Closed jeroen closed 3 years ago
R/bd_loglik_choosepar.R:1:1: style: Lines should not be more than 80 characters.
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik_choosepar.R:1:21: style: Use <-, not =, for assignment.
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
^
R/bd_loglik_choosepar.R:1:42: style: Commas should always have a space after.
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
^
R/bd_loglik_choosepar.R:1:52: style: Commas should always have a space after.
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
^
R/bd_loglik_choosepar.R:1:62: style: Commas should always have a space after.
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
^
R/bd_loglik_choosepar.R:1:72: style: Commas should always have a space after.
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
^
R/bd_loglik_choosepar.R:1:78: style: Commas should always have a space after.
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
^
R/bd_loglik_choosepar.R:1:83: style: Commas should always have a space after.
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
^
R/bd_loglik_choosepar.R:1:95: style: Commas should always have a space after.
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
^
R/bd_loglik_choosepar.R:2:1: style: Opening curly braces should never go on their own line and should always be followed by a new line.
{
^
R/bd_loglik_choosepar.R:3:12: style: Use <-, not =, for assignment.
trpars1 = rep(0,4)
^
R/bd_loglik_choosepar.R:3:20: style: Commas should always have a space after.
trpars1 = rep(0,4)
^
R/bd_loglik_choosepar.R:4:23: style: Use <-, not =, for assignment.
trpars1[idparsopt] = trparsopt
^
R/bd_loglik_choosepar.R:5:6: style: Place a space before left parenthesis, except in a function call.
if(length(idparsfix) != 0)
^
R/bd_loglik_choosepar.R:6:4: style: Opening curly braces should never go on their own line and should always be followed by a new line.
{
^
R/bd_loglik_choosepar.R:7:26: style: Use <-, not =, for assignment.
trpars1[idparsfix] = trparsfix
^
R/bd_loglik_choosepar.R:9:6: style: Place a space before left parenthesis, except in a function call.
if(max(trpars1) > 1 | min(trpars1) < 0)
^
R/bd_loglik_choosepar.R:10:4: style: Opening curly braces should never go on their own line and should always be followed by a new line.
{
^
R/bd_loglik_choosepar.R:11:14: style: Use <-, not =, for assignment.
loglik = -Inf
^
R/bd_loglik_choosepar.R:13:13: style: Use <-, not =, for assignment.
pars1 = trpars1/(1 - trpars1)
^
R/bd_loglik_choosepar.R:13:22: style: Put spaces around all infix operators.
pars1 = trpars1/(1 - trpars1)
~^~
R/bd_loglik_choosepar.R:13:23: style: Place a space before left parenthesis, except in a function call.
pars1 = trpars1/(1 - trpars1)
^
R/bd_loglik_choosepar.R:14:1: style: Lines should not be more than 80 characters.
loglik = bd_loglik(pars1 = pars1,pars2 = pars2[1:6],brts = brts,missnumspec = missnumspec, methode = methode)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik_choosepar.R:14:14: style: Use <-, not =, for assignment.
loglik = bd_loglik(pars1 = pars1,pars2 = pars2[1:6],brts = brts,missnumspec = missnumspec, methode = methode)
^
R/bd_loglik_choosepar.R:14:40: style: Commas should always have a space after.
loglik = bd_loglik(pars1 = pars1,pars2 = pars2[1:6],brts = brts,missnumspec = missnumspec, methode = methode)
^
R/bd_loglik_choosepar.R:14:59: style: Commas should always have a space after.
loglik = bd_loglik(pars1 = pars1,pars2 = pars2[1:6],brts = brts,missnumspec = missnumspec, methode = methode)
^
R/bd_loglik_choosepar.R:14:71: style: Commas should always have a space after.
loglik = bd_loglik(pars1 = pars1,pars2 = pars2[1:6],brts = brts,missnumspec = missnumspec, methode = methode)
^
R/bd_loglik_choosepar.R:15:9: style: Place a space before left parenthesis, except in a function call.
if(is.nan(loglik) || is.na(loglik))
^
R/bd_loglik_choosepar.R:16:7: style: Opening curly braces should never go on their own line and should always be followed by a new line.
