1,1564,2092
11,2147,2737,37,78.3,-1,761,58,1821,1909
4,1689,1414,42.1,47.6,-3,714,57,2577,2001
2,2566,1838,42.3,54.2,-1,797,58.9,2476,2254
7,2363,1480,37.3,48,19,984,67.5,1984,2217
example = data.frame(x1,x2,x3,x4,y)
How can I graph the variables x1, x2, x3 using scatter3D(x,y,z)?
I have tried:
library("plot3D")
with(example,scatter3D(y ~ x1 + x2 + x3))
But I get error:
Error in min(x,na.rm) : invalid 'type' (list) of argument
Looks like you want to plot a regression plane. The scatter3d function in package car will do that. You need to install car and rgl. First let's make your data more accessible:
dput(example)
structure(list(y = c(10L, 11L, 11L, 13L, 10L, 11L, 10L, 11L,
4L, 2L, 7L), x1 = c(2113L, 2003L, 2957L, 2285L, 2971L, 2309L,
2528L, 2147L, 1689L, 2566L, 2363L), x2 = c(1985L, 2855L, 1737L,
2905L, 1666L, 2927L, 2341L, 2737L, 1414L, 1838L, 1480L), x3 = c(38.9,
38.8, 40.1, 41.6, 39.2, 39.7, 38.1, 37, 42.1, 42.3, 37.3), x4 = c(64.7,
61.3, 60, 45.3, 53.8, 74.1, 65.4, 78.3, 47.6, 54.2, 48), x5 = c(4L,
3L, 14L, -4L, 15L, 8L, 12L, -1L, -3L, -1L, 19L), x6 = c(868L,
615L, 914L, 957L, 836L, 786L, 754L, 761L, 714L, 797L, 984L),
x7 = c(59.7, 55, 65.6, 61.4, 66.1, 61, 66.1, 58, 57, 58.9,
67.5), x8 = c(2205L, 2096L, 1847L, 1903L, 1457L, 1848L, 1564L,
1821L, 2577L, 2476L, 1984L), x9 = c(1917L, 1575L, 2175L,
2476L, 1866L, 2339L, 2092L, 1909L, 2001L, 2254L, 2217L)),
class = "data.frame", row.names = c(NA, -11L))
install.packages("car")
install.packages("rgl")
library(car)
library(rgl)
scatter3d(y~x1+x2, example)
The plot window will be small. Use the mouse to drag the lower right corner to make it bigger. You can drag within the plot to rotate it.
I'm trying to plot a graph with my data.
My code for that is
plot(birthRate$country_code, birthRate$yr2014, main = "Birth Rate by Countries 2014")
My out put is like this:
But I want to show all values in x axis.
dput(birthRate):
structure(list(series_code = structure(c(21L, 21L, 21L, 21L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L), .Label = c("NY.GNP.PCAP.CD",
"SE.PRM.ENRR", "SE.SEC.ENRR", "SE.TER.ENRR", "SE.TER.ENRR.FE",
"SH.ALC.PCAP.LI", "SH.DTH.COMM.ZS", "SH.DTH.INJR.ZS", "SH.DTH.NCOM.ZS",
"SH.IMM.IBCG", "SH.STA.MMRT.NE", "SH.STA.TRAF.P5", "SH.XPD.PCAP",
"SH.XPD.PRIV.ZS", "SH.XPD.PUBL.ZS", "SH.XPD.TOTL.ZS", "SL.UEM.TOTL.FE.ZS",
"SL.UEM.TOTL.MA.ZS", "SL.UEM.TOTL.ZS", "SP.ADO.TFRT", "SP.DYN.CBRT.IN",
"SP.DYN.CDRT.IN", "SP.DYN.LE00.FE.IN", "SP.DYN.LE00.IN",
"SP.DYN.LE00.MA.IN",
"SP.DYN.TFRT.IN"), class = "factor"), country_name = structure(c(1L,
2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 14L, 15L, 17L,
19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 28L, 29L), .Label = c("Australia",
"Brunei Darussalam", "Cambodia", "China", "Fiji", "Indonesia",
"Japan", "Kiribati", "Korea, Dem. People’s Rep.", "Korea, Rep.",
"Lao PDR", "Malaysia", "Marshall Islands", "Micronesia, Fed. Sts.",
"Mongolia", "Nauru", "New Zealand", "Palau", "Papua New Guinea",
"Philippines", "Samoa", "Singapore", "Solomon Islands", "Thailand",
"Timor-Leste", "Tonga", "Tuvalu", "Vanuatu", "Vietnam"), class = "factor"),