{
^
R/bd_loglik_choosepar.R:17:1: style: Lines should not be more than 80 characters.
cat("There are parameter values used which cause numerical problems.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik_choosepar.R:18:17: style: Use <-, not =, for assignment.
loglik = -Inf
^
R/bd_loglik.R:41:80: style: Trailing whitespace is superfluous.
#' \cr \cr \code{pars2[4]} sets whether the parameters and likelihood should be
^
R/bd_loglik.R:59:68: style: Trailing whitespace is superfluous.
#' bd_loglik(pars1 = c(0.5,0.1), pars2 = c(0,1,1,0,2), brts = 1:10,
^
R/bd_loglik.R:62:1: style: functions should have cyclomatic complexity of less than 15, this has 71.
bd_loglik <- function(pars1, pars2, brts, missnumspec, methode = "lsoda"){
^
R/bd_loglik.R:62:73: style: There should be a space between right parenthesis and an opening curly brace.
bd_loglik <- function(pars1, pars2, brts, missnumspec, methode = "lsoda"){
^
R/bd_loglik.R:66:1: style: Lines should not be more than 80 characters.
# - pars1[3] = la1 = parameter in exponential decay of speciation rate, OR K in
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:66:82: style: Trailing whitespace is superfluous.
# - pars1[3] = la1 = parameter in exponential decay of speciation rate, OR K in
^
R/bd_loglik.R:70:62: style: Trailing whitespace is superfluous.
# - pars1[5] = T0 = age at which lambda is lambda0 (default
^
R/bd_loglik.R:76:73: style: Trailing whitespace is superfluous.
# . tdmodel == 2: stepwise decline following diversity-dependence when
^
R/bd_loglik.R:77:7: style: Commented code should be removed.
# extinction = 0
^~~~~~~~~~~~~~
R/bd_loglik.R:78:80: style: Trailing whitespace is superfluous.
# . tdmodel == 3: decline in speciation rate following deterministic logistic
^
R/bd_loglik.R:80:1: style: Lines should not be more than 80 characters.
# . tdmodel == 4...8: change in speciation/extinction rate following ddmodel =
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:80:81: style: Trailing whitespace is superfluous.
# . tdmodel == 4...8: change in speciation/extinction rate following ddmodel =
^
R/bd_loglik.R:82:1: style: Lines should not be more than 80 characters.
# - pars2[2] = cond = conditioning on age (0), non-extinction of the clade and
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:82:81: style: Trailing whitespace is superfluous.
# - pars2[2] = cond = conditioning on age (0), non-extinction of the clade and
^
R/bd_loglik.R:86:79: style: Trailing whitespace is superfluous.
# - pars2[5] = likelihood is for a tree with crown age (2) or stem age (1) -
^
R/bd_loglik.R:89:1: style: Trailing whitespace is superfluous.
^~
R/bd_loglik.R:90:36: style: There should be a space between right parenthesis and an opening curly brace.
rhotaut <- function(tau, t1, pars){
^
R/bd_loglik.R:105:74: style: Trailing whitespace is superfluous.
rtt <- mu0 / mu1 * (exp(-mu1 * t1) - exp(-mu1 * tau)) - la0 / la1 *
^
R/bd_loglik.R:110:1: style: Trailing whitespace is superfluous.
^~
R/bd_loglik.R:111:3: style: Variable and function name style should be snake_case or symbols.
PtTint <- function(x, t1, pars){
^~~~~~
R/bd_loglik.R:111:33: style: There should be a space between right parenthesis and an opening curly brace.
PtTint <- function(x, t1, pars){
^
R/bd_loglik.R:112:5: style: Variable and function name style should be snake_case or symbols.
PtTint <- pars[2] * exp(-pars[4] * x) * exp(rhotaut(x, t1, pars))
^~~~~~
R/bd_loglik.R:115:1: style: Trailing whitespace is superfluous.
^~
R/bd_loglik.R:116:26: style: There should be a space between right parenthesis and an opening curly brace.
ff <- function(t1, pars){
^
R/bd_loglik.R:117:54: style: Place a space before left parenthesis, except in a function call.
ff <- 1 / pars[3] + (1 / 2 - 1 / pars[3]) * exp(-(pars[1] - pars[2]) * t1)
^
R/bd_loglik.R:120:1: style: Trailing whitespace is superfluous.
^~
R/bd_loglik.R:121:40: style: There should be a space between right parenthesis and an opening curly brace.
exprhotaut2 <- function(tau, t1, pars){
^
R/bd_loglik.R:125:1: style: Trailing whitespace is superfluous.
^~
R/bd_loglik.R:126:3: style: Variable and function name style should be snake_case or symbols.
intPtTint2 <- function(t1, T, pars){
^~~~~~~~~~
R/bd_loglik.R:126:30: style: Variable and function name style should be snake_case or symbols.
intPtTint2 <- function(t1, T, pars){
^
R/bd_loglik.R:126:37: style: There should be a space between right parenthesis and an opening curly brace.
intPtTint2 <- function(t1, T, pars){
^
R/bd_loglik.R:127:5: style: Variable and function name style should be snake_case or symbols.
intPtTint2 <- pars[2] / ff(t1,pars) *
^~~~~~~~~~
R/bd_loglik.R:127:35: style: Commas should always have a space after.
intPtTint2 <- pars[2] / ff(t1,pars) *
^
R/bd_loglik.R:127:42: style: Trailing whitespace is superfluous.
intPtTint2 <- pars[2] / ff(t1,pars) *
^
R/bd_loglik.R:128:11: style: Use TRUE instead of the symbol T.
( (T - t1) / pars[3] + (ff(t1, pars) - ff(T, pars)) /
~^
R/bd_loglik.R:128:50: style: Use TRUE instead of the symbol T.
( (T - t1) / pars[3] + (ff(t1, pars) - ff(T, pars)) /
~^
R/bd_loglik.R:128:60: style: Trailing whitespace is superfluous.
( (T - t1) / pars[3] + (ff(t1, pars) - ff(T, pars)) /
^
R/bd_loglik.R:129:30: style: Do not place spaces around code in parentheses or square brackets.
(pars[1] - pars[2]) )
^
R/bd_loglik.R:132:1: style: Trailing whitespace is superfluous.
^~
R/bd_loglik.R:134:61: style: There should be a space between right parenthesis and an opening curly brace.
if (min(pars1) < 0 | (tdmodel == 4 & pars1[1] <= pars1[2])){
^
R/bd_loglik.R:141:18: style: There should be a space between right parenthesis and an opening curly brace.
if (cond == 3){
^
R/bd_loglik.R:147:24: style: There should be a space between right parenthesis and an opening curly brace.
if (is.na(pars2[6])){
^
R/bd_loglik.R:148:16: style: Use <-, not =, for assignment.
pars2[6] = Inf
^
R/bd_loglik.R:150:1: style: Trailing whitespace is superfluous.
^~~~
R/bd_loglik.R:151:32: style: There should be a space between right parenthesis and an opening curly brace.
if (soc == 1 & tdmodel == 2){
^
R/bd_loglik.R:152:30: style: Commas should always have a space after.
pars1new <- c(pars1[1],1e-10,pars1[3])
^
R/bd_loglik.R:152:36: style: Commas should always have a space after.
pars1new <- c(pars1[1],1e-10,pars1[3])
^
R/bd_loglik.R:153:1: style: Lines should not be more than 80 characters.
pars2new <- c(min(10 * (1 + missnumspec + length(brts)),1000),1,pars2[2:5])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:153:63: style: Commas should always have a space after.
pars2new <- c(min(10 * (1 + missnumspec + length(brts)),1000),1,pars2[2:5])
^
R/bd_loglik.R:153:69: style: Commas should always have a space after.
pars2new <- c(min(10 * (1 + missnumspec + length(brts)),1000),1,pars2[2:5])
^
R/bd_loglik.R:153:71: style: Commas should always have a space after.
pars2new <- c(min(10 * (1 + missnumspec + length(brts)),1000),1,pars2[2:5])
^
R/bd_loglik.R:154:1: style: Lines should not be more than 80 characters.
loglik <- dd_loglik(pars1 = pars1new, pars2 = pars2new, brts = brts, missnumspec = missnumspec, methode = methode)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:154:17: warning: no visible global function definition for ‘dd_loglik’
loglik <- dd_loglik(pars1 = pars1new, pars2 = pars2new, brts = brts, missnumspec = missnumspec, methode = methode)
^~~~~~~~~
R/bd_loglik.R:156:12: style: Opening curly braces should never go on their own line and should always be followed by a new line.