country_code = structure(c(1L, 2L, 8L, 3L, 4L, 6L, 7L, 9L,
20L, 10L, 11L, 14L, 5L, 13L, 16L, 19L, 17L, 29L, 21L, 22L,
23L, 24L, 25L, 28L, 27L), .Label = c("AUS", "BRN", "CHN",
"FJI", "FSM", "IDN", "JPN", "KHM", "KIR", "KOR", "LAO", "MHL",
"MNG", "MYS", "NRU", "NZL", "PHL", "PLW", "PNG", "PRK", "SGP",
"SLB", "THA", "TLS", "TON", "TUV", "VNM", "VUT", "WSM"), class = "factor"),
yr2001 = c(12.7, 20.913, 27.327, 13.38, 24.41, 21.486, 9.3,
30.228, 17.414, 11.6, 30.999, 21.445, 29.21, 19.035, 14.36,
34.396, 29.301, 30.269, 11.8, 35.403, 14.025, 41.441, 28.365,
31.84, 17.13), yr2002 = c(12.8, 20.137, 26.793, 12.86, 24.103,
21.49, 9.3, 29.965, 16.92, 10.2, 30.287, 20.39, 28.453, 19.001,
13.67, 33.95, 28.892, 29.991, 11.4, 35.226, 13.653, 40.428,
28.468, 31.219, 16.921), yr2003 = c(12.6, 19.522, 26.44,
12.41, 23.804, 21.5, 9.2, 29.775, 16.431, 10.2, 29.753, 19.435,
27.669, 19.209, 13.94, 33.49, 28.404, 29.778, 10.5, 35.061,
13.32, 39.726, 28.565, 30.597, 16.839), yr2004 = c(12.3,
19.065, 26.24, 12.29, 23.508, 21.499, 8.6936, 29.647, 15.961,
9.8, 29.38, 18.62, 26.886, 19.627, 14.2, 33.03, 27.845, 29.624,
10.3, 34.889, 13.025, 39.368, 28.624, 29.993, 16.848), yr2005 = c(12.8,
18.738, 26.145, 12.4, 23.208, 21.476, 8.4133, 29.572, 15.532,
8.9, 29.134, 17.971, 26.139, 20.223, 13.96, 32.575, 27.238,
29.499, 10.2, 34.68, 12.764, 39.326, 28.611, 29.427, 16.919
), yr2006 = c(12.9, 18.499, 26.098, 12.09, 22.901, 21.429,
8.65, 29.537, 15.166, 9.2, 28.966, 17.498, 25.461, 20.959,
14.14, 32.121, 26.619, 29.355, 10.3, 34.409, 12.533, 39.509,
28.499, 28.92, 17.03), yr2007 = c(14.1, 18.292, 26.043, 12.1,
22.586, 21.364, 8.63, 29.528, 14.87, 10, 28.821, 17.171,
24.872, 21.769, 15.15, 31.659, 26.025, 29.148, 10, 34.063,
12.323, 39.752, 28.288, 28.475, 17.163), yr2008 = c(14, 18.07,
25.937, 12.14, 22.263, 21.283, 8.7, 29.526, 14.648, 9.4,
28.651, 16.954, 24.385, 22.576, 15.1, 31.186, 25.489, 28.845,
10.2, 33.637, 12.123, 39.92, 27.982, 28.091, 17.298), yr2009 = c(13.9,
17.809, 25.755, 12.13, 21.929, 21.177, 8.5, 29.513, 14.498,
9, 28.429, 16.828, 24.011, 23.311, 14.53, 30.706, 25.023,
28.442, 9.9, 33.132, 11.927, 39.95, 27.588, 27.766, 17.409
), yr2010 = c(13.7, 17.499, 25.491, 11.9, 21.583, 21.034,
8.5, 29.468, 14.411, 9.4, 28.142, 16.773, 23.751, 23.892,
14.68, 30.229, 24.634, 27.944, 9.3, 32.555, 11.725, 39.8,
27.112, 27.486, 17.473), yr2011 = c(13.6, 17.146, 25.164,
11.93, 21.221, 20.841, 8.3, 29.377, 14.374, 9.4, 27.8, 16.765,
23.598, 24.252, 14, 29.764, 24.315, 27.372, 9.5, 31.918,
11.51, 39.461, 26.57, 27.236, 17.477), yr2012 = c(13.7, 16.774,
24.812, 12.1, 20.846, 20.595, 8.2, 29.235, 14.363, 9.6, 27.43,
16.783, 23.528, 24.378, 13.87, 29.318, 24.041, 26.768, 10.1,
31.25, 11.281, 38.985, 25.992, 26.993, 17.424), yr2013 = c(13.3,
16.405, 24.462, 12.08, 20.463, 20.297, 8.2, 29.044, 14.358,
8.6, 27.051, 16.805, 23.511, 24.275, 13.2, 28.899, 23.79,
26.172, 9.3, 30.578, 11.041, 38.419, 25.409, 26.739, 17.318
), yr2014 = c(12.9, 16.043, 24.119, 12.4, 20.075, 19.955,
8, 28.8, 14.349, 8.6, 26.666, 16.811, 23.531, 23.949, 12.68,
28.51, 23.552, 25.608, 9.8, 29.921, 10.79, 37.783, 24.846,