} else {
^
R/bd_loglik.R:156:13: style: Trailing whitespace is superfluous.
} else {
^~~~~~~~
R/bd_loglik.R:158:34: style: There should be a space between right parenthesis and an opening curly brace.
if (brts[length(brts)] == 0){
^
R/bd_loglik.R:162:10: style: Place a space before left parenthesis, except in a function call.
for(i in 2:length(brts2)) {
^
R/bd_loglik.R:163:37: style: There should be a space between right parenthesis and an opening curly brace.
if (brts2[i] == brts2[i - 1]){
^
R/bd_loglik.R:167:19: style: There should be a space between right parenthesis and an opening curly brace.
if (soc == 2){
^
R/bd_loglik.R:170:7: style: Variable and function name style should be snake_case or symbols.
TT <- brts[1]
^~
R/bd_loglik.R:172:1: style: Trailing whitespace is superfluous.
^~~~~~
R/bd_loglik.R:173:7: style: Variable and function name style should be snake_case or symbols.
S <- length(brts)
^
R/bd_loglik.R:174:7: style: Variable and function name style should be snake_case or symbols.
N <- S + m
^
R/bd_loglik.R:176:7: style: Variable and function name style should be snake_case or symbols.
PtT <- rep(0, S)
^~~
R/bd_loglik.R:178:1: style: Trailing whitespace is superfluous.
^~~~~~
R/bd_loglik.R:179:7: warning: local variable ‘abstol’ assigned but may not be used
abstol <- 1e-16
^~~~~~
R/bd_loglik.R:180:7: warning: local variable ‘reltol’ assigned but may not be used
reltol <- 1e-10
^~~~~~
R/bd_loglik.R:181:1: style: Trailing whitespace is superfluous.
^~~~~~
R/bd_loglik.R:182:7: style: Variable and function name style should be snake_case or symbols.
T0 <- TT
^~
R/bd_loglik.R:185:28: style: There should be a space between right parenthesis and an opening curly brace.
if (length(pars1) > 2){
^
R/bd_loglik.R:187:9: style: Variable and function name style should be snake_case or symbols.
K <- pars1[3]
^
R/bd_loglik.R:189:31: style: There should be a space between right parenthesis and an opening curly brace.
if (length(pars1) == 5){
^
R/bd_loglik.R:190:11: style: Variable and function name style should be snake_case or symbols.
T0 <- pars1[5]
^~
R/bd_loglik.R:191:10: style: Trailing whitespace is superfluous.
}
^
R/bd_loglik.R:194:9: style: Variable and function name style should be snake_case or symbols.
K <- Inf
^
R/bd_loglik.R:196:31: style: Commas should always have a space after.
pars1 <- c(pars1, c(0,0))
^
R/bd_loglik.R:198:1: style: Trailing whitespace is superfluous.
^~~~~~
R/bd_loglik.R:199:9: style: Place a space before left parenthesis, except in a function call.
if(tdmodel == 1){
^
R/bd_loglik.R:199:22: style: There should be a space between right parenthesis and an opening curly brace.
if(tdmodel == 1){
^
R/bd_loglik.R:203:1: style: Trailing whitespace is superfluous.
^~~~~~
R/bd_loglik.R:205:1: style: Trailing whitespace is superfluous.
^~~~~~
R/bd_loglik.R:206:9: style: Place a space before left parenthesis, except in a function call.
if(tdmodel == 0 | (tdmodel == 1 & la1 == 0 & mu1 == 0))
^
R/bd_loglik.R:207:7: style: Opening curly braces should never go on their own line and should always be followed by a new line.
{
^
R/bd_loglik.R:208:11: style: Place a space before left parenthesis, except in a function call.
if(abs(la0 - mu0) < 1E-10){
^
R/bd_loglik.R:208:34: style: There should be a space between right parenthesis and an opening curly brace.
if(abs(la0 - mu0) < 1E-10){
^
R/bd_loglik.R:210:11: style: Variable and function name style should be snake_case or symbols.
PtT <- 1 / (1 + lamu * (TT - t))
^~~
R/bd_loglik.R:213:11: style: Variable and function name style should be snake_case or symbols.
PtT <- (la0 - mu0) / (la0 - mu0 * exp(-(la0 - mu0) * (TT - t)))
^~~
R/bd_loglik.R:213:50: style: Place a space before left parenthesis, except in a function call.
PtT <- (la0 - mu0) / (la0 - mu0 * exp(-(la0 - mu0) * (TT - t)))
^
R/bd_loglik.R:214:29: style: Place a space before left parenthesis, except in a function call.
ux <- la0 * (1 - exp(-(la0 - mu0) * (TT - t))) /
^
R/bd_loglik.R:215:27: style: Place a space before left parenthesis, except in a function call.
(la0 - mu0 * exp(-(la0 - mu0) * (TT - t)))
^
R/bd_loglik.R:218:47: style: There should be a space between right parenthesis and an opening curly brace.
if (tdmodel == 1 & (la1 != 0 | mu1 != 0)){
^
R/bd_loglik.R:219:12: style: Place a space before left parenthesis, except in a function call.
for(i in 1:S){
^
R/bd_loglik.R:221:46: style: Trailing whitespace is superfluous.
PtTint, lower = t[i], upper = TT,
^
R/bd_loglik.R:226:30: style: There should be a space between right parenthesis and an opening curly brace.
} else if (tdmodel == 2){
^
R/bd_loglik.R:227:27: style: There should be a space between right parenthesis and an opening curly brace.
if (N > ceiling(K)){
^
R/bd_loglik.R:231:22: style: Commas should always have a space after.
la <- pmax(0,la0 * (1 - (2:S) / K))
^
R/bd_loglik.R:232:33: style: Commas should always have a space after.
dx <- c(abs(diff(brts)),brts[S])[2:S]
^
R/bd_loglik.R:233:11: style: Commented code should be removed.
# mpfr(la, precBits = 500)
^~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:234:11: style: Commented code should be removed.
# mpfr(dx, precBits = 500)
^~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:236:9: style: Variable and function name style should be snake_case or symbols.
PtT <- rep(1,S)
^~~
R/bd_loglik.R:236:22: style: Commas should always have a space after.
PtT <- rep(1,S)
^
R/bd_loglik.R:237:12: style: Place a space before left parenthesis, except in a function call.
for(i in 2:S){
^
R/bd_loglik.R:241:30: style: There should be a space between right parenthesis and an opening curly brace.
} else if (tdmodel == 3){
^
R/bd_loglik.R:242:9: style: Variable and function name style should be snake_case or symbols.
PtT <- 1 / (1 + intPtTint2(t, TT, pars1))
^~~
R/bd_loglik.R:244:30: style: There should be a space between right parenthesis and an opening curly brace.
} else if (tdmodel == 4){
^
R/bd_loglik.R:245:9: style: Variable and function name style should be snake_case or symbols.
Kprime <- la0 / (la0 - mu0) * K
^~~~~~
R/bd_loglik.R:248:32: style: Trailing whitespace is superfluous.
ceiling(Kprime) < N |
^
R/bd_loglik.R:249:39: style: Trailing whitespace is superfluous.
K >= 0.9 * round(pars2[6]) |
^
R/bd_loglik.R:250:18: style: Trailing whitespace is superfluous.
K < 1 |
^
R/bd_loglik.R:251:22: style: Trailing whitespace is superfluous.
la0 < mu0 |
^
R/bd_loglik.R:253:9: style: There should be a space between right parenthesis and an opening curly brace.
){
^
R/bd_loglik.R:262:25: style: Trailing whitespace is superfluous.
latd[1] <- mu0 +
^
R/bd_loglik.R:264:12: style: Place a space before left parenthesis, except in a function call.
for(k in 2:np){
^
R/bd_loglik.R:268:1: style: Lines should not be more than 80 characters.