26.466, 17.157)), .Names = c("series_code", "country_name",
"country_code", "yr2001", "yr2002", "yr2003", "yr2004", "yr2005",
"yr2006", "yr2007", "yr2008", "yr2009", "yr2010", "yr2011", "yr2012",
"yr2013", "yr2014"), row.names = c(30L, 31L, 32L, 33L, 34L, 35L,
36L, 37L, 38L, 39L, 40L, 41L, 43L, 44L, 46L, 48L, 49L, 50L, 51L,
52L, 53L, 54L, 55L, 57L, 58L), class = "data.frame", na.action =
structure(c(13L, 16L, 18L, 27L), .Names = c("42", "45", "47", "56"), class = "omit"))
You could try plotting the x-axis labels horizontally.
Try this out:
plot(birthRate$country_code, birthRate$yr2014, main = "Birth Rate by Countries 2014", las=2)
Edit:
I was able to make this barplot using ggplot2.
Here's my code:
birthRate <- arrange(birthRate, yr2014)
p <- ggplot(birthRate, aes(y=yr2014, x=reorder(country_code, yr2014), fill=country_code)) +
geom_col()
p
Note: Your dput() output has 29 observations for the country_code variable, but only 25 for the yr2014 variable. I didn't know exactly where the missing data was, so I just removed the last four observations from the country_code variable to get things to line up. Your output may look slightly different based on where the NAs are...
I hope this was helpful!
When attempting to render a html app with crosstalk between leaflet/DT, I get the following error:
Error in datatable(sd, extensions = "Scroller", style = "bootstrap", class = "compact", : 'data' must be 2-dimensional (e.g. data frame or matrix)
data frame:
df2 <- data.frame(
structure(list(lat = c(-20.42, -20.62, -26, -17.97, -20.42, -19.68,
-11.7, -28.11, -28.74, -17.47, -21.44, -12.26, -18.54, -21, -20.7,
-15.94, -13.64, -17.83, -23.5, -22.63), long = c(181.62, 181.03,
184.1, 181.66, 181.96, 184.31, 166.1, 181.93, 181.74, 179.59,
180.69, 167, 182.11, 181.66, 169.92, 184.95, 165.96, 181.5, 179.78,
180.31), depth = c(562L, 650L, 42L, 626L, 649L, 195L, 82L, 194L,
211L, 622L, 583L, 249L, 554L, 600L, 139L, 306L, 50L, 590L, 570L,
598L), mag = c(4.8, 4.2, 5.4, 4.1, 4, 4, 4.8, 4.4, 4.7, 4.3,
4.4, 4.6, 4.4, 4.4, 6.1, 4.3, 6, 4.5, 4.4, 4.4), stations = c(41L,
15L, 43L, 19L, 11L, 12L, 43L, 15L, 35L, 19L, 13L, 16L, 19L, 10L,
94L, 11L, 83L, 21L, 13L, 18L)), .Names = c("lat", "long", "depth",
"mag", "stations"), row.names = c(NA, 20L), class = "data.frame")
)
Reproducible code:
library(crosstalk)
library(leaflet) #devtools::install_github('rstudio/leaflet', force = TRUE)
library(DT)
# Wrap data frame in SharedData
sd <- SharedData$new(quakes[sample(nrow(quakes), 10),])
# Create a filter input
filter_slider("mag", "Magnitude", sd, column=~mag, step=0.1, width=250)
# Use SharedData like a dataframe with Crosstalk-enabled widgets
bscols(
leaflet(sd) %>% addTiles() %>% addMarkers(),
datatable(sd, extensions="Scroller", style="bootstrap", class="compact", width="100%",
options=list(deferRender=TRUE, scrollY=300, scroller=FALSE))
)
And the platform and pkg versions:
R version 3.3.2 (2016-10-31)
crosstalk_1.0.1 (#installed from devtools/github)
leaflet_1.0.2.9010
DT_0.2
install 'DT' from devtool/github.
devtools::install_github('rstudio/DT')