#y2 = deSolve::ode(variables, c(t1, t2), td_loglik_rhs, c(pars1[1:min(4, length(pars1))], tdmodel - 3, lx), rtol = 1e-10, atol = 1e-16, method = methode)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:268:12: style: Commented code should be removed.
#y2 = deSolve::ode(variables, c(t1, t2), td_loglik_rhs, c(pars1[1:min(4, length(pars1))], tdmodel - 3, lx), rtol = 1e-10, atol = 1e-16, method = methode)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:285:19: style: Only use double-quotes.
cat('NA or NaN issues encountered.\n')
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:290:15: style: Place a space before left parenthesis, except in a function call.
if(verbose) cat('Probabilities smaller than 0 encountered\n')
^
R/bd_loglik.R:290:29: style: Only use double-quotes.
if(verbose) cat('Probabilities smaller than 0 encountered\n')
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:292:35: style: Commas should always have a space after.
variables <- rep(-Inf,length(variables))
^
R/bd_loglik.R:293:12: style: Trailing whitespace is superfluous.
}
^
R/bd_loglik.R:294:12: style: Commented code should be removed.
#variables2 = y2[2, 2:(lx + k)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:296:13: style: Trailing whitespace is superfluous.
#{
^
R/bd_loglik.R:297:15: style: Commented code should be removed.
# print(variables2 - variables)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:298:15: style: Commented code should be removed.
# unequal <- which(variables != variables2)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:299:14: style: Commented code should be removed.
# if(length(unequal) > 0) stop('Stop here')
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:303:11: style: Variable and function name style should be snake_case or symbols.
dEN_dt <- (la0 - mu0) * expn[k] - expn2 * (la0 - mu0) / K
^~~~~~
R/bd_loglik.R:306:40: style: Do not place spaces around code in parentheses or square brackets.
if (sum(variables[1:lx]) < 0.99 ) {
^
R/bd_loglik.R:307:12: style: Commented code should be removed.
#print(lx)
^~~~~~~~~
R/bd_loglik.R:308:12: style: Commented code should be removed.
#print(sum(variables[1:lx]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:309:15: style: Only use double-quotes.
cat('Leaking probabilities detected.')
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:313:9: style: Variable and function name style should be snake_case or symbols.
PtT <- 1 / (1 + sig)
^~~
R/bd_loglik.R:316:11: style: Variable and function name style should be snake_case or symbols.
PtT <- c(PtT[1], PtT)
^~~
R/bd_loglik.R:320:1: style: Trailing whitespace is superfluous.
^~~~~~
R/bd_loglik.R:322:11: style: Place a space before left parenthesis, except in a function call.
if(tdmodel == 0) {
^
R/bd_loglik.R:324:34: style: Opening curly braces should never go on their own line and should always be followed by a new line.
} else if (tdmodel == 1) {
^
R/bd_loglik.R:324:35: style: Trailing whitespace is superfluous.
} else if (tdmodel == 1) {
^
R/bd_loglik.R:328:18: style: Place a space before left parenthesis, except in a function call.
} else if(tdmodel == 3) {
^
R/bd_loglik.R:330:18: style: Place a space before left parenthesis, except in a function call.
} else if(tdmodel == 4) {
^
R/bd_loglik.R:333:9: style: Opening curly braces should never go on their own line and should always be followed by a new line.
{
^
R/bd_loglik.R:334:16: style: Only use double-quotes.
stop('The tdmodel you selected does not exist. Please check pars2.')
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:336:20: style: There should be a space between right parenthesis and an opening curly brace.
if (S > soc){
^
R/bd_loglik.R:337:64: style: Trailing whitespace is superfluous.
loglik <- loglik + sum(log(lavec[soc:length(lavec)]))
^
R/bd_loglik.R:340:1: style: Trailing whitespace is superfluous.
^~~~~~
R/bd_loglik.R:342:9: style: Place a space before left parenthesis, except in a function call.
if(cond == 1) {
^
R/bd_loglik.R:343:14: style: Use <-, not =, for assignment.
logp = soc * log(PtT[1])
^
R/bd_loglik.R:345:9: style: Place a space before left parenthesis, except in a function call.
if(cond == 2 | cond == 3) {
^
R/bd_loglik.R:346:11: style: Place a space before left parenthesis, except in a function call.
if(tdmodel == 2) {
^
R/bd_loglik.R:348:11: style: Variable and function name style should be snake_case or symbols.
K2 <- K
^~
R/bd_loglik.R:349:39: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (floor(K) == ceiling(K)) {
^
R/bd_loglik.R:349:40: style: Trailing whitespace is superfluous.
if (floor(K) == ceiling(K)) {
^
R/bd_loglik.R:350:13: style: Variable and function name style should be snake_case or symbols.
K2 <- K + eps
^~
R/bd_loglik.R:351:52: style: Opening curly braces should never go on their own line and should always be followed by a new line.
} else if (floor(K + eps) == ceiling(K)) {
^
R/bd_loglik.R:351:53: style: Trailing whitespace is superfluous.
} else if (floor(K + eps) == ceiling(K)) {
^
R/bd_loglik.R:352:13: style: Variable and function name style should be snake_case or symbols.
K2 <- K - eps
^~
R/bd_loglik.R:354:13: style: Variable and function name style should be snake_case or symbols.
K2 <- K + eps
^~
R/bd_loglik.R:364:12: style: Commented code should be removed.
#pB = max(50,round(3/la0))
^~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:365:12: style: Commented code should be removed.
#s = mpfr(s, precBits = pB)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:365:38: style: Trailing whitespace is superfluous.
#s = mpfr(s, precBits = pB)
^~~~~~
R/bd_loglik.R:366:12: style: Commented code should be removed.
#sgnsdiff = mpfr(sgnsdiff, precBits = pB)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:367:12: style: Commented code should be removed.
#logsdiff = mpfr(logsdiff, precBits = pB)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:368:12: style: Commented code should be removed.
#sgnsdiff2 = mpfr(sgnsdiff2, precBits = pB)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:369:12: style: Commented code should be removed.
#logsdiff2 = mpfr(logsdiff2, precBits = pB)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:370:12: style: Commented code should be removed.
#logsdiff3 = mpfr(logsdiff3, precBits = pB)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:372:26: style: Opening curly braces should never go on their own line and should always be followed by a new line.
for (i in 1:N) {
^
R/bd_loglik.R:372:27: style: Trailing whitespace is superfluous.
for (i in 1:N) {
^
R/bd_loglik.R:373:45: style: Commas should always have a space after.
sgnsdiff[i] <- prod(sign(s[-c(1,i)] - s[i]))
^
R/bd_loglik.R:374:47: style: Commas should always have a space after.
logsdiff[i] <- sum(log(abs(s[-c(1,i)] - s[i])))
^
R/bd_loglik.R:377:50: style: Put spaces around all infix operators.
logsdiff3[i] <- -sum(log(abs(1 - s[i]/s[-c(1,i,N)]))) -
~^~
R/bd_loglik.R:377:58: style: Commas should always have a space after.
logsdiff3[i] <- -sum(log(abs(1 - s[i]/s[-c(1,i,N)]))) -
^
R/bd_loglik.R:377:60: style: Commas should always have a space after.
logsdiff3[i] <- -sum(log(abs(1 - s[i]/s[-c(1,i,N)]))) -
^
R/bd_loglik.R:377:68: style: Trailing whitespace is superfluous.
logsdiff3[i] <- -sum(log(abs(1 - s[i]/s[-c(1,i,N)]))) -
^
R/bd_loglik.R:382:77: style: Trailing whitespace is superfluous.
# logp <- sum(log(s[2:(N-1)])) + log(sum(sgnsdiff[2:N] *
^
R/bd_loglik.R:384:1: style: Lines should not be more than 80 characters.
# logp <- log(sum(sgnsdiff[2:N] * exp(sum(log(s[2:(N-1)])) -
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:384:81: style: Trailing whitespace is superfluous.
# logp <- log(sum(sgnsdiff[2:N] * exp(sum(log(s[2:(N-1)])) -
^
R/bd_loglik.R:388:35: style: Put spaces around all infix operators.
logp <- sum(log(s[1:(N-1)])) +
~^~
R/bd_loglik.R:388:43: style: Trailing whitespace is superfluous.
logp <- sum(log(s[1:(N-1)])) +
^
R/bd_loglik.R:393:13: style: Place a space before left parenthesis, except in a function call.
if(cond == 2) {
^
R/bd_loglik.R:394:70: style: Trailing whitespace is superfluous.
logp <- (soc == 2) * log(S + m - 1) + soc * log(PtT[1]) +
^
R/bd_loglik.R:397:57: style: Trailing whitespace is superfluous.
logp <- log(PtT[1]) - log(S + missnumspec) -
^
R/bd_loglik.R:402:1: style: Trailing whitespace is superfluous.
^~~~~~
R/bd_loglik.R:404:1: style: Trailing whitespace is superfluous.
^~~~~~
R/bd_loglik.R:406:11: style: Place a space before left parenthesis, except in a function call.
if(tdmodel == 2) {
^
R/bd_loglik.R:408:60: style: Trailing whitespace is superfluous.
"Missing species in diversity-dependence models
^
R/bd_loglik.R:413:11: style: Place a space before left parenthesis, except in a function call.
if(cond == 3) {
^
R/bd_loglik.R:414:33: style: Put spaces around all infix operators.
x <- (1 - ux[1]^((0:m)+1)) / (1 - ux[1])
~^~
R/bd_loglik.R:418:12: style: Place a space before left parenthesis, except in a function call.
for(j in 2:S) {
^
R/bd_loglik.R:419:1: style: Lines should not be more than 80 characters.
#x = convolve(x,rev((1:(m + 1)) * ux[j]^(0:m)),type = 'open')[1:(m + 1)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:419:12: style: Commented code should be removed.
#x = convolve(x,rev((1:(m + 1)) * ux[j]^(0:m)),type = 'open')[1:(m + 1)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:420:16: warning: no visible global function definition for ‘conv’
x <- conv(x, (1:(m + 1)) * ux[j]^(0:m))[1:(m+1)]
^~~~
R/bd_loglik.R:420:55: style: Put spaces around all infix operators.
x <- conv(x, (1:(m + 1)) * ux[j]^(0:m))[1:(m+1)]
~^~
R/bd_loglik.R:422:59: style: Trailing whitespace is superfluous.
loglik <- loglik + lgamma(S + 1) + lgamma(m + 1) -
^
R/bd_loglik.R:424:1: style: Lines should not be more than 80 characters.
#loglik = loglik - log(S + m + 1) + log(S + 1) + log(S + m - 1) - log(S - 1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:424:10: style: Commented code should be removed.
#loglik = loglik - log(S + m + 1) + log(S + 1) + log(S + m - 1) - log(S - 1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:427:11: style: Place a space before left parenthesis, except in a function call.
if(tdmodel == 0) {
^
R/bd_loglik.R:428:25: style: Only use double-quotes.
s1 <- sprintf('Parameters: %f %f', pars1[1], pars1[2])
^~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:431:13: style: Only use double-quotes.
'Parameters: %f %f %f %f', pars1[1], pars1[2], pars1[3], pars1[4]
^~~~~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:434:25: style: Only use double-quotes.
s1 <- sprintf('Parameters: %f %f %f', pars1[1], pars1[2], pars1[3])
^~~~~~~~~~~~~~~~~~~~~~
R/bd_loglik.R:436:23: style: Only use double-quotes.
s2 <- sprintf(', Loglikelihood: %f', loglik)
^~~~~~~~~~~~~~~~~~~~~
R/bd_ML.R:3:3: style: Trailing whitespace is superfluous.
#'
^
R/bd_ML.R:8:3: style: Trailing whitespace is superfluous.
#'
^
R/bd_ML.R:14:3: style: Trailing whitespace is superfluous.
#'
^
Merging #25 (6aefd83) into master (659cbaa) will not change coverage. The diff coverage is
n/a
.
@@ Coverage Diff @@
## master #25 +/- ##
=======================================
Coverage 33.58% 33.58%
=======================================
Files 36 36
Lines 3278 3278
=======================================
Hits 1101 1101
Misses 2177 2177
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This is the best workaround that I can come up with. It works for now, maybe when an official fortran compiler is released for apple arm, you can come up with a more elegant solution.